Citations
This panel presents information regarding the papers that have cited the interatomic potential (IP) whose page you are on.
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This panel provides information on past usage of this interatomic potential (IP) powered by the OpenKIM Deep Citation framework. The word cloud indicates typical applications of the potential. The bar chart shows citations per year of this IP (bars are divided into articles that used the IP (green) and those that did not (blue)). The complete list of articles that cited this IP is provided below along with the Deep Citation determination on usage. See the Deep Citation documentation for more information.
693 Citations (538 used)
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USED (definite) M. A. Nejad and H. Urbassek, “Adsorption and Diffusion of Cisplatin Molecules in Nanoporous Materials: A Molecular Dynamics Study,” Biomolecules. 2019. link Times cited: 10 Abstract: Using molecular dynamics simulations, the adsorption and dif… read moreAbstract: Using molecular dynamics simulations, the adsorption and diffusion of cisplatin drug molecules in nanopores is investigated for several inorganic materials. Three different materials are studied with widely-varying properties: metallic gold, covalent silicon, and silica. We found a strong influence of both the van der Waals and the electrostatic interaction on the adsorption behavior on the pore walls, which in turn influence the diffusion coefficients. While van der Waals forces generally lead to a reduction of the diffusion coefficient, the fluctuations in the electrostatic energy induced by orientation changes of the cisplatin molecule were found to help desorb the molecule from the wall. read less USED (definite) G. Benetti et al., “Photoacoustic Sensing of Trapped Fluids in Nanoporous Thin Films: Device Engineering and Sensing Scheme.,” ACS applied materials & interfaces. 2018. link Times cited: 20 Abstract: Accessing fluid infiltration in nanogranular coatings is an … read moreAbstract: Accessing fluid infiltration in nanogranular coatings is an outstanding challenge, of relevance for applications ranging from nanomedicine to catalysis. A sensing platform, allowing quantifying the amount of fluid infiltrated in a nanogranular ultrathin coating, with thickness in the 10-40 nm range, is here proposed and theoretically investigated by multiscale modeling. The scheme relies on impulsive photoacoustic excitation of hypersonic mechanical breathing modes in engineered gas-phase-synthesized nanogranular metallic ultrathin films and time-resolved acousto-optical read-out of the breathing modes frequency shift upon liquid infiltration. A superior sensitivity, exceeding 26 × 103 cm2/g, is predicted upon equivalent areal mass loading of a few ng/mm2. The capability of the present scheme to discriminate among different infiltration patterns is discussed. The platform is an ideal tool to investigate nanofluidics in granular materials and naturally serves as a distributed nanogetter coating, integrating fluid sensing capabilities. The proposed scheme is readily extendable to other nanoscale and mesoscale porous materials. read less USED (definite) C. Meng, L. Liao, and C. Huang, “Study on failure mechanism of Cu-polyethylene-Cu sandwich structure by molecular dynamics simulation,” Computational Materials Science. 2018. link Times cited: 4 USED (definite) T. Li, J. Li, L. Wang, Y. Duan, and H. Li, “Coalescence of Immiscible Liquid Metal Drop on Graphene,” Scientific Reports. 2016. link Times cited: 34 USED (definite) M. Greif et al., “Following the molecular motion of near-resonant excited CO on Pt(111): A simulated x-ray photoelectron diffraction study based on molecular dynamics calculations,” Structural Dynamics. 2015. link Times cited: 8 Abstract: A THz-pump and x-ray-probe experiment is simulated where x-r… read moreAbstract: A THz-pump and x-ray-probe experiment is simulated where x-ray photoelectron diffraction (XPD) patterns record the coherent vibrational motion of carbon monoxide molecules adsorbed on a Pt(111) surface. Using molecular dynamics simulations, the excitation of frustrated wagging-type motion of the CO molecules by a few-cycle pulse of 2 THz radiation is calculated. From the atomic coordinates, the time-resolved XPD patterns of the C 1s core level photoelectrons are generated. Due to the direct structural information in these data provided by the forward scattering maximum along the carbon-oxygen direction, the sequence of these patterns represents the equivalent of a molecular movie. read less USED (definite) A. Mhashal and S. Roy, “Effect of Gold Nanoparticle on Structure and Fluidity of Lipid Membrane,” PLoS ONE. 2014. link Times cited: 47 Abstract: This paper deals with the effect of different size gold nano… read moreAbstract: This paper deals with the effect of different size gold nanoparticles on the fluidity of lipid membrane at different regions of the bilayer. To investigate this, we have considered significantly large bilayer leaflets and incorporated only one nanoparticle each time, which was subjected to all atomistic molecular dynamics simulations. We have observed that, lipid molecules located near to the gold nanoparticle interact directly with it, which results in deformation of lipid structure and slower dynamics of lipid molecules. However, lipid molecules far away from the interaction site of the nanoparticle get perturbed, which gives rise to increase in local ordering of the lipid domains and decrease in fluidity. The bilayer thickness and area per head group in this region also get altered. Similar trend, but with different magnitude is also observed when different size nanoparticle interact with the bilayer. read less USED (definite) S. Ju, H.-Y. Chen, and C. Shih, “Investigating mechanical properties of polymethylmethacrylate/silver nanoparticle composites by molecular dynamics simulation,” Journal of Nanoparticle Research. 2017. link Times cited: 41 USED (definite) “Effect of peptide length on the conjugation to the gold nanoparticle surface: a molecular dynamic study,” DARU Journal of Pharmaceutical Sciences. 2015. link Times cited: 0 USED (high confidence) Y. Noh and N. Aluru, “Ion transport in two-dimensional flexible nanoporous membranes.,” Nanoscale. 2023. link Times cited: 1 Abstract: Ion transport is a fundamental mechanism in living systems t… read moreAbstract: Ion transport is a fundamental mechanism in living systems that plays a role in cell proliferation, energy conversion, and maintaining homeostasis. This has inspired various nanofluidic applications such as electricity harvesting, molecular sensors, and molecular separation. Two dimensional (2D) nanoporous membranes are particularly promising for these applications due to their ultralow transport barriers. We investigated ion conduction across flexible 2D membranes via extensive molecular dynamics simulations. We found that the microscopic fluctuations of these membranes can significantly increase ion conductance, for example, by 320% in Cu-HAB with 0.5 M KCl. Our analysis of ion dynamics near the flexible membranes revealed that ion hydration is destabilized when the membrane fluctuated within a specific frequency range leading to improved ion conduction. Our results show that the dynamic coupling between the fluctuating membrane and ions can play a crucial role in ion conduction across 2D nanoporous membranes. read less USED (high confidence) R. Eschenbacher et al., “Thermal Stability and CO Permeability of [C4C1Pyr][NTf2]/Pd(111) Model SCILLs: from UHV to Ambient Pressure,” Topics in Catalysis. 2023. link Times cited: 1 USED (high confidence) H. Guo et al., “Non-reactive facet specific adsorption as a route to remediation of chlorinated organic contaminants,” Frontiers in Catalysis. 2023. link Times cited: 0 Abstract: The present work quantifies metal-contaminant interactions b… read moreAbstract: The present work quantifies metal-contaminant interactions between palladium substrates and three salient chlorinated organic contaminants, namely trichloroethylene 1,3,5-trichlorobenzene (TCB), and 3,3′,4,4′-tetrachlorobiphenyl (PCB77). Given that Pd is one of the conventional catalytically active materials known for contaminant removal, maximizing catalytic efficiency through optimal adsorption dynamics reduces the cost of remediation of contaminants that are persistent water pollutants chronically affecting public health. Adsorption efficiency analyses from all-atom molecular dynamics (MD) simulations advance the understanding of reaction mechanisms available from density functional theory (DFT) calculations to an extractable feature scale that can fit the parametric design of supported metal catalytic systems and feed into high throughput catalyst selection. Data on residence time, site-specific adsorption, binding energies, packing geometries, orientation profiles, and the effect of adsorbate size show the anomalous behaviour of organic contaminant adsorption on the undercoordinated {110} surface as compared to the {111} and {100} surfaces. The intermolecular interaction within contaminants from molecular dynamics simulation exhibits refreshing results than ordinary single molecule density functional theory calculation. Since complete adsorption and dechlorination is an essential step for chlorinated organic contaminant remediation pathways, the presented profiles provide essential information for designing efficient remediation systems through facet-controlled palladium nanoparticles. Graphical Abstract read less USED (high confidence) P. Kowalski et al., “Fundamentals of energy storage from first principles simulations: Challenges and opportunities,” Frontiers in Energy Research. 2023. link Times cited: 0 Abstract: Efficient electrochemical energy storage and conversion requ… read moreAbstract: Efficient electrochemical energy storage and conversion require high performance electrodes, electrolyte or catalyst materials. In this contribution we discuss the simulation-based effort made by Institute of Energy and Climate Research at Forschungszentrum Jülich (IEK-13) and partner institutions aimed at improvement of computational methodologies and providing molecular level understanding of energy materials. We focus on discussing correct computation of electronic structure, oxidation states and related redox reactions, phase transformation in doped oxides and challenges in computation of surface chemical reactions on oxides and metal surfaces in presence of electrolyte. Particularly, in the scope of this contribution we present new simulated data on Ni/Co and Am/U-bearing oxides, and Pb, Au and Ag metal surface materials. The computed results are combined with the available experimental data for thoughtful analysis of the computational methods performance. read less USED (high confidence) Q. Li et al., “Construction of Au/Cu hierarchically organized particles with dual-functional enzyme-like activity,” Science China Materials. 2023. link Times cited: 3 USED (high confidence) S. Moro et al., “The Effect of Glycol Side Chains on the Assembly and Microstructure of Conjugated Polymers,” ACS Nano. 2022. link Times cited: 6 Abstract: Conjugated polymers with glycol-based chains, are emerging a… read moreAbstract: Conjugated polymers with glycol-based chains, are emerging as a material class with promising applications as organic mixed ionic-electronic conductors, particularly in bioelectronics and thermoelectrics. However, little is still known about their microstructure and the role of the side chains in determining intermolecular interactions and polymer packing. Here, we use the combination of electrospray deposition and scanning tunneling microscopy to determine the microstructure of prototypical glycolated conjugated polymers (pgBTTT and p(g2T-TT)) with submonomer resolution. Molecular dynamics simulations of the same surface-adsorbed polymers exhibit an excellent agreement with the experimental images, allowing us to extend the characterization of the polymers to the atomic scale. Our results prove that, similarly to their alkylated counterparts, glycolated polymers assemble through interdigitation of their side chains, although significant differences are found in their conformation and interaction patterns. A model is proposed that identifies the driving force for the polymer assembly in the tendency of the side chains to adopt the conformation of their free analogues, i.e., polyethylene and polyethylene glycol, for alkyl or ethylene glycol side chains, respectively. For both classes of polymers, it is also demonstrated that the backbone conformation is determined to a higher degree by the interaction between the side chains rather than by the backbone torsional potential energy. The generalization of these findings from two-dimensional (2D) monolayers to three-dimensional thin films is discussed, together with the opportunity to use this type of 2D study to gain so far inaccessible, subnm-scale information on the microstructure of conjugated polymers. read less USED (high confidence) R. Cappabianca, P. D. Angelis, A. Cardellini, E. Chiavazzo, and P. Asinari, “Assembling Biocompatible Polymers on Gold Nanoparticles: Toward a Rational Design of Particle Shape by Molecular Dynamics,” ACS Omega. 2022. link Times cited: 4 Abstract: Gold nanoparticles (AuNPs) have received great attention in … read moreAbstract: Gold nanoparticles (AuNPs) have received great attention in a number of fields ranging from the energy sector to biomedical applications. As far as the latter is concerned, due to rapid renal clearance and a short lifetime in blood, AuNPs are often encapsulated in a poly(lactic-co-glycolic acid) (PLGA) matrix owing to its biocompatibility and biodegradability. A better understanding of the PLGA polymers on the AuNP surface is crucial to improve and optimize the above encapsulation process. In this study, we combine a number of computational approaches to explore the adsorption mechanisms of PLGA oligomers on a Au crystalline NP and to rationalize the PLGA coating process toward a more efficient design of the NP shape. Atomistic simulations supported by a recently developed unsupervised machine learning scheme show the temporal evolution and behavior of PLGA clusterization by tuning the oligomer concentration in aqueous solutions. Then, a detailed surface coverage analysis coupled with free energy landscape calculations sheds light on the anisotropic nature of PLGA adsorption onto the AuNP. Our results prove that the NP shape and topology may address and privilege specific sites of adsorption, such as the Au {1 1 1} crystal planes in selected NP samples. The modeling-based investigation suggested in this article offers a solid platform to guide the design of coated NPs. read less USED (high confidence) T. Miyata, Y. Kawagoe, T. Okabe, and H. Jinnai, “Morphologies of polymer chains adsorbed on inorganic nanoparticles in a polymer composite as revealed by atomic-resolution electron microscopy,” Polymer Journal. 2022. link Times cited: 2 USED (high confidence) I. Carrillo-Berdugo, J. Sampalo-Guzmán, R. Grau‐Crespo, D. Zorrilla, and J. Navas, “Interface chemistry effects in nanofluids: experimental and computational study of oil-based nanofluids with gold nanoplates,” Journal of Molecular Liquids. 2022. link Times cited: 1 USED (high confidence) Y. Liu et al., “Breaking the nanoparticle’s dispersible limit via rotatable surface ligands,” Nature Communications. 2022. link Times cited: 18 USED (high confidence) M. Kucherenko, “MODELING OF CONFORMATIONAL CHANGES OF POLYELECTROLYTES ON THE SURFACE OF A TRANSVERSELY POLARIZED METAL NANOWIRE IN AN EXTERNAL ELECTRIC FIELD,” Eurasian Physical Technical Journal. 2022. link Times cited: 0 Abstract: Gold nanowires with polyelectrolytes adsorbed on their surfa… read moreAbstract: Gold nanowires with polyelectrolytes adsorbed on their surface are widely used in various biomedical research. In this work, for the first time, conformationalchanges in polyelectrolytes on the surface of a gold nanowire transversely polarized in an external electric field were considered. The properties of a specially created analytical model of conformational rearrangements of a Gaussian macromolecular chain adsorbed on the surface of a cylindrical metal nanowire in an external electric field transverse to the axis of the nanowire were investigated. Conformational changes of uniformly charged polypeptides on the surface of a transversely polarized gold nanowire have been studied using molecular dynamics simulation. On the basis of the analytical model and the results of molecular dynamics simulation, the spatial distributions of the density of polyelectrolyte units on the surface of the nanowire were constructed. With an increase in the strength of the external electric field, an asymmetric stretching of the polyelectrolyte fringe in the direction of the dipole moment of the transversely polarized nanowire was observed. read less USED (high confidence) Y. Guo, C. Adessi, M. Cobian, and S. Merabia, “Atomistic simulation of phonon heat transport across metallic vacuum nanogaps,” Physical Review B. 2022. link Times cited: 11 Abstract: The understanding and modeling of the heat transport across … read moreAbstract: The understanding and modeling of the heat transport across nanometer and sub-nanometer gaps where the distinction between thermal radiation and conduction become blurred remains an open question. In this work, we present a three-dimensional atomistic simulation framework by combining the molecular dynamics (MD) and phonon nonequilibrium Green’s function (NEGF) methods. The relaxed atomic configuration and interaction force constants of metallic nanogaps are generated from MD as inputs into harmonic phonon NEGF. Phonon tunneling across gold-gold and copper-copper nanogaps is quantified, and is shown to be a significant heat transport channel below gap size of 1nm. We demonstrate that lattice anharmonicity contributes to within 20-30 % of phonon tunneling depending on gap size, whereas electrostatic interactions turn out to have negligible effect for the small bias voltage typically used in experimental measurements. This work provides detailed information of the heat current spectrum and interprets the recent experimental determination of thermal conductance across gold-gold nanogaps. Our study contributes to deeper insight into heat transport in the extremely near-field regime, as well as hints for the future experimental investigation. read less USED (high confidence) M. R. Brann, S. P. Hansknecht, X. Ma, and S. Sibener, “Differential Condensation of Methane Isotopologues Leading to Isotopic Enrichment under Non-equilibrium Gas–Surface Collision Conditions,” The Journal of Physical Chemistry. a. 2021. link Times cited: 2 Abstract: We examine the initial differential sticking probability of … read moreAbstract: We examine the initial differential sticking probability of CH4 and CD4 on CH4 and CD4 ices under nonequilibrium flow conditions using a combination of experimental methods and numerical simulations. The experimental methods include time-resolved in situ reflection–absorption infrared spectroscopy (RAIRS) for monitoring on-surface gaseous condensation and complementary King and Wells mass spectrometry techniques for monitoring sticking probabilities that provide confirmatory results via a second independent measurement method. Seeded supersonic beams are employed so that the entrained CH4 and CD4 have the same incident velocity but different kinetic energies and momenta. We found that as the incident velocity of CH4 and CD4 increases, the sticking probabilities for both molecules on a CH4 condensed film decrease systematically, but that preferential sticking and condensation occur for CD4. These observations differ when condensed CD4 is used as the target interface, indicating that the film’s phonon and rovibrational densities of states, and collisional energy transfer cross sections, have a role in differential energy accommodation between isotopically substituted incident species. Lastly, we employed a mixed incident supersonic beam composed of both CH4 and CD4 in a 3:1 ratio and measured the condensate composition as well as the sticking probability. When doing so, we see the same effect in the condensed mixed film, supporting an isotopic enrichment of the heavier isotope. We propose that enhanced multi-phonon interactions and inelastic cross sections between the incident CD4 projectile and the CH4 film allow for more efficacious gas–surface energy transfer. VENUS code MD simulations show the same sticking probability differences between isotopologues as observed in the gas–surface scattering experiments. Ongoing analyses of these trajectories will provide additional insights into energy and momentum transfer between the incident species and the interface. These results offer a new route for isotope enrichment via preferential condensation of heavier isotopes and isotopologues during gas–surface collisions under specifically selected substrate, gas-mixture, and incident velocity conditions. They also yield valuable insights into gaseous condensation under non-equilibrium conditions such as occur in aircraft flight in low-temperature environments. Moreover, these results can help to explain the increased abundance of deuterium in solar system planets and can be incorporated into astrophysical models of interstellar icy dust grain surface processes. read less USED (high confidence) M. L’opez-Su’arez, C. Melis, L. Colombo, and W. Tarantino, “Modeling charge transport in gold nanogranular films,” Physical Review Materials. 2021. link Times cited: 3 Abstract: Cluster-assembled metallic films show interesting electrical… read moreAbstract: Cluster-assembled metallic films show interesting electrical properties, both in the near-topercolation regime, when deposited clusters do not form a complete layer yet, and when the film thickness is well above the electrical percolation threshold. Correctly estimating their electrical conductivity is crucial, but, particularly for the latter regime, standard theoretical tools are not quite adequate. We therefore developed a procedure based on an atomically informed mesoscopic model in which ab-initio estimates of electronic transport at the nanoscale are used to reconstruct the conductivity of nanogranular gold films generated by molecular dynamics. An equivalent resistor network is developed, appropriately accounting for ballistic transport. The method is shown to correctly capture the non-monotonic behavior of the conductivity as a function of the film thickness, namely a signature feature of nanogranular films. read less USED (high confidence) S. D. Lecce, A. Kornyshev, M. Urbakh, and F. Bresme, “Structural effects in nanotribology of nanoscale films of ionic liquids confined between metallic surfaces.,” Physical chemistry chemical physics : PCCP. 2021. link Times cited: 3 Abstract: Room Temperature Ionic Liquids (RTILs) attract significant i… read moreAbstract: Room Temperature Ionic Liquids (RTILs) attract significant interest in nanotribology. However, their microscopic lubrication mechanism is still under debate. Here, using non-equilibrium molecular dynamics simulations, we investigate the lubrication performance of ultra-thin (<2 nm) films of [C2MIM]+ [NTf2]- confined between plane-parallel neutral surfaces of Au(111) or Au(100). We find that films consisting of tri-layers or bilayers, form ordered structures with a flat orientation of the imidazolium rings with respect to the gold surface plane. Tri-layers are unstable against loads >0.5 GPa, while bi-layers sustain pressures in the 1-2 GPa range. The compression of these films results in monolayers that can sustain loads of several GPa without significant loss in their lubrication performance. Surprisingly, in such ultra-thin films the imidazolium rings show higher orientational in-plane disorder, with and the rings adopting a tilted orientation with respect to the gold surface. The friction force and friction coefficient of the monolayers depends strongly on the structure of the gold plates, with the friction coefficient being four times higher for monolayers confined between Au(100) surfaces than for more compact Au(111) surfaces. We show that the general behaviour described here is independent of whether the metallic surfaces are modelled as polarizable or non-polarizable surfaces and speculate on the nature of this unexpected conclusion. read less USED (high confidence) A. Pecina et al., “On the Metal-Aided Catalytic Mechanism for Phosphodiester Bond Cleavage Performed by Nanozymes,” ACS Catalysis. 2021. link Times cited: 12 Abstract: Recent studies have shown that gold nanoparticles (AuNPs) fu… read moreAbstract: Recent studies have shown that gold nanoparticles (AuNPs) functionalized with Zn(II) complexes can cleave phosphate esters and nucleic acids. Remarkably, such synthetic nanonucleases appear to catalyze metal (Zn)-aided hydrolytic reactions of nucleic acids similar to metallonuclease enzymes. To clarify the reaction mechanism of these nanocatalysts, here we have comparatively analyzed two nanonucleases with a >10-fold difference in the catalytic efficiency for the hydrolysis of the 2-hydroxypropyl-4-nitrophenylphosphate (HPNP, a typical RNA model substrate). We have used microsecond-long atomistic simulations, integrated with NMR experiments, to investigate the structure and dynamics of the outer coating monolayer of these nanoparticles, either alone or in complex with HPNP, in solution. We show that the most efficient one is characterized by coating ligands that promote a well-organized monolayer structure, with the formation of solvated bimetallic catalytic sites. Importantly, we have found that these nanoparticles can mimic two-metal-ion enzymes for nucleic acid processing, with Zn ions that promote HPNP binding at the reaction center. Thus, the two-metal-ion-aided hydrolytic strategy of such nanonucleases helps in explaining their catalytic efficiency for substrate hydrolysis, in accordance with the experimental evidence. These mechanistic insights reinforce the parallelism between such functionalized AuNPs and proteins toward the rational design of more efficient catalysts. read less USED (high confidence) C. Schuschke et al., “A Molecular View of the Ionic Liquid Catalyst Interface of SCILLs: Coverage-Dependent Adsorption Motifs of [C4C1Pyr][NTf2] on Pd Single Crystals and Nanoparticles,” Journal of Physical Chemistry C. 2021. link Times cited: 6 USED (high confidence) X. Song, S. Wu, and R. Zhang, “Computational Study on Surface Bonding Based on Nanocone Arrays,” Nanomaterials. 2021. link Times cited: 3 Abstract: Surface bonding is an essential step in device manufacturing… read moreAbstract: Surface bonding is an essential step in device manufacturing and assembly, providing mechanical support, heat transfer, and electrical integration. Molecular dynamics simulations of surface bonding and debonding failure of copper nanocones are conducted to investigate the underlying adhesive mechanism of nanocones and the effects of separation distance, contact length, temperature, and size of the cones. It is found that van der Waals interactions and surface atom diffusion simultaneously contribute to bonding strength, and different adhesive mechanisms play a main role in different regimes. The results reveal that increasing contact length and decreasing separation distance can simultaneously contribute to increasing bonding strength. Furthermore, our simulations indicate that a higher temperature promotes diffusion across the interface so that subsequent cooling results in better adhesion when compared with cold bonding at the same lower temperature. It also reveals that maximum bonding strength was obtained when the cone angle was around 53°. These findings are useful in designing advanced metallic bonding processes at low temperatures and pressure with tenable performance. read less USED (high confidence) N. Kruchinin, “Molecular Dynamics Simulation of Uniformly Charged Polypeptides on the Surface of a Charged Metal Nanoparticle in an Alternating Electric Field,” Colloid Journal. 2021. link Times cited: 3 USED (high confidence) G. Zhou, L. Li, K. Peng, X. Wang, and Z. Yang, “Wettability Transition on Graphyne-Coated Au(111) Substrates with Different Pore Sizes: The Role of Interfacial Hydrogen Bonds,” Journal of Physical Chemistry C. 2021. link Times cited: 2 Abstract: The fabrication of solid surfaces with distinct wettability … read moreAbstract: The fabrication of solid surfaces with distinct wettability has critical implications in both science and technology. Recently, coatings have been widely employed to modulate the wettability of sol... read less USED (high confidence) S. Alfarano et al., “Stripping off of the Hydration Shells in the Double Layer Formation: Water Networks Matter,” ChemRxiv. 2021. link Times cited: 0 Abstract: The double layer at the solid/electrolyte interface is a key… read moreAbstract: The double layer at the solid/electrolyte interface is a key concept in electrochemistry. Here, we present an experimental study combined with simulations, which provides a molecular picture of the double-layer formation in operando processes. By THz spectroscopy we are able to follow the stripping off of the cation/anion hydration shells for a NaCl electrolyte at the Au surface when decreasing/increasing the bias potential. While Na+ is attracted toward the electrode already at the smallest applied negative potentials, stripping-off of the Cl- hydration shell is observed only at higher potential values. These phenomena are directly measured by in operando THz spectroscopy with ultra-bright synchrotron light as a source and rationalized by accompanying molecular-dynamics simulations and electronic-structure calculations. read less USED (high confidence) L. Li, A. Belcher, and D. Loke, “Simulating selective binding of a biological template to a nanoscale architecture: a core concept of a clamp-based binding-pocket-favored N-terminal-domain assembly.,” Nanoscale. 2020. link Times cited: 7 Abstract: The biological template and its mutants have vital significa… read moreAbstract: The biological template and its mutants have vital significance in next generation remediation, electrochemical, photovoltaic, catalytic, sensing and digital memory devices. However, a microscopic model describing the biotemplating process is generally lacking on account of modelling complexity, which has prevented widespread commercial use of biotemplates. Here, we demonstrate M13-biotemplating kinetics in atomic resolution by leveraging large-scale molecular dynamics (MD) simulations. The model reveals the assembly of gold nanoparticles on two experimentally-based M13 phage types using full M13-capsid structural models and with polarizable gold nanoparticles in explicit solvent. Both mechanistic and structural insights into the selective binding affinity of the M13 phage to gold nanoparticles are obtained based on a previously unconsidered clamp-based binding-pocket-favored N-terminal-domain assembly and also on surface-peptide flexibility. These results provide a deeper level of understanding of protein sequence-based affinity and open the route for genetically engineering a wide range of 3D electrodes for high-density low-cost device integration. read less USED (high confidence) A. Nemati, H. N. Pishkenari, A. Meghdari, and S. Ge, “Directional control of surface rolling molecules exploiting non-uniform heat-induced substrates.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 5 Abstract: Molecular machines, such as nanocars, have shown promising p… read moreAbstract: Molecular machines, such as nanocars, have shown promising potential for various tasks, including manipulation at the nanoscale. In this paper, we examined the influence of temperature gradients on nanocar and nanotruck motion as well as C60 - as their wheel - on a flat gold surface under various conditions. We also compared the accuracy and computational cost of two different approaches for generating the temperature gradient. The results show that severe vibrations and frequent impacts of gold atoms at high temperatures increase the average distance of C60 from the substrate, reducing its binding energy. Moreover, the temperature field drives C60 to move along the temperature variation; still, the diffusive motion of C60 remained unchanged in the direction perpendicular to the temperature gradient. Increasing the magnitude of the temperature gradient speeds up its motion parallel to the gradient, while raising the average temperature of the substrate increases the diffusion coefficient in all directions. The temperature field influences the nanocar motion in the same manner as C60. However, the nanocars have a substantially shorter motion range compared to C60. The relatively larger, heavier, and more flexible chassis of the nanocar makes it more sluggish than the nanotruck. In general, the motion of large and heavy surface rolling molecules is less affected by the temperature field compared to small and light molecules. The results of the study show that concentrated heat sources can be employed to push surface rolling molecules or break down their large clusters. We can exploit a temperature field as a driving force to push nanocars in a desired direction on prebuilt pathways. read less USED (high confidence) A. Serva, M. Salanne, M. Havenith, and S. Pezzotti, “Size dependence of hydrophobic hydration at electrified gold/water interfaces,” Proceedings of the National Academy of Sciences. 2020. link Times cited: 17 Abstract: Significance The optimization of “green” electrochemical pro… read moreAbstract: Significance The optimization of “green” electrochemical processes is one of the most important challenges in the transition toward renewable energy technologies. In many of these processes, including, e.g., CO2 and N2 reduction, small hydrophobic molecules are formed and react at the interface, and their hydration free energy modulates the associated thermodynamics. Here, we use molecular dynamics simulations to elucidate the mechanisms and energetics of hydrophobic hydration at an electrified gold/water interface. We propose an adaptation of the Lum–Chandler–Weeks theory that maps the changes in hydration free energies at the interface as a function of solute size and applied potential. Hydrophobic hydration at metal/water interfaces actively contributes to the energetics of electrochemical reactions, e.g. CO2 and N2 reduction, where small hydrophobic molecules are involved. In this work, constant applied potential molecular dynamics is employed to study hydrophobic hydration at a gold/water interface. We propose an adaptation of the Lum–Chandler–Weeks (LCW) theory to describe the free energy of hydrophobic hydration at the interface as a function of solute size and applied voltage. Based on this model we are able to predict the free energy cost of cavity formation at the interface directly from the free energy cost in the bulk plus an interface-dependent correction term. The interfacial water network contributes significantly to the free energy, yielding a preference for outer-sphere adsorption at the gold surface for ideal hydrophobes. We predict an accumulation of small hydrophobic solutes of sizes comparable to CO or N2, while the free energy cost to hydrate larger hydrophobes, above 2.5-Å radius, is shown to be greater at the interface than in the bulk. Interestingly, the transition from the volume dominated to the surface dominated regimes predicted by the LCW theory in the bulk is also found to take place for hydrophobes at the Au/water interface but occurs at smaller cavity radii. By applying the adapted LCW theory to a simple model addition reaction, we illustrate some implications of our findings for electrochemical reactions. read less USED (high confidence) K. Pivnic, F. Bresme, A. Kornyshev, and M. Urbakh, “Electrotunable Friction in Diluted Room Temperature Ionic Liquids: Implications for Nanotribology.” 2020. link Times cited: 12 Abstract: Using nonequilibrium molecular dynamics (NEMD) simulations, … read moreAbstract: Using nonequilibrium molecular dynamics (NEMD) simulations, we study the mechanism of electrotunable friction in the mixture of a room temperature ionic liquid (RTIL), BMIM PF6, and an organic solv... read less USED (high confidence) M. H. Dokoohaki, F. Mohammadpour, and A. R. Zolghadr, “New insight into electrosynthesis of ordered TiO2 nanotubes in EG-based electrolyte solutions: combined experimental and computational assessment.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 4 Abstract: To obtain a better understanding of TiO2 nanotube (TiO2-NT) … read moreAbstract: To obtain a better understanding of TiO2 nanotube (TiO2-NT) synthesis in different ethylene glycol (EG)-based electrolyte solutions by electrochemical anodization, the primary steps of TiO2-NT formation were studied by experimental techniques. In this regard, three different EG-based electrolyte solutions were used for anodic oxidation of titanium foil. The first electrolyte solution contains conventional ammonium fluoride (NH4F) dissolved in EG/water (98 : 2 v/v). In the second one, Ti foil anodization is performed in an electrolyte solution containing the 1-butyl-3-methyl-imidazolium tetrafluoroborate (Bmim-BF4) ionic liquid. Finally, the fluorine-containing species was replaced by the 1-butyl-3-methyl-imidazolium chloride (Bmim-Cl) ionic liquid. The results indicate that the TiO2-NTs did not form by anodization in the EG/H2O/Bmim-Cl electrolyte solution at 60 V. Interestingly, this electrolyte solution is less viscous than the fluorine-containing electrolyte solutions. In addition, we report a detailed study on the structural arrangement of electrolyte solution components near the solid surfaces using molecular dynamics (MD) simulation methods to reveal the factors governing the difference of the ionic species distribution. The MD results elucidate the role of the ionic constituents in the length of the nanotube arrays at a certain anodization condition. Furthermore, as reported herein for the first time, the lifetimes of ion-ion contacts and the interactions of ionic species with TiO2 walls have a substantial effect on the resulting nanotubes. These characteristics are analyzed by using radial distribution functions, density profiles, distance analysis, time correlation functions, and mean-square-displacements, complemented by DFT calculations. read less USED (high confidence) R. Tian, G. Hu, X. Ou, M. Luo, and J. Li, “Dynamic behaviors of interfacial water on the self-assembly monolayer (SAM) heterogeneous surface.,” The Journal of chemical physics. 2020. link Times cited: 3 Abstract: Dynamic behaviors of water molecules near the surface with m… read moreAbstract: Dynamic behaviors of water molecules near the surface with mixed hydrophobic and hydrophilic areas are studied by molecular dynamics simulation. More specifically, the diffusion coefficient and hydrogen bond lifetime of interfacial water on the self-assembly monolayer composed of hydrophobic and hydrophilic groups and their dependence on the mixing ratio are studied. The diffusion dramatically slows down, and the hydrogen bond lifetime considerably increases when a few hydrophilic groups are added to the hydrophobic surface. When the percentage of hydrophilic groups increases to 25%, the behavior of interfacial water is similar to the case of the pure hydrophilic surface. The sensitivity to the hydrophilic group can be attributed to the fact that the grafted hydrophilic groups can not only retard the directly bound water molecules but also affect indirectly bound water by stabilizing hydrogen bonds among interfacial water molecules. read less USED (high confidence) M. Izadyar, M. Rezaeian, and A. Victorov, “Theoretical study on the absorption of carbon dioxide by DBU-based ionic liquids.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 6 Abstract: In this article, 20 ns molecular dynamic (MD) simulations an… read moreAbstract: In this article, 20 ns molecular dynamic (MD) simulations and density functional theory (DFT) were used to investigate the absorption of CO2 molecules by some functionalized 1,8-diazabicyclo[5,4,0]-udec-7-ene (DBU)-based ILs. According to the MD results, the highest coordination number for NC is observed in the case of [DBUH+][Im-], which indicates that the functionalization of the imidazole anion by different alkyl groups decreases the interaction ability of the anion with CO2 molecules. The addition of water molecules to the ILs decreases the ability of the anion to interact with CO2 because of the hydrogen bond formation between the imidazole anions and water. Two different paths were proposed for CO2 absorption by the ILs, and the effect of alkyl groups on the kinetics and thermodynamics of the reaction was analyzed by using the M06-2X functional at the 6-311++G(d,p) level of theory in the gas phase and water. On the basis of the results, CO2 absorption is more favorable in [DBUH+][Im-], thermodynamically. Kinetic parameters show that the alkylation of the imidazole anion by ethyl, propyl, iso-propyl, and phenyl groups decreases the rate of CO2 absorption, because of the steric and electron-withdrawing effect of different alkyl groups. In the presence of water molecules, the lowest activation Gibbs energy is related to [DBUH+][Im-], which confirms the greater ability of this IL in CO2 absorption. read less USED (high confidence) Z. Li, V. G. Ruiz, M. Kanduč, and J. Dzubiella, “Ion-Specific Adsorption on Bare Gold (Au) Nanoparticles in Aqueous Solutions: Double-Layer Structure and Surface Potentials.,” Langmuir : the ACS journal of surfaces and colloids. 2020. link Times cited: 8 Abstract: We study the solvation and electrostatic properties of bare … read moreAbstract: We study the solvation and electrostatic properties of bare gold (Au) nanoparticles (NPs) of 1-2 nm in size in aqueous electrolyte solutions of sodium salts of various anions with large physicochemical diversity (Cl-, BF4-, PF6-, Nip- (nitrophenolate), 3- and 4-valent hexacyanoferrate (HCF)) using nonpolarizable, classical molecular dynamics computer simulations. We find a substantial facet selectivity in the adsorption structure and spatial distribution of the ions at the AuNPs: while sodium and some of the anions (e.g., Cl-, HCF3-) adsorb more at the "edgy" (100) and (110) facets of the NPs, where the water hydration structure is more disordered, other ions (e.g., BF4-, PF6-, Nip-) prefer to adsorb strongly on the extended and rather flat (111) facets. In particular, Nip-, which features an aromatic ring in its chemical structure, adsorbs strongly and perturbs the first water monolayer structure on the NP (111) facets substantially. Moreover, we calculate adsorptions, radially resolved electrostatic potentials as well as the far-field effective electrostatic surface charges and potentials by mapping the long-range decay of the calculated electrostatic potential distribution onto the standard Debye-Hückel form. We show how the extrapolation of these values to other ionic strengths can be performed by an analytical Adsorption-Grahame relation between the effective surface charge and potential. We find for all salts negative effective surface potentials in the range from -10 mV for NaCl down to about -80 mV for NaNip, consistent with typical experimental ranges for the zeta potential. We discuss how these values depend on the surface definition and compare them to the explicitly calculated electrostatic potentials near the NP surface, which are highly oscillatory in the ±0.5 V range. read less USED (high confidence) W. Zhou, S.-li Li, W. Lu, J. Zhu, and Y. Liu, “Molecular simulation of CH4 and CO2 adsorption in shale organic nanopores,” Molecular Simulation. 2020. link Times cited: 3 Abstract: ABSTRACT Using CO2 as an alternative working fluid to displa… read moreAbstract: ABSTRACT Using CO2 as an alternative working fluid to displace shale gas has been considered as a promising technology, which can not only enhance shale gas recovery but also geologically sequester CO2 in shale reservoirs. The adsorption behaviour of CH4 and CO2 in shale is the key to evaluate the efficiency of CH4 production and potential of CO2 sequestration. In the present work, the cylindrical and slit kerogen nanopores were constructed to represent the realistic organic nanopores existing in shale matrix. The adsorption behaviours of pure CH4 and CO2/CH4 mixture were investigated by employing the grand canonical Monte Carlo method. The results indicate that the adsorption capacities of CH4 in shale kerogen nanopores increase with the increment of pressure. However, temperature exhibits a negative impact on the gas adsorption capacity. The effects of pressure, temperature on competitive adsorption performances of CO2/CH4 mixture were discussed. It is found that the adsorption capacities of CO2 are significantly higher than that of CH4 at various pressure and temperature conditions. Both the adsorption capacity and selectivity should be taken into consideration to determine the proper conditions in the practical project. read less USED (high confidence) E. Zhu et al., “Enhancement of oxygen reduction reaction activity by grain boundaries in platinum nanostructures,” Nano Research. 2020. link Times cited: 16 USED (high confidence) K. Takahashi, H. Nakano, and H. Sato, “A polarizable molecular dynamics method for electrode-electrolyte interfacial electron transfer under the constant chemical-potential-difference condition on the electrode electrons.,” The Journal of chemical physics. 2020. link Times cited: 7 Abstract: Electron transfer (ET) at an electrode-electrolyte interface… read moreAbstract: Electron transfer (ET) at an electrode-electrolyte interface is a crucial step in electrochemical reactions. Computational simulations play an important role in unraveling the effects of the interfacial structure of the electrolyte solution and the applied voltage on the energetics and kinetics. In such simulations, it is important to know the chemical potentials of the electrons in the cathode and the anode and the nonequilibrium response of the interface to the abrupt change in the charge distribution in the system. We have developed a classical fully polarizable molecular dynamics method to deal with the interfacial nonadiabatic ET processes in which both the metal electrodes and the solvent molecules are electronically polarizable. The chemical potential of the electrons in each electrode is introduced based on the chemical potential equalization principle, and their difference between the cathode and the anode is kept equal to the applied voltage. We have investigated the effects of the electronic polarization of the solvent molecules on the interfacial structure of the electrolyte solution and the Marcus free energy curves. The effects are non-negligible for the accurate evaluation of the reorganization energies but become less significant as the redox species comes closer to the electrode surface, where the electronic polarization of the metal electrode plays a more dominant role. read less USED (high confidence) W. Ding et al., “Molecular dynamics study of anisotropic behaviours of water droplet on textured surfaces with various energies,” Molecular Physics. 2020. link Times cited: 12 Abstract: The anisotropic wetting behaviours of water droplets on six … read moreAbstract: The anisotropic wetting behaviours of water droplets on six surfaces with different solid–liquid interaction intensities are systemically investigated by molecular dynamics simulation. The six surfaces include Smooth, Square, Triangle, Sin, Sin-plus and Cylinder surfaces, and the interaction potentials between surface atoms and water molecules are adjusted to obtain various surface free energies. Moreover, the condensation process on those surfaces is investigated under a fixed solid-liquid interaction intensity. The wetting results indicate that surface energy plays an essential role in anisotropic wetting of the six surfaces. Moreover, under the fixed surface energy, the anisotropic wetting behaviours of water droplets are determined by the atom potential energy barrier and top area of solid substrate. The droplet on Square surface has most obvious anisotropic wetting behaviour because of its substantial atom potential energy barrier and large top area to support water droplet. In the condensation process, droplets nucleation, growth and coalescence processes are all visualised and quantitatively recorded, we find that texture creates lower atom potential energy on the surface and water molecules tend to nucleate on the area with low atom potential energy. Furthermore, the texture hinders the reunion of small clusters and consequently reduces the maximum cluster size. GRAPHICAL ABSTRACT read less USED (high confidence) H. Singh and S. Sharma, “Free energy profiles of adsorption of surfactant micelles at metal-water interfaces,” Molecular Simulation. 2020. link Times cited: 7 Abstract: ABSTRACT We have studied adsorption behaviour of cationic an… read moreAbstract: ABSTRACT We have studied adsorption behaviour of cationic and uncharged surfactant molecules and their micelles at metal-water interfaces via all-atom molecular dynamics (MD) simulations. Our simulations reveal that unaggregated surfactant molecules adsorb strongly on to the metal surface without any free energy barrier. The adsorption behaviour of micelles is quite different. Micelles of cationic surfactants experience a long-range free energy barrier to adsorption, which is attributed to the presence of a corona of counterions and hydration water around these micelles, which gets disturbed as the micelles approach the surface. Micelles of uncharged surfactants do not have a corona of counterions around them and therefore show a barrierless free energy profile of adsorption. The micelles of both cationic and uncharged surfactants strongly adsorb by disintegrating at the metal surface. In the disintegrated state, the molecules comprising the micelles re-arrange to attain either a lying down configuration in which the molecular axis is parallel to the surface or a standing up configuration in which the molecular axis is perpendicular to the surface. read less USED (high confidence) J. Qi et al., “Force-Activated Isomerization of a Single Molecule.,” Journal of the American Chemical Society. 2020. link Times cited: 10 Abstract: Understanding and controlling isomerization at single molecu… read moreAbstract: Understanding and controlling isomerization at single molecular level should provide new insight into molecular dynamics and design guidelines of functional devices. Scanning tunneling microscopy (STM) has been demonstrated to be a powerful tool to study isomerization of single molecules on substrate, by either electric field or inelastic electron tunneling mechanisms. Similar molecular isomerization process can in principle be induced by mechanical force, however relevant study has remained elusive. Here we demonstrate that isomerization of a N,N-dimethylamino-dianthryl-benzene molecule on Ag(100) can be mechanically driven by STM tip. The existence of out-of-plane dimethylamino group in the molecule is found to play a pivotal role in isomerization process by providing a steric hindrance effect for asymmetric interaction between the STM tip and molecule. This underlying mechanism is further confirmed by performing molecular dynamics simulations, showing agreement with experimental results. Our work opens up opportunity to manipulate molecular configuration based on mechanical force. read less USED (high confidence) S. Salassi, A. Cardellini, P. Asinari, R. Ferrando, and G. Rossi, “Water dynamics affects thermal transport at the surface of hydrophobic and hydrophilic irradiated nanoparticles,” Nanoscale Advances. 2020. link Times cited: 5 Abstract: Plasmonic nanoparticles, such as Au nanoparticles (NPs) coat… read moreAbstract: Plasmonic nanoparticles, such as Au nanoparticles (NPs) coated with bio-compatible ligands, are largely studied and tested in nanomedicine for photothermal therapies. Nevertheless, no clear physical interpretation is currently available to explain thermal transport at the nanoparticle surface, where a solid–liquid (core–ligand) interface is coupled to a liquid–liquid (ligand–solvent) interface. This lack of understanding makes it difficult to control the temperature increase imposed by the irradiated NPs to the surrounding biological environment, and it has so far hindered the rational design of the NP surface chemistry. Here, atomistic molecular dynamics simulations are used to show that thermal transport at the nanoparticle surface depends dramatically on solvent diffusivity at the ligand–solvent interface. Furthermore, using physical indicators of water confinement around hydrophobic and hydrophilic ligands, a predictive model is developed to allow the engineering of NP coatings with the desired thermal conductivities at the nanoscale. read less USED (high confidence) N. Kruchinin and M. Kucherenko, “Molecular-Dynamics Simulation of Rearrangements in the Conformational Structure of Polyampholytic Macromolecules on the Surface of a Polarized Metal Nanoparticle,” Colloid Journal. 2020. link Times cited: 5 USED (high confidence) N. Kruchinin and M. Kucherenko, “A Molecular Dynamics Simulation of Polyampholytic Polypeptides Associated with Atomic Clusters on the Surfaces of Metal-Like Nanoobjects,” Biophysics. 2020. link Times cited: 7 USED (high confidence) C.-H. Lin, S. Ju, J.-W. Su, and D.-E. Li, “Peptide Capping Agent Design for Gold (111) Facet by Molecular Simulation and Experimental Approaches,” Scientific Reports. 2020. link Times cited: 3 USED (high confidence) R. Rabani, G. Heidarinejad, J. Harting, and E. Shirani, “Effect of wall stiffness, mass and potential interaction strength on heat transfer characteristics of nanoscale-confined gas,” International Journal of Heat and Mass Transfer. 2020. link Times cited: 8 USED (high confidence) X. Wang, D. Venerus, I. Puri, and S. Murad, “On using the anisotropy in the thermal resistance of solid–fluid interfaces to more effectively cool nano-electronics,” Molecular Simulation. 2020. link Times cited: 1 Abstract: ABSTRACT As power-intensive electronic components are furthe… read moreAbstract: ABSTRACT As power-intensive electronic components are further miniaturised into nanodevices, their heat dissipation is a serious operational and safety concern. While nanochannels and nanofins are often used for facilitating heat dissipation, the liquid-solid interfaces that form (Kapitza resistance), become significant barriers to heat transfer. We demonstrate that the thermal resistance of these interfaces is strongly anisotropic. The resistance of an interface to heat transfer parallel to the interface (solid surface) is significantly smaller than the more well-known Kapitza resistance (associated with heat transfer across the interface – perpendicular to the solid surface) and is even lower than that of the bulk fluid. As a result, if devices are designed to dissipate heat parallel to an interface, heat dissipation can be significantly enhanced. Our studies are also able to explain the molecular basis of this observed anisotropy in interfacial resistance, which has hitherto remained unreported for solid–liquid interfaces. read less USED (high confidence) K. Pivnic, F. Bresme, A. Kornyshev, and M. Urbakh, “Structural Forces in Mixtures of Ionic Liquids with Organic Solvents.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 11 Abstract: Using molecular dynamics simulations, we study the impact of… read moreAbstract: Using molecular dynamics simulations, we study the impact of electrode charging and addition of solvent (acetonitrile, ACN) on structural forces of the BMIM PF6 ionic liquid (IL) confined by surfaces at nanometer separations. We establish microscopic relationships between the structural forces and the microscopic structure of the confined liquid. Depending on the structure of cations and anions across the nanofilm, the load-induced squeeze-out of liquid layers occurs via one layer or bilayer steps. The cations confined between charged plates orient with their aliphatic chain perpendicular to the surface planes, and link two adjacent IL layers. These structures facilitate the squeeze-out of single layers. For both pure IL and IL-ACN mixtures, we observe a strong dependence of nanofilm structure on the surface charge density, which affects the simulated pressure-displacement curves. Addition of solvent to the IL modifies the layering in the confined film. At high electrode charges and high dilution of IL (below 10% molar fraction) the layered structure of the nanofilm is less well defined. We predict a change in the squeeze-out mechanism under pressure, from a discontinuous squeeze-out (for high IL concentrations) to an almost continuous one (for low IL concentrations). Importantly, our simulations show that charged electrodes are coated with ions even at low IL concentrations. These ion rich layers adjacent to the charged plate surfaces are not squeezed-out even under very high normal pressures of ~5 GPa. Hence, we demonstrate the high performance of IL-solvent mixtures to protect surfaces from wear and to provide lubrication at high loads. read less USED (high confidence) S. Liu et al., “Different platinum crystal surfaces show very distinct protein denaturation capabilities.,” Nanoscale. 2019. link Times cited: 3 Abstract: Different platinum (Pt) surfaces of nanocrystals usually exh… read moreAbstract: Different platinum (Pt) surfaces of nanocrystals usually exhibit significant distinctions with regard to various biological, physical, and chemical characteristics, such as bio-recognition, surface wetting, and catalytic activities. In this study, we report for the first time that two shape-controlled Pt nanocrystals with the most common low-index surfaces, Pt(100) and Pt(111), show very dissimilar protein denaturation capabilities based on all-atom molecular dynamics simulations employing the widely used model protein, villin headpiece (HP35). We demonstrate that HP35 is well preserved on the Pt(100) crystal surface, whereas it is severely disrupted on the Pt(111) crystal surface. This surprising difference originates from the distinct water behavior in the first solvation shell (FSS) of the two Pt crystal surfaces. Within the FSS of the Pt(100) crystal surface, water molecules form a very compact and stable monolayer through a highly uniform rhombic hydrogen-bond network. This water monolayer prefers the adsorption of acidic residues (such as Glu and Asp) and acts as a shield to prevent other residues from directly coming into contact with the metal surface. On the other hand, the hydrogen bond network in the water monolayer in the FSS of the Pt(111) crystal surface is very sparse and quite defective, which makes it more vulnerable to the penetration of various residues, particularly those with planar side chains such as Phe, Trp and Arg due to strong dispersion interactions, leading to subsequent protein unfolding. The binding free energy calculations for some key amino acids on the two different crystal surfaces further uncover the molecular origin behind their distinct protein denaturation capability. Our study reveals the vital importance of interfacial water in determining the structure of proteins when binding to different metal crystal surfaces. The discovered molecular mechanisms may be helpful for the future development of a bio-assisted programmable synthetic strategy of sophisticated Pt nanostructures for biomedical applications. read less USED (high confidence) V. Rudyak and S. Krasnolutskii, “Simulation of Transport Coefficients of Aerosols and Nanofluids with Hollow Nanoparticles,” Atmospheric and Oceanic Optics. 2019. link Times cited: 1 USED (high confidence) E. Mervinetsky et al., “Direct Assembly and Metal-Ions Binding Properties of Oxytocin Monolayer on Gold Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 6 Abstract: Peptides are very common recognition entities which are usua… read moreAbstract: Peptides are very common recognition entities which are usually attached to surfaces using multistep processes. These processes require modification of the native peptides and of the substrates. Using functional groups in native peptides for their assembly on surfaces without affecting their biological activity can facilitate the preparation of biosensors. Herein we present a simple single-step formation of native oxytocin monolayer on gold surface. These surfaces were characterizations by atomic force spectroscopy, spectroscopic ellipsometry and x-ray photoelectron spectroscopy. We took advantage of the native disulfide bridge of the oxytocin for anchoring the peptide to the Au surface, while preserving the metal ion binding properties. Self-assembled oxytocin monolayer was used by electrochemical impedance spectroscopy for metal ion sensing leading to sub-nanomolar sensitivities for zinc or copper ions. read less USED (high confidence) T. Vasileiadis, “Ultrafast Energy Flow and Structural Changes in Nanoscale Heterostructures.” 2019. link Times cited: 0 Abstract: ............................................................… read moreAbstract: .......................................................................................................................... 9 Kurzfassung .................................................................................................................. 11 Chapter read less USED (high confidence) C. Qi, X. Lei, B. Zhou, C. Wang, and Y. Zheng, “Temperature regulation of the contact angle of water droplets on the solid surfaces.,” The Journal of chemical physics. 2019. link Times cited: 11 Abstract: We investigate theoretically the stability of the wetting pr… read moreAbstract: We investigate theoretically the stability of the wetting property, i.e., the contact angle values, as a function of the temperature. We find that the estimated temperature coefficient of the contact angle for the water droplets on an ordered water monolayer on a 100 surface of face-center cubic (FCC) is about one order of magnitude larger than that on a hydrophobic hexagonal surface in the temperature range between 290 K and 350 K, using molecular dynamics simulations. As temperature rises, the number of hydrogen bonds between the ordered water monolayer and the water droplet will increase, which therefore enhances the hydrophilicity of the ordered water monolayer at the FCC model surface. Our work thus provides an easily controllable and reversible way to control the degree of hydrophobicity of various solid surfaces exhibiting a similar wetting property of water droplets on the ordered water monolayer as such particular FCC (100) surfaces. read less USED (high confidence) J. Zhou et al., “Observing crystal nucleation in four dimensions using atomic electron tomography,” Nature. 2019. link Times cited: 198 USED (high confidence) M. Ehara and U. Priyakumar, “Gold-Palladium Nanocluster Catalysts for Homocoupling: Electronic Structure and Interface Dynamics.,” Chemical record. 2019. link Times cited: 10 Abstract: The gold-palladium (Au-Pd) bimetallic nanocluster (NC) catal… read moreAbstract: The gold-palladium (Au-Pd) bimetallic nanocluster (NC) catalyst in colloidal phase performs the homocoupling reaction of various aryl chlorides (Ar-Cl) under ambient conditions. We have systematically investigated various aspects of the Au-Pd NC catalysts with respect to this homocoupling reaction by using density functional theory (DFT) calculations, genetic algorithm (GA) approaches, and molecular dynamics (MD) simulations. Our findings include the geometric and electronic structures of the Au-Pd NC, the reactive Pd sites on the NC surface, the electron-donating effects of surrounding polymer matrix, the reaction mechanism of homocoupling reaction and rate-determining step, the inverse halogen dependence of the reaction, and the solvation dynamics at interface region between NC and polymer matrix in aqueous solution. read less USED (high confidence) N. Kruchinin and M. Kucherenko, “Molecular Dynamics Simulation of Electrically Induced Conformational Changes of Polyampholytic Polypeptides on Gold Nanoparticle Surface,” Colloid Journal. 2019. link Times cited: 9 USED (high confidence) B. A. Russell, K. Kubiak-Ossowska, Y. Chen, and P. Mulheran, “Critical role of tyrosine-20 in formation of gold nanoclusters within lysozyme: a molecular dynamics study.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 0 Abstract: Lysozyme is one of the most commonly used proteins for encap… read moreAbstract: Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20. read less USED (high confidence) Z. Gu et al., “Facet-regulated adhesion of double-stranded DNA on palladium surfaces.,” Nanoscale. 2019. link Times cited: 7 Abstract: A better understanding of interactions between metal-nanomat… read moreAbstract: A better understanding of interactions between metal-nanomaterial surfaces and biomolecules such as DNAs is critical for their biomedical applications. Here we investigated double-stranded DNA (dsDNA) adhering to palladium (Pd) nanosheets with two different exposed facets, {100} and {111}, using a combined computational and experimental approach. Different dsDNA binding modes on the two surfaces were observed, with a surprising "upright" conformation on Pd(100) and a "flat" conformation on Pd(111). Molecular dynamics simulations showed a stronger binding of the dsDNA on Pd(111) than Pd(100), which resulted in significant conformational changes and hydrogen bond breakage in the dsDNA on Pd(111). Further analyses revealed that the different binding strengths were caused by the number and arrangement of water molecules in the first solvation shell (FSS) of the two Pd surfaces. The water hydrogen bond network in the FSS of Pd(100) is compact and resists the embedding of dsDNA, while it is less compact on Pd(111), which allows penetration of dsDNA and its direct contact with Pd(111) surface atoms, thereby exhibiting stronger binding. Further free energy calculations with umbrella sampling supported these observations. Finally, these computational predictions on the adsorption capacity of dsDNA on Pd surfaces were confirmed by gel electrophoresis experiments. read less USED (high confidence) M. Nathanson, K. Kanhaiya, A. Pryor, J. Miao, and H. Heinz, “Atomic-Scale Structure and Stress Release Mechanism in Core-Shell Nanoparticles.,” ACS nano. 2018. link Times cited: 36 Abstract: Core-shell nanoparticles find applications in catalysts, sen… read moreAbstract: Core-shell nanoparticles find applications in catalysts, sensors, and theranostics. The full internal 3D atomic structure, however, cannot be resolved by current imaging and diffraction techniques. We analyzed the atomic positions and stress-release mechanism in a cubic Au-Pd core-shell nanoparticle in approximately 1000 times higher resolution than current experimental techniques using large-scale molecular dynamics simulation to overcome these limitations. The core-shell nanocube of 73 nm size was modeled similarly to solution synthesis by random epitaxial deposition of a 4 nm thick shell of Pd atoms onto a Au core of 65 nm side length using reliable interatomic potentials. The internal structure reveals specific deformations and stress relaxation mechanisms that are caused by the +4.8% lattice mismatch of gold relative to palladium and differential confinement of extended particle facets, edges, and corners by one, two, or three Au-Pd interfaces, respectively. The three-dimensional lattice strain causes long-range, arc-like bending of atomic rows along the faces and edges of the particle, especially near the Au-Pd interface, a bulging deformation of the Pd shell, and stacking faults in the Pd shell at the corners of the particle. The strain pattern and mechanism of stress release were further characterized by profiles of the atomic layer spacing in the principal crystallographic directions. Accordingly, strain in the Pd shell is several times larger in the extended facets than near the edges and corners of the nanoparticle, which likely affects adsorption, optical, and electrochemical properties. The findings are consistent with available experimental data, including 3D reconstructions of the same cubic nanoparticle by coherent diffractive imaging (CDI) and may be verified by more powerful experimental techniques in the future. The stress release mechanisms are representative for cubic core-shell nanoparticles with fcc structure and can be explored for different shapes by the same methods. read less USED (high confidence) L. Liu et al., “Effects of Solvent Molecules on the Interlayer Spacing of Graphene Oxide,” Transactions of Tianjin University. 2018. link Times cited: 11 USED (high confidence) L. Johnson et al., “Poling-induced birefringence in OEO materials under nanoscale confinement,” Organic Photonics + Electronics. 2018. link Times cited: 7 Abstract: Standard models for evaluating the electro-optic (EO) respon… read moreAbstract: Standard models for evaluating the electro-optic (EO) response of organic materials typically assume that the refractive index of the material in the absence of a RF modulation field is isotropic and homogeneous. Such assumptions work very well for low-concentration guest-host materials in bulk devices. However, current generation organic EO materials at high densities and under nanoscale confinement can show sufficient birefringence to affect device performance. We use computer simulations and spectroscopic experiments to characterize and predict changes in the index of refraction under poling. We also demonstrate that poling-induced birefringence can lead to a non-linear relationship between the apparent EO coefficient and poling field strength. read less USED (high confidence) L. Liao, C. Meng, and C. Huang, “Molecular Dynamics Simulations on the Tensile Deformation and Failure of a Polyethylene/Copper Interface,” Volume 4: 23rd Design for Manufacturing and the Life Cycle Conference; 12th International Conference on Micro- and Nanosystems. 2018. link Times cited: 0 Abstract: In this study, a microscale interface consisting of amorphou… read moreAbstract: In this study, a microscale interface consisting of amorphous polyethylene (PE) chains with the united-atom (UA) model and face-centered cubic (FCC) crystal copper as the substrate was established. Moving the copper layer with a given rate, the damage evolution of the interface during the tensile deformation was examined by molecular dynamics (MD) simulations. The stress-strain relationship was obtained to capture the evolution of tensile deformation. The distribution of the temperature field was adopted to predict the damage initiation and the failure mode. The phase diagram of the failure mode with respect to the thickness of the PE layer and the loading rate was provided. The results show that the PE layer with smaller thickness brings higher load-bearing capacity with larger yield strength. As for the rate-dependence, a rate-hardening followed by a rate-softening of yield strength was observed. In addition, the failure modes evolves from cohesive failure to interfacial one as the loading rate of tension increases progressively. It can be assumed that the control parameter on the failure mode changes from pure material strength of PE to the bonding strength between PE and copper. Furthermore, a larger thickness of PE layer leads to the cohesive failure with higher probability under a narrow range of loading rate with small values. However, the thickness-dependence of failure mode attenuates gradually and diminishes ultimately under higher loading rate, which leads to the transformation from mixed mode to interfacial one. read less USED (high confidence) A. F. Ferreira, M. Comune, A. Rai, L. Ferreira, and P. Simões, “Atomistic-Level Investigation of a LL37-Conjugated Gold Nanoparticle By Well-Tempered Metadynamics.,” The journal of physical chemistry. B. 2018. link Times cited: 9 Abstract: LL37 is a cathelicidin-derived antimicrobial peptide (AMP) w… read moreAbstract: LL37 is a cathelicidin-derived antimicrobial peptide (AMP) with a broad spectrum of antimicrobial activity and wound-healing potential. The enhancement of these characteristics was recently demonstrated for a cysteine (CYS)-modified cathelicidin-derived LL37-SH conjugated with gold nanoparticles (AuNPs). Considering the potential of this peptide, we hereby report a computational study in which well-tempered metadynamics was applied to unveil the interaction of LL37-SH and LL37 with a AuNP with atomistic detail. A structural analysis combined with the free energy surface (FES) characterization allowed the assessment of the role of CYS residue during the formation of the conjugate, as well as to understand how the AuNP improves the antimicrobial activity of the peptide. It was found that CYS promotes a lower conformational entropy (before and after adsorption onto the AuNP) and a faster adsorption process when compared to the LL37 without CYS. The FES for LL37-SH is characterized by one global minimum, while for LL37 a potential metastable state was found. The presence of the AuNP leads to an elongation of the peptides along with the adsorption, which translates into the increase of the solvent-accessible surface area. This elongation combined with the greater availability of positively charged residues upon adsorption rationalizes the observed enhancement of the activity of the LL37-SH/AuNP conjugate. read less USED (high confidence) G. Colherinhas, T. Malaspina, and E. Fileti, “Storing Energy in Biodegradable Electrochemical Supercapacitors,” ACS Omega. 2018. link Times cited: 39 Abstract: The development of green and biodegradable electrical compon… read moreAbstract: The development of green and biodegradable electrical components is one of the main fronts of research to overcome the growing ecological problem related to the issue of electronic waste. At the same time, such devices are highly desirable in biomedical applications such as integrated bioelectronics, for which biocompatibility is also required. Supercapacitors for storage of electrochemical energy, designed only with biodegradable organic matter would contemplate both aspects, that is, they would be ecologically harmless after their service lifetime and would be an important component for applications in biomedical engineering. By means of atomistic simulations of molecular dynamics, we propose a supercapacitor whose electrodes are formed exclusively by self-organizing peptides and whose electrolyte is a green amino acid ionic liquid. Our results indicate that this supercapacitor has a high potential for energy storage with superior performance than conventional supercapacitors. In particular its capacity to store energy was estimated to be almost 20 times greater than an analogue one of planar metallic electrodes. read less USED (high confidence) A. Nemati, A. Meghdari, H. N. Pishkenari, and S. Sohrabpour, “Investigation into thermally activated migration of fullerene-based nanocars,” Scientia Iranica. 2018. link Times cited: 11 Abstract: The rotational and translational motion of nanocars and nano… read moreAbstract: The rotational and translational motion of nanocars and nanotrucks as well as their motion regimes at different temperatures are investigated. In recent years, few similar types of molecular machines have been simulated. In contrast to previous studies which have used the Rigid-Body Molecular Dynamics (RB MD) method, an all-atom model and classic atomistic dynamics have been employed in this paper to achieve better accuracy. Our results demonstrated that the flexibility of the chassis and its attachment to the gold surface play important roles in the motion of a nanocar. In fact, a heavier and more flexible nanocar chassis reduces its speed compared to a nanotruck. In addition, simulations results are compared with available data from experimental studies done in recent years, and an acceptable agreement between the simulation results and experiments was observed. It was found that both molecules have three different regimes of motion, and the translational and rotational motion are not correlated. Results of this paper increase the knowledge and understanding of thermally-driven fullerene-based nanocars, and can be used to help design nanomachines with high controllability and maneuverability. read less USED (high confidence) D. Muñoz-Gacitúa et al., “Molecular dynamics characterization of silver colloidal interfaces for SERS applications. Gallic acid test,” Journal of Raman Spectroscopy. 2018. link Times cited: 1 Abstract: Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDE… read moreAbstract: Fondo Nacional de Desarrollo Cientifico y Tecnologico (FONDECYT)
1150138
Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT)
212832 read less USED (high confidence) G. Fang et al., “Differential Pd-nanocrystal facets demonstrate distinct antibacterial activity against Gram-positive and Gram-negative bacteria,” Nature Communications. 2018. link Times cited: 345 USED (high confidence) Q. Shao and C. Hall, “Selectivity of Glycine for Facets on Gold Nanoparticles.,” The journal of physical chemistry. B. 2017. link Times cited: 12 Abstract: The performance of nanoparticles in medical applications dep… read moreAbstract: The performance of nanoparticles in medical applications depends on their interactions with various molecules. Despite extensive research on this subject, it remains unclear where on an inhomogeneous nanoparticle molecules prefer to adsorb. Here we investigate the selectivity of glycine molecules for facets on five bare gold nanoparticles with diameters from 1.0 to 5.0 nm. Well-tempered metadynamics simulations are conducted to calculate the adsorption free-energy landscapes of a glycine molecule on various locations for the five gold nanoparticles in explicit water. We also calculate the glycine molecule's adsorption free energies on the five gold nanoparticles in vacuum and on three flat gold surfaces as a reference. The simulation results show that glycine molecules prefer to adsorb on the (110) facet for the 1.0 and 2.0 nm nanoparticles, the edges for the 3.0 nm nanoparticle, and the (111) facet for the 4.0 and 5.0 nm nanoparticles in water. The effect of water solvent on the selectivity is investigated through comparing the adsorption free-energy landscapes for glycine molecules on the nanoparticles in water and in vacuum. The area of the facet plays a key role in determining the selectivity of glycine molecules for the different facets, especially the shift of the selectivity as the nanoparticle diameter changes. Our simulations suggest that nanoparticle size and shape can be engineered to control the preferred adsorption location of molecules. read less USED (high confidence) A. Ruzanov et al., “On the thickness of the double layer in ionic liquids.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 31 Abstract: In this study, we examined the thickness of the electrical d… read moreAbstract: In this study, we examined the thickness of the electrical double layer (EDL) in ionic liquids using density functional theory (DFT) calculations and molecular dynamics (MD) simulations. We focused on BF4- anion adsorption from the 1-ethyl-3-methylimidazolium tetrafluoroborate (EMImBF4) ionic liquid on the Au(111) surface. At both DFT and MD levels, we evaluated the capacitance-potential dependence for the Helmholtz model of the interface. Using MD simulations, we also explored a more realistic, multilayer EDL model accounting for the ion layering. Concurrent analysis of the DFT and MD results provides a ground for thinking whether the electrical double layer in ionic liquids is one- or multi-ionic-layer thick. read less USED (high confidence) A. Berg, C. Peter, and K. Johnston, “Evaluation and Optimization of Interface Force Fields for Water on Gold Surfaces.,” Journal of chemical theory and computation. 2017. link Times cited: 27 Abstract: The structure and dynamics of water at gold surfaces are imp… read moreAbstract: The structure and dynamics of water at gold surfaces are important for a variety of applications, including lab on a chip and electrowetting. Classical molecular dynamics (MD) simulations are frequently used to investigate systems with water-gold interfaces, such as biomacromolecules in gold nanoparticle dispersions, but the accuracy of the simulations depends on the suitability of the force field. Density functional theory (DFT) calculations of a water molecule on gold were used as a benchmark to assess force field accuracy. It was found that Lennard-Jones potentials did not reproduce the DFT water-gold configurational energy landscape, whereas the softer Morse and Buckingham potentials allowed for a more accurate representation. MD simulations with different force fields exhibited rather different structural and dynamic properties of water on a gold surface. This emphasizes the need for experimental data and further effort on the validation of a realistic force field for water-gold interactions. read less USED (high confidence) X. Qi and K. Fichthorn, “Theory of the thermodynamic influence of solution-phase additives in shape-controlled nanocrystal synthesis.,” Nanoscale. 2017. link Times cited: 14 Abstract: Though many experimental studies have documented that certai… read moreAbstract: Though many experimental studies have documented that certain solution-phase additives can play a key role in the shape-selective synthesis of metal nanocrystals, the origins and mechanisms of this shape selectivity are still unclear. One possible role of such molecules is to thermodynamically induce the equilibrium shape of a nanocrystal by altering the interfacial free energies of the facets. Using a multi-scheme thermodynamic integration method that we recently developed [J. Chem. Phys., 2016, 145, 194108], we calculate the solid-liquid interfacial free energies γsl and investigate the propensity to achieve equilibrium shapes in such syntheses. We first apply this method to Ag(100) and Ag(111) facets in ethylene glycol solution containing polyvinylpyrrolidone (PVP), to mimic the environment in polyol synthesis of Ag nanocrystals. We find that although PVP has a preferred binding to Ag(100), its selectivity is not sufficient to induce a thermodynamic preference for {100}-faceted nanocubes, as has been observed experimentally. This indicates that PVP promotes Ag nanocube formation kinetically rather than thermodynamically. We further quantify the thermodynamic influence of adsorbed solution-phase additives for generic molecules, by building a γsl ratio/nanocrystal shape map as a function of zero-temperature binding energies. This map can be used to gauge the efficacy of candidate additive molecules for producing targeted thermodynamic nanocrystal shapes. The results indicate that only additives with a strong facet selectivity can impart significant thermodynamic-shape change. Therefore, many of the nanocrystals observed in experiments are likely kinetic products. read less USED (high confidence) F. Tavanti, A. Pedone, P. Matteini, and M. Menziani, “Computational Insight into the Interaction of Cytochrome C with Wet and PVP-Coated Ag Surfaces.,” The journal of physical chemistry. B. 2017. link Times cited: 18 Abstract: In this work, the adsorption of cytochrome C (CytC) on wet {… read moreAbstract: In this work, the adsorption of cytochrome C (CytC) on wet {100}, {111}, {110}, and {120} silver surfaces has been investigated by computational simulations. The effect of polyvinylpyrrolidone (PVP) coating has also been studied. The main results obtained can be summarized as follow: (a) CytC strongly interacts with wet bare high index facets, while the adsorption over the {100} surface is disfavored due to the strong water structuring at the surface; (b) a nonselective protein adsorption mechanism is highlighted; (c) the native structure of CytC is well preserved during adsorption; (d) the heme group of CytC is never found to interact directly with the surface; (e) the interactions with the PVP-capped {100} surface is weak and specific. These results can be exploited to better control biological responses at engineered nanosurface, allowing the development of improved diagnostic tools. read less USED (high confidence) M.-H. Wang, Y. Xie, and Y. Chen, “Thermal transport in twisted few-layer graphene,” Chinese Physics B. 2017. link Times cited: 16 Abstract: Twisted graphene possesses unique electronic properties and … read moreAbstract: Twisted graphene possesses unique electronic properties and applications, which have been studied extensively. Recently, the phonon properties of twisted graphene have received a great deal of attention. To the best of our knowledge, thermal transports in twisted graphene have been investigated little to date. Here, we study perpendicular and parallel transports in twisted few-layer graphene (T-FLG). It is found that perpendicular and parallel transports are both sensitive to the rotation angle θ between layers. When θ increases from 0° to 60°, perpendicular thermal conductivity κ ⊥ first decreases and then increases, and the transition angle is θ = 30°. For the parallel transport, the relation between thermal conductivity κ || and θ is complicated, because intra-layer thermal transport is more sensitive to the edge of layer than their stacking forms. However, the dependence of interlayer scattering on θ is similar to that of κ ⊥. In addition, the effect of layer number on the thermal transport is discussed. Our results may provide references for designing the devices of thermal insulation and thermal management based on graphene. read less USED (high confidence) M. Fitzner, L. Joly, M. Ma, G. Sosso, A. Zen, and A. Michaelides, “Communication: Truncated non-bonded potentials can yield unphysical behavior in molecular dynamics simulations of interfaces.,” The Journal of chemical physics. 2017. link Times cited: 14 Abstract: Non-bonded potentials are included in most force fields and … read moreAbstract: Non-bonded potentials are included in most force fields and therefore widely used in classical molecular dynamics simulations of materials and interfacial phenomena. It is commonplace to truncate these potentials for computational efficiency based on the assumption that errors are negligible for reasonable cutoffs or compensated for by adjusting other interaction parameters. Arising from a metadynamics study of the wetting transition of water on a solid substrate, we find that the influence of the cutoff is unexpectedly strong and can change the character of the wetting transition from continuous to first order by creating artificial metastable wetting states. Common cutoff corrections such as the use of a force switching function, a shifted potential, or a shifted force do not avoid this. Such a qualitative difference urges caution and suggests that using truncated non-bonded potentials can induce unphysical behavior that cannot be fully accounted for by adjusting other interaction parameters. read less USED (high confidence) X. Zhang and A. A. Gray-Weale, “Local hydrodynamics of solvent near diffusing dendrimers: A test of the new Stokes–Einstein relation,” Journal of Polymer Science Part B. 2017. link Times cited: 1 Abstract: We have reported a new Stokes–Einstein relation (SER) for si… read moreAbstract: We have reported a new Stokes–Einstein relation (SER) for size determination and tested it by different nanoparticles. We assumed that the breakdown for SER results from local increases in viscosity. Here we investigate hydrodynamics of solvent near dendrimers to further test generality of our new theory. We discuss simulations of dendrimers in comparison to nanoparticles, experimental data on dendrimers from literature, and our theory. Local viscosity and local diffusivity of solvent near dendrimers are estimated by persistence times and exchange times, respectively. We find that the local dynamics of solvent near dendrimers of low density stay almost the same as that of bulk solvent. While the motions of solvent particles slow down near dendrimers of high density. This is similar with changes in local dynamics of solvent near nanoparticles. According to the causes we proposed for the deviation of SER, this is consistent with our findings that the SER works for the dendrimers of low density, while it fails for the dendrimers of high density. The new SER is then tested to predict size of the dendrimers accurately. Taking this together with the results for the nanoparticles, we believe that the new theory is general. © 2017 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2017, 55, 1380–1392 read less USED (high confidence) G. Benetti et al., “Bottom-Up Mechanical Nanometrology of Granular Ag Nanoparticles Thin Films,” Journal of Physical Chemistry C. 2017. link Times cited: 33 Abstract: Ultrathin metal nanoparticles coatings, synthesized by gas-p… read moreAbstract: Ultrathin metal nanoparticles coatings, synthesized by gas-phase deposition, are emerging as go-to materials in a variety of fields ranging from pathogens control and sensing to energy storage. Predicting their morphology and mechanical properties beyond a trial-and-error approach is a crucial issue limiting their exploitation in real-life applications. The morphology and mechanical properties of Ag nanoparticle ultrathin films, synthesized by supersonic cluster beam deposition, are here assessed adopting a bottom-up, multitechnique approach. A virtual film model is proposed merging high resolution scanning transmission electron microscopy, supersonic cluster beam dynamics, and molecular dynamics simulations. The model is validated against mechanical nanometrology measurements and is readily extendable to metals other than Ag. The virtual film is shown to be a flexible and reliable predictive tool to access morphology-dependent properties such as mesoscale gas-dynamics and elasticity of ultrathin films sy... read less USED (high confidence) V. R. Ardham and F. Leroy, “Thermodynamics of atomistic and coarse-grained models of water on nonpolar surfaces.,” The Journal of chemical physics. 2017. link Times cited: 11 Abstract: In order to study the phenomena where interfaces play a domi… read moreAbstract: In order to study the phenomena where interfaces play a dominant role through molecular simulations, the proper representation of the interfacial thermodynamic properties of a given model is of crucial importance. The use of coarse-grained rather than atomistic models makes it possible to simulate interfacial systems with larger time and length scales. In the present work, we compare the structure and thermodynamic behavior of one atomistic and two single-site coarse-grained models of water on nonpolar surfaces, namely, graphite and the basal plane of molybdenum disulfide. The three models interact with the surfaces through Lennard-Jones potentials parametrized to reproduce recent experimental contact angle measurements. The models form a layered structure close to the surface, which is usually observed on sufficiently attractive nonpolar substrates. However, differences in the structure and thermodynamic behavior are observed between the models. These differences are explained by certain features of the water models, such as short range tetrahedral order and liquid density fluctuations. Besides these results, the approach employed in the present study may be used to assess the ability of coarse-grained models for solid-liquid systems to represent consistent interfacial thermodynamics. read less USED (high confidence) L. Riccardi et al., “Nanoparticle-Based Receptors Mimic Protein-Ligand Recognition,” Chem. 2017. link Times cited: 65 USED (high confidence) H. Lu, Y. Yimer, R. Berger, M. Bonn, J. Pfaendtner, and T. Weidner, “Thiolated Lysine‐Leucine Peptides Self‐Assemble into Biosilica Nucleation Pits on Gold Surfaces,” Advanced Materials Interfaces. 2017. link Times cited: 3 Abstract: Nanostructured silica architectures have led to many applica… read moreAbstract: Nanostructured silica architectures have led to many applications in electronic and optical devices, and catalysis. Recently, bioinspired approaches based on peptide‐assisted silica fabrication have attracted great attention because of low production cost and mild, sustainable fabrication methods. Herein it is demonstrated that biomimetic peptides can also exert control over silica mineralization when bounded to inorganic surfaces. The amphiphilic α‐helical peptide LKα14 (Ac‐LKKLLKLLKKLLKLC‐OH) is used, which is based on leucine and lysine and has been a model system for surface studies and mineralization in solution for several years. LKα14 has been anchored to gold surfaces via terminal cysteine groups as linkers. Using X‐ray photoelectron spectroscopy, vibrational sum frequency generation spectroscopy, scanning force microscopy, and molecular dynamic simulations, it is found that LKα14 peptides assemble into laterally ordered structures with ≈5 nm wide cavities which serve as effective nucleating sites for silica nanoparticles. read less USED (high confidence) A. Kyrychenko, D. A. Pasko, and O. Kalugin, “Poly(vinyl alcohol) as a water protecting agent for silver nanoparticles: the role of polymer size and structure.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 80 Abstract: Chemical modification of silver nanoparticles (AgNPs) with a… read moreAbstract: Chemical modification of silver nanoparticles (AgNPs) with a stabilizing agent, such as poly(vinyl alcohol) (PVA), plays an important role in shape-controlled seeded-growth and colloidal stability. However, theoretical aspects of the stabilizing mechanism of PVA are still poorly understood. To gain a better understanding of the role of PVA in water protecting effects for silver nanoparticles, we developed an atomistic model of a AgNP grafted with single-chain PVA of various lengths. Our model, designed for classical molecular dynamics (MD) simulations, approximates the AgNP as a quasi-spherical silver nanocrystal with 3.9 nm diameter and uses a united-atom representation for PVA with its polymer chain length varying from 220 up to 1540 repeating units. We found that PVA adsorbs onto the AgNP surface through multiple non-covalent interactions, among which non-covalent bonding of the hydroxyl groups plays a key role. The analysis of adsorption isotherms by using the Hill, Scatchard, and McGhee & von Hippel models exhibits evidence for positive binding cooperativity with the cooperativity parameter varying from 1.55 to 2.12. Our results indicate that the size of the PVA polymer rather than its structure plays a crucial role in providing water protecting effects for the AgNP core, varying from 40% up to 91%. The water-protecting efficiency was well approximated by the Langmuir-Freundlich equation, allowing us to predict that the saturated coverage of the nanoparticle of a given diameter of 3.9 nm should occur when the PVA molecular weight approaches 115 kDa, which corresponds to the number of vinyl alcohol monomers being equal to 3100 units. read less USED (high confidence) H. Zhao, J. Liu, Q. Ran, Y. Yang, and X. Shu, “Effect of methyl groups on conformational properties of small ionized comb-like polyelectrolytes at the atomic level,” Journal of Molecular Modeling. 2017. link Times cited: 3 USED (high confidence) W. Heni et al., “Nonlinearities of organic electro-optic materials in nanoscale slots and implications for the optimum modulator design.,” Optics express. 2017. link Times cited: 96 Abstract: The performance of highly nonlinear organic electro-optic (E… read moreAbstract: The performance of highly nonlinear organic electro-optic (EO) materials incorporated into nanoscale slots is examined. It is shown that EO coefficients as large as 190 pm/V can be obtained in 150 nm wide plasmonic slot waveguides but that the coefficients decrease for narrower slots. Possible mechanism that lead to such a decrease are discussed. Monte-Carlo computer simulations are performed, confirming that chromophore-surface interactions are one important factor influencing the EO coefficient in narrow plasmonic slots. These highly nonlinear materials are of particular interest for applications in optical modulators. However, in modulators the key parameters are the voltage-length product UπL and the insertion loss rather than the linear EO coefficients. We show record-low voltage-length products of 70 Vµm and 50 Vµm for slot widths in the order of 50 nm for the materials JRD1 and DLD164, respectively. This is because the nonlinear interaction is enhanced in narrow slot and thereby compensates for the reduced EO coefficient. Likewise, it is found that lowest insertion losses are observed for slot widths in the range 60 to 100 nm. read less USED (high confidence) A. S. Tascini, J. Armstrong, E. Chiavazzo, M. Fasano, P. Asinari, and F. Bresme, “Thermal transport across nanoparticle-fluid interfaces: the interplay of interfacial curvature and nanoparticle-fluid interactions.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 42 Abstract: We investigate the general dependence of the thermal transpo… read moreAbstract: We investigate the general dependence of the thermal transport across nanoparticle-fluid interfaces using molecular dynamics computations. We show that the thermal conductance depends strongly both on the wetting characteristics of the nanoparticle-fluid interface and on the nanoparticle size. Strong nanoparticle-fluid interactions, leading to full wetting states in the host fluid, result in high thermal conductances and efficient interfacial transport of heat. Weak interactions result in partial drying or full drying states, and low thermal conductances. The variation of the thermal conductance with particle size is found to depend on the fluid-nanoparticle interactions. Strong interactions coupled with large interfacial curvatures lead to optimum interfacial heat transport. This complex dependence can be modelled using an equation that includes the interfacial curvature as a parameter. In this way, we rationalise the existing experimental and computer simulation results and show that the thermal transport across nanoscale interfaces is determined by the correlations of both interfacial curvature and nanoparticle-fluid interactions. read less USED (high confidence) G. Yang, B. Liang, Q. Zhu, Y. Hu, and X. Ye, “Comprehensive Study of the Effects of Nanopore Structures on Enzyme Activity for the Enzyme Based Electrochemical Biosensors Based on Molecular Simulation.,” The journal of physical chemistry. A. 2016. link Times cited: 2 Abstract: Assembly of biocompatible nanostructures to retain the enzym… read moreAbstract: Assembly of biocompatible nanostructures to retain the enzyme activity and improve the biocatalytic ability is a decisive factor for enhancing the performance of enzyme biosensors. However, there is still a lack of molecular level understandings of the physicochemical interaction mechanism at the interface of biosensor electrodes and enzymes. Here, for the first time at molecular level, the effects of two classic biosensor electrode materials with different electrical properties and morphologies and glucose oxidase (GOD) on retaining the enzyme conformation were analyzed by molecular dynamics simulation. First, for the immobilization of GOD, the interfaces of zinc oxide (ZnO) with different electrical properties and 10 nm diameter ZnO nanopore were studied. Then, to simulate the sensing process when electric voltages are applied, positively charged gold planes and 10 nm diameter gold nanopore were investigated as well. The results showed that the nanopore structure was confirmed to be well adapted for the enzyme conformation retaining compared to the plane structure for both ZnO and gold materials, and they almost fit well with the sensitivity measurement results from many previously reported experimental studies. This study also indicates that molecular modeling of the interactions between biomolecules and functional nanostructures is helpful for developing high performance enzyme nanobiosensors. read less USED (high confidence) V. Rudyak and S. Krasnolutskii, “Simulation of nanoparticle thermal diffusion in dense gases and fluids by the molecular dynamics method,” Atmospheric and Oceanic Optics. 2016. link Times cited: 1 USED (high confidence) A. Mhashal and S. Roy, “Free Energy of Bare and Capped Gold Nanoparticles Permeating through a Lipid Bilayer.,” Chemphyschem : a European journal of chemical physics and physical chemistry. 2016. link Times cited: 7 Abstract: Herein, we study the permeation free energy of bare and octa… read moreAbstract: Herein, we study the permeation free energy of bare and octane-thiol-capped gold nanoparticles (AuNPs) translocating through a lipid membrane. To investigate this, we have pulled the bare and capped AuNPs from bulk water to the membrane interior and estimated the free energy cost. The adsorption of the bare AuNP on the bilayer surface is energetically favorable but further loading inside it requires energy. However, the estimated free-energy barrier for loading the capped AuNP into the lipid membrane is much higher compared to bare AuNP. We also demonstrate the details of the permeation process of bare and capped AuNPs. Bare AuNP induces the curvature in the lipid membrane whereas capped AuNP creates an opening in the interacting monolayer and get inserted into the membrane. The insertion of capped AuNP induces a partial unzipping of the lipid bilayer, which results in the ordering of the local lipids interacting with the nanoparticle. However, bare AuNP disrupts the lipid membrane by pushing the lipid molecules inside the membrane. We also analyze pore formation due to the insertion of capped AuNP into the membrane, which results in water molecules penetrating the hydrophobic region. read less USED (high confidence) V. Rudyak and S. Krasnolutskii, “Simulation of nanoparticle thermal diffusion in dense gases and fluids by the molecular dynamics method,” Atmospheric and Oceanic Optics. 2016. link Times cited: 0 USED (high confidence) T. Li, W. Wu, and H. Li, “Coalescence behavior of liquid immiscible metal drops in two-wall confinement.,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 19 Abstract: Molecular dynamics (MD) simulations are performed to investi… read moreAbstract: Molecular dynamics (MD) simulations are performed to investigate the coalescence of the liquid Al and Pb drops in the graphene (G) walls and pillared-graphene (PG) walls. The confining walls can affect the coalescence dynamics of two adjacent films by restricting the movement of one of the metal drops; however, the coalescence behavior is different in the G-walls and the PG-walls. Two un-contacted films can still merge into one bigger drop because of the restricting effect of the walls, in which the movement of the Pb drop plays a predominant role. The coalescence time decreases with the decrease of the confining space. Our findings demonstrate that the coalescence dynamics can be controlled by tuning the confining space or wall surface. read less USED (high confidence) Q. Zhang et al., “pH-induced conformational changes of comb-like polycarboxylate investigated by experiment and simulation,” Colloid and Polymer Science. 2016. link Times cited: 26 USED (high confidence) B. D. Ventura et al., “Simple and Flexible Model for Laser-Driven Antibody-Gold Surface Interactions: Functionalization and Sensing.,” ACS applied materials & interfaces. 2016. link Times cited: 5 Abstract: Interactions between biomolecules and between substrates and… read moreAbstract: Interactions between biomolecules and between substrates and biomolecules is a crucial issue in physics and applications to topics such as biotechnology and organic electronics. The efficiency of bio- and mechanical sensors, of organic electronics systems, and of a number of other devices critically depends on how molecules are deposited on a surface so that these acquire specific functions. Here, we tackle this vast problem by developing a coarse grained model of biomolecules having a recognition function, such as antibodies, capable to quantitatively describe in a simple manner essential phenomena: antigen-antibody and antibody substrate interactions. The model is experimentally tested to reproduce the results of a benchmark case, such as (1) gold surface functionalization with antibodies and (2) antibody-antigen immune-recognition function. The agreement between experiments and model prediction is excellent, thus unveiling the mechanism for antibody immobilization onto metals at the nanoscale in various functionalization schemes. These results shed light on the geometrical packing properties of the deposited molecules, and may open the way to a novel coarse-grained based approach to describe other processes where molecular packing is a key issue with applications in a huge number of fields from nano- to biosciences. read less USED (high confidence) A. F. Ferreira, A. Rai, L. Ferreira, and P. Simões, “Findings on the interaction of the antimicrobial peptide cecropin-melittin with a gold surface from molecular dynamics studies,” European Biophysics Journal. 2016. link Times cited: 6 USED (high confidence) A. Gupta, B. Boekfa, H. Sakurai, M. Ehara, and U. Priyakumar, “Structure, Interaction, and Dynamics of Au/Pd Bimetallic Nanoalloys Dispersed in Aqueous Ethylpyrrolidone, a Monomeric Moiety of Polyvinylpyrrolidone,” Journal of Physical Chemistry C. 2016. link Times cited: 25 Abstract: Bimetallic nanoparticles (NPs) have been shown to exhibit ce… read moreAbstract: Bimetallic nanoparticles (NPs) have been shown to exhibit certain advantages over pure NPs in catalysis due to a synergistic effect. It is common to disperse NPs in a polymer matrix such as polyvinylpyrrolidone (PVP) to prevent flocculation, which imparts considerable electronic effects on the NPs. In the present study, the interactions between aqueous solutions of N-ethylpyrrolidone (EP, system chosen to model the monomeric form of PVP) and Au/Pd bimetallic NPs, which are relevant in catalysis, have been investigated using molecular dynamics simulations and density functional theory (DFT) method. The adequacy of the force fields used was assessed based on their ability to reproduce the structures and adsorption energies obtained using DFT calculations. The interactions of NPs with the environment were studied at various concentrations of aqueous solutions of EP to examine the strength of NP–EP and NP–water interactions. Free energy calculations and local mole fraction enhancement values show that that th... read less USED (high confidence) V. Velachi, D. Bhandary, J. Singh, and M. Cordeiro, “Striped gold nanoparticles: New insights from molecular dynamics simulations.,” The Journal of chemical physics. 2016. link Times cited: 11 Abstract: Recent simulations have improved our knowledge of the molecu… read moreAbstract: Recent simulations have improved our knowledge of the molecular-level structure and hydration properties of mixed self-assembled monolayers (SAMs) with equal and unequal alkyl thiols at three different arrangements, namely, random, patchy, and Janus. In our previous work [V. Vasumathi et al., J. Phys. Chem. C 119, 3199-3209 (2015)], we showed that the bending of longer thiols over shorter ones clearly depends on the thiols' arrangements and chemical nature of their terminal groups. In addition, such a thiol bending revealed to have a strong impact on the structural and hydration properties of SAMs coated on gold nanoparticles (AuNPs). In this paper, we extend our previous atomistic simulation study to investigate the bending of longer thiols by increasing the stripe thickness of mixed SAMs of equal and unequal lengths coated on AuNPs. We study also the effect of stripe thickness on the structural morphology and hydration of the coated SAMs. Our results show that the structural and hydration properties of SAMs are affected by the stripe thickness for mixtures of alkyl thiols with unequal chain length but not for equal length. Hence, the stability of the stripe configuration depends on the alkyl's chain length, the length difference between the thiol mixtures, and solvent properties. read less USED (high confidence) S. M. Lavasani, H. N. Pishkenari, and A. Meghdari, “Mechanism of 1,12-Dicarba-closo-dodecaborane Mobility on Gold Substrate as a Nanocar Wheel,” Journal of Physical Chemistry C. 2016. link Times cited: 15 Abstract: We studied the mobility of p-carborane on a gold surface by … read moreAbstract: We studied the mobility of p-carborane on a gold surface by analyzing the potential energy surfaces (PES) and simulating the motion of p-carborane using the classical molecular dynamics (MD) method. In the first section, we calculated the PES of p-carborane molecules on a gold surface during pure translation (sliding) and pure rotation independently and then employed this PES to predict the probable motion of p-carborane. These calculations were performed in several major orientations during sliding as well as different fixed positions during rotational movements to enable us to find the p-carborane motion threshold on a gold surface. In the second section, we use classical MD in isothermal conditions to specify the regime of motion of p-carborane at different temperatures. We found that by raising the temperature, three different regimes of motion may be observed: jumps to adjacent cells, long jumps, and continuous motion. To better understand the change of motion regime of p-carborane on the gold surfac... read less USED (high confidence) V. Rudyak, “Molecular dynamics simulation of pressure isotherms for nanofluids,” Colloid Journal. 2016. link Times cited: 2 USED (high confidence) T. Wei, H. Ma, and A. Nakano, “Decaheme Cytochrome MtrF Adsorption and Electron Transfer on Gold Surface.,” The journal of physical chemistry letters. 2016. link Times cited: 17 Abstract: Emergent electrical properties of multiheme cytochromes have… read moreAbstract: Emergent electrical properties of multiheme cytochromes have promising applications. We performed hybrid simulations (molecular dynamics, free energy computation, and kinetic Monte Carlo) to study decaheme cytochrome, MtrF adsorption on an Au (111) surface in water and the electron transfer (ET) efficiency. Our results reveal that the gold surface's dehydration serves as a crucial driving force for protein adsorption due to large surface tension. The most possible adsorption orientation is with the ET terminal (heme5) approaching the gold surface, which yields a pathway for ET between the substrate and the aqueous environment. Upon adsorption, protein's secondary structures and central domains (II and IV) bonded with heme-residues remain relatively stable. MtrF surface mobility is dictated by thiol-gold interaction and strong binding between Au(111) and peptide aromatic groups. ET transfer rate across protein heme-network along the solvent-to-surface direction is slightly larger than that of the reverse direction, but lower than that of the solvation structure. read less USED (high confidence) H.-L. Chen et al., “Investigation on the Structural and Thermal Behaviors of Poly(amidoamine) Dendrimer-Encapsulated Au Nanoparticles of Different Sizes,” Industrial & Engineering Chemistry Research. 2015. link Times cited: 3 Abstract: The dynamical and thermal behaviors of Au nanoparticle (AuNP… read moreAbstract: The dynamical and thermal behaviors of Au nanoparticle (AuNP) and fourth generation poly(amidoamine) dendrimer (G4 PAMAM) of the dendrimer-encapsulated Au nanoparticle system under the dry environment were investigated by the molecular dynamics (MD) simulation. The consistent valence force field (CVFF) was used to describe the interaction of the G4 PAMAM dendrimer and the interaction between the dendrimer and the AuNP. The many-body tight-binding potential was adopted to describe the atomic interaction between the Au atoms of an AuNP. Three AuNPs, Au116, Au201, and Au405, with the diameters of 1.45, 1.8, and 2.3 nm were concerned, respectively. Au116 and Au201 are nearly completely covered by G4 PAMAM dendrimer, but the branching chains of the dendrimer are no longer able to wrap around the Au405.The conformation of G4 PAMAM dendrimer still possesses its unique spherical structure after encapsulating the AuNP, and the irregularity of the outer surface decreases as the size of the AuNP increases. For the t... read less USED (high confidence) A. A. Zeifman, F. Novikov, V. Stroylov, O. Stroganov, I. Svitanko, and G. Chilov, “An explicit account of solvation is essential for modeling Suzuki-Miyaura coupling in protic solvents.,” Dalton transactions. 2015. link Times cited: 3 Abstract: We compared explicit and implicit solvation approaches in mo… read moreAbstract: We compared explicit and implicit solvation approaches in modeling the free energy profile of the final step of Suzuki-Miyaura coupling. Both approaches produced similar ΔG(≠) in all the studied solvents (benzene, toluene, DMF, ethanol, and water). Solvation free energies of individual reaction components reasonably correlated for explicit and implicit models in aprotic solvents (RMSE = 30-50 kJ mol(-1), R(2) > 0.71). However for ethanol and water the correlation was poor. We attributed this difference to the formation of the PdH-O hydrogen bond with Pd(PPh3)2 which was surprisingly observed in explicit modeling. Further QM calculations of the Pd(PPh3)2-H2O system confirmed the direction (PdH) and stability of this bonding. Therefore we stress the need for considering explicit solvation for modeling Pd-catalyzed reactions in protic solvents. read less USED (high confidence) W. Xu, Z. Lan, B. Peng, R. Wen, and X. Ma, “Effect of surface free energies on the heterogeneous nucleation of water droplet: a molecular dynamics simulation approach.,” The Journal of chemical physics. 2015. link Times cited: 79 Abstract: Heterogeneous nucleation of water droplet on surfaces with d… read moreAbstract: Heterogeneous nucleation of water droplet on surfaces with different solid-liquid interaction intensities is investigated by molecular dynamics simulation. The interaction potentials between surface atoms and vapor molecules are adjusted to obtain various surface free energies, and the nucleation process and wetting state of nuclei on surfaces are investigated. The results indicate that near-constant contact angles are already established for nano-scale nuclei on various surfaces, with the contact angle decreasing with solid-liquid interaction intensities linearly. Meanwhile, noticeable fluctuation of vapor-liquid interfaces can be observed for the nuclei that deposited on surfaces, which is caused by the asymmetric forces from vapor molecules. The formation and growth rate of nuclei are increasing with the solid-liquid interaction intensities. For low energy surface, the attraction of surface atoms to water molecules is comparably weak, and the pre-existing clusters can depart from the surface and enter into the bulk vapor phase. The distribution of clusters within the bulk vapor phase becomes competitive as compared with that absorbed on surface. For moderate energy surfaces, heterogeneous nucleation predominates and the formation of clusters within bulk vapor phase is suppressed. The effect of high energy particles that embedded in low energy surface is also discussed under the same simulation system. The nucleation preferably initiates on the high energy particles, and the clusters that formed on the heterogeneous particles are trapped around their original positions instead of migrating around as that observed on smooth surfaces. This feature makes it possible for the heterogeneous particles to act as fixed nucleation sites, and simulation results also suggest that the number of nuclei increases monotonously with the number of high energy particles. The growth of nuclei on high energy particles can be divided into three sub-stages, beginning with the formation of a wet-spot, increase of contact angle with near-constant contact line, and finally growth with constant contact angle. The growth rate of nuclei also increases with the size of high energy particles. read less USED (high confidence) S. Förster et al., “Polymer adsorption on reconstructed Au(001): a statistical description of P3HT by scanning tunneling microscopy and coarse-grained Monte Carlo simulations.,” The Journal of chemical physics. 2014. link Times cited: 19 Abstract: We report on a combined theoretical and experimental charact… read moreAbstract: We report on a combined theoretical and experimental characterization of isolated Poly(3-hexylthiophene) (P3HT) chains weakly adsorbed on a reconstructed Au(001) surface. The local chain conformations of in situ deposited P3HT molecules were investigated by means of scanning tunneling microscopy. For comparison, Monte Carlo simulations of the system were performed up to a maximum chain length of 60 monomer units. The dependence of the end-to-end distance and the radius of gyration on the polymer chain length shows a good agreement between experiment and Monte Carlo simulations using simple updates for short chains. read less USED (high confidence) K. Gkionis, J. T. Obodo, C. Cucinotta, S. Sanvito, and U. Schwingenschlögl, “Molecular dynamics investigation of carbon nanotube junctions in non-aqueous solutions,” Journal of Materials Chemistry. 2014. link Times cited: 2 Abstract: The properties of liquids in a confined environment are know… read moreAbstract: The properties of liquids in a confined environment are known to differ from those in the bulk. Extending this knowledge to geometries defined by two metallic layers in contact with the ends of a carbon nanotube is important for describing a large class of nanodevices that operate in non-aqueous environments. Here we report a series of classical molecular dynamics simulations for gold-electrode junctions in acetone, cyclohexane and N,N-dimethylformamide solutions and analyze the structure and the dynamics of the solvents in different regions of the nanojunction. The presence of the nanotube has little effect on the ordering of the solvents along its axis, while in the transversal direction deviations are observed. Importantly, the orientational dynamics of the solvents at the electrode–nanotube interface differ dramatically from that found when only the electrodes are present. read less USED (high confidence) K. Tong, X. Song, S.-ying Sun, Y. Xu, and J. Yu, “Molecular dynamics study of linear and comb-like polyelectrolytes in aqueous solution: effect of Ca2+ ions,” Molecular Physics. 2014. link Times cited: 25 Abstract: All-atom molecular dynamics simulations were employed to pro… read moreAbstract: All-atom molecular dynamics simulations were employed to provide microscopic mechanism for the salt tolerance of polyelectrolytes dispersants. The conformational variation of polyelectrolytes and interactions between COO− groups and counterions/water molecules were also studied via radius of gyration and pair correlations functions. Sodium polyacrylate (NaPA) and sodium salts of poly(acrylic acid)–poly(ethylene oxide) (NaPA–PEO) were selected as the representative linear and comb-like polyelectrolyte, respectively. The results show that Ca2+ ions interact with COO− groups much stronger than Na+ ions and can bring ion-bridging interaction between intermolecular COO− groups in the NaPA systems. While in the NaPA–PEO systems, the introduced PEO side chains can prevent backbone chains from ion-bridging interactions and weaken the conformational changes. The present results can help in selecting and designing new-type efficient polyelectrolyte dispersants with good salt tolerance. read less USED (high confidence) E. Paek, A. Pak, and G. Hwang, “Large capacitance enhancement induced by metal-doping in graphene-based supercapacitors: a first-principles-based assessment.,” ACS applied materials & interfaces. 2014. link Times cited: 37 Abstract: Chemically doped graphene-based materials have recently been… read moreAbstract: Chemically doped graphene-based materials have recently been explored as a means to improve the performance of supercapacitors. In this work, we investigate the effects of 3d transition metals bound to vacancy sites in graphene with [BMIM][PF6] ionic liquid on the interfacial capacitance; these results are compared to the pristine graphene case with particular attention to the relative contributions of the quantum and electric double layer capacitances. Our study highlights that the presence of metal-vacancy complexes significantly increases the availability of electronic states near the charge neutrality point, thereby enhancing the quantum capacitance drastically. In addition, the use of metal-doped graphene electrodes is found to only marginally influence the microstructure and capacitance of the electric double layer. Our findings indicate that metal-doping of graphene-like electrodes can be a promising route toward increasing the interfacial capacitance of electrochemical double layer capacitors, primarily by enhancing the quantum capacitance. read less USED (high confidence) F. Ramezani, M. Amanlou, and H. Rafii-Tabar, “Gold nanoparticle shape effects on human serum albumin corona interface: a molecular dynamic study,” Journal of Nanoparticle Research. 2014. link Times cited: 28 USED (high confidence) J. Liu, C. Wang, P. Guo, G. Shi, and H. Fang, “Linear relationship between water wetting behavior and microscopic interactions of super-hydrophilic surfaces.,” The Journal of chemical physics. 2013. link Times cited: 10 Abstract: Using molecular dynamics simulations, we show a fine linear … read moreAbstract: Using molecular dynamics simulations, we show a fine linear relationship between surface energies and microscopic Lennard-Jones parameters of super-hydrophilic surfaces. The linear slope of the super-hydrophilic surfaces is consistent with the linear slope of the super-hydrophobic, hydrophobic, and hydrophilic surfaces where stable water droplets can stand, indicating that there is a universal linear behavior of the surface energies with the water-surface van der Waals interaction that extends from the super-hydrophobic to super-hydrophilic surfaces. Moreover, we find that the linear relationship exists for various substrate types, and the linear slopes of these different types of substrates are dependent on the surface atom density, i.e., higher surface atom densities correspond to larger linear slopes. These results enrich our understanding of water behavior on solid surfaces, especially the water wetting behaviors on uncharged super-hydrophilic metal surfaces. read less USED (high confidence) V. Petkov, Y. Lee, S. Sun, and Y. Ren, “Noncrystallographic Atomic Arrangement Driven Enhancement of the Catalytic Activity of Au Nanoparticles,” Journal of Physical Chemistry C. 2012. link Times cited: 8 Abstract: Determining the atomic-scale structure of nanosized particle… read moreAbstract: Determining the atomic-scale structure of nanosized particles remains a challenge and crucial goal for today’s science and technology. We investigate the atomic-scale structure of 3–8 nm Au particles obtained by a fast solution reaction and find it to be of a noncrystallographic icosahedral type, in particular, close to the particles’ surface. This noncrystallographic structure may well explain the previously observed but poorly understood enhancement of the particles’ catalytic properties. Our finding demonstrates that together with size the structure type of nanosized particles can be used as a tunable parameter for achieving improved functionality. read less USED (high confidence) E. J. Campos et al., “The role of Lys147 in the interaction between MPSA-gold nanoparticles and the α-hemolysin nanopore.,” Langmuir : the ACS journal of surfaces and colloids. 2012. link Times cited: 18 Abstract: Single channel recordings were used to determine the effect … read moreAbstract: Single channel recordings were used to determine the effect of direct electrostatic interactions between sulfonate-coated gold nanoparticles and the constriction of the Staphylococcus aureus α-hemolysin protein channel on the ionic current amplitude. We provide evidence that Lys147 of α-hemolysin can interact with the sulfonate groups at the nanoparticle surface, and these interactions can reversibly block 100% of the residual ionic current. Lys147 is normally involved in a salt bridge with Glu111. The capture of a nanoparticle leads to a partial current block at neutral pH values, but protonation of Glu111 at pH 2.8 results in a full current block when the nanoparticle is captured. At pH 2.8, we suggest that Lys147 is free to engage in electrostatic interactions with sulfonates at the nanoparticle surface. To verify our results, we engineered a mutation in the α-hemolysin protein, where Glu111 is substituted by Ala (E111A), thus removing Glu111-Lys147 interactions and facilitating Lys147-sulfonate electrostatic interactions. This mutation leads to a 100% current block at pH 2.8 and a 92% block at pH 8.0, showing that electrostatic interactions are formed between the nanopore and the nanoparticle surface. Besides demonstrating the effect of electrostatic interactions on cross channel ionic current, this work offers a novel approach to controlling open and closed states of the α-hemolysin nanopore as a function of external gears. read less USED (high confidence) H. Kim, B. Smit, and J. Jang, “Monte Carlo Study on the Water Meniscus Condensation and Capillary Force in Atomic Force Microscopy,” Journal of Physical Chemistry C. 2012. link Times cited: 42 Abstract: The water meniscus condensed between a nanoscale tip and an … read moreAbstract: The water meniscus condensed between a nanoscale tip and an atomically flat gold surface was examined under humid conditions using grand canonical Monte Carlo simulations. The molecular structure of the meniscus was investigated with particular focus on its width and stability. The capillary force due to the meniscus showed a dampened oscillation with increasing separation between the tip and surface because of the formation and destruction of water layers. The layering of water between the tip and the surface was different from that of the water confined between two plates. The humidity dependence of the capillary force exhibited a crossover behavior with increasing humidity, which is in agreement with the typical atomic force microscopy experiment on a hydrophilic surface. read less USED (high confidence) R. Nadler and J. Sanz, “Effect of dispersion correction on the Au(1 1 1)-H2O interface: a first-principles study.,” The Journal of chemical physics. 2012. link Times cited: 48 Abstract: A theoretical study of the H(2)O-Au(1 1 1) interface based o… read moreAbstract: A theoretical study of the H(2)O-Au(1 1 1) interface based on first principles density functional theory (DFT) calculations with and without inclusion of dispersion correction is reported. Three different computational approaches are considered. First, the standard generalized gradient approximation (GGA) functional PBE is employed. Second, an additional energy term is further included that adds a semi-empirically derived dispersion correction (PBE-D2), and, finally, a recently proposed functional that includes van der Waals (vdW) interactions directly in its functional form (optB86b-vdW) was used to represent the state-of-the art of DFT functionals. The monomeric water adsorption was first considered in order to explore the dependency of geometry on the details of the model slab used to represent it (size, thickness, coverage). When the dispersion corrections are included the Au-H(2)O interaction is stronger, as manifested by the smaller d(Au-O) and stronger adsorption energies. Additionally, the interfacial region between Au(1 1 1) slab surfaces and a liquid water layer was investigated with Born-Oppenheimer molecular dynamics (BOMD) using the same functionals. Two or three interfacial orientations can be determined, depending on the theoretical methodology applied. Closest to the surface, H(2)O is adsorbed O-down, whereas further away it is oriented with one OH bond pointing to the surface and the molecular plane parallel to the normal direction. For the optB86b-vdW functional a third orientation is found where one H atom points into the bulk water layer and the second OH bond is oriented parallel to the metal surface. As for the water density in the first adsorption layer we find a very small increase of roughly 8%. From the analysis of vibrational spectra a weakening of the H-bond network is observed upon the inclusion of the Au(1 1 1) slab, however, no disruption of H-bonds is observed. While the PBE and PBE-D2 spectra are very similar, the optB86b-vdW spectrum shows that the H-bonds are even more weakened. read less USED (high confidence) J. Saiz-Poseu et al., “Self-assembly of a catechol-based macrocycle at the liquid-solid interface: experiments and molecular dynamics simulations.,” Physical chemistry chemical physics : PCCP. 2012. link Times cited: 15 Abstract: This combined experimental (STM, XPS) and molecular dynamics… read moreAbstract: This combined experimental (STM, XPS) and molecular dynamics simulation study highlights the complex and subtle interplay of solvent effects and surface interactions on the 2-D self-assembly pattern of a Schiff-base macrocycle containing catechol moieties at the liquid-solid interface. STM imaging reveals a hexagonal ordering of the macrocycles at the n-tetradecane/Au(111) interface, compatible with a desorption of the lateral chains of the macrocycle. Interestingly, all the triangular-shaped macrocycles are oriented in the same direction, avoiding a close-packed structure. XPS experiments indicate the presence of a strong macrocycle-surface interaction. Also, MD simulations reveal substantial solvent effects. In particular, we find that co-adsorption of solvent molecules with the macrocycles induces desorption of lateral chains, and the solvent molecules act as spacers stabilizing the open self-assembly pattern. read less USED (high confidence) X. Aparicio-Anglès, P. Miró, A. Clotet, C. Bo, and J. Poblet, “Polyoxometalates adsorbed on metallic surfaces: immediate reduction of [SiW12O40]4− on Ag(100),” Chemical Science. 2012. link Times cited: 31 Abstract: Heterogenization of polyoxometalate clusters by means of ads… read moreAbstract: Heterogenization of polyoxometalate clusters by means of adsorption on surfaces is a necessary step prior to their use in heterogeneous catalysis and other applications. Herein, we introduce a general strategy to model the adsorption of polyoxometalates on surfaces, by combining periodic DFT calculations with classical molecular dynamics simulations so as to include the effects of counterions and solvent molecules. The specific case that we discuss here is the spontaneous reduction of the archetypal α-[SiW12O40]4− Keggin anion adsorbed on silver surfaces. Modelling the electron transfer between the surface and the anion is an excellent test of our approach, as it is necessary to place the Fermi level of the system at the right position. The immediate reduction of the anion, which we observed only when the environment is included, confirms the relevance of both the counterions and solvent to stabilise the adsorbed anion. The strategy used is a breakthrough in the computational modelling of polyoxometalates adsorbed on surfaces and it should be appropriate to study other properties of immobilised metal oxide anions on surfaces. read less USED (high confidence) J. Feng, J. Slocik, M. Sarikaya, R. Naik, B. Farmer, and H. Heinz, “Influence of the shape of nanostructured metal surfaces on adsorption of single peptide molecules in aqueous solution.,” Small. 2012. link Times cited: 90 Abstract: Self-assembly and function of biologically modified metal na… read moreAbstract: Self-assembly and function of biologically modified metal nanostructures depend on surface-selective adsorption; however, the influence of the shape of metal surfaces on peptide adsorption mechanisms has been poorly understood. The adsorption of single peptide molecules in aqueous solution (Tyr(12) , Ser(12) , A3, Flg-Na(3) ) is investigated on even {111} surfaces, stepped surfaces, and a 2 nm cuboctahedral nanoparticle of gold using molecular dynamics simulation with the CHARMM-METAL force field. Strong and selective adsorption is found on even surfaces and the inner edges of stepped surfaces (-20 to -60 kcal/mol peptide) in contrast to weaker and less selective adsorption on small nanoparticles (-15 to -25 kcal/mol peptide). Binding and selectivity appear to be controlled by the size of surface features and the extent of co-ordination of epitaxial sites by polarizable atoms (N, O, C) along the peptide chain. The adsorption energy of a single peptide equals a fraction of the sum of the adsorption energies of individual amino acids that is characteristic of surface shape, epitaxial pattern, and conformation constraints (often β-strand and random coil). The proposed adsorption mechanism is supported and critically evaluated by earlier sequence data from phage display, dissociation constants of small proteins as a function of nanoparticle size, and observed shapes of peptide-stabilized nanoparticles. Understanding the interaction of single peptides with shaped metal surfaces is a key step towards control over self-organization of multiple peptides on shaped metal surfaces and the assembly of superstructures from nanostructures. read less USED (high confidence) O.-S. Lee, V. Y. Cho, and G. Schatz, “A- to B-form transition in DNA between gold surfaces.,” The journal of physical chemistry. B. 2012. link Times cited: 24 Abstract: Molecular dynamics simulations have been performed to charac… read moreAbstract: Molecular dynamics simulations have been performed to characterize the conformation of DNA that is present when DNA links gold nanoparticles to form nanoparticle superlattice crystals. To model the DNA-linked gold nanoparticles, four strands of DNA are used to connect two gold surfaces, with a small interstrand separation and high added salt to match experiment. A-form DNA was assumed for the initial conformation, as this form of DNA has a length per base-pair that matches lengths that have been inferred from X-ray measurements. The DNA structure was monitored for 40 ns, and the distributions of the slide and z(p) coordinates were obtained from the simulations. We find that all the double-stranded DNA (ds-DNA) strands transform from A- to B-DNA during the simulations. In addition, single-stranded DNAa (ss-DNAs) that are used to connect the ds-DNA to each surface are found to become adsorbed on the gold surfaces during this process, and the ds-DNAs bend (∼143°) at their junctions with the two gold surfaces to accommodate the observed distance between gold surfaces using B-form DNA. We infer from this that the short length of DNA between the gold surfaces is not due to the presence of A-DNA. read less USED (high confidence) K. Lee and F. M. Ytreberg, “Effect of Gold Nanoparticle Conjugation on Peptide Dynamics and Structure,” Entropy. 2012. link Times cited: 25 Abstract: Molecular dynamics simulations were used to characterize the… read moreAbstract: Molecular dynamics simulations were used to characterize the structure and dynamics for several peptides and the effect of conjugating them to a gold nanoparticle. Peptide structure and dynamics were compared for two cases: unbound peptides in water, and peptides bound to the gold nanoparticle surface in water. The results show that conjugating the peptides to the gold nanoparticle usually decreases conformational entropy, but sometimes increases entropy. Conjugating the peptides can also result in more extended structures or more compact structures depending on the amino acid sequence of the peptide. The results also suggest that if one wishes to use peptide-nanoparticle conjugates for drug delivery it is important that the peptides contain secondary structure in solution because in our simulations the peptides with little to no secondary structure adsorbed to the nanoparticle surface. read less USED (high confidence) J. Yu, M. Becker, and G. Carri, “The influence of amino acid sequence and functionality on the binding process of peptides onto gold surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2012. link Times cited: 91 Abstract: We present a molecular dynamics study of the binding process… read moreAbstract: We present a molecular dynamics study of the binding process of peptide A3 (AYSSGAPPMPPF) and other similar peptides onto gold surfaces, and identify the functions of many amino acids. Our results provide a clear picture of the separate regimes present in the binding process: diffusion, anchoring, crawling and binding. Moreover, we explored the roles of individual residues. We found that tyrosine, methionine, and phenylalanine are strong binding residues; serine serves as an effective anchoring residue; proline acts as a dynamic anchoring point, while glycine and alanine give flexibility to the peptide backbone. We then show that our findings apply to unrelated phage-derived sequences that have been reported recently to facilitate AuNP synthesis. This new knowledge may aid in the design of new peptides for the synthesis of gold nanostructures with novel morphologies. read less USED (high confidence) R. Nadler and J. Sanz, “First-principles molecular dynamics simulations of the H2O / Cu(111) interface,” Journal of Molecular Modeling. 2011. link Times cited: 13 USED (high confidence) W. R. French, C. Iacovella, and P. Cummings, “The Influence of Molecular Adsorption on Elongating Gold Nanowires,” Journal of Physical Chemistry C. 2011. link Times cited: 24 Abstract: Using molecular dynamics simulations, we study the impact of… read moreAbstract: Using molecular dynamics simulations, we study the impact of physisorbing adsorbates on the structural and mechanical evolution of gold nanowires (AuNWs) undergoing elongation. We used various adsorbate models in our simulations, with each model giving rise to a different surface coverage and mobility of the adsorbed phase. We find that the local structure and mobility of the adsorbed phase remain relatively uniform across all segments of an elongating AuNW, except for the thinning region of the wire where the high mobility of Au atoms disrupts the monolayer structure, giving rise to higher solvent mobility. We analyzed the AuNW trajectories by measuring the ductile elongation of the wires and detecting the presence of characteristic structural motifs that appeared during elongation. Our findings indicate that adsorbates facilitate the formation of high-energy structural motifs and lead to significantly higher ductile elongations. In particular, our simulations result in a large number of monatomic chains... read less USED (high confidence) Y. Ahn, J. K. Saha, G. Schatz, and J. Jang, “Molecular Dynamics Study of the Formation of a Self-Assembled Monolayer on Gold,” Journal of Physical Chemistry C. 2011. link Times cited: 43 Abstract: Molecular dynamics simulations have been used to study the f… read moreAbstract: Molecular dynamics simulations have been used to study the formation of nanoscale islands of self-assembled monolayers (SAMs) starting from alkanethiol molecules initially lying down in a disordered physisorbed layer on gold. These islands form when tens of alkane thiols stand up together within tens of ns after chemisorption begins. The alkane chains in these islands are found to be tilted, and the tilt direction precesses around the center of the island. This precession, together with the packing of the sulfur atoms, signals the formation of a SAM island, occurring prior to the tilting and orientation ordering of the chains. read less USED (high confidence) J. Yu, M. Becker, and G. Carri, “A molecular dynamics simulation of the stability-limited growth mechanism of peptide-mediated gold-nanoparticle synthesis.,” Small. 2010. link Times cited: 36 USED (high confidence) A. Nemati, H. N. Pishkenari, A. Meghdari, and S. Sohrabpour, “Directing the diffusive motion of fullerene-based nanocars using nonplanar gold surfaces.,” Physical chemistry chemical physics : PCCP. 2017. link Times cited: 19 Abstract: A new method for guiding the motion of fullerene and fullere… read moreAbstract: A new method for guiding the motion of fullerene and fullerene-based nanocars is introduced in this paper. The effects of non-flat substrates on the motion of C60, a nanocar and a nanotruck are investigated at different conditions and temperatures. Their behavior is studied using two different approaches: analyzing the variation in potential energy and conducting all-atom classical molecular dynamics simulations. This paper proposes that the use of a stepped substrate will make their motion more predictable and controllable. The results of the simulations show that C60 stays on the top side of the step and cannot jump over the step at temperatures of 400 K and lower. However, at temperatures of 500 K and higher, C60 has sufficient energy to travel to the down side of the step. C60 attaches to the edge and moves just alongside of the edge when it is on the down side of the step. The edge also restricts the motion of C60 alongside the edge and reduces its range of motion. By considering the motion of C60, the general behavior of the nanocar and nanotruck is predictable. The nanocar stays on the top side of the step at temperatures of 400 K and less; at 500 K and higher temperatures, its wheels jump off the edge, and its range of motion is restricted. The relatively rigid chassis of the nanotruck does not allow the free individual motion of the wheels. As a result, the entire nanotruck stays on the top side of the step, even at 600 K. A pathway with the desired route can be fabricated for the motion of C60 and nanocars using the method presented in this paper. This represents a step towards the directional motion of C60 and nanocars. read less USED (high confidence) C. Cosenza, V. Lettera, F. Causa, P. L. Scognamiglio, E. Battista, and P. Netti, “Cell mechanosensory recognizes ligand compliance at biomaterial interface.,” Biomaterials. 2016. link Times cited: 6 USED (low confidence) J.-F. Shen, C.-M. Wu, and Y. Li, “Microscopic insight into mechanisms of heat and mass transfer improvement of dropwise condensation on a modified nanopillar surface,” International Journal of Heat and Mass Transfer. 2024. link Times cited: 0 USED (low confidence) K. Peng et al., “Molecular‐level insight on CO2 electroreduction to formate facilitated by triazole ionic liquid interfacial microhabitat,” AIChE Journal. 2023. link Times cited: 0 Abstract: The interfacial microhabitat induced by functionalized ionic… read moreAbstract: The interfacial microhabitat induced by functionalized ionic liquid (IL) electrolyte can effectively improve product selectivity for CO2 electroreduction. The multiple interactions in IL electrolytes affect the ions, CO2, proton distribution, and the protonation reaction, which are relevant to product selectivity. However, the specific effects are still unclear. Herein, molecular dynamics simulation and density functional theory were combined to reveal the regulatory mechanisms. The results showed that the dipolar interaction between CO2 and [124Triz]− cooperating the hydrogen bonds between [124Triz]− and H2O facilitates the accumulation of H atoms around C atoms of CO2. Moreover, the strong polar [124Triz]− induces protons to attack the C atoms of CO2, which results in lower free energy (−0.10 eV) for the formation of *HCOO intermediate and promotes the formation of formate, compared with the free energy of 0.43 eV for [NTf2]−. This work reveals the [124Triz]− regulatory mechanism for high formate selectivity. read less USED (low confidence) K. Goloviznina, E. Bendadesse, O. Sel, J. Tarascon, and M. Salanne, “Disclosing the Interfacial Electrolyte Structure of Na-Insertion Electrode Materials: Origins of the Desolvation Phenomenon.,” ACS applied materials & interfaces. 2023. link Times cited: 0 Abstract: Among a variety of promising cathode materials for Na-ion ba… read moreAbstract: Among a variety of promising cathode materials for Na-ion batteries, polyanionic Na-insertion compounds are among the preferred choices due to known fast sodium transfer through the ion channels along their framework structures. The most interesting representatives are Na3V2(PO4)3 (NVP) and Na3V2(PO4)2F3 (NVPF), which display large Na+ diffusion coefficients (up to 10-9 m2 s-1 in NVP) and high voltage plateaux (up to 4.2 V for NVPF). While the diffusion in the solid material is well-known to be the rate-limiting step during charging, already being thoroughly discussed in the literature, interfacial transport of sodium ions from the liquid electrolyte toward the electrode was recently shown to be important due to complex ion desolvation effects at the surface. In order to fill the blanks in the description of the electrode/electrolyte interface in Na-ion batteries, we performed a molecular dynamics study of the local nanostructure of a series of carbonate-based sodium electrolytes at the NVP and the NVPF interfaces along with careful examination of the desolvation phenomenon. We show that the tightness of solvent packing at the electrode surface is a major factor determining the height of the free energy barrier associated with desolvation, which explains the differences between the NVP and the NVPF structures. To rationalize and emphasize the remarkable properties of this family of cathode materials, a complementary comparative analysis of the same electrolyte system at the carbon electrode interface was also performed. read less USED (low confidence) F. Mollaamin and M. Monajjemi, “Carbenes trapping on Aluminum-Magnesium surface implanted with Silicon, Germanium, Tin: Promising of semiconductors by molecular modeling approach,” Applied Chemical Engineering. 2023. link Times cited: 0 Abstract: Al-Mg surface doped silicon, germanium and tin is theoretica… read moreAbstract: Al-Mg surface doped silicon, germanium and tin is theoretically studied using first-principles density functional theory (DFT) at the CAM-B3LYP/EPR-III, LANL2DZ,6-31+G(d,p) level of theory to explore the chemical adsorption and corrosion inhibition of organic carbenes through coating process. The fluctuation of NQR is estimated the inhibiting role of pyridine and its derivatives (picoline, 3-picoline,4-picoline,2,4-lutidine) for (Si, Ge, Sn)-doped Al-Mg alloy nanosheet due to concerning nitrogen in the benzene ring of related heterocyclic compounds becoming close to the monolayer nanosurface of Al-Mg-X (X = Si, Ge, Sn) nanoalloys. The NMR spectroscopy remarks that (Si, Ge, Sn)-doped Al-Mg alloy nanosheet has maximum band wavelengths approximately between 10 ppm–2000 ppm accompanying the sharpest peaks for inhibitors → Al-Mg-X which are between 10 ppm–100 ppm. IR spectroscopy has exhibited that (Si, Ge, Sn)-doped Al-Mg alloy nanosheet with the fluctuation in the frequency of intra-atomic interaction leads us to the most influence in the vicinage atoms generated due to inter-atomic interaction. The maximum IR spectrum for complexes of [inhibitor → Al-Mg-X (X = Si, Ge, Sn)] is observed in the frequency range between 500 cm−1–3500 cm−1. This work exhibits that proper monitoring of the coating mechanism by Langmuir adsorption can illustrate inhibiting the aluminum nanoalloys corrosion through an investigation of their structural and thermodynamic properties. This work investigates the characteristics, band structure, and projected density of state (PDOS) of Al-Mg nanoalloy doped with Si, Ge, Sn elements for increasing the corrosion inhibition of the surface through adsorption of organic molecules of carbenes in the surface coatings process. This article can be helpful in a range of applications which uses Al-Mg alloy for the study of energy storage and adsorption of air pollution or water contamination. Many different approaches such as surface coatings, alloying and doping can be adopted to protect the surface. read less USED (low confidence) O. Gutiérrez-Varela, J. Lombard, T. Biben, R. Santamaria, and S. Merabia, “Vapor Nanobubbles around Heated Nanoparticles: Wetting Dependence of the Local Fluid Thermodynamics and Kinetics of Nucleation.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 0 Abstract: Plasmonic nanobubbles are composite objects resulting from t… read moreAbstract: Plasmonic nanobubbles are composite objects resulting from the interaction between light and metallic nanoparticles immersed in a fluid. Plasmonic nanobubbles have applications in photothermal therapies, drug delivery, microfluidic manipulations, and solar energy conversion. Their early formation is, however, barely characterized due to the short time and length scales relevant to the process. Here, we investigate, using molecular dynamics (MD) simulations, the effect of nanoparticle wettability on both the local fluid thermodynamics and the kinetics of nanobubble generation in water. We first show that the local onset temperature of vapor nucleation decreases with the nanoparticle/water interfacial energy and may be 100 K below the water spinodal temperature in the case of weak nanoparticle/water interactions. Second, we demonstrate that vapor nucleation may be slower in the case of weak water/nanoparticle interactions. This result, which is qualitatively at odds with the predictions of isothermal classical nucleation theory, may be explained by the competition between two antagonist effects: while, classically, hydrophobicity increases the vapor nucleation rate, it also penalizes interfacial thermal transfer, slowing down kinetics. The kinetics of heat transfer from the nanoparticle to water is controlled by the interfacial thermal conductance. This quantity turns out not only to decrease with the nanoparticle hydrophobicity but also drops down prior to phase change, yielding even longer nucleation times. Such conclusions were reached by considering the comparison between MD and continuous heat transfer models. These results put forward the role of nanoparticle wettability in the generation of plasmonic nanobubbles observed experimentally and open the path to the control of boiling using nanopatterned surfaces. read less USED (low confidence) A. Codrignani et al., “Toward a continuum description of lubrication in highly pressurized nanometer-wide constrictions: The importance of accurate slip laws,” Science Advances. 2023. link Times cited: 1 Abstract: The Reynolds lubrication equation (RLE) is widely used to de… read moreAbstract: The Reynolds lubrication equation (RLE) is widely used to design sliding contacts in mechanical machinery. While providing an excellent description of hydrodynamic lubrication, friction in boundary lubrication regions is usually considered by empirical laws, because continuum theories are expected to fail for lubricant film heights h0 ≪ 10 nm, especially in highly loaded tribosystems with normal pressures pn ≫ 0.1 GPa. Here, the performance of RLEs is validated by molecular dynamics simulations of pressurized (with pn = 0.2 to 1 GPa) hexadecane in a gold converging-diverging channel with minimum gap heights h0 = 1.4 to 9.7 nm. For pn ≤ 0.4 GPa and h0 ≥ 5 nm, agreement with the RLE requires accurate constitutive laws for pressure-dependent density and viscosity. An additional nonlinear wall slip law relating wall slip velocities to local shear stresses extends the RLE’s validity to even the most severe loading condition pn = 1 GPa and h0 = 1.4 nm. Our results demonstrate an innovative route for continuum modeling of highly loaded tribological contacts under boundary lubrication. read less USED (low confidence) N. Kruchinin, “Rearrangement of the Conformations of Polyampholitic Macromolecules on the Surface of a Charged Spherical Metal Nanoparticle in an Alternating Electric Field: Molecular Dynamic Simulation,” Russian Journal of Physical Chemistry A. 2023. link Times cited: 0 USED (low confidence) N. Kruchinin, M. Kucherenko, and P. Neyasov, “Conformational Rearrangements of Adsorbed Polyampholytes under Periodic Changes in Polarity of a Charged Prolate Gold Nanospheroid,” High Energy Chemistry. 2023. link Times cited: 0 USED (low confidence) S. Sodomaco, S. Gómez, T. Giovannini, and C. Cappelli, “Computational Insights into the Adsorption of Ligands on Gold Nanosurfaces,” The Journal of Physical Chemistry. a. 2023. link Times cited: 0 Abstract: We study the adsorption process of model peptides, nucleobas… read moreAbstract: We study the adsorption process of model peptides, nucleobases, and selected standard ligands on gold through the development of a computational protocol based on fully atomistic classical molecular dynamics (MD) simulations combined with umbrella sampling techniques. The specific features of the interface components, namely, the molecule, the metallic substrate, and the solvent, are taken into account through different combinations of force fields (FFs), which are found to strongly affect the results, especially changing absolute and relative adsorption free energies and trends. Overall, noncovalent interactions drive the process along the adsorption pathways. Our findings also show that a suitable choice of the FF combinations can shed light on the affinity, position, orientation, and dynamic fluctuations of the target molecule with respect to the surface. The proposed protocol may help the understanding of the adsorption process at the microscopic level and may drive the in-silico design of biosensors for detection purposes. read less USED (low confidence) C. Du et al., “Accelerating Macroscale Superlubricity through Carbon Quantum Dots on Engineering Steel Surfaces,” Advanced Functional Materials. 2023. link Times cited: 0 Abstract: Macroscale superlubricity on engineering steel surfaces offe… read moreAbstract: Macroscale superlubricity on engineering steel surfaces offers a promising solution for minimizing friction and wear in engineering applications. However, achieving superlubricity typically requires a long running‐in period, which may result in significant wear for the friction pair. Herein, a new lubricant with superlubricating properties is rationally designed by using polyethylene glycol (PEG) and critic acid (CA) under complexing effect with a running‐in period of about 800 s. Importantly, the introduction of carbon quantum dots (CQDs) obtained from the pyrolysis of CA into PEG aqueous solution shortens the running‐in period for achieving macroscale superlubricity (µ ≈ 0.005) between steel/steel contact to 44 s. The corresponding wear rate (1.15 × 10−7 mm3 N−1 m−1) on the steel disk is reduced by 77% due to the shorter running‐in time. Furthermore, the surface analysis combined with the molecular dynamics simulations demonstrates that CQDs easily adsorb on the surface of the friction pair, forming a carbon film that reduces interaction energy between the lubricant molecules and the substrate. This work provides new insights into the lubrication mechanism of CQDs and contributes to the design of liquid superlubricants with short running‐in periods and low wear rates on engineering steel surfaces. read less USED (low confidence) T. Eggert, N. Hörmann, and K. Reuter, “Cavity formation at metal-water interfaces.,” The Journal of chemical physics. 2023. link Times cited: 0 Abstract: The free energy cost of forming a cavity in a solvent is a f… read moreAbstract: The free energy cost of forming a cavity in a solvent is a fundamental concept in rationalizing the solvation of molecules and ions. A detailed understanding of the factors governing cavity formation in bulk solutions has inter alia enabled the formulation of models that account for this contribution in coarse-grained implicit solvation methods. Here, we employ classical molecular dynamics simulations and multistate Bennett acceptance ratio free energy sampling to systematically study cavity formation at a wide range of metal-water interfaces. We demonstrate that the obtained size- and position-dependence of cavitation energies can be fully rationalized by a geometric Gibbs model, which considers that the creation of the metal-cavity interface necessarily involves the removal of interfacial solvent. This so-called competitive adsorption effect introduces a substrate dependence to the interfacial cavity formation energy that is missed in existing bulk cavitation models. Using expressions from scaled particle theory, this substrate dependence is quantitatively reproduced by the Gibbs model through simple linear relations with the adsorption energy of a single water molecule. Besides providing a better general understanding of interfacial solvation, this paves the way for the derivation and efficient parametrization of more accurate interface-aware implicit solvation models needed for reliable high-throughput calculations toward improved electrocatalysts. read less USED (low confidence) Y. Noh and N. Aluru, “Scaling of ionic conductance in a fluctuating single-layer nanoporous membrane,” Scientific Reports. 2023. link Times cited: 0 USED (low confidence) Q. Fan et al., “Effect of Modified Cellulose Nanocrystals on the Structure of Calcium Silicate Hydrate Studied by Molecular Dynamics Simulation and Experiment.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 0 Abstract: The interfacial bonding of the four cellulose nanocrystals (… read moreAbstract: The interfacial bonding of the four cellulose nanocrystals (CNCs) and calcium silicate hydrate (C-S-H) in vacuum and solution conditions was analyzed by molecular dynamics simulation. The binding energies were calculated, and the sources of interface strength were analyzed by the formation and lifetime of hydrogen bonds. The adsorption between CNC/C-S-H was characterized by the movement of interfacial atoms and CNC's adsorption conformation. The types of the functional group determine the bonding of the CNC/C-S-H, and the interface adsorption in two simulation conditions both followed: CNC-C (carboxyl) > CNC-O (hydroxyl) > CNC-N (amino) > CNC-S (sulfonic). The bonding of the interface affects the load transferred between the matrix and CNC, which can be reflected in the overall mechanical properties of the mortar. The mechanical strength of the mortar is in line with the simulation results. CNC-C has the strongest reinforcement effect, while CNC-S has the weakness effect. In the solution simulation, there is almost no chemical adsorption between C-S-H and CNC-S; instead, CNC-S decreased the bonding between the matrix and reduced the strength of the sample. Scanning electron microscopy found that CNC was interspersed in the matrix, riveting the matrix and enhanced the stability of the mortar structure. The influence of CNC on the mortar structure was analyzed by the calcium to silicon ratio (C/S) and it was showed that CNC-C, CNC-O, and CNC-N have an enhancement effect, while CNC-S decreased the coherence of the cement matrix. Durability and nuclear magnetic resonance tests further verified the effect of the four CNCs on the structure of mortar, and results indicated that CNC-C, CNC-O, and CNC-N can control the growth of hydration crystals, fill the cracks, and reduced porosity of samples, while CNC-S reduces the compactness of hydration products and ultimately decreased the mechanical and durability properties of the mortar. read less USED (low confidence) X. Chen, T. Vo, and P. Clancy, “A multiscale approach to uncover the self-assembly of ligand-covered palladium nanocubes.,” Soft matter. 2023. link Times cited: 0 Abstract: Ligand-mediated superlattice assemblies of metallic nanocrys… read moreAbstract: Ligand-mediated superlattice assemblies of metallic nanocrystals represent a new type of mesoscale materials whose structural ordering directly influence emergent collective properties. However, universal control over the spatial and orientational ordering of their constitutive components remains an open challenge. One major barrier contributing to the lack of programmability in these nanoscale building blocks revolves around a gap in fundamental understanding of how ligand-mediated interactions at the particle level propagate to macroscopic and mesoscale behaviors. Here, we employ a combination of scaling theory and coarse-grained simulations to develop a multiscale modeling framework capable of bridging across hierarchical assembly length scales for a model system of ligand-functionalized nanocubes (here, Pd). We first employ atomistic simulations to characterize how specific ligand-ligand interactions influence the local behaviors between neighboring Pd nanocubes. We then utilize a mean-field scaling theory to both rationalize the observed behaviors as well as compute a coarse-grained effective pairwise potential between nanocubes capable of reproducing atomistic behaviors at the mesoscale. Furthermore, our simulations reveal that a complex interplay between ligand-ligand interactions is directly responsible for a shift in macroscopic ordering between neighboring nanocubes. Our results, therefore, provides a critical step forward in establishing a multiscale understanding of ligand-functionalized nanocrystalline assemblies that can be subsequently leveraged to design targeted structures exhibiting novel, emergent collective properties. read less USED (low confidence) J.-F. Shen, C.-M. Wu, J. Song, J. Yu, and Y. Li, “Adsorption and capillary condensation transitions on nanostructures: Mechanisms of atomic evolution and meniscus growth,” International Communications in Heat and Mass Transfer. 2023. link Times cited: 0 USED (low confidence) M. Sekulla, M. Kohns, and M. Richter, “Adsorption of CO2 on Gold Surfaces: Adsorbate Density Assumption Investigated Using Molecular Dynamics Simulations,” Industrial & Engineering Chemistry Research. 2023. link Times cited: 0 USED (low confidence) X. Deng, X. Xu, Y. Huang, Y. Duan, C. Liu, and C. Dang, “A novel constant pressure control method for nucleation boiling of CO2/lubricant in molecular dynamics simulation,” International Journal of Refrigeration. 2023. link Times cited: 0 USED (low confidence) X. Wei and R. Hernandez, “Heat Transfer Enhancement in Tree-Structured Polymer Linked Gold Nanoparticle Networks.,” The journal of physical chemistry letters. 2023. link Times cited: 0 Abstract: Human brains use a tree-like neuron network for information … read moreAbstract: Human brains use a tree-like neuron network for information processing at high efficiency and low energy consumption. Tree-like structures have also been engineered to enhance mass and heat transfer in various applications. In this work, we reveal the heat transfer mechanism in tree-structured polymer linked gold nanoparticle (AuNP) networks using atomistic simulations. We report both upward and downward heat fluxes between root and leaf nodes in tree-structured polyethylene (PE) and poly(p-phenylene) (PPP) linked AuNP networks at tree levels from 1 to 5. We found that the heat conductance increases with an increasing polymer tree level. The heat transfer enhancement is due to the resulting increase in the low-frequency vibrational modes. This and other thermal properties are affected by the location of the AuNPs in the tree. Moreover, complex tree structures with at least five levels were found to be robust in the sense that disabling half of the leaves did not change the overall heat conductance. read less USED (low confidence) C. Zhang, H.-hong Jia, Y.-F. Zhang, and S. Du, “Capping Layer Determined Self-assembly of Au-Ag Bimetallic Janus Nanoparticles at An Oil/Water Interface by Molecular Dynamics Simulations.,” The journal of physical chemistry. B. 2023. link Times cited: 0 Abstract: Bimetallic Janus nanoparticles (BJNPs) have gained more atte… read moreAbstract: Bimetallic Janus nanoparticles (BJNPs) have gained more attention due to their unique catalytic and optical properties. The self-assembly of BJNPs is expected as an effective way to fabricate metamaterials suitable for different potential applications. However, the self-assembly dynamic process of BJNPs, which is key to achieving a controllable synthesis, is limited in both experimental and theoretical investigations. Herein, all-atom molecular dynamics (MD) simulations were employed to investigate the self-assembly process of 1-dodecanethiol (DDT)-decorated Au-Ag BJNPs at an oil-water interface. We demonstrate that DDT's van der Waals (vdW) interaction dominates the self-assembly process. BJNPs form close-packed structures at both fast and slow evaporation rates. Au-Ag BJNPs exhibit relatively larger rotations at a low evaporation rate than those at a high evaporation rate, suggesting that the evaporation rate influences the orientation of the Au-Ag BJNPs. BJNPs tend to orient their electric dipole moments toward the external electric field, according to the ab initio MD simulation results. Based on the energy comparison and model analysis, it is found that the parallel array is more stable than the antiparallel one for the Au-Ag BJNP arrays. The dipole-dipole interaction difference between the parallel and antiparallel BJNP arrays obtained according to dipole moment obtained from ab initio calculation is qualitatively consistent with that obtained from MD simulations, indicating that the dipole plays a decisive role in determining the orientation of the BJNP array. This work uncovers the self-assembly dynamic process of BJNPs, paving the way for future applications. read less USED (low confidence) X. Wang, S. Ham, H. Zhang, Y. Wang, and R. Qiao, “Adsorption of Model Polyfluoroalkyl Substances on Gold Electrodes for Electroanalytical Applications,” ChemElectroChem. 2023. link Times cited: 0 Abstract: Electrochemical methods can detect trace amounts of perfluor… read moreAbstract: Electrochemical methods can detect trace amounts of perfluoroalkyl and polyfluoroalkyl substances (PFAS) in the environment to help their management. PFAS adsorption on electrodes is an essential step in these methods, but is poorly understood. Here, we study the adsorption of perfluorooctanoic acid (PFOA), a model PFAS molecule, on gold substrates using metadynamics and equilibrium molecular dynamics simulations. The two‐dimensional free energy landscape obtained from metadynamics reveals that a PFOA molecule can adsorb on a neutral gold surface with the lowest free energy of −83.9 kJ/mol by adopting a co‐planar orientation, indicating a strong enrichment of PFOA occurs near the electrode. Spontaneous adsorption in other configurations, e. g., only a PFOA molecule‘s head attaches to the electrode, also occurs. However, a PFOA molecule generally must overcome energy barriers to become adsorbed. We show that energetic effects, particularly those associated with van der Waals PFOA‐gold interactions, are the primary driver for PFOA adsorption, and entropic effects associated with interfacial water molecules are the secondary driver. The implications of these results for the electrochemical detection and analysis of PFAS molecules are discussed. read less USED (low confidence) W. Liu and D. Jing, “Droplet Rolling Transport on Hydrophobic Surfaces Under Rotating Electric Fields: A Molecular Dynamics Study.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 0 Abstract: Driving droplets by electric fields is usually achieved by c… read moreAbstract: Driving droplets by electric fields is usually achieved by controlling their wettability, and realizing a flexible operation requires complex electrode designs. Here, we show by molecular dynamics methods the droplet transport on hydrophobic surfaces in a rolling manner under a rotating electric field, which provides a simpler and promising way to manipulate droplets. The droplet internal velocity field shows the rolling mode. When the contact angle on the solid surface is 144.4°, the droplet can be transported steadily at a high velocity under the rotating electric field (E = 0.5 V nm-1, ω = π/20 ps-1). The droplet center-of-mass velocities and trajectories, deformation degrees, dynamic contact angles, and surface energies were analyzed regarding the electric field strength and rotational angular frequency. Droplet transport with a complex trajectory on a two-dimensional surface is achieved by setting the electric field, which reflects the programmability of the driving method. Nonuniform wettability stripes can assist in controlling droplet trajectories. The droplet transport on the three-dimensional surface is studied, and the critical conditions for the droplet passing through the surface corners and the motion law on the curved surface are obtained. Droplet coalescence has been achieved by surface designs. read less USED (low confidence) L. Zhang, A. Zaoui, and W. Sekkal, “Synthesis of a chitosan-clay nanomembrane by pH control and its thermal stability in aqueous environments,” Applied Clay Science. 2023. link Times cited: 1 USED (low confidence) T. Li, “Molecular dynamics simulations of droplet coalescence and impact dynamics on the modified surfaces: A review,” Computational Materials Science. 2023. link Times cited: 0 USED (low confidence) F. Mollaamin and M. Monajjemi, “Coating of Al–X (X = Mg, Ga, Si) Alloys Nanosurface with Organic Corrosion Inhibitors Using TD-DFT Approach: Intra-Atomic and Interatomic Investigation through Langmuir Adsorption Study,” Russian Journal of Physical Chemistry A. 2023. link Times cited: 0 USED (low confidence) Z. Zhang et al., “Molecular dynamics study on the interaction of phosphorus building gypsum /surfactant composites.,” Journal of molecular graphics & modelling. 2023. link Times cited: 0 USED (low confidence) A. R. Zolghadr, S. Nozari, M. H. Dokoohaki, and H. Salari, “Investigating the performance of nickel molybdate nanostructure in dye sensitized solar cells: Computational and experimental analysis,” Journal of Photochemistry and Photobiology A: Chemistry. 2023. link Times cited: 0 USED (low confidence) M. Bakhtiari, S. N. Tavoosi, H. Shaygani, M. Tohidloo, S. Seifi, and A. Shamloo, “Effects of different wheels on the mobility of thermally driven fullerenes-based nanotrucks,” Sensors and Actuators A: Physical. 2023. link Times cited: 0 USED (low confidence) H.-guang Cao et al., “Wetting Behavior of CO2 Droplets on Smooth Solid Surface: Molecular Simulation Perspective,” Journal of Physics: Conference Series. 2023. link Times cited: 0 Abstract: The wettability of droplets on solid surfaces is important f… read moreAbstract: The wettability of droplets on solid surfaces is important for accurately revealing the microscopic mechanisms of gas condensation nucleation and droplet growth. During the contact condensation of CO2 gas on the heat exchanger surface in the pressurized liquefied natural gas technology, the wettability of CO2 droplets on the heat exchanger surface directly affects the heat transfer thermal resistance of the heat exchanger, which then affects the heat transfer efficiency of methane and ethane in the heat exchanger. Therefore, molecular dynamics simulations were used to study the spreading process and wetting patterns of nanoscale CO2 droplets on different energy surfaces. The results show that as the potential well depth ε of the wall atoms increases, the intensity of the solid-liquid interaction increases and the corresponding surface energy increases accordingly, showing different droplet spreading rates and wetting characteristics. Unlike the interfacial characteristics of macroscopic droplets, there are significant fluctuations at the gas-liquid interface of droplets on the molecular scale, but microdroplets can still form a specific contact angle after spreading on different energy surfaces in a statistical sense, and this contact angle decreases with increasing intensity of solid-liquid interaction. The low-energy surface at potential well depths ε less than 266 J·mol-1 exhibits a CO2-phobicity, and the surface becomes CO2-philic as the potential well depth continues to increase. The trend of the contact angle of CO2 droplets affected by temperature is the same as that of the center-of-mass height, which characterizes the spreading morphology of CO2 droplets. As the temperature increases, the contact angle decreases due to the further spreading and wetting of droplets on different energy surfaces. As the CO2-philicity of the surface gets higher, the contact angle decreases to a greater extent. read less USED (low confidence) S. Sarkar, A. Guha, R. Sadhukhan, T. N. Narayanan, and J. Mondal, “Osmolytes as Cryoprotectants under Salt Stress.,” ACS biomaterials science & engineering. 2023. link Times cited: 1 Abstract: Cryoprotecting agent (CPA)-guided preservation is essential … read moreAbstract: Cryoprotecting agent (CPA)-guided preservation is essential for effective protection of cells from cryoinjuries. However, current cryoprotecting technologies practiced to cryopreserve cells for biomedical applications are met with extreme challenges due to the associated toxicity of CPAs. Because of these limitations of present CPAs, the quest for nontoxic alternatives for useful application in cell-based biomedicines has been attracting growing interest. Toward this end, here, we investigate naturally occurring osmolytes' scope as biocompatible cryoprotectants under cold stress conditions in high-saline medium. Via a combination of the simulation and experiment on charged silica nanostructures, we render first-hand evidence that a pair of archetypal osmolytes, glycine and betaine, would act as a cryoprotectant by restoring the indigenous intersurface electrostatic interaction, which had been a priori screened due to the cold effect under salt stress. While these osmolytes' individual modes of action are sensitive to subtle chemical variation, a uniform augmentation in the extent of osmolytic activity is observed with an increase in temperature to counter the proportionately enhanced salt screening. The trend as noted in inorganic nanostructures is found to be recurrent and robustly transferable in a charged protein interface. In hindsight, our observation justifies the sufficiency of the reduced requirement of osmolytes in cells during critical cold conditions and encourages their direct usage and biomimicry for cryopreservation. read less USED (low confidence) W. Wang et al., “Regulating interfacial reaction through electrolyte chemistry enables gradient interphase for low-temperature zinc metal batteries,” Nature Communications. 2023. link Times cited: 2 USED (low confidence) K. Takahashi, H. Sato, and H. Nakano, “Iterative constant voltage molecular dynamics simulation on electrochemical interface at desired electrode potential,” Chemical Physics Letters. 2023. link Times cited: 0 USED (low confidence) Y. Kawagoe and T. Okabe, “Evaluations of atomic-resolution strain fields using molecular dynamics simulations combined with corrected smoothed particle hydrodynamics,” Computational Materials Science. 2023. link Times cited: 0 USED (low confidence) M. Fan et al., “Cationic-group-functionalized electrocatalysts enable stable acidic CO2 electrolysis,” Nature Catalysis. 2023. link Times cited: 3 USED (low confidence) F. Barbault, É. Brémond, J. Rey, P. Tufféry, and F. Maurel, “DockSurf: A Molecular Modeling Software for the Prediction of Protein/Surface Adhesion,” Journal of chemical information and modeling. 2023. link Times cited: 0 Abstract: The elucidation of structural interfaces between proteins an… read moreAbstract: The elucidation of structural interfaces between proteins and inorganic surfaces is a crucial aspect of bionanotechnology development. Despite its significance, the interfacial structures between proteins and metallic surfaces are yet to be fully understood, and the lack of experimental investigation has impeded the development of many devices. To overcome this limitation, we suggest considering the generation of protein/surface structures as a molecular docking problem with a homogenous plan as the target. To this extent, we propose a new software, DockSurf, which aims to quickly propose reliable protein/surface structures. Our approach considers the conformational exploration with Euler's angles, which provide a cartography instead of a unique structure. Interaction energies were derived from quantum mechanics computations for a set of small molecules that describe protein atom types and implemented in a Derjaguin, Landau, Verwey, and Overbeek potential for the consideration of large systems such as proteins. The validation of DockSurf software was conducted with molecular dynamics for corona proteins with gold surfaces and provided enthusiastic results. This software is implemented in the RPBS platform to facilitate widespread access to the scientific community. read less USED (low confidence) R. S. Janitra et al., “Multilayer Model of Gold Nanoparticles (AuNPs) and Its Application in the Classical Molecular Dynamics Simulation of Citrate-Capped AuNPs.,” The journal of physical chemistry. B. 2023. link Times cited: 0 Abstract: Studies on the interaction between gold nanoparticles (AuNPs… read moreAbstract: Studies on the interaction between gold nanoparticles (AuNPs) and functional proteins have been useful in developing diagnostic and therapeutic agents. Such studies require a realistic computational model of AuNPs for successful molecular design works. This study offers a new multilayer model of AuNPs to address the inconsistency between its molecular mechanics' interpretation and AuNP's plasmonic nature. We performed partial charge quantum calculation of AuNPs using Au13 and Au55 models. The result showed that it has partial negative charges on the surface and partial positive charges on the inner part, indicating that the AuNP model should be composed of multiatom types. We tested the partial charge parameters of these gold (Au) atoms in classical molecular dynamics simulation (CMD) of AuNPs. The result showed that our parameters performed better in simulating the adsorption of Na+ and dicarboxy acetone in terms of consistency with surface charge density than the zero charges Au in the interface force field (IFF). We proposed that the multiple-charged AuNP model can be developed further into a simpler four-atom type of Au in a larger AuNP size. read less USED (low confidence) L. Winter et al., “Tailoring the Selectivity of 1,3-Butadiene versus 1-Butene Adsorption on Pt(111) by Ultrathin Ionic Liquid Films,” ACS Catalysis. 2023. link Times cited: 0 USED (low confidence) Y. Zhang, D. Li, G. Xin, and S. Ren, “CO-Selective Catalytic Reduction of NOx in Fluid Catalytic Cracking Units and Applications of the Generated Exhaust Gas for Enhanced Shale Gas Recovery and Sequestration,” Energy & Fuels. 2023. link Times cited: 0 USED (low confidence) H. Cao et al., “Exploring the Effect of Surface Wettability on Heterogeneous Condensation of Carbon Dioxide: A Molecular Dynamics Study,” Journal of Molecular Liquids. 2023. link Times cited: 0 USED (low confidence) N. Li, M. Li, S. Lin, S. Cui, and X. Zhang, “Stoichiometric effect on the structural transformation and spatial variation of polyamide reverse osmosis membranes: A molecular dynamics study,” Journal of Membrane Science. 2023. link Times cited: 1 USED (low confidence) M. N. Jorabchi, M. Abbaspour, E. Goharshadi, I. Salahshoori, and S. Wohlrab, “Molecular dynamics simulation of Pt@Au nanoalloy in various solvents: Investigation of solvation, aggregation, and possible coalescence,” Journal of Materials Research and Technology. 2023. link Times cited: 0 USED (low confidence) J. Long, J. Wu, Y. Zhou, and X.-zhu Xie, “Hydrophilicity degradation and steam-induced rewetting during capillary-fed boiling,” Experimental Thermal and Fluid Science. 2023. link Times cited: 0 USED (low confidence) D. Meng et al., “Effect of anionic charge quantity on adsorption properties of PCE molecules on ettringite surface: a molecular dynamic simulation method,” Journal of Nanoparticle Research. 2023. link Times cited: 0 USED (low confidence) J. Tan, Y. Guo, and W. Guo, “Diameter-Optimum Spreading for the Impinging of Water Nanodroplets on Solid Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 0 Abstract: The impinging of water nanodroplets on solid surfaces is cru… read moreAbstract: The impinging of water nanodroplets on solid surfaces is crucial to many nanotechnologies. Through large-scale molecular dynamics simulations, the size effect on the spreading of water nanodroplets after impinging on hydrophilic, graphite, and hydrophobic surfaces under low impinging velocities has been systematically studied. The spreading rates of nanodroplets first increase and then decrease and gradually become constant with the increase of nanodroplet diameter. The nanodroplets with the diameters of 17-19 nm possess the highest spreading rates because of the combined effect of the strongest interfacial interaction and the strongest surface interaction within water molecules. The highest water molecule densities, hydrogen bond numbers, and dielectric constants of interface and surface layers mainly contribute to the lowest interface work of adhesion and surface tension values at optimal diameters. These results unveil the nonmonotonic characteristics of spreading velocity, interface work of adhesion and surface tension with nanodroplet diameter for nanodroplets on solid surfaces. read less USED (low confidence) V. Tiwari and T. Karmakar, “Understanding Molecular Aggregation of Ligand-Protected Atomically-Precise Metal Nanoclusters.,” The journal of physical chemistry letters. 2023. link Times cited: 1 Abstract: Monolayer-protected atomically precise nanoclusters (MPCs) a… read moreAbstract: Monolayer-protected atomically precise nanoclusters (MPCs) are an important class of molecules due to their unique structural features and diverse applications, including bioimaging, sensors, and drug carriers. Understanding the atomistic and dynamical details of their self-assembly process is crucial for designing system-specific applications. Here, we applied molecular dynamics and on-the-fly probability-based enhanced sampling simulations to study the aggregation of Au25(pMBA)18 MPCs in aqueous and methanol solutions. The MPCs interact via both hydrogen bonds and π-stacks between the aromatic ligands to form stable dimers, oligomers, and crystals. The dimerization free energy profiles reveal a pivotal role of the ligand charged state and solvent mediating the molecular aggregation. Furthermore, MPCs' ligands exhibit suppressed conformational flexibility in the solid phase due to facile intercluster hydrogen bonds and π-stacks. Our work provides unprecedented molecular-level dynamical details of the aggregation process and conformational dynamics of MPCs ligands in solution and crystalline phases. read less USED (low confidence) F. Liang, Y. Que, P. Li, and H. Chen, “The Thin Film Evaporation of R32/ R600 Mixture: A Molecular Dynamic Simulation,” 2023 IEEE/IAS Industrial and Commercial Power System Asia (I&CPS Asia). 2023. link Times cited: 0 Abstract: The utilization of mixed refrigerants in thermodynamic cycle… read moreAbstract: The utilization of mixed refrigerants in thermodynamic cycles is expected to improve the efficiency of the system. In the present paper, the evaporation behavior of the equimolar mixture of R32 and R600 on the copper surface is investigated by molecular dynamics approaches. The results denote that the evaporation process of the mixed R32/R600 liquid film can be roughly divided into the slow evaporation stage, stable evaporation stage and equilibrium stage. The evaporation rate of both R32 and R600 is maintained at a constant value during the stable evaporation phase, with the value of R32 being higher than that of R600. Besides, the evaporation of R32 and R600 is not synchronous. R600 enters both the stable evaporation phase and the equilibrium phase later than R32, indicating that the heat transfer thermal resistance of R600 is higher than that of R32. Furthermore, the three-dimensional vapor-liquid interface structure is obtained during the evaporation of the mixed R32/R600 liquid film. It is noticed that the undulation of the interface structure is greatest during the stable evaporation phase, where the vapor-liquid interface area is greater. read less USED (low confidence) W. Zhang, S. Cai, D. Zhang, and L. Gao, “Excellent performance of 8-hydroxyquinoline and alkyl polyglycolides hybrid electrolyte additives on aluminum-air battery,” Chemical Engineering Journal. 2023. link Times cited: 1 USED (low confidence) A. Gemma et al., “Full thermoelectric characterization of a single molecule,” Nature Communications. 2023. link Times cited: 2 USED (low confidence) M. R. Brann, X. Ma, and S. Sibener, “Isotopic Enrichment Resulting from Differential Condensation of Methane Isotopologues Involving Non-equilibrium Gas–Surface Collisions Modeled with Molecular Dynamics Simulations,” The Journal of Physical Chemistry C. 2023. link Times cited: 1 Abstract: : We employ molecular dynamics simulations to understand the… read moreAbstract: : We employ molecular dynamics simulations to understand the energy transfer processes involved during the collisions of CH 4 and CD 4 with CH 4 layered surfaces at 20 K in order to explain our experimental finding of preferential adsorption of CD 4 compared to CH 4 . There is good agreement between our MD simulations and our experimental results. We find that gas − surface collisional energy accommodation is dominated by exchange involving the translational degrees of freedom of the incident molecule and intermolecular vibrations of the interface. This observation allows us to understand that the cause of CD 4 preferential sticking arises from its propensity to lose more energy during its first impact with the surface, inducing longer residence times and leading to increased probability of becoming trapped and condensed onto the surface. Systematic trends are seen for sticking probabilities and energy transfer when we explore the behavior of the other H/D-substituted isotopologues of methane. These molecular insights provide context into the adsorption behavior occurring on icy dust grains in our solar system. Because adsorption is often the first step, trapping efficiency differences between isotopologues have notable implications for condensed phase reaction probabilities involving isotopically substituted species and subsequent events leading to increased molecular complexity. Aside from astrophysical significance, our findings have direct implications for novel isotope enrichment mechanisms under non-equilibrium conditions involving the preferential condensation of heavier isotopes and isotopologues during gas − surface collisions under specifically selected substrate, gas mixture, and incident kinematic conditions. read less USED (low confidence) C. Zhu, S. E. Hoff, M. Hémadi, and H. Heinz, “Accurate and Ultrafast Simulation of Molecular Recognition and Assembly on Metal Surfaces in Four Dimensions.,” ACS nano. 2023. link Times cited: 1 Abstract: Understanding molecular interactions with metal surfaces in … read moreAbstract: Understanding molecular interactions with metal surfaces in high reliability is critical for the development of catalysts, sensors, and therapeutics. Obtaining accurate experimental data for a wide range of surfaces remains a critical bottleneck and quantum-mechanical data remain speculative due to high uncertainties and limitations in scale. We report molecular dynamics simulations of adsorption energies and assembly of organic molecules on elemental metal surfaces using the INTERFACE force field (IFF). The force field-based simulations reach up to 8 times higher accuracy than density functional calculations at a million-fold faster speed, as well as more than 1 order of magnitude higher accuracy than other force fields relative to accurate measurements by single-crystal adsorption calorimetry. Uncertainties of prior computational methods are effectively reduced from on the order of 100% to less than 10% and validated by experimental data from multiple sources. Specifically, we describe the molecular interactions of benzene and naphthalene with even and defective platinum surfaces across a wide range of surface coverage in depth. We discuss molecular-scale influences on the heat of adsorption and clarify the definition of surface coverage. The methods can be applied to 18 metals to accurately predict binding and assembly of organic molecules, ligands, electrolytes, biological molecules, and gases without additional fit parameters. read less USED (low confidence) M. Kucherenko, P. Neyasov, and N. Kruchinin, “Modeling Conformational Rearrangements of a Macromolecule Adsorbed on a Metal Nanoparticle in an External Electric Field,” Russian Journal of Physical Chemistry B. 2023. link Times cited: 0 USED (low confidence) R. Rabani, M. Saidi, A. Rajabpour, L. Joly, and S. Merabia, “Enhanced Heat Flow between Charged Nanoparticles and an Aqueous Electrolyte.,” Langmuir : the ACS journal of surfaces and colloids. 2023. link Times cited: 1 Abstract: Heat transfer through the interface between a metallic nanop… read moreAbstract: Heat transfer through the interface between a metallic nanoparticle and an electrolyte solution has great importance in a number of applications, ranging from nanoparticle-based cancer treatments to nanofluids and solar energy conversion devices. However, the impact of the surface charge and dissolved ions on heat transfer has been scarcely explored so far. In this study, we compute the interface thermal conductance between hydrophilic and hydrophobic charged gold nanoparticles immersed in an electrolyte using equilibrium molecular dynamics simulations. Compared with an uncharged nanoparticle, we report a 3-fold increase of the Kapitza conductance for a nanoparticle surface charge of +320 mC/m2. This enhancement is shown to be approximately independent of the surface wettability, charge spatial distribution, and salt concentration. This allows us to express the Kapitza conductance enhancement in terms of the surface charge density on a master curve. Finally, we interpret the increase of the Kapitza conductance as a combined result of the shift of the water density distribution toward the charged nanoparticle and an accumulation of the counterions around the nanoparticle surface which increase the Coulombic interaction between the liquid and the charged nanoparticle. These considerations help us to apprehend the role of ions in heat transfer close to electrified surfaces. read less USED (low confidence) X. Ni et al., “Excluding the Trouble from Interfacial Water by Covalent Organic Polymer to Realize Extremely Reversible Zn Anode,” Advanced Functional Materials. 2023. link Times cited: 4 Abstract: The side reactions related to water are the major issue hind… read moreAbstract: The side reactions related to water are the major issue hindering practical application of Zn metal batteries. To exclude the trouble from interfacial water, a covalent organic polymer (COP) layer with N, N′‐Bis(salicylidene)ethylenediamine structure is designed, whose strong coordination ability with Zn2+ enhances the de‐solvation kinetics of solvated Zn2+ which is conducive to interfacial water removal thus alleviating the side reactions related to water. This function has been certified by density functional theory along with molecular dynamics analysis. Moreover, measurements including in situ electrochemical gas chromatography, in situ optical microscopy, in situ X‐ray diffraction and in situ Raman spectroscopy verify the weakened side reactions (including hydrogen evolution and corrosion) along with homogenous Zn deposition contributed from the covalent organic polymer layer. Benefiting from these merits, when assemble into cells based on common ZnSO4‐based aqueous electrolyte, the COP layer‐decorated anode exhibits excellent electrochemical performance of a high average Coulombic efficiency value 99.5% at a high capacity of 5.0 mA h cm−2. What's more, the symmetric cells can operate at −20 °C and the full cell with N/P ratio as low as 1.2 can cycle stably for 100 cycles, which would carry forward the promising practical application of Zn metal batteries. read less USED (low confidence) K. Yokoyama, J. Thomas, W. Ardner, M. Kieft, L. S. Neuwirth, and W. Liu, “An approach for in-situ detection of gold colloid aggregates amyloid formations within the hippocampus of the Cohen’s Alzheimer’s disease rat model by surface enhanced raman scattering methods,” Journal of Neuroscience Methods. 2023. link Times cited: 1 USED (low confidence) “Fabricating 2D Host −Guest Kagomé Packing for C2-Symmetric Aromatic Carboxylic Acids with Different Spatial Configuration: Different Ways, Same Destination,” The Journal of Physical Chemistry C. 2023. link Times cited: 0 USED (low confidence) S. R. Maalouf and S. Vel, “Nonlinear elastic behavior of 2D materials using molecular statics and comparisons with first principles calculations,” Physica E: Low-dimensional Systems and Nanostructures. 2023. link Times cited: 2 USED (low confidence) J. Shen, C.-M. Wu, J. Song, J. Yu, and Y. Li, “Characterizing the thermal transport and kinetics of droplet evaporation on a solid surface with hybrid wettability,” International Communications in Heat and Mass Transfer. 2023. link Times cited: 0 USED (low confidence) H. Zhao, Y. Yang, X. Shu, L. Dong, and Q. Ran, “Understanding the Adsorption of Air Entraining Agents on Portlandite: A Combined Dft and Molecular Dynamics Investigation,” SSRN Electronic Journal. 2023. link Times cited: 0 USED (low confidence) N. Kruchinin and M. Kucherenko, “Molecular Dynamics Simulation of the Conformational Structure of Polyampholyte Polypeptides at the Surface of a Charged Gold Nanoparticle in External Electric Field,” Polymer Science, Series A. 2023. link Times cited: 0 USED (low confidence) R. Liu, H. Zhai, M. Zhu, H. Shao, and T. H. Wang, “Inhibitory mechanism of n-MTAB AuNPs for α-synuclein aggregation,” Journal of Molecular Modeling. 2023. link Times cited: 0 USED (low confidence) H.-hong Jia, Y.-F. Zhang, C. Zhang, O. Min, and S. Du, “Ligand-Ligand-Interaction-Dominated Self-Assembly of Gold Nanoparticles at the Oil/Water Interface: An Atomic-Scale Simulation.,” The journal of physical chemistry. B. 2023. link Times cited: 2 Abstract: The self-assembly of nanoparticles (NPs) into ordered superl… read moreAbstract: The self-assembly of nanoparticles (NPs) into ordered superlattices is a powerful strategy to fabricate functional nanomaterials. Subtle variations in the interactions between NPs will influence the self-assembled superlattices. Using all-atom molecular dynamics simulations, we explore the self-assembly of 16 gold NPs, 4 nm in diameter, capped with ligands at the oil-water interface, and quantify the interactions between NPs at the atomic scale. We demonstrate that the interaction between capping ligands rather than that between NPs is dominant during the assembly process. For dodecanethiol (DDT)-capped Au NPs, the assembled superlattice is highly ordered in a close-packed configuration at a slow evaporation rate, while it is disordered at a fast evaporation rate. When replacing the capping ligands with stronger polarization than DDT molecules, the NPs form a robust ordered configuration at different evaporation rates due to the stronger electrostatic attraction between capping ligands from different NPs. Moreover, Au-Ag binary clusters exhibit similar assembly behavior with Au NPs. Our work uncovers the nonequilibrium nature of NP assembly at the atomic scale and would be helpful in rationally controlling NPs superlattice by changing passivating ligands, solvent evaporation rate, or both. read less USED (low confidence) Y. Ouyang, L. Qiu, X. Zhang, and Y. Feng, “Modulating heat transport inside CNT assemblies: Multi-level optimization and structural synergy,” Carbon. 2023. link Times cited: 4 USED (low confidence) Y. Shi et al., “Gold Nanorods Inhibit Tumor Metastasis by Regulating MMP-9 Activity: Implications for Radiotherapy.,” ACS applied materials & interfaces. 2023. link Times cited: 1 Abstract: Dysregulation of matrix metalloproteinase (MMP) is strongly … read moreAbstract: Dysregulation of matrix metalloproteinase (MMP) is strongly implicated in tumor invasion and metastasis. Nanomaterials can interact with proteins and have impacts on protein activity, which provides a potential strategy for inhibiting tumor invasion and metastasis. However, the regulation of MMP activity by nanomaterials has not been fully determined. Herein, we have found that gold nanorods (Au NRs) are able to induce the change of the secondary structure of MMP-9 and thereby inhibit their activity. Interestingly, the inhibition of MMP-9 activity is highly dependent on the aspect ratio of Au NRs, and an aspect ratio of 3.3 shows the maximum inhibition efficiency. Molecular dynamics simulations combined with mathematical statistics algorithm reveal the binding behaviors and interaction modes of MMP-9 with Au NRs in atomic details and disclose the mechanism of aspect ratio-dependent inhibition effect of Au NRs on MMP-9 activity. Au NRs with an aspect ratio of 3.3 successfully suppress the X-ray-activated invasion and metastasis of tumor by inhibiting MMP-9 activity. Our findings provide important guidance for the modulation of MMP-9 activity by tuning key parameters of nanomaterials and demonstrate that gold nanorods could be developed as potential MMP inhibitors. read less USED (low confidence) X. Yin et al., “Designing Robust Superhydrophobic Materials for Inhibiting Nucleation of Clathrate Hydrates by Imitating Glass Sponges,” ACS Central Science. 2023. link Times cited: 4 Abstract: Superhydrophobic surfaces are suggested to deal with hydrate… read moreAbstract: Superhydrophobic surfaces are suggested to deal with hydrate blockage because they can greatly reduce adhesion with the formed hydrates. However, they may promote the formation of fresh hydrate nuclei by inducing an orderly arrangement of water molecules, further aggravating hydrate blockage and meanwhile suffering from their fragile surfaces. Here, inspired by glass sponges, we report a robust anti-hydrate-nucleation superhydrophobic three-dimensional (3D) porous skeleton, perfectly resolving the conflict between inhibiting hydrate nucleation and superhydrophobicity. The high specific area of the 3D porous skeleton ensures an increase in terminal hydroxyl (inhibitory groups) content without damaging the superhydrophobicity, achieving the inhibition to fresh hydrates and antiadhesion to formed hydrates. Molecular dynamics simulation results indicate that terminal hydroxyls on a superhydrophobic surface can inhibit the formation of hydrate cages by disordering the arrangement of water molecules. And experimental data prove that the induction time of hydrate formation was prolonged by 84.4% and the hydrate adhesive force was reduced by 98.7%. Furthermore, this porous skeleton still maintains excellent inhibition and antiadhesion properties even after erosion for 4 h at 1500 rpm. Therefore, this research paves the way toward developing novel materials applied in the oil and gas industry, carbon capture and storage, etc. read less USED (low confidence) Y. Li, J.-N. Lin, M.-D. Xi, J. Wu, and J. Long, “Effects of surface nanotexturing on the wickability of microtextured metal surfaces.,” Journal of colloid and interface science. 2023. link Times cited: 3 USED (low confidence) N. Kruchinin and M. Kucherenko, “Rearrangements in the Conformational Structure of Polyelectrolytes on the Surface of a Flattened Metal Nanospheroid in an Alternating Electric Field,” Colloid Journal. 2023. link Times cited: 0 USED (low confidence) S. Saha, D. Bhadyopadhyay, and N. Choudhury, “Solvation Structure and Dynamics of Aqueous Solutions of Au^+ Ions: A Molecular Dynamics Simulation Study,” Journal of Solution Chemistry. 2023. link Times cited: 0 USED (low confidence) A. Farahvash, M. Agrawal, A. Peterson, and A. Willard, “Modeling Surface Vibrations and Their Role in Molecular Adsorption: A Generalized Langevin Approach.,” Journal of chemical theory and computation. 2023. link Times cited: 0 Abstract: The atomic vibrations of a solid surface can play a signific… read moreAbstract: The atomic vibrations of a solid surface can play a significant role in the reactions of surface-bound molecules, as well as their adsorption and desorption. Relevant phonon modes can involve the collective motion of atoms over a wide array of length scales. In this paper, we demonstrate how the generalized Langevin equation can be utilized to describe these collective motions weighted by their coupling to individual sites. Our approach builds upon the generalized Langevin oscillator (GLO) model originally developed by Tully. We extend the GLO by deriving parameters from atomistic simulation data. We apply this approach to study the memory kernel of a model platinum surface and demonstrate that the memory kernel has a bimodal form due to coupling to both low-energy acoustic modes and high-energy modes near the Debye frequency. The same bimodal form was observed across a wide variety of solids of different elemental compositions, surface structures, and solvation states. By studying how these dominant modes depend on the simulation size, we argue that the acoustic modes are frozen in the limit of macroscopic lattices. By simulating periodically replicated slabs of various sizes, we quantify the influence of phonon confinement effects in the memory kernel and their concomitant effect on simulated sticking coefficients. read less USED (low confidence) Y. Deng, D. Wang, and Y.-hua Han, “Molecular simulation on the effect of formation depth on methane adsorption by clay minerals,” AIP Advances. 2023. link Times cited: 0 Abstract: Shale gas is an unconventional natural gas with large reserv… read moreAbstract: Shale gas is an unconventional natural gas with large reserves. Recently, its production has increased rapidly, significantly impacting the international gas market and global energy landscape. In addition to organic matter and quartz, clay minerals constitute the majority of shale, and their production activities are effectively guided by evaluating their shale gas adsorption capabilities. To explore shale gas reserves and model their distribution, the variation in shale gas content with formation depth should be investigated. Currently, experimental methods are used to evaluate the effect of formation depth on shale gas adsorption, the data are substituted into a theoretical model, and the resulting mathematical model is used to estimate the variation in methane adsorption with formation depth, considering only temperature and pressure. However, the experimental method is flawed, and the true adsorption content cannot be obtained. The absolute methane adsorption amount was calculated using molecular dynamics and the grand-canonical Monte Carlo method for the corresponding temperature and pressure conditions. The supercritical Dubinin–Radushkevich (SDR) equation was fitted, yielding a temperature-dependent equation for the SDR parameter. Shale gas adsorption can be predicted using the developed mathematical model based on formation depth and temperature–pressure gradient. read less USED (low confidence) R. A. G. Carcamo et al., “Differences in solvation thermodynamics of oxygenates at Pt/Al2O3 perimeter versus Pt(111) terrace sites,” iScience. 2023. link Times cited: 1 USED (low confidence) Q. Xiong, O.-S. Lee, C. Mirkin, and G. Schatz, “Ethanol-Induced Condensation and Decondensation in DNA-Linked Nanoparticles: A Nucleosome-like Model for the Condensed State.,” Journal of the American Chemical Society. 2022. link Times cited: 4 Abstract: Inspired by the conventional use of ethanol to induce DNA pr… read moreAbstract: Inspired by the conventional use of ethanol to induce DNA precipitation, ethanol condensation has been applied as a routine method to dynamically tune "bond" lengths (i.e., the surface-to-surface distances between adjacent nanoparticles that are linked by DNA) and thermal stabilities of colloidal crystals involving DNA-linked nanoparticles. However, the underlying mechanism of how the DNA bond that links gold nanoparticles changes in this class of colloidal crystals in response to ethanol remains unclear. Here, we conducted a series of all-atom molecular dynamic (MD) simulations to explore the free energy landscape for DNA condensation and decondensation. Our simulations confirm that DNA condensation is energetically much more favorable under 80% ethanol conditions than in pure water, as a result of ethanol's role in enhancing electrostatic interactions between oppositely charged species. Moreover, the condensed DNA adopts B-form in pure water and A-form in 80% ethanol, which indicates that the higher-order transition does not affect DNA's conformational preferences. We further propose a nucleosome-like supercoiled model for the DNA condensed state, and we show that the DNA end-to-end distance derived from this model matches the experimentally measured DNA bond length of about 3 nm in the fully condensed state for DNA where the measured length is 16 nm in water. Overall, this study provides an atomistic understanding of the mechanism underlying ethanol-induced condensation and water-induced decondensation, while our proposed nucleosome-like model allows the design of new strategies for interpreting experimental studies of DNA condensation. read less USED (low confidence) C. Lionello, C. Perego, A. Gardin, R. Klajn, and G. Pavan, “Supramolecular Semiconductivity through Emerging Ionic Gates in Ion–Nanoparticle Superlattices,” ACS Nano. 2022. link Times cited: 7 Abstract: The self-assembly of nanoparticles driven by small molecules… read moreAbstract: The self-assembly of nanoparticles driven by small molecules or ions may produce colloidal superlattices with features and properties reminiscent of those of metals or semiconductors. However, to what extent the properties of such supramolecular crystals actually resemble those of atomic materials often remains unclear. Here, we present coarse-grained molecular simulations explicitly demonstrating how a behavior evocative of that of semiconductors may emerge in a colloidal superlattice. As a case study, we focus on gold nanoparticles bearing positively charged groups that self-assemble into FCC crystals via mediation by citrate counterions. In silico ohmic experiments show how the dynamically diverse behavior of the ions in different superlattice domains allows the opening of conductive ionic gates above certain levels of applied electric fields. The observed binary conductive/nonconductive behavior is reminiscent of that of conventional semiconductors, while, at a supramolecular level, crossing the “band gap” requires a sufficient electrostatic stimulus to break the intermolecular interactions and make ions diffuse throughout the superlattice’s cavities. read less USED (low confidence) N. Kruchinin, M. Kucherenko, and P. Neyasov, “Modeling Conformational Changes in Uniformly Charged Polyelectrolytes on the Surface of a Polarized Metallic Oblate Nanospheroid,” Russian Journal of Physical Chemistry A. 2022. link Times cited: 0 USED (low confidence) N. Kruchinin and M. Kucherenko, “Conformational Changes in Polyampholyte Macrochains on the Surface of an Oblate Metallic Nanospheroid in Alternating Electric Field,” High Energy Chemistry. 2022. link Times cited: 0 USED (low confidence) S. Guo, Y. Liu, Y. Wang, K. Dong, X. Zhang, and S. Zhang, “Interfacial Role of Ionic Liquids in CO2 Electrocatalytic Reduction: A Mechanistic Investigation,” Chemical Engineering Journal. 2022. link Times cited: 0 USED (low confidence) W. Cai, Z. He, J. Wang, Z. Wang, Q. Li, and Y. Wang, “Wetting characteristics of ethane droplet - A molecular dynamics study,” Journal of Molecular Liquids. 2022. link Times cited: 6 USED (low confidence) Y. Wang, J. Xu, and Q. Wang, “Molecular dynamics simulation and nonlinear analysis of density fluctuations in Lennard-Jones fluid system near the critical point,” Chinese Journal of Physics. 2022. link Times cited: 0 USED (low confidence) M. S. Gomes-Filho, A. O. Pereira, G. T. Feliciano, L. Pedroza, and M. Coutinho-Neto, “Extending the applicability of popular force fields for describing water/metal interfaces: application to water/Pd(111),” Physica Scripta. 2022. link Times cited: 0 Abstract: We propose a new method for constructing a polarizable class… read moreAbstract: We propose a new method for constructing a polarizable classical force field using data obtained from QM and QM/MM calculations to account for the charge redistribution at the water/metal interface. The induced charge effects are described by adding dipoles to the system topology following the Rod Model (Iori, F, et al J. Comput. Chem.2009, 30, 1465). Furthermore, the force field uses the TIP3P water model, and its functional form is compatible with popular force fields such as AMBER, CHARMM, GROMOS, OPLS-AA, CVFF and IFF. The proposed model was evaluated and validated for water/Pd(111) systems. We tuned the model parameters to reproduce a few critical water/Pd(111) geometries and energies obtained from DFT calculations using both PBE and a non-local van der Waals xc-functional. Our model can reproduce the hexagonal ice layer for the Pd(111)/water systems typically present in low-temperature experiments, in agreement with information available from the literature. Additionally, the model can also reproduce the experimental metal-water interfacial tension at room temperature. read less USED (low confidence) A. F. Qadikolae and S. Sharma, “Facet Selectivity of Cetyltrimethyl Ammonium Bromide Surfactants on Gold Nanoparticles Studied Using Molecular Simulations.,” The journal of physical chemistry. B. 2022. link Times cited: 2 Abstract: We have studied facet selectivity of cetyltrimethyl ammonium… read moreAbstract: We have studied facet selectivity of cetyltrimethyl ammonium bromide (CTAB) surfactants of varying alkyl tail lengths (C17TAB and C10TAB) during their adsorption on a spherical gold metal nanoparticle (MNP) using umbrella sampling and well-tempered metadynamics techniques in molecular simulations. We show that the surfactants strongly adsorb with their alkyl tails wrapped around the MNP. The adsorption morphologies are dictated by the strong preference of the polar head group of the surfactants to adsorb on to the atoms that lie between the facets of the MNP, that is, in the vicinity of low-coordinated gold atoms. The alkyl tails do not display any strong facet preference. Owing to the longer alkyl tails, C17TAB molecules pack together better than the C10TAB molecules in the adsorbed state on the MNP. These findings suggest that the regions near the edges of the facets and low-coordinated atoms are expected to be preferentially covered with the adsorbed surfactants. read less USED (low confidence) A. Sandupatla, P. K. A, S. Rana, and A. Chatterjee, “How the Facet Edge Controls the Overall CO Oxidation in Nanoporous Gold: Combined Atomistic Characterization/DFT Study of Residual Ag Distribution and Catalytic Activity,” ACS Catalysis. 2022. link Times cited: 1 USED (low confidence) X. Deng, Y. Liu, and C. Liu, “Evaporation behaviors of R32/R1234ze(E) mixtures on a copper surface using molecular dynamics simulations,” International Communications in Heat and Mass Transfer. 2022. link Times cited: 5 USED (low confidence) T. Zheng, X. Li, J. Gu, S. Liu, Y. Zhang, and H. Zhang, “Penetration of lubricating water molecules at the frictional interface of UHMWPE: Insights from molecular dynamics simulations,” Journal of Molecular Liquids. 2022. link Times cited: 2 USED (low confidence) X. Deng, X. Xu, X. Song, Q. Li, and C. Liu, “Boiling heat transfer of CO2/lubricant on structured surfaces using molecular dynamics simulations,” Applied Thermal Engineering. 2022. link Times cited: 6 USED (low confidence) J. Shen, C.-M. Wu, D. Mo, and Y. Li, “Molecular investigation on the formation and transition of condensation mode on the surface with nanostructure,” Journal of Molecular Liquids. 2022. link Times cited: 4 USED (low confidence) X. Wei, E. Harazinska, Y. Zhao, Z. Yi, and R. Hernandez, “Thermal Transport through Polymer-Linked Gold Nanoparticles,” The Journal of Physical Chemistry. C, Nanomaterials and Interfaces. 2022. link Times cited: 2 Abstract: Polymer–nanoparticle networks have potential applications in… read moreAbstract: Polymer–nanoparticle networks have potential applications in molecular electronics and nanophononics. In this work, we use all-atom molecular dynamics to reveal the fundamental mechanisms of thermal transport in polymer-linked gold nanoparticle (AuNP) dimers at the molecular level. Attachment of the polymers to AuNPs of varying sizes allows the determination of effects from the flexibility of the chains when their ends are not held fixed. We report heat conductance (G) values for six polymers—viz. polyethylene, poly(p-phenylene), polyacene, polyacetylene, polythiophene, and poly(3,4-ethylenedioxythiophene)—that represent a broad range of stiffness. We address the multimode effects of polymer type, AuNP size, polymer chain length, polymer conformation, system temperature, and number of linking polymers on G. The combination of the mechanisms for phonon boundary scattering and intrinsic phonon scattering has a strong effect on G. We find that the values of G are larger for conjugated polymers because of the stiffness in their backbones. They are also larger in the low-temperature region for all polymers owing to the quenching of segmental rotations at low temperature. Our simulations also suggest that the total G is additive as the number of linking polymers in the AuNP dimer increases from 1 to 2 to 3. read less USED (low confidence) A. Truszkowska, A. Boldini, and M. Porfiri, “Plating of Ion‐Exchange Membranes: A Molecular Dynamics Study,” Advanced Theory and Simulations. 2022. link Times cited: 0 Abstract: Electroless plating of membranes offers a viable pathway to … read moreAbstract: Electroless plating of membranes offers a viable pathway to create flexible electrodes for soft sensors and actuators, as well as flexible electronics and batteries. Ionic polymer metal composites are a promising class of active materials, realized through electroless plating of ion‐exchange membranes. The plating and electrode‐membrane interface play a key role on their performance, but computational tools to inform the selection of the plating material and optimize the plating process are currently lacking. Here, this gap is filled through the study of the electrode‐membrane interface in different types of ion‐exchange membranes via molecular dynamics simulations. Both commercially available cation‐ and research‐grade anion‐exchange membranes are studied here. For platinum coating, it is predicted that cation‐exchange membranes will have a superior interface than anion‐exchange membranes, in terms of metal penetration into the membrane, reliability of actuation performance, and interface stability. The results are in line with previous endeavors documenting the higher stability of the interface for cation‐ than for anion‐exchange membranes, easier plating processes, and better electrochemical performance when working with cation‐exchange membranes. The proposed computational framework offers a versatile environment for testing different types of coatings for specific membranes, toward optimizing the performance of electrochemical devices with plated flexible electrodes. read less USED (low confidence) X. Wang, S. Ham, W. Zhou, and R. Qiao, “Adsorption of rhodamine 6G and choline on gold electrodes: a molecular dynamics study,” Nanotechnology. 2022. link Times cited: 3 Abstract: The adsorption of analyte molecules on nano-optoelectrodes (… read moreAbstract: The adsorption of analyte molecules on nano-optoelectrodes (e.g. a combined nanoantenna and nanoelectrode device) significantly affects the signal characteristics in surface-enhanced Raman scattering (SERS) measurements. Understanding how different molecules adsorb on electrodes and their electrical potential modulation helps interpret SERS measurements better. We use molecular dynamics simulations to investigate the adsorption of prototypical analyte molecules (rhodamine 6G and choline) on gold electrodes with negative, neutral, and positive surface charges. We show that both molecules can readily adsorb on gold surfaces at all surface charge densities studied. Nevertheless, the configurations of the adsorbed molecules can differ for different surface charge densities, and adsorption can also change a molecule’s conformation. Rhodamine 6G molecules adsorb more strongly than choline molecules, and the adsorption of both molecules is affected by electrode charge in 0.25 M NaCl solutions. The mechanisms of these observations are elucidated, and their implications for voltage-modulated SERS measurements are discussed. read less USED (low confidence) J. M. Ortiz-Roldán et al., “Understanding the stability and structural properties of ordered nanoporous metals towards their rational synthesis,” Proceedings of the Royal Society A. 2022. link Times cited: 1 Abstract: Ordered Nanoporous Metals (ONMs) form a new family of nanopo… read moreAbstract: Ordered Nanoporous Metals (ONMs) form a new family of nanoporous materials composed only of pure metals. The expected impact is considerable from combining the ordered nanopore structure of MOFs, zeolites and carbon schwartzites with the robustness and electronic conductivity of metals. Little is known about their stability and structural features. Here we address these points to provide clues toward their rational synthesis, introducing an automatic atomistic design that uses model building and molecular dynamics structural relaxation, and is validated against the experimentally known ONMs. Analysing the properties of the 10 stable structures out of the 17 studied (14 of which are designed in this work) using four noble metals (Pt, Pd, Au and Ag), we have deciphered some key elements and structural descriptors that provide guidelines for the experimental synthesis of ONMS. The long-lived metastability of the stable ONMs is evidenced by the high free energy landscape, computed via Metadynamic simulations. The new ONMs permit molecular diffusion of various molecules of industrial relevance, increasing the expectation for their use in catalysis, separation, nanofiltration, batteries, fuel cells, etc. Stable low-cost ONMs are predicted using Earth-abundant Ni metal, which maintains the main features of their relative noble metal forms. read less USED (low confidence) R. Kariuki et al., “Behavior of Citrate-Capped Ultrasmall Gold Nanoparticles on a Supported Lipid Bilayer Interface at Atomic Resolution.,” ACS nano. 2022. link Times cited: 11 Abstract: Nanomaterials have the potential to transform biological and… read moreAbstract: Nanomaterials have the potential to transform biological and biomedical research, with applications ranging from drug delivery and diagnostics to targeted interference of specific biological processes. Most existing research is aimed at developing nanomaterials for specific tasks such as enhanced biocellular internalization. However, fundamental aspects of the interactions between nanomaterials and biological systems, in particular, membranes, remain poorly understood. In this study, we provide detailed insights into the molecular mechanisms governing the interaction and evolution of one of the most common synthetic nanomaterials in contact with model phospholipid membranes. Using a combination of atomic force microscopy (AFM) and molecular dynamics (MD) simulations, we elucidate the precise mechanisms by which citrate-capped 5 nm gold nanoparticles (AuNPs) interact with supported lipid bilayers (SLBs) of pure fluid (DOPC) and pure gel-phase (DPPC) phospholipids. On fluid-phase DOPC membranes, the AuNPs adsorb and are progressively internalized as the citrate capping of the NPs is displaced by the surrounding lipids. AuNPs also interact with gel-phase DPPC membranes where they partially embed into the outer leaflet, locally disturbing the lipid organization. In both systems, the AuNPs cause holistic perturbations throughout the bilayers. AFM shows that the lateral diffusion of the particles is several orders of magnitude smaller than that of the lipid molecules, which creates some temporary scarring of the membrane surface. Our results reveal how functionalized AuNPs interact with differing biological membranes with mechanisms that could also have implications for cooperative membrane effects with other molecules. read less USED (low confidence) P. Wang et al., “Controlling the condensation of vapor by electric field: A molecular dynamics simulation study,” Applied Surface Science. 2022. link Times cited: 4 USED (low confidence) Y. Wu, Y. He, T. Tang, and M. Zhai, “Molecular dynamic simulations of methane hydrate formation between solid surfaces: Implications for methane storage,” Energy. 2022. link Times cited: 13 USED (low confidence) M. Zare, M. Saleheen, N. Singh, M. Uline, M. Faheem, and A. Heyden, “Liquid-Phase Effects on Adsorption Processes in Heterogeneous Catalysis,” JACS Au. 2022. link Times cited: 7 Abstract: Aqueous solvation free energies of adsorption have recently … read moreAbstract: Aqueous solvation free energies of adsorption have recently been measured for phenol adsorption on Pt(111). Endergonic solvent effects of ∼1 eV suggest solvents dramatically influence a metal catalyst’s activity with significant implications for the catalyst design. However, measurements are indirect and involve adsorption isotherm models, which potentially reduces the reliability of the extracted energy values. Computational, implicit solvation models predict exergonic solvation effects for phenol adsorption, failing to agree with measurements even qualitatively. In this study, an explicit, hybrid quantum mechanical/molecular mechanical approach for computing solvation free energies of adsorption is developed, solvation free energies of phenol adsorption are computed, and experimental data for solvation free energies of phenol adsorption are reanalyzed using multiple adsorption isotherm models. Explicit solvation calculations predict an endergonic solvation free energy for phenol adsorption that agrees well with measurements to within the experimental and force field uncertainties. Computed adsorption free energies of solvation of carbon monoxide, ethylene glycol, benzene, and phenol over the (111) facet of Pt and Cu suggest that liquid water destabilizes all adsorbed species, with the largest impact on the largest adsorbates. read less USED (low confidence) A. R. Zolghadr, N. Azari, and M. H. Dokoohaki, “The Use of 1-Ethyl-3-Methylimidazolium Iodide Ionic Liquid in Dye Sensitized Solar Cells: A Joint Experimental and Computational Perspective,” Journal of Molecular Liquids. 2022. link Times cited: 5 USED (low confidence) M. T. Darby and C. Cucinotta, “The role of water at electrified metal-water interfaces unravelled from first principles,” Current Opinion in Electrochemistry. 2022. link Times cited: 4 USED (low confidence) A. Yamada, “Computational Analyses of Plasmonics of a Silver Nanoparticle in a Vacuum and in a Water Solution by Classical Electronic and Molecular Dynamics Simulations.,” The journal of physical chemistry. A. 2022. link Times cited: 0 Abstract: We present basic optical responses of a silver nanoparticle … read moreAbstract: We present basic optical responses of a silver nanoparticle (Ag309) in a vacuum and a water solution obtained by classical electronic and molecular dynamics (CEMD) calculations, where the CEMD is our previously developed force-field based molecular dynamics simulation method that incorporates the classical equation of motion for free electrons in metal and an interaction with the applied oscillating electric field (Yamada, A. J. Chem. Phys. 2021, 155, 174118)). The present work is the follow-up of the previous study. Calculated absorption spectra in the visible region with various conditions are reported together with parameter determination for realistic analyses as well as the verification of the method. Time-domain optical responses of Ag309 in water solvent are as well analyzed in terms of the plasmon resonance excitation under a subpicosecond light pulse and its thermal relaxation. read less USED (low confidence) N. Kalčec et al., “Transformation of L-DOPA and Dopamine on the Surface of Gold Nanoparticles: An NMR and Computational Study.,” Inorganic chemistry. 2022. link Times cited: 1 Abstract: Gold nanoparticles (AuNPs) have found applications in biomed… read moreAbstract: Gold nanoparticles (AuNPs) have found applications in biomedicine as diagnostic tools, but extensive research efforts have been also directed toward their development as more efficient drug delivery agents. The high specific surface area of AuNPs may provide dense loading of molecules like catechols (L-DOPA and dopamine) on nanosurfaces, enabling functionalization strategies for advancing conventional therapy and diagnostic approaches of neurodegenerative diseases. Despite numerous well-described procedures in the literature for preparation of different AuNPs, possible transformation and structural changes of surface functionalization agents have not been considered thoroughly. As a case in point, the catechols L-DOPA and dopamine were selected because of their susceptibility to oxidation, cyclization, and polymerization. To assess the fate of coating and functionalization agents during the preparation of AuNPs or interaction at the nano-bio interface, a combination of spectroscopy, light scattering, and microscopy techniques was used while structural information and reaction mechanism were obtained by NMR in combination with computational tools. The results revealed that the final form of catechol on the AuNP nanosurface depends on the molar ratio of Au used for AuNP preparation. A large molar excess of L-DOPA or dopamine is needed to prepare AuNPs funtionalized with fully reduced catechols. In the case of molar excess of Au, the oxidation of catechols to dopamine quinone and dopaquinone was promoted, and dopaquinone underwent intramolecular cyclization in which additional oxidation products, leukodopachrome, dopachrome, or its tautomer, were formed because of the larger intrinsic acidity of the more nucleophilic amino group in dopaquinone. MD simulations showed that, of the oxidation products, dopachrome had the highest affinity for binding to the AuNPs surface. The results highlight how a more versatile methodological approach, combining experimental and in silico techniques, allows more reliable characterization of binding events at the surface of AuNPs for possible applications in biomedicine. read less USED (low confidence) W. Liu, Z. Sun, N. Li, Z. Qi, Z. Wang, and Z. Wang, “Binary droplet interactions in shear water-in-oil emulsion: A molecular dynamics study,” Journal of Molecular Liquids. 2022. link Times cited: 5 USED (low confidence) N. Farhadian, M. Kazemi, F. Moosavi, and M. Khalaj, “Molecular dynamics simulation of drug delivery across the cell membrane by applying gold nanoparticle carrier: Flutamide as hydrophobic and glutathione as hydrophilic drugs as the case studies.,” Journal of molecular graphics & modelling. 2022. link Times cited: 8 USED (low confidence) N. Kruchinin and M. Kucherenko, “Modeling of electrical induced conformational changes of macromolecules on the surface of metallic nanospheroids,” Materials Today: Proceedings. 2022. link Times cited: 0 USED (low confidence) M. M. Aksoy and Y. Bayazitoglu, “Temperature and Heat Flux Dependence of Interfacial Thermal Resistance for Water Between Platinum, Palladium, Lead and Nickel Nanochannel Walls,” International Journal of Thermophysics. 2022. link Times cited: 1 USED (low confidence) M. Sokolová et al., “Photochemical synthesis of pink silver and its use for monitoring peptide nitration via surface enhanced Raman spectroscopy (SERS),” Amino Acids. 2022. link Times cited: 1 USED (low confidence) K. Kanhaiya and H. Heinz, “Adsorption and Diffusion of Oxygen on Pure and Partially Oxidized Metal Surfaces in Ultrahigh Resolution.,” Nano letters. 2022. link Times cited: 2 Abstract: The interaction of gas molecules with metal and oxide surfac… read moreAbstract: The interaction of gas molecules with metal and oxide surfaces plays a critical role in corrosion, catalysis, sensing, and heterogeneous materials. However, insights into the dynamics of O2 from picoseconds to microseconds have remained unavailable to date. We obtained 3D potential energy surfaces for adsorption of O2 on 11 common pristine and partially oxidized (hkl) surfaces of Ni and Al in picometer resolution and high accuracy of 0.1 kcal/mol, identified binding sites, and surface mobility from 25 to 300 °C. We explain relative oxidation rates and parameters for oxide growth. We employed over 150 000 molecular mechanics and molecular dynamics simulations with the interface force field (IFF) using structural data from X-ray diffraction (XRD) and low-energy electron diffraction (LEED). The methods reach 10 to 50 times higher accuracy than possible before and are suited to analyze gas interactions with metals up to the micrometer scale including defects and irregular nanostructures. read less USED (low confidence) S. Sarkar, A. Guha, T. N. Narayanan, and J. Mondal, “Zwitterionic Osmolytes Revive Surface Charges under Salt Stress via Dual Mechanisms.,” The journal of physical chemistry letters. 2022. link Times cited: 2 Abstract: To counter the stress of a salt imbalance, the cell often pr… read moreAbstract: To counter the stress of a salt imbalance, the cell often produces low molecular weight osmolytes to resuscitate homeostasis. However, how zwitterionic osmolytes would tune the electrostatic interactions among charged biomacromolecular surfaces under salt stress has eluded mainstream investigations. Here, via combination of molecular simulation and experiment, we demonstrate that a set of zwitterionic osmolytes is able to restore the electrostatic interaction between two negatively charged surfaces that had been masked in the presence of salt. Interestingly, the mechanisms of resurrecting charge interaction under excess salt are revealed to be mutually divergent and osmolyte specific. In particular, glycine is found to competitively desorb the salt ions from the surface via its direct interaction with the surface. On the contrary, TMAO and betaine counteract salt stress by retaining adsorbed cations but partially neutralizing their charge density via ion-mediated interaction. These access to alternative modes of osmolytic actions would provide the cell the required flexibility in combating salt stress. read less USED (low confidence) V. Reshetniak, O. Reshetniak, A. Aborkin, V. Nederkin, and A. Filippov, “Effect of the Interface on the Compressibility of Substances with Spherical Nano-Inhomogeneities on the Example of Al/C60,” Nanomaterials. 2022. link Times cited: 3 Abstract: The paper examines the compressibility of media with nano-in… read moreAbstract: The paper examines the compressibility of media with nano-inhomogeneities using the example of an aluminum melt and C60 fullerenes immersed in it. The results of molecular dynamics simulations indicate a significant effect of the interface on the effective compressibility of a heterogeneous medium. It is found that the application of the rule of mixture for the Al/C60 system results in an incorrect qualitative picture of the dependence of compressibility on the concentration of fullerenes. To explain this effect, an analytical model is proposed that takes into account the reduction in distances between atoms of different components during compression. The model makes it possible to estimate the effective mechanical characteristics of a liquid with nano-inhomogeneities within the framework of the mechanical approach, and correctly predicts the nature of the change in the dependence of compressibility on concentration. read less USED (low confidence) S. E. Hoff, D. D. Silvio, R. Ziolo, S. Moya, and H. Heinz, “Patterning of Self-Assembled Monolayers of Amphiphilic Multisegment Ligands on Nanoparticles and Design Parameters for Protein Interactions.,” ACS nano. 2022. link Times cited: 5 Abstract: Functionalization of nanoparticles with specific ligands is … read moreAbstract: Functionalization of nanoparticles with specific ligands is helpful to control specific diagnostic and therapeutic responses such as protein adsorption, cell targeting, and circulation. Precision delivery critically depends on a fundamental understanding of the interplay between surface chemistry, ligand dynamics, and interaction with the biochemical environment. Due to limited atomic-scale insights into the structure and dynamics of nanoparticle-bound ligands from experiments, relationships of grafting density and ligand chemistry to observable properties such as hydrophilicity and protein interactions remain largely unknown. In this work, we uncover how self-assembled monolayers (SAMs) composed of multisegment ligands such as thioalkyl-PEG-(N-alkyl)amides on gold nanoparticles can mimic mixed hydrophobic and hydrophilic ligand coatings, including control of patterns, hydrophilicity, and specific recognition properties. Our results are derived from molecular dynamics simulations with the INTERFACE-CHARMM36 force field at picometer resolution and comparisons to experiments. Small changes in ligand hydrophobicity, via adjusting the length of the N-terminal alkyl groups, tune water penetration by multiples and control superficial ordering of alkyl chains from 0 to 70% regularity. Further parameters include the grafting density of the ligands, curvature of the nanoparticle surfaces, type of solvent, and overall ligand length, which were examined in detail. We explain the thermodynamic origin of the formation of heterogeneous patterns of multisegment ligand SAMs and illustrate how different degrees of ligand order on the nanoparticle surface affect interactions with bovine serum albumin. The resulting design principles can be applied to a variety of ligand chemistries to customize the behavior of functionalized nanoparticles in biological media and enhance therapeutic efficiency. read less USED (low confidence) Y. Onabuta et al., “Analysis of the behavior of Zn atoms with a Pb additive on the surface during Zn electrodeposition,” Electrochemistry Communications. 2022. link Times cited: 1 USED (low confidence) W. Zhou, X. Yang, and X. Liu, “Multiscale modeling of gas flow behaviors in nanoporous shale matrix considering multiple transport mechanisms.,” Physical review. E. 2022. link Times cited: 5 Abstract: This study proposes a multiscale model combining molecular s… read moreAbstract: This study proposes a multiscale model combining molecular simulation and the lattice Boltzmann method (LBM) to explore gas flow behaviors with multiple transport mechanisms in nanoporous media of shale matrix. The gas adsorption characteristics in shale nanopores are first investigated by molecular simulations, which are then integrated and upscaled into the LBM model through a local adsorption density parameter. In order to adapt to high Knudsen number and nanoporous shale matrix, a multiple-relaxation-time pore-scale LBM model with a regularization procedure is developed. The combination of bounce-back and full diffusive boundary condition is adopted to take account of gas slippage and surface diffusion induced by gas adsorption. Molecular simulation results at the atomic scale show that gas adsorption behaviors are greatly affected by the pressure and pore size of the shale organic nanopore. At the pore scale, the gas transport behaviors with multiple transport mechanisms in nanoporous shale matrix are explored by the developed multiscale model. Simulation results indicate that pressure exhibits more significant influences on the transport behaviors of shale gas than temperature does. Compared with porosity, the average pore size of nanoporous shale matrix plays a more significant role in determining the apparent permeability of gas transport. The roles of the gas adsorption layer and surface diffusion in shale gas transport are discussed. It is observed that under low pressure, the gas adsorption layer has a positive influence on gas transport in shale matrix due to the strong surface diffusion effect. The nanoporous structure with the anisotropy characteristic parallel to the flow direction can enhance gas transport in shale matrix. The obtained results may provide underlying and comprehensive understanding of gas flow behaviors considering multiple transport mechanisms in shale matrix. Also, the proposed multiscale model can be considered as a powerful tool to invesigate the multiscale and multiphysical flow behaviors in porous media. read less USED (low confidence) M. Farouq, K. Kubiak-Ossowska, M. M. A. Qaraghuli, V. Ferro, and P. Mulheran, “Functionalisation of Inorganic Material Surfaces with Staphylococcus Protein A: A Molecular Dynamics Study,” International Journal of Molecular Sciences. 2022. link Times cited: 0 Abstract: Staphylococcus protein A (SpA) is found in the cell wall of … read moreAbstract: Staphylococcus protein A (SpA) is found in the cell wall of Staphylococcus aureus bacteria. Its ability to bind to the constant Fc regions of antibodies means it is useful for antibody extraction, and further integration with inorganic materials can lead to the development of diagnostics and therapeutics. We have investigated the adsorption of SpA on inorganic surface models such as experimentally relevant negatively charged silica, as well as positively charged and neutral surfaces, by use of fully atomistic molecular dynamics simulations. We have found that SpA, which is itself negatively charged at pH7, is able to adsorb on all our surface models. However, adsorption on charged surfaces is more specific in terms of protein orientation compared to a neutral Au (111) surface, while the protein structure is generally well maintained in all cases. The results indicate that SpA adsorption is optimal on the siloxide-rich silica surface, which is negative at pH7 since this keeps the Fc binding regions free to interact with other species in solution. Due to the dominant role of electrostatics, the results are transferable to other inorganic materials and pave the way for new diagnostic and therapeutic designs where SpA might be used to conjugate antibodies to nanoparticles. read less USED (low confidence) Y. Coskuner, E. Dean, X. Yin, and E. Ozkan, “Water Alternating Alkane Injection: A Molecular Dynamics Simulation Study,” Day 3 Wed, April 27, 2022. 2022. link Times cited: 0 Abstract:
In a recent study, we observed that the diffusion coeffici… read moreAbstract:
In a recent study, we observed that the diffusion coefficient of common hydrocarbons in crude oils are more affected by the presence of different hydrocarbon components than the effect of confinement. Based on our previous observations, in this study, we investigated the efficiency of smaller-chain alkane injection into oil-soaked sandstone pores to dilute the oil with alkane. We used molecular dynamics simulations of C2, C3, C4 and C5 as well as a mixture of C3 and C4 to rank the effects of different alkanes on the diffusion and distribution of oil molecules in pore. As water-alternating-alkane injection would bring water into the pores, our simulations included water. Our results indicate that alkane injection into sandstone reservoirs has a significant potential due to the fact that it effectively dilutes the oil. Water always wets quartz surface relative to the oils. Injection of water therefore should be effective in detaching oil molecules on the surface. Presence of water layers did not affect the diffusion coefficients of oil molecules. read less USED (low confidence) Y. Cao, Y. Qiao, S. Cui, and J. Ge, “Origin of Metal Cluster Tuning Enzyme Activity at the Bio-Nano Interface,” JACS Au. 2022. link Times cited: 4 Abstract: Detailed understanding of how the bio-nano interface orchest… read moreAbstract: Detailed understanding of how the bio-nano interface orchestrates the function of both biological components and nanomaterials remains ambiguous. Here, through a combination of experiments and molecular dynamics simulations, we investigated how the interface between Candida Antarctic lipase B and palladium (Pd) nanoparticles (NPs) tunes the structure, dynamics, and catalysis of the enzyme. Our simulations show that the metal binding to protein is a shape matching behavior and there is a transition from saturated binding to unsaturated binding along with the increase in the size of metal NPs. When we engineered the interface with the polymer, not only did the critical size of saturated binding of metal NPs become larger, but also the disturbance of the metal NPs to the enzyme function was reduced. In addition, we found that an enzyme–metal interface engineered with the polymer can boost bio-metal cascade reactions via substrate channeling. Understanding and control of the bio-nano interface at the molecular level enable us to rationally design bio-nanocomposites with prospective properties. read less USED (low confidence) D. García‐Lojo et al., “Bolaform Surfactant‐Induced Au Nanoparticle Assemblies for Reliable Solution‐Based Surface‐Enhanced Raman Scattering Detection,” Advanced Materials Technologies. 2022. link Times cited: 0 Abstract: Solution‐based surface‐enhanced Raman scattering (SERS) dete… read moreAbstract: Solution‐based surface‐enhanced Raman scattering (SERS) detection typically involves the aggregation of citrate‐stabilized Au nanoparticles into colloidal assemblies. Although this sensing methodology offers excellent prospects for sensitivity, portability, and speed, it is still challenging to control the assembly process by a salting‐out effect, which affects the reproducibility of the assemblies and, therefore, the reliability of the analysis. This work presents an alternative approach that uses a bolaform surfactant, B20, to induce the plasmonic assembly. The decrease of the surface charge and the bridging effect, both promoted by the adsorption of B20, are hypothesized as the key points governing the assembly. Furthermore, molecular dynamic simulations supported the bridging effect of the B20 by showing the preferential bridging of surfactant monomers between two adjacent Au(111) slabs. The colloidal assemblies showed excellent SERS capabilities towards the rapid, on‐site detection and quantification of beta‐blockers and analgesic drugs in the nanomolar regime, with a portable Raman device. Interestingly, the application of state‐of‐the‐art convolutional neural networks, such as ResNet, allows a 100% accuracy in classifying the concentration of different binary mixtures. Finally, the colloidal approach was successfully implemented in a millifluidic chip allowing the automation of the whole process, as well as improving the performance of the sensor in terms of speed, reliability, and reusability without affecting its sensitivity. read less USED (low confidence) N. Kruchinin and M. Kucherenko, “Statistical and Molecular-Dynamics Simulation of Electrically Induced Changes in the Conformational Structure of Polyampholytes on the Surface of a Flattened Metal Nanospheroid,” Colloid Journal. 2022. link Times cited: 1 USED (low confidence) Z. Chen et al., “Investigation of Multilayered Structures of Ionic Liquids on Graphite and Platinum Using Atomic Force Microscopy and Molecular Simulations.,” Langmuir : the ACS journal of surfaces and colloids. 2022. link Times cited: 4 Abstract: The molecular-level orientation and structure of ionic liqui… read moreAbstract: The molecular-level orientation and structure of ionic liquids (ILs) at liquid-solid interfaces are significantly different than in the bulk. The interfacial ordering influences both IL properties, such as dielectric constants and viscosity, and their efficacy in devices, such as fuel cells and electrical capacitors. Here, we report the layered structures of four ILs on unbiased, highly ordered pyrolytic graphite (HOPG) and Pt(111) surfaces, as determined by atomic force microscopy. The ILs investigated are 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ([emim][Tf2N]), 1-ethyl-3-methylimidazolium perfluorobutylsulfonate ([emim][C4F9SO3]), 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene bis(trifluoromethylsulfonyl)imide ([MTBD][Tf2N]), and 7-methyl-1,5,7-triazabicyclo[4.4.0]dec-5-ene perfluorobutylsulfonate ([MTBD][C4F9SO3]). Molecular dynamics simulations provide complementary information on the position and orientation of the ions. These ILs form a cation layer at the IL-solid interface, followed by a layer of anions. [Emim]+ and [MTBD]+ have similar orientations at the surface, but [MTBD]+ forms a thinner layer compared to [emim]+ on both HOPG and Pt(111). In addition, [Tf2N]- shows stronger interactions with Pt(111) surfaces than [C4F9SO3]-. read less USED (low confidence) T. Tanaka, Y. Hamanaka, T. Kato, and K. Uchida, “Simultaneous Detection of Mixed-Gas Components by Ionic-Gel Sensors with Multiple Electrodes.,” ACS sensors. 2022. link Times cited: 5 Abstract: The sensing of gas components in a mixed gas is required for… read moreAbstract: The sensing of gas components in a mixed gas is required for breath-based health monitoring and diagnosis. In this work, we report the simultaneous detection of mixed-gas components using a sensor consisting of [EMIM][BF4]-based ionic gel with four electrodes made of Au, Pt, Rh, and Cr. The voltage between any given pair of electrodes depends on the gas molecules absorbed in the ionic gel and the elements the electrodes are made of. When the voltage signals between all pairs of electrodes were used, H2, NH3, and C2H5OH concentrations were simultaneously estimated by a neural-network-based inference. From molecular dynamics simulations, the origin of the voltage signal was attributed to the catalytically generated adsorbates on the electrodes. read less USED (low confidence) A. Chew, J. Pedersen, and R. V. V. Lehn, “Predicting the Physicochemical Properties and Biological Activities of Monolayer-Protected Gold Nanoparticles Using Simulation-Derived Descriptors.,” ACS nano. 2022. link Times cited: 8 Abstract: Gold nanoparticles are versatile materials for biological ap… read moreAbstract: Gold nanoparticles are versatile materials for biological applications because their properties can be modulated by assembling ligands on their surface to form monolayers. However, the physicochemical properties and behaviors of monolayer-protected nanoparticles in biological environments are difficult to anticipate because they emerge from the interplay of ligand-ligand and ligand-solvent interactions that cannot be readily inferred from ligand chemical structure alone. In this work, we demonstrate that quantitative nanostructure-activity relationship (QNAR) models can employ descriptors calculated from molecular dynamics simulations to predict nanoparticle properties and cellular uptake. We performed atomistic molecular dynamics simulations of 154 monolayer-protected gold nanoparticles and calculated a small library of simulation-derived descriptors that capture nanoparticle structural and chemical properties in aqueous solution. We then parametrized QNAR models using interpretable regression algorithms to predict experimental measurements of nanoparticle octanol-water partition coefficients, zeta potentials, and cellular uptake obtained from a curated database. These models reveal that simulation-derived descriptors can accurately predict experimental trends and provide physical insight into what descriptors are most important for obtaining desired nanoparticle properties or behaviors in biological environments. Finally, we demonstrate model generalizability by predicting cell uptake trends for 12 nanoparticles not included in the original data set. These results demonstrate that QNAR models parametrized with simulation-derived descriptors are accurate, generalizable computational tools that could be used to guide the design of monolayer-protected gold nanoparticles for biological applications without laborious trial-and-error experimentation. read less USED (low confidence) H. Singh and S. Sharma, “Determination of Equilibrium Adsorbed Morphologies of Surfactants at Metal-Water Interfaces Using a Modified Umbrella Sampling-Based Methodology.,” Journal of chemical theory and computation. 2022. link Times cited: 5 Abstract: Surfactants adsorb to metal-water interfaces in various morp… read moreAbstract: Surfactants adsorb to metal-water interfaces in various morphologies, including self-assembled monolayers (SAMs), cylindrical and spherical micelles, or hemimicelles. Current molecular simulation methods are unable to efficiently sample the formation of these morphologies because of the large diffusive/energetic barriers. We introduce a modified umbrella sampling-based methodology that allows sampling of these morphologies from any initial configuration and provides free energy differences between them. Using this methodology, we have studied adsorption behavior of cationic [quaternary ammonium (quat) of 4 and 12 carbon long alkyl tails], uncharged [decanethiol], and anionic [phosphate monoester] surfactants and their mixtures at a gold-water interface. We find that while Coulombic repulsion between the charged head groups of quat-4 limits their adsorption to a sparse layer, stronger hydrophobic interactions between the alkyl tails of quat-12 promote adsorption resulting in a morphology with adsorbed hemispherical micelles sitting atop a monolayer. Decanethiol molecules adsorb in a densely packed bilayer with the molecules standing-up on the surface in the first layer and lying parallel to the surface in the second layer. Cationic and anionic surfactant mixtures display a synergistic adsorption behavior. These results elucidate the role of molecular characteristics in dictating the nature of adsorbed morphologies of surfactants at metal-water interfaces. read less USED (low confidence) X. Wei, A. Popov, and R. Hernandez, “Electric Potential of Citrate-Capped Gold Nanoparticles Is Affected by Poly(allylamine hydrochloride) and Salt Concentration.,” ACS applied materials & interfaces. 2022. link Times cited: 8 Abstract: The structure near polyelectrolyte-coated gold nanoparticles… read moreAbstract: The structure near polyelectrolyte-coated gold nanoparticles (AuNPs) is of significant interest because of the increased use of AuNPs in technological applications and the possibility that the acquisition of polyelectrolytes can lead to novel chemistry in downstream environments. We use all-atom molecular dynamics (MD) simulations to reveal the electric potential around citrate-capped gold nanoparticles (cit-AuNPs) and poly(allylamine hydrochloride) (PAH)-wrapped cit-AuNP (PAH-AuNP). We focus on the effects of the overall ionic strength and the shape of the electric potential. The ionic number distributions for both cit-AuNP and PAH-AuNP are calculated using MD simulations at varying salt concentrations (0, 0.001, 0.005, 0.01, 0.05, 0.1, and 0.2 M NaCl). The net charge distribution (Z(r)) around the nanoparticle is determined from the ionic number distribution observed in the simulations and allows for the calculation of the electric potential (ϕ(r)). We find that the magnitude of ϕ(r) decreases with increasing salt concentration and upon wrapping by PAH. Using a hydrodynamic radius (RH) estimated from the literature and fits to the Debye-Hü̈ckel expression, we found and report the ζ potential for both cit-AuNP and PAH-AuNP at varying salt concentrations. For example, at 0.001 M NaCl, MD simulations suggest that ζ = -25.5 mV for cit-AuNP. Upon wrapping of cit-AuNP by one PAH chain, the resulting PAH-AuNP exhibits a reduced ζ potential (ζ = -8.6 mV). We also compare our MD simulation results for ϕ(r) to the classic Poisson-Boltzmann equation (PBE) approximation and the well-known Derjaguin-Landau-Verwey-Overbeek (DLVO) theory. We find agreement with the limiting regimes─with respect to surface charge, salt concentration and particle size─in which the assumptions of the PBE and DLVO theory are known to be satisfied. read less USED (low confidence) W. Liu, N. Li, Z. Sun, Z. Wang, and Z. Wang, “Binary droplet coalescence in shear gas flow: A molecular dynamics study,” Journal of Molecular Liquids. 2022. link Times cited: 5 USED (low confidence) W. Schmickler, G. Belletti, and P. Quaino, “The approach of alkali ions towards an electrode surface – a molecular dynamics study,” Chemical Physics Letters. 2022. link Times cited: 4 USED (low confidence) B. Xi, T. Zhao, Q. Gao, Z. Wei, and S. Zhao, “Surface Wettability Effect on Heat Transfer across Solid-Water Interfaces,” Chemical Engineering Science. 2022. link Times cited: 3 USED (low confidence) N. Liu, T. Li, T. Liu, and L. Yang, “Molecular dynamics simulations of metal nanoparticles effects on methane hydrate formation,” Journal of Molecular Liquids. 2022. link Times cited: 1 USED (low confidence) N. Kruchinin and M. Kucherenko, “Molecular Dynamics Simulation of the Conformational Structure of Uniform Polypeptides on the Surface of a Polarized Metal Prolate Nanospheroid with Varying pH,” Russian Journal of Physical Chemistry A. 2022. link Times cited: 2 USED (low confidence) M. Moulod and S. Moghaddam, “High directional water transport graphene oxide biphilic stack,” Molecular Simulation. 2022. link Times cited: 0 Abstract: ABSTRACT It is a widely held view that the hydrophilicity of… read moreAbstract: ABSTRACT It is a widely held view that the hydrophilicity of graphene oxide (GO) enhances the water transport properties. In this study, it is shown that a combination of graphene and GO can yield superior transport properties including high mass flow rate and directionality. First, different membrane characteristics such as the smallest pore diameter for water molecules sieving and mass flow rate are evaluated. Furthermore, a combination of graphene and GO, a biphilic stack of hydrophobic and hydrophilic layers, is used to evaluate the mass flow rates and results are compared with that of normal GO laminates. This structure acts as a water diode i.e. conducts water molecules in the desired direction and increases the mass flow rate several times. The effects of interatomic potential, oxidation level and charge, and the spacing between layers on mass flow rate and directionality are examined. It is found that an optimized structure conducts water in the desired direction and increases mass flow rate up to 10 times for small interlayer distance of 7 Å compared with normal GO laminates. The given structures can be used in a wide range of filtration applications, where selective water sieving with a high mass flow rate is desired. read less USED (low confidence) N. Kruchinin and M. Kucherenko, “Conformational Changes of Polyelectrolyte Macromolecules on the Surface of Charged Prolate Metal Nanospheroid in Alternating Electric Field,” Polymer Science, Series A. 2022. link Times cited: 1 USED (low confidence) S. Sarkar, A. Guha, T. N. Narayanan, and J. Mondal, “Zwitterionic Osmolytes Employ Dual Mechanisms for Resurrection of Surface Charge under Salt-stress.” 2022. link Times cited: 0 Abstract: Salt imbalance in cells is a major detrimental abiotic stres… read moreAbstract: Salt imbalance in cells is a major detrimental abiotic stress which causes ionic toxicity and disrupts important cellular functions. To counter this saline stress, cell often produces low molecular weight cosolutes, known as osmolytes, which have the ability to resuscitate homeostasis. Here we combine atomistic computer simulation, contact angle measurements and Raman spectroscopic analysis to identify the mechanistic role of multiple osmolytes (glycine, TMAO and betaine) in modulating the electrostatic interaction under salt stress, a slowly emerging aspect of osmoprotection. By utilising a pair of negatively charged silica surfaces in a ternary mixture of osmolyte and KCl solution as a proxy of charged surface of biomacromolecule, our investigation reveals that all three osmolytes are able to resurrect the electrostatic interaction between the two surfaces, which had been otherwise charge-screened by excess salt. The joint venture of experiment and simulation discover dual and mutually exclusive mechanisms of recovering charge interaction by zwitter-ionic osmolytes. However, the relative ability and the underlying mechanism of revival of electrostatic interactions are found to be strongly dependent of chemical nature of osmolyte. Specifically, glycine was found to competitively desorb the salt-ions from the surface via its direct interaction with the surface. On the other hand, TMAO and betaine counter-act salt stress by retaining adsorbed cations but partially neutralising their charge-density via ion-mediated interaction. We believe that the access to dual and mutually alternative modes of osmolytic actions, as elucidated here, would provide the cell the required adaptability in combating salt-stress. read less USED (low confidence) J. G, R. S. Varatharaj, and M. J, “Influence of elemental composition on structural, thermal and hydration behavior of gold-silver bimetallic nanoparticles,” Journal of Molecular Modeling. 2022. link Times cited: 1 USED (low confidence) D. Martí, E. Martín-Martinez, J. Torras, O. Betran, P. Turon, and C. Aléman, “In silico study of substrate chemistry effect on the tethering of engineered antibodies for SARS-CoV-2 detection: Amorphous silica vs gold,” Colloids and Surfaces. B, Biointerfaces. 2022. link Times cited: 1 USED (low confidence) A. Gross and S. Sakong, “Ab Initio Simulations of Water/Metal Interfaces.,” Chemical reviews. 2022. link Times cited: 38 Abstract: Structures and processes at water/metal interfaces play an i… read moreAbstract: Structures and processes at water/metal interfaces play an important technological role in electrochemical energy conversion and storage, photoconversion, sensors, and corrosion, just to name a few. However, they are also of fundamental significance as a model system for the study of solid-liquid interfaces, which requires combining concepts from the chemistry and physics of crystalline materials and liquids. Particularly interesting is the fact that the water-water and water-metal interactions are of similar strength so that the structures at water/metal interfaces result from a competition between these comparable interactions. Because water is a polar molecule and water and metal surfaces are both polarizable, explicit consideration of the electronic degrees of freedom at water/metal interfaces is mandatory. In principle, ab initio molecular dynamics simulations are thus the method of choice to model water/metal interfaces, but they are computationally still rather demanding. Here, ab initio simulations of water/metal interfaces will be reviewed, starting from static systems such as the adsorption of single water molecules, water clusters, and icelike layers, followed by the properties of liquid water layers at metal surfaces. Technical issues such as the appropriate first-principles description of the water-water and water-metal interactions will be discussed, and electrochemical aspects will be addressed. Finally, more approximate but numerically less demanding approaches to treat water at metal surfaces from first-principles will be briefly discussed. read less USED (low confidence) P. Sarker, M. S. J. Sajib, X. Tao, and T. Wei, “Multiscale Simulation of Protein Corona Formation on Silver Nanoparticles: Study of Ovispirin-1 Peptide Adsorption.,” The journal of physical chemistry. B. 2022. link Times cited: 6 Abstract: The exposure of nanoparticles (NPs) to biofluids leads to th… read moreAbstract: The exposure of nanoparticles (NPs) to biofluids leads to the rapid coverage of proteins, named protein corona, which alters the NPs' chemicophysical and biological properties. Fundamental studies of the protein corona are thus critical to the increasing applications of NPs in nanotechnology and nanomedicines. The present work utilizes multiscale simulations of a model biological system, small ovispirin-1 peptides, and bare silver nanoparticles (AgNPs) to examine the NPs' size and surface hydrophilicity effects on formation dynamics and the structure of the peptide corona. Our simulations revealed the different adsorption dynamics of ovispirin-1 peptides on the NPs, including the direct adsorption of a single peptide and peptide aggregates and multistep adsorption, as well as an intermediate cycle of desorption and readsorption. Notably, the whole process of peptide adsorption on hydrophilic AgNP surfaces can be generalized as three stages: diffusion to the surface, initial landing via hydrophilic residues, and the final attachment. The decrease in AgNP's size leads to faster adsorption with more heterogeneous peptide interfacial dynamics, a denser and inhomogeneous peptide packing structure, and a wider distribution of adsorption orientations. Subsequent atomistic molecular dynamics simulations demonstrated that on the hydrophilic AgNP surfaces, adsorbed peptides display moderate changes in their secondary structure, resulting in further changes of corona composition, i.e., amino acid residue distribution on the surface. read less USED (low confidence) I. M. P. Espinosa, S. Azadehranjbar, R. Ding, A. Baker, T. Jacobs, and A. Martini, “Platinum nanoparticle compression: Combining in situ TEM and atomistic modeling,” Applied Physics Letters. 2022. link Times cited: 6 USED (low confidence) S. M. Hatam-Lee, F. Jabbari, and A. Rajabpour, “Interfacial thermal conductance between gold and SiO2: A molecular dynamics study,” Nanoscale and Microscale Thermophysical Engineering. 2022. link Times cited: 2 Abstract: ABSTRACT Silica coating on a gold nanoparticle can improve i… read moreAbstract: ABSTRACT Silica coating on a gold nanoparticle can improve its thermal application in cancer thermotherapy. In this paper, the interfacial thermal conductance between gold and silica is calculated utilizing classical non-equilibrium molecular dynamics. It is revealed that the results of molecular dynamics are different from what has been predicted by the conventional diffuse mismatch model. Furthermore, the interfacial thermal conductance between amorphous SiO2 and gold is approximately twice that of crystalline silica, which is explained by calculating the vibrational density of state mismatches. The interfacial thermal conductance variations in terms of van der Waals interaction strength between gold and silica are also investigated. It is revealed that the conductance increases by about 30% by increasing the simulation temperature from 300 to 700 K. The results of this paper can be useful in nanofluid systems, in addition to the application of silica-coated gold nanoparticles in cancer thermal therapy. read less USED (low confidence) W. Deng, S. Ahmad, H. Liu, J. Chen, and W. Zhao, “Improving boiling heat transfer with hydrophilic/hydrophobic patterned flat surface: A molecular dynamics study,” International Journal of Heat and Mass Transfer. 2022. link Times cited: 13 USED (low confidence) S. Lyu, Z. Yang, and Y. Duan, “The sliding mode and dissipative force of moving nanodroplets on smooth and striped hydrophobic surfaces,” Journal of Molecular Liquids. 2022. link Times cited: 4 USED (low confidence) K. Haseena, M. Gupta, A. Madhu, A. Narang, M. I. Alam, and M. Haider, “Understanding Catalyst Inhibition from Biogenic Impurities in Transfer Hydrogenation of a Biorenewable Platform Chemical,” Journal of Environmental Chemical Engineering. 2022. link Times cited: 0 USED (low confidence) H. Zhang, L. Pan, and X. Xie, “Molecular Dynamics Simulation on Behaviors of Water Nanodroplets Impinging on Moving Surfaces,” Nanomaterials. 2022. link Times cited: 2 Abstract: Droplets impinging on solid surfaces is a common phenomenon.… read moreAbstract: Droplets impinging on solid surfaces is a common phenomenon. However, the motion of surfaces remarkably influences the dynamical behaviors of droplets, and related research is scarce. Dynamical behaviors of water nanodroplets impinging on translation and vibrating solid copper surfaces were investigated via molecular dynamics (MD) simulation. The dynamical characteristics of water nanodroplets with various Weber numbers were studied at five translation velocities, four vibration amplitudes, and five vibration periods of the surface. The results show that when water nanodroplets impinge on translation surfaces, water molecules not only move along the surfaces but also rotate around the centroid of the water nanodroplet at the relative sliding stage. Water nanodroplets spread twice in the direction perpendicular to the relative sliding under a higher surface translation velocity. Additionally, a formula for water nanodroplets velocity in the translation direction was developed. Water nanodroplets with a larger Weber number experience a heavier friction force. For cases wherein water nanodroplets impinge on vibration surfaces, the increase in amplitudes impedes the spread of water nanodroplets, while the vibration periods promote it. Moreover, the short-period vibration makes water nanodroplets bounce off the surface. read less USED (low confidence) W. Liu, N. Li, Z. Sun, Z. Wang, and Z. Wang, “Molecular Dynamics Study on Regimes of Head-on Droplet Collision.,” Langmuir : the ACS journal of surfaces and colloids. 2021. link Times cited: 2 Abstract: The head-on collision of two water droplets with a diameter … read moreAbstract: The head-on collision of two water droplets with a diameter of 10 nm in an atmospheric environment was investigated via molecular dynamics simulations. The gas molecules between droplets were visualized, and the phenomena of gas extrusion and gas molecules being captured were found. By observing and analyzing the holes regime, a "periphery-sucking" mechanism was proposed to explain the thinning in the middle of the expanding disk and the holes appearing. It was found that the splattering regime can be divided into the limited splattering regime and the divergent splattering regime. The splattering modes and droplet characteristics of the two regimes are markedly different. The non-bonded interactions and intermolecular hydrogen bond were analyzed, and it was found that increasing the Weber number (We) can effectively promote the mixing of the two droplets, promote the formation of an intermolecular hydrogen bond between the two droplets, and reduce the average lifetime of the intermolecular hydrogen bond. The radial distribution function between the water molecules was plotted, showing that increasing the We makes the water molecules more dispersed as a whole in the collision process. read less USED (low confidence) Y. Noh and N. Aluru, “Phonon-Fluid Coupling Enhanced Water Desalination in Flexible Two-Dimensional Porous Membranes.,” Nano letters. 2021. link Times cited: 14 Abstract: Water purification using 2D nanoporous membranes has been dr… read moreAbstract: Water purification using 2D nanoporous membranes has been drawing significant attention for over a decade because of fast water transport in ultrathin membranes. We perform a comprehensive study using molecular dynamics (MD) simulations on water desalination using 2D flexible membranes where the coupling between the fluid dynamics and mechanics of the membrane plays an important role. We observe that a considerable deformation and fluctuation in the 2D membrane results in an enhanced water permeability (up to 122%) along with a slight decrease in the salt rejection rate (less than 11%). Simulations on harmonically vibrating membranes indicate that the vibrational match at the membrane-water interface can significantly increase the permeance. We conduct mechanical stability tests and discuss the maximum endurable pressure of 2D porous membranes for water desalination. These findings will contribute to advances in applications using ultrathin membranes, such as energy harvesting and molecular separation. read less USED (low confidence) X.-lei He et al., “Effects of Nanodroplet Sizes on Wettability, Electrowetting Transition, and Spontaneous Dewetting Transition on Nanopillar-Arrayed Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2021. link Times cited: 6 Abstract: In this study, the wetting and dewetting behaviors of water … read moreAbstract: In this study, the wetting and dewetting behaviors of water nanodroplets containing various molecule numbers on nanopillar-arrayed surfaces in the presence or absence of an external electric field are investigated via molecular dynamics (MD) simulations, aiming to examine whether there is a scale effect. The results show that, in the absence of an electric field, nanodroplets on coexisting Cassie/Wenzel surfaces may be in the Cassie or the Wenzel state depending on their initial states, and apparent contact angles of the Cassie or Wenzel nanodroplets increase monotonously with increasing the droplet size. Energy analysis shows that on the same coexisting Cassie/Wenzel surface, when an electric field is imposed, a small nanodroplet possesses a lower energy barrier separating the Cassie state from the Wenzel state. Therefore, the small nanodroplet is easier to collapse into the Wenzel state. Moreover, the spontaneous Wenzel-to-Cassie dewetting transition is not observed for the nanodroplets after the removal of the electric field because the Wenzel state is a globally stable energetic state. With the same pillar geometry, both the wetting transition and the dewetting transition are significantly modified for liquids with higher intrinsic contact angles. The energy barrier of the wetting transition increases for both the large and small nanodroplets, meaning that the Cassie state becomes more robust. The energy curve shows that the Wenzel state of the large nanodroplet has higher energy so that the droplet can return to the Cassie state when removing the electric field. Intriguingly, although the small Wenzel nanodroplet has lower energy in the presence of the electric field, the dewetting transition still occurs. The increased solid-liquid interfacial tension when removing the electric field is responsible for this abnormal result. The wetting and dewetting transitions follow different energy pathways, leading to a hysteresis energy loop. There exists a critical water molecule number separating the unstable/stable Wenzel configurations, above which the Cassie state is energetically favorable and the dewetting transition can occur spontaneously after removing the electric field. read less USED (low confidence) Y. Choi et al., “CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems.,” Journal of chemical theory and computation. 2021. link Times cited: 38 Abstract: Molecular modeling and simulation are invaluable tools for n… read moreAbstract: Molecular modeling and simulation are invaluable tools for nanoscience that predict mechanical, physicochemical, and thermodynamic properties of nanomaterials and provide molecular-level insight into underlying mechanisms. However, building nanomaterial-containing systems remains challenging due to the lack of reliable and integrated cyberinfrastructures. Here we present Nanomaterial Modeler in CHARMM-GUI, a web-based cyberinfrastructure that provides an automated process to generate various nanomaterial models, associated topologies, and configuration files to perform state-of-the-art molecular dynamics simulations using most simulation packages. The nanomaterial models are based on the interface force field, one of the most reliable force fields (FFs). The transferability of nanomaterial models among the simulation programs was assessed by single-point energy calculations, which yielded 0.01% relative absolute energy differences for various surface models and equilibrium nanoparticle shapes. Three widely used Lennard-Jones (LJ) cutoff methods are employed to evaluate the compatibility of nanomaterial models with respect to conventional biomolecular FFs: simple truncation at r = 12 Å (12 cutoff), force-based switching over 10 to 12 Å (10-12 fsw), and LJ particle mesh Ewald with no cutoff (LJPME). The FF parameters with these LJ cutoff methods are extensively validated by reproducing structural, interfacial, and mechanical properties. We find that the computed density and surface energies are in good agreement with reported experimental results, although the simulation results increase in the following order: 10-12 fsw <12 cutoff < LJPME. Nanomaterials in which LJ interactions are a major component show relatively higher deviations (up to 4% in density and 8% in surface energy differences) compared with the experiment. Nanomaterial Modeler's capability is also demonstrated by generating complex systems of nanomaterial-biomolecule and nanomaterial-polymer interfaces with a combination of existing CHARMM-GUI modules. We hope that Nanomaterial Modeler can be used to carry out innovative nanomaterial modeling and simulations to acquire insight into the structure, dynamics, and underlying mechanisms of complex nanomaterial-containing systems. read less USED (low confidence) L. A. A. Kury et al., “Single-Walled Carbon Nanotubes Inhibit TRPC4-Mediated Muscarinic Cation Current in Mouse Ileal Myocytes,” Nanomaterials. 2021. link Times cited: 2 Abstract: Single-walled carbon nanotubes (SWCNTs) are characterized by… read moreAbstract: Single-walled carbon nanotubes (SWCNTs) are characterized by a combination of rather unique physical and chemical properties, which makes them interesting biocompatible nanostructured materials for various applications, including in the biomedical field. SWCNTs are not inert carriers of drug molecules, as they may interact with various biological macromolecules, including ion channels. To investigate the mechanisms of the inhibitory effects of SWCNTs on the muscarinic receptor cation current (mICAT), induced by intracellular GTPγs (200 μM), in isolated mouse ileal myocytes, we have used the patch-clamp method in the whole-cell configuration. Here, we use molecular docking/molecular dynamics simulations and direct patch-clamp recordings of whole-cell currents to show that SWCNTs, purified and functionalized by carboxylation in water suspension containing single SWCNTs with a diameter of 0.5–1.5 nm, can inhibit mICAT, which is mainly carried by TRPC4 cation channels in ileal smooth muscle cells, and is the main regulator of cholinergic excitation–contraction coupling in the small intestinal tract. This inhibition was voltage-independent and associated with a shortening of the mean open time of the channel. These results suggest that SWCNTs cause a direct blockage of the TRPC4 channel and may represent a novel class of TRPC4 modulators. read less USED (low confidence) Z. Wang, P. Wang, H.-S. Song, and Z. Chen, “Dynamic wetting behavior of nanofluid droplet on a vertically vibrating surface: A molecular dynamics study,” Journal of Molecular Liquids. 2021. link Times cited: 2 USED (low confidence) T. Zheng, S. Wang, L. Zhou, X. Li, and H. Zhang, “The disentanglement and shear properties of amorphous polyethylene during friction: Insights from molecular dynamics simulations,” Applied Surface Science. 2021. link Times cited: 6 USED (low confidence) S. Alfarano et al., “Stripping away ion hydration shells in electrical double-layer formation: Water networks matter,” Proceedings of the National Academy of Sciences of the United States of America. 2021. link Times cited: 13 Abstract: Significance For centuries the double layer at the solid/ele… read moreAbstract: Significance For centuries the double layer at the solid/electrolyte interface has been a central concept in electrochemistry. Today, it is still crucial for virtually all renewable energy storage and conversion technologies. Here, the double-layer formation is probed by THz spectroscopy with ultrabright synchrotron light as a source. Our results capture the molecular details of double-layer formation at positively/negatively charged Au electrodes for an NaCl electrolyte. We reveal a contrasting response applying positive versus negative bias, which is dictated by the interfacial water network and rationalized by accompanying molecular dynamics simulations and electronic-structure calculations. While Na+ is directly attracted toward the negatively charged electrode, stripping of the Cl− hydration shell is observed only at larger potential values. The double layer at the solid/electrolyte interface is a key concept in electrochemistry. Here, we present an experimental study combined with simulations, which provides a molecular picture of the double-layer formation under applied voltage. By THz spectroscopy we are able to follow the stripping away of the cation/anion hydration shells for an NaCl electrolyte at the Au surface when decreasing/increasing the bias potential. While Na+ is attracted toward the electrode at the smallest applied negative potentials, stripping of the Cl− hydration shell is observed only at higher potential values. These phenomena are directly measured by THz spectroscopy with ultrabright synchrotron light as a source and rationalized by accompanying molecular dynamics simulations and electronic-structure calculations. read less USED (low confidence) A. Yamada, “Classical electronic and molecular dynamics simulation for optical response of metal system.,” The Journal of chemical physics. 2021. link Times cited: 3 Abstract: An extended molecular dynamics simulation that incorporates … read moreAbstract: An extended molecular dynamics simulation that incorporates classical free electron dynamics in the framework of the force-field model has been developed to enable us to describe the optical response of metal materials under the visible light electric field. In the simulation, dynamical atomic point charges follow equations of motion of classical free electrons that include Coulomb interactions with the oscillating field and surrounding atomic sites and collision effects from nearby electrons and ions. This scheme allows us to simulate an interacting system of metals with molecules using an ordinary polarizable force-field and preserves energy conservation in the case without applying an external electric field. As the first applications, we show that the presented simulation accurately reproduces (i) the classical image potential in a metal-charge interaction system and (ii) the dielectric function of bulk metal. We also demonstrate (iii) calculations of absorption spectra of metal nano-particles with and without a water solvent at room temperature, showing reasonable red-shift by the solvent effect, and (iv) plasmon resonant excitation of the metal nano-particle in solution under the visible light pulse and succeeding energy relaxation of the absorbed light energy from electrons to atoms on the metal and to the water solvent. Our attempt thus opens the possibility to expand the force-field based molecular dynamics simulation to an alternative tool for optical-related fields. read less USED (low confidence) R. Singh, C. Hano, F. Tavanti, and B. Sharma, “Biogenic Synthesis and Characterization of Antioxidant and Antimicrobial Silver Nanoparticles Using Flower Extract of Couroupita guianensis Aubl.,” Materials. 2021. link Times cited: 6 Abstract: Couroupita guianensis Aubl. is an important medicinal tree. … read moreAbstract: Couroupita guianensis Aubl. is an important medicinal tree. This tree is rich in various phytochemicals, and is therefore used as a potent antioxidant and antibacterial agent. This plant is also used for the treatment of various diseases. Here, we have improved its medicinal usage with the biosynthesis of silver nanoparticles (AgNPs) using Couroupita guianensis Aubl. flower extract as a reducing and capping agent. The biosynthesis of the AgNPs reaction was carried out using 1 mM of silver nitrate and flower extract. The effect of the temperature on the biosynthesis of AgNPs was premeditated by room temperature (25 °C) and 60 °C. The continuous stirring of the reaction mixture at room temperature for approximately one hour resulted in the successful formation of AgNPs. A development of a yellowish brown color confirmed the formation of AgNPs. The efficacious development of AgNPs was confirmed by the characteristic peaks of UV–Vis, X-ray diffraction (XRD) and Fourier transform infrared (FT-IR) spectroscopy spectra. The biosynthesized AgNPs exhibited significant free radical scavenging activity through a DPPH antioxidant assay. These AgNPs also showed potent antibacterial activity against many pathogenic bacterial species. The results of molecular dynamics simulations also proved the average size of NPs and antibacterial potential of the flower extract. The observations clearly recommended that the green biosynthesized AgNPs can serve as effective antioxidants and antibacterial agents over the plant extract. read less USED (low confidence) S. Rabet and G. Raabe, “Comparison of the GAFF, OPLSAA and CHARMM27 Force Field for the Reproduction of the Thermodynamics Properties of Furfural, 2-Methylfuran, 2,5-Dimethylfuran and 5-Hydroxymethylfurfural,” Fluid Phase Equilibria. 2021. link Times cited: 3 USED (low confidence) N. Kruchinin and M. Kucherenko, “Modeling the Conformational Rearrangement of Polyampholytes on the Surface of a Prolate Spheroidal Metal Nanoparticle in Alternating Electric Field,” High Energy Chemistry. 2021. link Times cited: 4 USED (low confidence) R. Zhao, J. Li, Z. Zhang, R. Long, W. Liu, and Z. Liu, “Harvesting net power and desalinating water by pressure-retarded membrane distillation,” Science China Technological Sciences. 2021. link Times cited: 2 USED (low confidence) R. Zhao, J. Li, Z. Zhang, R. Long, W. Liu, and Z. Liu, “Harvesting net power and desalinating water by pressure-retarded membrane distillation,” Science China Technological Sciences. 2021. link Times cited: 0 USED (low confidence) X. Wei, Y. Zhao, Y. Zhuang, and R. Hernandez, “Building blocks for autonomous computing materials: Dimers, trimers, and tetramers.,” The Journal of chemical physics. 2021. link Times cited: 4 Abstract: Autonomous computing materials for data storage and computin… read moreAbstract: Autonomous computing materials for data storage and computing offer an opportunity for next generation of computing devices. Patchy nanoparticle networks, for example, have been suggested as potential candidates for emulating neuronal networks and performing brain-like computing. Here, we use molecular dynamics (MD) simulations to show that stable dimers, trimers, and tetramers can be built from citrate capped gold nanoparticles (cit-AuNPs) linked by poly(allylamine hydrochloride) (PAH) chains. We use different lengths of PAHs to build polymer-networked nanoparticle assemblies that can emulate a complex neuronal network linked by axons of varying lengths. We find that the tetramer structure can accommodate up to 11 different states when the AuNP pairs are connected by either of two polymer linkers, PAH200 and PAH300. We find that the heavy AuNPs contribute to the assembly's structure stability. To further illustrate the stability, the AuNP-AuNP distances in dimer, trimer, and tetramer structures are reduced by steering the cit-AuNPs closer to each other. At different distances, these steered structures are all locally stable in a 10 ns MD simulation time scale because of their connection to the AuNPs. We also find that the global potential energy minimum is at short AuNP-AuNP distances where AuNPs collapse because the -NH3 + and -COO- attraction reduces the potential energy. The stability and application of these fundamental structures remain to be further improved through the use of alternative polymer linkers and nanoparticles. read less USED (low confidence) Y. Pan, A. S. Blum, L. Simine, and J. Mauzeroll, “Nanometals Templated by Tobacco Mosaic Virus Coat Protein with Enhanced Catalytic Activity,” ECS Meeting Abstracts. 2021. link Times cited: 6 USED (low confidence) H. Liu, W. Deng, P. Ding, and W. Zhao, “Investigation of the effects of surface wettability and surface roughness on nanoscale boiling process using molecular dynamics simulation,” Nuclear Engineering and Design. 2021. link Times cited: 7 USED (low confidence) X. Deng, Y. Xiao, Q. Li, C. He, and S. Wang, “Evaporation of R1234yf, R1234ze(E) and R1234ze(Z) on Cu surface: A molecular dynamics study,” Journal of Molecular Liquids. 2021. link Times cited: 7 USED (low confidence) N. Kruchinin and M. Kucherenko, “REARRANGEMENTS IN THE CONFORMATIONAL STRUCTURE OF POLYAMPHOLYTIC POLYPEPTIDES ON THE SURFACE OF A UNIFORMLY CHARGED AND POLARIZED NANOWIRE: MOLECULAR DYNAMICS SIMULATION,” Surfaces and Interfaces. 2021. link Times cited: 10 USED (low confidence) H. A, Z. Yang, R. Hu, and Y. F. Chen, “Roles of energy dissipation and asymmetric wettability in spontaneous imbibition dynamics in a nanochannel.,” Journal of colloid and interface science. 2021. link Times cited: 4 USED (low confidence) J. Touzeau et al., “Theoretical and Experimental Elucidation of the Adsorption Process of a Bioinspired Peptide on Mineral Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2021. link Times cited: 2 Abstract: Inorganic materials used for biomedical applications such as… read moreAbstract: Inorganic materials used for biomedical applications such as implants generally induce the adsorption of proteins on their surface. To control this phenomenon, the bioinspired peptidomimetic polymer 1 (PMP1), which aims to reproduce the adhesion of mussel foot proteins, is commonly used to graft specific proteins on various surfaces and to regulate the interfacial mechanism. To date and despite its wide application, the elucidation at the atomic scale of the PMP1 mechanism of adsorption on surfaces is still unknown. The purpose of the present work was thus to unravel this process through experimental and computational investigations of adsorption of PMP1 on gold, TiO2, and SiO2 surfaces. A common mechanism of adsorption is identified for the adsorption of PMP1 which emphasizes the role of electrostatics to approach the peptide onto the surface followed by a full adhesion process where the entropic desolvation step plays a key role. Besides, according to the fact that mussel naturally controls the oxidation states of its proteins, further investigations were performed for two distinct redox states of PMP1, and we conclude that even if both states are able to allow interaction of PMP1 with the surfaces, the oxidation of PMP1 leads to a stronger interaction. read less USED (low confidence) A. O. Tipeev, J. Rino, and E. D. Zanotto, “Direct determination of Lennard-Jones crystal surface free energy by a computational cleavage method.,” The Journal of chemical physics. 2021. link Times cited: 4 Abstract: The surface free energy of solids, γ, plays a crucial role i… read moreAbstract: The surface free energy of solids, γ, plays a crucial role in all physical and chemical processes involving material surfaces. For the first time, we obtained γ directly from molecular dynamics simulations using a crystal cleavage method. The approach was successfully realized in a Lennard-Jones system by inserting two movable external walls, each consisting of a single crystal layer, into a bulk crystal to create flat, defect-free surfaces. The cleavage technique designed allowed us to calculate the surface free energy according to its definition and avoid surface premelting. The temperature dependence of γ was determined for the (100) and (110) crystal planes along the whole sublimation line and its metastable extension, up to T = 1.02 · Tm, where Tm is the melting point. Good agreement with indirect values of γ(T) was found. The proposed computational cleavage method can be applied to other solids of interest, providing valuable insight into the understanding of chemical and physical surface processes, and demonstrates the successful import of the cleavage method, traditionally used in technical preparation and study of crystal surfaces, into a modern atomistic simulation. read less USED (low confidence) S. Salassi et al., “A Martini Coarse Grained Model of Citrate-Capped Gold Nanoparticles Interacting with Lipid Bilayers,” Journal of Chemical Theory and Computation. 2021. link Times cited: 14 Abstract: Citrate capping is one of the most common strategies to achi… read moreAbstract: Citrate capping is one of the most common strategies to achieve the colloidal stability of Au nanoparticles (NPs) with diameters ranging from a few to hundreds of nanometers. Citrate-capped Au nanoparticles (CNPs) represent a step of the synthesis of Au NPs with specific functionalities, as CNPs can be further functionalized via ligand-exchange reactions, leading to the replacement of citrate with other organic ligands. In vitro, CNPs are also used to address the fundamental aspects of NP–membrane interactions, as they can directly interact with cells or model cell membranes. Their affinity for the bilayer is again mediated by the exchange of citrate with lipid molecules. Here, we propose a new computational model of CNPs compatible with the coarse grained Martini force field. The model, which we develop and validate through an extensive comparison with new all-atom molecular dynamics (MD) simulations and UV–vis and Fourier transform infrared spectroscopy data, is aimed at the MD simulation of the interaction between citrate-capped NPs and model phosphatidylcholine lipid membranes. As a test application we show that, during the interaction between a single CNP and a flat planar 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine bilayer, the citrate coating is spontaneously replaced by lipids on the surface of Au NPs, while the NP size and shape determine the final structural configuration of the NP–bilayer complex. read less USED (low confidence) Y. Zhou, G. Luo, Y. Hu, D. Wu, and Z. Yao, “Interaction properties between molten metal and quartz by molecular dynamics simulation,” Journal of Molecular Liquids. 2021. link Times cited: 2 USED (low confidence) N. Kruchinin and M. Kucherenko, “Molecular Dynamics Simulation of Conformational Rearrangements in Polyelectrolyte Macromolecules on the Surface of a Charged or Polarized Prolate Spheroidal Metal Nanoparticle,” Colloid Journal. 2021. link Times cited: 4 USED (low confidence) Z. Jiang et al., “Penetration and Displacement Behavior of N2 in Porous Interlayer Structures Containing Water/Salt Component by Molecular Dynamics Simulation,” Molecules. 2021. link Times cited: 0 Abstract: The penetration and displacement behavior of N2 molecules in… read moreAbstract: The penetration and displacement behavior of N2 molecules in porous interlayer structures containing a water/salt component with porosities of 4.29%, 4.73%, 5.17%, 7.22%, and 11.38% were explored using molecular dynamics simulations. The results demonstrated that the large porosity of the interlayer structures effectively enhanced the permeation and diffusion characteristics of N2. The water and salt in the interlayer structures were displaced during the injection of N2 in the porosity sequence of 4.29% < 4.73% < 5.17% < 7.22% < 11.38%. The high permeance of 7.12 × 10−6 indicated that the interlayer structures with a porosity of 11.38% have better movability. The strong interaction of approximately 15 kcal/mol between N2 and H2O had a positive effect on the diffusion of N2 and the displacement of H2O before it reached a stable equilibrium state. The distribution of N2 in porous interlayer structures and the relationship between the logarithm of permeability and breakthrough pressure were presented. This work highlighted the effects of porosity on the permeability and diffusion of N2/H2O in the interlayer, thus providing theoretical guidance for the development of petroleum resources. read less USED (low confidence) A. R. Zolghadr, O. Estakhr, M. H. Dokoohaki, and H. Salari, “Comparison between Bi2WO6 and TiO2 Photoanodes in Dye-Sensitized Solar Cells: Experimental and Computational Studies,” Industrial & Engineering Chemistry Research. 2021. link Times cited: 6 USED (low confidence) B. Huang et al., “Cation- and pH-Dependent Hydrogen Evolution and Oxidation Reaction Kinetics,” JACS Au. 2021. link Times cited: 66 Abstract: The production of molecular hydrogen by catalyzing water spl… read moreAbstract: The production of molecular hydrogen by catalyzing water splitting is central to achieving the decarbonization of sustainable fuels and chemical transformations. In this work, a series of structure-making/breaking cations in the electrolyte were investigated as spectator cations in hydrogen evolution and oxidation reactions (HER/HOR) in the pH range of 1 to 14, whose kinetics was found to be altered by up to 2 orders of magnitude by these cations. The exchange current density of HER/HOR was shown to increase with greater structure-making tendency of cations in the order of Cs+ < Rb+ < K+ < Na+ < Li+, which was accompanied by decreasing reorganization energy from the Marcus–Hush–Chidsey formalism and increasing reaction entropy. Invoking the Born model of reorganization energy and reaction entropy, the static dielectric constant of the electrolyte at the electrified interface was found to be significantly lower than that of bulk, decreasing with the structure-making tendency of cations at the negatively charged Pt surface. The physical origin of cation-dependent HER/HOR kinetics can be rationalized by an increase in concentration of cations on the negatively charged Pt surface, altering the interfacial water structure and the H-bonding network, which is supported by classical molecular dynamics simulation and surface-enhanced infrared absorption spectroscopy. This work highlights immense opportunities to control the reaction rates by tuning interfacial structures of cation and solvents. read less USED (low confidence) R. Tesch, P. Kowalski, and M. Eikerling, “Properties of the Pt(111)/electrolyte electrochemical interface studied with a hybrid DFT–solvation approach,” Journal of Physics: Condensed Matter. 2021. link Times cited: 11 Abstract: Self-consistent modeling of the interface between solid meta… read moreAbstract: Self-consistent modeling of the interface between solid metal electrode and liquid electrolyte is a crucial challenge in computational electrochemistry. In this contribution, we adopt the effective screening medium reference interaction site method (ESM–RISM) to study the charged interface between a Pt(111) surface that is partially covered with chemisorbed oxygen and an aqueous acidic electrolyte. This method proves to be well suited to describe the chemisorption and charging state of the interface at controlled electrode potential. We present an in-depth assessment of the ESM–RISM parameterization and of the importance of computing near-surface water molecules explicitly at the quantum mechanical level. We found that ESM–RISM is able to reproduce some key interface properties, including the peculiar, non-monotonic charging relation of the Pt(111)/electrolyte interface. The comparison with independent theoretical models and explicit simulations of the interface reveals strengths and limitations of ESM–RISM for modeling electrochemical interfaces. read less USED (low confidence) M. H. Dokoohaki, F. Mohammadpour, and A. R. Zolghadr, “Dye-Sensitized Solar Cells Based on Deep Eutectic Solvent Electrolytes: Insights from Experiment and Simulation,” The Journal of Physical Chemistry C. 2021. link Times cited: 10 USED (low confidence) T. Murono, K. Hongo, K. Nakano, and R. Maezono, “Interface Modeling for the Ab Initio Evaluation of the Water Contact Angle on a Metallic Cu(111) Surface.” 2021. link Times cited: 0 Abstract:
Controlling the water contact angle on a surface is import… read moreAbstract:
Controlling the water contact angle on a surface is important for regulating its wettability in industrial applications. Therefore, it is crucial to develop ab initio evaluation methods that can accurately predict this angle. The ab initio predictions require an adsorption structure model for the adsorption of liquid molecules on a surface, but the construction of this model depends on whether the test surface comprises an insulating or metallic material because the surface reconstruction takes quite a different form in each case. Previous studies have focused on the estimation of the water contact angle on insulators; however, this study elucidates the water contact angle on a metallic surface, Cu(111). Because the feasibility of ab initio evaluations depends on the approximation of liquid–gas interface energy, which can be roughly estimated through the interface energy of crystal ice, it is natural to use the periodic-honeycomb array of water molecules as the adsorption model for the water on the surface. However, despite the successful application of the periodic model for ab initio prediction of the water contact angle on insulating surfaces, applying this model to metallic surfaces has not provided satisfactory predictions that reproduce experimental values. Therefore, in this study, we propose the use of models with isolated water oligomers for the ab initio prediction of the water contact angle on a metallic surface, which achieved an accurate prediction. The ambiguity of the models based on the size and coverage of the oligomers was small (∼ ±10 °), which was averaged out to give a plausible value based on the Boltzmann weight with the adsorbing energies. The proposed procedure can be used to estimate the wettability of the surfaces of other metallic materials. read less USED (low confidence) M. Dewapriya and R. E. Miller, “Energy absorption mechanisms of nanoscopic multilayer structures under ballistic impact loading,” Computational Materials Science. 2021. link Times cited: 22 USED (low confidence) L. Morillas-Becerril et al., “Specific and nondisruptive interaction of guanidium-functionalized gold nanoparticles with neutral phospholipid bilayers,” Communications Chemistry. 2021. link Times cited: 6 USED (low confidence) P. Molaghan, M. Jahanshahi, and M. Ahangari, “H2 and H2S separation by adsorption using graphene and zinc oxide sheets: Molecular dynamic simulations,” Physica B-condensed Matter. 2021. link Times cited: 3 USED (low confidence) R. Liu et al., “Study on novel PtNP-Sorafenib and its interaction with VEGFR2.,” Journal of biochemistry. 2021. link Times cited: 1 Abstract: With the developments of nanodrugs, some drugs have combined… read moreAbstract: With the developments of nanodrugs, some drugs have combined with nanoparticles (NPs) to reduce their side effects and increase their therapeutic activities. Here, a novel nano-drug PtNP-sorafenib (PtNP-SOR) was proposed for the first time. By means of molecular dynamics simulation, the stability and biocompatibility of PtNP-SOR were investigated. Then, the interaction mechanism between PtNP-SOR and vascular endothelial growth factor receptor 2 (VEGFR2) was explored and compared with that of the peptide 2a coated PtNPs (PtNP-2a). The results showed that PtNP-SOR could bind to VEGFR2 more stably, which was driven by the Coulombic (Coul) and strong dispersion interaction between PtNP-SOR and VEGFR2. According to their contributions obtained from the decomposition of binding free energies, the key residues in VEGFR2 were identified to form the specific space, which increased the affinity with PtNP-SOR. This study provided useful insights to the design of PtNP-drugs as well as important theoretical proofs to the interaction between PtNP-SOR and VEGFR2 at a molecular level, which can be of large help during the development and optimization of novel nanodrugs. read less USED (low confidence) J. Li et al., “Stack Thermo-Osmotic System for Low-Grade Thermal Energy Conversion.,” ACS applied materials & interfaces. 2021. link Times cited: 13 Abstract: Thermo-osmotic energy conversion (TOEC) technology, develope… read moreAbstract: Thermo-osmotic energy conversion (TOEC) technology, developed from membrane distillation, is an emerging method that has the potential of obtaining electricity efficiently from a low-grade heat source but faces the difficult problem of pump power loss. In this study, we build a novel TOEC system with a multistage architecture that can work without pump assistance. The experiment system, made of cheap commercial materials, can obtain a power density of 1.39 ± 0.25 W/m2, with a heating temperature of 80 °C, and its efficiency increased linearly with the total stage number. A theory calculation shows that a 30-stage system with a specific membrane and a working pressure of 5.0 MPa can obtain an efficiency of 2.72% with a power density of 14.0 W/m2. By a molecular dynamics simulation, it is shown that a high-performance membrane has the potential to work at 40 MPa. This study proves that TOEC technology is a practical and competitive approach to covert low-grade thermal energy into power efficiently. read less USED (low confidence) T. Yan and K. Fichthorn, “Self-Assembly of a Linear Alkylamine Bilayer around a Cu Nanocrystal: Molecular Dynamics.,” The journal of physical chemistry. B. 2021. link Times cited: 2 Abstract: Copper nanocrystals are often grown with the help of alkylam… read moreAbstract: Copper nanocrystals are often grown with the help of alkylamine capping agents, which direct the nanocrystal shape. However, the role of these molecules is still unclear. We characterized the assembly of aqueous tetradecylamine (TDA) around a Cu nanocrystal and found that TDA exhibits a temperature-dependent bilayer structure. The bilayer involves an inner layer, in which TDA binds to Cu via the amine group and tends to orient the alkyl tail perpendicular to the surface, and an outer layer whose structure depends on temperature. At low temperatures, alkylamines in the inner layer form bundles with no apparent relation to the crystal facets. Alkylamines in the outer layer tend to orient their long axes perpendicular to the Cu surfaces, with interdigitation into the inner layer. At high temperatures, alkylamines in the inner layer lose their bundle structure, and outer-layer alkylamines tend to orient themselves tangential to the Cu surfaces, forming a "web" above inner-layer TDA. TDA exhibits a rapid interlayer exchange at typical synthesis temperatures, consistent with experiment. The variety in the assemblies seen here and in other studies of alkanethiols around gold nanocrystals indicates a richness in the assemblies that can be achieved by modulating the interaction between the strongly binding end group and the surface. read less USED (low confidence) Z. Li, V. G. Ruiz, M. Kanduč, and J. Dzubiella, “Highly Heterogeneous Polarization and Solvation of Gold Nanoparticles in Aqueous Electrolytes.,” ACS nano. 2021. link Times cited: 3 Abstract: The performance of gold nanoparticles (NPs) in applications … read moreAbstract: The performance of gold nanoparticles (NPs) in applications depends critically on the structure of the NP-solvent interface, at which the electrostatic surface polarization is one of the key characteristics that affects hydration, ionic adsorption, and electrochemical reactions. Here, we demonstrate significant effects of explicit metal polarizability on the solvation and electrostatic properties of bare gold NPs in aqueous electrolyte solutions of sodium salts of various anions (Cl-, BF4-, PF6-, nitrophenolate, and 3- and 4-valent hexacyanoferrate), using classical molecular dynamics simulations with a polarizable core-shell model for the gold atoms. We find considerable spatial heterogeneity of the polarization and electrostatic potentials on the NP surface, mediated by a highly facet-dependent structuring of the interfacial water molecules. Moreover, ion-specific, facet-dependent ion adsorption leads to considerable alterations of the interfacial polarization. Compared to nonpolarizable NPs, surface polarization modifies water local dipole densities only slightly but has substantial effects on the electrostatic surface potentials and leads to significant lateral redistributions of ions on the NP surface. Besides, interfacial polarization effects cancel out in the far field for monovalent ions but not for polyvalent ions, as anticipated from continuum "image-charge" concepts. Far-field effective Debye-Hückel surface potentials change accordingly in a valence-specific fashion. Hence, the explicit charge response of metal NPs is crucial for the accurate description and interpretation of interfacial electrostatics (e.g., for charge transfer and interfacial polarization in catalysis and electrochemistry). read less USED (low confidence) P. Wang, L. He, and Z. Wang, “The effect of surface structure and arrangement on wettability of substrate surface,” Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2021. link Times cited: 8 USED (low confidence) C. A. Lochbaum, A. Chew, X. Zhang, V. Rotello, R. V. V. Lehn, and J. Pedersen, “Lipophilicity of Cationic Ligands Promotes Irreversible Adsorption of Nanoparticles to Lipid Bilayers.,” ACS nano. 2021. link Times cited: 20 Abstract: A mechanistic understanding of the influence of the surface … read moreAbstract: A mechanistic understanding of the influence of the surface properties of engineered nanomaterials on their interactions with cells is essential for designing materials for applications such as bioimaging and drug delivery as well as for assessing nanomaterial safety. Ligand-coated gold nanoparticles have been widely investigated because their highly tunable surface properties enable investigations into the effect of ligand functionalization on interactions with biological systems. Lipophilic ligands have been linked to adverse biological outcomes through membrane disruption, but the relationship between ligand lipophilicity and membrane interactions is not well understood. Here, we use a library of cationic ligands coated on 2 nm gold nanoparticles to probe the impact of ligand end group lipophilicity on interactions with supported phosphatidylcholine lipid bilayers as a model for cytoplasmic membranes. Nanoparticle adsorption to and desorption from the model membranes were investigated by quartz crystal microbalance with dissipation monitoring. We find that nanoparticle adsorption to model membranes increases with ligand lipophilicity. The effects of ligand structure on gold nanoparticle attachment were further analyzed using atomistic molecular dynamics simulations, which showed that the increase in ligand lipophilicity promotes ligand intercalation into the lipid bilayer. Together, the experimental and simulation results could be described by a two-state model that accounts for the initial attachment and subsequent conversion to a quasi-irreversibly bound state. We find that only nanoparticles coated with the most lipophilic ligands in our nanoparticle library undergo conversion to the quasi-irreversible state. We propose that the initial attachment is governed by interaction between the ligands and phospholipid tail groups, whereas conversion into the quasi-irreversibly bound state reflects ligand intercalation between phospholipid tail groups and eventual lipid extraction from the bilayer. The systematic variation of ligand lipophilicity enabled us to demonstrate that the lipophilicity of cationic ligands correlates with nanoparticle-bilayer adsorption and suggested that changing the nonpolar ligand R group promotes a mechanism of ligand intercalation into the bilayer associated with irreversible adsorption. read less USED (low confidence) D. Biriukov and Z. Futera, “Adsorption of Amino Acids at the Gold/Aqueous Interface: Effect of an External Electric Field,” Journal of Physical Chemistry C. 2021. link Times cited: 6 Abstract: Gaining accurate molecular descriptions of metal/bio interfa… read moreAbstract: Gaining accurate molecular descriptions of metal/bio interfaces is a necessary step toward numerous important applications, particularly in electrochemistry and bionanotechnology. Here, using atomi... read less USED (low confidence) S. Dutta, S. Corni, and G. Brancolini, “Molecular Dynamics Simulations of a Catalytic Multivalent Peptide–Nanoparticle Complex,” International Journal of Molecular Sciences. 2021. link Times cited: 11 Abstract: Molecular modeling of a supramolecular catalytic system is c… read moreAbstract: Molecular modeling of a supramolecular catalytic system is conducted resulting from the assembling between a small peptide and the surface of cationic self-assembled monolayers on gold nanoparticles, through a multiscale iterative approach including atomistic force field development, flexible docking with Brownian Dynamics and µs-long Molecular Dynamics simulations. Self-assembly is a prerequisite for the catalysis, since the catalytic peptides do not display any activity in the absence of the gold nanocluster. Atomistic simulations reveal details of the association dynamics as regulated by defined conformational changes of the peptide due to peptide length and sequence. Our results show the importance of a rational design of the peptide to enhance the catalytic activity of peptide–nanoparticle conjugates and present a viable computational approach toward the design of enzyme mimics having a complex structure–function relationship, for technological and nanomedical applications. read less USED (low confidence) M. Foroutan, F. Esmaeilian, and M. T. Rad, “The change in the wetting regime of a nanodroplet on a substrate with varying wettability: A molecular dynamics investigation,” Physics of Fluids. 2021. link Times cited: 16 Abstract: The effect of the triple-phase contact line (TPCL) on the we… read moreAbstract: The effect of the triple-phase contact line (TPCL) on the wetting phenomenon has been extensively discussed during the past decade. Numerous attempts have also been made to quantify its characteristics based on thermodynamic or mechanical definitions. In this research, molecular dynamics simulation was used to define the term “vicinity of the TPCL” and its effect on the hydrophilic and hydrophobic behaviors of a water nanodroplet. A nanodroplet was placed on a substrate that was modified in a stepwise manner by growing a patch of heterogeneity from either the center of the substrate or from the sides. The relative direction of motion of the TPCL and the patch determined the pathway that the nanodroplet chooses in order to change its wetting regime from hydrophilic to hydrophobic and vice versa. A gradual change occurs when the TPCL and the heterogeneity move in the same direction, and an abrupt change takes place otherwise. In addition to the insights into the wetting phenomenon, the width of the TPCL is also discussed. The obtained data suggest that the effective width of the TPCL, δ, is different inside the perimeter of the nanodroplet from outside of it. Moreover, the value of δ for the abrupt pathway is twice as large as the gradual one. In conclusion, the width, or vicinity, of the TPCL depends on the type of the pathway and the configuration of the substrate-patch system and cannot be treated similarly in both cases. read less USED (low confidence) I. V. Voroshylova et al., “Ionic liquid–metal interface: The origins of capacitance peaks,” Electrochimica Acta. 2021. link Times cited: 18 USED (low confidence) N. Liu, H. Zhu, J. Zhou, L. Yang, and D. Liu, “Molecular dynamics simulations on formation of CO2 hydrate in the presence of metal particles,” Journal of Molecular Liquids. 2021. link Times cited: 16 USED (low confidence) S. Deguchi et al., “A new mechanism for reduced cell adhesion: Adsorption dynamics of collagen on a nanoporous gold surface.,” Materials science & engineering. C, Materials for biological applications. 2021. link Times cited: 3 USED (low confidence) N. Kruchinin, M. Kucherenko, and P. Neyasov, “Conformational Changes of Uniformly Charged Polyelectrolyte Chains on the Surface of a Polarized Gold Nanoparticle: Molecular Dynamics Simulation and the Theory of a Gaussian Chain in a Field,” Russian Journal of Physical Chemistry A. 2021. link Times cited: 4 USED (low confidence) C. Seidl, J. Hörmann, and L. Pastewka, “Molecular Simulations of Electrotunable Lubrication: Viscosity and Wall Slip in Aqueous Electrolytes,” Tribology Letters. 2021. link Times cited: 5 USED (low confidence) M. V. Slavgorodska, Y. O. Gurova, and A. Kyrychenko, “γ-Cyclodextrin as a capping agent for gold nanoparticles,” Computational and Theoretical Chemistry. 2021. link Times cited: 7 USED (low confidence) N. Kruchinin and M. Kucherenko, “Rearrangements in the Conformational Structure of Polypeptides on the Surface of a Metal Nanowire in Rotating Electric Field: Molecular Dynamics Simulation,” Colloid Journal. 2021. link Times cited: 4 USED (low confidence) A. S. Abdelsattar, A. Dawoud, and M. Helal, “Interaction of nanoparticles with biological macromolecules: a review of molecular docking studies,” Nanotoxicology. 2020. link Times cited: 36 Abstract: The high frequency of using engineered nanoparticles in vari… read moreAbstract: The high frequency of using engineered nanoparticles in various medical applications entails a deep understanding of their interaction with biological macromolecules. Molecular docking simulation is now widely used to study the binding of different types of nanoparticles with proteins and nucleic acids. This helps not only in understanding the mechanism of their biological action but also in predicting any potential toxicity. In this review, the computational techniques used in studying the nanoparticles interaction with biological macromolecules are covered. Then, a comprehensive overview of the docking studies performed on various types of nanoparticles will be offered. The implication of these predicted interactions in the biological activity and/or toxicity is also discussed for each type of nanoparticles. read less USED (low confidence) W. Wang, X. Zhang, Y. Li, R. Huang, J.-J. Xu, and L. Yang, “Effects of molecular structures of poly α-olefin mixture on nano-scale thin film lubrication,” Materials today communications. 2020. link Times cited: 4 USED (low confidence) H. Liu, S. Ahmad, J. Chen, and J. Zhao, “Molecular dynamics study of the nanoscale boiling heat transfer process on nanostructured surfaces,” International Communications in Heat and Mass Transfer. 2020. link Times cited: 26 USED (low confidence) M. Zare, M. Saleheen, S. Kundu, and A. Heyden, “Dependency of solvation effects on metal identity in surface reactions,” Communications Chemistry. 2020. link Times cited: 10 USED (low confidence) M. Rezaeian, M. Izadyar, and M. Housaindokht, “Exploring the interaction of amino acid-based ionic liquids in water and organic solvents: Insight from MD simulations and QM calculations,” Journal of Molecular Liquids. 2020. link Times cited: 0 USED (low confidence) M. R. Khan, H. Singh, S. Sharma, and K. L. A. Cimatu, “Direct Observation of Adsorption Morphologies of Cationic Surfactants at the Gold Metal-Liquid Interface.,” The journal of physical chemistry letters. 2020. link Times cited: 10 Abstract: Understanding interfacial phenomena is important in processe… read moreAbstract: Understanding interfacial phenomena is important in processes like corrosion, catalysis, and electrochemical reactions. Specifically, in corrosion inhibition, the assembly of adsorbed surfactants at metal-water interfaces in well-packed, ordered layers is desired. We provide direct evidence of the role of alkyl tails of surfactants in the formation of ordered adsorbed layers at metal-water interfaces. We have employed surface-specific sum frequency generation (SFG) spectroscopy to probe the in situ adsorption and self-assembly of cationic surfactants, alkyldimethylbenzyl ammonium bromides of tail lengths n = 4 (C4) and 12 (C12), without any applied potential or stimulus, at the gold-water interface. Our SFG measurements show that C12 Quat adsorbs as an ordered monolayer, whereas C4 Quat adsorbs in a disordered monolayer. All-atom molecular dynamics (MD) simulations of these surfactants corroborate with SFG results. These findings provide new insights on how hydrophobic interactions between alkyl tails of surfactants affect their self-assembly at metal-water interfaces. read less USED (low confidence) G. V. Huerta and G. Raabe, “Genetic Parameterization of Interfacial Force Fields Based on Classical Bulk Force Fields and Ab Initio Data: Application to the Methanol-ZnO Interfaces,” Journal of chemical information and modeling. 2020. link Times cited: 2 Abstract: Despite the high advances of classical molecular simulation … read moreAbstract: Despite the high advances of classical molecular simulation to study bulk phases, classical force fields (FFs) to describe interactions at interfaces are rarely available in the literature. In this study, FFs to describe fluid | solid interfaces are developed by matching forces and energies from ab initio simulation and by using a newly developed genetic algorithm (GA). The interfacial FFs are parameterized to be combined with existing classical bulk FFs. Our procedure is tested on the methanol (CH3OH) | ZnO interface. The results for the forces, energies, and some structural adsorption properties calculated using an own parameterized interfacial FF are comparable with results from ab initio and experimental data. With this, we illustrate the potential of the proposed procedure to yield accurate models for interfacial systems to be combined with available bulk FFs. read less USED (low confidence) M. S. J. Sajib, P. Sarker, Y. Wei, X. Tao, and T. Wei, “Protein Corona on Gold Nanoparticles Studied with Coarse-Grained Simulations.,” Langmuir : the ACS journal of surfaces and colloids. 2020. link Times cited: 20 Abstract: Understanding protein corona formation in an aqueous environ… read moreAbstract: Understanding protein corona formation in an aqueous environment at the molecular and atomistic levels is critical to applications such as biomolecule-detection and drug delivery. In this work, we employed mesoscopic coarse-grained simulations to study ovispirin-1 and lysozyme protein coronas on bare gold nanoparticles. Our study showed that protein corona formation is governed by protein-surface and protein-protein interactions, as well as the surface hydrophobic effect. The corona structure was found to be dependent on protein types and the size of nanoparticles. Ovispirin proteins form homogeneous single-layered adsorption in comparison with the lysozyme's inhomogeneous multilayered aggregates on gold NP surfaces. The decrease in nanoparticle size leads to more angular degrees of freedom for protein adsorption orientation. Subsequent atomistic molecular dynamics simulations further demonstrate the loss of secondary structure of ovispirin upon adsorption and the heterogeneity of its local structure. read less USED (low confidence) F. Valencia, M. Ramírez, A. Varas, J. Rogan, and M. Kiwi, “Thermal Stability of Hollow Porous Gold Nanoparticles: A Molecular Dynamics Study,” Journal of chemical information and modeling. 2020. link Times cited: 5 Abstract: Hollow nanoparticle structures play a major role in nanotech… read moreAbstract: Hollow nanoparticle structures play a major role in nanotechnology and nanoscience since their surface to volume ratio is significantly larger than that of filled ones. While porous hollow nanoparticles offer a significant improvement of the available surface area, there is a lack of theoretical understanding, and scarce experimental information, on how the porosity controls or dominates the stability. Here we use classical molecular dynamics simulations to shed light on the particular characteristics and properties of gold porous hollow nanoparticles and how they differ from the nonporous ones. Adopting gold as a prototype, we show how, as the temperature increases, the porosity introduces surface stress and minor transitions that lead to various scenarios, from partial shrinkage for small filling factors to abrupt compression and the loss of spherical shape for large filling. Our work provides new insights into the stability limits of porous hollow nanoparticles, with important implications for the design and practical use of these enhanced geometries. read less USED (low confidence) L. Guo et al., “On-surface synthesis of size- and shape-controlled two-dimensional Aun nanoclusters using a flexible fullerene molecular template.,” Nanoscale. 2020. link Times cited: 0 Abstract: Synthesizing nano-clusters with a well-defined size, shape, … read moreAbstract: Synthesizing nano-clusters with a well-defined size, shape, and composition is an important and challenging goal in nanotechnology. Here we report the application of a single layer C60 molecule as an effective molecular template for the synthesis of size- and shape-selected two-dimensional gold clusters (Aun) on a graphite substrate. This molecular template facilitates the preferential formation of Au19 clusters with a selectivity as high as 90%. Density-functional-theory (DFT) calculations found an energy minimum associated with C60-stabilized two-dimensional Au19 clusters. read less USED (low confidence) A. Raj, N. Dhandia, and K. Balani, “Adhesin Protein Interaction of Staphylococcus Aureus Bacteria with Various Biomaterial Surfaces.,” ACS biomaterials science & engineering. 2020. link Times cited: 1 Abstract: The primary stage of adhesion during implant infection is do… read moreAbstract: The primary stage of adhesion during implant infection is dominated by interactions of the surface proteins of the bacteria with the substrate atoms. In the current work, molecular dynamics (MD) simulations have been utilized to investigate the mechanics of the associated adhesion forces of bacteria on different surfaces. The unfolding of these adhesion proteins is investigated in order to map these events to earlier experiments on bacterial de-adhesion (using single cell force spectroscopy) with real-life substrates (i.e., ultrahigh molecular weight polyethylene, hydroxyapatite, Ti alloy, and stainless steel). The adhesion of Staphylococcus aureus adhesin (i.e., SpA) is observed by altering their orientation on the silica substrate through MD simulations, followed by capturing unfolding events of three adhesins (SpA, ClfA, and SraP) of variable lengths possessing different secondary structures. The output long-range and short-range interaction forces and consequent visualization of changes in the secondary structure of protein segments are presented during the de-adhesion process. Simulation results are correlated with extracted short-range forces (using Poisson regression) from real-life bacterial de-adhesion experiments. Insights into such protein-substrate interactions may allow for engineering of biomaterials and designing of nonbiofouling surfaces. read less USED (low confidence) J. D. D. Silva, M. Meneghetti, and C. M. Soares, “Molecular Dynamics Simulations Suggest a Possible Role for NO in the Polyol Synthesis of Silver Nanostructures,” The Journal of Physical Chemistry C. 2020. link Times cited: 2 Abstract: Polyol synthesis allows the preparation of silver nanostruct… read moreAbstract: Polyol synthesis allows the preparation of silver nanostructures with different well-controlled morphologies and opens a window to explore their potential in various emerging applications. Despite ... read less USED (low confidence) H. A, Z. Yang, R. Hu, Y. F. Chen, and L. Yang, “Effect of Solid–Liquid Interactions on Substrate Wettability and Dynamic Spreading of Nanodroplets: A Molecular Dynamics Study,” Journal of Physical Chemistry C. 2020. link Times cited: 16 Abstract: Solid–liquid interaction plays a key role in substrate wetta… read moreAbstract: Solid–liquid interaction plays a key role in substrate wettability and spreading dynamics of liquid droplets. Yet, how the solid–liquid interaction controls wettability and the spreading process is... read less USED (low confidence) T. Murono, K. Hongo, K. Nakano, and R. Maezono, “Ab-initio-based interface modeling and statistical analysis for estimate of the water contact angle on a metallic Cu(111) surface,” Surfaces and Interfaces. 2020. link Times cited: 3 USED (low confidence) W. Chen et al., “Atomic Insights into Robust Pt–PdO Interfacial Site-Boosted Hydrogen Generation,” ACS Catalysis. 2020. link Times cited: 14 Abstract: Suppression of catalyst deactivation without compromising ac… read moreAbstract: Suppression of catalyst deactivation without compromising activity has been a long-standing yet elusive goal in heterogeneous catalysis. Herein, we report a remarkable achievement of both hydrogen ... read less USED (low confidence) F. M. Colombari, A. Lozada-Blanco, K. Bernardino, W. R. Gomes, and A. F. de Moura, “Themis: A Software to Assess Association Free Energies via Direct Estimative of Partition Functions.” 2020. link Times cited: 2 Abstract: We present the program Themis - a computer implementation of… read moreAbstract: We present the program Themis - a computer implementation of a standard statistical mechanics framework to compute free energies, average energies and entropic contributions for association processes of two atom-based structures. The partition functions are computed analytically using a discrete grid in the phase space, whose size and degree of coarseness can be controlled to allow efficient calculations and to achieve the desired level of accuracy. With this strategy, applications ranging from molecular recognition, chiral discrimination, surface adsorption and even the interactions involving molecules in electronic excited states can be handled. read less USED (low confidence) M. Uranagase and S. Ogata, “FE-CLIP: A tool for the calculation of the solid-liquid interfacial free energy,” Comput. Phys. Commun. 2020. link Times cited: 0 USED (low confidence) J. Wu et al., “Revealing the Role of Surface Co-modification in Boosting the Gas Sensing Performance of Graphene Using Experimental and Theoretical Evidences,” Sensors and Actuators B-chemical. 2020. link Times cited: 6 USED (low confidence) X. Liu et al., “Uniform, anti-corrosive and anti-abrasive coatings on metallic surfaces for cation-metal and cation-π interactions.,” ACS applied materials & interfaces. 2020. link Times cited: 10 Abstract: Metals are widely used from daily life to modern industry. G… read moreAbstract: Metals are widely used from daily life to modern industry. Great efforts have been made to protect the metals with various coatings. However, the well-known conventional electrochemical corrosion induced by cations and the ubiquitous nature of the coffee-ring effect make these processes very difficult. Here, a scheme by two bridges of cations and ethylenediamine (EDA) is proposed to overcome coffee-ring effect and electrochemical corrosion and experimentally achieve uniform, anti-corrosive and anti-abrasive coatings on metallic surfaces. Anti-corrosive capability reaches about 26 times higher than that without cation-controlled coatings at 12 hours in extremely acidic, high-temperature and high-humidity conditions, and still enhances to 2.7 times over a week. Anti-abrasive capability also reaches 2.5 times. Theoretical calculations show that the suspended materials are uniformly adsorbed on the surface mediated by complexed cations through strong cation-metal and cation-π interactions. Notably, the well-known conventional electrochemical corrosion induced by cations is avoided by EDA to control cations solubility in different coating processes. These findings provide a new efficient, cost-effective, facile, and scalable method to fabricate protective coatings on metallic materials and a methodology to study metallic nanostructures in solutions, benefitting practical applications including coatings, printing, dyeing, electrochemical protection and biosensors. read less USED (low confidence) H. Liu, F. Chu, J. Zhang, and D. Wen, “Nanodroplets impact on surfaces decorated with ridges,” Physical Review Fluids. 2020. link Times cited: 13 Abstract: Molecular dynamics is employed to investigate the impact of … read moreAbstract: Molecular dynamics is employed to investigate the impact of nanodroplets on superhydrophobic surfaces decorated with nanoridges. It is concluded that the decorated nanoridges can significantly promote the bouncing performance of nanodroplets. Five distinct bounce modes are identified, and they determine the variation laws of contact time and bounce velocity of nanodroplets. read less USED (low confidence) A. Nemati, H. N. Pishkenari, A. Meghdari, and S. Ge, “Influence of Vacancies and Grain Boundaries on the Diffusive Motion of Surface Rolling Molecules,” Journal of Physical Chemistry C. 2020. link Times cited: 7 Abstract: Molecular machines and surface rolling molecules show great … read moreAbstract: Molecular machines and surface rolling molecules show great potential to accomplish different tasks in several fields, such as bottom-up assembly and nano-manipulation. Many researchers have invest... read less USED (low confidence) N. Kruchinin and M. Kucherenko, “Electrically Induced Conformational Changes in Gold Cluster–Bonded Polyampholytic Polypeptides on a Surface of Gold: Molecular Dynamic Simulation,” Russian Journal of Physical Chemistry A. 2020. link Times cited: 6 USED (low confidence) R. Rabani, G. Heidarinejad, J. Harting, and E. Shirani, “Interplay of wall force field and wall physical characteristics on interfacial phenomena of a nano-confined gas medium,” International Journal of Thermal Sciences. 2020. link Times cited: 5 USED (low confidence) P. Clabaut, B. Schweitzer, A. Götz, C. Michel, and S. Steinmann, “Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid QM-MM Simulations.,” Journal of chemical theory and computation. 2020. link Times cited: 11 Abstract: Modeling adsorption at the metal/water interfaces is a corne… read moreAbstract: Modeling adsorption at the metal/water interfaces is a corner-stone towards an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in gas phase at the DFT level with the variation in solvation from the bulk phase to the interface evaluated using a molecular mechanics based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation, but also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H2O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our QM-MM hybrid scheme is limited to 6 kcal/mol through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (-0.46 J/m2) is in good agreement with the experimental estimate (-0.32 J/m2). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy, but with opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ~30 and 40 kcal/mol for our QM/MM hybrid scheme and experiment, respectively, but ~0 with the implicit solvent) at the solid/liquid compared to the solid/gas interface. This reduction is mainly due to the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semi-quantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM-MM scheme. read less USED (low confidence) C. Tietz, M. Sekulla, X. Yang, R. Schmid, and M. Richter, “Linking Fluid Densimetry and Molecular Simulation: Adsorption Behavior of Carbon Dioxide on Planar Gold Surfaces,” Industrial & Engineering Chemistry Research. 2020. link Times cited: 6 Abstract: Phase equilibria of fluid substances and their mixtures are … read moreAbstract: Phase equilibria of fluid substances and their mixtures are important in numerous scientific as well as industrial applications and are, therefore, a major focus of thermophysical property research... read less USED (low confidence) D. T. Yarullin, B. N. Galimzyanov, and A. Mokshin, “Direct evaluation of attachment and detachment rate factors of atoms in crystallizing supercooled liquids.,” The Journal of chemical physics. 2020. link Times cited: 9 Abstract: Kinetic rate factors of crystallization have a direct effect… read moreAbstract: Kinetic rate factors of crystallization have a direct effect on formation and growth of an ordered solid phase in supercooled liquids and glasses. Using the crystallizing Lennard-Jones liquid as an example, in the present work, we perform a direct quantitative estimation of values of the key crystallization kinetic rate factors-the rate g+ of particle attachments to a crystalline nucleus and the rate g- of particle detachments from a nucleus. We propose a numerical approach, according to which a statistical treatment of the results of molecular dynamics simulations was performed without using any model functions and/or fitting parameters. This approach allows one to accurately estimate the critical nucleus size nc. We find that for the growing nuclei, whose sizes are larger than the critical size nc, the dependence of these kinetic rate factors on the nucleus size n follows a power law. In the case of the subnucleation regime, when the nuclei are smaller than nc, the n-dependence of the quantity g+ is strongly determined by the inherent microscopic properties of a system, and this dependence cannot be described in the framework of any universal law (for example, a power law). It has been established that the dependence of the growth rate of a crystalline nucleus on its size goes into the stationary regime at the size n > 3nc particles. read less USED (low confidence) Z. Cao, V. Liu, and A. B. Farimani, “Why is Single-Layer MoS2 a More Energy Efficient Membrane for Water Desalination?,” ACS energy letters. 2020. link Times cited: 55 Abstract: Water desalination technologies are extensively utilized to … read moreAbstract: Water desalination technologies are extensively utilized to solve water scarcity problems in many regions of the world. Discovery and application of two-dimensional (2D) nanoporous materials provid... read less USED (low confidence) Y. Kawagoe, D. Surblys, H. Matsubara, G. Kikugawa, and T. Ohara, “Cross-plane and in-plane heat conductions in layer-by-layer membrane: Molecular dynamics study.,” Langmuir : the ACS journal of surfaces and colloids. 2020. link Times cited: 12 Abstract: A material with anisotropic heat conduction characteristics,… read moreAbstract: A material with anisotropic heat conduction characteristics, which is determined by molecular scale structure, provides a way of controlling heat flow in nanoscale spaces. As such, here we consider layer-by-layer (LbL) membranes, which are an electrostatic assembly of polyelectrolyte multilayers and are expected to have different heat conduction characteristics between cross-plane and in-plane directions. We constructed models of a polyacrylic acid/polyethylenimine (PAA/PEI) LbL membrane sandwiched by charged solid walls and investigated their anisotropic heat conduction using molecular dynamics simulations. In the cross-plane direction, the thermal boundary resistance between the solid wall and the LbL membrane and that between the constituent PAA and PEI layers decrease with increasing degree of ionization (solid surface charge density and the number of electric charges per PAA/PEI molecule). When the degree of ionization is low, the cross-plane thermal conductivity of a constituent layer is higher than that of bulk state. As the degree of ionization increases, however, the cross-plane thermal conductivity of PAA, a linear polymer, decreases because of the increase in the number of in-plane oriented polymer chains. In the in-plane direction, we investigated heat conduction of each layer, and found the enhancement of effective in-plane thermal conductivity again due to the in-plane oriented chain alignment. The heat conduction in the LbL membrane is three-dimensionally enhanced when compared with those in the bulk states of the constituent polymers, because of the electrostatic interactions in the cross-plane direction and the molecular alignment in the in-plane direction. read less USED (low confidence) J. D. D. Silva, M. Meneghetti, and P. Netz, “Molecular Dynamics Simulations of the Structural Arrangement and Density of Alkylamine Surfactants on Copper Surfaces: Implications for Anisotropic Growth of Copper Nanowires.” 2020. link Times cited: 10 Abstract: The understanding of the role of alkylamine surfactants in t… read moreAbstract: The understanding of the role of alkylamine surfactants in the anisotropic growth mechanism of copper nanowires (CuNWs) in solution-phase synthesis has implications for the tuning of properties tha... read less USED (low confidence) F. Ávila-Salas, R. González, P. Ríos, I. Araya-Durán, and M. B. Camarada, “Effect of the Generation of PAMAM Dendrimers on the Stabilization of Gold Nanoparticles,” Journal of chemical information and modeling. 2020. link Times cited: 19 Abstract: The behavior of small and intermediate generations of poly(a… read moreAbstract: The behavior of small and intermediate generations of poly(amidoamine) (PAMAM) dendrimers and PAMAM|gold nanocomposites was studied by computational tools and experimental techniques. Molecular dynamics simulations were used to characterize at the atomic level the stabilization mechanism of gold nanoparticles by dendrimeric platforms. Low PAMAM generations create a stabilization sphere around the nanoparticle, while upper PAMAM sizes provide stabilization sites through the internal voids. These results can help in the understanding of the stabilization process of metallic nanoparticles for the design and contribution of new nanotechnological applications. read less USED (low confidence) C. Su et al., “The Mechanical Behaviors of Polyethylene/Silver Nanoparticle Composites: an Insight from Molecular Dynamics study,” Scientific Reports. 2020. link Times cited: 14 USED (low confidence) X. Dou, Y. Chen, and Y. Han, “Modification of glycerol force Field for simulating silver nucleation under a diffusion limited condition,” Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2020. link Times cited: 2 USED (low confidence) H.-hong Jia, Q. Guo, and S. Du, “Thermally Driven Diffusion of a Magic Number Gold–Fullerene Cluster on a Au(111) Surface,” Journal of Physical Chemistry C. 2020. link Times cited: 0 Abstract: Metal clusters stabilized by surface passivation with organi… read moreAbstract: Metal clusters stabilized by surface passivation with organic molecules have potential applications in diverse fields such as optics, microelectronics, catalysis, and biochemical analysis. The diff... read less USED (low confidence) L. O. Mark, C. Zhu, J. Medlin, and H. Heinz, “Understanding the Surface Reactivity of Ligand-Protected Metal Nanoparticles for Biomass Upgrading,” ACS Catalysis. 2020. link Times cited: 27 Abstract: Ligand-protected metal nanoparticles are widely used in hete… read moreAbstract: Ligand-protected metal nanoparticles are widely used in heterogeneous catalysis and biomass upgrading. Thiolate surfactants can greatly improve the overall yield; however, the dynamics of the react... read less USED (low confidence) S. Ntim and M. Sulpizi, “Role of image charges in ionic liquid confined between metallic interfaces.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 11 Abstract: The peculiar properties of ionic liquids in confinement have… read moreAbstract: The peculiar properties of ionic liquids in confinement have not only become essential for energy storage, catalysis and tribology, but still pose fundamental questions. Recently, an anomalous liquid-solid phase transition has been observed in atomic force microscopy experiments for 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]), the transition being more pronounced for metallic surfaces. Image charges have been suggested as the key element driving the anomalous freezing. Using atomistic molecular dynamics simulations, we investigate the impact of image charges on structure, dynamics and thermodynamics of [BMIM][BF4] confined between gold electrodes. Our results not only unveil a minor role played by the metal polarisation, but also provide a novel description of the interfacial layer. Although no diffuse layer can be defined in terms of the electrostatic potential, long range effects are clearly visible in the dynamical properties up to 10 nanometers away from the surface, and are expected to influence viscous forces in the experiments. read less USED (low confidence) R. Liu et al., “Tribological behaviour of Ag–BN coatings prepared by plasma spraying,” Surface Engineering. 2020. link Times cited: 3 Abstract: ABSTRACT Hexagonal boron nitride (h-BN) particles were added… read moreAbstract: ABSTRACT Hexagonal boron nitride (h-BN) particles were added to a sliver metal matrix to improve the tribological properties of the prepared Ag–BN coatings, which were deposited via plasma spraying technique. The morphology, flowability and apparent density of Ag–BN composite powders were characterized, as well as the phase composition, microstructure and friction properties of Ag–BN coatings were systematically investigated. Results of XRD showed that Ag–BN coatings were successfully prepared, morphologies of SEM showed dense structures of Ag–BN coatings. The friction and wear behaviour of Ag–BN coatings was investigated from ambient temperature up to 800°C. The results showed that the coatings exhibited excellent tribological properties in this temperature range. The main wear mechanisms of Ag–BN coating were adhesive wear and ploughing. Layered h-BN reduced the friction coefficient and improved abradable property of Ag–BN coatings. Ag as the metal phase effectively protected the Si3N4 ball from wear. read less USED (low confidence) C.-C. Yen et al., “Lattice distortion effect on elastic anisotropy of high entropy alloys,” Journal of Alloys and Compounds. 2020. link Times cited: 25 USED (low confidence) S. M. Nejad, S. Nedea, A. Frijns, and D. Smeulders, “The Influence of Gas–Wall and Gas–Gas Interactions on the Accommodation Coefficients for Rarefied Gases: A Molecular Dynamics Study,” Micromachines. 2020. link Times cited: 10 Abstract: Molecular dynamics (MD) simulations are conducted to determi… read moreAbstract: Molecular dynamics (MD) simulations are conducted to determine energy and momentum accommodation coefficients at the interface between rarefied gas and solid walls. The MD simulation setup consists of two parallel walls, and of inert gas confined between them. Different mixing rules, as well as existing ab-initio computations combined with interatomic Lennard-Jones potentials were employed in MD simulations to investigate the corresponding effects of gas-surface interaction strength on accommodation coefficients for Argon and Helium gases on a gold surface. Comparing the obtained MD results for accommodation coefficients with empirical and numerical values in the literature revealed that the interaction potential based on ab-initio calculations is the most reliable one for computing accommodation coefficients. Finally, it is shown that gas–gas interactions in the two parallel walls approach led to an enhancement in computed accommodation coefficients compared to the molecular beam approach. The values for the two parallel walls approach are also closer to the experimental values. read less USED (low confidence) M. Davari and M. A. Jabbareh, “Modeling the interfacial energy of embedded metallic nanoparticles,” Journal of Physics and Chemistry of Solids. 2020. link Times cited: 4 USED (low confidence) H. Singh and S. Sharma, “Disintegration of Surfactant Micelles at Metal-Water Interfaces Promotes their Strong Adsorption.,” The journal of physical chemistry. B. 2020. link Times cited: 15 Abstract: We have studied adsorption behavior of micelles of cationic … read moreAbstract: We have studied adsorption behavior of micelles of cationic surfactants at metal-water interfaces via fully atomistic simulations. We show that the micelles experience a free energy barrier to adsorption. Near the metal surface, surfactant molecules in the micelles slowly rearrange leading to complete disintegration of the micelles. Disintegration of the micelles results in much stronger adsorption. After the disintegration, surfactant molecules adsorb by lying flat on the metal surface. Additional simulations performed by treating the micelles as rigid bodies results in a weak adsorption. This confirms our result that disintegration of the micelles is necessary for their strong adsorption. read less USED (low confidence) M. Bahrami, M. Ghatee, and S. Ayatollahi, “Simulation of Wetting and Interfacial Behavior of Quaternary Ammonium and Phosphonium Ionic Liquids Nano-Droplets over FCC Metal Surfaces.,” The journal of physical chemistry. B. 2020. link Times cited: 6 Abstract: We studied the behavior of quaternary ammonium- and phosphon… read moreAbstract: We studied the behavior of quaternary ammonium- and phosphonium-based ([N2225][NTf2] and [P2225][NTf2]) ionic liquids (ILs) nano-droplets on Copper (Cu) and Platinum (Pt) metals surface using classical MD simulations. Solid-liquid interactions were underpinned by studying the dynamic spreading, contact angle, time-dependent binding energies, MSDs, number and charge density profiles, and orientational distribution of these two ILs nano-droplets with the particular wetting feature. In particular, the role and importance of different crystallographic facets of FCC metal surfaces (Cu(100), Cu(111), Pt(100) and Pt(111)) were investigated. The results indicate a vast variety of properties that are dictated highly by the structure of different crystallography facet of the metals substrate. The nature of the facet (e.g., the atomic arrangement symmetry, the extent of closed-packed, and unit cell size) leads to an extended scale spreading of the ILs on the surface with (111) index but not with (100) index while the nature of metals itself play roles. read less USED (low confidence) G. Zhou, B. H. Schoen, Z. Yang, and L. Huang, “First Adsorbed Water Layer and Its Wettability Transition under Compressive Lattice Strain,” Journal of Physical Chemistry C. 2020. link Times cited: 3 Abstract: A molecular-level description of a near-surface water struct… read moreAbstract: A molecular-level description of a near-surface water structure and a handy manipulation of its properties are relevant to a broad range of scientific and technological phenomena. Here, through a s... read less USED (low confidence) A. Kyrychenko, M. M. Blazhynska, and O. Kalugin, “Protonation-dependent adsorption of polyarginine onto silver nanoparticles,” Journal of Applied Physics. 2020. link Times cited: 11 Abstract: Polyarginine (poly-Arg) and arginine-rich peptides have been… read moreAbstract: Polyarginine (poly-Arg) and arginine-rich peptides have been attracting enormous interest in chemical and cell biology as cell-penetrating peptides capable of direct intracellular penetration. Owing to advances in protein engineering, arginine-rich fragments are often incorporated into multifunctional bioorganic/inorganic core–shell nanoparticles, enabling them the novel unique ability to cross cells and deliver biopharmaceutical cargos. Therefore, understanding the molecular details of the adsorption, packing, and release of poly-Arg onto or from metal nanoparticles is one of the current challenges. In this work, we carry out atomistic molecular dynamics simulations to identify the most favorable location, orientation, and conformation of poly-Arg adsorbed onto a silver nanoparticle (AgNP). Herein, we utilize the constant protonation approach to identify the role of protonation of side chain arginine moieties in the adsorption of poly-Arg to AgNP as a function of pH. The strong adsorption of unprotonated poly-Arg30 onto the quasispherical surface of AgNP with an average diameter of 3.9 nm is primarily governed by multiple interactions of side chain guanidinium (Gdm) moieties, which get stacked and align flat onto the surface. The protonation of the arginine side chain enhances the protein–solvent interactions and promotes the weakening of the protein–nanoparticle binding. The formation of multiple H-bonds between the protonated Arg residues and water molecules favors exposing the charged Gdm+ moieties to the solvent. Protonated poly-Arg30 is found to be partially bound to AgNP due to some weak protein–nanoparticle contacts, maintained by binding of the amide oxygen atoms of the peptide bond. These results suggest that reversible acid–base switching between the arginine protonation states is able to drive the rearrangement of the polyarginine coating around AgNPs, which could be important for a rational design of “intelligent” multifunctional core–shell nanosystems.Polyarginine (poly-Arg) and arginine-rich peptides have been attracting enormous interest in chemical and cell biology as cell-penetrating peptides capable of direct intracellular penetration. Owing to advances in protein engineering, arginine-rich fragments are often incorporated into multifunctional bioorganic/inorganic core–shell nanoparticles, enabling them the novel unique ability to cross cells and deliver biopharmaceutical cargos. Therefore, understanding the molecular details of the adsorption, packing, and release of poly-Arg onto or from metal nanoparticles is one of the current challenges. In this work, we carry out atomistic molecular dynamics simulations to identify the most favorable location, orientation, and conformation of poly-Arg adsorbed onto a silver nanoparticle (AgNP). Herein, we utilize the constant protonation approach to identify the role of protonation of side chain arginine moieties in the adsorption of poly-Arg to AgNP as a function of pH. The strong adsorption of unprotonated... read less USED (low confidence) R. Qiu, J. Xiao, and X. Chen, “Multi-Peptide Adsorption on Uncharged Solid Surfaces: A Coarse-Grained Simulation Study,” Engineering. 2020. link Times cited: 5 USED (low confidence) S.-ying Sun, X.-Y. Nie, J. Huang, and J. Yu, “Molecular simulation of diffusion behavior of counterions within polyelectrolyte membranes used in electrodialysis,” Journal of Membrane Science. 2020. link Times cited: 25 USED (low confidence) L. K. Scarbath-Evers, R. Hammer, D. Golze, M. Brehm, D. Sebastiani, and W. Widdra, “From flat to tilted: gradual interfaces in organic thin film growth.,” Nanoscale. 2020. link Times cited: 5 Abstract: We investigate domain formation and local morphology of thin… read moreAbstract: We investigate domain formation and local morphology of thin films of α-sexithiophene (α-6T) on Au(100) beyond monolayer coverage by combining high resolution scanning tunneling microscopy (STM) experiments with electronic structure theory calculations and computational structure search. We report a layerwise growth of highly-ordered enantiopure domains. For the second and third layer, we show that the molecular orbitals of individual α-6T molecules can be well resolved by STM, providing access to detailed information on the molecular orientation. We find that already in the second layer the molecules abandon the flat adsorption structure of the monolayer and adopt a tilted conformation. Although the observed tilted arrangement resembles the orientation of α-6T in the bulk, the observed morphology does not yet correspond to a well-defined surface of the α-6T bulk structure. A similar behavior is found for the third layer indicating a growth mechanism where the bulk structure is gradually adopted over several layers. read less USED (low confidence) C. Dharmawardhana, J. Zhou, M. Taylor, J. Miao, J. Perepezko, and H. Heinz, “Reactive modeling of Mo3Si oxidation and resulting silica morphology,” Acta Materialia. 2020. link Times cited: 5 USED (low confidence) M. Buraschi, S. Sansotta, and D. Zahn, “Polarization Effects in Dynamic Interfaces of Platinum Electrodes and Ionic Liquid Phases: A Molecular Dynamics Study,” Journal of Physical Chemistry C. 2020. link Times cited: 6 Abstract: We outline molecular dynamics simulations of electrode–ionic… read moreAbstract: We outline molecular dynamics simulations of electrode–ionic liquid interfaces with explicit consideration of electronic polarization effects. For this, conventional molecular mechanics are extended by the charge equilibrium approach, leading to moderate computational demand that still allows 10 ns scale dynamics studies of 10 nm scale models of atomic detail. The importance of local charge fluctuations is illustrated by comparing our models with the simplified picture of identical atom charges at the electrode surfaces. Already at idealized flat (110) and (111) platinum surfaces, we find that the migration of anions and cations induces local charge fluctuations on the electrode within a range of −0.2 to +0.2e, respectively. Heterogeneous charge distribution becomes even more critical when investigating rough surfaces. By the example of (1-butyl-3-methylimidazolium), acetate, and hexafluorophosphate, we show selective ion association from the ionic liquid phase to the surface steps of platinum electrodes ... read less USED (low confidence) A. Alkurdi, C. Adessi, F. Tabatabaei, S. Li, K. Termentzidis, and S. Merabia, “Thermal transport across nanometre gaps: Phonon transmission vs. air conduction,” International Journal of Heat and Mass Transfer. 2020. link Times cited: 15 USED (low confidence) Z. Hazarika and A. Jha, “Computational Analysis of the Silver Nanoparticle–Human Serum Albumin Complex,” ACS Omega. 2019. link Times cited: 27 Abstract: Drug delivery in excess concentrations and at not-specified … read moreAbstract: Drug delivery in excess concentrations and at not-specified sites inside the human body adversely affects the body and gives rise to other diseases. Several methods have been developed to deliver the drugs in required amounts and at specific targets. Nanoparticle-mediated drug delivery is one such approach and has gained success at primary levels. The effect of nanoparticles on the human body needs important apprehension, and it has been unraveled by assessing the protein–nanoparticle interactions. Here, we have measured the impact of silver nanoparticles (AgNPs) on the human serum albumin (HSA) structure and function with the help of all-atom molecular dynamics simulations (MDS). HSA is a transport protein, and any change in the structure may obstruct its function. The post MD analyses showed that the NP interacts with HSA and the conjugated system got stabilized with time evolution of trajectories. The present investigation confirms that the AgNP interacts with HSA without affecting its tertiary and secondary structures and in turn the protein function as well. AgNP application is recommended in transporting conjugated drug molecules as it has no adverse effect on serum proteins. Since HSA is present in the circulatory system, it may open various applications of AgNPs in the biomedical field. read less USED (low confidence) Q. Zhang, B. Yang, Q. Ran, C. Yu, and H. Zhao, “Effect of side chain on conformational properties of comb-like polycarboxylate in salt solutions,” Journal of Dispersion Science and Technology. 2019. link Times cited: 5 Abstract: To investigate the effect of side-chain structure of comb-li… read moreAbstract: To investigate the effect of side-chain structure of comb-like polycarboxylates (PCE) on conformational properties in salt solutions, PCE with polyethyleneoxide (PEO) of different lengths were synthesized using methallyl polyethylene glycol (MPEG, Mw = 1200, 2400, 4000). Adding counter-ions (i.e., Na+, Ca2+) to dilute PCE solutions was found to induce a more complicated conformational changes, since the screening of the electrostatic intramolecular repulsion and the different complexation behaviors of Ca2+ with carboxylic groups. Laser light scattering (LLS) and conductivity measurements were used to investigate the conformations of PCE at various pH values. PCE of a long side chain polymer and the sparse grafting studied herein possesses a more coiled polymer backbone due to the intramolecular steric hindrance, which resulted in a more exposed extent of carboxylic groups on the backbone at the same pH values. Obviously, the solution conformation of PCE strongly impacts the accessible carboxylic groups contribution to complexation of the carboxylic oxygen atoms of PCE with Ca2+. In this way it may provide a new insight to design the polymer dispersants. Graphical Abstract read less USED (low confidence) J. D. D. Silva, P. Netz, and M. Meneghetti, “Growth mechanism of gold nanorods: the effect of tip-surface curvature as revealed by molecular dynamics simulations.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 18 Abstract: To understand the anisotropic growth mechanism of gold nanor… read moreAbstract: To understand the anisotropic growth mechanism of gold nanorods (AuNRs) during colloidal synthesis is critical for controlling the nanocrystal size and shape and thus has implications in tuning the properties for applications in a wide range of research and technology fields. In order to investigate the role of the cetyltrimethylammonium bromide (CTAB) coating in the anisotropic growth mechanism of AuNRs, we used molecular dynamics (MD) simulations and built a computational model that considered explicitly the effect of the curvature of the gold surface on CTAB adsorption and therefore differentiated the CTAB arrangements on flat and curved surfaces, representing the lateral and tip facets of growing AuNRs, respectively. We verified that on a curved surface, a lower CTAB coverage density and larger intermicellar channels are generated compared to those on a flat surface. Using umbrella sampling simulations, we measured the free energy profile and verified that the environment around a curved surface corresponds to an easier migration from the solution to the gold surface for the [AuBr2] species than does a flat surface. Long unbiased molecular dynamics simulations also corroborated the umbrella sampling results. Therefore, the [AuBr2]- diffusion through the environment of the tips is much more favorable than in the case of lateral facets. This shows that the surface curvature is an essential component of the anisotropic growth mechanism. read less USED (low confidence) N. A. Azman, N. Thanh, and J. C. Y. Kah, “Sequestration of Cetyltrimethylammonium Bromide on Gold Nanorods by Human Serum Albumin Causes its Conformation Change.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 5 Abstract: Serum albumin could potentially be exploited to form a prote… read moreAbstract: Serum albumin could potentially be exploited to form a protein corona on gold nanorods (AuNRs) for drug delivery due to its endogenous functionality as a small molecule carrier. However, the cetyltrimethylammonium bromide (CTAB) surfactant, which is a synthesis by-product passivating AuNRs to confer colloidal stability, could also cause its conformational change upon interaction with serum albumin during the process of corona formation, thus altering its biological functions. Unfortunately, a clear understanding of how exactly human serum albumin (HSA) would change its conformation as it interacts with AuNR-CTAB is presently lacking. Here, we made use of coarse-grain molecular dynamics (CGMD) simulation to elucidate the interaction between HSA and AuNR-CTAB leading to its widely-reported conformational change. We showed that HSA could sequester CTAB from the surface of AuNR and form HSA-CTAB complex, which could also interact with other adjacent complexes through "cross-linking" by the clusters of CTAB. Such HSA-CTAB complex resulted in the observed conformational change of HSA, which we verified empirically with an esterase activity assay and by analyzing the root-mean-square-deviation (RMSD) of the HSA molecules from CGMD. Conformational change of HSA was not observed in AuNRs passivated with other negatively or positively charged surface ligands such as polystyrene sulfonate (PSS) and polydiallyldimethylammonium chloride (PDADMAC) respectively. Therefore, our study revealed that conformational change experienced by HSA may not necessarily be attributed to protein unfolding on the surface of the AuNR due to charge interactions, but rather to the instability of the surface ligands on the AuNRs which allows them to be sequestered by HSA to form HSA-CTAB complexes. read less USED (low confidence) H. Liu, X. Qin, S. Ahmad, Q. Tong, and J. Zhao, “Molecular dynamics study about the effects of random surface roughness on nanoscale boiling process,” International Journal of Heat and Mass Transfer. 2019. link Times cited: 46 USED (low confidence) E. S. Muckley et al., “Hierarchical TiO2:Cu2O nanostructures for gas/vapor sensing and CO2 sequestration.,” ACS applied materials & interfaces. 2019. link Times cited: 12 Abstract: We investigate the effect of high-surface-area self-assemble… read moreAbstract: We investigate the effect of high-surface-area self-assembled TiO2:Cu2O nanostructures for CO2¬ and relative humidity (RH) gravimetric detection using polyethylenimine (PEI), 1-ethyl-3-methylimidazolium (EMIM), and polyacrylamide (PAAm). Introduction of hierarchical TiO2:Cu2O nanostructures on the surface of quartz crystal microbalance (QCM) sensors is found to significantly improve sensitivity to CO2 and to H2O vapor. The response of EMIM to CO2 increases 5-fold for 100 nm thick TiO2:Cu2O as compared to gold. At ambient CO2 concentrations the hierarchical assembly operates as a sensor with excellent reversibility, while at higher pressures the CO2 desorption rate decreases, suggesting possible application for CO2 sequestration under those conditions. The gravimetric response of PEI to CO2 increases by a factor of 3 upon introduction of a 50 nm TiO2:Cu2O layer. The PAAm gravimetric response to water vapor also increases by a factor of 3 and displays improved reversibility with the addition of 50 nm TiO2:Cu2O structures. We found that TiO2:Cu2O can be used to lower the detection limits for CO2 sensing with EMIM and PEI and lower detection limits for H2O sensing with PAAm by over a factor of two. Coarse-grained and all-atom molecular dynamics simulations indicate the dissociative character of ionic liquid assembly on TiO2:Cu2O interfaces and different distributions of CO2 and H2O molecules on bare and ionic liquid-coated surfaces, confirming experimental observations. Overall, our results show high potential of hierarchical assemblies of TiO2:Cu2O / room temperature ionic liquid and polymer films for sensors and CO2 sequestration. read less USED (low confidence) Z. Cao, V. Liu, and A. B. Farimani, “Water Desalination with Two-dimensional Metal Organic Framework Membranes.,” Nano letters. 2019. link Times cited: 90 Abstract: Providing fresh and drinkable water is a grand challenge the… read moreAbstract: Providing fresh and drinkable water is a grand challenge the world is facing today. Development in nano-materials can create possibilities of using energy-efficient nanoporous materials for water desalination. In this work, we demonstrated that ultrathin Metal Organic Framework (MOF) is capable of efficiently rejecting ions while giving access to high water flux. Through molecular dynamic simulation, we discovered perfect ion rejection rate by two-dimensional multi-layer MOF. The naturally porous structure of 2D MOF enables significantly 3 to 6 orders of magnitude higher water permeation compared to that of traditional membranes. Few layers MOF membranes show one order of magnitude higher water flux compared to single layer nanoporous graphene or molybdenum disulfide without the requirement of drilling pores. The excellent performance of 2D MOF membranes is supported by water permeation calculations, water density/velocity profiles at the pore and the water interfacial diffusion near the pore. The performance of MOF offers a potential solution for energy-efficient water desalination. read less USED (low confidence) K. Yokoyama et al., “Examination of Adsorption Orientation of Amyloidogenic Peptides Over Nano-Gold Colloidal Particle Surfaces,” International Journal of Molecular Sciences. 2019. link Times cited: 9 Abstract: The adsorption of amyloidogenic peptides, amyloid beta 1–40 … read moreAbstract: The adsorption of amyloidogenic peptides, amyloid beta 1–40 (Aβ1–40), alpha-synuclein (α-syn), and beta 2 microglobulin (β2m), was attempted over the surface of nano-gold colloidal particles, ranging from d = 10 to 100 nm in diameter (d). The spectroscopic inspection between pH 2 and pH 12 successfully extracted the critical pH point (pHo) at which the color change of the amyloidogenic peptide-coated nano-gold colloids occurred due to aggregation of the nano-gold colloids. The change in surface property caused by the degree of peptide coverage was hypothesized to reflect the ΔpHo, which is the difference in pHo between bare gold colloids and peptide coated gold colloids. The coverage ratio (Θ) for all amyloidogenic peptides over gold colloid of different sizes was extracted by assuming Θ = 0 at ΔpHo = 0. Remarkably, Θ was found to have a nano-gold colloidal size dependence, however, this nano-size dependence was not simply correlated with d. The geometric analysis and simulation of reproducing Θ was conducted by assuming a prolate shape of all amyloidogenic peptides. The simulation concluded that a spiking-out orientation of a prolate was required in order to reproduce the extracted Θ. The involvement of a secondary layer was suggested; this secondary layer was considered to be due to the networking of the peptides. An extracted average distance of networking between adjacent gold colloids supports the binding of peptides as if they are “entangled” and enclosed in an interfacial distance that was found to be approximately 2 nm. The complex nano-size dependence of Θ was explained by available spacing between adjacent prolates. When the secondary layer was formed, Aβ1–40 and α-syn possessed a higher affinity to a partially negative nano-gold colloidal surface. However, β2m peptides tend to interact with each other. This difference was explained by the difference in partial charge distribution over a monomer. Both Aβ1–40 and α-syn are considered to have a partial charge (especially δ+) distribution centering around the prolate axis. The β2m, however, possesses a distorted charge distribution. For a lower Θ (i.e., Θ <0.5), a prolate was assumed to conduct a gyration motion, maintaining the spiking-out orientation to fill in the unoccupied space with a tilting angle ranging between 5° and 58° depending on the nano-scale and peptide coated to the gold colloid. read less USED (low confidence) H. A. El-Mageed and M. Taha, “Exploring the intermolecular interaction of serine and threonine dipeptides with gold nanoclusters and nanoparticles of different shapes and sizes by quantum mechanics and molecular simulations,” Journal of Molecular Liquids. 2019. link Times cited: 12 USED (low confidence) A. Nemati, H. N. Pishkenari, A. Meghdari, and S. Ge, “Controlling the Diffusive Motion of Fullerene-Wheeled Nanocars Utilizing a Hybrid Substrate,” The Journal of Physical Chemistry C. 2019. link Times cited: 14 Abstract: In the previous years, a few types of nanocars have been bui… read moreAbstract: In the previous years, a few types of nanocars have been built with the promising potential to transport other molecules, to provide bottom-up assembly, or to perform other mechanical tasks. In this study, we propose a method to convert the diffusive displacement of nanocars to a guided motion in a desired path by adding some impurity atoms in the substrate. We investigated the motion of C60 as well as the nanotruck and the nanocar on a flat gold substrate containing silver contamination and conversely a silver substrate containing gold contamination at the different temperatures. The results showed that silver impurity on the gold substrate act as a repellent obstacle in the path of C60 making it unable to enter the silver region even at high temperatures, although at 600 K and higher temperatures, it was finally able to enter the silver segment. Nevertheless, a big enough silver impurity proved to be an impenetrable barrier for the nanocar and the nanotruck even at 600 K. The study of motion on the silv... read less USED (low confidence) S. Min et al., “Simulation of electrical conductivity for nanoparticles and nanotubes composite sensor according to geometrical properties of nanomaterials,” Composites Part B: Engineering. 2019. link Times cited: 7 USED (low confidence) I. V. Voroshylova et al., “On the role of the surface charge plane position at Au(hkl)–BMImPF6 interfaces,” Electrochimica Acta. 2019. link Times cited: 12 USED (low confidence) T. Vasileiadis et al., “Ultrafast rotational motions of supported nanoclusters probed by electron diffraction,” Nanoscale Horizons. 2019. link Times cited: 4 Abstract: Femtosecond electron diffraction is established as goniomete… read moreAbstract: Femtosecond electron diffraction is established as goniometer of ultrafast nanocrystal rotations. read less USED (low confidence) R. Liu, L. Song, Y. Meng, M. Zhu, and H. Zhai, “The Study on Biocompatibility of AuNPs and Theoretical Design of Multi-CDRs-Functional Nanobody.,” The journal of physical chemistry. B. 2019. link Times cited: 4 Abstract: The investigation on protein-like specific functions of nano… read moreAbstract: The investigation on protein-like specific functions of nano-particles (NPs) has been a huge challenge. Here, the biocompatibility of Au nano-particles (AuNPs) to antigens HEWL and EGFR was studied firstly by molecular dynamics (MD) simulations, and the research results revealed that antigens could form quickly a stable binding with the AuNPs and kept the structural integrity of protein, which noted better biocompatibility of AuNPs. Then, two types of complementary-determining regions (CDRs) were grafted onto the AuNPs to design a novel multi-CDRs-functional nanobody. By means of MD simulations under physiological condition, we found that the bindings of the designed nanobody and the antigens were stable and safe. Compared with the results of antigens interacted with natural antibody, the redundant CDRs on AuNPs bound with non-active site in the antigens to form stable conformation, which leaded to the powerful binding capacity of the designed nanobody than that of natural antibody. This study provided available insights on the biocompatibility of AuNPs and important theoretical proofs to the multi-CDRs-functional nanobody applied in biological systems, which were expected to help the design of novel multi-functional nanobodies. read less USED (low confidence) M. Balonis, G. Sant, and O. B. Isgor, “Mitigating steel corrosion in reinforced concrete using functional coatings, corrosion inhibitors, and atomistic simulations,” Cement and Concrete Composites. 2019. link Times cited: 29 USED (low confidence) F. Teixeira and M. Salvadori, “Nucleation of gold nanoclusters in PMMA during energetic plasma deposition: A molecular dynamics and tfMC-Monte Carlo study,” Physica E: Low-dimensional Systems and Nanostructures. 2019. link Times cited: 4 USED (low confidence) I.-C. Yeh, J. L. Lenhart, J. Orlicki, and B. Rinderspacher, “Molecular Dynamics Simulation Study of Adsorption of Bioinspired Oligomers on Alumina Surfaces.,” The journal of physical chemistry. B. 2019. link Times cited: 10 Abstract: The adsorption of small oligomers on a model metal oxide sur… read moreAbstract: The adsorption of small oligomers on a model metal oxide surface was studied with atomistically detailed molecular dynamics simulations. The oligomers consisted of two different repeat units: a maleimide, which contains a catechol functional group as in the dopamine residue found in marine adhesive proteins, and a methyl acrylate. A hydroxylated alumina surface was used as the model metal oxide surface. Adsorption interactions were investigated in aqueous as well as anhydrous conditions. In anhydrous conditions, the model oligomers displayed strong adsorption interactions with the surface. However, in aqueous conditions, the adsorption interactions were significantly weakened because of the competition with the water molecules for adsorption sites near the surface. Catechol functional groups in the model oligomers were found to play an important role in adsorption interactions with the alumina surface via hydrogen bonds. read less USED (low confidence) M. Saleheen, M. Zare, M. Faheem, and A. Heyden, “Computational Investigation of Aqueous Phase Effects on the Dehydrogenation and Dehydroxylation of Polyols over Pt(111),” The Journal of Physical Chemistry C. 2019. link Times cited: 19 Abstract: Prediction of solvation effects on the kinetics of elementar… read moreAbstract: Prediction of solvation effects on the kinetics of elementary reactions occurring at metal–water interfaces is of high importance for the rational design of catalysts for the biomass and electrocatalysis communities. A lack of knowledge of the reliability of various computational solvation schemes for processes on metal surfaces is currently a limiting factor. Using a multilevel quantum mechanical/molecular mechanical (QM/MM) description of the potential energy surface, we determined characteristic time and length scales for typical free-energy perturbation (FEP) calculations of bond cleavages in ethylene glycol, a sugar surrogate molecule, over Pt(111). Our approach is based on our explicit solvation model for metal surfaces and the repetition of FEP calculations to estimate confidence intervals. Results indicate that aqueous phase effects on the free energies of elementary processes can be determined with 95% confidence intervals from limited configuration space sampling and the fixed charge approximati... read less USED (low confidence) M. Lasich and K. Tumba, “Single-site Langmuir-type adsorption in structure-I clathrate hydrates: A molecular simulation study using a general self-consistent force field,” Fluid Phase Equilibria. 2019. link Times cited: 0 USED (low confidence) Y. Noh, T. Vo, and B. H. Kim, “Subatomic-Level Solid/Fluid Boundary of Lennard-Jones Atoms: A Molecular Dynamics Study of Metal-Inert Fluid Interface,” Applied Sciences. 2019. link Times cited: 5 Abstract: At the molecular scale, the definition of solid/fluid bounda… read moreAbstract: At the molecular scale, the definition of solid/fluid boundary is ambiguous since its defining precision is comparable to the size of the electron orbitals. It is important to figure out the sub-atomic-level solid/fluid boundary as the definition of the solid/fluid interface is related to estimating various properties such as slip length, Kapitza resistance, confined volume, thermodynamic properties, and material properties. In this work, molecular dynamics (MD) simulations were conducted to show the effects of the solid/fluid boundary on estimating thermodynamic properties. Our results reveal that the different definitions of solid/fluid boundary can cause a considerable impact on quantitative analysis and even qualitative analysis of a nanoscale system. The solid/fluid boundary for Lennard-Jones atoms is determined within sub-atomic precision via heat transfer MD simulations and microscopic heat flux relation. The result shows that solid/fluid boundary is slightly shifted to the fluid regime as the temperature increase. We suggested a mathematical expression of solid/fluid boundary of LJ atom that is theoretically estimated by ignoring the thermal vibration. The results presented in this work are expected to improve the accuracy of analyzing nanoscale phenomena as well as the continuum-based models for nanoscale heat and mass transport. read less USED (low confidence) M. Zhou, X. Xiong, D. Drummer, and B. Jiang, “Interfacial interaction and joining property of direct injection-molded polymer-metal hybrid structures: A molecular dynamics simulation study,” Applied Surface Science. 2019. link Times cited: 46 USED (low confidence) Y.-Z. Tang, X. Zhang, Y. Lin, J. Xue, Y. He, and L. Ma, “Molecular Dynamics Simulation of Nanofilm Boiling on Graphene‐Coated Surface,” Advanced Theory and Simulations. 2019. link Times cited: 12 Abstract: Molecular dynamics (MD) simulations are conducted to investi… read moreAbstract: Molecular dynamics (MD) simulations are conducted to investigate the effect of graphene coating on nanofilm boiling on an atomically smooth surface. Transition of boiling modes from normal evaporation to explosive boiling is observed on both bare and graphene‐coated surfaces. The onset temperature of explosive boiling on the graphene‐coated surface is approximately 170 K, which is extremely close to the value of approximately 160 K on the bare surface. A hydrophobic surface is also artificially fabricated to verify the effect of surface wettability on nanofilm boiling and the significance of graphene coating. The onset temperature of explosive boiling on the hydrophobic surface is much higher than that on the hydrophilic and graphene‐coated surfaces. Additionally, the critical heat flux of the nanofilm boiling on the graphene‐coated surface is slightly lower than that on the bare hydrophilic surface. Results confirm that graphene coating is almost useless, and even harmful to the heat transfer enhancement of the nanofilm boiling. read less USED (low confidence) L. Zhao and J. Cheng, “Characterizing the bifurcating configuration of hydrogen bonding network in interfacial liquid water and its adhesion on solid surfaces,” RSC Advances. 2019. link Times cited: 1 Abstract: The interfacial structures of liquid water molecules adjacen… read moreAbstract: The interfacial structures of liquid water molecules adjacent to a solid surface contribute significantly to the interfacial properties of aqueous solutions, and are of prime importance in a wide spectrum of applications. In this work, we use molecular dynamics (MD) simulations to explore the interfacial structures, mainly in term of hydrogen bonding network, of a liquid water film interacting intimately with solid surfaces, which are composed of [100] face centered cubic (FCC) lattices. We disclose the formation of a bifurcating configuration of hydrogen bonds in interfacial liquid water and ascribe its occurrence to the collective effects of water density depletion, hydrogen bonds and local polarization. Such bifurcating configuration of interfacial water molecules consists of repetitive layer by layer water sheets with intra-layer hydrogen bonding network being formed in each layer, and inter-layer defects, i.e., hydrogen bonds formed between two neighboring layers of interfacial water. A lower bound of 2.475 for the average number of hydrogen bonds per interfacial water molecule is expected. Our MD study on the interfacial configuration of water on solid surfaces reveals a quadratic dependence of adhesion on the solid–liquid affinity, bridging the gap between the macroscopic interfacial property Wadh and the microscopic parameter εSL of the depth of the Lennard-Jones solid–liquid potential. read less USED (low confidence) M. Lasich, C. Narasigadu, and S. Moodley, “Adsorption of humid air in compacted montmorillonite: A Monte Carlo simulation study,” Fluid Phase Equilibria. 2019. link Times cited: 4 USED (low confidence) S. Vahidi, M. Bozorgmehr, A. Morsali, and S. Beyramabadi, “Study of alpha-amylase and gold nanoparticles interaction at two different temperatures through molecular dynamics.,” Journal of molecular graphics & modelling. 2019. link Times cited: 2 USED (low confidence) M. Yoneya and S. Sugisawa, “Simulation of Colloidal Silver Nanoparticle Formation from a Precursor Complex,” The Journal of Physical Chemistry C. 2019. link Times cited: 7 Abstract: The formation of oleylamine-stabilized colloidal silver nano… read moreAbstract: The formation of oleylamine-stabilized colloidal silver nanoparticles (Ag-NPs), which are the most promising metal NP inks for printed electronics, was modeled and simulated to investigate the shell structure of the oleylamine coating of the Ag-NPs. Our simulation results showed that Ag-NP growth occurred by the coalescence of silver clusters. We also found that the oleylamine shell structure surrounding the Ag-NPs was not the commonly assumed radially extending structure with a single amine group adsorbed to the silver surface but rather a partially lying-down structure with multiple adsorbed groups. The latter structure results in a thinner shell and contains fewer stabilizing agents than the former, which may contribute to the low-temperature sintering characteristics of Ag-NP inks. read less USED (low confidence) S. Ju, J.-W. Su, C.-H. Lin, and H.-Y. Chen, “Revealing the interaction mechanism of peptide with specific platinum facets by stochastic tunneling-basin hopping method,” Applied Surface Science. 2019. link Times cited: 2 USED (low confidence) M. V. Slavgorodska and A. Kyrychenko, “Binding Preference of α-Cyclodextrin onto Gold Nanoparticles,” Nanosistemi, Nanomateriali, Nanotehnologii. 2019. link Times cited: 3 Abstract: The binding preference of -cyclodextrin ( -CD) onto the … read moreAbstract: The binding preference of -cyclodextrin ( -CD) onto the surface of a gold nanoparticle is studied by means of molecular dynamics (MD) simulations. As found, the -CD molecules bind onto the nanoparticle surface at the nanosecond time scale. Adsorption onto the gold nanoparticle surface occurs through multiple non-covalent interactions, among which non-covalent bonding of the aliphatic carbon atoms of -CD play a key role. The analysis shows that a -CD molecule prefers to bind onto the gold surface by its cone side. In addi-tion, the MD simulations reveal that, upon the increase in concentration, the self-aggregation and steric repulsion among adsorbed -CD molecules affect its binding preference onto read less USED (low confidence) M. Tang, N. S. Gandhi, K. Burrage, and Y. T. Gu, “Adsorption of Collagen-like Peptides onto Gold Nanosurfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 18 Abstract: The molecular behavior of proteins in the presence of inorga… read moreAbstract: The molecular behavior of proteins in the presence of inorganic surfaces is of fundamental biological significance. Examples include extracellular matrix proteins interacting with gold nanoparticles and metallic implant biomaterials, such as titanium and stainless steels. Uncharged inorganic surfaces that interact strongly with the solution phase (hydrophilic surfaces) have been commonly used in disease treatments. A deep understanding of the molecular behavior of body proteins in the presence of hydrophilic surfaces is important in terms of clinical applications. However, the adsorption mechanism of proteins onto hydrophilic surfaces remains not fully understood. Here, comprehensive molecular dynamics simulations are carried out to study the molecular response of a human collagen molecule segment (CMS) to the presence of a planar gold surface (AuNS) in explicit solvent, aiming to unravel the adsorption mechanism of proteins onto hydrophilic surfaces. The results demonstrate that in the presence of AuNS, the CMS first biasedly diffuses toward AuNS, followed by anchoring to the gold surface, and finally adsorbs stepwise onto AuNS, where the protein adjusts its structure to maximize the interaction with AuNS. We conclude that adsorption of proteins onto hydrophilic surfaces adheres to three steps, namely, biased diffusion, anchoring, and stepwise adsorption accompanied by structural adaptation. The obtained adsorption mechanism provides insights into the development of inorganic surfaces for biomedical and therapeutic applications. read less USED (low confidence) A. Brant and M. Sundaram, “Molecular dynamics study of direct localized overpotential deposition for nanoscale electrochemical additive manufacturing process,” Precision Engineering. 2019. link Times cited: 7 USED (low confidence) S. M. H. Lavasani, H. N. Pishkenari, and A. Meghdari, “How Chassis Structure and Substrate Crystalline Direction Affect the Mobility of Thermally Driven p-Carborane-Wheeled Nanocars,” The Journal of Physical Chemistry C. 2019. link Times cited: 14 Abstract: In recent years, various nanocars have been synthesized in o… read moreAbstract: In recent years, various nanocars have been synthesized in order to provide controlled mechanical function, transport other nanoparticles, or enable bottom-up assembly capability. There have even been racing competitions among well-known nanocars in which the wheels play an influential role. In this paper, the motion of thermally driven nanocars equipped with p-carborane wheels on Au(111) and Au(001) substrates is investigated. For the sake of comparison, classical all-atom molecular dynamics (MD) and rigid-body MD (RBMD) have been used to study the motion threshold as well as to analyze the effect of temperature, substrate crystalline direction, and chassis shape on the diffusive motion of a nanocooper, trimer, nanocaterpillar, and angled nanocar. It was observed that the motion regime of the nanocars on a gold substrate is a function of temperature and translational diffusion as well as the rotational diffusion coefficient, which shows non-Arrhenius behavior. Nanocar motion has three main regimes, trapp... read less USED (low confidence) A. Kyrychenko, M. M. Blazhynska, M. V. Slavgorodska, and O. Kalugin, “Stimuli-responsive adsorption of poly(acrylic acid) onto silver nanoparticles: Role of polymer chain length and degree of ionization,” Journal of Molecular Liquids. 2019. link Times cited: 23 USED (low confidence) M. Wu et al., “Solution NMR Analysis of Ligand Environment in Quaternary Ammonium-Terminated Self-Assembled Monolayers on Gold Nanoparticles: The Effect of Surface Curvature and Ligand Structure.,” Journal of the American Chemical Society. 2019. link Times cited: 51 Abstract: We report a solution NMR-based analysis of (16-mercaptohexad… read moreAbstract: We report a solution NMR-based analysis of (16-mercaptohexadecyl)trimethylammonium bromide (MTAB) self-assembled monolayers on colloidal gold nanospheres (AuNSs) with diameters from 1.2 to 25 nm and gold nanorods (AuNRs) with aspect ratios from 1.4 to 3.9. The chemical shift analysis of the proton signals from the solvent-exposed headgroups of bound ligands suggests that the headgroups are saturated on the ligand shell as the sizes of the nanoparticles increase beyond ∼10 nm. Quantitative NMR shows that the ligand density of MTAB-AuNSs is size-dependent. Ligand density ranges from ∼3 molecules per nm2 for 25 nm particles to up to 5-6 molecules per nm2 in ∼10 nm and smaller particles for in situ measurements of bound ligands; after I2/I- treatment to etch away the gold cores, ligand density ranges from ∼2 molecules per nm2 for 25 nm particles to up to 4-5 molecules per nm2 in ∼10 nm and smaller particles. T2 relaxation analysis shows greater hydrocarbon chain ordering and less headgroup motion as the diameter of the particles increases from 1.2 nm to ∼13 nm. Molecular dynamics simulations of 4, 6, and 8 nm (11-mercaptoundecyl)trimethylammonium bromide-capped AuNSs confirm greater hydrophobic chain packing order and saturation of charged headgroups within the same spherical ligand shell at larger nanoparticle sizes and higher ligand densities. Combining the NMR studies and MD simulations, we suggest that the headgroup packing limits the ligand density, rather than the sulfur packing on the nanoparticle surface, for ∼10 nm and larger particles. For MTAB-AuNRs, no chemical shift data nor ligand density data suggest that two populations of ligands that might correspond to side-ligands and end-ligands exist; yet T2 relaxation dynamics data suggest that headgroup mobility depends on aspect ratio and absolute nanoparticle dimensions. read less USED (low confidence) M. Tang, N. S. Gandhi, K. Burrage, and Y. T. Gu, “Interaction of gold nanosurfaces/nanoparticles with collagen-like peptides.,” Physical chemistry chemical physics : PCCP. 2019. link Times cited: 17 Abstract: Nanotechnology has quickly emerged as a promising research f… read moreAbstract: Nanotechnology has quickly emerged as a promising research field with potential effects in disease treatments. For example, gold nanoparticles (AuNPs) have been extensively used in diagnostics and therapeutics. When administrated into human tissues, AuNPs first encounter extracellular matrix (ECM) molecules. Amongst all the ECM components, collagen is the main tension-resisting constituent, whose biofunctional and mechanical properties are strongly dependent on its hierarchical structure. Therefore, an in-depth understanding of the structural response of collagen to the presence of gold nanosurfaces (AuNS) and AuNPs is crucial in terms of clinical applications of AuNPs. However, detailed understanding of the molecular-level and atomic-level interaction between AuNS/AuNPs and collagen in the ECM is elusive. In this study, comprehensive molecular dynamics (MD) simulations have been performed to investigate the molecular behaviour of a collagen molecule segment (CMS) in the presence of AuNS/AuNPs in explicit water, aiming to explore the interaction of AuNS/AuNPs with collagen triple helices at the molecular and atomic levels. The results show that the CMS forms a rapid association with AuNS/AuNPs and undergoes a severe unfolding upon adsorption on AuNS/AuNPs, indicating an unfolding propensity of gold surfaces. We conclude that collagen triple helices unfold readily on AuNS and bare AuNPs, due to the interaction of gold surfaces with the protein backbone. The revealed clear unfolding nature and the unravelled atomic-level unfolding mechanism of collagen triple helices onto AuNPs contribute to the development of AuNPs for biomedical and therapeutic applications, and the design of gold-binding proteins. read less USED (low confidence) S. Franco-Ulloa, L. Riccardi, F. Rimembrana, M. Pini, and M. D. Vivo, “NanoModeler: A Webserver for Molecular Simulations and Engineering of Nanoparticles.,” Journal of chemical theory and computation. 2019. link Times cited: 24 Abstract: Functionalized nanoparticles (NPs) are at the frontier of na… read moreAbstract: Functionalized nanoparticles (NPs) are at the frontier of nanoscience. They hold the promise of innovative applications for human health and technology. In this context, molecular dynamics (MD) simulations of NPs are increasingly employed to understand the fundamental structural and dynamical features of NPs. While informative, such simulations demand a laborious two-step process for their setup. In-house scripts are required to (i) construct complex 3D models of the inner metal core and outer layer of organic ligands, and (ii) correctly assign force-field parameters to these composite systems. Here, we present NanoModeler ( www.nanomodeler.it ), the first Webserver designed to automatically generate and parametrize model systems of monolayer-protected gold NPs and gold nanoclusters. The only required input is a structure file of one or two ligand(s) to be grafted onto the gold core, with the option of specifying homogeneous or heterogeneous NP morphologies. NanoModeler then generates 3D models of the nanosystem and the associated topology files. These files are ready for use with the Gromacs MD engine, and they are compatible with the AMBER family of force fields. We illustrate NanoModeler's capabilities with MD simulations of selected representative NP model systems. NanoModeler is the first platform to automate and standardize the construction and parametrization of realistic models for atomistic simulations of gold NPs and gold nanoclusters. read less USED (low confidence) K. Nishio, A. K. A. Lu, and T. Miyazaki, “Entropy-driven docosahedral short-range order in simple liquids and glasses.,” Physical review. E. 2019. link Times cited: 7 Abstract: The energetically favored icosahedral structure has been see… read moreAbstract: The energetically favored icosahedral structure has been seen as the central figure for describing the local structure of simple liquids and glasses. Although regular icosahedral structures are rarely found, it is accepted that distorted icosahedral structures occur in simple liquids and glasses. However, which local structure dominates and why it is more frequent than the others remain unanswered questions. In this study, by using a recently developed structure descriptor, we show that docosahedral structures are the most favored not only in models of simple liquids and glasses but also in an experimental colloid glass. We also show that the the predominance of docosahedral structures is entropy-driven. Our findings represent a significant milestone towards comprehending mysterious phenomena such as supercooling, glass transition, and crystallization, where local structures play a key role. read less USED (low confidence) O. A. Perfilieva, D. Pyshnyi, and A. Lomzov, “Molecular Dynamics Simulation of Polarizable Gold Nanoparticles Interacting with Sodium Citrate.,” Journal of chemical theory and computation. 2019. link Times cited: 30 Abstract: To study the structure of a citrate-capped gold nanoparticle… read moreAbstract: To study the structure of a citrate-capped gold nanoparticle and forces involved in citrate-gold interactions, we performed a molecular dynamics simulation of a truncated-octahedron nanoparticle containing Au(111) and Au(100) surfaces with sodium citrate. In this paper, we employed an approach to the modeling of interactions of a gold nanoparticle with citrate molecules taking into account the image charge effect in the metal. First, we built models of 6 and 14 nm nanoparticles, which can reproduce the polarization effects, based on a rigid-rod gold model and the GolP-CHARMM force field. To verify the simulation results, we analyzed density plots, radial distributions, distributions perpendicular to Au(111) and Au(100) surfaces, the electric potential of the system, and the dynamics of citrate crown formation. We observed formation of a stable citrate crown around the nanoparticle and detected nonuniform surface distribution of citrate ions with the preference for Au(111) facets over Au(100) ones. Testing of the model of the citrate-capped gold nanoparticle in a simulation at high concentrations of Na+ and Cl- ions (0.8 M) showed incorporation of chloride anions into the citrate crown. We compared the results of citrate crown formation between polarizable and nonpolarizable gold models and noticed a difference in the citrate distribution on the surface of the gold nanoparticle. We found that polarization effects in the metal are involved in the mechanism of interaction of the gold nanoparticle and citrate ions. The obtained results are in good agreement with experimental data and computer simulations from a number of other studies, which prove the validity of the proposed model. read less USED (low confidence) A. Terzyk et al., “Water Nanodroplet on a Hydrocarbon ‘Carpet’-The Mechanism of Water Contact Angle Stabilization by Airborne Contaminations on Graphene, Au, and PTFE Surfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2019. link Times cited: 16 Abstract: Wetting is very common phenomenon, and it is well documented… read moreAbstract: Wetting is very common phenomenon, and it is well documented that the wettability of a solid depends on the surface density of adsorbed airborne hydrocarbons. This "hydrocarbon hypothesis" has been experimentally confirmed for different surfaces, for example, graphene, TiO2, and SiO2; however, there are no scientific reports describing the influence of airborne contaminants on the water contact angle (WCA) value measured on the polytetrafluoroethylene (PTFE) surface. Using experimental data showing the influence of airborne hydrocarbons on the wettability of graphene, gold and PTFE by water, together with Molecular Dynamics simulation results we prove that the relation between the WCA and the surface concentration of hydrocarbons ( n-decane, n-tridecane, and n-tetracosane) is more complex than has been assumed up until now. We show, in contrast to commonly approved opinion, that adsorbed hydrocarbons can increase (graphene, Au) or decrease (PTFE) the WCA of a nanodroplet sitting on a surface. Using classical thermodynamics, a simple theoretical approach is developed. It is based on two adsorbed hydrocarbon states, namely, "carpet" and "dimple". In the "carpet" state a uniform layer of alkane molecules covers the entire substrate. In contrast, in the "dimple" state, the preadsorbed layer of alkane molecules covers only the open surface. Simple thermodynamic balance between the two states explains observed experimental and simulation results, forming a good starting point for future studies. read less USED (low confidence) M. A. Nejad and H. Urbassek, “Diffusion of cisplatin molecules in silica nanopores: Molecular dynamics study of a targeted drug delivery system.,” Journal of molecular graphics & modelling. 2019. link Times cited: 11 USED (low confidence) P. Zhang, L. Jin, L. Zhou, X. Du, and Y. Yang, “Heat transfer around copper nanoparticle with high superheat in water pool: A molecular dynamics simulation,” Thermal Science and Engineering Progress. 2018. link Times cited: 6 USED (low confidence) E. Zhu et al., “Long-Range Hierarchical Nanocrystal Assembly Driven by Molecular Structural Transformation.,” Journal of the American Chemical Society. 2018. link Times cited: 14 Abstract: The hierarchical control in biogenic minerals, from precise … read moreAbstract: The hierarchical control in biogenic minerals, from precise nanomorphology control to subsequent macroscopic assembly, remains a formidable challenge in artificial synthesis. Studies in biomineralization, however, are largely limited to atomic andmolecular scale crystallization, devoting little attention to biomolecular higher-order structures (HOSs) which critically impact long-range assembly of biominerals. Here we demonstrate a biomimetic route and quantitative simulations that explore peptide HOSs on guiding nanocrystal formation and anisotropic assembly into hierarchical structures. It is found that the Pt{100}-specific peptide T7 (Ac-TLTTLTN-CONH2) adopts ST-turn secondary structure, promoting cubic Pt nanocrystal formation at low concentration, and spontaneously transforms into a β-sheet with increased concentration. The β-sheet T7-Pt{100} specificity drives cubic Pt nanocrystals to self-assemble into large-area, long-range, [100] linear assemblies. This study provides a robust demonstration for bio/nonbiogenic material specificity, nanoscale synthesis, and long-range self-organization with biomolecular HOSs and opens vast opportunities for multiscale programmable structures. read less USED (low confidence) A. Aggarwal, S. Bag, and P. Maiti, “Remarkable similarity of force induced dsRNA conformational changes to stretched dsDNA and their detection using electrical measurements.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 10 Abstract: In spite of the striking difference between twist-stretch co… read moreAbstract: In spite of the striking difference between twist-stretch coupling of dsRNA and dsDNA under external force, dsRNA shows similar structural polymorphism to dsDNA under different pulling protocols. Our atomistic MD simulations show that overstretching dsRNA along the 3' direction of the opposite strands (OS3) leads to the emergence of S-RNA whereas overstretching along the 5' directions of the opposite strands (OS5) leads to melting of dsRNA at lower forces. Using the dsRNA morphology from pulling MD simulations, we use a multiscale method involving ab initio calculations and Kinetic Monte Carlo (KMC) simulations to estimate the conductance of dsRNA and find that the conformational changes drastically affect its conductance. The current through dsRNA chains drastically drops after a critical stretching length and critically depends on the pulling protocol. The critical stretching length for the OS3 pulling case is around 65% higher than that of the OS5 case. read less USED (low confidence) A. K. Giri and E. Spohr, “Influence of Chain Length and Branching on the Structure of Functionalized Gold Nanoparticles,” The Journal of Physical Chemistry C. 2018. link Times cited: 18 Abstract: Functionalized gold nanoparticles (GNPs) in aqueous NaCl sol… read moreAbstract: Functionalized gold nanoparticles (GNPs) in aqueous NaCl solutions have been studied using molecular dynamics simulations to assess the suitability of various functionalization chemistries to effec... read less USED (low confidence) A. Chew and R. V. V. Lehn, “Effect of Core Morphology on the Structural Asymmetry of Alkanethiol Monolayer-Protected Gold Nanoparticles,” The Journal of Physical Chemistry C. 2018. link Times cited: 18 Abstract: Gold nanoparticles (GNPs) are versatile materials suitable f… read moreAbstract: Gold nanoparticles (GNPs) are versatile materials suitable for various biological applications due to their tunable surface properties, but structure–function relationships between specific GNP components and GNP behavior are largely lacking. In this work, atomistic molecular dynamics simulations were used to study the influence of gold core morphology, size, and ligand length on the structure of uniformly nonpolar alkanethiol monolayer-protected GNPs in water. By use of a generalized system preparation workflow, three gold core models were selected for this study: (1) a uniformly spherical hollow gold core, (2) a spherical gold core cut from a bulk gold lattice, and (3) a faceted gold core obtained from variance-constrained semigrand-canonical simulations. Independent of the gold core morphology, we found that long alkanethiol ligands exhibit increased ligand order and form quasi-crystalline domains, or bundles, in which ligands orient in the same direction, leading to asymmetric monolayer structures. Fa... read less USED (low confidence) M. Jagannath, S. N. Divi, and A. Chatterjee, “Kinetic Map for Destabilization of Pt-Skin Au Nanoparticles via Atomic Scale Rearrangements,” The Journal of Physical Chemistry C. 2018. link Times cited: 7 Abstract: A commonly used strategy to enhance the mass activity of Pt-… read moreAbstract: A commonly used strategy to enhance the mass activity of Pt-based catalysts involves the synthesis of Au nanoparticles (NPs) with a monolayer-thick Pt-skin layer. The synergistic effect of Au and Pt results in a higher catalytic activity and better Pt utilization. However, the stability of the Pt-skin layer is questionable as our recent equilibrium Monte Carlo simulations predict that eventually the surface Pt is replaced by Au. The role of Au during destabilization of Pt-skin in vacuum and solution is investigated with the help of molecular dynamics. Different starting Au–Pt arrangements are studied mimicking various NP synthesis approaches. Beyond a critical number of atoms in a Pt cluster, the ideal Pt monolayer rapidly transforms to a three-dimensional (3D) Pt cluster. This is supported by our model predicting transition from the Pt monolayer to Volmer–Weber growth in the Au–Pt system. At room temperature, Pt atoms move into the subsurface layer at second timescales mainly via the exchange mechanism i... read less USED (low confidence) M. Khavani, M. Izadyar, and M. Housaindokht, “Modeling of the Functionalized Gold Nanoparticle Aggregation in the Presence of Dopamine: A Joint MD/QM Study,” The Journal of Physical Chemistry C. 2018. link Times cited: 14 Abstract: The investigation of gold nanoparticle (AuNP) aggregation at… read moreAbstract: The investigation of gold nanoparticle (AuNP) aggregation at the atomic level is a great challenge from the experimental view, while theoretical methods facilitate our understanding of the AuNP aggregation process. In this article, by applying full atomistic molecular dynamics simulations, the aggregation process and the stability of the functionalized AuNPs with 4-amino-3-hydrazino-5-mercapto-1,2,4-triazole (AT) was investigated. Moreover, the ability of AT–AuNPs toward selective detection of dopamine was analyzed. Theoretical results showed that AT groups on the surface of the AuNPs increase the resistance of nanoparticles against the aggregation. Also, AT–AuNPs are only accumulated in the presence of dopamine in a mixture of different analytes. In this process, dopamine acts as a molecular bridge between the AT–AuNPs, which facilitates nanoparticle aggregation through hydrogen bond interactions. Quantum chemistry calculations confirmed that the structural feature of dopamine is a more effective factor ... read less USED (low confidence) R. Palacios-Rivera et al., “Enantiopure Supramolecular Motifs of Self-Assembled Diamine-Based Chiral Molecules on Cu(100),” The Journal of Physical Chemistry C. 2018. link Times cited: 2 Abstract: The assembly of two diphenylethylenediamine enantiomers, sep… read moreAbstract: The assembly of two diphenylethylenediamine enantiomers, separately deposited on Cu(100), is investigated from the first stages of two-dimensional crystallization to the nucleation and growth of the second layer. By means of scanning tunneling microscopy, we show that the chirality of enantiomers is expressed at different levels of molecular organization. Below the monolayer completion, a disordered phase coexists with domains of a square lattice aligned with the principal crystallographic directions of the substrate. The intrinsic chirality of the molecules is only manifested through specific features contained within the corresponding unit cell. For increasing coverage, this arrangement is accompanied by a second square structure, which appears to be clockwise or counterclockwise rotated with respect to the Cu(100) directions depending on the enantiomer. The nucleation of molecular chains on top of the aligned square structure gives rise to a second layer exhibiting a stripelike configuration with remar... read less USED (low confidence) T. Avanessian and G. Hwang, “Thermal diode using controlled capillary in heterogeneous nanopores,” International Journal of Heat and Mass Transfer. 2018. link Times cited: 9 USED (low confidence) V. Imandi, M. Jagannath, and A. Chatterjee, “Role of solvent in metal-on-metal surface diffusion: A case for rational solvent selection for materials synthesis,” Surface Science. 2018. link Times cited: 7 USED (low confidence) T. Avanessian and G. Hwang, “Adsorption and capillary transition in heterogeneous nanostructures using Grand Canonical Monte Carlo simulation,” International Journal of Heat and Mass Transfer. 2018. link Times cited: 9 USED (low confidence) M. S. Googheri, M. S. Googheri, and S. H. Araghi, “Configurational effect on ion-pair interaction energies and intermolecular potential energy functions in imidazolium-based ionic liquids: A theoretical study,” Journal of Molecular Liquids. 2018. link Times cited: 7 USED (low confidence) H. Mori and N. Matubayasi, “Resin filling into nano-sized pore on metal surface analyzed by all-atom molecular dynamics simulation over a variety of resin and pore sizes,” Polymer. 2018. link Times cited: 14 USED (low confidence) M. S. Googheri, M. S. S. Googheri, and S. H. Araghi, “Configurational effect on ion-pair interaction energies and intermolecular potential energy functions in imidazolium-based ionic liquids: A theoretical study,” Journal of Molecular Liquids. 2018. link Times cited: 0 USED (low confidence) G. Chong and R. Hernandez, “Adsorption Dynamics and Structure of Polycations on Citrate-Coated Gold Nanoparticles,” The Journal of Physical Chemistry C. 2018. link Times cited: 20 Abstract: Despite the widespread application of engineered multilayere… read moreAbstract: Despite the widespread application of engineered multilayered polyelectrolyte-coated gold nanoparticles (AuNPs), their interparticle interaction is not fully understood in part because of a lack of molecular scale observation of the layer-by-layer assembly of the polyelectrolyte coating. While top-down coarse-grained models of polyelectrolyte-coated AuNPs have focused on polyelectrolytes of short length, from 10 to a 100 monomers represented as one charged bead per monomer, here we use molecular dynamics and bottom-up coarse-grained approaches to access more typical polymer lengths on the order of 200 monomers. Specifically, we simulate the adsorption dynamics and structure of one or two such long polycations on negatively charged 4 nm citrate-coated AuNPs within implicit or explicit solvents. The first polycation coats approximately half of the AuNP surface regardless of solvent model and leaves a significant part of the anionic citrate layer exposed to absorption by a second polycation. We find that the... read less USED (low confidence) L. Su, J. Krim, and D. Brenner, “Interdependent Roles of Electrostatics and Surface Functionalization on the Adhesion Strengths of Nanodiamonds to Gold in Aqueous Environments Revealed by Molecular Dynamics Simulations.,” The journal of physical chemistry letters. 2018. link Times cited: 11 Abstract: Molecular dynamics simulations demonstrate that adhesion str… read moreAbstract: Molecular dynamics simulations demonstrate that adhesion strengths as a function of charge for aqueous nanodiamonds (NDs) interacting with a gold substrate result from an interdependence of electrostatics and surface functionalization. The simulations reveal a water layer containing Na+ counterions between a negative ND with surface -COO- functional groups that is not present for a positively charged ND with -NH3+ functional groups. The closer proximity of the positive ND to the gold surface and the lack of cancelation of electrostatic interactions due to counterions and the water layer lead to an electrostatic adhesion force for the positive ND that is nearly three times larger than that of the negative ND. Prior interpretations of experimental tribological studies of ND-gold systems suggested that electrostatics or surface functionalization could be responsible for observed adhesion strength differences. The present work demonstrates how these two effects work together in determining adhesion for this system. read less USED (low confidence) M. Atilhan and S. Aparicio, “Molecular Dynamics Simulations of Metal Nanoparticles in Deep Eutectic Solvents,” The Journal of Physical Chemistry C. 2018. link Times cited: 16 Abstract: A molecular dynamics study on the solvation of metal nanopar… read moreAbstract: A molecular dynamics study on the solvation of metal nanoparticles in deep eutectic solvents is reported in this work. The solvation process was analyzed in terms of the type of metal, geometry of the nanoparticles and properties of the deep eutectic solvent. Simulations results in the microsecond range allowed to infer the properties of the solvation shells and the effects of the nanoparticles on the liquid structuring. The possible aggregation of metal nanoparticles in the studied solvents was analyzed and discussed in terms of the screening effect of the solvents and the efficient nanoparticle–solvent intermolecular forces. The reported results show deep eutectic solvents acting as metal nanoparticle stabilizers, thus providing a new platform for nanoparticles technologies. read less USED (low confidence) M. A. M. Abdalla, H.-qing Peng, D. Wu, L. Abusin, and T. J. Mbah, “Prediction of Hydrophobic Reagent for Flotation Process Using Molecular Modeling,” ACS Omega. 2018. link Times cited: 15 Abstract: The interaction or nonbonded energies of base organic ions a… read moreAbstract: The interaction or nonbonded energies of base organic ions and water molecules during the flotation process of minerals have important meanings for organizing hydrophobic and stable collectors. Furthermore, the interaction, cross-term, and valence energies of optimized structures are important for understanding the properties and structures of selective collectors. The simulation of pure scheelite mineral (PSM) surfaces with four different negative ions, using an adsorption locator module is demonstrated. The interaction energies for base organic ions and water molecules were resolved and detected by shaping the best hydrophobic interaction and the most stable suspension over the PSM surface (112) and (101). The adsorption locator results for base organic ions and water molecules on PSM surfaces (112) and (101) using buffer width 0.5 Å and temperature range from 318.15 to 283.15 K confirmed the results obtain from Forcite calculations. The results have demonstrated that the possibilities of using consistent valence force field implemented by Forcite and adsorption locator modules in the selection of flotation reagents are cost saving. Furthermore, hydrophobicity of the main negative ions in soaps were solved by the simulation methods and results are in a good agreement with the experimental methods that proved that mustard soap is more selective on the mineral surfaces than sunflower soap when used as a collector. Increasing the molecular weight of negative ions increases the interaction energy between base collector ions and PSM surfaces (112) and (101) significantly. read less USED (low confidence) T. Avanessian and G. Hwang, “Thermal switch using controlled capillary transition in heterogeneous nanostructures,” International Journal of Heat and Mass Transfer. 2018. link Times cited: 14 USED (low confidence) R. Wang, S. Bi, V. Presser, and G. Feng, “Systematic comparison of force fields for molecular dynamic simulation of Au(111)/Ionic liquid interfaces,” Fluid Phase Equilibria. 2018. link Times cited: 19 USED (low confidence) Y. Kurapati and S. Sharma, “Adsorption Free Energies of Imidazolinium-Type Surfactants in Infinite Dilution and in Micellar State on Gold Surface.,” The journal of physical chemistry. B. 2018. link Times cited: 19 Abstract: We report adsorption behavior of imidazolinium-type surfacta… read moreAbstract: We report adsorption behavior of imidazolinium-type surfactant molecules in different aggregation states on metal-water interfaces studied using all-atom molecular dynamics simulations. Surfactant molecules with two different alkyl tail lengths, a 10-carbon and a 17-carbon tail (henceforth referred to as imid-10 and imid-17, respectively), have been considered. Six layers of face-centered cubic lattice of gold atoms submerged in water represent the metal-water interface. Our simulations reveal that, in infinite dilution, both types of surfactant molecules strongly adsorb onto the metal-water interface in a configuration with their alkyl tail lying parallel to the surface. This adsorption occurs through a barrierless transition with an adsorption free energy of ∼30 kB T and is found to be enthalpically driven and entropically unfavorable. Surfactant micelles, on the other hand, experience a long-range repulsion from the metal surface at distances as large as 50-60 Å due to the presence of a large "corona" around the micelles that comprises counterions and their solvation layer. Surfactant micelles have an adsorption free energy barrier of ∼13-16 kB T, which is associated with the removal of adsorbed water from the metal surface. Micelles are thermodynamically stable in the bulk aqueous phase, and the adsorbed micellar state is only metastable. read less USED (low confidence) L. Zhao and J. Cheng, “The mechanism and universal scaling law of the contact line friction for the Cassie-state droplets on nanostructured ultrahydrophobic surfaces.,” Nanoscale. 2018. link Times cited: 11 Abstract: Besides the Wenzel state, liquid droplets on micro/nanostruc… read moreAbstract: Besides the Wenzel state, liquid droplets on micro/nanostructured surfaces can stay in the Cassie state and consequently exhibit intriguing characteristics such as a large contact angle, small contact angle hysteresis and exceptional mobility. Here we report molecular dynamics (MD) simulations of the wetting dynamics of Cassie-state water droplets on nanostructured ultrahydrophobic surfaces with an emphasis on the genesis of the contact line friction (CLF). From an ab initio perspective, CLF can be ascribed to the collective effect of solid-liquid retarding and viscous damping. Solid-liquid retarding is related to the work of adhesion, whereas viscous damping arises from the viscous force exerted on the liquid molecules within the three-phase (liquid/vapor/solid) contact zone. In this work, a universal scaling law is derived to generalize the CLF on nanostructured ultrahydrophobic surfaces. With the decreasing fraction of solid-liquid contact (i.e., the solid fraction), CLF for a Cassie-state droplet gets enhanced due to the fact that viscous damping is counter-intuitively intensified while solid-liquid retarding remains unchanged. Nevertheless, the overall friction between a Cassie-state droplet and the structured surface is indeed reduced since the air cushion formed in the interstices of the surface roughness underneath the Cassie-state droplet applies negligible resistance to the contact line. Our results have revealed the genesis of CLF from an ab initio perspective, demonstrated the effects of surface structures on a moving contact line and justified the critical role of CLF in the analysis of wetting-related situations. read less USED (low confidence) S. Sadeghzadeh, “Geometric Effects on Nanopore Creation in Graphene and on the Impact-withstanding Efficiency of Graphene Nanosheets.” 2018. link Times cited: 3 Abstract: Single- and multilayer graphene sheets (MLGSs) are projectil… read moreAbstract: Single- and multilayer graphene sheets (MLGSs) are projectile-resisting materials that can be bombarded by nanoparticles to produce graphene sheets of various sizes and distributions of nanopores. These sheets are used in a variety of applications, including DNA sequencing, water desalination, and phase separation. Here, the impact-withstanding efficiency of graphene nanosheets and the primary factors affecting creation of nanopores in these sheets were studied using a molecular dynamics method. The velocity of impacting nanoparticles and resulting displacement in graphene nanosheets are not sufficient criteria for evaluating the impact resistance of sheets with more than six layers. Instead, visual inspection of the bottom side of a graphene sheet should be used. Self-healing is the most important aspect of MLGSs because it closes the paths of penetrating nanoparticles in the upper layers of the sheets. For nanosheets with few layers, self-healing is observed only at very small nanoparticle velocities; however, when the number of layers is more than six, self-healing occurs even at high nanoparticle velocities. In nanoribbon simulations, it was found that layer boundaries improve resistance against projectile impacts that create well-defined oval shapes. By increasing the distance between layers, the carbon atoms of each layer experience more collisions with the carbon atoms of other layers. Thus, increasing the interlayer distance causes the number of unwanted collisions between carbon atoms to increase and the graphene nanosheets to disintegrate. Additionally, as the circularity of nanopores increases, they become more circular and homogeneous, in turn increasing interlayer spacing, the impact-withstanding efficiency of the sheets, and the circular shape of created nanopores. read less USED (low confidence) S. Steinmann et al., “Force Field for Water over Pt(111): Development, Assessment, and Comparison.,” Journal of chemical theory and computation. 2018. link Times cited: 36 Abstract: Metal/water interfaces are key in many natural and industria… read moreAbstract: Metal/water interfaces are key in many natural and industrial processes, such as corrosion, atmospheric, or environmental chemistry. Even today, the only practical approach to simulate large interfaces between a metal and water is to perform force-field simulations. In this work, we propose a novel force field, GAL17, to describe the interaction of water and a Pt(111) surface. GAL17 builds on three terms: (i) a standard Lennard-Jones potential for the bonding interaction between the surface and water, (ii) a Gaussian term to improve the surface corrugation, and (iii) two terms describing the angular dependence of the interaction energy. The 12 parameters of this force field are fitted against a set of 210 adsorption geometries of water on Pt(111). The performance of GAL17 is compared to several other approaches that have not been validated against extensive first-principles computations yet. Their respective accuracy is evaluated on an extended set of 802 adsorption geometries of H2O on Pt(111), 52 geometries derived from icelike layers, and an MD simulation of an interface between a c(4 × 6) Pt(111) surface and a water layer of 14 Å thickness. The newly developed GAL17 force field provides a significant improvement over previously existing force fields for Pt(111)/H2O interactions. Its well-balanced performance suggests that it is an ideal candidate to generate relevant geometries for the metal/water interface, paving the way to a representative sampling of the equilibrium distribution at the interface and to predict solvation free energies at the solid/liquid interface. read less USED (low confidence) A. Nicholas, D. Welch, X. Li, and H. Patterson, “Host lattice effects on the design of different metallophilic nanoclusters with novel photonic properties,” Inorganica Chimica Acta. 2018. link Times cited: 6 USED (low confidence) M. Uranagase and S. Ogata, “Smart MD-Sampling Method for Interfacial Free Energy between Polymer-Grafted Substrate and Liquid,” MRS Advances. 2018. link Times cited: 2 Abstract: A novel and efficient scheme for evaluating the work of adhe… read moreAbstract: A novel and efficient scheme for evaluating the work of adhesion between a liquid and a polymer-grafted surface is proposed. A set of spherically symmetric potentials are gradually inserted at the interface to separate the liquid molecules from the surface according to its shape. This method is applied to the interface between the water and the gold substrate modified by poly(ethylene glycol). We find that the work of adhesion becomes maximum at the intermediate density of grafted poly(ethylene glycol). This is attributed to penetration of the water molecules into grafted poly(ethylene glycol) and hydrophilic interaction between them. read less USED (low confidence) T. Roussel and J. Faraudo, “SANO Methodology for Simulating Self‐Assembly Patterns of Organic Molecules over Metal Surfaces.” 2017. link Times cited: 0 USED (low confidence) M. H. Anvari, Q. Liu, Z. Xu, and P. Choi, “Line tensions of galena (001) and sphalerite (110) surfaces: A molecular dynamics study,” Journal of Molecular Liquids. 2017. link Times cited: 11 USED (low confidence) H. Manzano, A. Mohamed, R. K. Mishra, and P. Bowen, “A discussion on the paper ‘Role of porosity on the stiffness and stability of (001) surface of the nanogranular C–S–H gel,’” Cement and Concrete Research. 2017. link Times cited: 6 USED (low confidence) P. Bhadra and S. Siu, “Comparison of Biomolecular Force Fields for Alkanethiol Self-Assembled Monolayer Simulations,” Journal of Physical Chemistry C. 2017. link Times cited: 11 Abstract: Reasonable all-atom or united-atom biomolecular force fields… read moreAbstract: Reasonable all-atom or united-atom biomolecular force fields have been developed to represent the properties of proteins and lipid membranes in molecular dynamics simulations. However, since they have not been parametrized for self-assembled monolayers (SAMs), their utility in simulating SAMs and protein–SAM systems has not been confirmed. Here, we compared six popular biomolecular force fields, Lipid14, GAFF, L-OPLS, CHARMM36, Slipids, and GROMOS54a7, to simulate alkanethiol SAMs of short to long chains (C10–C18). Our results show that none of these force fields reproduce the chain length dependence of the tilt angle, and twist angle. Although the droplet contact angles on SAMs are well represented by all force fields, only GAFF and Lipid14 yield phase transition temperatures that are reasonably close to the experimental values. Overall, our comprehensive comparison suggests that GAFF and Lipid14 are better choices for SAM simulations; further improvements in the force field parameters for SAMs are requi... read less USED (low confidence) S. J. Chen, X. Yao, C. Zheng, and W. Duan, “Quantification of evaporation induced error in atom probe tomography using molecular dynamics simulation.,” Ultramicroscopy. 2017. link Times cited: 4 USED (low confidence) I. Moncayo-Riascos and B. Hoyos, “Effect of collector molecular structure on the wettability of gold for froth flotation,” Applied Surface Science. 2017. link Times cited: 25 USED (low confidence) S. Gao, Q. Liao, W. Liu, and Z. Liu, “Effects of Solid Fraction on Droplet Wetting and Vapor Condensation: A Molecular Dynamic Simulation Study.,” Langmuir : the ACS journal of surfaces and colloids. 2017. link Times cited: 57 Abstract: Recently, numerous studies focused on the wetting process of… read moreAbstract: Recently, numerous studies focused on the wetting process of droplets on various surfaces at a microscale level. However, there are a limited number of studies about the mechanism of condensation on patterned surfaces. The present study performed the dynamic wetting behavior of water droplets and condensation process of water molecules on substrates with different pillar structure parameters, through molecular dynamic simulation. The dynamic wetting results indicated that droplets exhibit Cassie state, PW state, and Wenzel state successively on textured surfaces with decreasing solid fraction. The droplets possess a higher static contact angle and a smaller spreading exponent on textured surfaces than those on smooth surfaces. The condensation processes, including the formation, growth, and coalescence of a nanodroplet, are simulated and quantitatively recorded, which are difficult to be observed by experiments. In addition, a wetting transition and a dewetting transition were observed and analyzed in condensation on textured surfaces. Combining these simulation results with previous theoretical and experimental studies will guide us to understand the hypostasis and mechanism of the condensation more clearly. read less USED (low confidence) L. Zhao and J. Cheng, “Analyzing the Molecular Kinetics of Water Spreading on Hydrophobic Surfaces via Molecular Dynamics Simulation,” Scientific Reports. 2017. link Times cited: 23 USED (low confidence) P.-Y. Yang, S. Ju, Y. Chuang, and H.-Y. Chen, “Molecular dynamics simulations of PAMAM dendrimer-encapsulated Au nanoparticles of different sizes under different pH conditions,” Computational Materials Science. 2017. link Times cited: 15 USED (low confidence) M. Dehghani, M. Asghari, A. Mohammadi, and M. Mokhtari, “Molecular simulation and Monte Carlo study of structural-transport-properties of PEBA-MFI zeolite mixed matrix membranes for CO2, CH4 and N2 separation,” Comput. Chem. Eng. 2017. link Times cited: 27 USED (low confidence) M. Gupta, T. Khan, S. Gupta, M. I. Alam, M. Agarwal, and M. Haider, “Non-bonding and bonding interactions of biogenic impurities with the metal catalyst and the design of bimetallic alloys,” Journal of Catalysis. 2017. link Times cited: 10 USED (low confidence) T. Walsh, “Pathways to Structure-Property Relationships of Peptide-Materials Interfaces: Challenges in Predicting Molecular Structures.,” Accounts of chemical research. 2017. link Times cited: 49 Abstract: An in-depth appreciation of how to manipulate the molecular-… read moreAbstract: An in-depth appreciation of how to manipulate the molecular-level recognition between peptides and aqueous materials interfaces, including nanoparticles, will advance technologies based on self-organized metamaterials for photonics and plasmonics, biosensing, catalysis, energy generation and harvesting, and nanomedicine. Exploitation of the materials-selective binding of biomolecules is pivotal to success in these areas and may be particularly key to producing new hierarchically structured biobased materials. These applications could be accomplished by realizing preferential adsorption of a given biomolecule onto one materials composition over another, one surface facet over another, or one crystalline polymorph over another. Deeper knowledge of the aqueous abiotic-biotic interface, to establish clear structure-property relationships in these systems, is needed to meet this goal. In particular, a thorough structural characterization of the surface-adsorbed peptides is essential for establishing these relationships but can often be challenging to accomplish via experimental approaches alone. In addition to myriad existing challenges associated with determining the detailed molecular structure of any molecule adsorbed at an aqueous interface, experimental characterization of materials-binding peptides brings new, complex challenges because many materials-binding peptides are thought to be intrinsically disordered. This means that these peptides are not amenable to experimental techniques that rely on the presence of well-defined secondary structure in the peptide when in the adsorbed state. To address this challenge, and in partnership with experiment, molecular simulations at the atomistic level can bring complementary and critical insights into the origins of this abiotic/biotic recognition and suggest routes for manipulating this phenomenon to realize new types of hybrid materials. For the reasons outlined above, molecular simulation approaches also face challenges in their successful application to model the biotic-abiotic interface, related to several factors. For instance, simulations require a plausible description of the chemistry and the physics of the interface, which comprises two very different states of matter, in the presence of liquid water. Also, it is essential that the conformational ensemble be comprehensively characterized under these conditions; this is especially challenging because intrinsically disordered peptides do not typically admit one single structure or set of structures. Moreover, a plausible structural model of the substrate is required, which may require a high level of detail, even for single-element materials such as Au surfaces or graphene. Developing and applying strategies to make credible predictions of the conformational ensemble of adsorbed peptides and using these to construct structure-property relationships of these interfaces have been the goals of our efforts. We have made substantial progress in developing interatomic potentials for these interfaces and adapting advanced conformational sampling approaches for these purposes. This Account summarizes our progress in the development and deployment of interfacial force fields and molecular simulation techniques for the purpose of elucidating these insights at biomolecule-materials interfaces, using examples from our laboratories ranging from noble-metal interfaces to graphitic substrates (including carbon nanotubes and graphene) and oxide materials (such as titania). In addition to the well-established application areas of plasmonic materials, biosensing, and the production of medical implant materials, we outline new directions for this field that have the potential to bring new advances in areas such as energy materials and regenerative medicine. read less USED (low confidence) H. Han, S. Merabia, and F. Müller-Plathe, “Thermal transport at a solid-nanofluid interface: from increase of thermal resistance towards a shift of rapid boiling.,” Nanoscale. 2017. link Times cited: 23 Abstract: We use molecular dynamics simulations to investigate interfa… read moreAbstract: We use molecular dynamics simulations to investigate interfacial thermal transport between an ethanol suspension containing gold atomic clusters and a gold surface, using both realistic and simplified molecular models of nanoparticles. The interfacial thermal conductance was determined via a thermal relaxation method for a variety of nanoparticle-nanoparticle and nanoparticle-surface interaction strengths. The Kapitza resistance is found to increase due to the presence of nanoparticles in the vicinity of the solid-liquid interface. The heat flow from the solid to the nanoparticles is separated from its counterpart from the solid to the liquid to discriminate their respective contribution to the total heat current. A per-vibrational-mode analysis highlights a shift of major heat carriers from low frequencies towards higher frequencies due to the coupling of the internal nanoparticle dynamics to the gold surface, in addition to stronger particle-surface interactions. Finally, we demonstrate that the increase of the Kapitza resistance significantly shifts the nanofluid/solid surface explosive boiling temperature to higher temperatures compared to pure ethanol. read less USED (low confidence) S. Meena et al., “Nanophase Segregation of Self-Assembled Monolayers on Gold Nanoparticles.,” ACS nano. 2017. link Times cited: 30 Abstract: Nanophase segregation of a bicomponent thiol self-assembled … read moreAbstract: Nanophase segregation of a bicomponent thiol self-assembled monolayer is predicted using atomistic molecular dynamics simulations and experimentally confirmed. The simulations suggest the formation of domains rich in acid-terminated chains, on one hand, and of domains rich in amide-functionalized ethylene glycol oligomers, on the other hand. In particular, within the amide-ethylene glycol oligomers region, a key role is played by the formation of interchain hydrogen bonds. The predicted phase segregation is experimentally confirmed by the synthesis of 35 and 15 nm gold nanoparticles functionalized with several binary mixtures of ligands. An extensive study by transmission electron microscopy and electron tomography, using silica selective heterogeneous nucleation on acid-rich domains to provide electron contrast, supports simulations and highlights patchy nanoparticles with a trend toward Janus nano-objects depending on the nature of the ligands and the particle size. These results validate our computational platform as an effective tool to predict nanophase separation in organic mixtures on a surface and drive further exploration of advanced nanoparticle functionalization. read less USED (low confidence) H. Zhao, Y. Wang, Y. Yang, X. Shu, Y. Han, and Q. Ran, “Effect of hydrophobic groups on the adsorption conformation of modified polycarboxylate superplasticizer investigated by molecular dynamics simulation,” Applied Surface Science. 2017. link Times cited: 68 USED (low confidence) H. Wei, S. Wei, X. Zhu, and X. Lu, “Investigation of Structural, Thermal, and Dynamical Properties of Pd–Au–Pt Ternary Metal Nanoparticles Confined in Carbon Nanotubes Based on MD Simulation,” Journal of Physical Chemistry C. 2017. link Times cited: 12 Abstract: We apply molecular dynamics (MD) simulations to investigate … read moreAbstract: We apply molecular dynamics (MD) simulations to investigate structural, thermal, and dynamical properties of Pd–Au–Pt trimetallic nanoparticles confined in armchair single-walled carbon tubes ((n,n)-SWNTs). The metal–carbon interactions are described by a Lennard-Jones (LJ) potential, while the metal–metal interactions are represented by the second-moment approximation of the tight-binding (TB-SMA) potentials. Results illustrate that the confined Pd–Au–Pt metal nanoparticles appear to be of cylindrical multishelled structure, similar to those of gold (or Au–Pt) nanoparticles confined in SWNT and different from free Pd–Au–Pt nanoparticles or bulk gold. For each confined Pd–Au–Pt nanoparticle, gold atoms preferentially accumulate near the tube center, while Pt atoms preferentially distribute near the tube wall. These results are in qualitative agreement with previous observations on Au–Pt nanoparticles confined in SWNT. Importantly, Pd atoms disperse thorough the confined Pd–Au–Pt nanoparticle, which is con... read less USED (low confidence) H. Han et al., “Solid-Liquid Interface Thermal Resistance Affects the Evaporation Rate of Droplets from a Surface: A Study of Perfluorohexane on Chromium Using Molecular Dynamics and Continuum Theory.,” Langmuir : the ACS journal of surfaces and colloids. 2017. link Times cited: 28 Abstract: We study the role of solid-liquid interface thermal resistan… read moreAbstract: We study the role of solid-liquid interface thermal resistance (Kapitza resistance) on the evaporation rate of droplets on a heated surface by using a multiscale combination of molecular dynamics (MD) simulations and analytical continuum theory. We parametrize the nonbonded interaction potential between perfluorohexane (C6F14) and a face-centered-cubic solid surface to reproduce the experimental wetting behavior of C6F14 on black chromium through the solid-liquid work of adhesion (quantity directly related to the wetting angle). The thermal conductances between C6F14 and (100) and (111) solid substrates are evaluated by a nonequilibrium molecular dynamics approach for a liquid pressure lower than 2 MPa. Finally, we examine the influence of the Kapitza resistance on evaporation of droplets in the vicinity of a three-phase contact line with continuum theory, where the thermal resistance of liquid layer is comparable with the Kapitza resistance. We determine the thermodynamic conditions under which the Kapitza resistance plays an important role in correctly predicting the evaporation heat flux. read less USED (low confidence) P. Schäfer et al., “Trimesic acid on Cu in ethanol: Potential-dependent transition from 2-D adsorbate to 3-D metal-organic framework,” Journal of Electroanalytical Chemistry. 2017. link Times cited: 5 USED (low confidence) S. B. Kang et al., “Ostwald-ripening sintering kinetics of Pd-based three-way catalyst: Importance of initial particle size of Pd,” Chemical Engineering Journal. 2017. link Times cited: 36 USED (low confidence) M. Ebadi, L. T. Costa, C. M. Araujo, and D. Brandell, “Modelling the Polymer Electrolyte/Li-Metal Interface by Molecular Dynamics simulations,” Electrochimica Acta. 2017. link Times cited: 38 USED (low confidence) H. Han, S. Merabia, and F. Müller-Plathe, “Thermal Transport at Solid-Liquid Interfaces: High Pressure Facilitates Heat Flow through Nonlocal Liquid Structuring.,” The journal of physical chemistry letters. 2017. link Times cited: 47 Abstract: The integration of three-dimensional microelectronics is ham… read moreAbstract: The integration of three-dimensional microelectronics is hampered by overheating issues inherent to state-of-the-art integrated circuits. Fundamental understanding of heat transfer across soft-solid interfaces is important for developing efficient heat dissipation capabilities. At the microscopic scale, the formation of a dense liquid layer at the solid-liquid interface decreases the interfacial heat resistance. We show through molecular dynamics simulations of n-perfluorohexane on a generic wettable surface that enhancement of the liquid structure beyond a single adsorbed layer drastically enhances interfacial heat conductance. Pressure is used to control the extent of the liquid layer structure. The interfacial thermal conductance increases with pressure values up to 16.2 MPa at room temperature. Furthermore, it is shown that liquid structuring enhances the heat-transfer rate of high-energy lattice waves by broadening the transmission peaks in the heat flux spectrum. Our results show that pressure is an important external parameter that may be used to control interfacial heat conductance at solid-soft interfaces. read less USED (low confidence) R. Qiu, J. Xiao, and X. Chen, “Further understanding of the biased diffusion for peptide adsorption on uncharged solid surfaces that strongly interact with water molecules,” Colloids and Surfaces A: Physicochemical and Engineering Aspects. 2017. link Times cited: 5 USED (low confidence) S. Salassi, F. Simonelli, D. Bochicchio, R. Ferrando, and G. Rossi, “Au Nanoparticles in Lipid Bilayers: a Comparison between Atomistic and Coarse Grained Models,” arXiv: Biological Physics. 2017. link Times cited: 53 Abstract: The computational study of the interaction between charged, … read moreAbstract: The computational study of the interaction between charged, ligand-protected metal nanoparticles and model lipid membranes has been recently addressed both at atomistic and coarse grained level. Here we compare the performance of three versions of the coarse grained Martini force field at describing the nanoparticle-membrane interaction. The three coarse-grained models differ in terms of treatment of long-range electrostatic interactions and water polarizability. The NP-membrane interaction consists in the transition from a metastable NP- membrane complex, in which the NP is only partially embedded in the membrane, to a configuration in which the NP is anchored to both membrane leaflets. All the three coarse grained models provide a description of the metastable NP-membrane complex that is consistent with that obtained using an atomistic force field. As for the anchoring transition, the polarizable- water Martini correctly describes the molecular mechanisms and the energetics of the transition. The standard version of the Martini model, instead, underestimates the free energy barriers for anchoring and does not completely capture the membrane deformations involved in the transition process. read less USED (low confidence) X. Shu et al., “Effect of hydrophobic units of polycarboxylate superplasticizer on the flow behavior of cement paste,” Journal of Dispersion Science and Technology. 2017. link Times cited: 36 Abstract: ABSTRACT For the tuning of conformation of polycarboxylate (… read moreAbstract: ABSTRACT For the tuning of conformation of polycarboxylate (PCE) superplasticizers, hydrophobic groups of different stiffness were incorporated, including styrene (St), methyl methacrylate (MMA), ethyl acrylate (EA), and n-butyl acrylate (n-BA) units. The effect of these hydrophobic groups on the dispersing performance, adsorption process and, rheology of cement paste were investigated. Investigation on the solution conformation and adsorption layer thickness indicated the action mechanism of these groups. High backbone stiffness resulted in a lower extent of conformation condensation from pure aqueous solution to pore solution, and therefore more carboxylic groups could be accessible for adsorption. However, the conformation change after adsorption might also be limited and the size of single molecule after adsorption should be small. Hydrophobic groups always resulted in a coiled PCE conformation in salt solution, which indicated a lower adsorption affinity and thinner adsorption layer for these PCE molecules. GRAPHICAL ABSTRACT read less USED (low confidence) F. Fu et al., “Molecular-Level Insights into Size-Dependent Stabilization Mechanism of Gold Nanoparticles in 1-Butyl-3-methylimidazolium Tetrafluoroborate Ionic Liquid,” Journal of Physical Chemistry C. 2017. link Times cited: 24 Abstract: Here we report a series of classical molecular dynamics simu… read moreAbstract: Here we report a series of classical molecular dynamics simulations for the icosahedral Au nanoparticles with four different diameters of 1.0, 1.4, 1.8, and 2.3 nm in 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim][BF4]) room-temperature ionic liquid (RTIL). Our simulation results reveal for the first time a size-dependent stabilization mechanism of the Au nanoparticles in the [bmim][BF4] RTIL, which may help to clarify the relevant debate on the stabilization mechanism from various experimental observations. By comparison, the alkyl chains in the [bmim]+ cations are found to dominate the stabilization of the smallest Au13 nanoparticle in the RTIL while the imidazolium rings should be mainly responsible for the stabilization of other larger nanoparticles in the RTIL. Compared to the [bmim]+ cations, the [BF4]− anions are found to have an indirect influence on stabilizing the Au nanoparticles in the RTIL because of the weak interaction between the Au nanoparticles and the anions. However, such differ... read less USED (low confidence) A. Iakovlev, D. Bedrov, and M. Müller, “Molecular Dynamics Simulation of Alkylthiol Self-Assembled Monolayers on Liquid Mercury.,” Langmuir : the ACS journal of surfaces and colloids. 2017. link Times cited: 5 Abstract: We report computer simulation of the self-assembly of alkylt… read moreAbstract: We report computer simulation of the self-assembly of alkylthiols on the surface of liquid mercury. Here we focus mainly on the alkylthiol behavior on mercury as a function of the surfactant surface coverage, which we study by means of large-scale molecular dynamics simulations of the equilibrium structure at room temperature. The majority of the presented results are obtained for octa- and dodecanethiol surfactants. This topic is particularly interesting because the properties of the alkylthiol self-assembled monolayers on liquid mercury are relevant for practical applications (e.g., in organic electronics) and can be controlled by mechanically manipulating the monolayer, i.e., by changing its structure. Our computer simulation results shed additional light on the alkylthiol self-assembly on liquid mercury by revealing the coexistence of a dense agglomerated laying-down alkylthiols with a very dilute 2D vapor on mercury surface rather than a single vapor phase in the low surface coverage regime. In the regimes of the high surface coverage we observe the coexistence of the laying-down liquid phase and crystalline phases with alkylthiols standing tilted at a sharp angle to the surface normal, which agrees with the phase behavior previously seen in X-ray and tensiometry experiments. We also discuss the influence of finite-size effects, which one inevitably encounters in molecular simulations. Our findings agree well with the general predictions of the condensation/evaporation theory for finite systems. The temperature dependence of the stability of the crystalline alkylthiol phases and details of the surfactant chemical binding to the surface are discussed. The equilibrium structure of the crystalline phase is investigated in detail for the alkylthiols of various tail lengths. read less USED (low confidence) E. Colangelo et al., “Computational and Experimental Investigation of the Structure of Peptide Monolayers on Gold Nanoparticles.,” Langmuir : the ACS journal of surfaces and colloids. 2017. link Times cited: 23 Abstract: The self-assembly and self-organization of small molecules o… read moreAbstract: The self-assembly and self-organization of small molecules on the surface of nanoparticles constitute a potential route toward the preparation of advanced proteinlike nanosystems. However, their structural characterization, critical to the design of bionanomaterials with well-defined biophysical and biochemical properties, remains highly challenging. Here, a computational model for peptide-capped gold nanoparticles (GNPs) is developed using experimentally characterized Cys-Ala-Leu-Asn-Asn (CALNN)- and Cys-Phe-Gly-Ala-Ile-Leu-Ser-Ser (CFGAILSS)-capped GNPs as a benchmark. The structure of CALNN and CFGAILSS monolayers is investigated using both structural biology techniques and molecular dynamics simulations. The calculations reproduce the experimentally observed dependence of the monolayer secondary structure on the peptide capping density and on the nanoparticle size, thus giving us confidence in the model. Furthermore, the computational results reveal a number of new features of peptide-capped monolayers, including the importance of sulfur movement for the formation of secondary structure motifs, the presence of water close to the gold surface even in tightly packed peptide monolayers, and the existence of extended 2D parallel β-sheet domains in CFGAILSS monolayers. The model developed here provides a predictive tool that may assist in the design of further bionanomaterials. read less USED (low confidence) Q. Shao and C. Hall, “Allosteric effects of gold nanoparticles on human serum albumin.,” Nanoscale. 2017. link Times cited: 34 Abstract: The ability of nanoparticles to alter protein structure and … read moreAbstract: The ability of nanoparticles to alter protein structure and dynamics plays an important role in their medical and biological applications. We investigate allosteric effects of gold nanoparticles on human serum albumin protein using molecular simulations. The extent to which bound nanoparticles influence the structure and dynamics of residues distant from the binding site is analyzed. The root mean square deviation, root mean square fluctuation and variation in the secondary structure of individual residues on a human serum albumin protein are calculated for four protein-gold nanoparticle binding complexes. The complexes are identified in a brute-force search process using an implicit-solvent coarse-grained model for proteins and nanoparticles. They are then converted to atomic resolution and their structural and dynamic properties are investigated using explicit-solvent atomistic molecular dynamics simulations. The results show that even though the albumin protein remains in a folded structure, the presence of a gold nanoparticle can cause more than 50% of the residues to decrease their flexibility significantly, and approximately 10% of the residues to change their secondary structure. These affected residues are distributed on the whole protein, even on regions that are distant from the nanoparticle. We analyze the changes in structure and flexibility of amino acid residues on a variety of binding sites on albumin and confirm that nanoparticles could allosterically affect the ability of albumin to bind fatty acids, thyroxin and metals. Our simulations suggest that allosteric effects must be considered when designing and deploying nanoparticles in medical and biological applications that depend on protein-nanoparticle interactions. read less USED (low confidence) C. T. Lai et al., “Molecular Dynamics Simulation and Experimental Studies of Gold Nanoparticle Templated HDL-like Nanoparticles for Cholesterol Metabolism Therapeutics.,” ACS applied materials & interfaces. 2017. link Times cited: 13 Abstract: High-density lipoprotein (HDL) plays an important role in th… read moreAbstract: High-density lipoprotein (HDL) plays an important role in the transport and metabolism of cholesterol. Mimics of HDL are being explored as potentially powerful therapeutic agents for removing excess cholesterol from arterial plaques. Gold nanoparticles (AuNPs) functionalized with apolipoprotein A-I and with the lipids 1,2-dipalmitoyl-sn-glycero-3-phosphocholine and 1,2-dipalmitoyl-sn-glycero-3-phosphoethanolamine-N-[3-(2-pyridyldithio)propionate] have been demonstrated to be robust acceptors of cellular cholesterol. However, detailed structural information about this functionalized HDL AuNP is still lacking. In this study, we have used X-ray photoelectron spectroscopy and lecithin/cholesterol acyltransferase activation experiments together with coarse-grained and all-atom molecular dynamics simulations to model the structure and cholesterol uptake properties of the HDL AuNP construct. By simulating different apolipoprotein-loaded AuNPs, we find that lipids are oriented differently in regions with and without apoA-I. We also show that in this functionalized HDL AuNP, the distribution of cholesteryl ester maintains a reverse concentration gradient that is similar to the gradient found in native HDL. read less USED (low confidence) L. Separdar and S. Davatolhagh, “Effect of gold nanoparticles on structure and dynamics of binary Lennard-Jones liquid: Wave-vector space analysis,” Physica A-statistical Mechanics and Its Applications. 2016. link Times cited: 2 USED (low confidence) K. Krishnadas, A. Baksi, A. Ghosh, G. Natarajan, and T. Pradeep, “Structure-conserving spontaneous transformations between nanoparticles,” Nature Communications. 2016. link Times cited: 82 USED (low confidence) M. Schneemilch and N. Quirke, “Free energy of adsorption of supported lipid bilayers from molecular dynamics simulation,” Chemical Physics Letters. 2016. link Times cited: 17 USED (low confidence) T. Zhang et al., “Protein–Ligand Interaction Detection with a Novel Method of Transient Induced Molecular Electronic Spectroscopy (TIMES): Experimental and Theoretical Studies,” ACS Central Science. 2016. link Times cited: 23 Abstract: Protein–ligand interaction detection without disturbances (e… read moreAbstract: Protein–ligand interaction detection without disturbances (e.g., surface immobilization, fluorescent labeling, and crystallization) presents a key question in protein chemistry and drug discovery. The emergent technology of transient induced molecular electronic spectroscopy (TIMES), which incorporates a unique design of microfluidic platform and integrated sensing electrodes, is designed to operate in a label-free and immobilization-free manner to provide crucial information for protein–ligand interactions in relevant physiological conditions. Through experiments and theoretical simulations, we demonstrate that the TIMES technique actually detects protein–ligand binding through signals generated by surface electric polarization. The accuracy and sensitivity of experiments were demonstrated by precise measurements of dissociation constant of lysozyme and N-acetyl-d-glucosamine (NAG) ligand and its trimer, NAG3. Computational fluid dynamics (CFD) computation is performed to demonstrate that the surface’s electric polarization signal originates from the induced image charges during the transition state of surface mass transport, which is governed by the overall effects of protein concentration, hydraulic forces, and surface fouling due to protein adsorption. Hybrid atomistic molecular dynamics (MD) simulations and free energy computation show that ligand binding affects lysozyme structure and stability, producing different adsorption orientation and surface polarization to give the characteristic TIMES signals. Although the current work is focused on protein–ligand interactions, the TIMES method is a general technique that can be applied to study signals from reactions between many kinds of molecules. read less USED (low confidence) S. Sadeghzadeh and L.-L. Liu, “Resistance and rupture analysis of single- and few-layer graphene nanosheets impacted by various projectiles,” Superlattices and Microstructures. 2016. link Times cited: 22 USED (low confidence) D. Tunega, M. Gerzabek, G. Haberhauer, H. Lischka, and A. Aquino, “Organic and Contaminant Geochemistry.” 2016. link Times cited: 5 USED (low confidence) X. Shu et al., “Tailoring the solution conformation of polycarboxylate superplasticizer toward the improvement of dispersing performance in cement paste,” Construction and Building Materials. 2016. link Times cited: 90 USED (low confidence) Q. Shao and C. Hall, “Binding Preferences of Amino Acids for Gold Nanoparticles: A Molecular Simulation Study.,” Langmuir : the ACS journal of surfaces and colloids. 2016. link Times cited: 51 Abstract: A better understanding of the binding preference of amino ac… read moreAbstract: A better understanding of the binding preference of amino acids for gold nanoparticles of different diameters could aid in the design of peptides that bind specifically to nanoparticles of a given diameter. Here we identify the binding preference of 19 natural amino acids for three gold nanoparticles with diameters of 1.0, 2.0, and 4.0 nm, and investigate the mechanisms that govern these preferences. We calculate potentials of mean force between 36 entities (19 amino acids and 17 side chains) and the three gold nanoparticles in explicit water using well-tempered metadynamics simulations. Comparing these potentials of mean force determines the amino acids' nanoparticle binding preferences and if these preferences are controlled by the backbone, the side chain, or both. Twelve amino acids prefer to bind to the 4.0 nm gold nanoparticle, and seven prefer to bind to the 2.0 nm one. We also use atomistic molecular dynamics simulations to investigate how water molecules near the nanoparticle influence the binding of the amino acids. The solvation shells of the larger nanoparticles have higher water densities than those of the smaller nanoparticles while the orientation distributions of the water molecules in the shells of all three nanoparticles are similar. The nanoparticle preferences of the amino acids depend on whether their binding free energy is determined mainly by their ability to replace or to reorient water molecules in the nanoparticle solvation shell. The amino acids whose binding free energy depends mainly on the replacement of water molecules are likely to prefer to bind to the largest nanoparticle and tend to have relatively simple side chain structures. Those whose binding free energy depends mainly on their ability to reorient water molecules prefer a smaller nanoparticle and tend to have more complex side chain structures. read less USED (low confidence) Z. E. Hughes and T. Walsh, “Non-covalent adsorption of amino acid analogues on noble-metal nanoparticles: influence of edges and vertices.,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 20 Abstract: The operation of many nanostructured biomolecular sensors an… read moreAbstract: The operation of many nanostructured biomolecular sensors and catalysts critically hinges on the manipulation of non-covalent adsorption of biomolecules on unfunctionalised noble-metal nanoparticles (NMNPs). Molecular-level structural details of the aqueous biomolecule/NMNP interface are pivotal to the successful realisation of these technologies, but such experimental data are currently scarce and challenging to obtain. Molecular simulations can generate these details, but are limited by the assumption of non-preferential adsorption to NMNP features. Here, via first principles calculations using a vdW-DF functional, and based on nanoscale sized NMNPs, we demonstrate that adsorption preferences to NP features vary with adsorbate chemistry. These results show a clear distinction between hydrocarbons, that prefer adsorption to facets over edges/vertices, over heteroatomic molecules that favour adsorption onto vertices over facets. Our data indicate the inability of widely used force-fields to correctly capture the adsorption of biomolecules onto NMNP surfaces under aqueous conditions. Our findings introduce a rational basis for the development of new force-fields that will reliably capture these phenomena. read less USED (low confidence) K. Sebeck, C. Shao, and J. Kieffer, “Alkane-Metal Interfacial Structure and Elastic Properties by Molecular Dynamics Simulation.,” ACS applied materials & interfaces. 2016. link Times cited: 9 Abstract: The structure of amorphous materials near the interface with… read moreAbstract: The structure of amorphous materials near the interface with an ordered substrate can be affected by various characteristics of the adjoining phases, such as the lattice spacing of the adherent surface, polymer chain length, and adhesive strength. To discern the influence of each of these factors, four FCC metal lattices are examined for three chain lengths of n-alkane and van der Waals interfacial interactions are controlled by adjusting the Lennard-Jones 12-6 potential parameters. The role of interaction strength is investigated for a single chain length and substrate combination. Four nanoconfined systems are also analyzed in terms of their mechanical strength. A strong layering effect is observed near the interface for all systems. The distinctiveness of polymer layering, i.e., the maximum density and spatial extent, exhibits a logarithmic dependence on the interaction strength between polymer and substrate. Congruency with the substrate lattice parameter further enhances this effect. Moreover, the elastic modulus of the alkane phase as a function of layer thickness indicates that the effects of ordering within the structure extend beyond the immediately obvious interfacial region. read less USED (low confidence) C. Li, J. Huang, and Z. Li, “A Relation for Nanodroplet Diffusion on Smooth Surfaces,” Scientific Reports. 2016. link Times cited: 16 USED (low confidence) V. Petkov et al., “Structural dynamics and activity of nanocatalysts inside fuel cells by in operando atomic pair distribution studies.,” Nanoscale. 2016. link Times cited: 16 Abstract: Here we present the results from a study aimed at clarifying… read moreAbstract: Here we present the results from a study aimed at clarifying the relationship between the atomic structure and activity of nanocatalysts for chemical reactions driving fuel cells, such as the oxygen reduction reaction (ORR). In particular, using in operando high-energy X-ray diffraction (HE-XRD) we tracked the evolution of the atomic structure and activity of noble metal-transition metal (NM-TM) nanocatalysts for ORR as they function at the cathode of a fully operational proton exchange membrane fuel cell (PEMFC). Experimental HE-XRD data were analysed in terms of atomic pair distribution functions (PDFs) and compared to the current output of the PEMFC, which was also recorded during the experiments. The comparison revealed that under actual operating conditions, NM-TM nanocatalysts can undergo structural changes that differ significantly in both length-scale and dynamics and so can suffer losses in their ORR activity that differ significantly in both character and magnitude. Therefore we argue that strategies for reducing ORR activity losses should implement steps for achieving control not only over the length but also over the time-scale of the structural changes of NM-TM NPs that indeed occur during PEMFC operation. Moreover, we demonstrate how such a control can be achieved and thereby the performance of PEMFCs improved considerably. Last but not least, we argue that the unique capabilities of in operando HE-XRD coupled to atomic PDF analysis to characterize active nanocatalysts inside operating fuel cells both in a time-resolved manner and with atomic level resolution, i.e. in 4D, can serve well the ongoing search for nanocatalysts that deliver more with less platinum. read less USED (low confidence) M. Makaremi, M. Jhon, M. Mauter, and L. Biegler, “Surface Wetting Study via Pseudocontinuum Modeling,” Journal of Physical Chemistry C. 2016. link Times cited: 12 Abstract: An accurate estimation of contact angle and surface wettabil… read moreAbstract: An accurate estimation of contact angle and surface wettability for various degrees of hydrophobicity becomes increasingly important in the molecular design of solid surfaces. In this study, we develop a simple, yet physically realistic, model for estimating contact angle via hybridizing molecular dynamics and pseudocontinuum theory. Molecular dynamics simulations were carried out to compute the macroscale contact angle between a water droplet and smooth walls from the nanoscale calculations. A macrolevel droplet including numerous degrees of freedom due to a large number of molecules cannot be directly studied using atomistic simulations. To resolve this issue, we employed two approaches consisting of the pseudocontinuum approximation and the modified Young–Laplace equation. The former involves the 9–3 Lennard-Jones potential and can drastically reduce the degrees of freedom in molecular simulations, while the latter relates the mesoscale contact angle to the realistic one. We altered different parameter... read less USED (low confidence) M. Atilhan and S. Aparicio, “Deep Eutectic Solvents on the Surface of Face Centered Cubic Metals,” Journal of Physical Chemistry C. 2016. link Times cited: 23 Abstract: The properties of the deep eutectic solvent based on choline… read moreAbstract: The properties of the deep eutectic solvent based on choline chloride and levulinic acid, for 1:2 molar ratio, on the (100) surfaces of metals with face centered cubic crystal structures (Ag, Al, and Pt) are studied using classic molecular dynamics simulations. The densification, molecular arrangements and orientations, and electronic density at the metal interfaces are analyzed. Likewise, the dynamic properties of the involved molecules at the metal surfaces are quantified through self-diffusion coefficients and compared with the behavior in the bulk liquid phases. Strong preferential adsorption at the metal surfaces by the molecules forming the deep eutectic solvents is inferred, which characteristics are analyzed as a function of the type of metal, the strength on metal–solvent interactions, and the changes in the nanoscopic properties of the solvent upon adsorption. The reported results show for the very first time the characteristics of metal–deep eutectic solvent hybrid materials. read less USED (low confidence) P. Charchar, A. Christofferson, N. Todorova, and I. Yarovsky, “Understanding and Designing the Gold-Bio Interface: Insights from Simulations.,” Small. 2016. link Times cited: 57 Abstract: Gold nanoparticles (AuNPs) are an integral part of many exci… read moreAbstract: Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications. read less USED (low confidence) L. J. Martin, M. Bilek, A. Weiss, and S. Kuyucak, “Force fields for simulating the interaction of surfaces with biological molecules,” Interface Focus. 2016. link Times cited: 28 Abstract: The interaction of biomolecules with solid interfaces is of … read moreAbstract: The interaction of biomolecules with solid interfaces is of fundamental importance to several emerging biotechnologies such as medical implants, anti-fouling coatings and novel diagnostic devices. Many of these technologies rely on the binding of peptides to a solid surface, but a full understanding of the mechanism of binding, as well as the effect on the conformation of adsorbed peptides, is beyond the resolution of current experimental techniques. Nanoscale simulations using molecular mechanics offer potential insights into these processes. However, most models at this scale have been developed for aqueous peptide and protein simulation, and there are no proven models for describing biointerfaces. In this review, we detail the current research towards developing a non-polarizable molecular model for peptide–surface interactions, with a particular focus on fitting the model parameters as well as validation by choice of appropriate experimental data. read less USED (low confidence) J. Vera and Y. Bayazitoglu, “Molecular Dynamics Simulations for Water–Metal Interfacial Thermal Resistance.” 2016. link Times cited: 0 USED (low confidence) Y. Qian et al., “Silver nanoparticle-induced hemoglobin decrease involves alteration of histone 3 methylation status.,” Biomaterials. 2015. link Times cited: 78 USED (low confidence) A. K. Giri, “Conformational Equilibria of Organic Adsorbates on Nanostructures in Aqueous Solution: MD Simulations,” Journal of Physical Chemistry C. 2015. link Times cited: 16 Abstract: Atomistic molecular dynamics (MD) simulations of bulk aqueou… read moreAbstract: Atomistic molecular dynamics (MD) simulations of bulk aqueous solution of NaCl and functionalized gold nanoparticles (GNPs) in aqueous solution were conducted at 300 K. Bulk NaCl solution systems of different concentration have been studied using various force field parameter sets to investigate aggregation of ions and to choose suitable force field parameters for ions. Gold nanoparticles functionalized with linear and branched hydrocarbon chains with different grafting density (d f =1, 2/3 and 1/3), chain length ((CH 2 ) l , l=5, 11, 17 and 23), position of the branching point (4th, 8th and 12th carbon) and terminal groups (CH 3 , COO − and NH +3 ) were modeled to investigate various phenomena at the microscopic level. The solution of a functionalized GNP with ionic terminations was neutralized by excess Na + and Cl − ions. Focus has been given to the penetration depth of water and ions into the diffuse shell of alkanethiols as a function of grafting density, functionalization and chain length. Special focus has been given to the relative accessibility of the gold core by water in dependence of grafting density, chain length and chain shape. The orientation of water molecules inside the hydrocarbon chain environment (from the surface of the gold core to the terminal groups) and near the terminal groups has been studied in detail. Hydrogen bonds between water and polar terminal groups have also been studied. Special attention has been given to the solvent accessible surface area (SASA) of functionalized GNPs, and the coating asymmetry and ways to prevent it.
It is observed that the penetration of water and ions into the hydration shell of alkanethiols increases with decreasing grafting density, irrespective of the terminal group of the hydrocarbon chains. High grafting densities lead to more extended hydrocarbon chains which behave more rigidly. The solvent accessible surface area (SASA) is dependent on the chain length and the terminal group. SASA (per unit chain length) of COO − group terminated GNPs with chain length (C l ) 5 is the highest among all GNP coated with linear chains. Water molecules orient near the surface of the gold core pointing one hydrogen towards the center of the gold core irrespective of chain length, terminal group and grafting density. Water molecules cannot access the surface of the gold core of a branched chain GNP as easily as in the linear chain GNP. Branched chains protect the core better than the corresponding linear chains. Among all studied systems, nonpolar group terminated branched chains with chain length 17 and branched at the 4th carbon atom provide the best protection to the nanoparticle core. Coating asymmetry is generally more prominent for longer chains (>11), and the asymmetry can be prevented by introducing branching points. read less USED (low confidence) M. Cuerva, R. García‐Fandiño, C. Vázquez-Vázquez, M. López‐Quintela, J. Montenegro, and J. Granja, “Self-Assembly of Silver Metal Clusters of Small Atomicity on Cyclic Peptide Nanotubes.,” ACS nano. 2015. link Times cited: 36 Abstract: Subnanometric noble metal clusters, composed by only a few a… read moreAbstract: Subnanometric noble metal clusters, composed by only a few atoms, behave like molecular entities and display magnetic, luminescent and catalytic activities. However, noncovalent interactions of molecular metal clusters, lacking of any ligand or surfactant, have not been seen at work. Theoretically attractive and experimentally discernible, van der Waals forces and noncovalent interactions at the metal/organic interfaces will be crucial to understand and develop the next generation of hybrid nanomaterials. Here, we present experimental and theoretical evidence of noncovalent interactions between subnanometric metal (0) silver clusters and aromatic rings and their application in the preparation of 1D self-assembled hybrid architectures with ditopic peptide nanotubes. Atomic force microscopy, fluorescence experiments, circular dichroism and computational simulations verified the occurrence of these interactions in the clean and mild formation of a novel peptide nanotube and metal cluster hybrid material. The findings reported here confirmed the sensitivity of silver metal clusters of small atomicity toward noncovalent interactions, a concept that could find multiple applications in nanotechnology. We conclude that induced supramolecular forces are optimal candidates for the precise spatial positioning and properties modulation of molecular metal clusters. The reported results herein outline and generalize the possibilities that noncovalent interactions will have in this emerging field. read less USED (low confidence) D. A. Cannon, N. Ashkenasy, and T. Tuttle, “Influence of Solvent in Controlling Peptide-Surface Interactions.,” The journal of physical chemistry letters. 2015. link Times cited: 16 Abstract: Protein binding to surfaces is an important phenomenon in bi… read moreAbstract: Protein binding to surfaces is an important phenomenon in biology and in modern technological applications. Extensive experimental and theoretical research has been focused in recent years on revealing the factors that govern binding affinity to surfaces. Theoretical studies mainly focus on examining the contribution of the individual amino acids or, alternatively, the binding potential energies of the full peptide, which are unable to capture entropic contributions and neglect the dynamic nature of the system. We present here a methodology that involves the combination of nonequilibrium dynamics simulations with strategic mutation of polar residues to reveal the different factors governing the binding free energy of a peptide to a surface. Using a gold-binding peptide as an example, we show that relative binding free energies are a consequence of the balance between strong interactions of the peptide with the surface and the ability for the bulk solvent to stabilize the peptide. read less USED (low confidence) N. Nerngchamnong et al., “Nonideal electrochemical behavior of ferrocenyl-alkanethiolate SAMs maps the microenvironment of the redox unit,” Journal of Physical Chemistry C. 2015. link Times cited: 49 Abstract: We studied the electrochemical behavior of self-assembled mo… read moreAbstract: We studied the electrochemical behavior of self-assembled monolayers (SAMs) of n-alkanethiolates with ferrocenyl (Fc) termini on gold (S(CH2)nFc, n = 0–15) in relation to their supramolecular structures (characterized by photoemission spectroscopy (PES) supported by molecular dynamics (MD) simulations) to elucidate the origin of nonideal features commonly observed in cyclic voltammograms (CVs) of these SAMs by systematically changing n from 0 to 15. For all SAMs the CV data are dominated by a main peak for Fc units directly in contact with the electrolyte solution and interacting with neighboring Fc units. A second peak is observed for SAMs with n ≥ 2 ascribed to partially buried Fc units as a result of lattice strain due to the different sizes of the lattices of the Fc units and the sulfur atoms. For thick SAMs with strong molecule–molecule interactions, the strain is large, resulting in a third peak due to Fc units that are well shielded from the electrolyte by other Fc units. Our results do not agree w... read less USED (low confidence) E. S. C. Ferreira, C. Pereira, M. Cordeiro, and D. J. V. A. dos Santos, “Molecular Dynamics Study of the Gold/Ionic Liquids Interface.,” The journal of physical chemistry. B. 2015. link Times cited: 33 Abstract: The results of a systematic molecular dynamics study of the … read moreAbstract: The results of a systematic molecular dynamics study of the interfacial structure between the gold (100) surface and two room-temperature ionic liquids, namely, 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) and 1-butyl-3-methylimadazolium bis(trifluoromethylsulfonyl)imide ([BMIm][NTf2]), are herein reported. It is found that near an uncharged surface the IL structure differs from its bulk, having an enhanced density extended until the two first layers. Interfacial layering is clearly observed at the gold surface, with a higher effect for the [BMIm][NTf2] IL but a higher packing for [BMIm][PF6]. In both ILs the alkyl side chains are oriented parallel to the interface while the imidazolium rings tend to be parallel to the interface in about 60% of the cases. The presence of the interface has a higher impact on the orientation of the cations than on the chemical properties of the counterion. The surface potential drop across the interface is more pronounced toward a negative value for ([BMIm][PF6]) than for ([BMIm][NTf2]), due to relatively larger local density of the anions for ([BMIm][PF6]) near the gold surface. read less USED (low confidence) J. Vera and Y. Bayazitoglu, “Temperature and heat flux dependence of thermal resistance of water/metal nanoparticle interfaces at sub-boiling temperatures,” International Journal of Heat and Mass Transfer. 2015. link Times cited: 31 USED (low confidence) P. Nirmalraj, D. Thompson, and H. Riel, “Capturing the embryonic stages of self-assembly - design rules for molecular computation,” Scientific Reports. 2015. link Times cited: 12 USED (low confidence) N. Bedford et al., “Elucidation of peptide-directed palladium surface structure for biologically tunable nanocatalysts.,” ACS nano. 2015. link Times cited: 89 Abstract: Peptide-enabled synthesis of inorganic nanostructures repres… read moreAbstract: Peptide-enabled synthesis of inorganic nanostructures represents an avenue to access catalytic materials with tunable and optimized properties. This is achieved via peptide complexity and programmability that is missing in traditional ligands for catalytic nanomaterials. Unfortunately, there is limited information available to correlate peptide sequence to particle structure and catalytic activity to date. As such, the application of peptide-enabled nanocatalysts remains limited to trial and error approaches. In this paper, a hybrid experimental and computational approach is introduced to systematically elucidate biomolecule-dependent structure/function relationships for peptide-capped Pd nanocatalysts. Synchrotron X-ray techniques were used to uncover substantial particle surface structural disorder, which was dependent upon the amino acid sequence of the peptide capping ligand. Nanocatalyst configurations were then determined directly from experimental data using reverse Monte Carlo methods and further refined using molecular dynamics simulation, obtaining thermodynamically stable peptide-Pd nanoparticle configurations. Sequence-dependent catalytic property differences for C-C coupling and olefin hydrogenation were then elucidated by identification of the catalytic active sites at the atomic level and quantitative prediction of relative reaction rates. This hybrid methodology provides a clear route to determine peptide-dependent structure/function relationships, enabling the generation of guidelines for catalyst design through rational tailoring of peptide sequences. read less USED (low confidence) P. Xiao, J. Wang, R. Yang, F. Ke, and Y.-long Bai, “Transition of mechanisms underlying the rate effects and its significance,” Computational Materials Science. 2015. link Times cited: 8 USED (low confidence) V. Velachi, D. Bhandary, J. Singh, and M. Cordeiro, “Structure of Mixed Self-Assembled Monolayers on Gold Nanoparticles at Three Different Arrangements,” Journal of Physical Chemistry C. 2015. link Times cited: 26 Abstract: In this work, we performed atomistic simulations to study th… read moreAbstract: In this work, we performed atomistic simulations to study the structural properties of mixed self-assembled monolayers (SAM) of hydrophilic and hydrophobic alkylthiols, with two different chain lengths (C5 and C11), on gold nanoparticles (NPs) at three different arrangements, namely: random, patchy, and Janus domains. In particular, we report the effect of mixing of thiols with unequal carbon chain lengths (C5 and C11) at three different arrangements on the structural properties and hydration of SAMs. Our simulation study reveals that the arrangement of thiols having unequal carbon chains in mixed SAMs is a key parameter in deciding the hydrophilicity of the coated gold NPs. Thus, our findings suggest that the hydration of the SAMs-protected gold NPs is not only dependent on the molecular composition of the thiols, but also on the organization of their mixing. In addition, our results show that the bending of longer thiols, when these are mixed with shorter thiols, depends on the arrangement of thiols as ... read less USED (low confidence) F. Ramezani, M. Habibi, H. Rafii-Tabar, and M. Amanlou, “Effect of peptide length on the conjugation to the gold nanoparticle surface: a molecular dynamic study,” DARU Journal of Pharmaceutical Sciences. 2015. link Times cited: 15 USED (low confidence) Z. E. Hughes and T. Walsh, “Structure of the electrical double layer at aqueous gold and silver interfaces for saline solutions.,” Journal of colloid and interface science. 2014. link Times cited: 11 USED (low confidence) P. Nirmalraj et al., “Nanoelectrical analysis of single molecules and atomic-scale materials at the solid/liquid interface.,” Nature materials. 2014. link Times cited: 29 USED (low confidence) M. E. Grady, P. Geubelle, P. Braun, and N. Sottos, “Molecular tailoring of interfacial failure.,” Langmuir : the ACS journal of surfaces and colloids. 2014. link Times cited: 17 Abstract: Self-assembled monolayers (SAMs) provide an enabling platfor… read moreAbstract: Self-assembled monolayers (SAMs) provide an enabling platform for molecular tailoring of the chemical and physical properties of an interface. In this work, we systematically vary SAM end-group functionality and quantify the corresponding effect on interfacial failure between a transfer printed gold (Au) film and a fused silica substrate. SAMs with four different end groups are investigated: 11-amino-undecyltriethoxysilane (ATES), dodecyltriethoxysilane (DTES), 11-bromo-undecyltrimethoxysilane (BrUTMS), and 11-mercapto-undecyltrimethoxysilane (MUTMS). In addition to these four end groups, mixed monolayers of increasing molar ratio of MUTMS to DTES in solution are investigated. The failure of each SAM-mediated interface is initiated by a noncontact laser-induced spallation method at strain rates in excess of 10(6) s(-1). By making multiple measurements at increasing stress amplitudes (controlled by the laser fluence), we measure interface strengths of 19 ± 1.7, 20 ± 1.3, 52 ± 5.4, and 80 ± 6.5 MPa for interfaces functionalized with ATES, DTES, BrUTMS, and MUTMS, respectively. The interface strength is effectively tuned between the low strength of DTES and the high strength of MUTMS by controlling the concentration of MUTMS in solution. X-ray photoelectron spectroscopy of the failed interfaces reveals the influence of end group functionality on molecular dissociation, which significantly alters the failure process. read less USED (low confidence) X.-yong Zhang and Y. Ding, “Thickness-dependent structural and transport behaviors in the platinum–Nafion interface: a molecular dynamics investigation,” RSC Advances. 2014. link Times cited: 17 Abstract: Structures and transport behaviors around the ionomer–cataly… read moreAbstract: Structures and transport behaviors around the ionomer–catalyst interface in polymer electrolyte membrane fuel cells (PEMFCs) have aroused great research interests in recent years. Herein, classical molecular dynamics simulation method is used to investigate the interfacial self-assembly phenomena of three fully hydrated (λ = 23) Nafion films with thicknesses of 2.4, 5.0 and 7.3 nm on the platinum surface. Interestingly, it is found that in the vicinity of the platinum surface, there is an ultra-dense adhesive ionomer layer with a thickness of 0.5 nm, whose compositions are not affected by the hydration levels and film thickness. Due to the lack of sulfonate groups, the Nafion ionomer in regions away from the Pt slab are reorganized in different patterns for films with different thicknesses. Besides this, we have found a thickness-dependence of the wetability of the surfaces exposed to the air in these fully hydrated films. It is also shown that the transport properties of hydronium ions and water molecules in the interfacial films are closely related to film morphologies. Water molecules in the 5.0 nm film are found to possess the lowest mobility as a result of the weakest connectivity of the hydrophilic channels, while in the 7.3 nm film, water diffusion is the fastest since the water channels are most ideally connected throughout this film. Notably, though water molecules cannot be retained inside the ultrathin 2.4 nm film, they could mostly develop into linear hydrophilic channels over the ionomer matrix, which can also provide transport pathways for hydrophilic species without interruption. read less USED (low confidence) Z. Tang, Q. Zhang, Y. Yin, and C. A. Chang, “Facet Selectivity of Ligands on Silver Nanoplates: Molecular Mechanics Study,” Journal of Physical Chemistry C. 2014. link Times cited: 13 Abstract: Colloidal nanomaterials with well-defined shapes have wide a… read moreAbstract: Colloidal nanomaterials with well-defined shapes have wide applications in many fields. However, the exact role of capping ligands, which often dictates the shape of products in colloidal syntheses, is often unclear. Here we use a classical molecular-mechanics force-field method, mining minima (M2), to compute the binding free energy of the ligands such as citrate, monocarboxylates, dicarboxylates, and tricarboxylates to both (111) and (100) facets of silver and to investigate the mechanisms of the anisotropic growth of silver nanoplates. The distribution of partial charges on a ligand, the geometry complementation in the complex, and the entropic penalty on binding played crucial roles in discriminating the two facets and determining a good or poor ligand. Our finding allows rational design of capping ligands that may perform as well as citrate in promoting the anisotropic growth of nanoplates; however, designing a compound that outperforms citrate is found to be challenging. read less USED (low confidence) K. Kubiak-Ossowska, P. Mulheran, and W. Nowak, “Fibronectin module FN(III)9 adsorption at contrasting solid model surfaces studied by atomistic molecular dynamics.,” The journal of physical chemistry. B. 2014. link Times cited: 26 Abstract: The mechanism of human fibronectin adhesion synergy region (… read moreAbstract: The mechanism of human fibronectin adhesion synergy region (known as integrin binding region) in repeat 9 (FN(III)9) domain adsorption at pH 7 onto various and contrasting model surfaces has been studied using atomistic molecular dynamics simulations. We use an ionic model to mimic mica surface charge density but without a long-range electric field above the surface, a silica model with a long-range electric field similar to that found experimentally, and an Au {111} model with no partial charges or electric field. A detailed description of the adsorption processes and the contrasts between the various model surfaces is provided. In the case of our model silica surface with a long-range electrostatic field, the adsorption is rapid and primarily driven by electrostatics. Because it is negatively charged (-1e), FN(III)9 readily adsorbs to a positively charged surface. However, due to its partial charge distribution, FN(III)9 can also adsorb to the negatively charged mica model because of the absence of a long-range repulsive electric field. The protein dipole moment dictates its contrasting orientation at these surfaces, and the anchoring residues have opposite charges to the surface. Adsorption on the model Au {111} surface is possible, but less specific, and various protein regions might be involved in the interactions with the surface. Despite strongly influencing the protein mobility, adsorption at these model surfaces does not require wholesale FN(III)9 conformational changes, which suggests that the biological activity of the adsorbed protein might be preserved. read less USED (low confidence) V. Petkov et al., “Solving the nanostructure problem: exemplified on metallic alloy nanoparticles.,” Nanoscale. 2014. link Times cited: 28 Abstract: With current technology moving rapidly toward smaller scales… read moreAbstract: With current technology moving rapidly toward smaller scales nanometer-size materials, hereafter called nanometer-size particles (NPs), are being produced in increasing numbers and explored for various useful applications ranging from photonics and catalysis to detoxification of wastewater and cancer therapy. Nature also is a prolific producer of useful NPs. Evidence can be found in ores on the ocean floor, minerals and soils on land and in the human body that, when water is excluded, is mostly made of proteins that are 6-10 nm in size and globular in shape. Precise knowledge of the 3D atomic-scale structure, that is how atoms are arranged in space, is a crucial prerequisite for understanding and so gaining more control over the properties of any material, including NPs. In the case of bulk materials such knowledge is fairly easy to obtain by Bragg diffraction experiments. Determining the 3D atomic-scale structure of NPs is, however, still problematic spelling trouble for science and technology at the nanoscale. Here we explore this so-called "nanostructure problem" from a practical point of view arguing that it can be solved when its technical, that is the inapplicability of Bragg diffraction to NPs, and fundamental, that is the incompatibility of traditional crystallography with NPs, aspects are both addressed properly. As evidence we present a successful and broadly applicable, 6-step approach to determining the 3D atomic-scale structure of NPs based on a suitable combination of a few experimental and computational techniques. This approach is exemplified on 5 nm sized Pd(x)Ni(100-x) particles (x = 26, 56 and 88) explored for catalytic applications. Furthermore, we show how once an NP atomic structure is determined precisely, a strategy for improving NP structure-dependent properties of particular interest to science and technology can be designed rationally and not subjectively as frequently done now. read less USED (low confidence) M. Sha, Q. Dou, F. Luo, G. Zhu, and G. Wu, “Molecular insights into the electric double layers of ionic liquids on Au(100) electrodes.,” ACS applied materials & interfaces. 2014. link Times cited: 43 Abstract: The electric double layer structure and differential capacit… read moreAbstract: The electric double layer structure and differential capacitance of single crystalline Au(100) electrodes in the ionic liquid 1-butyl-3-methyl-imidazolium hexafluorophosphate are investigated using molecular dynamics simulations. Results show strong adsorption on the electrode surface. The potential of zero charge (pzc) and maxima of differential capacitance are strongly dependent on the adsorption layer structure. At potentials near the pzc, cations and anions adjacent to the electrode surface are coadsorbed on the same screening layer. This strong adsorption layer results in overscreening effects on the compact layer and induces both a bell-shaped differential capacitance curve and a positive pzc. Moreover, the potential required for transition from overscreening to overcrowding is about 4.0 V. This transition potential may be attributed to the higher interaction energy between the Au(100) electrode and ions compared with the binding energy in our cation-anion system. read less USED (low confidence) T. Huong, V. V. Hoang, and P. N. K. Cát, “Molecular dynamics simulations of crystallization of Lennard-Jones nanoparticles,” European Physical Journal-applied Physics. 2014. link Times cited: 1 Abstract: Crystallization of Lennard-Jones nanoparticles has been stud… read moreAbstract: Crystallization of Lennard-Jones nanoparticles has been studied by molecular dynamics (MD) simulations. Spherical models with free surface are cooled from the melt to crystalline state. In the cooling process, thermodynamics, structural properties and atomic mechanism of the crystallization are investigated. We found that crystallization in nanoparticles follows the Ostwald’s step rule like that found in the past. Due to free surface contribution, the solidification exhibits non-homogeneous behavior which proceeds in different manners between core and surface: homogeneous crystallization in the core and heterogeneous one in the surface layer of nanoparticles. It is due to the discrepancy between structures of two parts: highly ordered structure dominates in the core region while the surface exhibits defective one with a high fraction of undercoordinated sites. Also, our results are consistent with previous ones about the free surface-induced phenomena. read less USED (low confidence) T. Roussel, E. Barrena, C. Ocal, and J. Faraudo, “Predicting supramolecular self-assembly on reconstructed metal surfaces.,” Nanoscale. 2014. link Times cited: 25 Abstract: The prediction of supramolecular self-assembly onto solid su… read moreAbstract: The prediction of supramolecular self-assembly onto solid surfaces is still challenging in many situations of interest for nanoscience. In particular, no previous simulation approach has been capable to simulate large self-assembly patterns of organic molecules over reconstructed surfaces (which have periodicities over large distances) due to the large number of surface atoms and adsorbing molecules involved. Using a novel simulation technique, we report here large scale simulations of the self-assembly patterns of an organic molecule (DIP) over different reconstructions of the Au(111) surface. We show that on particular reconstructions, the molecule-molecule interactions are enhanced in a way that long-range order is promoted. Also, the presence of a distortion in a reconstructed surface pattern not only induces the presence of long-range order but also is able to drive the organization of DIP into two coexisting homochiral domains, in quantitative agreement with STM experiments. On the other hand, only short range order is obtained in other reconstructions of the Au(111) surface. The simulation strategy opens interesting perspectives to tune the supramolecular structure by simulation design and surface engineering if choosing the right molecular building blocks and stabilising the chosen reconstruction pattern. read less USED (low confidence) L. Wright, N. A. Merrill, M. R. Knecht, and T. Walsh, “Structure of arginine overlayers at the aqueous gold interface: implications for nanoparticle assembly.,” ACS applied materials & interfaces. 2014. link Times cited: 23 Abstract: Adsorption of small biomolecules onto the surface of nanopar… read moreAbstract: Adsorption of small biomolecules onto the surface of nanoparticles offers a novel route to generation of nanoparticle assemblies with predictable architectures. Previously, ligand-exchange experiments on citrate-capped gold nanoparticles with the amino acid arginine were reported to support linear nanoparticle assemblies. Here, we use a combination of atomistic modeling with experimental characterization to explore aspects of the assembly hypothesis for these systems. Using molecular simulation, we probe the structural and energetic characteristics of arginine overlayers on the Au(111) surface under aqueous conditions at both low- and high-coverage regimes. In the low-density regime, the arginines lie flat on the surface. At constant composition, these overlayers are found to be lower in energy than the densely packed films, although the latter case appears kinetically stable when arginine is adsorbed via the zwitterion group, exposing the charged guanidinium group to the solvent. Our findings suggest that zwitterion-zwitterion hydrogen bonding at the gold surface and minimization of the electrostatic repulsion between adjacent guanidinium groups play key roles in determining arginine overlayer stability at the aqueous gold interface. Ligand-exchange experiments of citrate-capped gold nanoparticles with arginine derivatives agmatine and N-methyl-l-arginine reveal that modification at the guanidinium group significantly diminishes the propensity for linear assembly of the nanoparticles. read less USED (low confidence) V. Rudyak and S. Krasnolutskii, “Dependence of the viscosity of nanofluids on nanoparticle size and material,” Physics Letters A. 2014. link Times cited: 128 USED (low confidence) G. Vilé, N. Almora‐Barrios, S. Mitchell, N. López, and J. Pérez–Ramírez, “From the Lindlar catalyst to supported ligand-modified palladium nanoparticles: selectivity patterns and accessibility constraints in the continuous-flow three-phase hydrogenation of acetylenic compounds.,” Chemistry. 2014. link Times cited: 134 Abstract: Site modification and isolation through selective poisoning … read moreAbstract: Site modification and isolation through selective poisoning comprise an effective strategy to enhance the selectivity of palladium catalysts in the partial hydrogenation of triple bonds in acetylenic compounds. The recent emergence of supported hybrid materials matching the stereo- and chemoselectivity of the classical Lindlar catalyst holds promise to revolutionize palladium-catalyzed hydrogenations, and will benefit from an in-depth understanding of these new materials. In this work, we compare the performance of bare, lead-poisoned, and ligand-modified palladium catalysts in the hydrogenation of diverse alkynes. Catalytic tests, conducted in a continuous-flow three-phase reactor, coupled with theoretical calculations and characterization methods, enable elucidation of the structural origins of the observed selectivity patterns. Distinctions in the catalytic performance are correlated with the relative accessibility of the active site to the organic substrate, and with the adsorption configuration and strength, depending on the ensemble size and surface potentials. This explains the role of the ligand in the colloidally prepared catalysts in promoting superior performance in the hydrogenation of terminal and internal alkynes, and short-chain alkynols. In contrast, the greater accessibility of the active surface of the Pd-Pb alloy and the absence of polar groups are shown to be favorable in the conversion of alkynes containing long aliphatic chains and/or ketone groups. These findings provide detailed insights for the advanced design of supported nanostructured catalysts. read less USED (low confidence) C. Shao, Y. Jin, K. Pipe, M. Shtein, and J. Kieffer, “Simulation of crystalline and amorphous copper phthalocyanine: Force field development and analysis of thermal transport mechanisms,” Journal of Physical Chemistry C. 2014. link Times cited: 8 Abstract: The thermal conductivities of crystalline and amorphous CuPc… read moreAbstract: The thermal conductivities of crystalline and amorphous CuPc structures have been studied using molecular dynamics simulations. To this end, a Hybrid-COMPASS force field for the CuPc molecule has been developed and parametrized using ab initio and empirical parametrization techniques. The valence parameters and atomic partial charges were derived by fitting to ab initio calculation results, and the van der Waals (vdW) parameters were derived by comparing MD simulations of CuPc crystal structures to experimentally determined characteristics. The resulting force field successfully predicts accurate molecular structure, crystal structure, and vibration density of states (VDOS) of CuPc molecule in isolation and in condensed phase. Thermal conductivities calculated using the Green–Kubo formalism show a significant difference between crystalline and amorphous CuPc. Further analysis of the thermal conductivity spectral modes reveals that this difference mainly stems from the scattering of acoustic phonons, and t... read less USED (low confidence) V. Vasumathi and M. Cordeiro, “Molecular dynamics study of mixed alkanethiols covering a gold surface at three different arrangements,” Chemical Physics Letters. 2014. link Times cited: 15 USED (low confidence) R. K. Mishra, L. Fernández-Carrasco, R. Flatt, and H. Heinz, “A force field for tricalcium aluminate to characterize surface properties, initial hydration, and organically modified interfaces in atomic resolution.,” Dalton transactions. 2014. link Times cited: 84 Abstract: Tricalcium aluminate (C3A) is a major phase of Portland ceme… read moreAbstract: Tricalcium aluminate (C3A) is a major phase of Portland cement clinker and some dental root filling cements. An accurate all-atom force field is introduced to examine structural, surface, and hydration properties as well as organic interfaces to overcome challenges using current laboratory instrumentation. Molecular dynamics simulation demonstrates excellent agreement of computed structural, thermal, mechanical, and surface properties with available experimental data. The parameters are integrated into multiple potential energy expressions, including the PCFF, CVFF, CHARMM, AMBER, OPLS, and INTERFACE force fields. This choice enables the simulation of a wide range of inorganic-organic interfaces at the 1 to 100 nm scale at a million times lower computational cost than DFT methods. Molecular models of dry and partially hydrated surfaces are introduced to examine cleavage, agglomeration, and the role of adsorbed organic molecules. Cleavage of crystalline tricalcium aluminate requires approximately 1300 mJ m(-2) and superficial hydration introduces an amorphous calcium hydroxide surface layer that reduces the agglomeration energy from approximately 850 mJ m(-2) to 500 mJ m(-2), as well as to lower values upon surface displacement. The adsorption of several alcohols and amines was examined to understand their role as grinding aids and as hydration modifiers in cement. The molecules mitigate local electric fields through complexation of calcium ions, hydrogen bonds, and introduction of hydrophobicity upon binding. Molecularly thin layers of about 0.5 nm thickness reduce agglomeration energies to between 100 and 30 mJ m(-2). Molecule-specific trends were found to be similar for tricalcium aluminate and tricalcium silicate. The models allow quantitative predictions and are a starting point to provide fundamental understanding of the role of C3A and organic additives in cement. Extensions to impure phases and advanced hydration stages are feasible. read less USED (low confidence) F. Ramezani, M. Amanlou, and H. Rafii-Tabar, “Comparison of amino acids interaction with gold nanoparticle,” Amino Acids. 2014. link Times cited: 31 USED (low confidence) Y. Yimer, K. C. Jha, and M. Tsige, “Epitaxial transfer through end-group coordination modulates the odd-even effect in an alkanethiol monolayer assembly.,” Nanoscale. 2014. link Times cited: 8 Abstract: Short spacer length and high end-group coordination lead to … read moreAbstract: Short spacer length and high end-group coordination lead to the top network acting as a template for the buried sulfur-gold interface of n-alkanethiols (SH-(CH2)n-OH or SH-(CH2)n-CH3) on gold {111}. Annealing and templating both drive toward a higher sampling of the spatially favorable bridge adsorption sites. The hydrogen-bonded network increases in strength by increasing the number of hydrogens participating per oxygen, from 1.75 to 1.98 for n = 14-30. Higher n leads to better packing (five times for hydroxyl-terminated and seven times for methyl-terminated for n = 14-30) and stability of monolayers, while lower n results in better epitaxial transfer (transfer coefficient ratio = 13.5 for {SH-(CH2)14-OH}/{SH-(CH2)30-CH3}) and actuation. Odd values of n for the hydroxyl-terminated n-alkanethiols lead to lattice spacing of an average of 0.04 ± 0.01 Å higher than even values. There is a structural transition in properties around spacer length n = 24-27. Characterization of monolayer assembly through correlation between adatom and network layers provides recursive design principles for actuation and sensing applications. read less USED (low confidence) V. Petkov, Y. Ren, S. Shan, J. Luo, and C. Zhong, “A distinct atomic structure-catalytic activity relationship in 3-10 nm supported Au particles.,” Nanoscale. 2014. link Times cited: 25 Abstract: Bulk Au is very inert but Au nanoparticles less than 5 nm in… read moreAbstract: Bulk Au is very inert but Au nanoparticles less than 5 nm in size have been found to be catalytically active for several reactions, in particular for low-temperature oxidation of CO. Using high-energy X-ray diffraction coupled with atomic pair distribution function analysis and computer simulations we determine the structure of 3 nm and 10 nm Au particles supported on titania and silica as typical representatives of reducible and irreducible supports, respectively. We find that the synthesis protocol adopted in our work affects strongly and differently the structure of the Au nanoparticles on the different supports. This leads to clearly distinct dependences of the catalytic activity of the nanoparticles on their size. In the case of the silica support the catalytic activity of Au nanoparticles increases and in the case of the titania support it decreases with decreasing nanoparticle size. The experimental results are considered in terms of current theoretical predictions and found to be in good accord with them. read less USED (low confidence) S. Meena and M. Sulpizi, “Understanding the microscopic origin of gold nanoparticle anisotropic growth from molecular dynamics simulations.,” Langmuir : the ACS journal of surfaces and colloids. 2013. link Times cited: 89 Abstract: We use molecular dynamics simulations in order to understand… read moreAbstract: We use molecular dynamics simulations in order to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. We provide the first atomistic model of different surfaces on gold nanoparticles in a growing electrolyte solution, and we describe the interaction of the metal with the surfactants, namely, cetyltrimethylammonium bromide (CTAB) and the ions. An innovative aspect is the inclusion of the role of the surfactants, which are explicitly modeled. We find that on all the investigated surfaces, namely, (111), (110), and (100), CTAB forms a layer of distorted cylindrical micelles where channels among micelles provide direct ion access to the surface. In particular, we show how AuCl2(-) ions, which are found in the growth solution, can freely diffuse from the bulk solution to the gold surface. We also find that the (111) surface exhibits a higher CTAB packing density and a higher electrostatic potential. Both elements would favor the growth of gold nanoparticles along the (111) direction. These findings are in agreement with the growth mechanisms proposed by the experimental groups of Murphy and Mulvaney. read less USED (low confidence) V. Petkov et al., “Noble-transition metal nanoparticle breathing in a reactive gas atmosphere.,” Nanoscale. 2013. link Times cited: 20 Abstract: In situ high-energy X-ray diffraction coupled to atomic pair… read moreAbstract: In situ high-energy X-ray diffraction coupled to atomic pair distribution function analysis is used to obtain fundamental insight into the effect of the reactive gas environment on the atomic-scale structure of metallic particles less than 10 nm in size. To substantiate our recent discovery we investigate a wide range of noble-transition metal nanoparticles and confirm that they expand and contract radially when treated in oxidizing (O2) and reducing (H2) atmospheres, respectively. The results are confirmed by supplementary XAFS experiments. Using computer simulations guided by the experimental diffraction data we quantify the effect in terms of both relative lattice strain and absolute atomic displacements. In particular, we show that the effect leads to a small percent of extra surface strain corresponding to several tenths of Ångström displacements of the atoms at the outmost layer of the particles. The effect then gradually decays to zero within 4 atomic layers inside the particles. We also show that, reminiscent of a breathing type structural transformation, the effect is reproducible and reversible. We argue that because of its significance and widespread occurrence the effect should be taken into account in nanoparticle research. read less USED (low confidence) Y. Wu and N. Aluru, “Graphitic carbon-water nonbonded interaction parameters.,” The journal of physical chemistry. B. 2013. link Times cited: 139 Abstract: In this study, we develop graphitic carbon-water nonbonded i… read moreAbstract: In this study, we develop graphitic carbon-water nonbonded interaction parameters entirely from ab initio calculation data of interaction energies between graphene and a single water molecule. First, we employ the Møller-Plesset perturbation theory of the second order (MP2) method to compute the polycyclic aromatic hydrocarbon (PAH)-water interaction energies, with proper size of basis sets and energy component analysis to extrapolate to infinite-sized graphene limit. Then, we develop graphitic carbon-water interaction parameters based on the MP2 data from this work and the ab initio data available in the literature from other methods such as random-phase approximation (RPA), density functional theory-symmetry-adapted perturbation theory (DFT-SAPT), and coupled cluster treatment with single and double excitations and perturbative triples (CCSD(T)). The accuracy of the interaction parameters is evaluated by predicting water contact angle on graphite and carbon nanotube (CNT) radial breathing mode (RBM) frequency shift and comparing them with experimental data. The interaction parameters obtained from MP2 data predict the CNT RBM frequency shift that is in good agreement with experiments. The interaction parameters obtained from RPA and DFT-SAPT data predict the contact angles and the CNT RBM frequency shift that agree well with experiments. The interaction parameters obtained from CCSD(T) data underestimate the contact angles and overestimate the CNT RBM frequency shift probably due to the use of small basis sets in CCSD(T) calculations. read less USED (low confidence) M. Siwko and S. Corni, “Cytochrome C on a gold surface: investigating structural relaxations and their role in protein-surface electron transfer by molecular dynamics simulations.,” Physical chemistry chemical physics : PCCP. 2013. link Times cited: 19 Abstract: Proteins immobilized on inorganic surfaces are important in … read moreAbstract: Proteins immobilized on inorganic surfaces are important in technological fields such as biosensors, enzymatic biofuel cells and biomolecular electronics. In these frameworks, it has been demonstrated that some proteins are able to keep their functionality, although the latter may be somewhat modified by the interaction with the surface. Cytochrome C, an heme-based electron transfer protein, has been found to be able to exchange electrons with the gold surface on which it is immobilized, but some deviations from the expected electron transfer rates were evidenced [C. A. Bortolotti, et al., J. Phys. Chem. C 2007, 111, 12100-12105]. In this work we have used molecular dynamics simulations of (native and mutated) yeast cytochrome C supported on Au(111) to investigate the microscopic picture behind the experimental behavior of the molecule. In particular, we have focused on the structural re-arrangements due to the interactions with the surface. We found that, despite being secondary-structure preserving, they can profoundly affect protein-surface electronic coupling and, in turn, electron transfer rates, explaining experimental findings. The conformational flexibility of the protein in the region of the protein-surface bond is thus pivotal in determining the resulting ET functionality of the immobilized protein. read less USED (low confidence) H. Ramezani-Dakhel, P. Mirau, R. Naik, M. R. Knecht, and H. Heinz, “Stability, surface features, and atom leaching of palladium nanoparticles: toward prediction of catalytic functionality.,” Physical chemistry chemical physics : PCCP. 2013. link Times cited: 55 Abstract: Surfactant-stabilized metal nanoparticles have shown promise… read moreAbstract: Surfactant-stabilized metal nanoparticles have shown promise as catalysts although specific surface features and their influence on catalytic performance have not been well understood. We quantify the thermodynamic stability, the facet composition of the surface, and distinct atom types that affect rates of atom leaching for a series of twenty near-spherical Pd nanoparticles of 1.8 to 3.1 nm size using computational models. Cohesive energies indicate higher stability of certain particles that feature an approximate 60/20/20 ratio of {111}, {100}, and {110} facets while less stable particles exhibit widely variable facet composition. Unique patterns of atom types on the surface cause apparent differences in binding energies and changes in reactivity. Estimates of the relative rate of atom leaching as a function of particle size were obtained by the summation of Boltzmann-weighted binding energies over all surface atoms. Computed leaching rates are in good qualitative correlation with the measured catalytic activity of peptide-stabilized Pd nanoparticles of the same shape and size in Stille coupling reactions. The agreement supports rate-controlling contributions by atom leaching in the presence of reactive substrates. The computational approach provides a pathway to estimate the catalytic activity of metal nanostructures of engineered shape and size, and possible further refinements are described. read less USED (low confidence) D. Poger and A. Mark, “Study of Proteins and Peptides at Interfaces by Molecular Dynamics Simulation Techniques.” 2013. link Times cited: 1 Abstract: This chapter discusses the study of the interaction of pepti… read moreAbstract: This chapter discusses the study of the interaction of peptides and proteins at interfaces using molecular dynamics (MD) simulation techniques. First, the chapter discusses how computational methods, in particular MD simulation techniques, complement experimental methods. Then it focuses on three main areas of research: the interaction of peptides and proteins with (i) biological membranes and lipid bilayers, (ii) airâwater and oilâwater interfaces, and (iii) organic and inorganic sorbents. read less USED (low confidence) L. Ruan et al., “Tailoring molecular specificity toward a crystal facet: a lesson from biorecognition toward Pt111.,” Nano letters. 2013. link Times cited: 104 Abstract: Surfactants with preferential adsorption to certain crystal … read moreAbstract: Surfactants with preferential adsorption to certain crystal facets have been widely employed to manipulate morphologies of colloidal nanocrystals, while mechanisms regarding the origin of facet selectivity remain an enigma. Similar questions exist in biomimetic syntheses concerning biomolecular recognition to materials and crystal surfaces. Here we present mechanistic studies on the molecular origin of the recognition toward platinum {111} facet. By manipulating the conformations and chemical compositions of a platinum {111} facet specific peptide, phenylalanine is identified as the dominant motif to differentiate {111} from other facets. The discovered recognition motif is extended to convert nonspecific peptides into {111} specific peptides. Further extension of this mechanism allows the rational design of small organic molecules that demonstrate preferential adsorption to the {111} facets of both platinum and rhodium nanocrystals. This work represents an advance in understanding the organic-inorganic interfacial interactions in colloidal systems and paves the way to rational and predictable nanostructure modulations for many applications. read less USED (low confidence) K. Gkionis, I. Rungger, S. Sanvito, and U. Schwingenschlögl, “Protocol for classical molecular dynamics simulations of nano-junctions in solution,” Journal of Applied Physics. 2012. link Times cited: 2 Abstract: Modeling of nanoscale electronic devices in water requires t… read moreAbstract: Modeling of nanoscale electronic devices in water requires the evaluation of the transport properties averaged over the possible configurations of the solvent. They can be obtained from classical molecular dynamics for water confined in the device. A series of classical molecular dynamics simulations is performed to establish a methodology for estimating the average number of water molecules N confined between two static and semi-infinite gold electrodes. Variations in key parameters of the simulations, as well as simulations with non-static infinite gold surfaces of constant area and with anisotropically fluctuating cell dimensions lead to less than 1% discrepancies in the calculated N. Our approach is then applied to a carbon nanotube placed between the gold electrodes. The atomic density profile along the axis separating the slabs shows the typical pattern of confined liquids, irrespective of the presence of the nanotube, while parallel to the slabs the nanotube perturbs the obtained profile. read less USED (low confidence) R. K. Mishra, H. Heinz, J. Zimmermann, T. Müller, and R. Flatt, “Understanding the Effectiveness of Polycarboxylates as Grinding Aids,” SP-288: Tenth International Conference on Superplasticizers and other Chemical Admixtures. 2012. link Times cited: 15 Abstract: Over recent years, polycarboxylate superplasticizers have fo… read moreAbstract: Over recent years, polycarboxylate superplasticizers have found their way into grinding aids used in cement production to reduce the electrical energy consumption. The effectiveness of these large molecules challenges the pre-existing theories concerning the factors that govern the performance of grinding aids. This paper reports on molecular dynamics simulations to examine a physical property believed to control the effective¬ness of grinding aids, namely their adsorption energy. The molecules selected are TIPA (Triisopropanol amine), TEA (Triethanol amine) and glycerine. The surfaces examined are dry and hydroxylated C3S surfaces, which are believed to be more representative of reality, since some humidity is always present during the grinding. Detailed results of this part of the work show that glycerine interacts relatively more with dry as well as hydroxylated surfaces of C3S both at 25°C, ambient temperature and 110°C, grinding temperature with respect to TIPA and TEA. These result help to better understand the specific interaction of these molecules with cement surfaces. In the second part of this work oligomers of some PCE superplasticizers are examined with similar numerical tools on dry and hydroxylated surfaces of C3S. Results for different types of these oligomers, together with the previous results, shed light onto the reasons why polycarboxylate superplasticizers have found to also be effective grinding aids in cement production. read less USED (low confidence) Y. Chen, E. R. Cruz-Chú, J. C. Woodard, M. Gartia, K. Schulten, and L. Liu, “Electrically induced conformational change of peptides on metallic nanosurfaces.,” ACS nano. 2012. link Times cited: 58 Abstract: Surface immobilized biomolecular probes are used in many are… read moreAbstract: Surface immobilized biomolecular probes are used in many areas of biomedical research, such as genomics, proteomics, immunology, and pathology. Although the structural conformations of small DNA and peptide molecules in free solution are well studied both theoretically and experimentally, the conformation of small biomolecules bound on surfaces, especially under the influence of external electric fields, is poorly understood. Using a combination of molecular dynamics simulation and surface-enhanced Raman spectroscopy, we study the external electric field-induced conformational change of dodecapeptide probes tethered to a nanostructured metallic surface. Surface-tethered peptides with and without phosphorylated tyrosine residues are compared to show that peptide conformational change under electric field is sensitive to biochemical modification. Our study proposes a highly sensitive in vitro nanoscale electro-optical detection and manipulation method for biomolecule conformation and charge at bio-nano interfaces. read less USED (low confidence) V. Petkov et al., “Pt-Au alloying at the nanoscale.,” Nano letters. 2012. link Times cited: 91 Abstract: The formation of nanosized alloys between a pair of elements… read moreAbstract: The formation of nanosized alloys between a pair of elements, which are largely immiscible in bulk, is examined in the archetypical case of Pt and Au. Element specific resonant high-energy X-ray diffraction experiments coupled to atomic pair distribution functions analysis and computer simulations prove the formation of Pt-Au alloys in particles less than 10 nm in size. In the alloys, Au-Au and Pt-Pt bond lengths differing in 0.1 Å are present leading to extra structural distortions as compared to pure Pt and Au particles. The alloys are found to be stable over a wide range of Pt-Au compositions and temperatures contrary to what current theory predicts. The alloy-type structure of Pt-Au nanoparticles comes along with a high catalytic activity for electrooxidation of methanol making an excellent example of the synergistic effect of alloying at the nanoscale on functional properties. read less USED (low confidence) G. Cicero, A. Calzolari, S. Corni, and A. Catellani, “Anomalous Wetting Layer at the Au(111) Surface,” Journal of Physical Chemistry Letters. 2011. link Times cited: 48 Abstract: In this paper we present a microscopic picture of the interf… read moreAbstract: In this paper we present a microscopic picture of the interface between liquid water and a Au(111) surface at room temperature conditions, as obtained from ab initio molecular dynamics simulations. We find that the first wetting layer has peculiar structural and electronic features that can be revealed only by considering the dynamical evolution of the system. Surface phonons and molecular vibrations lead to instantaneous charge density distortions that are pivotal to explain the features of such an atypical wetting layer, and, in turn, the surface hydrophilicity. read less USED (low confidence) R. H. Coppage et al., “Crystallographic recognition controls peptide binding for bio-based nanomaterials.,” Journal of the American Chemical Society. 2011. link Times cited: 92 Abstract: The ability to control the size, shape, composition, and act… read moreAbstract: The ability to control the size, shape, composition, and activity of nanomaterials presents a formidable challenge. Peptide approaches represent new avenues to achieve such control at the synthetic level; however, the critical interactions at the bio/nano interface that direct such precision remain poorly understood. Here we present evidence to suggest that materials-directing peptides bind at specific time points during Pd nanoparticle (NP) growth, dictated by material crystallinity. As such surfaces are presented, rapid peptide binding occurs, resulting in the stabilization and size control of single-crystal NPs. Such specificity suggests that peptides could be engineered to direct the structure of nanomaterials at the atomic level, thus enhancing their activity. read less USED (low confidence) F. Delogu, “Melting of Pb clusters encapsulated in large fullerenes,” Chemical Physics. 2011. link Times cited: 0 USED (low confidence) J. Feng et al., “Effects of oligopeptide’s conformational changes on its adsorption.,” Colloids and surfaces. B, Biointerfaces. 2011. link Times cited: 2 USED (low confidence) J. Feng, R. Pandey, R. Berry, B. Farmer, R. Naik, and H. Heinz, “Adsorption mechanism of single amino acid and surfactant molecules to Au 111 surfaces in aqueous solution: design rules for metal-binding molecules,” Soft Matter. 2011. link Times cited: 190 Abstract: The adsorption mechanism of twenty amino acids and four surf… read moreAbstract: The adsorption mechanism of twenty amino acids and four surfactants was examined on a {111} surface of gold in dilute aqueous solution using molecular dynamics simulation with a broadly applicable intermolecular potential CHARMM–METAL. All molecules are attracted to the surface between −3 and −26 kcal mol−1. The adsorption strength correlates with the degree of coordination of polarizable atoms (O, N, C) to multiple epitaxial sites. Therefore, the molecular size and geometry rather than the specific chemistry determine the adsorption energy. Large molecules with planar sp2 hybridized groups (Arg, Trp, Gln, Tyr, Asn, and PPh3) adsorb most strongly, followed by molecules with polar sp3 hybridized groups, and short molecules with sp3 hybridized alkyl groups exhibit least attraction. Conformationally flexible, extended molecules such as hexadecyltrimethylammonium bromide (CTAB) also showed significant attraction to the metal surface related to accommodation in epitaxial grooves and coordination with numerous epitaxial sites. Computational results are consistent with combinatorial binding experiments, observations in the growth and stabilization of metal nanoparticles, and ab initio data. The mechanism of adsorption conforms to soft epitaxy observed for peptides on metal surfaces (H. Heinz et al., J. Am. Chem. Soc., 2009, 131, 9704) and enables the de novo design of molecules for binding to a given metal surface. In addition to soft epitaxy, contributions to adsorption are possible by covalent bonding and induced charges. read less USED (low confidence) H. Heinz, K. C. Jha, J. Luettmer-Strathmann, B. Farmer, and R. Naik, “Polarization at metal–biomolecular interfaces in solution,” Journal of The Royal Society Interface. 2011. link Times cited: 69 Abstract: Metal surfaces in contact with water, surfactants and biopol… read moreAbstract: Metal surfaces in contact with water, surfactants and biopolymers experience attractive polarization owing to induced charges. This fundamental physical interaction complements stronger epitaxial and covalent surface interactions and remains difficult to measure experimentally. We present a first step to quantify polarization on even gold (Au) surfaces in contact with water and with aqueous solutions of peptides of different charge state (A3 and Flg-Na3) by molecular dynamics simulation in all-atomic resolution and a posteriori computation of the image potential. Attractive polarization scales with the magnitude of atomic charges and with the length of multi-poles in the aqueous phase such as the distance between cationic and anionic groups. The polarization energy per surface area is similar on aqueous Au {1 1 1} and Au {1 0 0} interfaces of approximately −50 mJ m−2 and decreases to −70 mJ m−2 in the presence of charged peptides. In molecular terms, the polarization energy corresponds to −2.3 and −0.1 kJ mol−1 for water in the first and second molecular layers on the metal surface, and to between −40 and 0 kJ mol−1 for individual amino acids in the peptides depending on the charge state, multi-pole length and proximity to the surface. The net contribution of polarization to peptide adsorption on the metal surface is determined by the balance between polarization by the peptide and loss of polarization by replaced surface-bound water. On metal surfaces with significant epitaxial attraction of peptides such as Au {1 1 1}, polarization contributes only 10–20% to total adsorption related to similar polarity of water and of amino acids. On metal surfaces with weak epitaxial attraction of peptides such as Au {1 0 0}, polarization is a major contribution to adsorption, especially for charged peptides (−80 kJ mol−1 for peptide Flg-Na3). A remaining water interlayer between the metal surface and the peptide then reduces losses in polarization energy by replaced surface-bound water. Computed polarization energies are sensitive to the precise location of the image plane (within tenths of Angstroms near the jellium edge). The computational method can be extended to complex nanometre and micrometer-size surface topologies. read less USED (low confidence) X. Yin, A. Opara, H. Du, and J. D. Miller, “Molecular dynamics simulations of metal–cyanide complexes: Fundamental considerations in gold hydrometallurgy,” Hydrometallurgy. 2011. link Times cited: 33 USED (low confidence) H. Heinz, S. Patnaik, R. Pandey, and B. Farmer, “Modeling of Polymer Matrix Nanocomposites.” 2010. link Times cited: 3 USED (low confidence) A. Calzolari, G. Cicero, C. Cavazzoni, R. D. Felice, A. Catellani, and S. Corni, “Hydroxyl-rich beta-sheet adhesion to the gold surface in water by first-principle simulations.,” Journal of the American Chemical Society. 2010. link Times cited: 50 Abstract: Proteins able to recognize inorganic surfaces are of paramou… read moreAbstract: Proteins able to recognize inorganic surfaces are of paramount importance for living organisms. Mimicking nature, surface-recognizing proteins and peptides have also been man-made by combinatorial biochemistry. However, to date the recognition mechanisms remain elusive, and the underlying physicochemical principles are still unknown. Selectivity of gold-binding peptides (cysteine-free and rich in hydroxyl amino acids) is particularly puzzling, since the most relevant gold surface, Au(111), is known to be chemically inert and atomically flat. Using atomistic first-principle simulations we show that weak chemical interactions of dative-bond character confer to a prototype secondary structure (an antiparallel beta-sheet made of hydroxyl amino acids) and its hydration layer the capability of discriminating among gold surface sites. Our results highlight the unexpected role of hydration water in this process, suggesting that hydrophilic amino acids and their hydration shell cooperate to contribute to protein-gold surface recognition. read less USED (low confidence) S. Takakusagi, K. Kitamura, and K. Uosaki, “Electrodeposition of Ag and Pd on a reconstructed Au(111) electrode surface studied by in situ scanning tunneling microscopy,” Electrochimica Acta. 2009. link Times cited: 4 USED (low confidence) R. Rabani, S. Merabia, and A. Pishevar, “Conductive heat transfer through nanoconfined argon gas: From continuum to free-molecular regime,” International Journal of Thermal Sciences. 2023. link Times cited: 1 USED (low confidence) F. Mollaamin and M. Monajjemi, “Application of DFT and TD-DFT on Langmuir Adsorption of Nitrogen and Sulfur Heterocycle Dopants on an Aluminum Surface Decorated with Magnesium and Silicon,” Comput. 2023. link Times cited: 3 Abstract: In this study, we investigated the abilities of nitrogen and… read moreAbstract: In this study, we investigated the abilities of nitrogen and sulfur heterocyclic carbenes of benzotriazole, 2-mercaptobenzothiazole, 8-hydroxyquinoline, and 3-amino-1,2,4-triazole-5-thiol regarding adsorption on an Al-Mg-Si alloy toward corrosion inhibition of the surface. Al-Si(14), Al-Si(19), and Al-Si(21) in the Al-Mg-Si alloy surface with the highest fluctuation in the shielding tensors of the “NMR” spectrum generated by intra-atomic interaction directed us to the most influence in the neighbor atoms generated by interatomic reactions of N→ Al, O→ Al, and S→ Al through the coating and adsorbing process of Langmuir adsorption. The values of various thermodynamic properties and dipole moments of benzotriazole, 2-mercaptobenzothiazole, 8-hydroxyquinoline, and 3-amino-1,2,4-triazole-5-thiol adsorbed on the Al-Mg-Si increased by enhancing the molecular weight of these compounds as well as the charge distribution between organic compounds (electron donor) and the alloy surface (electron acceptor). Finally, this research can build up our knowledge of the electronic structure, relative stability, and surface bonding of various metal alloy surfaces, metal-doped alloy nanosheets, and other dependent mechanisms such as heterogeneous catalysis, friction lubrication, and biological systems. read less USED (low confidence) S. Guan, Z. Zhang, R. Wu, X. Gu, and C. Y. Zhao, “Boiling on nano-porous structures: Theoretical analysis and molecular dynamics simulations,” International Journal of Heat and Mass Transfer. 2022. link Times cited: 1 USED (low confidence) W. Deng, S. Ma, W. Li, H. Liu, and W. Zhao, “A molecular dynamics investigation of boiling heat transfer over wettability thermo-responsive surface,” International Journal of Heat and Mass Transfer. 2022. link Times cited: 2 USED (low confidence) P. Clabaut, B. Schweitzer, A. Götz, C. Michel, Stéphan, and Steinmann, “Solvation Free Energies and Adsorption Energies at the Metal/Water Interface from Hybrid Quantum-Mechanical/Molecular Mechanics Simulations.” 2022. link Times cited: 12 Abstract: Modeling adsorption at the metal/water interfaces is a corne… read moreAbstract: Modeling adsorption at the metal/water interfaces is a corner-stone towards an improved understanding in a variety of fields from heterogeneous catalysis to corrosion. We propose and validate a hybrid scheme that combines the adsorption free energies obtained in gas phase at the DFT level with the variation in solvation from the bulk phase to the interface evaluated using a molecular mechanics based alchemical transformation, denoted MMsolv. Using the GAL17 force field for the platinum/water interaction, we retrieve a qualitatively correct interaction energy of the water solvent at the interface. This interaction is of near chemisorption character and thus challenging, both for the alchemical transformation, but also for the fixed point-charge electrostatics. Our scheme passes through a state characterized by a well-behaved physisorption potential for the Pt(111)/H 2 O interaction to converge the free energy difference. The workflow is implemented in the freely available SolvHybrid package. We first assess the adsorption of a water molecule at the Pt/water interface, which turns out to be a stringent test. The intrinsic error of our QM-MM hybrid scheme is limited to 6 kcal · mol − 1 through the introduction of a correction term to attenuate the electrostatic interaction between near-chemisorbed water molecules and the underlying Pt atoms. Next, we show that the MMsolv solvation free energy of Pt (-0.46 J · m − 2 ) is in good agreement with the experimental estimate (-0.32 J · m − 2 ). Furthermore, we show that the entropy contribution at room temperature is roughly of equal magnitude as the free energy, but with opposite sign. Finally, we compute the adsorption energy of benzene and phenol at the Pt(111)/water interface, one of the rare systems for which experimental data are available. In qualitative agreement with experiment, but in stark contrast with a standard implicit solvent model, the adsorption of these aromatic molecules is strongly reduced (i.e., less exothermic by ∼ 30 and 40 kcal · mol − 1 for our QM/MM hybrid scheme and experiment, respectively, but ∼ 0 with the implicit solvent) at the solid/liquid compared to the solid/gas interface. This reduction is mainly due to the competition between the organic adsorbate and the solvent for adsorption on the metallic surface. The semi-quantitative agreement with experimental estimates for the adsorption energy of aromatic molecules thus validates the soundness of our hybrid QM-MM scheme. read less USED (low confidence) R. K. Mishra, K. Kanhaiya, J. Winetrout, R. Flatt, and H. Heinz, “Force field for calcium sulfate minerals to predict structural, hydration, and interfacial properties,” Cement and Concrete Research. 2021. link Times cited: 28 USED (low confidence) “Molecular Dynamics Simulation of Metal Matrix Composites Using BIOVIA Materials Studio, LAMMPS, and GROMACS,” Molecular Dynamics Simulation of Nanocomposites Using BIOVIA Materials Studio, Lammps and Gromacs. 2019. link Times cited: 0 USED (low confidence) H. Poblete and J. Comer, “Computational modeling of the adsorption of capping agent biomolecules to inorganic nanoparticles,” Photoactive Inorganic Nanoparticles. 2019. link Times cited: 0 USED (low confidence) S. Krasnolutskii and V. Rudyak, “Kinetic calculation of transport processes in rarefied gas suspensions with hollow nanoparticles.” 2018. link Times cited: 0 USED (low confidence) H. Mori and N. Matubayasi, “MD simulation analysis of resin filling into nano-sized pore formed on metal surface,” Applied Surface Science. 2018. link Times cited: 13 USED (low confidence) R. Latour, “3.14 Molecular Simulation Methods to Investigate Protein Adsorption Behavior at the Atomic Level.” 2017. link Times cited: 6 USED (low confidence) N. M. Bedford, C. J. Munro, and M. R. Knecht, “Peptide Binding for Bio-Based Nanomaterials.,” Methods in enzymology. 2016. link Times cited: 7 USED (low confidence) W. Janke, “Computer Simulation Studies of Polymer Adsorption and Aggregation - From Flexible to Stiff,” Physics Procedia. 2015. link Times cited: 3 USED (low confidence) M. Griep, A. L. West, M. Sellers, M. Karna, E. Zhan, and N. Hoque, “Biomediated Atomic Metal Nanoclusters: Synthesis and Theory.” 2015. link Times cited: 4 USED (low confidence) A. Dohn, “Treating Relativistic Effects in Transition Metal Complexes.” 2015. link Times cited: 0 USED (low confidence) A. Hallil, J. Raulot, and M. Cherkaoui, “Atomistic simulations of Cu2O bulk and Cu/Cu2O interface properties by using a new interatomic potential,” Computational Materials Science. 2014. link Times cited: 10 USED (low confidence) P. Mirau, “Interfacial Structure Determination.” 2014. link Times cited: 3 USED (low confidence) H. Heinz, “Understanding Molecular Recognition on Metallic and Oxidic Nanostructures from a Perspective of Computer Simulation and Theory.” 2014. link Times cited: 0 USED (low confidence) R. Latour, “3.311 – Molecular Simulation Methods to Investigate Protein Adsorption Behavior at the Atomic Level,” Comprehensive Biomaterials. 2011. link Times cited: 5 NOT USED (low confidence) K. Kanhaiya et al., “Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale.,” Journal of chemical theory and computation. 2023. link Times cited: 0 Abstract: The simulation of metals, oxides, and hydroxides can acceler… read moreAbstract: The simulation of metals, oxides, and hydroxides can accelerate the design of therapeutics, alloys, catalysts, cement-based materials, ceramics, bioinspired composites, and glasses. Here we introduce the INTERFACE force field (IFF) and surface models for α-Al2O3, α-Cr2O3, α-Fe2O3, NiO, CaO, MgO, β-Ca(OH)2, β-Mg(OH)2, and β-Ni(OH)2. The force field parameters are nonbonded, including atomic charges for Coulomb interactions, Lennard-Jones (LJ) potentials for van der Waals interactions with 12-6 and 9-6 options, and harmonic bond stretching for hydroxide ions. The models outperform DFT calculations and earlier atomistic models (Pedone, ReaxFF, UFF, CLAYFF) up to 2 orders of magnitude in reliability, compatibility, and interpretability due to a quantitative representation of chemical bonding consistent with other compounds across the periodic table and curated experimental data for validation. The IFF models exhibit average deviations of 0.2% in lattice parameters, <10% in surface energies (to the extent known), and 6% in bulk moduli relative to experiments. The parameters and models can be used with existing parameters for solvents, inorganic compounds, organic compounds, biomolecules, and polymers in IFF, CHARMM, CVFF, AMBER, OPLS-AA, PCFF, and COMPASS, to simulate bulk oxides, hydroxides, electrolyte interfaces, and multiphase, biological, and organic hybrid materials at length scales from atoms to micrometers. The nonbonded character of the models also enables the analysis of mixed oxides, glasses, and certain chemical reactions, and well-performing nonbonded models for silica phases, SiO2, are introduced. Automated model building is available in the CHARMM-GUI Nanomaterial Modeler. We illustrate applications of the models to predict the structure of mixed oxides, and energy barriers of ion migration, as well as binding energies of water and organic molecules in outstanding agreement with experimental data and calculations at the CCSD(T) level. Examples of model building for hydrated, pH-sensitive oxide surfaces to simulate solid-electrolyte interfaces are discussed. read less NOT USED (low confidence) J. D. Olarte-Plata, J. Gabriel, P. Albella, and F. Bresme, “Spatial Control of Heat Flow at the Nanoscale Using Janus Particles.,” ACS nano. 2021. link Times cited: 3 Abstract: Janus nanoparticles (JNPs) feature heterogeneous composition… read moreAbstract: Janus nanoparticles (JNPs) feature heterogeneous compositions, bringing opportunities in technological and medical applications. We introduce a theoretical approach based on nonequilibrium molecular dynamics simulations and heat transfer continuum theory to investigate the temperature fields generated around heated spherical JNPs covering a wide range of particle sizes, from a few nm to 100 nm. We assess the performance of these nanoparticles to generate anisotropic heating at the nanoscale. We demonstrate that the contrasting interfacial thermal conductances of the fluid-material interfaces arising from the heterogeneous composition of the JNPs can be exploited to control the thermal fields around the nanoparticle, leading to a temperature difference between both sides of the nanoparticle (temperature contrast) that is significant for particles comprising regions with disparate hydrophilicity. We illustrate this idea using coarse-grained and atomistic models of gold nanoparticles with hydrophobic and hydrophilic coatings, in water. Furthermore, we introduce a continuum model to predict the temperature contrast as a function of the interfacial thermal conductance and nanoparticle size. We further show that, unlike homogeneous nanoparticles, the interfacial fluid temperature depends on the interfacial thermal conductance of Janus nanoparticles. read less NOT USED (low confidence) S. Wang, K. Hou, and H. Heinz, “Accurate and Compatible Force Fields for Molecular Oxygen, Nitrogen, and Hydrogen to Simulate Gases, Electrolytes, and Heterogeneous Interfaces.,” Journal of chemical theory and computation. 2021. link Times cited: 26 Abstract: Gas molecules and interfaces with liquids and solids play a … read moreAbstract: Gas molecules and interfaces with liquids and solids play a critical role in living organisms, sorption, catalysis, and the environment. Monitoring adsorption and heterogeneous interfaces remains difficult in experiments, and earlier models for molecular simulations lead to errors over 100% in fundamental molecular properties. We introduce conceptually new force field parameters for molecular oxygen, nitrogen, and hydrogen that reduce deviations to <5%. We employ a combination of a harmonic bond stretching potential and Lennard-Jones parameters with 12-6 and 9-6 options, leading to computed bond lengths, Raman peaks, liquid densities, vaporization enthalpies, and free energies of hydration in impressive agreement with experiments. Reliable free energies of hydration were obtained upon validation of density and vaporization energy without significant further parameter adjustments. We illustrate applications to O2 adsorption on Pt electrocatalysts and N2 adsorption in zeolites, showing <5% deviation in adsorption energies measured in experiments without additional fitting parameters. We discuss the chemical interpretation of all parameters and explain the reasons for discrepancies in earlier models. Compatibility with the Interface Force Field (IFF), CHARMM, AMBER, OPLS-AA, GROMOS, DREIDING, CVFF, PCFF, COMPASS, and QM/MM methods enables reliable simulations of gases and liquid/solid interfaces with biopolymers, minerals, and metals. The parametrization protocol can be applied to similar molecules. read less NOT USED (low confidence) J. Rey, S. Blanck, P. Clabaut, S. Loehlé, S. Steinmann, and C. Michel, “Transferable Gaussian Attractive Potentials for Organic/Oxide Interfaces.,” The journal of physical chemistry. B. 2021. link Times cited: 7 Abstract: Organic/oxide interfaces play an important role in many area… read moreAbstract: Organic/oxide interfaces play an important role in many areas of chemistry and in particular for lubrication and corrosion. Molecular dynamics simulations are the method of choice for providing complementary insight to experiments. However, the force fields used to simulate the interaction between molecules and oxide surfaces tend to capture only weak physisorption interactions, discarding the stabilizing Lewis acid/base interactions. We here propose a simple complement to the straightforward molecular mechanics description based on "out-of-the-box" Lennard-Jones potentials and electrostatic interactions: the addition of an attractive Gaussian potential between reactive sites of the surface and heteroatoms of adsorbed organic molecules, leading to the Gaussian Lennard-Jones (GLJ) potential. The interactions of four oxygenated and four amine molecules with the typical and widespread hematite and γ-alumina surfaces are investigated. The root mean square deviation (RMSD) for all probed molecules is only 5.7 kcal/mol, which corresponds to an error of 23% over hematite. On γ-alumina, the RMSD is 11.2 kcal/mol using a single parameter for all five chemically inequivalent surface aluminum atoms. Applying GLJ to the simulation of organic films on oxide surfaces demonstrates that the mobility of the surfactants is overestimated by the simplistic LJ potential, while GLJ and other qualitatively correct potentials show a strong structuration and slow dynamics of the surface films, as could be expected from the first-principles adsorption energies for model head groups. read less NOT USED (low confidence) C. Zhang et al., “Low-Temperature Charging Dynamics of the Ionic Liquid and Its Gating Effect on FeSe0.5Te0.5 Superconducting Films.,” ACS applied materials & interfaces. 2019. link Times cited: 10 Abstract: Ionic liquids (ILs) have been investigated extensively becau… read moreAbstract: Ionic liquids (ILs) have been investigated extensively because of their unique ability to form the electric double layer (EDL), which induces high electrical field. For certain materials, low-temperature IL charging is needed to limit the electrochemical etching. Here, we report our investigation of the low-temperature charging dynamics in two widely used ILs-DEME-TF2N and C4mim-TF2N. Results show that the formation of the EDL at ∼220 K requires several hours relative to milliseconds at room temperature, and an equivalent voltage Ve is introduced as a measure of the EDL formation during the biasing process. The experimental observation is supported by molecular dynamics simulation, which shows that the dynamics are logically a function of gate voltage, time, and temperature. To demonstrate the importance of understanding the charging dynamics, a 140 nm thick FeSe0.5Te0.5 film was biased using the DEME IL, showing a tunable Tc between 18 and 35 K. Notably, this is the first observation of the tunability of the Tc in thick film FeSe0.5Te0.5 superconductors. read less NOT USED (low confidence) B. Briggs et al., “Toward a modular multi-material nanoparticle synthesis and assembly strategy via bionanocombinatorics: bifunctional peptides for linking Au and Ag nanomaterials.,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 8 Abstract: Materials-binding peptides represent a unique avenue towards… read moreAbstract: Materials-binding peptides represent a unique avenue towards controlling the shape and size of nanoparticles (NPs) grown under aqueous conditions. Here, employing a bionanocombinatorics approach, two such materials-binding peptides were linked at either end of a photoswitchable spacer, forming a multi-domain materials-binding molecule to control the in situ synthesis and organization of Ag and Au NPs under ambient conditions. These multi-domain molecules retained the peptides' ability to nucleate, grow, and stabilize Ag and Au NPs in aqueous media. Disordered co-assemblies of the two nanomaterials were observed by TEM imaging of dried samples after sequential growth of the two metals, and showed a clustering behavior that was not typically observed without both metals and the linker molecules. While TEM evidence suggested the formation of AuNP/AgNP assemblies upon drying, SAXS analysis indicated that no extended assemblies existed in solution, suggesting that sample drying plays an important role in facilitating NP clustering. Molecular simulations and experimental data revealed tunable materials-binding based upon the isomerization state of the photoswitchable unit and metal employed. This work is a first step in generating externally actuated biomolecules with specific material-binding properties that could be used as the building blocks to achieve multi-material switchable NP assemblies. read less NOT USED (low confidence) H. Heinz and H. Ramezani-Dakhel, “Simulations of inorganic-bioorganic interfaces to discover new materials: insights, comparisons to experiment, challenges, and opportunities.,” Chemical Society reviews. 2016. link Times cited: 139 Abstract: Natural and man-made materials often rely on functional inte… read moreAbstract: Natural and man-made materials often rely on functional interfaces between inorganic and organic compounds. Examples include skeletal tissues and biominerals, drug delivery systems, catalysts, sensors, separation media, energy conversion devices, and polymer nanocomposites. Current laboratory techniques are limited to monitor and manipulate assembly on the 1 to 100 nm scale, time-consuming, and costly. Computational methods have become increasingly reliable to understand materials assembly and performance. This review explores the merit of simulations in comparison to experiment at the 1 to 100 nm scale, including connections to smaller length scales of quantum mechanics and larger length scales of coarse-grain models. First, current simulation methods, advances in the understanding of chemical bonding, in the development of force fields, and in the development of chemically realistic models are described. Then, the recognition mechanisms of biomolecules on nanostructured metals, semimetals, oxides, phosphates, carbonates, sulfides, and other inorganic materials are explained, including extensive comparisons between modeling and laboratory measurements. Depending on the substrate, the role of soft epitaxial binding mechanisms, ion pairing, hydrogen bonds, hydrophobic interactions, and conformation effects is described. Applications of the knowledge from simulation to predict binding of ligands and drug molecules to the inorganic surfaces, crystal growth and shape development, catalyst performance, as well as electrical properties at interfaces are examined. The quality of estimates from molecular dynamics and Monte Carlo simulations is validated in comparison to measurements and design rules described where available. The review further describes applications of simulation methods to polymer composite materials, surface modification of nanofillers, and interfacial interactions in building materials. The complexity of functional multiphase materials creates opportunities to further develop accurate force fields, including reactive force fields, and chemically realistic surface models, to enable materials discovery at a million times lower computational cost compared to quantum mechanical methods. The impact of modeling and simulation could further be increased by the advancement of a uniform simulation platform for organic and inorganic compounds across the periodic table and new simulation methods to evaluate system performance in silico. read less NOT USED (low confidence) R. Cortes-Huerto, J. Goniakowski, and C. Noguera, “An efficient many-body potential for the interaction of transition and noble metal nano-objects with an environment.,” The Journal of chemical physics. 2013. link Times cited: 13 Abstract: We present a mean-field model for the description of transit… read moreAbstract: We present a mean-field model for the description of transition or noble metal nano-objects interacting with an environment. It includes a potential given by the second-moment approximation to the tight-binding Hamiltonian for metal-metal interactions, and an additional many-body potential that depends on the local atomic coordination for the metal-environment interaction. The model does not refer to a specific type of chemical conditions, but rather provides trends as a function of a limited number of parameters. The capabilities of the model are highlighted by studying the relative stability of semi-infinite gold surfaces of various orientations and formation energies of a restricted set of single-faceted gold nanoparticles. It is shown that, with only two parameters and in a very efficient way, it is able to generate a great variety of stable structures and shapes, as the nature of the environment varies. It is thus expected to account for formation energies of nano-objects of various dimensionalities (surfaces, thin films, nano-rods, nano-wires, nanoparticles, nanoribbons, etc.) according to the environment. read less NOT USED (low confidence) C. Kramer, P. Gedeck, and M. Meuwly, “Multipole-Based Force Fields from ab Initio Interaction Energies and the Need for Jointly Refitting All Intermolecular Parameters.,” Journal of chemical theory and computation. 2013. link Times cited: 38 Abstract: Distributed atomic multipole (MTP) moments promise significa… read moreAbstract: Distributed atomic multipole (MTP) moments promise significant improvements over point charges (PCs) in molecular force fields, as they (a) more realistically reproduce the ab initio electrostatic potential (ESP) and (b) allow to capture anisotropic atomic properties such as lone pairs, conjugated systems, and σ holes. The present work focuses on the question of whether multipolar electrostatics instead of PCs in standard force fields leads to quantitative improvements over point charges in reproducing intermolecular interactions. To this end, the interaction energies of two model systems, benzonitrile (BZN) and formamide (FAM) homodimers, are characterized over a wide range of dimer conformations. It is found that although with MTPs the monomer ab initio ESP can be captured better by about an order of magnitude compared to point charges (PCs), this does not directly translate into better describing ab initio interaction energies compared to PCs. Neither ESP-fitted MTPs nor refitted Lennard-Jones (LJ) parameters alone demonstrate a clear superiority of atomic MTPs. We show that only if both electrostatic and LJ parameters are jointly optimized in standard, nonpolarizable force fields, atomic are MTPs clearly beneficial for reproducing ab initio dimerization energies. After an exhaustive exponent scan, we find that for both BZN and FAM, atomic MTPs and a 9-6 LJ potential can reproduce ab initio interaction energies with ∼30% (RMSD 0.13 vs 0.18 kcal/mol) less error than point charges (PCs) and a 12-6 LJ potential. We also find that the improvement due to using MTPs with a 9-6 LJ potential is considerably more pronounced than with a 12-6 LJ potential (≈ 10%; RMSD 0.19 versus 0.21 kcal/mol). read less NOT USED (high confidence) Y. Li et al., “Molecular dynamics simulation of the transformation of Fe-Co alloy by machine learning force field based on atomic cluster expansion,” Chemical Physics Letters. 2023. link Times cited: 0 NOT USED (high confidence) V. Tiwari, S. Garg, and T. Karmakar, “Insights into the Interactions of Peptides with Monolayer-Protected Metal Nanoclusters,” bioRxiv. 2022. link Times cited: 3 Abstract: Monolayer-protected atomically precise metal nanoclusters (M… read moreAbstract: Monolayer-protected atomically precise metal nanoclusters (MPC) are an important class of molecules that have potential applications in catalysis, imaging, and drug delivery. Recent studies have shown that peptide-based drugs can be complexed with MPCs to avoid enzymatic degradation and get delivered to targeted cells. Although the MPCs potential role in imaging and drug delivery processes have been studied, for their impactful use, specific molecular interactions between MPCs and biomolecules, mainly proteins and peptides should be explored in detail. In this work, we have carried out atomistic molecular dynamics simulations to investigate the interactions between Au-based MPCs and an anticancer peptide, melittin. The MEL peptides get attached to the MPCs surface by the formation of multiple hydrogen bonds between the peptide amino acid residues with MPCs ligands. Additionally, the positively charged residues such as Lys and Arg, the Trp, and the N-terminal of the peptide anchor strongly to the MPC core playing a crucial role in the peptide’s overall stabilization on the MPC surface. read less NOT USED (high confidence) B. Feng, J. Liu, Y. Zeng, and L. Fan, “Atomistic Insights into the Heat Conductance Across the Interfaces between Erythritol and Different Metals: A Non-Equilibrium Molecular Dynamics Study,” SSRN Electronic Journal. 2022. link Times cited: 0 NOT USED (high confidence) M. Bakhtiari, S. Seifi, M. Tohidloo, and A. Shamloo, “Investigation of the motion of fullerene-wheeled nano-machines on thermally activated curved gold substrates,” Scientific Reports. 2022. link Times cited: 3 NOT USED (high confidence) A. Takamatsu, M. Higashi, and H. Sato, “Free Energy and Solvation Structure Analysis for Adsorption of Aromatic Molecules at Pt(111)/Water Interface by 3D-RISM Theory,” Chemistry Letters. 2022. link Times cited: 1 NOT USED (high confidence) G. Jeanmairet, B. Rotenberg, and M. Salanne, “Microscopic Simulations of Electrochemical Double-Layer Capacitors,” Chemical Reviews. 2022. link Times cited: 54 Abstract: Electrochemical double-layer capacitors (EDLCs) are devices … read moreAbstract: Electrochemical double-layer capacitors (EDLCs) are devices allowing the storage or production of electricity. They function through the adsorption of ions from an electrolyte on high-surface-area electrodes and are characterized by short charging/discharging times and long cycle-life compared to batteries. Microscopic simulations are now widely used to characterize the structural, dynamical, and adsorption properties of these devices, complementing electrochemical experiments and in situ spectroscopic analyses. In this review, we discuss the main families of simulation methods that have been developed and their application to the main family of EDLCs, which include nanoporous carbon electrodes. We focus on the adsorption of organic ions for electricity storage applications as well as aqueous systems in the context of blue energy harvesting and desalination. We finally provide perspectives for further improvement of the predictive power of simulations, in particular for future devices with complex electrode compositions. read less NOT USED (high confidence) N. R. Kern, J. Lee, Y. Choi, and W. Im, “CHARMM-GUI Multicomponent Assembler for Modeling and Simulation of Complex Multicomponent Systems,” bioRxiv. 2022. link Times cited: 1 Abstract: Atomic-scale molecular modeling and simulation are powerful … read moreAbstract: Atomic-scale molecular modeling and simulation are powerful tools for computational biology. However, constructing models with large, densely packed molecules, non-water solvents, or with combinations of multiple biomembranes, polymers, and nanomaterials remains challenging and requires significant time and expertise. Furthermore, existing tools do not support such assemblies under the periodic boundary conditions (PBC) necessary for molecular simulation. Here, we describe Multicomponent Assembler in CHARMM-GUI that automates complex molecular assembly and simulation input preparation under the PBC. We demonstrate its versatility by preparing 6 challenging systems with varying density of large components: (1) solvated proteins, (2) solvated proteins with a pre-equilibrated membrane, (3) solvated proteins with a sheet-like nanomaterial, (4) solvated proteins with a sheet-like polymer, (5) a mixed membrane-nanomaterial system, and (6) a sheet-like polymer with gaseous solvent. Multicomponent Assembler is expected to be a unique cyberinfrastructure to facilitate innovative studies of complex interactions between small (organic and inorganic) molecules, biomacromolecules, polymers, and nanomaterials. read less NOT USED (high confidence) V. Reshetnyak, O. Reshetnyak, A. Aborkin, and A. Filippov, “Interatomic Interaction at the Aluminum–Fullerene C60 Interface,” Journal of Experimental and Theoretical Physics. 2022. link Times cited: 1 NOT USED (high confidence) R. Rabani, S. Merabia, and A. Pishevar, “Conductive Heat Transfer Through Nanoconfined Gas: From Continuum to Free-Molecular Regime,” SSRN Electronic Journal. 2021. link Times cited: 0 Abstract: : In the past few decades, great efforts have been devoted t… read moreAbstract: : In the past few decades, great efforts have been devoted to studying heat transfer on the nanoscale due to its importance in multiple technologies such as thermal control and sensing applications. Heat conduction through the nanoconfined gas medium differs from macroscopic predictions due to several reasons. The continuum assumption is broken down; the surface forces which extend deeper through the gas medium become prominent due to the large surface-to-volume ratio, and, finally, the gas molecules are accumulated nonuniformly on the solid surfaces. In this work, to better understand the combination of these phenomena on the heat conduction through the nanoconfined gas medium, we present a series of molecular dynamics simulations of argon gas confined between either metals or silicon walls. The gas density is set so that gas experiences a wide range of Knudsen numbers from continuum to the free molecular regime. It is observed that the intrinsic characteristics of the solid determine the gas density distribution near the walls and consequently in the bulk region, and these distributions control the heat conduction through the gas medium. While the nanochannel walls have their most significant impact on the density and temperature distributions of the rarefied gas, the pressure and the heat flux across the gas domain converge toward a plateau as the gas becomes denser. We propose new analytical formulas for calculating the gas pressure, induced heat flux, and effective thermal conductivity through the strongly nanoconfined gas, which incorporates the wall force field impacts on the gas transport characteristics for the Knudsen number in the range of 0.05 to 20. continuum to rarefied gas conditions. read less NOT USED (high confidence) M. Khenner and L. Hebenstiel, “A mesoscopic model of nanoclusters self-assembly on a graphene Moiré,” Journal of Applied Physics. 2021. link Times cited: 2 Abstract: A continuum, post-deposition mesoscopic model of a Moiré-reg… read moreAbstract: A continuum, post-deposition mesoscopic model of a Moiré-regulated self-assembly of metal nanoclusters on a twisted bilayer graphene is presented. Quasi-two-dimensional nanocluster-like steady states at a low adsorbate coverage are analytically determined for Pt, Ni, and Pb adsorbates, pointing that nanoclusters self-assemble at the Moiré cells centers. This is followed by the computations of nanoclusters self-assembly dynamics. Differences in the self-assembly efficiency for three chosen metals are highlighted across three typical values of an initial submonolayer coverage and for three temperature regimes. Accounting for the adsorption potential of metal atoms onto graphene leads to a significantly faster nanoclusters self-assembly and has a transient impact on the nanoclusters morphologies. A model extensions to the cases of nanoclusters self-assembly on a Moiré formed by a monolayer graphene over a metal substrate, and the electromigration-guided self-assembly on such Moiré are proposed. read less NOT USED (high confidence) T. Bian et al., “Electrostatic co-assembly of nanoparticles with oppositely charged small molecules into static and dynamic superstructures,” Nature chemistry. 2021. link Times cited: 79 NOT USED (high confidence) S. Wang, E. Zhu, Y. Huang, and H. Heinz, “Direct correlation of oxygen adsorption on platinum-electrolyte interfaces with the activity in the oxygen reduction reaction,” Science Advances. 2021. link Times cited: 31 Abstract: The adsorption of oxygen molecules to Pt nanostructures in s… read moreAbstract: The adsorption of oxygen molecules to Pt nanostructures in solution is shown to predict the relative ORR activity in fuel cells. The oxygen reduction reaction (ORR) on platinum catalysts is essential in fuel cells. Quantitative predictions of the relative ORR activity in experiments, in the range of 1 to 50 times, have remained challenging because of incomplete mechanistic understanding and lack of computational tools to account for the associated small differences in activation energies (<2.3 kilocalories per mole). Using highly accurate molecular dynamics (MD) simulation with the Interface force field (0.1 kilocalories per mole), we elucidated the mechanism of adsorption of molecular oxygen on regular and irregular platinum surfaces and nanostructures, followed by local density functional theory (DFT) calculations. The relative ORR activity is determined by oxygen access to platinum surfaces, which greatly depends on specific water adlayers, while electron transfer occurs at a similar slow rate. The MD methods facilitate quantitative predictions of relative ORR activities of any platinum nanostructures, are applicable to other catalysts, and enable effective MD/DFT approaches. read less NOT USED (high confidence) K. Kanhaiya, S. Kim, W.-G. Im, and H. Heinz, “Accurate simulation of surfaces and interfaces of ten FCC metals and steel using Lennard–Jones potentials,” npj Computational Materials. 2021. link Times cited: 32 NOT USED (high confidence) J. Kim, B. Savoie, and T. F. Miller, “Interfacial Electron Transfer and Ion Solvation in the Solid Electrolyte Interphase,” The Journal of Physical Chemistry C. 2020. link Times cited: 3 Abstract: As a chemically and structurally well-defined model for redo… read moreAbstract: As a chemically and structurally well-defined model for redox processes in the solid electrolyte interphase of battery electrodes, we investigate electron transfer to lithium ions at the interface between a platinum metal anode and a solid polymer electrolyte. Studied electrolytes include LiTFSI (lithium bis(trifluoromethane)sulfonimide) salts in polyethylene oxide and poly(diethylene oxide-alt-oxymethylene), as well as in the as- sociated liquid electrolytes 1,2-dimethoxyethane and tetraglyme. read less NOT USED (high confidence) C. Trapalis, E. Lidorikis, and D. Papageorgiou, “Structural and energetic properties of P3HT and PCBM layers on the Ag(1 1 1) surface,” Computational and Theoretical Chemistry. 2020. link Times cited: 1 NOT USED (high confidence) A. Khelfa et al., “Selective shortening of gold nanorods: when surface functionalization dictates the reactivity of nanostructures.,” Nanoscale. 2020. link Times cited: 8 Abstract: The selective shortening of gold nanorods (NRs) is a directi… read moreAbstract: The selective shortening of gold nanorods (NRs) is a directional etching process that has been intensively studied by UV-Vis spectroscopy because of its direct impact on the optical response of these plasmonic nanostructures. Here, liquid-cell transmission electron microscopy is exploited to visualize this peculiar corrosion process at the nanoscale and study the impacts of reaction kinetics on the etching mechanisms. In situ imaging reveals that anisotropic etching requires a chemical environment with a low etching power to make the tips of NRs the only reaction site for the oxidation process. Then, aberration-corrected TEM and atomistic simulations were combined to demonstrate that the disparity between the reactivity of the body and the ends of NRs does not derive from their crystal structure but results from an inhomogeneous surface functionalization. In a general manner, this work highlights the necessity to consider the organic/inorganic natures of nanostructures to understand their chemical reactivity. read less NOT USED (high confidence) F. Font, W. Micou, and F. Bresme, “Non-equilibrium molecular dynamics and continuum modelling of transient freezing of atomistic solids,” International Journal of Heat and Mass Transfer. 2020. link Times cited: 2 NOT USED (high confidence) L. Scalfi, M. Salanne, and B. Rotenberg, “Molecular Simulation of Electrode-Solution Interfaces.,” Annual review of physical chemistry. 2020. link Times cited: 40 Abstract: Many key industrial processes, from electricity production, … read moreAbstract: Many key industrial processes, from electricity production, conversion, and storage to electrocatalysis or electrochemistry in general, rely on physical mechanisms occurring at the interface between a metallic electrode and an electrolyte solution, summarized by the concept of an electric double layer, with the accumulation/depletion of electrons on the metal side and of ions on the liquid side. While electrostatic interactions play an essential role in the structure, thermodynamics, dynamics, and reactivity of electrode-electrolyte interfaces, these properties also crucially depend on the nature of the ions and solvent, as well as that of the metal itself. Such interfaces pose many challenges for modeling because they are a place where quantum chemistry meets statistical physics. In the present review, we explore the recent advances in the description and understanding of electrode-electrolyte interfaces with classical molecular simulations, with a focus on planar interfaces and solvent-based liquids, from pure solvent to water-in-salt-electrolytes. Expected final online publication date for the Annual Review of Physical Chemistry, Volume 72 is April 2021. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates. read less NOT USED (high confidence) J. Liu, J. Zeng, C. Zhu, J. Miao, Y. Huang, and H. Heinz, “Interpretable molecular models for molybdenum disulfide and insight into selective peptide recognition†,” Chemical Science. 2020. link Times cited: 13 Abstract: Molybdenum disulfide (MoS2) is a layered material with outst… read moreAbstract: Molybdenum disulfide (MoS2) is a layered material with outstanding electrical and optical properties. Numerous studies evaluate the performance in sensors, catalysts, batteries, and composites that can benefit from guidance by simulations in all-atom resolution. However, molecular simulations remain difficult due to lack of reliable models. We introduce an interpretable force field for MoS2 with record performance that reproduces structural, interfacial, and mechanical properties in 0.1% to 5% agreement with experiments. The model overcomes structural instability, deviations in interfacial and mechanical properties by several 100%, and empirical fitting protocols in earlier models. It is compatible with several force fields for molecular dynamics simulation, including the interface force field (IFF), CVFF, DREIDING, PCFF, COMPASS, CHARMM, AMBER, and OPLS-AA. The parameters capture polar covalent bonding, X-ray structure, cleavage energy, infrared spectra, bending stability, bulk modulus, Young's modulus, and contact angles with polar and nonpolar solvents. We utilized the models to uncover the binding mechanism of peptides to the MoS2 basal plane. The binding strength of several 7mer and 8mer peptides scales linearly with surface contact and replacement of surface-bound water molecules, and is tunable in a wide range from −86 to −6 kcal mol−1. The binding selectivity is multifactorial, including major contributions by van-der-Waals coordination and charge matching of certain side groups, orientation of hydrophilic side chains towards water, and conformation flexibility. We explain the relative attraction and role of the 20 amino acids using computational and experimental data. The force field can be used to screen and interpret the assembly of MoS2-based nanomaterials and electrolyte interfaces up to a billion atoms with high accuracy, including multiscale simulations from the quantum scale to the microscale. read less NOT USED (high confidence) N. Kruchinin and M. Kucherenko, “Conformational Rearrangements of Polyampholytic Polypeptides on Metal Nanoparticle Surface in Microwave Electric Field: Molecular-Dynamics Simulation,” Colloid Journal. 2020. link Times cited: 3 NOT USED (high confidence) G. González‐Rubio et al., “Micelle-directed chiral seeded growth on anisotropic gold nanocrystals,” Science. 2020. link Times cited: 143 Abstract: Groovy chiral gold particles Although plasmonic optical acti… read moreAbstract: Groovy chiral gold particles Although plasmonic optical activity can arise from chiral assemblies of gold and silver nanoparticles, there are few examples of gold nanoparticles with intrinsic chirality and high optical activity. González-Rubio et al. show that morphological chirality can be induced during the seeded growth of gold nanoparticles, particularly for highly anisotropic nanorods. Chiral additives as cosurfactants formed helical micelles that directed the seeded growth to create grooves that maintained a chiral morphology. The resulting particles displayed high-intensity circular dichroism with anisotropy factors near 0.2 at near-infrared wavelengths. Science, this issue p. 1472 Seeded growth with gold nanorods and chiral micelle cosurfactants created nanoparticles with high chiroplasmonic activity. Surfactant-assisted seeded growth of metal nanoparticles (NPs) can be engineered to produce anisotropic gold nanocrystals with high chiroptical activity through the templating effect of chiral micelles formed in the presence of dissymmetric cosurfactants. Mixed micelles adsorb on gold nanorods, forming quasihelical patterns that direct seeded growth into NPs with pronounced morphological and optical handedness. Sharp chiral wrinkles lead to chiral plasmon modes with high dissymmetry factors (~0.20). Through variation of the dimensions of chiral wrinkles, the chiroptical properties can be tuned within the visible and near-infrared electromagnetic spectrum. The micelle-directed mechanism allows extension to other systems, such as the seeded growth of chiral platinum shells on gold nanorods. This approach provides a reproducible, simple, and scalable method toward the fabrication of NPs with high chiral optical activity. read less NOT USED (high confidence) N. A. Azman, L. Bekale, T. X. Nguyen, and J. Kah, “Polyelectrolyte stiffness on gold nanorods mediates cell membrane damage.,” Nanoscale. 2020. link Times cited: 9 Abstract: Charge and surface chemistry of gold nanorods (AuNRs) are of… read moreAbstract: Charge and surface chemistry of gold nanorods (AuNRs) are often considered the predictive factors for cell membrane damage. Unfortunately, extensive research on AuNR passivated with polyelectrolyte (PE) ligand shell (AuNR-PE) has hitherto left a vital knowledge gap between the mechanical stability of the ligand shell and the cytotoxicity of AuNR-PEs. Here, the agreement between unbiased coarse-grained molecular dynamics (CGMD) simulation and empirical outcomes on hemolysis of red blood cells by AuNR-PEs demonstrates for the first time, a direct impact of the mechanical stability of the PE shell passivating the AuNRs on the lipid membrane rupture. Such mechanical stability is ultimately modulated by the rigidity of the PE components. The CGMD simulation results also reveal the mechanism where the PE chain adsorbs near the surface of the lipid bilayer without penetrating the hydrophobic core of the bilayer, which allows the hydrophobic AuNR core to be in direct contact with the hydrophobic interior of the lipid bilayer, thereby perforating the lipid membrane to induce membrane damage. read less NOT USED (high confidence) G. Jayabalaji, L. Ramya, and J. M. Devi, “Investigation on the structural, thermal and hydration properties of gold-fullerene nanocomposite,” Journal of Chemical Sciences. 2020. link Times cited: 1 NOT USED (high confidence) A. Nicholas et al., “Understanding the vapochromic response of mixed copper(i) iodide/silver(i) Iodide nanoparticles toward dimethyl sulfide.,” Physical chemistry chemical physics : PCCP. 2020. link Times cited: 1 Abstract: We report on the vapochromic behavior of a series of homo- a… read moreAbstract: We report on the vapochromic behavior of a series of homo- and heterometallic copper(i) iodide/silver(i) iodide nanoparticles when exposed to dimethyl sulfide (DMS) vapor. These systems show remarkable colorimetric sensing behavior via emission color upon DMS exposure, shifting from pink to green emission. Kinetics measurements of CuI/AgI nanoparticle reactions with DMS show a significant rate increase with increasing Ag(i) content. However, luminescence spectroscopy and X-ray diffraction of the post-exposure samples with varying Ag(i) content reveal that the luminophore is identical in all cases and contains no Ag(i) ions. To rationalize the experimental observations and determine the vapochromic response mechanism, molecular dynamic calculations were performed on model (111) cation-terminated surfaces of copper iodide crystals doped with variable amounts of silver. Computational studies indicate that heterometallic Cu/Ag systems have a stronger binding affinity towards DMS vapor molecules than homometallic CuI and that embedding of the DMS molecules into the surface is the primary intermediate by which the vapochromic response occurs. read less NOT USED (high confidence) P. Clabaut, R. Staub, J. Galiana, É. Antonetti, and S. Steinmann, “Water adlayers on noble metal surfaces: Insights from energy decomposition analysis.,” The Journal of chemical physics. 2020. link Times cited: 9 Abstract: Water molecules adsorbed on noble metal surfaces are of fund… read moreAbstract: Water molecules adsorbed on noble metal surfaces are of fundamental interest in surface science, in heterogeneous catalysis, and as a model for the metal/water interface. Herein, we analyze 28 water structures adsorbed on five noble metal surfaces (Cu, Ag, Au, Pd, and Pt) via density functional theory and energy decomposition analysis based on the block localized wave function technique. Structures, ranging from monomers to ice adlayers, reveal that the charge transfer from water to the surface is nearly independent from the charge transfer between the water molecules, while the polarization energies are cooperative. Dense water-water networks with small surface dipoles, such as the 39×39 unit cell [experimentally observed on Pt(111)], are favored compared to the highly ordered and popular Hup and Hdown phases. The second main result of our study is that the many-body interactions, which stabilize the water assemblies on the metal surfaces, are dominated by the polarization energies, with the charge transfer scaling with the polarization energies. Hence, if an empirical model could be found that reproduces the polarization energies, the charge transfer could be predicted as well, opening exciting perspectives for force field development. read less NOT USED (high confidence) M. Semenov, V. Kraposhin, A. Talis, and N. D. Simich-Lafitskii, “Transfer of Diagonals in a Rhombus: Elementary Act of Polymorphic Transformation. Analysis of the Energy Threshold of Transformation in Metals,” Metal Science and Heat Treatment. 2020. link Times cited: 6 NOT USED (high confidence) L. Su, J. Krim, and D. Brenner, “Dynamics of Neutral and Charged Nanodiamonds in Aqueous Media Confined between Gold Surfaces under Normal and Shear Loading,” ACS Omega. 2020. link Times cited: 3 Abstract: The dynamics of cubo-octahedral nanodiamonds (NDs) with thre… read moreAbstract: The dynamics of cubo-octahedral nanodiamonds (NDs) with three different surface treatments and confined in aqueous environments between gold surfaces under shear and normal loading conditions have been characterized via molecular dynamics (MD) simulations. The treatments consisted of carboxyl (−COO–) or amino (−NH3+) groups attached to the NDs, producing either negatively or positively charged NDs, respectively, and hydrogen-terminated surfaces producing neutral NDs. Simulations were performed in the presence and absence of induced image charges to explore the impact of electrostatic interactions on friction and surface deformation. Significant deformation of the gold surfaces was observed for negatively charged NDs placed between gold surfaces under external loads that were sufficient to displace water from the contact. Rolling and relatively high friction levels were also observed for the negatively charged NDs under the same conditions. In contrast, the neutral and positively charged NDs exhibited sliding behavior with only minor deformation of the gold surfaces. The results suggest that the size of the surface functional group plays a major role in determining whether NDs slide or roll on solid contacts. Higher friction levels were also observed in conjunction with induced image charges in the gold contacts. The results demonstrate how surface functionalization and surface-induced charges can work in combination to profoundly influence tribological performance. read less NOT USED (high confidence) S. Franco-Ulloa et al., “Dispersion state phase diagram of citrate-coated metallic nanoparticles in saline solutions,” Nature Communications. 2020. link Times cited: 30 NOT USED (high confidence) J.-L. Liu and B. Eisenberg, “Molecular Mean-Field Theory of Ionic Solutions: A Poisson-Nernst-Planck-Bikerman Model,” Entropy. 2020. link Times cited: 43 Abstract: We have developed a molecular mean-field theory—fourth-order… read moreAbstract: We have developed a molecular mean-field theory—fourth-order Poisson–Nernst–Planck–Bikerman theory—for modeling ionic and water flows in biological ion channels by treating ions and water molecules of any volume and shape with interstitial voids, polarization of water, and ion-ion and ion-water correlations. The theory can also be used to study thermodynamic and electrokinetic properties of electrolyte solutions in batteries, fuel cells, nanopores, porous media including cement, geothermal brines, the oceanic system, etc. The theory can compute electric and steric energies from all atoms in a protein and all ions and water molecules in a channel pore while keeping electrolyte solutions in the extra- and intracellular baths as a continuum dielectric medium with complex properties that mimic experimental data. The theory has been verified with experiments and molecular dynamics data from the gramicidin A channel, L-type calcium channel, potassium channel, and sodium/calcium exchanger with real structures from the Protein Data Bank. It was also verified with the experimental or Monte Carlo data of electric double-layer differential capacitance and ion activities in aqueous electrolyte solutions. We give an in-depth review of the literature about the most novel properties of the theory, namely Fermi distributions of water and ions as classical particles with excluded volumes and dynamic correlations that depend on salt concentration, composition, temperature, pressure, far-field boundary conditions etc. in a complex and complicated way as reported in a wide range of experiments. The dynamic correlations are self-consistent output functions from a fourth-order differential operator that describes ion-ion and ion-water correlations, the dielectric response (permittivity) of ionic solutions, and the polarization of water molecules with a single correlation length parameter. read less NOT USED (high confidence) E. N. Skountzos, F. Wrochem, and V. Mavrantzas, “Structure and Conformation of a Crystalline P3HT Film Adsorbed on an Alkanethiol Self‐Assembled Monolayer Deposited on Gold,” Macromolecular Theory and Simulations. 2020. link Times cited: 6 NOT USED (high confidence) F. Sohraby et al., “Application of Molecular Dynamics in Coating Ag-Conjugated Nanoparticles with Potential Therapeutic Applications,” Nano Biomedicine and Engineering. 2020. link Times cited: 10 Abstract: Drug delivery systems may benefit from nanoparticles synthes… read moreAbstract: Drug delivery systems may benefit from nanoparticles synthesized using biological methods. While chemical reduction of particles is facilitated by some active compounds present in the bio-extract, other active compounds, with potential therapeutic activities, may be adsorbed onto the surface of nanoparticles. However, the mechanism of bio-based nanoparticle synthesis is still under debate. Here, we first employed a molecular dynamics (MD) approach to theoretically predict the coating of a hypothetical 4.5 nm silver nanoparticle with four selected rosemary (Rosmarinus Officinalis L.) active compounds (rosmanol, isorosmanol, carnosol, and carnosic acid). Analysis of density maps and radial distribution functions (RDF) values suggested that the examined compounds had strong hydrophobic properties and could instantaneously be adsorbed to the nanoparticle surfaces. Next, we experimentally examined the capacity of rosemary leaf extract to synthesize and coat Ag-conjugated nanoparticles. The data obtained from ultraviolet–visible spectroscopy, transmission electron microscopy, Fourier-transform infrared spectroscopy and X-ray powder diffraction analyses confirmed the production of spherical Ag-conjugated nanoparticles with an average size of 12-15 nm, coated with proteins, secondary metabolites and other active compounds. Since this method can predict the dynamic behavior of therapeutic compounds when they are in contact with nanoparticles, we believe it provides a valid and new avenue to designing new therapeutic nanoparticles. read less NOT USED (high confidence) A. Fraile and T. Polcar, “Volume and pressure of helium bubbles inside liquid Pb16Li. A molecular dynamics study,” Nuclear Fusion. 2020. link Times cited: 4 Abstract: The behaviour of helium impurities inside metals has been we… read moreAbstract: The behaviour of helium impurities inside metals has been well studied in the last 30 years, however, little attention has been devoted to helium atoms inside liquid metals. Here we have investigated the nucleation and coalescence processes of helium atoms inside liquid eutectic lithium–lead alloys using atomistic simulations. Several key findings regarding He bubbles inside liquid PbLi eutectic are presented. The radius versus the number of atoms has been calculated in the temperature range 600–1000 K. The trend can be fitted and likely extrapolated to larger bubbles (micrometer size). The value of thermal expansion of He bubbles is given as well and compared to the thermal expansion of bulk He. The pressure inside He bubbles has been calculated as a function of bubble size. Finally, the importance of accurate interatomic potentials for the He–metal interaction is discussed. read less NOT USED (high confidence) P. Clabaut, P. Fleurat‐Lessard, C. Michel, and S. Steinmann, “Ten Facets, One Force Field: The GAL19 Force Field for Water - Noble Metal Interfaces.,” Journal of chemical theory and computation. 2020. link Times cited: 23 Abstract: Understanding the structure of the water/metal interfaces pl… read moreAbstract: Understanding the structure of the water/metal interfaces plays an important role in many areas ranging from surface chemistry to environmental processes. The size, required phase-space sampling and the slow diffusion of molecules at the water/metal interfaces motivate the development of accurate force-fields. We develop and parametrize GAL19, a novel force-field to describe the interaction of water with two facets (111 and 100) of five metals (Pt, Pd, Au, Ag, Cu). To increase transferability compared to its predecessor GAL17, the water-metal interaction is described as a sum of pair-wise terms. The interaction energy has three contributions: (i) physisorption is described via a Tang and Toennies potential, (ii) chemisorption and surface corrugation relies on an attractive Gaussian term and (iii) the angular dependence is explicitly included as a truncated Fourier series. 13 parameters are used for each metal surface and were fitted on 250 water adsorption energies computed at the PBE+dDsC level. The performance of GAL19 was evaluated on a set of more than 600 DFT adsorption energies for each surface, leading to an average root mean square deviation (RMSD) of only 1 kcal/mol, correctly reproducing the adsorption trends: strong on Pt and Pd but weaker on Ag, Au and Cu. This force-field was then used to simulate the water/metal interface for all ten surfaces for 1 ns. Structural analyses reveal similar tendencies for all surfaces: a first, dense water layer that is mostly adsorbed on the metal top sites, and a second layer up to around 6 Å, which is less structured. On Pt and Pd, the first layer is strongly organized with water lying flat on the surface. The pairwise additive functional form allows to simulate the water adsorption on alloys, which is demonstrated at the example of Ag/Cu and Au/Pt alloys. The water/Ag-Cu interface is predicted to be disordered with water mostly adsorbed on Cu which should exacerbate the Ag reactivity. On the contrary, incorporating Pt into Au materials leads to a structuring of the water interface. Our promising results make GAL19 an ideal candidate to get representative sampling of complex metal/water interfaces as a first step towards accurate estimation of free energies of reactions in solution at the metal interface. read less NOT USED (high confidence) X. Wang, C. Jameson, and S. Murad, “Interfacial Thermal Conductivity and Its Anisotropy,” Processes. 2019. link Times cited: 2 Abstract: There is a significant effort in miniaturizing nanodevices, … read moreAbstract: There is a significant effort in miniaturizing nanodevices, such as semi-conductors, currently underway. However, a major challenge that is a significant bottleneck is dissipating heat generated in these energy-intensive nanodevices. In addition to being a serious operational concern (high temperatures can interfere with their efficient operation), it is a serious safety concern, as has been documented in recent reports of explosions resulting from many such overheated devices. A significant barrier to heat dissipation is the interfacial films present in these nanodevices. These interfacial films generally are not an issue in macro-devices. The research presented in this paper was an attempt to understand these interfacial resistances at the molecular level, and present possibilities for enhancing the heat dissipation rates in interfaces. We demonstrated that the thermal resistances of these interfaces were strongly anisotropic; i.e., the resistance parallel to the interface was significantly smaller than the resistance perpendicular to the interface. While the latter is well-known—usually referred to as Kapitza resistance—the anisotropy and the parallel component have previously been investigated only for solid-solid interfaces. We used molecular dynamics simulations to investigate the density profiles at the interface as a function of temperature and temperature gradient, to reveal the underlying physics of the anisotropy of thermal conductivity at solid-liquid, liquid-liquid, and solid-solid interfaces. read less NOT USED (high confidence) G. Fernandez, “Abstract,” Journal of the ICRU. 2019. link Times cited: 0 Abstract: Dosimetry methods for use in dose assessment for individuals… read moreAbstract: Dosimetry methods for use in dose assessment for individuals following acute exposure to radiation are described. Primary methods include biodosimetry and physical dosimetry techniques, while additional supplementary methods are bioassays, neutron activation, and radiation field mapping. Biodosimetry methods include the established techniques of dicentric chromosome assay, cytokinesis-block micronucleus assay, translocation analysis by fluorescent in-situ hybridization, premature chromosome condensation, and the γ-H2AX assay. Emerging techniques include RNA expression-based, protein-based, and metabolomic-based assays. Physical dosimetry methods include electron paramagnetic resonance and the luminescence-based techniques of thermoluminescence and optically stimulated luminescence. Electron paramagnetic resonance methods are used to assess absorbed dose in biologically derived materials, such as bone, teeth, and keratinous tissue, as well as non-biologically derived materials such as sugars, glasses, and polymeric materials used in fabrics and other personal items. Thermoluminescence and optically stimulated luminescence techniques are used to assess absorbed dose in the components of personal electronics, along with other items such as plastic cards, fabrics, and clothing. There have also been similar efforts for teeth and dental repair ceramics. Since the above-listed techniques cannot distinguish between exposure to internal and external sources, bioassays may be used to assess exposure from internal contamination, including thyroid counting, chest counting, and excretion analysis methods. When a neutron exposure is expected, neutron activation analysis in blood, hair, or other non-biological items is useful. Radiation field mapping can be a useful method for determining locations where doses to individuals may be expected to be high and may complement radiation transport calculations performed for that purpose. Since immediate medical assessment is concerned with tissue reactions (deterministic effects), the quantity of interest for the above dosimetry methods is absorbed dose (expressed in gray). This Report concludes with a summary of the various methods and a brief discussion of the uses of such information in the aftermath of acute radiation exposure. read less NOT USED (high confidence) W. Zhou, Z. Zhang, H. Wang, and X. Yang, “Molecular Investigation of CO2/CH4 Competitive Adsorption and Confinement in Realistic Shale Kerogen,” Nanomaterials. 2019. link Times cited: 23 Abstract: The adsorption behavior and the mechanism of a CO2/CH4 mixtu… read moreAbstract: The adsorption behavior and the mechanism of a CO2/CH4 mixture in shale organic matter play significant roles to predict the carbon dioxide sequestration with enhanced gas recovery (CS-EGR) in shale reservoirs. In the present work, the adsorption performance and the mechanism of a CO2/CH4 binary mixture in realistic shale kerogen were explored by employing grand canonical Monte Carlo (GCMC) and molecular dynamics (MD) simulations. Specifically, the effects of shale organic type and maturity, temperature, pressure, and moisture content on pure CH4 and the competitive adsorption performance of a CO2/CH4 mixture were investigated. It was found that pressure and temperature have a significant influence on both the adsorption capacity and the selectivity of CO2/CH4. The simulated results also show that the adsorption capacities of CO2/CH4 increase with the maturity level of kerogen. Type II-D kerogen exhibits an obvious superiority in the adsorption capacity of CH4 and CO2 compared with other type II kerogen. In addition, the adsorption capacities of CO2 and CH4 are significantly suppressed in moist kerogen due to the strong adsorption strength of H2O molecules on the kerogen surface. Furthermore, to characterize realistic kerogen pore structure, a slit-like kerogen nanopore was constructed. It was observed that the kerogen nanopore plays an important role in determining the potential of CO2 subsurface sequestration in shale reservoirs. With the increase in nanopore size, a transition of the dominated gas adsorption mechanism from micropore filling to monolayer adsorption on the surface due to confinement effects was found. The results obtained in this study could be helpful to estimate original gas-in-place and evaluate carbon dioxide sequestration capacity in a shale matrix. read less NOT USED (high confidence) H. Nakano and H. Sato, “A chemical potential equalization approach to constant potential polarizable electrodes for electrochemical-cell simulations.,” The Journal of chemical physics. 2019. link Times cited: 11 Abstract: Atomistic modeling of electrochemical systems is one of the … read moreAbstract: Atomistic modeling of electrochemical systems is one of the most challenging topics in the field of molecular simulations. We derive the equations for modeling constant potential polarizable electrodes in electrochemical-cell simulations based on the chemical potential equalization principle. They reduce to those derived by Siepmann and Sprik [J. Chem. Phys. 102, 511 (1995)], later arranged by Reed, Lanning, and Madden [J. Chem. Phys. 126, 084704 (2007)] under some assumptions. The present approach clarifies the physical meaning of the total energy of a system that includes classical polarizable electrodes, which is important in order to analyze the energetics of chemical phenomena at electrode-electrolyte interfaces. The effects of the Hubbard U parameter of an electrode atom are discussed in connection with the perfect conductor limit for a metal electrode. read less NOT USED (high confidence) S. Gim, K. J. Cho, H.-K. Lim, and H. Kim, “Structure, Dynamics, and Wettability of Water at Metal Interfaces,” Scientific Reports. 2019. link Times cited: 35 NOT USED (high confidence) H. Mori and N. Matubayasi, “Local viscoelasticity at resin-metal interface analyzed with spatial-decomposition formula for relaxation modulus.,” The Journal of chemical physics. 2019. link Times cited: 0 Abstract: A spatial-decomposition formula is presented for viscoelasti… read moreAbstract: A spatial-decomposition formula is presented for viscoelasticity. In this formula, the relaxation modulus is decomposed with respect to a spatial coordinate and the local viscoelasticity is analyzed with the spatially decomposed stress-stress time correlation function. The spatial-decomposition formula is then applied to a planar interface between resin and metal by using the Kremer-Grest model at a variety of adhesion strengths. It was observed that when the resin-metal interaction is strong, the resin forms a layer structure extending over a spatial range which is larger by an order of magnitude than the segment size of the resin. The motion of the resin is suppressed there, and the effect of the interface is localized near the wall only when the adhesion is weak. Actually, the layer region is more viscous than the bulk when the resin interacts strongly with the wall, in the sense that the stress-stress correlation in the former region persists over longer times. The resin-metal interaction in the spatial scale corresponding to the segment size does not affect the equal-time correlation of the local stress significantly and modifies mainly the decay with time of the local stress of the resin within the layers. The present work demonstrates that the spatially decomposed relaxation modulus can be a general framework for analyzing the viscoelasticity at the interface and revealing the relationship of the adhesion to the stress-stress correlation in the segment-scale space and time. read less NOT USED (high confidence) J. Liu et al., “Incorporation of clusters within inorganic materials through their addition during nucleation steps,” Nature Chemistry. 2019. link Times cited: 69 NOT USED (high confidence) M. M. Blazhynska, A. Kyrychenko, and O. Kalugin, “Polarizable force field for molecular dynamics simulations of silver nanoparticles,” Kharkov University Bulletin Chemical Series. 2019. link Times cited: 3 Abstract: Contact of silver metal surfaces with water, ions and organi… read moreAbstract: Contact of silver metal surfaces with water, ions and organic ligands experiences induced charges, leading to attractive polarization. These forces play an important role at inorganic/organic interfaces and complement other non-bonded surface interactions. Despite the importance of these interactions, it, however, remains difficult to implement polarization effects to classical molecular dynamics (MD) simulations. In this contribution, we first present an overview of two popular polarizable models, such as Drude oscillator and the rigid rod model, which are utilized to mimic the polarizability of bulk metals. Second, we implemented the rigid rod model to the polarizable force field (FF) for a silver atom, which was further adapted for atomistic MD simulations of silver nanoparticles (AgNPs) composed of 1397 atoms. In our model, induced charge polarization is represented by the displacement of a charge-carrying virtual site attached rigidly to an original Ag atom. To explore the role of polarization, we compared the performance of the classical nonpolarizable FF and the new polarizable model in the MD simulations of adsorption of water and ions onto quasi-spherical AgNP and the flat crystalline silver surface. The analysis of the radial distribution function of Ag-Ag atoms demonstrated that the introduction of the polarization effect had minor effects on face-centered cubic (fcc) packing of silver atoms of bare and water-solvated AgNPs. We found that the polarizable FF causes some increase in attractive interactions between the silver surface and water molecules and Na+ ions. As a crucial test of the developed polarizable model, the structure of adsorbed interfacial water molecules was analyzed. Our data suggest that the environment-induced polarization of the silver surface contributes significantly to the structure of adsorbed interfacial water layers and it also plays an important role in the adsorption of positive ions. However, it was also found out that the polarization effect has a rather short-range effect, so that a minor contribution of silver polarization was seen for adsorption of water molecules and ions from distant solvation shells. read less NOT USED (high confidence) T. Inagaki and M. Nagaoka, “Electrode polarization effects on interfacial kinetics of ionic liquid at graphite surface: An extended lagrangian‐based constant potential molecular dynamics simulation study,” Journal of Computational Chemistry. 2019. link Times cited: 6 Abstract: Computational models including electrode polarization can be… read moreAbstract: Computational models including electrode polarization can be essential to study electrode/electrolyte interfacial phenomena more realistically. We present here a constant‐potential classical molecular dynamics simulation method based on the extended Lagrangian formulation where the fluctuating electrode atomic charges are treated as independent dynamical variables. The method is applied to a graphite/ionic liquid system for the validation and the interfacial kinetics study. While the correct adiabatic dynamics is achieved with a sufficiently small fictitious mass of charge, static properties have been shown to be almost insensitive to the fictitious mass. As for the kinetics study, electrical double layer (EDL) relaxation and ion desorption from the electrode surface are considered. We found that the polarization slows EDL relaxation greatly whereas it has little impact on the ion desorption kinetics. The findings suggest that the polarization is essential to estimate the kinetics in nonequilibrium processes, not in equilibrium. © 2019 Wiley Periodicals, Inc. read less NOT USED (high confidence) R. Khatib, A. Kumar, S. Sanvito, M. Sulpizi, and C. Cucinotta, “The nanoscale structure of the Pt-water double layer under bias revealed,” arXiv: Chemical Physics. 2019. link Times cited: 15 NOT USED (high confidence) W. Wei et al., “Regulating Second-Harmonic Generation by van der Waals Interactions in Two-dimensional Lead Halide Perovskite Nanosheets.,” Journal of the American Chemical Society. 2019. link Times cited: 62 Abstract: The flexible organic amine cations on the interfaces of two-… read moreAbstract: The flexible organic amine cations on the interfaces of two-dimensional (2D) hybrid organic-inorganic perovskite nanosheets could form relaxed structures, which would lead to exotic optoelectronic properties but are hard to understand. Here, the unusual interfacial relaxation of nanosheets exfoliated from an orthorhombic 2D lead halide perovskite, [(C6H5CH2NH3)2]PbCl4, is interrogated via ultrafast second-harmonic generation (SHG) spectroscopy. The in-plane SHG intensity anisotropy of these nanosheets is found to decrease with reducing layer thickness. Combined first-principles calculations and Monte Carlo simulations reveal that the induced second-order polarization arises primarily from the (C6H5CH2NH3)+ cations; and these organic amine cations form significantly reorganized conformations with decreasing nanosheet thickness due to weakened van der Waals interactions. Because the orientations of organic components at the interface determine their electric properties and specifically the dipolar susceptibility, the resulting structure leads to striking changes in the SHG properties. read less NOT USED (high confidence) R. E. Jones, W. C. Tucker, M. J. L. Mills, and S. Mukerjee, “Insight into hydrogen production through molecular simulation of an electrode-ionomer electrolyte system.,” The Journal of chemical physics. 2019. link Times cited: 2 Abstract: In this work, we examine metal electrode-ionomer electrolyte… read moreAbstract: In this work, we examine metal electrode-ionomer electrolyte systems at high voltage (negative surface charge) and at high pH to assess factors that influence hydrogen production efficiency. We simulate the hydrogen evolution electrode interface investigated experimentally in the work of Bates et al. [J. Phys. Chem. C 119, 5467 (2015)] using a combination of first principles calculations and classical molecular dynamics. With this detailed molecular information, we explore the hypotheses posed in the work of Bates et al. In particular, we examine the response of the system to increased bias voltage and oxide coverage in terms of the potential profile, changes in solvation and species concentrations away from the electrode, surface concentrations, and orientation of water at reactive surface sites. We discuss this response in the context of hydrogen production. read less NOT USED (high confidence) S. Tewari, J. Bakermans, C. Wagner, F. Galli, and J. V. van Ruitenbeek, “Intuitive human interface to a scanning tunnelling microscope: observation of parity oscillations for a single atomic chain,” Beilstein Journal of Nanotechnology. 2019. link Times cited: 3 Abstract: A new way to control individual molecules and monoatomic cha… read moreAbstract: A new way to control individual molecules and monoatomic chains is devised by preparing a human–machine augmented system in which the operator and the machine are connected by a real-time simulation. Here, a 3D motion control system is integrated with an ultra-high vacuum (UHV) low-temperature scanning tunnelling microscope (STM). Moreover, we coupled a real-time molecular dynamics (MD) simulation to the motion control system that provides a continuous visual feedback to the operator during atomic manipulation. This allows the operator to become a part of the experiment and to make any adaptable tip trajectory that could be useful for atomic manipulation in three dimensions. The strength of this system is demonstrated by preparing and lifting a monoatomic chain of gold atoms from a Au(111) surface in a well-controlled manner. We have demonstrated the existence of Fabry–Pérot-type electronic oscillations in such a monoatomic chain of gold atoms and determined its phase, which was difficult to ascertain previously. We also show here a new geometric procedure to infer the adatom positions and therefore information about the substrate atoms, which are not easily visible on clean metallic surfaces such as gold. This method enables a new controlled atom manipulation technique, which we will refer to as point contact pushing (PCP) technique. read less NOT USED (high confidence) Z. Futera and J. Blumberger, “Adsorption of Amino Acids on Gold: Assessing the Accuracy of the GolP-CHARMM Force Field and Parametrization of Au-S Bonds.,” Journal of chemical theory and computation. 2018. link Times cited: 18 Abstract: The interaction of amino acids with metal electrodes plays a… read moreAbstract: The interaction of amino acids with metal electrodes plays a crucial role in bioelectrochemistry and the emerging field of bionanoelectronics. Here we present benchmark calculations of the adsorption structure and energy of all natural amino acids on Au(111) in vacuum using a van-der-Waals density functional (revPBE-vdW) that showed good performance on the S22 set of weakly bound dimers (mean relative unsigned error (MRUE) wrt CCSD(T)/CBS = 13.3%) and adsorption energies of small organic molecules on Au(111) (MRUE wrt experiment = 11.2%). The vdW-DF results are then used to assess the accuracy of a popular force field for Au-amino acid interactions, GolP-CHARMM, which explicitly describes image charge interactions via rigid-rod dipoles. We find that while the force field underestimates adsorption distances, it does reproduce the binding energy rather well (MRUE wrt revPBE-vdW = 11.3%) with the MRUE decreasing in the order Cys, Met > amines > aliphatic > carboxylic > aromatic. We also present a parametrization of the bonding interaction between sulfur-containing molecules and the Au(111) surface and report force field parameters that are compatible with GolP-CHARMM. We believe the vdW-DF calculations presented herein will provide useful reference data for further force field development, and that the new Au-S bonding parameters will enable improved simulations of proteins immobilized on Au-electrodes via S-linkages. read less NOT USED (high confidence) M. Lasich, “Sorption of natural gas in cement hydrate by Monte Carlo simulation,” The European Physical Journal B. 2018. link Times cited: 6 NOT USED (high confidence) I. L. Geada, I. Petit, M. Sulpizi, and F. Tielens, “Unravelling the GLY-PRO-GLU tripeptide induced reconstruction of the Au(110) surface at the molecular scale,” Surface Science. 2018. link Times cited: 1 NOT USED (high confidence) H. Zhao et al., “Binding of calcium cations with three different types of oxygen-based functional groups of superplasticizers studied by atomistic simulations,” Journal of Molecular Modeling. 2018. link Times cited: 16 NOT USED (high confidence) M. Uranagase, S. Ogata, K. Tanaka, H. Mori, and S. Tajima, “Efficient scheme for calculating work of adhesion between a liquid and polymer-grafted substrate.,” The Journal of chemical physics. 2018. link Times cited: 5 Abstract: We propose a method for calculating the work of adhesion bet… read moreAbstract: We propose a method for calculating the work of adhesion between a liquid and solid surface by using molecular simulations. Two ideas are introduced for efficient calculation when the proposed method is applied at the interface between a liquid and a polymer-grafted substrate. First, the liquid molecules are separated from the solid surface based on its shape by placing spherically symmetric potentials around the atoms selected from the substrate and the polymers grafted onto it. Second, to avoid deterioration of accuracy during numerical integration of the work, the parameters that appear in the potential are updated so that variations in the gradient of the work are suppressed. This method is applied to the interface between water and a gold substrate modified by poly(ethylene oxide) (PEO), and it is found that the work of adhesion is greater at intermediate PEO densities. read less NOT USED (high confidence) T. Raeker, B. Jansen, D. Behrens, and B. Hartke, “Simulations of optically switchable molecular machines for particle transport,” Journal of Computational Chemistry. 2018. link Times cited: 3 Abstract: A promising application for design and deployment of molecul… read moreAbstract: A promising application for design and deployment of molecular machines is nanoscale transport, driven by artificial cilia. In this contribution, we present several further steps toward this goal, beyond our first‐generation artificial cilium (Raeker et al., J. Phys. Chem. A 2012, 116, 11241). Promising new azobenzene‐derivatives were tested for use as cilium motors. Using a QM/MM partitioning in on‐the‐fly photodynamics, excited‐state surface‐hopping trajectories were calculated for each isomerization direction and each motor version. The methods used were reparametrized semiempirical quantum chemistry together with floating‐occupation configuration interaction as the QM part and the OPLSAA‐L forcefield as MM part. In addition, we simulated actual particle transport by a single cilium attached to a model surface, with varying attachment strengths and modes, and with transport targets ranging from single atoms to multi‐molecule arrangements. Our results provide valuable design guidelines for cilia‐driven nanoscale transport and emphasize the need to carefully select the whole setup (not just the cilium itself, but also its surface attachment and the dynamic cilium‐target interaction) to achieve true transport. © 2018 Wiley Periodicals, Inc. read less NOT USED (high confidence) F. Font and F. Bresme, “Transient Melting at the Nanoscale: A Continuum Heat Transfer and Nonequilibrium Molecular Dynamics Approach,” The Journal of Physical Chemistry C. 2018. link Times cited: 12 Abstract: Transient melting is an ubiquitous phenomenon in nature, whi… read moreAbstract: Transient melting is an ubiquitous phenomenon in nature, which plays an increasingly important role in the processing of nanomaterials. A sound theoretical description of this process is therefore important, both from fundamental and applied points of view. We present a numerical study of transient melting in simple atomic solids using both, continuum theory based on the heat diffusion equation and transient nonequilibrium molecular dynamics simulations. We show that continuum theory provides an accurate description of relevant properties, temperature relaxation, time-dependent internal energy, and dynamics of the melting front. However, deviations between the continuum approach and the molecular dynamics simulations are observed in picosecond time scales depending on the initial temperature used to melt the solid. These deviations are due to the emergence of new time scales associated with the activated character of the melting process. Consistently with this notion, we observe that the closer the initia... read less NOT USED (high confidence) J. Liu, E. Tennessen, J. Miao, Y. Huang, J. Rondinelli, and H. Heinz, “Understanding Chemical Bonding in Alloys and the Representation in Atomistic Simulations,” The Journal of Physical Chemistry C. 2018. link Times cited: 29 Abstract: Alloys are widely used in catalysts and structural materials… read moreAbstract: Alloys are widely used in catalysts and structural materials. The nature of chemical bonding and the origin of alloy formation energies, defect energies, and interfacial properties have not been well understood to date but are critical to material performance. In this contribution, we explain the polar nature of chemical bonding and an implementation in classical and reactive atomistic simulations to understand such properties more quantitatively. Electronegativity differences between metal atoms lead to polar bonding, and exothermic alloy formation energies are related to charge transfer between the different elements. These differences can be quantified by atomic charges using pairwise charge increments, determined by matching the computed alloy formation energy to experimentally measured alloy formation energies using pair potentials for the pure metals. The polar character of alloys is comparable to organic molecules and partially ionic minerals, for example, AlNi and AlNi3 alloys assume significant a... read less NOT USED (high confidence) L. Liu, R. Zhang, Y. Liu, W. Tan, and G. Zhu, “Insight into hydrogen bonds and characterization of interlayer spacing of hydrated graphene oxide,” Journal of Molecular Modeling. 2018. link Times cited: 25 NOT USED (high confidence) M. M. Blazhynska, A. Kyrychenko, and O. Kalugin, “Molecular dynamics simulation of the size-dependent morphological stability of cubic shape silver nanoparticles,” Molecular Simulation. 2018. link Times cited: 25 Abstract: The morphological stability of sharp-edged silver nanopartic… read moreAbstract: The morphological stability of sharp-edged silver nanoparticles is examined by the classical molecular dynamics (MD) simulations. The crystalline structure and the perfect fcc atom packing of a series of silver nanocubes (AgNC) of different sizes varying from 63 up to 1099 atoms are compared against quasi-spherical nanoparticles of the same sizes at temperature 303 K. Our MD simulations demonstrate that starting from the preformed perfect crystalline structures the cubic shape is preserved for AgNCs composed of 365–1099 atoms. Surprisingly, the rapid loss of the cubic shape morphology and transformation into the non-fcc-structure are found for smaller AgNCs composed of less than ~256 atoms. No such loss of the preformed crystalline structure is seen for quasi-spherical nanoparticles composed of 38–1007 atoms. The analysis of the temperature dependence and the binding energy of outermost Ag surface atoms suggests that the loss of the perfect cubic shape, rounding and smoothing of sharp edges and corners are driven by the tendency towards the increase in their coordination number. In addition, we revealed that AgNC1099 partially loses its sharp edges and corners in the aqueous environment; however, the polymer coating with poly(vinyl alcohol) (PVA) was able to preserve the well-defined cubic morphology. Finally, these results help improve the understanding of the role of surface capping agents in solution phase synthesis of Ag nanocubes. read less NOT USED (high confidence) N. Miyazawa, M. Hakamada, and M. Mabuchi, “Antimicrobial mechanisms due to hyperpolarisation induced by nanoporous Au,” Scientific Reports. 2018. link Times cited: 25 NOT USED (high confidence) I. L. Geada, H. Ramezani-Dakhel, T. Jamil, M. Sulpizi, and H. Heinz, “Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard–Jones potential,” Nature Communications. 2018. link Times cited: 100 NOT USED (high confidence) H. Gao, H. Liu, H. Qian, G.-S. Jiao, and Z.-yuan Lu, “Multiscale simulations of ligand adsorption and exchange on gold nanoparticles.,” Physical chemistry chemical physics : PCCP. 2018. link Times cited: 8 Abstract: We have developed a multiscale model that combines first-pri… read moreAbstract: We have developed a multiscale model that combines first-principles methods with atomistic and mesoscopic simulations to explore the molecular structures and packing density of the ligands present on the gold nanoparticle (AuNP) surface, as well as the adsorption/exchange reaction kinetics of cetyltrimethylammonium bromide (CTAB)/PEG-SH ligands on different facets of gold, namely, Au(111), Au(100), and Au(110). Our model predicts that on clean gold surfaces, CTAB adsorption is diffusion limited. Specifically, CTAB has the preferentially higher adsorption rate and coverage density on Au(100) and Au(110) surfaces, forming a more compact layer with respect to that on the Au(111) surface, which could result in greater growth of gold nanoparticles along the (111) direction. As opposed to CTAB adsorption, the exchange reaction between PEG-SH with CTAB shows no selectivity to different crystal faces, and the reaction process follows Langmuir diffusion kinetics. Kinetic analysis reveals that, in water, the exchange reaction is zeroth order with respect to the concentration of an incoming PEG-SH, indicative of a dissociative exchange mechanism. The observed rate constant decreases exponentially with the PEG-SH chain length, consistent with a diffusion process for the free PEG-SH in water. In particular, we show that the exchange efficiency increases as the chain rigidness and size of the incoming ligand and/or steric bulk of the initial protecting ligand shell are decreased. Our objectives are to provide a model to assess the kinetics and thermodynamics of the adsorption/exchange reaction process, and we expect that these findings will have important implications for routine surface characterization of AuNPs. read less NOT USED (high confidence) H.-ming Ding and Y.-qiang Ma, “Computational approaches to cell-nanomaterial interactions: keeping balance between therapeutic efficiency and cytotoxicity.,” Nanoscale horizons. 2018. link Times cited: 32 Abstract: Owing to their unique properties, nanomaterials have been wi… read moreAbstract: Owing to their unique properties, nanomaterials have been widely used in biomedicine since they have obvious inherent advantages over traditional ones. However, nanomaterials may also cause dysfunction in proteins, genes and cells, resulting in cytotoxic and genotoxic responses. Recently, more and more attention has been paid to these potential toxicities of nanomaterials, especially to the risks of nanomaterials to human health and safety. Therefore, when using nanomaterials for biomedical applications, it is of great importance to keep the balance between therapeutic efficiency and cytotoxicity (i.e., increase the therapeutic efficiency as well as decrease the potential toxicity). This requires a deeper understanding of the interactions between various types of nanomaterials and biological systems at the nano/bio interface. In this review, from the point of view of theoretical researchers, we will present the current status regarding the physical mechanism of cytotoxicity caused by nanomaterials, mainly based on recent simulation results. In addition, the strategies for minimizing the nanotoxicity naturally and artificially will also be discussed in detail. Furthermore, we should notice that toxicity is not always bad for clinical use since causing the death of specific cells is the main way of treating disease. Enhancing the targeting ability of nanomaterials to diseased cells and minimizing their side effects on normal cells will always be hugely challenging issues in nanomedicine. By combining the latest computational studies with some experimental verifications, we will provide special insights into recent advances regarding these problems, especially for the design of novel environment-responsive nanomaterials. read less NOT USED (high confidence) R. K. Mishra et al., “cemff: A force field database for cementitious materials including validations, applications and opportunities,” Cement and Concrete Research. 2017. link Times cited: 168 NOT USED (high confidence) D. R. Nieto, A. Lindbråthen, and M. B. Hägg, “Effect of Water Interactions on Polyvinylamine at Different pHs for Membrane Gas Separation,” ACS Omega. 2017. link Times cited: 25 Abstract: In our previous work, it was shown that the separation perfo… read moreAbstract: In our previous work, it was shown that the separation performance of the fixed-site-carrier polyvinylamine (PVAm) composite membrane increases exponentially with increasing relative humidity content in the gas. Through these efforts, it has been important to develop a greater understanding of the relationship between the water, structural, and interfacial properties of the PVAm surface. The degree of hydrophilicity of a given surface plays a crucial role in the separation performance of the membrane when exposed to a humidified gas. Therefore, in the current work, the wettability properties of PVAm at different pHs have been studied by experimental measurements and molecular dynamic simulations. It was confirmed that the intramolecular interactions are not linearly dependent on pH. As well as the H-bonding between protonated and unprotonated amine groups, the conformation polymer chain and the distribution charge density play a crucial role in the surface stability and wettability properties. read less NOT USED (high confidence) V. Rudyak and S. Krasnolutskii, “Simulation of the thermal conductivity of a nanofluid with small particles by molecular dynamics methods,” Technical Physics. 2017. link Times cited: 15 NOT USED (high confidence) S.-H. Liu and K. Fichthorn, “Interaction of Alkylamines with Cu Surfaces: A Metal–Organic Many-Body Force Field,” Journal of Physical Chemistry C. 2017. link Times cited: 18 Abstract: Hexadecylamine (HDA) and alkylamines, in general, are key mo… read moreAbstract: Hexadecylamine (HDA) and alkylamines, in general, are key molecules in the shape-selective synthesis of Cu nanostructures. To resolve certain aspects of these syntheses, we develop a classical many-body force field to describe the interactions of HDA with Cu surfaces. We parametrize the force field through force and energy matching to results from first-principles density functional theory (DFT). Our force field reproduces the DFT binding energies and configurations of self-assembled HDA layers on Cu(100) and Cu(111) at various coverages. We implemented the force field in classical molecular dynamics (MD) simulations to resolve various HDA self-assembled-layer structures on Cu(100) in vacuum, and we find that HDA layers undergo a continuous structural transition through various ordered layers at high coverage to disordered layers at lower coverages. We probed pentylamine (PA), decylamine (DA), and HDA binding on Cu surfaces in vacuum with MD and find that DA forms self-assembled layers, but PA layers diso... read less NOT USED (high confidence) T. Walsh and M. R. Knecht, “Biointerface Structural Effects on the Properties and Applications of Bioinspired Peptide-Based Nanomaterials.,” Chemical reviews. 2017. link Times cited: 140 Abstract: Peptide sequences are known to recognize and bind different … read moreAbstract: Peptide sequences are known to recognize and bind different nanomaterial surfaces, which has resulted in the screening and identification of hundreds of peptides with the ability to bind to a wide range of metallic, metal oxide, mineral, and polymer substrates. These biomolecules are able to bind to materials with relatively high affinity, resulting in the generation of a complex biointerface between the biotic and abiotic components. While the number of material-binding sequences is large, at present, quantitative materials-binding characterization of these peptides has been accomplished only for a relatively small number of sequences. Moreover, it is currently very challenging to determine the molecular-level structure(s) of these peptides in the materials adsorbed state. Despite this lack of data related to the structure and function of this remarkable biointerface, several of these peptide sequences have found extensive use in creating functional nanostructured materials for assembly, catalysis, energy, and medicine, all of which are dependent on the structure of the individual peptides and collective biointerface at the material surface. In this Review, we provide a comprehensive overview of these applications and illustrate how the versatility of this peptide-mediated approach for the growth, organization, and activation of nanomaterials could be more widely expanded via the elucidation of biointerfacial structure/property relationships. Future directions and grand challenges to realize these goals are highlighted for both experimental characterization and molecular-simulation strategies. read less NOT USED (high confidence) W. Shi, Y. H. Lee, X. Ling, and S. Li, “Quantitative prediction of the position and orientation for an octahedral nanoparticle at liquid/liquid interfaces.,” Nanoscale. 2017. link Times cited: 7 Abstract: Shape-controlled polyhedral particles and their assembled st… read moreAbstract: Shape-controlled polyhedral particles and their assembled structures have important applications in plasmonics and biosensing, but the interfacial configurations that will critically determine their resultant assembled structures are not well-understood. Hence, a reliable theory is desirable to predict the position and orientation of a polyhedron at the vicinity of a liquid/liquid interface. Here we demonstrate that the free energy change theory can quantitatively predict the position and orientation of an isolated octahedral nanoparticle at a liquid/liquid interface, whose vertices and facets can play crucial roles in biosensing. We focus on two limiting orientations of an octahedral nanoparticle, vertex up and facet up. Our proposed theory indicates that the surface wettability (hydrophilic/hydrophobic ratio) of the nanoparticle determines its most stable position and the preferred orientation at a water/oil interface. The surface wettability of an octahedron is adjusted from extremely hydrophobic to extremely hydrophilic by changing the amount of charge on the Ag surface in molecular dynamics (MD) simulations. The MD simulations results are in excellent agreement with our theoretical prediction for an Ag octahedral nanoparticle at a hexane/water interface. Our proposed theory bridges the gap between molecular-level simulations and equilibrium configurations of polyhedral nanoparticles in experiments, where insights from nanoparticle intrinsic wettability details can be used to predict macroscopic superlattice formation experimentally. This work advances our ability to precisely predict the final structures of the polyhedral nanoparticle assemblies at a liquid/liquid interface. read less NOT USED (high confidence) H. Ramezani-Dakhel, N. Bedford, T. Woehl, M. R. Knecht, R. Naik, and H. Heinz, “Nature of peptide wrapping onto metal nanoparticle catalysts and driving forces for size control.,” Nanoscale. 2017. link Times cited: 16 Abstract: Colloidal metal nanocrystals find many applications in catal… read moreAbstract: Colloidal metal nanocrystals find many applications in catalysis, energy conversion devices, and therapeutics. However, the nature of ligand interactions and implications on shape control have remained uncertain at the atomic scale. Large differences in peptide adsorption strength and facet specificity were found on flat palladium surfaces versus surfaces of nanoparticles of 2 to 3 nm size using accurate atomistic simulations with the Interface force field. Folding of longer peptides across many facets explains the formation of near-spherical particles with local surface disorder, in contrast to the possibility of nanostructures of higher symmetry with shorter ligands. The average particle size in TEM correlates inversely with the surface coverage with a given ligand and with the strength of ligand adsorption. The role of specific amino acids and sequence mutations on the nanoparticle size and facet composition is discussed, as well as the origin of local surface disorder that leads to large differences in catalytic reactivity. read less NOT USED (high confidence) C. Dharmawardhana et al., “Reliable computational design of biological-inorganic materials to the large nanometer scale using Interface-FF,” Molecular Simulation. 2017. link Times cited: 33 Abstract: The function of nanomaterials and biomaterials greatly depen… read moreAbstract: The function of nanomaterials and biomaterials greatly depends on understanding nanoscale recognition mechanisms, crystal growth and surface reactions. The Interface Force Field (IFF) and surface model database are the first collection of transferable parameters for inorganic and organic compounds that can be universally applied to all materials. IFF uses common energy expressions and achieves best accuracy among classical force fields due to rigorous validation of structural and energetic properties of all compounds in comparison to perpetually valid experimental data. This paper summarises key aspects of parameterisation, including atomic charges and transferability of parameters and current coverage. Examples of biomolecular recognition at metal and mineral interfaces, surface reactions of alloys, as well as new models for graphitic materials and pi-conjugated molecules are described. For several metal–organic interfaces, a match in accuracy of computed binding energies between of IFF and DFT results is demonstrated at ten million times lower computational cost. Predictive simulations of biomolecular recognition of peptides on phosphate and silicate surfaces are described as a function of pH. The use of IFF for reactive molecular dynamics is illustrated for the oxidation of Mo3Si alloys at high temperature, showing the development of specific porous silica protective layers. The introduction of virtual pi electrons in graphite and pi-conjugated molecules enables improvements in property predictions by orders of magnitude. The inclusion of such molecule-internal polarity in IFF can reproduce cation–pi interactions, pi-stacking in graphite, DNA bases, organic semiconductors and the dynamics of aqueous and biological interfaces for the first time. read less NOT USED (high confidence) K. S. Austin, J. Zierenberg, and W. Janke, “Interplay of Adsorption and Semiflexibility: Structural Behavior of Grafted Polymers under Poor Solvent Conditions,” Macromolecules. 2017. link Times cited: 10 Abstract: We analyze the structural behavior of isolated semiflexible … read moreAbstract: We analyze the structural behavior of isolated semiflexible polymers grafted to an impenetrable surface. Employing a parallel multicanonical algorithm, we find a rich phase behavior for both purely entropic and attractive surface–polymer interactions. The corresponding conformations range from very compact ones, to folded bundles, to adsorbed and desorbed weakly bent rods. The case of a polymer grafted to a flat, noninteracting surface differs only marginally from the case of a completely free and isolated polymer. Introducing surface attraction, we find that below the adsorption transition temperature stiffer polymers are completely adsorbed and confined to an effectively two-dimensional conformation space. This ultimately holds true over the full range of semiflexibility for increasing surface attraction, in accordance with recent experimental findings. read less NOT USED (high confidence) H. Joshi, D. Bhatia, Y. Krishnan, and P. Maiti, “Probing the structure and in silico stability of cargo loaded DNA icosahedra using MD simulations.,” Nanoscale. 2017. link Times cited: 14 Abstract: Platonic solids such as polyhedra based on DNA have been dep… read moreAbstract: Platonic solids such as polyhedra based on DNA have been deployed for multifarious applications such as RNAi delivery, biological targeting and bioimaging. All of these applications hinge on the capability of DNA polyhedra for molecular display with high spatial precision. Therefore high resolution structural models of such polyhedra are critical to widen their applications in both materials and biology. Here, we present an atomistic model of a well-characterized DNA icosahedron, with demonstrated versatile functionalities in biological systems. We study the structure and dynamics of this DNA icosahedron using fully atomistic molecular dynamics (MD) simulation in explicit water and ions. The major modes of internal motion have been identified using principal component analysis. We provide a quantitative estimate of the radius of gyration (Rg), solvent accessible surface area (SASA) and volume of the icosahedron which is essential to estimate its maximal cargo carrying capacity. Importantly, our simulation of gold nanoparticles (AuNPs) encapsulated within DNA icosahedra revealed enhanced stability of the AuNP loaded DNA icosahedra compared to empty icosahedra. This is consistent with the experimental results that show high yields of cargo-encapsulated DNA icosahedra that have led to its diverse applications for precision targeting. These studies reveal that the stabilizing interactions between the cargo and the DNA scaffold powerfully position DNA polyhedra as targetable nanocapsules for payload delivery. These insights can be exploited for precise molecular display for diverse biological applications. read less NOT USED (high confidence) H. Heinz et al., “Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications,” Surface Science Reports. 2017. link Times cited: 381 NOT USED (high confidence) W. Alexander, “Performance of a rigid rod statistical mechanical treatment to predict monolayer ordering: a study of chain interactions and comparison with molecular dynamics simulation,” Journal of Mathematical Chemistry. 2017. link Times cited: 0 NOT USED (high confidence) Y.-lei Wang, M. Golets, B. Li, S. Sarman, and A. Laaksonen, “Interfacial Structures of Trihexyltetradecylphosphonium-bis(mandelato)borate Ionic Liquid Confined between Gold Electrodes.,” ACS applied materials & interfaces. 2017. link Times cited: 28 Abstract: Atomistic molecular dynamics simulations have been performed… read moreAbstract: Atomistic molecular dynamics simulations have been performed to study microscopic the interfacial ionic structures, molecular arrangements, and orientational preferences of trihexyltetradecylphosphonium-bis(mandelato)borate ([P6,6,6,14][BMB]) ionic liquid confined between neutral and charged gold electrodes. It was found that both [P6,6,6,14] cations and [BMB] anions are coabsorbed onto neutral electrodes at different temperatures. The hexyl and tetradecyl chains in [P6,6,6,14] cations lie preferentially flat on neutral electrodes. The oxalato and phenyl rings in [BMB] anions are characterized by alternative parallel-perpendicular orientations in the mixed innermost ionic layer adjacent to neutral electrodes. An increase in temperature has a marginal effect on the interfacial ionic structures and molecular orientations of [P6,6,6,14][BMB] ionic species in a confined environment. Electrifying gold electrodes leads to peculiar changes in the interfacial ionic structures and molecular orientational arrangements of [P6,6,6,14] cations and [BMB] anions in negatively and positively charged gold electrodes, respectively. As surface charge density increases (but lower than 20 μC/cm2), the layer thickness of the mixed innermost interfacial layer gradually increases due to a consecutive accumulation of [P6,6,6,14] cations and [BMB] anions at negatively and positively charged electrodes, respectively, before the formation of distinct cationic and anionic innermost layers. Meanwhile, the molecular orientations of two oxalato rings in the same [BMB] anions change gradually from a parallel-perpendicular feature to being partially characterized by a tilted arrangement at an angle of 45° from the electrodes and finally to a dominant parallel coordination pattern along positively charged electrodes. Distinctive interfacial distribution patterns are also observed accordingly for phenyl rings that are directly connected to neighboring oxalato rings in [BMB] anions. read less NOT USED (high confidence) J. A. Nash, A. Kwansa, J. S. Peerless, H. Kim, and Y. G. Yingling, “Advances in Molecular Modeling of Nanoparticle-Nucleic Acid Interfaces.,” Bioconjugate chemistry. 2017. link Times cited: 19 Abstract: Nanoparticles (NPs) play increasingly important roles in nan… read moreAbstract: Nanoparticles (NPs) play increasingly important roles in nanotechnology and nanomedicine in which nanoparticle surface chemistry allows for control over interactions with other nanoparticles and biomolecules. In particular, for applications in drug and gene delivery, a fundamental understanding of the NP-nucleic acid interface allows for development of more efficient and effective nanoparticle carriers. Computational modeling can provide insights of processes occurring at the inorganic NP-nucleic interface in detail that is difficult to access by experimental methods. With recent advances such as the use of graphics processing units (GPUs) for simulations, computational modeling has the potential to give unprecedented insight into inorganic-biological interfaces via the examination of increasingly large and complex systems. In this Topical Review, we briefly review computational methods relevant to the interactions of inorganic NPs and nucleic acids and highlight recent insights obtained from various computational methods that were applied to studies of inorganic nanoparticle-nanoparticle and nanoparticle-nucleic acid interfaces. read less NOT USED (high confidence) P. Li and K. Merz, “Metal Ion Modeling Using Classical Mechanics,” Chemical Reviews. 2017. link Times cited: 230 Abstract: Metal ions play significant roles in numerous fields includi… read moreAbstract: Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems. read less NOT USED (high confidence) Y. Xia, K. Gilroy, H. C. Peng, and X. Xia, “Seed-Mediated Growth of Colloidal Metal Nanocrystals.,” Angewandte Chemie. 2017. link Times cited: 485 Abstract: Seed-mediated growth is a powerful and versatile approach fo… read moreAbstract: Seed-mediated growth is a powerful and versatile approach for the synthesis of colloidal metal nanocrystals. The vast allure of this approach mainly stems from the staggering degree of control one can achieve over the size, shape, composition, and structure of nanocrystals. These parameters not only control the properties of nanocrystals but also determine their relevance to, and performance in, various applications. The ingenuity and artistry inherent to seed-mediated growth offer extensive promise, enhancing a number of existing applications and opening the door to new developments. This Review demonstrates how the diversity of metal nanocrystals can be expanded with endless opportunities by using seeds with well-defined and controllable internal structures in conjunction with a proper combination of capping agent and reduction kinetics. New capabilities and future directions are also highlighted. read less NOT USED (high confidence) Y. Xia, K. D. Gilroy, H.-C. Peng, and X. Xia, “Keimvermitteltes Wachstum kolloidaler Metallnanokristalle,” Angewandte Chemie. 2017. link Times cited: 39 Abstract: Beim keimvermittelten Wachstum handelt es sich um eine leist… read moreAbstract: Beim keimvermittelten Wachstum handelt es sich um eine leistungsfahige und vielseitige Vorgehensweise zur Synthese kolloidaler Metallnanokristalle. Der grose Reiz dieser Methode resultiert aus dem erstaunlichen Ausmas an Kontrolle, das uber die Grose, Form, Zusammensetzung und Struktur von Nanokristallen erzielt werden kann. Diese Parameter kontrollieren nicht nur die Eigenschaften von Nanokristallen, sondern entscheiden auch uber deren Relevanz und Leistungsfahigkeit in diversen Anwendungen. Das keimvermittelte Wachstum bietet hervorragende Aussichten fur die Erweiterung zahlreicher Anwendungen und offnet zugleich Turen fur neue Entwicklungen. Dieser Aufsatz veranschaulicht die schier endlos erweiterbare Diversitat von Metallnanokristallen auf Basis von Keimen mit genau definierten und kontrollierbaren internen Strukturen in Verbindung mit einer geeigneten Kombination aus Bedeckungsmittel und Reduktionskinetik. Daruber hinaus werden neue Einsatzmoglichkeiten und zukunftige Richtungen aufgezeigt. read less NOT USED (high confidence) T. Avanessian and G. Hwang, “Thermal diode in gas-filled nanogap with heterogeneous surfaces using nonequilibrium molecular dynamics simulation,” Journal of Applied Physics. 2016. link Times cited: 16 Abstract: A thermal diode serves as a basic building block to design a… read moreAbstract: A thermal diode serves as a basic building block to design advanced thermal management systems in energy-saving applications. However, the main challenges of existing thermal diodes are poor steady-state performance, slow transient response, and/or extremely difficult manufacturing. In this study, the thermal diode is examined by employing an argon gas-filled nanogap with heterogeneous surfaces in the Knudsen regime, using nonequilibrium molecular dynamics simulation. The asymmetric gas pressure and thermal accommodation coefficients changes are found due to asymmetric adsorptions onto the heterogeneous nanogap with respect to the different temperature gradient directions, and these in turn result in the thermal diode. The maximum degree of diode (or rectification) is Rmax ∼ 7, at the effective gas-solid interaction ratio between the two surfaces of e* = 0.75. This work could pave the way to designing advanced thermal management systems such as thermal switches (transistors). read less NOT USED (high confidence) B. Calmettes, N. Estrampes, C. Coudret, T. Roussel, J. Faraudo, and R. Coratger, “Observation and modeling of conformational molecular structures driving the self-assembly of tri-adamantyl benzene on Ag(111).,” Physical chemistry chemical physics : PCCP. 2016. link Times cited: 4 Abstract: The self-organization of tri-adamantyl (TAB) benzene molecul… read moreAbstract: The self-organization of tri-adamantyl (TAB) benzene molecules has been investigated using low temperature scanning tunneling microscopy (LT-STM). The molecular structures have also been studied using molecular modeling. In particular, these calculations have been performed on large areas (1000 nm(2)) from the atomic structure of the molecular building block, combining molecular dynamics (MD) and Monte-Carlo (MC) approaches. These investigations show that the structure of the molecule and its flexibility allow for the formation of different networks as a function of surface coverage. The calculations demonstrate that the stability of the largest structures is obtained through the increase of the interfacial energy induced by the rotation of the adamantyl groups, a behavior whose consequences explain the subtle contrasts observed in the experimental STM images. read less NOT USED (high confidence) F. Šebesta, V. Sláma, J. Melcr, Z. Futera, and J. Burda, “Estimation of Transition-Metal Empirical Parameters for Molecular Mechanical Force Fields.,” Journal of chemical theory and computation. 2016. link Times cited: 21 Abstract: Force-field parameters of the first row transition metals to… read moreAbstract: Force-field parameters of the first row transition metals together with a few additional common elements such as those from the second (Rh, Ru) and third (Hg, Pt) rows of elements in ligated forms were determined based on the density functional theory calculations. Bonding characteristics were determined by averaging metal-ligand force constants in optimal geometries from several chosen complexes of each metal in the most common oxidation numbers and structural arrangements. Parameters of Lennard-Jones potential were determined based on a supermolecular model. Our determined molecular mechanical parameters are compared with presently available parameters published by other groups. We performed two different kinds of testing in order to demonstrate the reliability of these parameters in the case of ligated metallo complexes. First, the nonbonding potential was constructed for an additional set of 19 larger systems containing common complexes with organic molecules. The second test compares the Pt-O and Pt-H radial distribution functions for cisplatin in a box of TIP3P water with lately published studies. read less NOT USED (high confidence) A. Iakovlev, D. Bedrov, and M. Müller, “Alkyl-Based Surfactants at a Liquid Mercury Surface: Computer Simulation of Structure, Self-Assembly, and Phase Behavior.,” The journal of physical chemistry letters. 2016. link Times cited: 4 Abstract: Self-assembled organic films on liquid metals feature a very… read moreAbstract: Self-assembled organic films on liquid metals feature a very rich phase behavior, which qualitatively differs from the one on crystalline metals. In contrast to conventional crystalline supports, self-assembled alkylthiol monolayers on liquid metals possess a considerably higher degree of molecular order, thus enabling much more robust metal-molecule-semiconductor couplings for organic electronics applications. Yet, compared to crystalline substrates, the self-assembly of organic surfactants on liquid metals has been studied to a much lesser extent. In this Letter we report the first of its kind molecular simulation investigation of alkyl-based surfactants on a liquid mercury surface. The focus of our investigation is the surfactant conformations as a function of surface coverage and surfactant type. First, we consider normal alkanes because these systems set the basis for simulations of all other organic surfactants on liquid mercury. Subsequently, we proceed with the discussion of alkylthiols that are the most frequently used surfactants in the surface science of hybrid organometallic interfaces. Our results indicate a layering transition of normal alkanes as well as alkylthiols from an essentially bare substrate to a completely filled monolayer of laying molecules. As the surface coverage increases further, we observe a partial wetting of the laying monolayer by the bulk phase of alkanes. In the case of alkylthiols, we clearly see the coexistence of molecules in laying-down and standing-up conformations, in which the sulfur headgroups of the thiols are chemically bound to mercury. In the standing-up phase, the headgroups form an oblique lattice. For the first time we were able to explicitly characterize the molecular-scale structure and transitions between phases of alkyl-based surfactants and to demonstrate how the presence of a thiol headgroup qualitatively changes the phase equilibrium and structure in these systems. The observed phenomena are consistent with available direct and indirect experimental evidence. read less NOT USED (high confidence) E. Pohjolainen, X. Chen, S. Malola, G. Groenhof, and H. Häkkinen, “A Unified AMBER-Compatible Molecular Mechanics Force Field for Thiolate-Protected Gold Nanoclusters.,” Journal of chemical theory and computation. 2016. link Times cited: 62 Abstract: We present transferable AMBER-compatible force field paramet… read moreAbstract: We present transferable AMBER-compatible force field parameters for thiolate-protected gold nanoclusters. Five different sized clusters containing both organo-soluble and water-soluble thiolate ligands served as test systems in MD simulations, and parameters were validated against DFT and experimental results. The cluster geometries remain intact during the MD simulations in various solvents, and structural fluctuations and energetics showed agreement with DFT calculations. Experimental diffusion coefficients and crystal structures were also reproduced with sufficient accuracy. The presented parameter set contains the minimum number of cluster-specific parameters enabling the use of these parameters for several different gold nanoclusters. The parameterization of ligands can also be extended to different types of ligands. read less NOT USED (high confidence) M. Ozboyaci, D. Kokh, S. Corni, and R. Wade, “Modeling and simulation of protein–surface interactions: achievements and challenges,” Quarterly Reviews of Biophysics. 2016. link Times cited: 128 Abstract: Understanding protein–inorganic surface interactions is cent… read moreAbstract: Understanding protein–inorganic surface interactions is central to the rational design of new tools in biomaterial sciences, nanobiotechnology and nanomedicine. Although a significant amount of experimental research on protein adsorption onto solid substrates has been reported, many aspects of the recognition and interaction mechanisms of biomolecules and inorganic surfaces are still unclear. Theoretical modeling and simulations provide complementary approaches for experimental studies, and they have been applied for exploring protein–surface binding mechanisms, the determinants of binding specificity towards different surfaces, as well as the thermodynamics and kinetics of adsorption. Although the general computational approaches employed to study the dynamics of proteins and materials are similar, the models and force-fields (FFs) used for describing the physical properties and interactions of material surfaces and biological molecules differ. In particular, FF and water models designed for use in biomolecular simulations are often not directly transferable to surface simulations and vice versa. The adsorption events span a wide range of time- and length-scales that vary from nanoseconds to days, and from nanometers to micrometers, respectively, rendering the use of multi-scale approaches unavoidable. Further, changes in the atomic structure of material surfaces that can lead to surface reconstruction, and in the structure of proteins that can result in complete denaturation of the adsorbed molecules, can create many intermediate structural and energetic states that complicate sampling. In this review, we address the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems. In this context, we discuss the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches. We examine uses of different sampling methods, as well as free energy calculations. Furthermore, we review computational studies of protein–surface interactions and discuss the successes and limitations of current approaches. read less NOT USED (high confidence) D. Potdar and M. Sammalkorpi, “Asymmetric heat transfer from nanoparticles in lipid bilayers,” Chemical Physics. 2015. link Times cited: 12 NOT USED (high confidence) M. J. Guberman‐Pfeffer, J. R. W. Ulcickas, and J. A. Gascón, “Connectivity-Based Biocompatible Force Field for Thiolated Gold Nanoclusters,” Journal of Physical Chemistry C. 2015. link Times cited: 8 Abstract: Thiolated gold nanoclusters (AuNCs), sub-2 nm Au particles c… read moreAbstract: Thiolated gold nanoclusters (AuNCs), sub-2 nm Au particles capped by Au(I) thiolate complexes, promise to have a myriad of applications in biomedical diagnosis and therapy as well as industrial catalysis, energy production, and monitoring of environmental pollutants. Computational simulations are a valuable tool in elucidating design principles for optimizing application-specific physicochemical properties. However, thiolated AuNCs protected, conjugated, and/or interacting with macromolecules often exceed the limit of computational tractability with present-day quantum chemistry software. To facilitate theoretical studies, a molecular mechanics force field, AuSBio, is presented that reasonably reproduces, and retains, characteristic structural features of perhaps the most intensively studied thiolated AuNC, Au25L18 (L = alkylthiolate), over 2 ns finite temperature molecular dynamics simulations. AuSBio was parametrized within the framework of force fields for (bio)organic simulations to reproduce equilibr... read less NOT USED (high confidence) X. Qi, T. Balankura, Y. Zhou, and K. Fichthorn, “How Structure-Directing Agents Control Nanocrystal Shape: Polyvinylpyrrolidone-Mediated Growth of Ag Nanocubes.,” Nano letters. 2015. link Times cited: 89 Abstract: The importance of structure-directing agents (SDAs) in the s… read moreAbstract: The importance of structure-directing agents (SDAs) in the shape-selective synthesis of colloidal nanostructures has been well documented. However, the mechanisms by which SDAs actuate shape control are poorly understood. In the polyvinylpyrrolidone (PVP)-mediated growth of {100}-faceted Ag nanocrystals, this capability has been attributed to preferential binding of PVP to Ag(100). We use molecular dynamics simulations to probe the mechanisms by which Ag atoms add to Ag(100) and Ag(111) in ethylene glycol solution with PVP. We find that PVP induces kinetic Ag nanocrystal shapes by regulating the relative Ag fluxes to these facets. Stronger PVP binding to Ag(100) leads to a larger Ag flux to Ag(111) and cubic nanostructures through two mechanisms: enhanced Ag trapping by more extended PVP films on Ag(111) and a reduced free-energy barrier for Ag to cross lower-density films on Ag(111). These flux-regulating capabilities depend on PVP concentration and chain length, consistent with experiment. read less NOT USED (high confidence) Z. Xu, Y. Gao, C. Wang, and H. Fang, “Nanoscale Hydrophilicity on Metal Surfaces at Room Temperature: Coupling Lattice Constants and Crystal Faces,” Journal of Physical Chemistry C. 2015. link Times cited: 38 Abstract: It is generally accepted that the metal–water interface tens… read moreAbstract: It is generally accepted that the metal–water interface tensions are quite high; thus, the metal surfaces are usually regarded as hydrophilic. Using the molecular dynamics simulations, we have investigated the microscopic wetting behaviors of a series of metal surfaces at room temperature, including Ni, Cu, Pd, Pt, Al, Au, Ag, and Pb with three crystal faces of (100), (110), and (111). We have found that the wetting of the metals is greatly dependent on both the lattice constants and crystal surfaces. Particularly, stable water droplets are found forming on the first ordered water layer, serving as an evidence of room temperature “ordered water monolayer that does not completely wet water” on Pd(100), Pt(100), and Al(100) surfaces, while water films without ordered water monolayer are found on (110) and (111) faces of all metal surfaces and even (100) face of other metal surfaces (Ni, Cu, Au, Ag, and Pb). The formation of water droplets is attributed to the rhombic ordered water layers on the surfaces, re... read less NOT USED (high confidence) B. A. Russell et al., “Locating the nucleation sites for protein encapsulated gold nanoclusters: a molecular dynamics and fluorescence study.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 39 Abstract: Fluorescent gold nanoclusters encapsulated by proteins have … read moreAbstract: Fluorescent gold nanoclusters encapsulated by proteins have attracted considerable attention in recent years for their unique properties as new fluorescence probes for biological sensing and imaging. However, fundamental questions, such as the nucleation sites of gold nanoclusters within proteins and the fluorescence mechanism remain unsolved. Here we present a study of the location of gold nanoclusters within bovine serum albumin (BSA) combining both fully atomistic molecular dynamic (MD) simulations and fluorescence spectroscopic studies. The MD simulations show gold clusters growing close to a number of cysteine sites across all three domains of BSA, although just two major sites in domains IIB and IA were found to accommodate large clusters comprising more than 12 atoms. The dependence of the fluorescence on pH is found to be compatible with possible nucleation sites in domains IIB and IA. Furthermore, the energy transfer between tryptophan and gold nanoclusters reveals a separation of 29.7 Å, further indicating that gold nanoclusters were most likely located in the major nucleation site in domain IIB. The disclosure of the precise location of the gold nanoclusters and their surrounding amino acid residues should help better understanding of their fluorescence mechanism and aid their optimization as fluorescent nanoprobes. read less NOT USED (high confidence) X. Li and H. Ågren, “Molecular Dynamics Simulations Using a Capacitance–Polarizability Force Field,” Journal of Physical Chemistry C. 2015. link Times cited: 10 Abstract: We present molecular dynamics (MD) simulations using a capac… read moreAbstract: We present molecular dynamics (MD) simulations using a capacitance–polarizability force field. This force field allows an atomistic description of charge migration within a particle and hence the image charge effects at the interface of such a particle. By employing atomic capacitance and polarizability as the key parameters that describe fluctuating charges and dipoles, we can thus explore the effect of charge migration on the structural dynamics. We illustrate the method by exploring gold nanoparticles in aqueous solutions and compare with previous simulation work. We reach the conclusion that the capacitance–polarizability force field MD method serves as a promising tool for simulating gold–water systems, indicating probable extensions to other metal solutions and for studies of more complicated systems provided that a proper parametrization of the capacitance force field can be made. For the particular system studied, it is found that the water molecules interact with the surface through oxygen atoms,... read less NOT USED (high confidence) E. G. Brandt and A. Lyubartsev, “Systematic Optimization of a Force Field for Classical Simulations of TiO2-Water Interfaces,” Journal of Physical Chemistry C. 2015. link Times cited: 47 Abstract: Atomistic force field parameters were developed for the TiO2… read moreAbstract: Atomistic force field parameters were developed for the TiO2–water interface by systematic optimization with respect to experimentally determined crystal structures (lattice parameters) and surface thermodynamics (water adsorption enthalpy). Optimized force field parameters were determined for the two cases where TiO2 was modeled with or without covalent bonding. The nonbonded TiO2 model can be used to simulate different TiO2 phases, while the bonded TiO2 model is particularly useful for simulations of nanosized TiO2 and biomatter, including protein–surface and nanoparticle–biomembrane simulations. The procedure is easily generalized to parametrize interactions between other inorganic surfaces and biomolecules. read less NOT USED (high confidence) F. Leroy and F. Müller-Plathe, “Dry-Surface Simulation Method for the Determination of the Work of Adhesion of Solid-Liquid Interfaces.,” Langmuir : the ACS journal of surfaces and colloids. 2015. link Times cited: 50 Abstract: We introduce a methodology, referred to as the dry-surface m… read moreAbstract: We introduce a methodology, referred to as the dry-surface method, to calculate the work of adhesion of heterogeneous solid-liquid interfaces by molecular simulation. This method employs a straightforward thermodynamic integration approach to calculate the work of adhesion as the reversible work to turn off the attractive part of the actual solid-liquid interaction potential. It is formulated in such a way that it may be used either to evaluate the ability of force fields to reproduce reference values of the work of adhesion or to optimize force-field parameters with reference values of the work of adhesion as target quantities. The methodology is tested in the case of water on a generic model of nonpolar substrates with the structure of gold. It is validated through a quantitative comparison to phantom-wall calculations and against a previous characterization of the thermodynamics of the gold-water interface. It is found that the work of adhesion of water on nonpolar substrates is a nonlinear function of the microscopic solid-liquid interaction energy parameter. We also comment on the ability of mean-field approaches to predict the work of adhesion of water on nonpolar substrates. In addition, we discuss in detail the information on the solid-liquid interfacial thermodynamics delivered by the phantom-wall approach. We show that phantom-wall calculations yield the solid-liquid interfacial tension relative to the solid surface tension rather than the absolute solid-liquid interfacial tension as previously believed. read less NOT USED (high confidence) V. Rudyak and S. Krasnolutskii, “Simulation of the nanofluid viscosity coefficient by the molecular dynamics method,” Technical Physics. 2015. link Times cited: 43 NOT USED (high confidence) R. Grenier, Q. To, M. P. de Lara-Castells, and C. Léonard, “Argon Interaction with Gold Surfaces: Ab Initio-Assisted Determination of Pair Ar-Au Potentials for Molecular Dynamics Simulations.,” The journal of physical chemistry. A. 2015. link Times cited: 17 Abstract: Global potentials for the interaction between the Ar atom an… read moreAbstract: Global potentials for the interaction between the Ar atom and gold surfaces are investigated and Ar-Au pair potentials suitable for molecular dynamics simulations are derived. Using a periodic plane-wave representation of the electronic wave function, the nonlocal van-der-Waals vdW-DF2 and vdW-OptB86 approaches have been proved to describe better the interaction. These global interaction potentials have been decomposed to produce pair potentials. Then, the pair potentials have been compared with those derived by combining the dispersionless density functional dlDF for the repulsive part with an effective pairwise dispersion interaction. These repulsive potentials have been obtained from the decomposition of the repulsive interaction between the Ar atom and the Au2 and Au4 clusters and the dispersion coefficients have been evaluated by means of ab initio calculations on the Ar+Au2 complex using symmetry adapted perturbation theory. The pair potentials agree very well with those evaluated through periodic vdW-DF2 calculations. For benchmarking purposes, CCSD(T) calculations have also been performed for the ArAu and Ar+Au2 systems using large basis sets and extrapolations to the complete basis set limit. This work highlights that ab initio calculations using very small surface clusters can be used either as an independent cross-check to compare the performance of state-of-the-art vdW-corrected periodic DFT approaches or, directly, to calculate the pair potentials necessary in further molecular dynamics calculations. read less NOT USED (high confidence) A. Kyrychenko, “NANOGOLD decorated by pHLIP peptide: comparative force field study.,” Physical chemistry chemical physics : PCCP. 2015. link Times cited: 23 Abstract: The potential of gold nanoparticles (AuNPs) in therapeutic a… read moreAbstract: The potential of gold nanoparticles (AuNPs) in therapeutic and diagnostic cancer applications is becoming increasingly recognized, which focuses on their efficient and specific delivery from passive accumulation in tumour tissue to directly targeting tumor-specific biomarkers. AuNPs functionalized by pH low insertion peptide (pHLIP) have recently revealed the capability of targeting acidic tissues and inserting into cell membranes. However, the structure of AuNP-pHLIP conjugates and fundamental gold-peptide interactions still remain unknown. In this study, we have developed a series of molecular dynamics (MD) models reproducing a small gold nanoparticle coupled to pHLIP. We focus on Au135 nanoparticles that comprise a nearly spherical Au core (diameter ∼ 1.4 nm) functionalized with a monomaleimide moiety, mimicking a commercially available monomaleimido NANOGOLD® labelling agent. To probe the structure and folding of pHLIP, which is attached covalently to the maleimide NANOGOLD particle, we have benchmarked the performances of a series of popular, all-atom force fields (FF), including those of OPLS-AA, AMBER03, three variations of CHARMM FFs, as well as united-atom GROMOS G53A6 FF. We found that CHARMMs and OPLSAA FFs predict that in an aqueous salt solution at a neutral pH, pHLIP is partially bound onto the gold surface through some short hydrophobic peptide stretches, while at the same time, a large portion of peptide remains in solution. In contrast, AMBER03 and G53A6 FFs revealed the formation of compact, tightly bound peptide configurations adsorbed onto the nanoparticle core. To reproduce the experimental physical picture of the peptide adsorption onto gold in unfolded and unstructured conformations, our study suggests CHARMM36 and OPLS-AA FFs as a tool of choice for the computational studies of NANOGOLD decorated by pHLIP. read less NOT USED (high confidence) A. Kyrychenko, O. M. Korsun, I. Gubin, S. Kovalenko, and O. Kalugin, “Atomistic Simulations of Coating of Silver Nanoparticles with Poly(vinylpyrrolidone) Oligomers: Effect of Oligomer Chain Length,” Journal of Physical Chemistry C. 2015. link Times cited: 115 Abstract: Silver nanoparticles (AgNPs) possess unique physicochemical … read moreAbstract: Silver nanoparticles (AgNPs) possess unique physicochemical properties, which are different from those of matter of the same chemical composition on a larger scale. These features open up the opportunity for their use in many promising chemical and biomedical applications. In this study we have developed an atomistic model for molecular dynamics (MD) simulations of AgNP coated by poly(N-vinyl-2-pyrrolidone) (PVP) oligomers. We focus on identifying the relative length of PVP oligomers, enabling effective protecting of a crystalline silver core of 4.5 nm diameter from water contacts. Three different PVP-coated AgNP systems have been compared: (i) a nanoparticle coated by a mixture of short-chain PVP oligomers of the varying size and (ii,iii) the silver core wrapped by a single, long-chain PVP polymer with the number of monomers equal to 816 and 1440, respectively. We have validated the MD models of the PVP–AgNPs using a series of MD simulations reproducing adsorption, wrapping, and coating of PVP around a s... read less NOT USED (high confidence) I.-C. Yeh, J. L. Lenhart, and B. Rinderspacher, “Molecular Dynamics Simulations of Adsorption of Catechol and Related Phenolic Compounds to Alumina Surfaces,” Journal of Physical Chemistry C. 2015. link Times cited: 38 Abstract: We performed atomistically detailed molecular dynamics simul… read moreAbstract: We performed atomistically detailed molecular dynamics simulations to study adsorption behaviors of catechol, which is a key functional group in marine bioadhesives, to two different alumina surfaces in both anhydrous and aqueous conditions. In anhydrous conditions, without competing interactions from water molecules, catechol adsorbed to both hydroxylated and nonhydroxylated alumina surfaces. In aqueous conditions, catechol and several analogous phenolic compounds displaced water molecules and were strongly attracted to the nonhydroxylated alumina surface, which is more hydrophobic. When comparing the phenolic moieties near the hydroxylated alumina surface in aqueous conditions, the catechol molecules displayed the strongest adsorptions mainly through cooperative hydrogen bonding interactions of two neighboring hydroxyl groups with the surface hydroxyl groups of alumina as evidenced by the longer hydrogen bonding lifetimes and the larger number of adsorbed molecules near the surface. Insights gained from... read less NOT USED (high confidence) H. Ramezani-Dakhel, L. Ruan, Y. Huang, and H. Heinz, “Molecular Mechanism of Specific Recognition of Cubic Pt Nanocrystals by Peptides and of the Concentration‐Dependent Formation from Seed Crystals,” Advanced Functional Materials. 2015. link Times cited: 60 Abstract: Metal nanocrystals enable new functionality in sensors, biom… read moreAbstract: Metal nanocrystals enable new functionality in sensors, biomarkers, and catalysts while mechanisms of shape‐control in synthesis remain incompletely understood. This study explains mechanisms of biomolecule recognition and ligand‐directed growth of cubic platinum nanocrystals in atomic detail using molecular dynamics simulation (MD), synthesis, and characterization. Peptide T7 is shown to selectively recognize {100} bounded nanocubes through preferential adsorption near the edges as opposed to facet centers. Spatial preferences in peptide binding are related to differences in the binding of water molecules and conformational matching of polarizable atoms in the peptide to {100} epitaxial sites. Changes in peptide concentration also have profound impact on attraction versus repulsion on a given surface. As an example, the selective synthesis of cubes in the presence of peptide T7 demonstrates that only intermediate T7 concentration leads to high yield. High‐resolution transmission electron microscopy (HRTEM) shows concentration‐dependent changes in crystal shape, yield, and size. Large‐scale MD simulations explain associated differences in facet coverage and in adsorption energies of T7 peptides on cuboctahedral seed crystals, supporting a growth mechanism of adatom deposition. A similar analysis using a different peptide S7 is presented as well. Emerging computational opportunities to predict ligand binding to metal nanocrystals and rationalize growth preferences are summarized. read less NOT USED (high confidence) D. J. V. A. dos Santos and M. N. D. Cordeiro, “Effect of replacing [NTf2] by [PF6] anion on the [BMIm][NTf2] ionic liquid confined by gold,” Molecular Simulation. 2015. link Times cited: 14 Abstract: The effect of replacing bis(trifluoromethylsulphonyl)imide (… read moreAbstract: The effect of replacing bis(trifluoromethylsulphonyl)imide ([NTf2]) by hexafluorophosphate ([PF6]) in room temperature ionic liquid (IL) 1-butyl-3-methylimidazolium bis(trifluoromethylsulphonyl)imide ([BMIm][NTf2]) confined between two gold interfaces is herein reported through molecular dynamics simulations using all-atom non-polarisable force-fields. Five systems were studied ranging from pure [BMIm][NTf2] to pure [BMIm][PF6], with [PF6] molar fractions of 0, 0.125, 0.25, 0.375 and 0.5. Special attention was drawn to investigate the impact of the [PF6] anion on the IL, in particular on the first layers of the liquid in close contact with the solid gold surface. read less NOT USED (high confidence) T. Milek and D. Zahn, “Molecular simulation of AG nanoparticle nucleation from solution: redox-reactions direct the evolution of shape and structure.,” Nano letters. 2014. link Times cited: 30 Abstract: The association of Ag(+) ions and the early stage of Ag nano… read moreAbstract: The association of Ag(+) ions and the early stage of Ag nanoparticle nucleation are investigated from molecular dynamics simulations. Combining special techniques for tackling crystal nucleation from solution with efficient approaches to model redox-reactions, we unravel the structural evolution of forming silver nanoparticles as a function of the redox-potential in the solution. Within a range of only 1 eV, the redox-potential is demonstrated to have a drastic effect on both the inner structure and the overall shape of the forming particles. On the basis of our simulations we identify surface charge and its distribution as an atomic scale mechanism that accounts for creating/avoiding 5-fold coordination polyhedra and thus the degree of (multiple)-twinning in silver nanoparticles. read less NOT USED (high confidence) L. Ruan et al., “A rational biomimetic approach to structure defect generation in colloidal nanocrystals.,” ACS nano. 2014. link Times cited: 45 Abstract: Controlling the morphology of nanocrystals (NCs) is of param… read moreAbstract: Controlling the morphology of nanocrystals (NCs) is of paramount importance for both fundamental studies and practical applications. The morphology of NCs is determined by the seed structure and the following facet growth. While means for directing facet formation in NC growth have been extensively studied, rational strategies for the production of NCs bearing structure defects in seeds have been much less explored. Here, we report mechanistic investigations of high density twin formation induced by specific peptides in platinum (Pt) NC growth, on the basis of which we derive principles that can serve as guidelines for the rational design of molecular surfactants to introduce high yield twinning in noble metal NC syntheses. Two synergistic factors are identified in producing twinned Pt NCs with the peptide: (1) the altered reduction kinetics and crystal growth pathway as a result of the complex formation between the histidine residue on the peptide and Pt ions, and (2) the preferential stabilization of {111} planes upon the formation of twinned seeds. We further apply the discovered principles to the design of small organic molecules bearing similar binding motifs as ligands/surfactants to create single and multiple twinned Pd and Rh NCs. Our studies demonstrate the rich information derived from biomimetic synthesis and the broad applicability of biomimetic principles to NC synthesis for diverse property tailoring. read less NOT USED (high confidence) H. Heinz, “The role of chemistry and pH of solid surfaces for specific adsorption of biomolecules in solution—accurate computational models and experiment,” Journal of Physics: Condensed Matter. 2014. link Times cited: 26 Abstract: Adsorption of biomolecules and polymers to inorganic nanostr… read moreAbstract: Adsorption of biomolecules and polymers to inorganic nanostructures plays a major role in the design of novel materials and therapeutics. The behavior of flexible molecules on solid surfaces at a scale of 1–1000 nm remains difficult and expensive to monitor using current laboratory techniques, while playing a critical role in energy conversion and composite materials as well as in understanding the origin of diseases. Approaches to implement key surface features and pH in molecular models of solids are explained, and distinct mechanisms of peptide recognition on metal nanostructures, silica and apatite surfaces in solution are described as illustrative examples. The influence of surface energies, specific surface features and protonation states on the structure of aqueous interfaces and selective biomolecular adsorption is found to be critical, comparable to the well-known influence of the charge state and pH of proteins and surfactants on their conformations and assembly. The representation of such details in molecular models according to experimental data and available chemical knowledge enables accurate simulations of unknown complex interfaces in atomic resolution in quantitative agreement with independent experimental measurements. In this context, the benefits of a uniform force field for all material classes and of a mineral surface structure database are discussed. read less NOT USED (high confidence) H. K. Liu et al., “Interaction of substituted poly(phenyleneethynylene)s with ligand-stabilized CdS nanoparticles,” Journal of Materials Chemistry. 2014. link Times cited: 13 Abstract: The interfacial region between surface-modified semiconducti… read moreAbstract: The interfacial region between surface-modified semiconducting nanoparticles and polymers remains difficult to characterize experimentally in atomic resolution and contributes to the limited efficiency of hybrid photovoltaic cells and luminescent devices. Therefore, molecular dynamics simulation was employed to investigate the structure of cadmium sulfide nanoparticles capped with 3-mercaptopropyltrimethoxysilane (MPS) in contact with four substituted poly(phenyleneethynylene)s using a new force field for CdS and the polymer consistent force field. The results show that polymers with long alkyl side chains tend to wrap around the nanoparticles, and reduce backbone bending as well as polymer diffusion. The absence of alkyl side chains decreases the distance of conjugated backbones from the surface. Differences in the preferred location of functional groups of the polymers on the nanoparticle surface and of covalent versus non-covalent bonding were also monitored. Polymers containing terminal hydroxyl groups on alkyl side chains approach the surfactant corona and the core of the CdS-MPS nanoparticles. Close contact supports the formation of silyl ether cross-links although the interfacial structure upon bond formation remains similar to that of the non-covalently attached polymers. Ester groups bound to aromatic rings in the poly(phenyleneethynylene) backbone did not closely approach the nanoparticle surface. The results are the first step to understand nanoparticle–polymer interfaces at length scales of 10 nm and explore correlations with photovoltaic performance. read less NOT USED (high confidence) L. Bellucci and S. Corni, “Interaction with a gold surface reshapes the free energy landscape of alanine dipeptide,” Journal of Physical Chemistry C. 2014. link Times cited: 29 Abstract: The adsorption of the alanine dipeptide onto a gold surface … read moreAbstract: The adsorption of the alanine dipeptide onto a gold surface in aqueous conditions was explored by using molecular dynamics simulations. In particular, using Metadynamics, we reconstructed a three-dimensional free energy landscape to investigate the effect of the metal surface on such landscape. The results show that the adsorption process is able to strongly modify the internal free energy surface of the molecule, even changing its qualitative appearance. The new free energy global minimum corresponds to elongated conformations of the biomolecule, arranged in preferred orientations with respect to the surface. Therefore, the surface-induced changes in the relative stability of the local free energy minima and in the free-energy barriers between them show that the entire conformational ensemble and the interconformer dynamics are also affected by the presence of the surface. The alanine dipeptide is the simplest molecule that exhibits the main features shown by larger peptides. Therefore, these findings pr... read less NOT USED (high confidence) F. Emami et al., “Force Field and a Surface Model Database for Silica to Simulate Interfacial Properties in Atomic Resolution,” Chemistry of Materials. 2014. link Times cited: 322 Abstract: Silica nanostructures find applications in drug delivery, ca… read moreAbstract: Silica nanostructures find applications in drug delivery, catalysis, and composites, however, understanding of the surface chemistry, aqueous interfaces, and biomolecule recognition remain difficult using current imaging techniques and spectroscopy. A silica force field is introduced that resolves numerous shortcomings of prior silica force fields over the last 30 years and reduces uncertainties in computed interfacial properties relative to experiment from several 100% to less than 5%. In addition, a silica surface model database is introduced for the full range of variable surface chemistry and pH (Q2, Q3, Q4 environments with adjustable degree of ionization) that have shown to determine selective molecular recognition. The force field enables accurate computational predictions of aqueous interfacial properties of all types of silica, which is substantiated by extensive comparisons to experimental measurements. The parameters are integrated into multiple force fields for broad applicability to biomolecu... read less NOT USED (high confidence) M. Rosa, S. Corni, and R. D. Felice, “Enthalpy-Entropy Tuning in the Adsorption of Nucleobases at the Au(111) Surface.,” Journal of chemical theory and computation. 2014. link Times cited: 30 Abstract: The interaction of DNA molecules with hard substrates is of … read moreAbstract: The interaction of DNA molecules with hard substrates is of paramount importance both for the study of DNA itself and for the variety of possible technological applications. Interaction with inorganic surfaces strongly modifies the helical shape of DNA. Hence, an accurate understanding of DNA structure and function at interfaces is a fundamental question with enormous impact in science and society. This work sets the fundamentals for the simulation of entire DNA oligomers on gold surfaces in dry and wet conditions. Thanks to the new GolDNA-AMBER force field, which was derived from first principles and includes dispersion interactions and polarization effects, we simulated self-assembled guanine and adenine monolayers on Au(111) in vacuo and the adsorption of all nucleobases on the same substrate in aqueous conditions. The periodic monolayers obtained from classical simulations match very well those from first principle calculations and experiments, assessing the robustness of the force field and motivating the application to more complex systems for which quantum calculations are not affordable and experiments are elusive. The energetics of nucleobases on Au(111) in solution reveal fundamental physicochemical effects: we find that the adsorption paradigm shifts from purely enthalpic to dominantly entropic by changing the environment and aggregation phase. read less NOT USED (high confidence) T. Milek, T. Döpper, C. Neiss, A. Görling, and D. Zahn, “Charge distribution analysis in Agnm+$ \mathbfAg_\mathbfn^\mathbfm+ $clusters: molecular modeling and DFT calculations,” Journal of Molecular Modeling. 2014. link Times cited: 4 NOT USED (high confidence) N. Plattner and M. Meuwly, “The effect of classical and quantum dynamics on vibrational frequency shifts of H2 in clathrate hydrates.,” The Journal of chemical physics. 2014. link Times cited: 8 Abstract: Vibrational frequency shifts of H2 in clathrate hydrates are… read moreAbstract: Vibrational frequency shifts of H2 in clathrate hydrates are important to understand the properties and elucidate details of the clathrate structure. Experimental spectra of H2 in clathrate hydrates have been measured for different clathrate compositions, temperatures, and pressures. In order to establish reliable relationships between the clathrate structure, dynamics, and observed frequencies, calculations of vibrational frequency shifts in different clathrate environments are required. In this study, a combination of classical molecular dynamics simulations, electronic structure calculations, and quantum dynamical simulation is used to calculate relative vibrational frequencies of H2 in clathrate hydrates. This approach allows us to assess dynamical effects and simulate the change of vibrational frequencies with temperature and pressure. The frequency distributions of the H2 vibrations in the different clathrate cage types agree favorably with experiment. Also, the simulations demonstrate that H2 in the 5(12) cage is more sensitive to the details of the environment and to quantum dynamical effects, in particular when the cage is doubly occupied. We show that for the 5(12) cage quantum effects lead to frequency increases and double occupation is unlikely. This is different for the 5(12)6(4) cages for which higher occupation numbers than one H2 per cage are likely. read less NOT USED (high confidence) S. Ramakrishnan, M. Martin, T. Cloitre, L. Firlej, F. Cuisinier, and C. Gergely, “Insights on the Facet Specific Adsorption of Amino Acids and Peptides toward Platinum,” Journal of chemical information and modeling. 2013. link Times cited: 21 Abstract: Engineering shape-controlled bionanomaterials requires compr… read moreAbstract: Engineering shape-controlled bionanomaterials requires comprehensive understanding of interactions between biomolecules and inorganic surfaces. We explore the origin of facet-selective binding of peptides adsorbed onto Pt(100) and Pt(111) crystallographic planes. Using molecular dynamics simulations, we show that upon adsorption the peptides adopt a predictable conformation. We compute the binding energies of the amino acids constituting two adhesion peptides for Pt, S7, and T7 and demonstrate that peptides' surface recognition behavior that makes them unique among populations originates from differential adsorption of their building blocks. We find that the degree of peptide binding is mainly due to polar amino acids and the molecular architecture of the peptides close to the Pt facets. Our analysis is a first step in the prediction of enhanced affinity between inorganic materials and a peptides, toward the synthesis of novel nanomaterials with programmable shape, structure, and properties. read less NOT USED (high confidence) K. C. Jha, H. K. Liu, M. Bockstaller, and H. Heinz, “Facet Recognition and Molecular Ordering of Ionic Liquids on Metal Surfaces,” Journal of Physical Chemistry C. 2013. link Times cited: 73 Abstract: Ionic liquids are widely used as solvents and reaction media… read moreAbstract: Ionic liquids are widely used as solvents and reaction media due to low volatility, stability up to high temperature, and large dipole moment. Emergent applications also aim at the anisotropic growth of metal nanostructures in ionic liquids through facet-selective interactions although the governing mechanisms remain poorly understood. We employed a combination of quantum mechanical and classical simulations to analyze the structure and energetics of the self-assembly of ionic liquids on metal surfaces from single ion pairs to multilayers, using the example of 1-ethyl-3-methylimidazolium ethyl sulfate ([EMIM][ES]) on the crystallographic {111}, {100}, and {110} facets of gold. Adsorption is controlled by the interplay of soft epitaxy, ionic interactions, induced charges, and steric effects related to the geometry of the cation and anion. These factors lead to characteristic molecular patterns on individual surfaces. Binding energies are similar irrespective of surface coverage and only slightly increase f... read less NOT USED (high confidence) L. Wright, P. Rodger, T. Walsh, and S. Corni, “First-principles-based force field for the interaction of proteins with Au(100)(5 × 1) : an extension of GolP-CHARMM,” Journal of Physical Chemistry C. 2013. link Times cited: 54 Abstract: Noncovalent recognition between peptides and inorganic mater… read moreAbstract: Noncovalent recognition between peptides and inorganic materials is an established phenomenon. Key to exploiting these interactions in a wide range of materials self-assembly applications would be to harness the facet-selective control of peptide binding onto these materials. Fundamental understanding of what drives facet-selectivity in peptide binding is developing, but as yet is not sufficient to enable design of predictable facet-specific sequences. Computational simulation of the aqueous peptide–gold interface, commonly used to understand the mechanisms driving adsorption at an atomic level, has thus far neglected the role that surface reconstruction might play in facet specificity. Here the polarizable GolP-CHARMM suite of force fields is extended to include the reconstructed Au(100) surface. The force field, compatible with the bio-organic force field CHARMM, is parametrized using first-principles data. Our extended force field is tailored to reproduce the heterogeneity of weak chemisorbing N and S ... read less NOT USED (high confidence) L. Wright, C. Freeman, and T. Walsh, “Benzene adsorption at the aqueous (0 1 1) α-quartz interface: is surface flexibility important?,” Molecular Simulation. 2013. link Times cited: 15 Abstract: Atomistic simulations of molecular adsorption onto inorganic… read moreAbstract: Atomistic simulations of molecular adsorption onto inorganic substrates under aqueous conditions can be used to guide the rational design of new materials, fabricated using biomimetic methods. The success of such work depends critically on the model used. Here, we investigate the impact of using a rigid structural model of the (0 1 1) α-quartz surface, over a fully flexible model, on the calculated free energy change in the adsorption of a single molecule of benzene (a simple analogue of the amino acid phenylalanine) from liquid water. Subtle differences in the mobility of the adsorbate close to the surface result in the free energy of adsorption being overestimated by the rigid model, relative to the fully flexible case. Moreover, we find that the distribution of bound configurations of the adsorbate at their respective free energy minima is different between the two models. read less NOT USED (high confidence) Z. Tang et al., “Biomolecular recognition principles for bionanocombinatorics: an integrated approach to elucidate enthalpic and entropic factors.,” ACS nano. 2013. link Times cited: 129 Abstract: Bionanocombinatorics is an emerging field that aims to use c… read moreAbstract: Bionanocombinatorics is an emerging field that aims to use combinations of positionally encoded biomolecules and nanostructures to create materials and devices with unique properties or functions. The full potential of this new paradigm could be accessed by exploiting specific noncovalent interactions between diverse palettes of biomolecules and inorganic nanostructures. Advancement of this paradigm requires peptide sequences with desired binding characteristics that can be rationally designed, based upon fundamental, molecular-level understanding of biomolecule-inorganic nanoparticle interactions. Here, we introduce an integrated method for building this understanding using experimental measurements and advanced molecular simulation of the binding of peptide sequences to gold surfaces. From this integrated approach, the importance of entropically driven binding is quantitatively demonstrated, and the first design rules for creating both enthalpically and entropically driven nanomaterial-binding peptide sequences are developed. The approach presented here for gold is now being expanded in our laboratories to a range of inorganic nanomaterials and represents a key step toward establishing a bionanocombinatorics assembly paradigm based on noncovalent peptide-materials recognition. read less NOT USED (high confidence) Z. E. Hughes, L. Wright, and T. Walsh, “Biomolecular adsorption at aqueous silver interfaces: first-principles calculations, polarizable force-field simulations, and comparisons with gold.,” Langmuir : the ACS journal of surfaces and colloids. 2013. link Times cited: 65 Abstract: The molecular simulation of biomolecules adsorbed at noble m… read moreAbstract: The molecular simulation of biomolecules adsorbed at noble metal interfaces can assist in the development of bionanotechnology applications. In line with advances in polarizable force fields for adsorption at aqueous gold interfaces, there is scope for developing a similar force field for silver. One way to accomplish this is via the generation of in vacuo adsorption energies calculated using first-principles approaches for a wide range of different but biologically relevant small molecules, including water. Here, we present such first-principles data for a comprehensive range of bio-organic molecules obtained from plane-wave density functional theory calculations using the vdW-DF functional. As reported previously for the gold force field, GolP-CHARMM (Wright, L. B.; Rodger, P. M.; Corni, S.; Walsh, T. R. GolP-CHARMM: first-principles based force-fields for the interaction of proteins with Au(111) and Au(100). J. Chem. Theory Comput. 2013, 9, 1616-1630), we have used these data to construct a a new force field, AgP-CHARMM, suitable for the simulation of biomolecules at the aqueous Ag(111) and Ag(100) interfaces. This force field is derived to be consistent with GolP-CHARMM such that adsorption on Ag and Au can be compared on an equal footing. Our force fields are used to evaluate the water overlayer stability on both silver and gold, finding good agreement with known behaviors. We also calculate and compare the structuring (spatial and orientational) of liquid water adsorbed at both silver and gold. Finally, we report the adsorption free energy of a range of amino acids at both the Au(111) and Ag(111) aqueous interfaces, calculated using metadynamics. Stronger adsorption on gold was noted in most cases, with the exception being the carboxylate group present in aspartic acid. Our findings also indicate differences in the binding free energy profile between silver and gold for some amino acids, notably for His and Arg. Our analysis suggests that the relatively stronger structuring of the first water layer on silver, relative to gold, could give rise to these differences. read less NOT USED (high confidence) V. Petkov et al., “Resolving Atomic Ordering Differences in Group 11 Nanosized Metals and Binary Alloy Catalysts by Resonant High-Energy X-ray Diffraction and Computer Simulations,” Journal of Physical Chemistry C. 2013. link Times cited: 25 Abstract: Resonant high-energy X-ray diffraction coupled to atomic pai… read moreAbstract: Resonant high-energy X-ray diffraction coupled to atomic pair distribution function analysis and computer simulations is used to study the atomic-scale structure of group 11 nanosized metals and binary alloy catalysts. We find that nanosized Cu is quite disordered structurally whereas nanosized Ag and especially Au exhibit a very good degree of crystallinity. We resolve Cu–Cu and Ag–Ag atomic correlations from Au-involving ones in Au–Cu and Au–Ag nanoalloys and show that depending on the synthetic route group 11 binary alloys may adopt structural states that obey or markedly violate Vegard’s law. In the latter case, Cu and Ag atoms undergo substantial size expansion and contraction by as much as 0.3 and 0.03 A, respectively, while heavier Au atoms remain practically intact. The size change of Cu and Ag atoms does not follow Pauling’s rule of electronegativity predicting charge flow toward the more electronegative Au but occurs in a way such that Cu/Au and Ag/Au atomic size ratios in the nanoalloys become ... read less NOT USED (high confidence) R. H. Coppage et al., “Exploiting localized surface binding effects to enhance the catalytic reactivity of peptide-capped nanoparticles.,” Journal of the American Chemical Society. 2013. link Times cited: 84 Abstract: Peptide-based methods represent new approaches to selectivel… read moreAbstract: Peptide-based methods represent new approaches to selectively produce nanostructures with potentially important functionality. Unfortunately, biocombinatorial methods can only select peptides with target affinity and not for the properties of the final material. In this work, we present evidence to demonstrate that materials-directing peptides can be controllably modified to substantially enhance particle functionality without significantly altering nanostructural morphology. To this end, modification of selected residues to vary the site-specific binding strength and biological recognition can be employed to increase the catalytic efficiency of peptide-capped Pd nanoparticles. These results represent a step toward the de novo design of materials-directing peptides that control nanoparticle structure/function relationships. read less NOT USED (high confidence) T. Mandal, C. Dasgupta, and P. Maiti, “Engineering Gold Nanoparticle Interaction by PAMAM Dendrimer,” Journal of Physical Chemistry C. 2013. link Times cited: 44 Abstract: Bare faceted gold nanoparticles (AuNPs) have a tendency to a… read moreAbstract: Bare faceted gold nanoparticles (AuNPs) have a tendency to aggregate through a preferred attachment of the [111] surfaces. We have used fully atomistic classical molecular dynamics simulations to obtain a quantitative estimate of this surface interaction using umbrella sampling (US) at various temperatures. To tune this surface interaction, we use polyamidoamine (PAMAM) dendrimer to coat the gold surface under various conditions. We observe a spontaneous adsorption of the protonated as well as nonprotonated PAMAM dendrimer on the AuNP surface. The adsorbed dendrimer on the nanoparticle surface strongly alters the interaction between the nanoparticles. We calculate the interaction between dendrimer-coated AuNPs using US and show how the interaction between two bare faceted AuNPs can be tuned as a function of dendrimer concentration and charge (pH-dependent). With appropriate choice of the dendrimer concentration and charge, two strongly interacting AuNPs can be made effectively noninteracting. Our simulati... read less NOT USED (high confidence) C. Herbers, C. Li, and N. V. D. Vegt, “Grand challenges in quantum‐classical modeling of molecule–surface interactions,” Journal of Computational Chemistry. 2013. link Times cited: 5 Abstract: A detailed understanding of the adsorption of small molecule… read moreAbstract: A detailed understanding of the adsorption of small molecules or macromolecules to a materials surface is of importance, for example, in the context of material and biomaterial research. Classical atomistic simulations in principle provide microscopic insight in the complex entropic and enthalpic interplay at the interface. However, an application of classical atomistic simulation techniques to such interface systems is a nontrivial problem, mostly because commonly used force fields cannot be straightforwardly applied, as they are usually developed to reproduce bulk properties of either solids or liquids but not the interfacial region between two phases. Therefore, a dual‐scale modeling approach has often been the method of choice in the past, in which the classical force field is parameterized such that quantum chemical information on near‐surface conformations and adsorption energies is reproduced by the classical force field. We will discuss in this review the current state‐of‐the‐art of quantum‐classical modeling of molecule–surface interactions and outline the major challenges in this field. In this context, we will, among other things, lay emphasis on discussing ways to obtain representable force fields and propose systematic and system‐independent strategies to optimize the quantum‐classical fitting procedure. © 2013 Wiley Periodicals, Inc. read less NOT USED (high confidence) T. Roussel and L. Vega, “Modeling the Self-Assembly of Nano Objects: Applications to Supramolecular Organic Monolayers Adsorbed on Metal Surfaces.,” Journal of chemical theory and computation. 2013. link Times cited: 24 Abstract: We present here the implementation of a code developed for t… read moreAbstract: We present here the implementation of a code developed for the simulation of the self-assembly of nano objects (SANO). The code has the ability to predict the molecular self-assembly of different structural motifs by tuning the molecular building blocks as well as the metallic substrate. It consists in a two-dimensional grand canonical Monte Carlo (GCMC) approach developed to perform atomistic simulations of thousands of large organic molecules self-assembling on metal surfaces. By computing adsorption isotherms at room temperature and spanning over the characteristic submicrometric scales, we confront the robustness of the approach with three different well-known systems: ZnPcCl8 on Ag(111), CuPcF16 on Au(111), and PTBC on Ag(111). We retrieve respectively their square, oblique, and hexagonal supramolecular tilling. The code incorporates generalized force fields to describe the molecular interactions, which provides transferability to many organic building blocks and metal surfaces. Ultimately, the method is versatile and can be an interesting multiscale approach if one aims to bridge quantum level calculations to the experimental scales and within a treatment in temperature. read less NOT USED (high confidence) R. K. Mishra, R. Flatt, and H. Heinz, “Force Field for Tricalcium Silicate and Insight into Nanoscale Properties: Cleavage, Initial Hydration, and Adsorption of Organic Molecules,” Journal of Physical Chemistry C. 2013. link Times cited: 140 Abstract: Improvements in the sustainability and durability of buildin… read moreAbstract: Improvements in the sustainability and durability of building materials depend on understanding interfacial properties of various mineral phases at the nanometer scale. Tricalcium silicate (C3S) is the major constituent of cement clinker and we present and validate a force field for atomistic simulations that provides excellent agreement with available experimental data, including X-ray structures, cleavage energies, elastic moduli, and IR spectra. Using this model and available measurements, we quantify key surface and interface properties of the dry and superficially hydrated mineral. An extensive set of possible cleavage planes shows cleavage energies in a range of 1300 to 1600 mJ/m2 that are consistent with the observation of faceted crystallites with an aspect ratio near one. Using pure and hydroxylated surface models that represent the first step in the hydration reaction, we examined the adsorption mechanism of several organic amines and alcohols at different temperatures. Strong attraction between... read less NOT USED (high confidence) L. Wright, P. Rodger, S. Corni, and T. Walsh, “GolP-CHARMM: First-Principles Based Force Fields for the Interaction of Proteins with Au(111) and Au(100).,” Journal of chemical theory and computation. 2013. link Times cited: 202 Abstract: Computational simulation of peptide adsorption at the aqueou… read moreAbstract: Computational simulation of peptide adsorption at the aqueous gold interface is key to advancing the development of many applications based on gold nanoparticles, ranging from nanomedical devices to smart biomimetic materials. Here, we present a force field, GolP-CHARMM, designed to capture peptide adsorption at both the aqueous Au(111) and Au(100) interfaces. The force field, compatible with the bio-organic force field CHARMM, is parametrized using a combination of experimental and first-principles data. Like its predecessor, GolP (Iori, F.; et al. J. Comput. Chem.2009, 30, 1465), this force field contains terms to describe the dynamic polarization of gold atoms, chemisorbing species, and the interaction between sp(2) hybridized carbon atoms and gold. A systematic study of small molecule adsorption at both surfaces using the vdW-DF functional (Dion, M.; et al. Phys. Rev. Lett.2004, 92, 246401-1. Thonhauser, T.; et al. Phys. Rev. B2007, 76, 125112) is carried out to fit and test force field parameters and also, for the first time, gives unique insights into facet selectivity of gold binding in vacuo. Energetic and spatial trends observed in our DFT calculations are reproduced by the force field under the same conditions. Finally, we use the new force field to calculate adsorption energies, under aqueous conditions, for a representative set of amino acids. These data are found to agree with experimental findings. read less NOT USED (high confidence) R. Cardia, C. Melis, and L. Colombo, “Neutral-cluster implantation in polymers by computer experiments,” Journal of Applied Physics. 2013. link Times cited: 14 Abstract: In this work, we perform atomistic model potential molecular… read moreAbstract: In this work, we perform atomistic model potential molecular dynamics simulations by means of state-of-the art force-fields to study the implantation of a single Au nanocluster on a polydimethylsiloxane substrate. All the simulations have been performed on realistic substrate models containing up to ∼4.6 × 106 of atoms having depths up to ∼90 nm and lateral dimensions up to ∼25 nm. We consider both entangled-melt and cross-linked polydimethylsiloxane amorphous structures. We show that even a single cluster impact on the polydimethylsiloxane substrate remarkably changes the polymer local temperature and pressure. Moreover, we observe the presence of craters created on the polymer surface having lateral dimensions comparable to the cluster radius and depths strongly dependent on the implantation energy. Present simulations suggest that the substrate morphology is largely affected by the cluster impact and that most-likely such modifications favour the penetration of the next impinging clusters. read less NOT USED (high confidence) H. Heinz, T.-J. Lin, R. K. Mishra, and F. Emami, “Thermodynamically consistent force fields for the assembly of inorganic, organic, and biological nanostructures: the INTERFACE force field.,” Langmuir : the ACS journal of surfaces and colloids. 2013. link Times cited: 635 Abstract: The complexity of the molecular recognition and assembly of … read moreAbstract: The complexity of the molecular recognition and assembly of biotic-abiotic interfaces on a scale of 1 to 1000 nm can be understood more effectively using simulation tools along with laboratory instrumentation. We discuss the current capabilities and limitations of atomistic force fields and explain a strategy to obtain dependable parameters for inorganic compounds that has been developed and tested over the past decade. Parameter developments include several silicates, aluminates, metals, oxides, sulfates, and apatites that are summarized in what we call the INTERFACE force field. The INTERFACE force field operates as an extension of common harmonic force fields (PCFF, COMPASS, CHARMM, AMBER, GROMACS, and OPLS-AA) by employing the same functional form and combination rules to enable simulations of inorganic-organic and inorganic-biomolecular interfaces. The parametrization builds on an in-depth understanding of physical-chemical properties on the atomic scale to assign each parameter, especially atomic charges and van der Waals constants, as well as on the validation of macroscale physical-chemical properties for each compound in comparison to measurements. The approach eliminates large discrepancies between computed and measured bulk and surface properties of up to 2 orders of magnitude using other parametrization protocols and increases the transferability of the parameters by introducing thermodynamic consistency. As a result, a wide range of properties can be computed in quantitative agreement with experiment, including densities, surface energies, solid-water interface tensions, anisotropies of interfacial energies of different crystal facets, adsorption energies of biomolecules, and thermal and mechanical properties. Applications include insight into the assembly of inorganic-organic multiphase materials, the recognition of inorganic facets by biomolecules, growth and shape preferences of nanocrystals and nanoparticles, as well as thermal transitions and nanomechanics. Limitations and opportunities for further development are also described. read less NOT USED (high confidence) C. Huaigang, S. Huiping, and C. Fangqin, “The effect of ion charge-mass ratio on adsorption of heavy metals on magnetotactic bacteria,” African Journal of Microbiology Research. 2012. link Times cited: 1 Abstract: The magnetotactic bacteria have the properties of both captu… read moreAbstract: The magnetotactic bacteria have the properties of both capturing heavy metal ions and being quickly separated out from the wastewater, which makes them high quality adsorbents. The adsorption of ions usually shows selectivity in the multi component aqueous solutions. This paper investigated the mechanism of adsorption selectivity using the molecular dynamics method on the basis of periodic law of elements. A universal equation with respect to the mass, volume and charge of ions was deduced. Based on the analysis of the surficial properties, a model was built to describe the structure of magnetotactic bacteria using the organic groups. Then, the interface system of bacterium surface, aqueous solutions and heavy metal ions was developed and dynamics simulation was performed. It was found that the ion having smaller charge-mass ratio according to the periodic system of elements might be easier to be adsorbed. The ionic thermal motion could depress the adsorption of ions and might be one of the reasons which cause adsorption selectivity. Furthermore, the larger charge-mass ions were more inclined to be drifting away from the bacteria in the simulation. read less NOT USED (high confidence) S. V. Patwardhan et al., “Chemistry of aqueous silica nanoparticle surfaces and the mechanism of selective peptide adsorption.,” Journal of the American Chemical Society. 2012. link Times cited: 338 Abstract: Control over selective recognition of biomolecules on inorga… read moreAbstract: Control over selective recognition of biomolecules on inorganic nanoparticles is a major challenge for the synthesis of new catalysts, functional carriers for therapeutics, and assembly of renewable biobased materials. We found low sequence similarity among sequences of peptides strongly attracted to amorphous silica nanoparticles of various size (15-450 nm) using combinatorial phage display methods. Characterization of the surface by acid base titrations and zeta potential measurements revealed that the acidity of the silica particles increased with larger particle size, corresponding to between 5% and 20% ionization of silanol groups at pH 7. The wide range of surface ionization results in the attraction of increasingly basic peptides to increasingly acidic nanoparticles, along with major changes in the aqueous interfacial layer as seen in molecular dynamics simulation. We identified the mechanism of peptide adsorption using binding assays, zeta potential measurements, IR spectra, and molecular simulations of the purified peptides (without phage) in contact with uniformly sized silica particles. Positively charged peptides are strongly attracted to anionic silica surfaces by ion pairing of protonated N-termini, Lys side chains, and Arg side chains with negatively charged siloxide groups. Further, attraction of the peptides to the surface involves hydrogen bonds between polar groups in the peptide with silanol and siloxide groups on the silica surface, as well as ion-dipole, dipole-dipole, and van-der-Waals interactions. Electrostatic attraction between peptides and particle surfaces is supported by neutralization of zeta potentials, an inverse correlation between the required peptide concentration for measurable adsorption and the peptide pI, and proximity of cationic groups to the surface in the computation. The importance of hydrogen bonds and polar interactions is supported by adsorption of noncationic peptides containing Ser, His, and Asp residues, including the formation of multilayers. We also demonstrate tuning of interfacial interactions using mutant peptides with an excellent correlation between adsorption measurements, zeta potentials, computed adsorption energies, and the proposed binding mechanism. Follow-on questions about the relation between peptide adsorption on silica nanoparticles and mineralization of silica from peptide-stabilized precursors are raised. read less NOT USED (high confidence) P. Skrdla, “Roles of nucleation, denucleation, coarsening, and aggregation kinetics in nanoparticle preparations and neurological disease.,” Langmuir : the ACS journal of surfaces and colloids. 2012. link Times cited: 29 Abstract: Kinetic models for nucleation, denucleation, Ostwald ripenin… read moreAbstract: Kinetic models for nucleation, denucleation, Ostwald ripening (OR), and nanoparticle (NP) aggregation are presented and discussed from a physicochemical standpoint, in terms of their role in current NP preparations. Each of the four solid-state mechanisms discussed predict a distinct time dependence for the evolution of the mean particle radius over time. Additionally, they each predict visually different particle size distributions (PSDs) under limiting steady-state (time-independent) conditions. While nucleation and denucleation represent phase transformation mechanisms, OR and NP aggregation do not. Thus, when modeling solid-state kinetics relevant to NP processing, either the time evolution of the mean particle radius or the fractional conversion data should be fit using appropriate models (discussed herein), without confusing/combining the two classes of models. Experimental data taken from the recent literature are used to demonstrate the usefulness of the models in real-world applications. Specifically, the following examples are discussed: the preparation of bismuth NPs, the synthesis of copper indium sulfide nanocrystals, and the aggregation of neurological proteins. Because the last process is found to obey reaction-limited colloid aggregation (RLCA) kinetics, potential connections between protein aggregation rates, the onset of neurological disease, and population lifespan dynamics are suggested by drawing a parallel between RLCA kinetics and Gompertz kinetics. The physical chemistry underpinning NP aggregation is investigated, and a detailed definition of the rate constant of aggregation, k(a), is put forth that provides insight into the origin of the activation energy barrier of aggregation. For the two nanocrystal preparations investigated, the initial kinetics are found to be well-described by the author's dispersive kinetic model for nucleation-and-growth, while the late-stage NP size evolution is dominated by OR. At intermediate times, it is thought that the two mechanisms both contribute to the NP growth, resulting in PSD focusing as discussed in a previous work [Skrdla, P. J. J. Phys. Chem. C2012, 116, 214-225]. On the basis of these two mechanisms, a synthetic procedure for obtaining monodisperse NP PSDs, of small and/or systematically targeted mean sizes, is proposed. read less NOT USED (high confidence) V. Barone, M. Casarin, D. Forrer, S. Monti, and G. Prampolini, “Molecular Dynamics Simulations of the Self-Assembly of Tetraphenylporphyrin-Based Monolayers and Bilayers at a Silver Interface,” Journal of Physical Chemistry C. 2011. link Times cited: 19 Abstract: A theoretical study of the adsorption and dynamics of tetrap… read moreAbstract: A theoretical study of the adsorption and dynamics of tetraphenylporphyrins on a Ag(111) substrate and the subsequent aggregation of the formed monolayers with fullerene molecules is reported. Classical molecular dynamics simulations were able to reveal the various phases of monolayer and bilayer formation and succeeded in identifying all the interactions responsible for self-assembling and surface binding. Possible supramolecular configurations extracted from the molecular dynamics trajectories were classified and characterized in detail and revealed to be in satisfactory agreement with experimental data. read less NOT USED (high confidence) S. Laref, Y. Li, M. Bocquet, F. Delbecq, P. Sautet, and D. Loffreda, “Nature of adhesion of condensed organic films on platinum by first-principles simulations.,” Physical chemistry chemical physics : PCCP. 2011. link Times cited: 8 Abstract: Understanding the nature of the adhesion of an organic liqui… read moreAbstract: Understanding the nature of the adhesion of an organic liquid on a metal surface is of paramount importance for elucidating the stability and chemical reactivity at these complex interfaces. However, to date, the morphology, layering and chemical properties at organic liquid metal interfaces have been rarely known. Using semi-empirical dispersion corrected density functional theory calculations and ab initio molecular dynamics simulations, we show that carbon tetrachloride and ethanol films confined to a platinum surface alter their intrinsic properties and exhibit interfacial reactivity. A few interface carbon tetrachloride (ethanol) molecules adsorb dissociatively (molecularly) on platinum thanks to the surrounding medium. The adsorption strength of the interfacial molecules is consequently increased in the condensed phase as compared to the gas phase. This remarkable effect is rationalized by an interaction energy decomposition model and an electrostatic potential analysis. read less NOT USED (high confidence) R. Felice and S. Corni, “Simulation of Peptide–Surface Recognition,” Journal of Physical Chemistry Letters. 2011. link Times cited: 70 Abstract: The interaction between proteins and the surfaces of inorgan… read moreAbstract: The interaction between proteins and the surfaces of inorganic materials is of paramount importance in natural systems. In recent years, the scope of polypeptide–surface interactions has been enlarged in different directions also in synthetic systems toward technological contexts. Despite the pivotal role of protein–surface interactions in several technologically and socially relevant fields, they are still poorly understood, hindering a rational approach to fully exploit their potential and preventing the related technologies from taking off. Crucial questions remain open, related to the association mechanisms, control of binding events, and preservation of functionality. In this Perspective, we present a concise overview of the current knowledge in this field with emphasis on the computational modeling. We first introduce the motivations for studying peptide–surface recognition, and we then illustrate the experimental evidence and the open issues, which lead to the establishment of a theoretical plan fo... read less NOT USED (high confidence) P. Posocco, Z. Posel, M. Fermeglia, M. Lísal, and S. Pricl, “A molecular simulation approach to the prediction of the morphology of self-assembled nanoparticles in diblock copolymers,” Journal of Materials Chemistry. 2010. link Times cited: 34 Abstract: Mixing microphase-separating diblock copolymers and nanopart… read moreAbstract: Mixing microphase-separating diblock copolymers and nanoparticles can lead to the self-assembly of organic/inorganic hybrid materials that are spatially organized on the nanometre scale. Controlling particle location and patterns within the polymeric matrix domains remains, however, an unmet need. Computer simulation of such systems constitutes an interesting challenge since an appropriate technique would require the capturing of both the formation of the diblock mesophases and the copolymer–particle and particle–particle interactions, which can affect the ultimate structure of the material. In this work we discuss the application of Dissipative Particle Dynamics (DPD) to the study of the distribution of nanoparticles with different degree of functionality and volume fraction in a lamellar microsegregated copolymer template. The DPD parameters of the systems were calculated according to a multi-step modelling approach, i.e., from lower scale (atomistic) simulations. The results show that positioning and ordering of the nanoparticles, as well as the dimensions of the block domains depend on covering extent and volume fraction, in full agreement with experiments. The overall results provide molecular-level information for the rational, a priori design of new polymer–particle nanocomposites with ad hoc, tailored properties. read less NOT USED (high confidence) M. Hoefling, F. Iori, S. Corni, and K. Gottschalk, “The conformations of amino acids on a gold(111) surface.,” Chemphyschem : a European journal of chemical physics and physical chemistry. 2010. link Times cited: 58 Abstract: The interactions of amino acids with inorganic surfaces are … read moreAbstract: The interactions of amino acids with inorganic surfaces are of interest for biologists and biotechnologists alike. However, the structural determinants of peptide-surface interactions have remained elusive, but are important for a structural understanding of the interactions of biomolecules with gold surfaces. Molecular dynamics simulations are a tool to analyze structures of amino acids on surfaces. However, such an approach is challenging due to lacking parameterization for many surfaces and the polarizability of metal surfaces. Herein, we report DFT calculations of amino acid fragments in vacuo and molecular dynamics simulations of the interaction of all amino acids with a gold(111) surface in explicit solvent, using the recently introduced polarizable gold force field GolP. We describe preferred orientations of the amino acids on the metal surface. We find that all amino acids preferably interact with the gold surface at least partially with their backbone, underlining an unfolding propensity of gold surfaces. read less NOT USED (high confidence) P. V. Komarov, V. Alekseev, S. Khizhnyak, M. Ovchinnikov, and P. Pakhomov, “Study of silver mercaptide nanocluster formation in cystein-silver solution by atomistic molecular dynamics simulation,” Nanotechnologies in Russia. 2010. link Times cited: 2 NOT USED (high confidence) H. Heinz, “Computational screening of biomolecular adsorption and self‐assembly on nanoscale surfaces,” Journal of Computational Chemistry. 2009. link Times cited: 62 Abstract: The quantification of binding properties of ions, surfactant… read moreAbstract: The quantification of binding properties of ions, surfactants, biopolymers, and other macromolecules to nanometer‐scale surfaces is often difficult experimentally and a recurring challenge in molecular simulation. A simple and computationally efficient method is introduced to compute quantitatively the energy of adsorption of solute molecules on a given surface. Highly accurate summation of Coulomb energies as well as precise control of temperature and pressure is required to extract the small energy differences in complex environments characterized by a large total energy. The method involves the simulation of four systems, the surface‐solute–solvent system, the solute–solvent system, the solvent system, and the surface‐solvent system under consideration of equal molecular volumes of each component under NVT conditions using standard molecular dynamics or Monte Carlo algorithms. Particularly in chemically detailed systems including thousands of explicit solvent molecules and specific concentrations of ions and organic solutes, the method takes into account the effect of complex nonbond interactions and rotational isomeric states on the adsorption behavior on surfaces. As a numerical example, the adsorption of a dodecapeptide on the Au {111} and mica {001} surfaces is described in aqueous solution. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 read less NOT USED (high confidence) H. Heinz et al., “Nature of molecular interactions of peptides with gold, palladium, and Pd-Au bimetal surfaces in aqueous solution.,” Journal of the American Chemical Society. 2009. link Times cited: 330 Abstract: We investigated molecular interactions involved in the selec… read moreAbstract: We investigated molecular interactions involved in the selective binding of several short peptides derived from phage-display techniques (8-12 amino acids, excluding Cys) to surfaces of Au, Pd, and Pd-Au bimetal. The quantitative analysis of changes in energy and conformation upon adsorption on even {111} and {100} surfaces was carried out by molecular dynamics simulation using an efficient computational screening technique, including 1000 explicit water molecules and physically meaningful peptide concentrations at pH = 7. Changes in chain conformation from the solution to the adsorbed state over the course of multiple nanoseconds suggest that the peptides preferably interact with vacant sites of the face-centered cubic lattice above the metal surface. Residues that contribute to binding are in direct contact with the metal surfaces, and less-binding residues are separated from the surface by one or two water layers. The strength of adsorption ranges from 0 to -100 kcal/(mol peptide) and scales with the surface energy of the metal (Pd surfaces are more attractive than Au surfaces), the affinity of individual residues versus the affinity of water, and conformation aspects, as well as polarization and charge transfer at the metal interface (only qualitatively considered here). A hexagonal spacing of approximately 1.6 A between available lattice sites on the {111} surfaces accounts for the characteristic adsorption of aromatic side groups and various other residues (including Tyr, Phe, Asp, His, Arg, Asn, Ser), and a quadratic spacing of approximately 2.8 A between available lattice sites on the {100} surface accounts for a significantly lower affinity to all peptides in favor of mobile water molecules. The combination of these factors suggests a "soft epitaxy" mechanism of binding. On a bimetallic Pd-Au {111} surface, binding patterns are similar, and the polarity of the bimetal junction can modify the binding energy by approximately 10 kcal/mol. The results are semiquantitatively supported by experimental measurements of the affinity of peptides and small molecules to metal surfaces as well as results from quantum-mechanical calculations on small peptide and surface fragments. Interfaces were modeled using the consistent valence force field extended for Lennard-Jones parameters for fcc metals which accurately reproduce surface and interface energies [Heinz, H.; Vaia, R. A.; Farmer, B. L.; Naik, R. R. J. Phys. Chem. C 2008, 112, 17281-17290]. read less NOT USED (high confidence) R. Pandey et al., “Adsorption of peptides (A3, Flg, Pd2, Pd4) on gold and palladium surfaces by a coarse-grained Monte Carlo simulation.,” Physical chemistry chemical physics : PCCP. 2009. link Times cited: 88 Abstract: Monte Carlo simulations are performed to study adsorption an… read moreAbstract: Monte Carlo simulations are performed to study adsorption and desorption of coarse-grained peptide chains on generic gold and palladium surfaces in the presence of solvent. The atomistic structural details are ignored within the amino acid residues; however, their specificity and hydrophobicity are incorporated via an interaction matrix guided by atomistic simulation. Adsorption probabilities of the peptides A3, Flg, Pd2, Pd4, Gly10, Pro10 on gold and palladium surfaces are studied via analysis of the mobility of each residue, the interaction energy with the surface, profiles of the proximity to the surface, the radius of gyration, and comparisons to homopolymers. In contrast to the desorption of Gly10 and Pro10 (with faster global dynamics), peptides Pd2, Pd4, Flg, and A3 exhibit various degrees of adsorption on gold and palladium surfaces (with relatively slower dynamics). Adsorption on both gold and palladium occurs through aromatic anchoring residues Tyr2 and Phe12 in A3, Tyr2 in Flg, Phe2, His10 and His12 in Pd2, and His6 and His11 in Pd4. A lower (more negative) surface-interaction energy of these residues and lower mobility on palladium lead us to conclude that they are slightly more likely to be adsorbed on palladium surfaces than on gold. read less NOT USED (high confidence) D. Roccatano, “The Molecular Dynamics Simulation of Peptides on Gold Nanosurfaces.,” Methods in molecular biology. 2020. link Times cited: 1 NOT USED (high confidence) L. Kahle, “Modeling, understanding, and screening fast lithium-ion conductors for solid-state electrolytes.” 2019. link Times cited: 0 Abstract: The Li-ion batteries within the consumer electronics used in… read moreAbstract: The Li-ion batteries within the consumer electronics used in our everyday life suffer from well-known deficiencies due to the prevalent use of organic liquid electrolytes: the narrow electrochemical stability windows of the organic solvents used in these electrolytes prevent the use of high-voltage cathodes, and the flammability and volatility of the solvent molecules constitute a safety hazard. Replacing the organic liquid electrolytes with inorganic solid-state electrolytes could lead to significantly safer batteries with a higher energy density. However, most known solid-state Li-ion conductors are not yet suitable for application as electrolytes, since no material satisfies the stringent requirements for safety in a high-performance battery: a wide electrochemical stability window, high mechanical stability, very low electronic mobility, and fast Li-ion conduction. Searching for materials that satisfy those requirements by via experiment is too human-labor intensive to be done on a large scale due to the time-consuming materials synthesis and experimental characterization. Computational approaches can be easily parallelized, enabling the screening of thousands of materials to find new solid-state electrolytes for Li-ion batteries. Such a computational high-throughput screening requires an automated framework and methods that are accurate enough to predict the quantities of interest but also of sufficient computational efficiency to be applied on many materials. However, known methods to predict the Li-ion conductivity in a material are either computationally too expensive to be applied on a large scale, as is the case for first-principles molecular dynamics, or are not general enough to be performed across a wide range of materials. We present a model to calculate the Li-ion diffusion coefficient and conductivity efficiently by applying physically motivated approximations to the Hamiltonian of density-functional theory. The results obtained using this “pinball model” compare well to those from accurate first-principles molecular dynamics. This agreement provides interesting insights into the dependence of the valence electronic charge density of an ionic system on the motion of Li ions and suggests that the model can be used for screening applications. After its derivation and validation, we use the pinball model in a computational high-throughput screening to find structures with promising Li-ion diffusion. These candidate solid-state electrolytes are characterized with first-principles molecular dynamics to obtain more accurate predictions of the diffusion coefficients and pathways in these materials. The pinball model, combined with the efforts to automate molecular dynamics simulations, results in a large quantity of data stored in the form of molecular dynamics trajectories, motivating a read less NOT USED (high confidence) S. Ramakrishnan, J. Zhu, and C. Gergely, “Organic–inorganic interface simulation for new material discoveries,” Wiley Interdisciplinary Reviews: Computational Molecular Science. 2017. link Times cited: 12 Abstract: Organic–inorganic interactions are of high importance in sev… read moreAbstract: Organic–inorganic interactions are of high importance in several biological processes and in modern nanobiotechnological applications. Despite its significance in interface sciences, the basic mechanism of biomolecules’ specific binding to a surface is still not well understood. Current experimental methods have not reached the level either to follow the dynamics of interactions at the picosecond scale or to observe the surface morphology at the nanoscale level. The increasing interest in bio‐interfaces particularly for engineering applications demands proteins or peptides to be designed to recognize the inorganic surface with high specificity. Molecular simulation has been well adopted in the past couple of decades to decipher the protein–surface interactions at different levels of time and length scales. Several molecular simulation methods such as quantum mechanics, atomistic, and coarse grain simulations were employed in this domain of research, but the continuous improvements in interfacial force field (FF) development, availability of experimental data and new sampling methods make the atomistic simulation more attractive due to the offered accurate representation of protein adsorption behavior at the atomic level. However, the exactitude of such simulations entirely depends on the applied FF parameters, conformational sampling, and the solvation effects. In this overview, we briefly summarize the applicability of different simulation methods and of interface FFs. We also present the recent advances in the simulation of protein–surface interactions, and the challenges posed by the current simulation methods to reproduce the exact phenomenon. Future directions in this research field are also discussed. WIREs Comput Mol Sci 2017, 7:e1277. doi: 10.1002/wcms.1277 read less NOT USED (high confidence) A. Awarke, M. Wittler, S. Pischinger, and J. Bockstette, “A 3D Mesoscale Model of the Collector-Electrode Interface in Li-Ion Batteries,” Journal of The Electrochemical Society. 2012. link Times cited: 19 Abstract: To gain insight into the collector-electrode interface in Li… read moreAbstract: To gain insight into the collector-electrode interface in Li-ion batteries, a mesoscale model resolved at the particle scale in a representative volume element domain was developed. The underlying microstructure was first generated using a random packing and a dynamic collision algorithm. A finite element stress analysis was then used to calculate the deformations which are induced by Li-ion concentrations. The collector-electrode mechanical interaction was modeled using an adhesive contact law which was derived from the atomistic Lennard-Jones energy potential considering Van der Waals attractions. A finite element electrical analysis followed to calculate the collector contact resistance considering quantum tunneling currents. As a model application, we elaborated the role of the electrode microstructure by evaluating the damage and contact resistances for 8 various LiFeP0 4 based cathodes. We found that optimum interfaces would be achieved using a rough collector, low porosity, small particle sizes with disk like shapes and conductive additives in the interstitial sites. Pressure application was also beneficial. The developed model could be used either separately prior to commonly used porous electrode electrochemical models which require the collector-contact resistance as a parameter, or coupled in a 3D mesoscale electrochemical analysis so that a mechanical-electrochemical interaction would be considered. read less NOT USED (definite) J. Puibasset, “Elastic Compliance and Stiffness Matrix of the FCC Lennard-Jones Thin Films: Influence of Thickness and Temperature,” The Journal of Physical Chemistry C. 2019. link Times cited: 1 Abstract: The face-centered cubic (fcc) Lennard-Jones crystal is used … read moreAbstract: The face-centered cubic (fcc) Lennard-Jones crystal is used as a generic model of a solid to study the elastic properties of thin films as a function of thickness and temperature. The Monte Carlo algorithm is used to calculate the average deformations along the axes in the isostress–isothermal ensemble that mimics a real uniaxial loading experiment. Four independent parameters (tetragonal symmetry without shear) have been calculated for film thicknesses ranging from 4 to 12 atomic layers and for five reduced temperatures between 0 and 0.5 e/kB, where e is the energetic parameter of the Lennard-Jones potential and kB is Boltzmann’s constant. These parameters (Poisson’s ratio and moduli) give the compliance matrix, which is inverted to obtain the stiffness coefficients. It is shown that the three Poisson’s ratios exhibit a good linearity with the inverse of the film thickness, while this is not the case for the moduli and the compliance coefficients. Remarkably, the stiffness coefficients do exhibit a good linearity with the inverse of the film thickness, including the limiting value of infinite thickness (bulk solid) obtained by applying periodic boundary conditions in all directions. This linearity suggests to interpret the results in terms of a bulk + surface decomposition. However, the surface stiffness matrix deduced from the slopes has nonzero components along the out-of-plane direction—an unexpected observation in the framework of the surface stress theory. read less NOT USED (definite) V. Hitaishi et al., “Controlling Redox Enzyme Orientation at Planar Electrodes,” Catalysts. 2018. link Times cited: 62 Abstract: Redox enzymes, which catalyze reactions involving electron t… read moreAbstract: Redox enzymes, which catalyze reactions involving electron transfers in living organisms, are very promising components of biotechnological devices, and can be envisioned for sensing applications as well as for energy conversion. In this context, one of the most significant challenges is to achieve efficient direct electron transfer by tunneling between enzymes and conductive surfaces. Based on various examples of bioelectrochemical studies described in the recent literature, this review discusses the issue of enzyme immobilization at planar electrode interfaces. The fundamental importance of controlling enzyme orientation, how to obtain such orientation, and how it can be verified experimentally or by modeling are the three main directions explored. Since redox enzymes are sizable proteins with anisotropic properties, achieving their functional immobilization requires a specific and controlled orientation on the electrode surface. All the factors influenced by this orientation are described, ranging from electronic conductivity to efficiency of substrate supply. The specificities of the enzymatic molecule, surface properties, and dipole moment, which in turn influence the orientation, are introduced. Various ways of ensuring functional immobilization through tuning of both the enzyme and the electrode surface are then described. Finally, the review deals with analytical techniques that have enabled characterization and quantification of successful achievement of the desired orientation. The rich contributions of electrochemistry, spectroscopy (especially infrared spectroscopy), modeling, and microscopy are featured, along with their limitations. read less NOT USED (definite) A. Gooneie, J. Gonzalez-Gutierrez, and C. Holzer, “Atomistic Modelling of Confined Polypropylene Chains between Ferric Oxide Substrates at Melt Temperature,” Polymers. 2016. link Times cited: 18 Abstract: The interactions and conformational characteristics of confi… read moreAbstract: The interactions and conformational characteristics of confined molten polypropylene (PP) chains between ferric oxide (Fe2O3) substrates were investigated by molecular dynamics (MD) simulations. A comparative analysis of the adsorbed amount shows strong adsorption of the chains on the high-energy surface of Fe2O3. Local structures formed in the polymer film were studied utilizing density profiles, orientation of bonds, and end-to-end distance of chains. At interfacial regions, the backbone carbon-carbon bonds of the chains preferably orient in the direction parallel to the surface while the carbon-carbon bonds with the side groups show a slight tendency to orient normal to the surface. Based on the conformation tensor data, the chains are compressed in the normal direction to the substrates in the interfacial regions while they tend to flatten in parallel planes with respect to the surfaces. The orientation of the bonds as well as the overall flattening of the chains in planes parallel to the solid surfaces are almost identical to that of the unconfined PP chains. Also, the local pressure tensor is anisotropic closer to the solid surfaces of Fe2O3 indicating the influence of the confinement on the buildup imbalance of normal and tangential pressures. read less NOT USED (definite) N. M. Bedford et al., “Peptide-Directed PdAu Nanoscale Surface Segregation: Toward Controlled Bimetallic Architecture for Catalytic Materials.,” ACS nano. 2016. link Times cited: 53 Abstract: Bimetallic nanoparticles are of immense scientific and techn… read moreAbstract: Bimetallic nanoparticles are of immense scientific and technological interest given the synergistic properties observed when two different metallic species are mixed at the nanoscale. This is particularly prevalent in catalysis, where bimetallic nanoparticles often exhibit improved catalytic activity and durability over their monometallic counterparts. Yet despite intense research efforts, little is understood regarding how to optimize bimetallic surface composition and structure synthetically using rational design principles. Recently, it has been demonstrated that peptide-enabled routes for nanoparticle synthesis result in materials with sequence-dependent catalytic properties, providing an opportunity for rational design through sequence manipulation. In this study, bimetallic PdAu nanoparticles are synthesized with a small set of peptides containing known Pd and Au binding motifs. The resulting nanoparticles were extensively characterized using high-resolution scanning transmission electron microscopy, X-ray absorption spectroscopy, and high-energy X-ray diffraction coupled to atomic pair distribution function analysis. Structural information obtained from synchrotron radiation methods was then used to generate model nanoparticle configurations using reverse Monte Carlo simulations, which illustrate sequence dependence in both surface structure and surface composition. Replica exchange with solute tempering molecular dynamics simulations were also used to predict the modes of peptide binding on monometallic surfaces, indicating that different sequences bind to the metal interfaces via different mechanisms. As a testbed reaction, electrocatalytic methanol oxidation experiments were performed, wherein differences in catalytic activity are clearly observed in materials with identical bimetallic composition. Taken together, this study indicates that peptides could be used to arrive at bimetallic surfaces with enhanced catalytic properties, which could be leveraged for rational bimetallic nanoparticle design using peptide-enabled approaches. read less NOT USED (definite) S. Jarvis et al., “Physisorption controls the conformation and density of states of an adsorbed porphyrin,” Journal of Physical Chemistry C. 2015. link Times cited: 34 Abstract: Conformational changes caused by adsorption can dramatically… read moreAbstract: Conformational changes caused by adsorption can dramatically affect a molecule’s properties. Despite extensive study, however, the exact mechanisms underpinning conformational switching are often unclear. Here we show that the conformation of a prototypical flexible molecule, the free-base tetra(4-bromophenyl) porphyrin, adsorbed on Cu(111), depends critically on its precise adsorption site and that, remarkably, large conformational changes are dominated by van der Waals interactions between the molecule and the substrate surface. A combination of scanning probe microscopy, single-molecule manipulation, DFT with dispersion density functional theory, and molecular dynamics simulations show that van der Waals forces drive significant distortions of the molecular architecture so that the porphyrin can adopt one of two low-energy conformations. We find that adsorption driven by van der Waals forces alone is capable of causing large shifts in the molecular density of states, despite the apparent absence of che... read less NOT USED (definite) T.-J. Lin and H. Heinz, “Accurate Force Field Parameters and pH Resolved Surface Models for Hydroxyapatite to Understand Structure, Mechanics, Hydration, and Biological Interfaces,” arXiv: Materials Science. 2015. link Times cited: 118 Abstract: Mineralization of bone and teeth involves interactions betwe… read moreAbstract: Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior models for atomistic simulations are limited in the representation of chemical bonding, surface chemistry, and interfacial interactions. This work introduces an accurate force field along with pH-resolved surface models for hydroxyapatite to represent chemical bonding, structural, surface, interfacial, and mechanical properties in quantitative agreement with experiment. The accuracy is orders of magnitude higher in comparison to earlier models to facilitate quantitative monitoring of inorganic-biological assembly. The force field is integrated into the CHARMM, AMBER, OPLS-AA, PCFF, and INTERFACE force fields to enable realistic simulations of apatite-biological systems of any composition and ionic strength. Specifically, the parameters reproduce lattice constants (<0.5% deviation), IR spectrum, cleavage energies, immersion energies in water (<5% deviation), and elastic constants (<10% deviation) of hydroxyapatite in comparison to experiment. Interactions between mineral, water, and organic compounds are represented by standard combination rules in the force field without additional adjustable parameters and shown to achieve quantitative accuracy. Surface models for common (001), (010), (020), (101) facets and nanocrystals are introduced as a function of pH on the basis of extensive experimental data. New insight into surface and immersion energies, the structure of aqueous interfaces, density profiles, and superficial dissolution is described. Mechanisms of specific binding of peptides, drugs, and mineralization can be analyzed and the force field is extensible to substituted and defective apatites as well as to other calcium phosphate phases. read less NOT USED (definite) G. Nawrocki and M. Cieplak, “Aqueous Amino Acids and Proteins Near the Surface of Gold in Hydrophilic and Hydrophobic Force Fields,” Journal of Physical Chemistry C. 2014. link Times cited: 32 Abstract: We calculate potentials of the mean force for 20 amino acids… read moreAbstract: We calculate potentials of the mean force for 20 amino acids in the vicinity of the (111) surface of gold, for several dipeptides, and for some analogues of the side chains, using molecular dynamics simulations and the umbrella sampling method. We compare results obtained within three different force fields: one hydrophobic (for a contaminated surface) and two hydrophilic. All of these fields lead to good binding with very different specificities and different patterns in the density and polarization of water. The covalent bond with the sulfur atom on cysteine is modeled by the Morse potential. We demonstrate that binding energies of dipeptides are different than the combined binding energies of their amino acidic components. For the hydrophobic gold, adsorption events of a small protein are driven by attraction to the strongest binding amino acids. This is not so in the hydrophilic cases—a result of smaller specificities combined with the difficulty for proteins, but not for single amino acids, to penetr... read less NOT USED (definite) “Diagonal flipping of a Rhombus as elementary act of a polymorphic transformation. Calculation of energy threshold for the transformation in metals,” arXiv: Materials Science. 2018. link Times cited: 0 Abstract: Diagonal flipping of a rhombus consisting of two triangles s… read moreAbstract: Diagonal flipping of a rhombus consisting of two triangles sharing a common edge with atoms (ions) in vertices of the triangles is considered as an elementary act of the polymorphic transformation in metals. The estimation of the energy threshold for the diagonal flipping has been carried out for various combination of rhombus vertices occupation by Fe, Cr, and Mn atoms. The energy threshold has been calculated in the framework of Morse interatomic pair potential. Numerical coefficients for the approximation of the pair potential function have been scaled by experimental values of the sublimation energy and temperature dependencies of elastic constants for Fe, Cr, Mn. Values of the energy threshold at 1193 K were estimated equal to 195, 150 and 94 kJ/mole for pure Cr, Fe and Mn respectively, i.e. in the same sequence as values of elastic bulk modulus for these metals. The substitution of one Fe atom by Cr or Mn atom results in alteration of the energy threshold. This alteration is dependent on the angle type at this vertex (an acute or obtuse angle), as well as on the ratio of bulk modulus values of iron and alloying element. read less |