Abstract: Zinc oxide nanostructures are used in an ever increasing line of applications in technology and biomedical fields. This requires a detailed understanding of the phenomena that occur at the surface particularly in aqueous environments and in contact with biomolecules. In this work, we used ab initio molecular dynamics (AIMD) simulations to determine structural details of ZnO surfaces in water and to develop a general and transferable classical force field for hydrated ZnO surfaces. AIMD simulations show that water molecules dissociate near unmodified ZnO surfaces, forming hydroxyl groups at about 65% of the surface Zn atoms and protonating 3-coordinated surface oxygen atoms, while the rest of the surface Zn atoms bind molecularly adsorbed waters. Several force field atom types for ZnO surface atoms were identified by analysis of the specific connectivities of atoms. The analysis of the electron density was then used to determine partial charges and Lennard-Jones parameters for the identified force field atom types. The obtained force field was validated by comparison with AIMD results and with available experimental data on adsorption and immersion enthalpies, as well as adsorption free energies of several amino acids in methanol. The developed force field can be used for modeling of ZnO in aqueous and other fluid environments and in interaction with biomolecules. read less

Abstract: A deep understanding of surface catalysis recombination characteristics is significant for accurately predicting the aeroheating between hypersonic non-equilibrium flow and thermal protection materials, while a de-coupling sensitivity analysis of various influential factors is still lacking. A gas–solid interface (GSI) model with a hyperthermal flux boundary was established to investigate the surface catalysis recombination mechanisms on nanoscale silica surfaces. Using the reactive molecular dynamics (RMD) simulation method, the effects of solid surface temperature, gas incident angle, and translational energy on the silica surface catalysis recombination were qualified under hyperthermal atomic oxygen (AO), atomic nitrogen (AN), and various AN/AO gas mixtures’ influence. It can be found that, though the Eley–Rideal (E–R) recombination mechanism plays a dominant role over the Langmuir–Hinshelwood (L–H) mechanism for all the sensitivity analyses, a non-linear increasing pattern of AO recombination coefficient γO2 with the increase in incident angle θin and translational energy Ek is observed. Compared with the surface catalysis under hyperthermal AO impact, the AN surface adsorption fraction shows an inverse trend with the increase in surface temperature, which suggests the potential inadequacy of the traditional proportional relationship assumptions between the surface adsorption concentration and the surface catalysis recombination coefficient for other species’ impact instead of AOs. For the incoming bi-component AO/AN gas mixtures, the corresponding surface catalysis coefficient is not the simple superposition of the effects of individual gases but is affected by both the intramolecular bond energies (e.g., O2, N2) and intermolecular energies (e.g., Si/N, Si/O). read less

Abstract: A reactive field force potential has been created in order to model the structural effects of low percentage dopant aluminium in a zinc oxide (ZnO) system. The potential’s parameters were fitted to configurations computed with density functional theory: binding energies were considered for surface structures and for Al in ZnO bulk crystals. Energies for Zn–Al alloys were also considered. Forces were fit to zero for all equilibrium structures and were also fitted for some non-equilibrium structures. As a first application of the model, the energetic deposition (0.1–40 eV) of an aluminium atom onto the polar surface of a ZnO (0001¯) is considered. For low energies the Al atom attaches to two preferred sites on the surface but as the energy increases above ≈15 eV subplantation is preferred at near normal incidence, with high diffusion barriers between stable sites. At these energies, reflection of the Al atom occurs at incident angles above ≈55° . read less

Abstract: Metal oxide nanoparticles have great potential for selective adsorption and catalytic degradation of contaminants from aqueous solutions. In this study, we employ mass spectrometry and molecular dynamics simulations to better understand the chemical and physical mechanisms determining the affinity of chlorobenzenes and polychlorinated biphenyls (PCBs) for zinc oxide nanoparticles (ZnO NPs). The experiments and simulations both demonstrate that the adsorption coefficients for chlorobenzenes increase steadily with the number of chlorine atoms, while, for PCBs, the relation is more complex. The simulations link this complexity to chlorine atoms at ortho positions hindering coplanar conformations. For a given number of chlorine atoms, the simulations predict decreasing adsorption affinity with increasing numbers of ortho substitutions. Consequently, the simulations predict that some of the highest adsorption affinities for ZnO NPs are exhibited by dioxin-like PCBs, suggesting the possibility of selective sequestration of these most acutely toxic PCBs. Remarkably, the experiments show that the PCB adsorption coefficients of ZnO NPs with diameters ≤ 80 nm exceed those of a soil sample by 5–7 orders of magnitude, meaning that a single gram of ZnO NPs could sequester low levels of PCB contamination from as much as a ton of soil. read less

Abstract: Nanowires are an increasingly prevalent class of nanomaterials in composites and devices, with arrays and other complex geometries used in various applications. Little investigation has been done regarding the mechanical behavior of micron-sized nanowire structures. We conduct in situ microcompression experiments on vertically aligned dense microbundles of 300 nm diameter single-crystalline zinc oxide nanowires to gain insights into their structural failure. Experiments demonstrate that bundles containing approximately 10-130 nanowires experience two failure regimes: (1) localized noncatastrophic interfacial splitting and (2) global structural failure. Utilizing Weibull statistics and experimental results, we develop a technique for analyzing flaw distribution and use it to predict the expected range of bundle failure stress. This analysis provides guidelines for nanowire arrays' susceptibility to failure, sensitivity to flaw size, interfacial interactions of constituents, and degree of alignment. This work develops insights to understand and predict fundamental failure mechanisms in highly aligned, dense structures. read less

Abstract: Combined quantum mechanical/molecular mechanical (QM/MM) models using semiempirical and ab initio methods have been extensively reported on over the past few decades. These methods have been shown to be capable of providing unique insights into a range of problems, but they are still limited to relatively short time scales, especially QM/MM models using ab initio methods. An intermediate approach between a QM based model and classical mechanics could help fill this time-scale gap and facilitate the study of a range of interesting problems. Reactive force fields represent the intermediate approach explored in this paper. A widely used reactive model is ReaxFF, which has largely been applied to materials science problems and is generally used as a stand-alone (i.e., the full system is modeled using ReaxFF). We report a hybrid ReaxFF/AMBER molecular dynamics (MD) tool, which introduces ReaxFF capabilities to capture bond breaking and formation within the AMBER MD software package. This tool enables us to study local reactive events in large systems at a fraction of the computational costs of QM/MM models. We describe the implementation of ReaxFF/AMBER, validate this implementation using a benzene molecule solvated in water, and compare its performance against a range of similar approaches. To illustrate the predictive capabilities of ReaxFF/AMBER, we carried out a Claisen rearrangement study in aqueous solution. In a first for ReaxFF, we were able to use AMBER's potential of mean force (PMF) capabilities to perform a PMF study on this organic reaction. The ability to capture local reaction events in large systems using combined ReaxFF/AMBER opens up a range of problems that can be tackled using this model to address both chemical and biological processes. read less

Abstract: Concrete gains its strength from the precipitation of a calcium-alumino-silicate-hydrate (C-A-S-H) colloidal gel, which acts as its binding phase. However, despite concrete's ubiquity in the building environment, the atomic-scale mechanism of C-A-S-H precipitation is still unclear. Here, we use reactive molecular dynamics simulations to model the early-age precipitation of a C-A-S-H gel. We find that, upon gelation, silicate and aluminate precursors condensate and polymerize to form an aluminosilicate gel network. Notably, we demonstrate that the gelation reaction is driven by the existence of a mismatch of atomic-level internal stress between Si and Al polytopes, which are initially experiencing some local tension and compression, respectively. The polymerization of Si and Al polytopes enables the release of these competitive stresses. read less

Abstract: Currently, there is a great interest in nanoparticle-based vaccine delivery. Recent studies suggest that nanoparticles when introduced into the biological milieu are not simply passive carriers but may also contribute immunological activity themselves or of their own accord. For example there is considerable interest in the biomedical applications of one of the physiologically-based inorganic metal oxide nanoparticle, zinc oxide (ZnO). Indeed zinc oxide (ZnO) NP are now recognized as a nanoscale chemotherapeutic or anticancer nanoparticle (ANP) and several recent reports suggest ZnO NP and/or its complexes with drug and RNA induce a potent antitumor response in immuno-competent mouse models. A variety of cell culture studies have shown that ZnO NP can induce cytokines such as IFN-γ, TNF-α, IL-2, and IL-12 which are known to regulate the tumor microenvironment. Much less work has been done on magnesium oxide (MgO), cobalt oxide (Co3O4), or nickel oxide (NiO); however, despite the fact that these physiologically-based metal oxide NP are reported to functionally load and assemble RNA and protein onto their surface and may thus also be of potential interest as nanovaccine platform. Here we initially compared in vitro immunogenicity of ZnO and Co3O4 NP and their effects on cancer-associated or tolerogenic cytokines. Based on these data we moved ZnO NP forward to testing in the ex vivo splenocyte assay relative to MgO and NiO NP and these data showed significant difference for flow cytometry sorted population for ZnO-NP, relative to NiO and MgO. These data suggesting both molecular and cellular immunogenic activity, a double-stranded anticancer RNA (ACR), polyinosinic:poly cytidylic acid (poly I:C) known to bind ZnO NP; when ZnO-poly I:C was injected into B16F10-BALB/C tumor significantly induced, IL-2 and IL-12 as shown by Cohen’s d test. LL37 is an anticancer peptide (ACP) currently in clinical trials as an intratumoral immuno-therapeutic agent against metastatic melanoma. LL37 is known to bind poly I:C where it is thought to compete for receptor binding on the surface of some immune cells, metastatic melanoma and lung cells. Molecular dynamic simulations revealed association of LL37 onto ZnO NP confirmed by gel shift assay. Thus using the well-characterized model human lung cancer model cell line (BEAS-2B), poly I:C RNA, LL37 peptide, or LL37-poly I:C complexes were loaded onto ZnO NP and delivered to BEAS-2B lung cells, and the effect on the main cancer regulating cytokine, IL-6 determined by ELISA. Surprisingly ZnO-LL37, but not ZnO-poly I:C or the more novel tricomplex (ZnO-LL37-poly I:C) significantly suppressed IL-6 by >98–99%. These data support the further evaluation of physiological metal oxide compositions, so-called physiometacomposite (PMC) materials and their formulation with anticancer peptide (ACP) and/or anticancer RNA (ACR) as a potential new class of immuno-therapeutic against melanoma and potentially lung carcinoma or other cancers. read less

Abstract: The very first stages of nucleation and growth of ZnO nanoparticles in a plasma reactor are studied by means of a multiscale computational paradigm where the DFT-GGA approach is used to evaluate structure and electronic energy of small (ZnO) N clusters ( N ≤ 24) that are employed as a training set (TS) for the optimization of a Reactive Force Field (ReaxFF). Reactive Molecular Dynamics (RMD) simulations based on this tuned ReaxFF are carried out to reproduce nucleation and growth in a realistic environment. Inside the reaction chamber the temperature is around 1200 K, and the zinc atoms are oxidized in an oxygen-rich atmosphere at high pressure (about 20 atm), whereas in the quenching chamber where the temperature is lower (about 800 K) the ZnO embryo-nanoclusters are grown. The main processes ruling gas-phase nucleation and growth of ZnO nanoclusters are identified and discussed together with the dependence of the inception time and average stoichiometry of nanoclusters of different size on the composition of precursor material and physical parameters. read less

Abstract: An approach is presented to construct stoichiometric and saturated clusters as representative models for nanoparticles based on quantum-chemical surface energy calculations. The procedure consists of three steps. In the first step, the shape of the cluster is determined by applying the Wulff theorem based on calculated surface energies of the solid compound. Stoichiometry is recovered by adding selected atoms on the cluster surface. If the particles in solution are to be modeled, solvent molecules may be added. A global optimization is then performed to allow for full reconstruction of the cluster structure. As an example, we studied the spectroscopic properties of chalcopyrite (CuFeS2) nanoparticles and compared our calculated results to experimental O 1s X-ray photoelectron spectroscopy, IR, and optical spectra. read less

Abstract: The reaction dynamics of a liquid-solid interface with the example of an acetic acid/water solution interacting with a ZnO(101̅0) surface was investigated using ReaxFF reactive force field-based molecular dynamics. The interactions were studied over a broad temperature range to assess the kinetics and reaction pathways. Two different acetic acid dissociation mechanisms are observed in the simulations: (1) deprotonation to surface cation, which produces a terminal hydroxyl and (2) deprotonation to a bridging hydroxyl, which results in water production. An increase in temperature promotes the dissociation of acetic acids and its adsorption to surface at first, but as the temperature increase continues, the surface coverage by acetates decreases due to evaporation from the surface or decomposition. The acetate decomposition starts with a nucleophilic attack of oxygen to methyl carbon and results in the production of carbon dioxide, which is consistent with experimental findings in the literature. The coverage of the surface by water molecules decreases as the system is heated up, which is also observed in other molecular dynamics studies. At elevated temperatures, acetate molecules are more stable than water molecules or bridging hydroxyls on the surface. These simulations validate the ReaxFF method for the water/organic mixture and metal oxide surface interactions and provide insights into structure and reactivity of aqueous solvents on metal oxide surfaces at elevated temperatures. Adsorption trends that are observed in this study are consistent with phenomenological Langmuir models. The reaction of acetic acid decomposition to smaller molecules such as CO2 and CH2O agrees with experimental observations. Understanding the details of these dynamic surface reactions are critical to understand important new cold sintering processes that utilize transient liquid and solid reactions, and the latter could be used to predict solvent selection for cold sintering. read less

Abstract: To overcome the limitation of conventional fixed charge potential methods for the study of Li-ion battery cathode materials, a dynamic charge potential method, charge-transfer modified embedded atom method (CT-MEAM), has been developed and applied to the Li–Co–O ternary system. The accuracy of the potential has been tested and validated by reproducing a variety of structural and electrochemical properties of LiCoO2. A detailed analysis on the local charge distribution confirmed the capability of this potential for dynamic charge modeling. The transferability of the potential is also demonstrated by its reliability in describing Li-rich Li2CoO2 and Li-deficient LiCo2O4 compounds, including their phase stability, equilibrium volume, charge states and cathode voltages. These results demonstrate that the CT-MEAM dynamic charge potential could help to overcome the challenge of modeling complex ternary transition metal oxides. This work can promote molecular dynamics studies of Li ion cathode materials and other important transition metal oxides systems that involve complex electrochemical and catalytic reactions. read less

Abstract: Ultralong ZnO nanowires with lengths of 20–80 μm and aspect ratios of 200–500 were synthesized within 15 minutes via a low-temperature hydrothermal method. With the assistance of sodium dodecyl sulfonate (SDSN) as the capping ligand, ZnO nanowires were formed by the initial nucleation of nanocrystals followed by the ligand-directed oriented attachment. Head-to-head attachment, side-by-side coalescence and nanocrystals attached to the surfaces were observed at different growth stages. ZnO microrods (lengths: 2–10 μm, diameters: 0.5 to 5 μm) were formed in the absence of SDSN. FT-IR spectra, XPS analysis and molecular dynamics simulations revealed that SDSN molecules were preferentially adsorbed onto the (100) planes rather than polar (001) planes, with their sulfonate groups coordinating with the surface zinc ions and possibly forming Zn–SO3 complexes. Such selective adsorption not only protected the initially nucleated ZnO nanocrystals from rapid aggregation, but also directed their subsequent self-assembly into highly-anisotropic nanowires. The as-prepared ZnO nanowires exhibited improved photoluminescence properties compared to the microrods. I–V characteristics indicated that the ZnO nanowires exhibited a much lower dark current, while an enhanced photocurrent upon 360 nm light illumination compared to the microrods. In addition, UV photodetectors using ZnO nanowires showed 27 times higher photo-sensitivity and 15.4/13.8 times higher rise/decay rates compared to those using ZnO microrods, which were attributed to the morphological effects in addition to the improved optical properties. read less

Abstract: Transparent conducting oxides (TCO) are a critical component of many organic electronic devices including organic solar cells and light-emitting diodes. In this Perspective, we discuss what we have learned from our theoretical investigations, at the density functional theory (DFT) level, of the electronic structures of several technologically relevant transparent conducting oxides and their interfaces with organic layers. In particular, we describe how DFT calculations can be used to provide a detailed understanding of (i) the impact of surface modification by an organic monolayer on the interfacial electronic structure and the work function; (ii) the electronic characteristics of TCO surfaces as a function of surface hydroxylation and the presence of various intrinsic and extrinsic defects; and (iii) the nature of the charge transfer taking place between an organic semiconducting layer and a TCO electrode when considering the physisorption of a monolayer of π-conjugated organic molecules on the TCO surfaces. read less

Abstract: In this study, the effect of oxygen vacancies on the water wettability of a hydrated ZnO(100) surface has been examined via molecular dynamics simulations with a reactive force field (ReaxFF). The results show that the oxygen vacancies on the ZnO surface change the structures of the ZnO surface and subsequently its water adsorption capability. While a 1 : 1 ratio of water to hydroxyl is observed for a water monolayer absorbed on ZnO(100) without oxygen vacancies, additional water adsorption as coordinate hydroxyl that resides on the vacancy site and bonds with three lattice zinc atoms is observed on the surfaces with oxygen vacancies. The results also show that the energy of the interaction per unit area between water and the hydrated ZnO surface is 55.1% higher in the presence of the oxygen vacancies than that without oxygen vacancies. This leads to a water contact angle of ~115° for the hydrated ZnO(100) surface in the absence of vacancies and ~21° with vacancies. The wetting kinetics of a water droplet on a ZnO(100) surface with and without oxygen vacancies are compared with the diffusion-limited reactive wetting and molecular kinetics models, respectively. In addition, the ordering of the vacancy sites is found not to significantly affect the wettability of the ZnO(100) surface. read less

Abstract: We determine potentials of the mean force for interactions of amino acids with four common surfaces of ZnO in aqueous solutions. The method involves all-atom molecular dynamics simulations combined with the umbrella sampling technique. The profiled nature of the density of water with the strongly adsorbed first layer affects the approach of amino acids to the surface and generates either repulsion or weak binding. The largest binding energy is found for tyrosine interacting with the surface in which the Zn ions are at the top. It is equal to 7 kJ mol(-1) which is comparable to that of the hydrogen bonds in a protein. This makes the adsorption of amino acids onto the ZnO surface much weaker than onto the well studied surface of gold. Under vacuum, binding energies are more than 40 times stronger (for one of the surfaces). The precise manner in which water molecules interact with a given surface influences the binding energies in a way that depends on the surface. Among the four considered surfaces the one with Zn at the top is recognized as binding almost all amino acids with an average binding energy of 2.60 kJ mol(-1). Another (O at the top) is non-binding for most amino acids. For binding situations the average energy is 0.66 kJ mol(-1). The remaining two surfaces bind nearly as many amino acids as they do not and the average binding energies are 1.46 and 1.22 kJ mol(-1). For all of the surfaces the binding energies vary between amino acids significantly: the dispersion in the range of 68-154% of the mean. A small protein is shown to adsorb onto ZnO only intermittently and with only a small deformation. Various adsorption events lead to different patterns in mobilities of amino acids within the protein. read less

Abstract: A new polarizable water model is developed for molecular dynamics (MD) simulations of the proton transport process. The interatomic potential model has three important submodels corresponding to electrostatic interactions, making and breaking of covalent bonds, and treatment of electron exchange and correlation through a van der Waals potential. A polarizable diffuse charge density function was used to describe Coulombic interactions between atoms. Most of the model parameters were obtained from ab initio data for a lone water molecule. Molecules respond realistically to their electrochemical environment by the use of coupled fluctuating charge and fluctuating dipole dynamics, which controlled the charge density. The main purpose of the work is to develop a general model and framework for future studies, though some validation work was performed here. We applied the model to a MD simulation study of bulk properties of liquid water at room temperature and model gave good agreement with thermodynamic and transport properties at the same conditions. The model was then applied to a preliminary study of proton transfer, in which multiple proton transfer events were observed, though the rate of proton transfer was under-predicted by a factor of 5. read less

Abstract: The development of innovative carbon-based materials can be greatly facilitated by molecular modeling techniques. Although the Reax Force Field (ReaxFF) can be used to simulate the chemical behavior of carbon-based systems, the simulation settings required for accurate predictions have not been fully explored. Using the ReaxFF, molecular dynamics (MD) simulations are used to simulate the chemical behavior of pure carbon and hydrocarbon reactive gases that are involved in the formation of carbon structures such as graphite, buckyballs, amorphous carbon, and carbon nanotubes. It is determined that the maximum simulation time step that can be used in MD simulations with the ReaxFF is dependent on the simulated temperature and selected parameter set, as are the predicted reaction rates. It is also determined that different carbon-based reactive gases react at different rates, and that the predicted equilibrium structures are generally the same for the different ReaxFF parameter sets, except in the case of the predicted formation of large graphitic structures with the Chenoweth parameter set under specific conditions. read less

Abstract: Simulations of the initial oxidation process of a SiC surface exposed to O2 and H2O molecules was studied with ReaxFF, an atomically detailed reactive molecular dynamics method that naturally models the breaking and forming of bonds. In this work, the ReaxFF forcefield was first expanded by training it with new quantum mechanics data of the binding energy, equation of state, and heat of formation of the SiC crystal, along with data from earlier studies that describes Si – Si, Si – O, and Si – H interactions. This expanded ReaxFF forcefield is capable of simultaneously describing both Si–C–O and Si–O–H bonding interactions. Using the forcefield, oxidation simulations were performed at various temperatures (in the range of 500 to 5000 K), and the trajectories were analyzed. The analyses showed that SiC gradually transforms into the oxides of silicon with simultaneous formation of a graphite-like layer. In presence of excess O2, the graphite-like layer was further oxidized to CO and CO2. We also analyzed the... read less

Abstract: The ability to understand the phonon behavior in small metal oxide nanostructures and their surfaces is of great importance for thermal and microelectronic applications in successively smaller devi ... read less

Abstract: We have conducted quantum chemistry calculations and gas- and solution-phase reactive molecular dynamics simulation studies of reactions involving the ethylene carbonate (EC) radical anion EC(-) using the reactive force field ReaxFF. Our studies reveal that the substantial barrier for transition from the closed (cyclic) form, denoted c-EC(-), of the radical anion to the linear (open) form, denoted o-EC(-), results in a relatively long lifetime of the c-EC(-) allowing this compound to react with other singly reduced alkyl carbonates. Using ReaxFF, we systematically investigate the fate of both c-EC(-) and o-EC(-) in the gas phase and EC solution. In the gas phase and EC solutions with a relatively low concentration of Li(+)/x-EC(-) (where x = o or c), radical termination reactions between radical pairs to form either dilithium butylene dicarbonate (CH(2)CH(2)OCO(2)Li)(2) (by reacting two Li(+)/o-EC(-)) or ester-carbonate compound (by reacting Li(+)/o-EC(-) with Li(+)/c-EC(-)) are observed. At higher concentrations of Li(+)/x-EC(-) in solution, we observe the formation of diradicals which subsequently lead to formation of longer alkyl carbonates oligomers through reaction with other radicals or, in some cases, formation of (CH(2)OCO(2)Li)(2) through elimination of C(2)H(4). We conclude that the local ionic concentration is important in determining the fate of x-EC(-) and that the reaction of c-EC(-) with o-EC(-) may compete with the formation of various alkyl carbonates from o-EC(-)/o-EC(-) reactions. read less

Abstract: Copper ions play crucial roles in many enzymatic and aqueous processes. A critical analysis of the fundamental properties of copper complexes is essential to understand their impact on a wide range of chemical interactions. However the study of copper complexes is complicated by the presence of strong polarization and charge transfer effects, multiple oxidation states, and quantum effects like Jahn-Teller distortions. These complications make the experimental observations difficult to interpret. In order to provide a computationally inexpensive yet reliable method for simulation of aqueous-phase copper chemistry, ReaxFF reactive force field parameters have been developed. The force field parameters have been trained against a large set of DFT-derived energies for condensed-phase copper-chloride clusters as well as chloride/water and copper-chloride/water clusters sampled from molecular dynamics (MD) simulations. The parameters were optimized by iteratively training them against configurations generated from ReaxFF MD simulations that are performed multiple times with improved sets of parameters. This cycle was repeated until the ReaxFF results were in accordance with the DFT-derived values. We have performed MD simulations on chloride/water and copper-chloride/water systems to validate the optimized force field. The structural properties of the chloride/water system are in accord with previous experimental and computational studies. The properties of copper-chloride/water agreed with the experimental observations including evidence of the Jahn-Teller distortion. The results of this study demonstrate the applicability of ReaxFF for the precise characterization of aqueous copper chloride. This force field provides a base for the design of a computationally inexpensive tool for the investigation of various properties and functions of metal ions in industrial, environmental, and biological environments. read less

Abstract: Computational techniques have been applied to study a broad range of chemical and physical properties of zinc oxide. Both interatomic‐potential and density functional theory methods are used to investigate structural, thermodynamic, surface, and defect properties. We survey the structures and energies of nano‐particulate zinc oxide. © 2008 Wiley Periodicals, Inc. J Comput Chem 2008 read less

Abstract: Modeling the adsorption processes and luminescence properties of Zinc Oxide (ZnO) can provide valuable insights into its applications. We used Molecular Dynamics (MD) method to investigate the adsorption processes on ZnO nanoclusters under di(cid:27)erent initial conditions. To ensure the nanoclusters were correctly structured, we applied Radial Distribution Functions (RDF) and Central Symmetry Parameter (CSP) methods. It was discovered that the number of defects in the samples had a major in(cid:29)uence on the simulated photoluminescence (PL) spectra, which were created using a bi-Gaussian function. To assess the amount of vacancies on the surfaces of the sample, we used the relative luminescence intensity of the secondary peak in the PL spectra. To analyze the simulated PL spectra, we utilized a Gaussian (cid:28)tting technique. The self-activated PL band peaking was divided by Gaussian deconvolution, which was utilized for a more in-depth analysis of the data. By researching the consequences of varying conditions on the PL spectra, we were able to obtain a better comprehension of the mechanisms behind adsorption processes on ZnO nanoclusters. Furthermore, this research enabled us to gain insight into the in(cid:29)uences that di(cid:27)erent conditions can have on the adsorption of oxygen atoms on the nanoclusters and helped us in creating new generation gas sensors based on ZnO nanopowders and its compounds. read less

Abstract: Developing effective device architectures for energy technologies—such as solar cells, rechargeable batteries or fuel cells—does not only depend on the performance of a single material, but on the performance of multiple materials working together. A key part of this is understanding the behaviour at the interfaces between these materials. In the context of a solar cell, efficient charge transport across the interface is a pre-requisite for devices with high conversion efficiencies. There are several methods that can be used to simulate interfaces, each with an in-built set of approximations, limitations and length-scales. These methods range from those that consider only composition (e.g. data-driven approaches) to continuum device models (e.g. drift-diffusion models using the Poisson equation) and ab-initio atomistic models (developed using e.g. density functional theory). Here we present an introduction to interface models at various levels of theory, highlighting the capabilities and limitations of each. In addition, we discuss several of the various physical and chemical processes at a heterojunction interface, highlighting the complex nature of the problem and the challenges it presents for theory and simulation. read less

Abstract: Observing non-classical nucleation pathways remains challenging in simulations of complex materials with technological interests. This is because it requires very accurate force fields that can capture the whole complexity of their underlying interatomic interactions and an advanced structural analysis. Here, we first report the construction of a machine-learning force field for zinc oxide interactions using the Physical LassoLars Interaction Potentials approach which allows us to be predictive even for untrained structures. Then, we carried out freezing simulations from a liquid and observed the crystal formation with atomistic precision. Our results, which are analyzed using a data-driven approach based on bond order parameters, demonstrate the presence of both prenucleation clusters and two-step nucleation scenarios thus retrieving seminal predictions of non-classical nucleation pathways made on much simpler models. read less

Abstract: ABSTRACT Tensile properties of hydrogenated hybrid graphene–hexagonal boron nitride (h-BN) nanosheets were investigated atomistically using molecular dynamics simulations in conjunction with a reactive force field (ReaxFF). ReaxFF was chosen to provide more reliable results compared to those of previous studies that used simpler atomistic potential models to predict mechanical properties. The hydrogenation site that provides the most significant reduction in Young’s modulus of the hybrid structures has been identified. The results show that fully hydrogenated hybrid nanosheet has the lowest Young’s modulus compared to partially hydrogenated or pristine configurations. It was also seen that hydrogenation reduces Young’s modulus of hybrid nanosheets regardless of the hydrogenation configuration. However, hydrogenated graphene was found to be stiffer than the equivalent hydrogenated BN structures on account of the stronger C–C bond compared to C–B, C–N and BN bonds. Significant differences in the deformation behaviour are observed for various hydrogenation regimes examined as also their temperature dependencies. Pristine hybrid nanosheet exhibits brittle failure whereas the hydrogenated hybrid nanosheets show ductile failures. The lowering of Young’s modulus due to hydrogenation of the hybrids becomes less significant with increasing temperature. It is expected that the present results provide useful knowledge for suggested applications of hydrogenated hybrids as nanodiodes and nanotransitors. read less

Abstract: To investigate the chemical isotope-exchange reactions within a system composed of a mixture of hydrogen and deuterium (H/D) in the plasma media, the ReaxFFHD potential was parameterized against an appropriate quantum mechanics (QM)-based training set. These QM data involve structures and energies related to bond dissociation, angle distortion, and an exchange reaction of the tri-atomic molecular ions, H3 +, D3 +, H2D+, and D2H+, produced in the hydrogen plasma. Using the ReaxFFHD potential, a range of reactive molecular dynamics simulations were performed on different mixtures of H/D systems. Analysis of the reactions involved in the production of these tri-atomic molecular ions was carried out over 1 ns simulations. The results show that the ReaxFFHD potential can properly model isotope-exchange reactions of tri-atomic molecular ions and that it also has a perfect transferability to reactions taking place in these systems. In our simulations, we observed some intermediate molecules (H2, D2, and HD) that undergo secondary reactions to form the tri-atomic molecular ions as the most likely products in the hydrogen plasma. Moreover, there remains a preference for D in the produced molecular ions, which is related to the lower zero-point energy of the D-enriched species, showing the isotope effects at the heart of the ReaxFFHD potential. read less

Abstract: Cold Sintering Process (CSP) densifies ceramics at extremely low temperatures relative to conventional sintering processes. Several ceramics and composite systems have been successfully densified under cold sintering; in the case of zinc oxide grain growth kinetics, reduced activation energies are shown, and yet, the mechanism behind this growth is unknown. Herein, we investigate these mechanisms in more detail with experiments and ReaxFF molecular dynamics simulations. We investigated the recrystallization of zinc cations at various acidic conditions and found that its adsorption to surface can be a rate-limiting factor for cold sintering. Our studies show that surface hydroxylation in CSP does not inhibit crystallization; in contrast, by creating a surface complex, it creates an orders of magnitude acceleration in surface diffusion, and in turn, accelerate recrystallization. read less

Abstract: The interface between transition metal oxides (TMO) and liquid water plays a crucial role in environmental chemistry, catalysis, and energy science. Yet, the mechanism and energetics of chemical transformations at solvated TMO surfaces is often unclear, largely because of the difficulty to characterize the active surface species experimentally. The hematite (α-Fe2O3)-liquid water interface is a case in point. Here we demonstrate that ab initio molecular dynamics is a viable tool for determining the protonation states of complex interfaces. The p Ka values of the oxygen-terminated (001) surface group of hematite, ≡OH, and half-layer terminated (012) surface groups, ≡2OH and ≡1OH2, are predicted to be (18.5 ± 0.3), (18.9 ± 0.6), and (10.3 ± 0.5) p Ka units, respectively. These are in good agreement with recent bond-valence theory based estimates, and suggest that the deprotonation of these surfaces require significantly more free energy input than previously thought. read less

Abstract: The atomistic processes that form the basis of thin film growth often involve complex multi-atom movements of atoms or groups of atoms on or close to the surface of a substrate. These transitions and their pathways are often difficult to predict in advance. By using an adaptive kinetic Monte Carlo (AKMC) approach, many complex mechanisms can be identified so that the growth processes can be understood and ultimately controlled. Here the AKMC technique is briefly described along with some special adaptions that can speed up the simulations when, for example, the transition barriers are small. Examples are given of such complex processes that occur in different material systems especially for the growth of metals and metallic oxides. read less

Abstract: Morphologically reproducible wurtzite-structured zinc oxide nanowires (ZnO NWs) can be synthesized by different methods. Since ZnO NWs have been found to possess piezoelectricity, a comprehensive study of their mechanical properties, e.g. deformations caused by external compression or stretching, is one of the actual tasks of this paper. We have calculated wurtzite-structured [0 0 0 1]-oriented ZnO NWs whose diameters have been varied within 1–5 nm and 1–20 nm ranges when using either ab initio (hybrid DFT-LCAO) or force-field (molecular mechanical) methods, respectively (the minimum diameter dNW of experimentally synthesized NWs has been estimated on average to be ~20 nm). When using both chosen calculation approaches, the values of Young’s moduli determined for the mentioned ranges of NW diameters have been found to be qualitatively compatible (168–169 GPa for 5 nm NW thickness), whereas results of molecular mechanical simulations on YNW for 20 nm-thick NWs (160–162 GPa) have been qualitatively comparable with those experimentally measured along the [0 0 0 1] direction of NW loading. In all the cases, a gradual increase of the NW diameter has resulted in an asymptotic decrease of Young’s modulus consequently approaching that (Yb) of wurtzite-structured ZnO bulk along its [0 0 0 1] axis. The novelty of this study is that we combine the computation methods of quantum chemistry and molecular mechanics, while the majority of previous studies with the same aim have focused on the application of different classical molecular dynamical methods. read less

Abstract: There is a long standing contradiction on the tensile response of zinc oxide nanowires between theoretical prediction and experimental observations. Although it is proposed that there is a ductile behavior dominated by phase transformation, only an elastic deformation and brittle fracture was witnessed in experiments. Using molecular dynamics simulations, we clarified that, as the lateral dimension of zinc oxide nanowires increases to a critical value, an unambiguous ductile-to-brittle transition occurs. The critical value increases with decreasing the strain rate. Factors including planar defects and surface contamination induce brittle fracture prior to the initiation of phase transformation. These findings are consistent with previous atomistic standpoints and experimental results. read less

Abstract: 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

Abstract: Large scale quantum calculations for molar enthalpy of formation (Delta(f) H-0), standard entropy (S-0), and heat capacity (C-V) are presented. A large data set may help to evaluate quantum thermoc ... read less

Abstract: MgCl2 hydrates are considered as high-potential candidates for seasonal heat storage materials. These materials have high storage capacity and fast dehydration kinetics. However, as a side reaction to dehydration, hydrolysis may occur. Hydrolysis is an irreversible reaction, which produces HCl gas thus affecting the durability of heat storage systems. In this study, we present the parameterization of a reactive force field (ReaxFF) for MgCl2 hydrates to study the dehydration and hydrolysis kinetics of MgCl2·H2O and MgCl2·2H2O. The ReaxFF parameters have been derived by training against quantum mechanics data obtained from Density Functional Theory (DFT) calculations consisting of bond dissociation curves, angle bending curves, reaction enthalpies, and equation of state. A single-parameter search algorithm in combination with a Metropolis Monte Carlo algorithm is successfully used for this ReaxFF parameterization. The newly developed force field is validated by examining the elastic properties of MgCl2 hydrates and the proton transfer reaction barrier, which is important for the hydrolysis reaction. The bulk moduli of MgCl2·H2O and MgCl2·2H2O obtained from ReaxFF are in close agreement with the bulk moduli obtained from DFT. A barrier of 20.24 kcal mol(-1) for the proton transfer in MgCl2·2H2O is obtained, which is in good agreement with the barrier (19.55 kcal mol(-1)) obtained from DFT. Molecular dynamics simulations using the newly developed ReaxFF on 2D-periodic slabs of MgCl2·H2O and MgCl2·2H2O show that the dehydration rate increases more rapidly with temperature in MgCl2·H2O than in MgCl2·2H2O, in the temperature range 300-500 K. The onset temperature of HCl formation, a crucial design parameter in seasonal heat storage systems, is observed at 340 K for MgCl2·H2O, which is in agreement with experiments. The HCl formation is not observed for MgCl2·2H2O. The diffusion coefficient of H2O through MgCl2·H2O is lower than through MgCl2·2H2O, and can become a rate-limiting step. The diffusion coefficient increases with temperature and follows the Arrhenius law both for MgCl2·H2O and MgCl2·2H2O. These results indicate the validity of the ReaxFF approach for studying MgCl2 hydrates and provide important atomistic-scale insight of reaction kinetics and H2O transport in these materials. read less

Abstract: A ReaxFF reactive force field is developed and used for molecular dynamics studies of reactions that occur when diethyl zinc is exposed to a graphene surface that has been functionalized with epoxide groups. From past experiments, it is known that these conditions lead to zinc oxide nanoparticle formation. Molecular dynamics simulations are used to provide atom-level detail into the nanoparticle formation process, including the mechanisms whereby oxygen is abstracted from the graphene surface, thus enabling condensation reactions in which multiple zinc-containing species form zinc oxide fragments and ultimately nanoparticles. Structural properties of the nanoparticles show nonstoichiometric zinc oxide structures with average coordination numbers of 3.6 around each zinc. Time-dependent density functional theory calculations show that the absorption spectra of these clusters are red-shifted by a few tenths of an electronvolt compared to that of a wurtzite crystal structure, representing transitions from oxy... read less

Abstract: The aim of the study described in this thesis is to obtain a profound understanding of transformations in NCs at the atomic level, by performing molecular simulations for such transformations, and by comparing the simulation results with available experimental high resolution transmission electron microscopy (HRTEM) data to validate the simulations and to reveal underlying physical mechanisms. These transformations include structural and morphological transitions and cation exchange processes in ionic nanocrystals (II-VI and IV-VI semiconductors). The main simulation method used is classical Molecular Dynamics (MD) simulation. First principles density functional theory (DFT) calculations were used to develop empirical force fields that are able to accurately reproduce phase transitions. Using these newly developed force fields, large scaled classical MD simulations were carried out and linked to HRTEM experiments. The partially charged rigid ion model (PCRIM) was chosen for the force fields. This PCRIM approach has a simple functional form with a few number of parameters and has a clear physical meaning for ionic crystals. To simulate cation exchange in colloidal NC systems at the NC/solution interface, we used a combination of all-atom force fields and a coarse-grained model. In Chapter 2, an ab-initio based force field for ZnO is developed within the framework of the PCRIM approach. The values of the partial charges were determined by Bader charge analysis of DFT calculations on various ZnO phases. Beside Coulombic interactions, only short-ranged pairwise interatomic interactions were included. An initial guess of the parameters of the short-ranged pair potentials were first obtained by the lattice inversion method. The parameters were further adjusted by an ab-initio potential surface fitting procedure. The new ZnO force field has a very simple functional form is able to accurately reproduce several important physical properties of ZnO materials. These physical properties include the lattice parameters and phase stability of several ZnO polymorphs, as well as the elastic constants, bulk moduli, phonon dispersion, and melting points of wurtzite ZnO. The transition pressure of the wurtzite-to-rocksalt transition calculated with the force field equals 12.3 GPa, in agreement with experimental measurements and DFT calculations. A wurtzite-to-honeycomb phase transition is predicted at an uniaxial pressure of 8.8 GPa. We found a rational and effective way to derive force fields with simple functional forms for accurate simulations of phase transitions in ionic crystals. In Chapter 3, we developed a transferable force field for CdS-CdSe-PbSPbSe solid systems. The selection of the force field and the fitting procedure are similar to that of the ZnO force field in Chapter 2. The challenges when developing this force field were to maintain the transferability of this force field for four materials (CdS, CdSe, PbS, and PbSe) and to describe their mixed phases. This was solved by assuming that different cations/anions have the same values of the partial charges, and that shortranged interatomic interactions between two cations/anions are the same in different materials. For the mixed phases, DFT calculations of the mixed phases were included in both the training and validation sets. This work is the first step for further simulation studies of these II-VI and IV-VI semiconductor NCs and heteronanocrystals (HNCs). In Chapter 4, a thermally induced morphological and structural transition of CdSe NCs was investigated using MD simulations. In MD simulations, a CdSe nanosphere with the ZB structure transforms into a tetrapodlike morphology at 800 K. In a CdSe tetrapod, four WZ legs attach to the {111} facets of a tetrahedral ZB core. This transformation is achieved by a layer-by-layer slip of the ZB-{111} bilayer. Simulations show that the slips are mediated by the formation of Cd vacancies on the surface of the NCs to overcome the potentially large energy barriers associated with slip. The morphology of the annealed NCs is found to be temperature and size-dependent. An octapod-like morphology is found in NCs with a relatively large NC size and in a certain range of the heating temperature. Surprisingly, nanoscale transformations of CdSe NCs have been directly observed in HRTEM in situ heating experiments. Our findings provide a simple method to modify the morphology of ionic NCs and can potentially be used in the synthesis of branched NCs. The cation exchange process of PbSe/CdSe HNCs has been investigated by HRTEM in situ heating experiments in combination with MD simulations and DFT calculations in Chapter 5. In the HRTEM experiments, we bserved that Cd atoms in PbSe/CdSe nanodumbbells (CdSe rods with one or two PbSe tip(s)) are replaced by Pb atoms. The exchange rate depends on the heating temperature and the amount of Pb atoms present in the system. Sometimes, fully converted PbSe nanodumbells can be observed. MD simulations were performed to investigate the mechanism of this cation exchange process. It was found that the the CdSe domains near the PbSe/CdSe interfaces have significant structural disorder. These findings are in line with the experimental observation that the exchange process proceeds in a layer-by-layer fashion along the WZ- direction. We concluded that cation exchange in PbSe/CdSe HNCs is mediated by the local structural disorder which enables the formation of vacancies and accelerated the motion of cations. In Chapter 6, a coarse-grained psuedoligand model was introduced to simulate cation exchange in PbS colloidal NCs taking into account the cation-solvent interactions. Modelling colloidal NC systems including interactions with the solvent has long been a challenge due to the large system size and long time scales. Here, we incorporated the effects of ligands and solvents into negatively charged large spherical coarse-grained psuedoligands. MD simulations combining coarse-grained and all-atom models can successfully reproduce the cation exchange process in PbS colloidal NCs. Simulations show that the exchange rate and system equilibrium can be controlled by the temperature and by changing ligands. The exchange process is directly related to vacancy formation and the high mobility of Cd ions at the PbS/CdS interface. Our simulations also predict that high-pressure conditions will be beneficial for achieving fast exchange at elevated temperatures. Our coarse-grained model can be easily extended to other systems for the computational investigation of transformations in nanostructures. read less

Abstract: We assess the consequences of the interface model—embedded‐cluster or periodic‐slab model—on the ability of DFT calculations to describe charge transfer (CT) in a particularly challenging case where periodic‐slab calculations indicate a delocalized charge‐transfer state. Our example is Cu atom adsorption on ZnO(10 1¯ 0), and in fact the periodic slab calculations indicate three types of CT depending on the adsorption site: full CT, partial CT, and no CT. Interestingly, when full CT occurs in the periodic calculations, the calculated Cu atom adsorption energy depends on the underlying ZnO substrate supercell size, since when the electron enters the ZnO it delocalizes over as many atoms as possible. In the embedded‐cluster calculations, the electron transferred to the ZnO delocalizes over the entire cluster region, and as a result the calculated Cu atom adsorption energy does not agree with the value obtained using a large periodic supercell, but instead to the adsorption energy obtained for a periodic supercell of roughly the same size as the embedded cluster. Different density functionals (of GGA and hybrid types) and basis sets (local atom‐centered and plane‐waves) were assessed, and we show that embedded clusters can be used to model Cu adsorption on ZnO(10 1¯ 0), as long as care is taken to account for the effects of CT. © 2015 Wiley Periodicals, Inc. read less

Abstract: The mechanism of (100) and (000) zinc oxide surface growth from ethanolic solution is investigated by molecular simulation. Growth steps are modelled at the maximum level of detail, i.e. by association of individual Zn2+ and OH− ions. Apart from structural relaxation, a mixed quantum/classical approach is used to explicitly study the proton-transfer reactions during crystal growth. Starting from idealized surfaces, we find that the (000) face evolves into rough landscapes composed of small islands separated by ~1 nm. On the other hand, the (100) growth front shows the formation of ridges encompassed by analogous 100 planes of the wurtzite structure. Contrary to idealized surface models, such rough surfaces obtained from explicit growth simulations enable us to identify considerable differences in both the binding site and energy for the association of growth-controlling additives. Using acetate and citrate ions as examples, we demonstrated the preferential association with peaks and kinks, respectively. read less

Abstract: The mechanical response of zinc oxide nanowires under uniaxial tensile loading is investigated by molecular dynamics and supported by density functional calculations. Previous theoretical works predict a stress-induced phase transition which has not been observed experimentally in zinc oxide nanowires up to date. Here, we report an explanation for such a discrepancy. Our simulations reveal brittle failure at room temperature without phase transformation, in agreement with experiments. Interestingly, we also find that if the temperature is raised to 600 K, the phase transition occurs. A detailed reaction mechanism is proposed. For the first time, the associated rate constant has been calculated. Based on these results we propose an experimental procedure to finally observe the predicted phase transformation. read less

Abstract: A second-moment, tight-binding charge equilibration (SMTB-Q) model for the atomic interactions in TiO2 is refined by comparison with results of density functional theory (DFT) calculations within t... read less

Abstract: ReaxFF force field parameters describing Pt-Pt and Pt-O interactions have been developed and tested. The Pt-Pt parameters are shown to accurately account for the chemical nature, atomic structures and other materials properties of bulk platinum phases, low and high-index platinum surfaces and nanoclusters. The Pt-O parameters reliably describe bulk platinum oxides, as well as oxygen adsorption and oxide formation on Pt(111) terraces and the {111} and {100} steps connecting them. Good agreement between the force field and both density functional theory (DFT) calculations and experimental observations is demonstrated in the relative surface free energies of high symmetry Pt-O surface phases as a function of the oxygen chemical potential, making ReaxFF an ideal tool for more detailed investigations of more complex Pt-O surface structures. Validation for its application to studies of the kinetics and dynamics of surface oxide formation in the context of either molecular dynamics (MD) or Monte Carlo simulations are provided in part by a two-part investigation of oxygen diffusion on Pt(111), in which nudged elastic band (NEB) calculations and MD simulations are used to characterize diffusion processes and to determine the relevant diffusion coefficients and barriers. Finally, the power of the ReaxFF reactive force field approach in addressing surface structures well beyond the reach of routine DFT calculations is exhibited in a brief proof-of-concept study of oxygen adsorbate displacement within ordered overlayers. read less

Abstract: A set of interatomic pair potentials is developed for ZnO based on the partially charged rigid ion model (PCRIM). The derivation of the potentials combines lattice inversion, empirical fitting, and ab initio energy surface fitting. We show that, despite the low number of parameters in this model (8), a wide range of physical properties is accurately reproduced using the new potential model. The calculated lattice parameters and elastic constants of ZnO in the wurtzite (WZ) phase, as well as the lattice parameters and stabilities of ZnO in other high-pressure and metastable phases, agree well with experiments and with density functional theory (DFT) calculations. The calculated transition pressure of the wurtzite-to-rocksalt (WZ-to-RS) transition is 12.3 GPa. A wurtzite-to-honeycomb (WZ-to-HC) phase transition induced by uniaxial pressure along the c-axis is simulated by means of molecular dynamics (MD) simulations. The WZ-to-HC transition takes place at an uniaxial pressure of 8.8 GPa while the reverse tr... read less

Abstract: The effects of surface and interface on the thermodynamics of small particles require a deeper understanding. This step is crucial for the development of models that can be used for decision-making support to design nanomaterials with original properties. On the basis of experimental results for phase transitions in compressed ZnO nanoparticles, we show the limitations of classical thermodynamics approaches (Gibbs and Landau). We develop a new model based on the Ginzburg-Landau theory that requires the consideration of several terms, such as the interaction between nanoparticles, pressure gradients, defect density, and so on. This phenomenological approach sheds light on the discrepancies in the literature as it identifies several possible parameters that should be taken into account to properly describe the transformations. For the sake of clarity and standardization, we propose an experimental protocol that must be followed during high-pressure investigations of nanoparticles in order to obtain coherent, reliable data that can be used by the scientific community. read less

Abstract: We present here a reactive force field based metadynamics study of pressure-induced amorphization in β-eucryptite, a lithium aluminum silicate that exhibits negative thermal expansion, i.e., volumetric contraction upon heating. From our simulations, we found that β-eucryptite amorphizes under a moderate applied pressure of ∼3 GPa. A careful inspection of the amorphous phase showed that it contains AlO3, AlO4, AlO5, and SiO4 polyhedra, indicating clear short-range order. We have also identified the atomic-scale processes responsible for the amorphization of β-eucryptite. These processes are (a) tilting and distortion of tetrahedra centered at Al/Si, (b) change in atomic coordination around Al, and (c) disordering of Li atoms with the formation of Li-Li, Li-O, and Li-O-Li linkages. We discuss our results in the context of a possible general link between negative thermal expansion, radiation tolerance, and pressure-induced amorphization in flexible network structures. read less

Abstract: Oxide formation on palladium surfaces impacts the activity and selectivity of Pd-based catalysts, which are widely employed under oxygen rich operating conditions. To investigate oxidation processes over Pd catalysts at time and length scales inaccessible to quantum based computational methods, we have developed a Pd∕O interaction potential for the ReaxFF reactive force field. The parameters of the ReaxFF potential were fit against an extensive set of quantum data for both bulk and surface properties. Using the resulting potential, we conducted molecular dynamics simulations of oxide formation on Pd(111), Pd(110), and Pd(100) surfaces. The results demonstrate good agreement with previous experimental observations; oxygen diffusion from the surface to the subsurface occurs faster on the Pd(110) surface than on the Pd(111) and Pd(100) surfaces under comparable conditions at high temperatures and pressures. Additionally, we developed a ReaxFF-based hybrid grand canonical Monte Carlo∕molecular dynamics (GC-MC∕MD) approach to assess the thermodynamic stability of oxide formations. This method is used to derive a theoretical phase diagram for the oxidation of Pd935 clusters in temperatures ranging from 300 K to 1300 K and oxygen pressures ranging from 10(-14) atm to 1 atm. We observe good agreement between experiment and ReaxFF, which validates the Pd∕O interaction potential and demonstrates the feasibility of the hybrid GC-MC∕MD method for deriving theoretical phase diagrams. This GC-MC∕MD method is novel to ReaxFF, and is well suited to studies of supported-metal-oxide catalysts, where the extent of oxidation in metal clusters can significantly influence catalytic activity, selectivity, and stability. read less

Abstract: We have developed a reactive force field within the ReaxFF framework to accurately describe reactions involving aluminum–molybdenum alloy, which are part parameters of Al–O–Mo ternary system metastable intermolecular composites. The parameters are optimized from a training set, whose data come from density functional theory (DFT) calculations and experimental value, such as heat of formation, geometry data, and equation of states, which are reproduced well by ReaxFF. Body-centered cubic molybdenum’s surface energy, vacancy formation, and two transformational paths, Bain and trigonal paths are calculated to validate the ReaxFF ability describing the defects and deformations. Some structures’ elastic constant and phonon are calculated by DFT and ReaxFF to predict the structures’ mechanics and kinetic stability. All those results indicate that the fitted parameters can describe the energy difference of various structures under various circumstances and generally represent the diffusion property but cannot reproduce the elasticity and phonon spectra so well. read less

Abstract: Biology implements intriguing structural design principles that allow for attractive mechanical properties—such as high strength, toughness, and extensibility despite being made of weak and brittle constituents, as observed in biomineralized structures. For example, diatom algae contain nanoporous hierarchical silicified shells, called frustules, which provide mechanical protection from predators and virus penetration. These frustules generally have a morphology resembling honeycombs within honeycombs, meshes, or wavy shapes, and are surprisingly tough when compared to bulk silica, which is one of the most brittle materials known. However, the reason for its extreme extensibility has not been explained from a molecular level upwards. By carrying out a series of molecular dynamics simulations with the first principles‐based reactive force field ReaxFF, the mechanical response of the structures is elucidated and correlated with underlying deformation mechanisms. Specifically, it is shown that for wavy silica, unfolding mechanisms are achieved for increasing amplitude and allow for greater ductility of up to 270% strain. This mechanism is reminiscent to the uncoiling of hidden length from proteins that allows for enhanced energy dissipation capacity and, as a result, toughness. We report the development of an analytical continuum model that captures the results from atomistic simulations and can be used in multiscale models to bridge to larger scales. Our results demonstrate that tuning the geometric parameters of amplitude and width in wavy silica nanostructures are beneficial in improving the mechanical properties, including enhanced deformability, effectively overcoming the intrinsic shortcomings of the base material that features extreme brittleness. read less

Abstract: A new reactive force field has been derived that allows the modelling of speciation in the aqueous-calcium carbonate system. Using the ReaxFF methodology, which has now been implemented in the program GULP, calcium has been simulated as a fixed charge di-cation species in both crystalline phases, such as calcite and aragonite, as well as in the solution phase. Excluding calcium from the charge equilibration process appears to have no adverse effects for the simulation of species relevant to the aqueous environment. Based on this model, the speciation of carbonic acid, bicarbonate and carbonate have been examined in microsolvated conditions, as well as bulk water. When immersed in a droplet of 98 water molecules and two hydronium ions, the carbonate ion is rapidly converted to bicarbonate, and ultimately carbonic acid, which is formed as the metastable cis-trans isomer under kinetic control. Both first principles and ReaxFF calculations exhibit the same behaviour, but the longer timescale accessible to the latter allows the diffusion of the carbonic acid to the surface of the water to be observed, where it is more stable at the interface. Calcium carbonate is also examined as ion pairs in solution for both CaCO(3)(0)((aq)) and CaHCO(3)(+)((aq)), in addition to the (1014) surface in contact with water. read less

Abstract: We have parameterized a reactive force field (ReaxFF) for lithium–aluminum silicates using density functional theory (DFT) calculations of structural properties of a number of bulk phase oxides, silicates and aluminates, as well as of several representative clusters. The force field parameters optimized in this study were found to predict lattice parameters and heats of formation of selected condensed phases in excellent agreement with previous DFT calculations and with experiments. We have used the newly developed force field to study the eucryptite phases in terms of their thermodynamic stability and their elastic properties. We have found that (a) these ReaxFF parameters predict the correct order of stability of the three crystalline polymorphs of eucryptite, α, β and γ, and (b) that upon indentation, a new phase appears at applied pressures ⩾7 GPa. The high-pressure phase obtained upon indentation is amorphous, as illustrated by the radial distribution functions calculated for different pairs of elements. In terms of elastic properties analysis, we have determined the elements of the stiffness tensor for α- and β-eucryptite at the level of ReaxFF, and discussed the elastic anisotropy of these two polymorphs. Polycrystalline average properties of these eucryptite phases are also reported to serve as ReaxFF predictions of their elastic moduli (in the case of α-eucryptite), or as tests against values known from experiments or DFT calculations (β-eucrypite). The ReaxFF potential reported here can also describe well single-species systems (e.g. Li-metal, Al-metal and condensed phases of silicon), which makes it suitable for investigating structure and properties of suboxides, atomic-scale mechanisms responsible for phase transformations, as well as oxidation–reduction reactions. read less

Abstract: The need for greater fuel economy in automotive vehicles has driven a surge in the development of diesel and lean-burn gasoline engines. Coupled with the increase in fuel efficiency, an increase in the air to fuel ratio also results in heightened production of NOx. [1] Several different strategies have been proposed for the handling of the higher NOx levels in lean-burn automotive emissions. One such strategy is the NOx storage reduction (NSR) system whereby excess NO is further oxidized to NO2 over the exhaust catalyst, which is typically platinum, and then NO2 is stored on a carrier material, such as BaO. [2] The catalyst system operates in this fashion for some minutes until the storage material has been fully converted. The system then cycles to a rich mode, during which a reductant is injected into the exhaust stream and reacts with the stored NOx, possibly at the interface between the carrier material and the metal particle, to produce the traditional exhaust products of N2, H2O, and CO2, all in a matter of seconds. Therefore, a requirement of a successful NSR catalyst is that the catalyst must be active for both NO oxidation and NOx reduction. In recent years, a debate has emerged as to the role of metal oxides in oxidation catalysis. [3–6] Although there have been some indications that oxide surfaces may be more active in simple oxidation reactions such as CO oxidation, [7] platinum catalysts have been preferred as the metal component in the NOx storage reduction system for their combination of high activity and ability to resist deactivation through oxidation. Ribeiro et al. have studied Pt NO-oxidation catalysts for NSR applications in considerable detail. They determined that large Pt particles are more active and that single crystal Pt(111) and Pt(100) outperform disperse Pt particles. [8, 9] One possible explanation for the higher activity of the single crystal surfaces is that oxygen is bound less strongly and that the catalysts do not deactivate due to oxide formation. Reports of platinum deactivation as a NO oxidation catalyst, however, concern catalysts that have been exposed to oxygen (and NO) for long periods. [9] As NSR systems operate under a cyclic operation read less

Abstract: We review the growing role of computational techniques in modelling the structures and properties of nano-particulate oxides and sulphides. We describe the main methods employed, including those based on both electronic structure and interatomic potential approaches. Particular attention is paid to the techniques used in searching for global minima in the energy landscape defined by the nano-particle cluster. We summarise applications to the widely studied ZnO and ZnS systems, to silica nanochemistry and to group IV oxides including TiO(2). We also consider the special case of silica cluster chemistry in solution and its importance in understanding the hydrothermal synthesis of microporous materials. The work summarised, together with related experimental studies, demonstrates a rich and varied nano-cluster chemistry for these materials. read less

Abstract: High temperatures caused by partial discharge results in the decomposition of insulating epoxy resins in electrical equipment. In this paper, the ReaxFF force field is used to investigate the decomposition process of epoxy resins cured by anhydride and the formation mechanisms of small-molecule gases. Results show that the initiation reaction is the cleavage of an ester bond linked with an epoxy resin. Produced by the decomposition of ester groups, CO2 is the first and most abundant product. Meanwhile, CH2O can be generated through three main ways, although the process still depends on the decomposition of epoxy functional groups. H2O is produced by free radical collision and dehydration. The production of small-molecule gases has the following sequence: CO2, CH2O, CO, and H2O. The produced gases have the following order according to amount: CO2, CH2O, H2O, and CO. read less

Abstract: We have developed an efficient scheme for the generation of accurate repulsive potentials for self-consistent charge density-functional-based tight-binding calculations, which involves energy-volume scans of bulk polymorphs with different coordination numbers. The scheme was used to generate an optimized parameter set for various ZnO polymorphs. The new potential was subsequently tested for ZnO bulk, surface, and nanowire systems as well as for water adsorption on the low-index wurtzite (101̅0) and (112̅0) surfaces. By comparison to results obtained at the density functional level of theory, we show that the newly generated repulsive potential is highly transferable and capable of capturing most of the relevant chemistry of ZnO and the ZnO/water interface. read less