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Development and Application of a ReaxFF Reactive Force Field for Ni-Doped MoS 2
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Formation of AlF x Gaseous Phases during High Temperature Etching: A Reactive Force Field Based Molecular Dynamics Study
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Identification of the Selective Sites for Electrochemical Reduction of CO to C 2+ Products on Copper Nanoparticles by Combining Reactive Force Fields, Density Functional Theory, and Machine Learning
Recent experiments have shown that CO reduction on oxide derived Cu nanoparticles (NP) are highly selective toward C 2+ products. However, understanding of the active sites on such NPs is limited, because the NPs have ~200 000 atoms with more than 10 000 surface sites, far too many for direct quantum mechanical calculations and experimental identifications. We show here how to overcome the computational limitation by combining multiple levels of theoretical computations with machine learning. This approach allows us to map the machine learned CO adsorption energies on the surface of the copper nanoparticle to construct the active site visualization (ASV). Furthermore, we identify the structural criteria for optimizing selective reduction by predicting the reaction energies of the potential determining step, $ΔE_{OCCOH}$, for the C 2+ product. Based on this structural criterion, we design a new periodic copper structure for CO reduction with a theoretical faradaic efficiency of 97%.
Multiobjective genetic training and uncertainty quantification of reactive force fields
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Reactive force fields for aqueous and interfacial magnesium carbonate formation
Here we develop Mg/C/O/H ReaxFF parameter sets for two environments: an aqueous force field for magnesium ions in solution and an interfacial force field for minerals and mineral–water interfaces. Since magnesium is highly ionic, we choose to fix the magnesium charge and model its interaction with C/O/H through Coulomb, Lennard-Jones, and Buckingham potentials. We parameterize the forcefields against several crystal structures, including brucite, magnesite, magnesia, magnesium hydride, and magnesium carbide, as well as Mg 2+ water binding energies for the aqueous forcefield. Then, we test the forcefield for other magnesium-containing crystals, solvent separated and contact ion-pairs and single-molecule/multilayer water adsorption energies on mineral surfaces. We also apply the forcefield to the forsterite–water and brucite–water interface that contains a bicarbonate ion. We observe that a long-range proton transfer mechanism deprotonates the bicarbonate ion to carbonate at the interface. Free energy calculations show that carbonate can attach to the magnesium surface with an energy barrier of about 0.22 eV, consistent with the free energy required for aqueous Mg–CO 3 ion pairing. Also, the diffusion constant of the hydroxide ions in the water layers formed on the forsterite surface are shown to be anisotropic and heterogeneous. These findings can help explain the experimentally observed fast nucleation and growth of magnesite at low temperature at the mineral–water–CO 2 interface in water-poor conditions.
Lithiation of Sulfur-Graphene Compounds Using Reactive Force-Field Molecular Dynamics Simulations
We performed molecular dynamics simulations of lithium-sulfur-graphene compounds using reactive force fields, providing a time scale to observe atomistic features relevant to the microscopic behavior of the of the bulk of sulfur-based cathodes to be used beyond our present Li-ion batteries. The samples we used were set to realistic geometries through sophisticated protocols to simulate ultrafast reactions that occur within the picosecond range, thus allowing us to get some insights into the characteristics of the bulk material in working cathodes of Li–S batteries, which are mixed with carbon to increase the poor electronic conductivity of S. We report chemical speciation and geometrical data at atomistic levels. We observed that slowly lithiated cathodes were more stable and with higher density than those that were suddenly fully-lithiated. We did not observe molecular Li 2 S formation; however, we observed an amorphous solid arrangement with the same stoichiometry of Li and S, with S–Li–S angles of ~111° and smaller ones due to the interaction between polysulfides that did not reacted totally. In addition, graphene keeps its planar shape; however, S8 changes its shape from rings to chains. Lithiated structures are more stable with lower energies, and more close-packed structures than structures with Li already inserted.
Structural features of sodium silicate glasses from reactive force field-based molecular dynamics simulations
Atomistic computer simulations can offer insights into silicate glass-environment interactions with the recent development of reactive potentials. Yet, the accuracy of generated glass structures with these potential was usually not fully examined. In this paper, the capability of the reactive force field (ReaxFF) to describe the short and medium range structure features of sodium silicate glasses in molecular dynamics simulations is investigated by comparing a widely used partial charge pairwise potential and available experimental data. Glass structure information such as pair distribution function (PDF), coordination number, Qn species, neutron broadened structure factor, and X-ray broadened structure factor of the glass structures from ReaxFF simulations were calculated and compared to evaluate the generated glass structure. Advantages and limitations of the potentials and glass forming procedures, as well as areas of further improvement, were discussed. The results show that the recently refined ReaxFF parameters through the proposed procedure enable the simulations of sodium silicate glass structures with minimal defects, which paves the way to investigate water-glass interaction mechanisms with the reactive enabled potentials.
Hydrogen irradiation-driven computational surface chemistry of lithium oxide and hydroxide
We have investigated, using molecular dynamics, the surface chemistry of hydrogen incident on the amorphous and crystalline lithium oxide and lithium hydroxide surfaces upon being slowed down by a collision cascade and retained in the amorphous surface of either Li 2 O or LiOH. We looked for the bonding of H to the resident structures in the surface to understand a possible chain of chemical reactions that can lead to surface transformation upon H atom impact. Our findings, using Density-Functional Theory (DFT) trained ReaxFF force field/electronegativity equalization method potentials, stress the importance of inclusion of polarization in the dynamics of a Li–O–H system, which is also illustrated by DFT energy minimization and quantum–classical molecular dynamics using tight binding DFT. The resulting polar-covalent chemistry of the studied systems is complex and very sensitive to the instantaneous positions of all atoms as well as the ratio of concentrations of various resident atoms in the surface.
Active learning of reactive Bayesian force fields applied to heterogeneous catalysis dynamics of H/Pt
Abstract Atomistic modeling of chemically reactive systems has so far relied on either expensive ab initio methods or bond-order force fields requiring arduous parametrization. Here, we describe a Bayesian active learning framework for autonomous “on-the-fly” training of fast and accurate reactive many-body force fields during molecular dynamics simulations. At each time-step, predictive uncertainties of a sparse Gaussian process are evaluated to automatically determine whether additional ab initio training data are needed. We introduce a general method for mapping trained kernel models onto equivalent polynomial models whose prediction cost is much lower and independent of the training set size. As a demonstration, we perform direct two-phase simulations of heterogeneous H 2 turnover on the Pt(111) catalyst surface at chemical accuracy. The model trains itself in three days and performs at twice the speed of a ReaxFF model, while maintaining much higher fidelity to DFT and excellent agreement with experiment.
Iodine recombination in xenon solvent: Clusters in the gas to liquid-like state transition
Supercritical fluids (SCFs) have attracted significant attention as solvents for chemical reactions due to their unique properties, such as high diffusivity, low viscosity, and tunable solvation properties. These properties profoundly influence reaction kinetics and are often attributed to the formation of molecular clusters within SCFs. To study the effect of supercritical solvent on chemical reactivity and dynamics of reactions, one needs to understand the dynamics of clusters in supercritical fluid. Extensive experiments on the photodissociation and recombination of iodine in supercritical fluids served as a model system for understanding these effects. Experimental studies have been complemented by theoretical and computational investigations, which mostly employ Monte Carlo or empirical molecular dynamics simulations. However, computational studies using non-reactive force fields and ab initio approaches present challenges in capturing reactive processes at larger scales within supercritical fluids. Here, in this work, we developed the ReaxFF parameters by training against quantum mechanics data. ReaxFF reactive force field based molecular dynamics simulations were performed, studying the dynamics of a xenon solvent and cage effect at different thermodynamic conditions for the iodine recombination reaction. We show that the conditions near the critical point are the optimal conditions to study the cage effect. We show that the average lifetime of xenon clusters ranging between 5 and 11 ps is comparable to iodine geminate recombination. Our simulation results of iodine recombination in xenon solvent demonstrate the higher probability of iodine molecule formation in the presence of xenon clusters. Finally, we show that the supercritical condition exhibits the highest recombination rate for iodine atoms.
Nanoporous silica gel structures and evolution from reactive force field-based molecular dynamics simulations
Nanoporous silica-rich gel formed on silicate glass surfaces during dissolution in aqueous environment is critical in elucidating the corrosion mechanisms and the long-term residual dissolution behaviors. Silica gel models were created using two types of methods with reactive force field-based molecular dynamics simulations. The results show that the remnant silica gels created from the ISG bulk structure have a more isolated and closed pore morphology and slightly higher glass network connectivity. This contrasts with the gel structures created by hydrogarnet defect formation that exhibit more connected pore morphologies. The remnant gel structures show lower water diffusivity which was explained by the nano-confinement effect of water molecules due to frequent interactions of water molecules with adjacent silica walls and the more isolated pore morphology in the remnant gel structures. These results reveal the complexity in terms of micro and atomic structures of these silica gels, and both structure features have impact on water transport in the gel layer hence the passivating effect that controls the long-term dissolution behavior of these glasses.
High-temperature active oxidation of nanocrystalline silicon-carbide: A reactive force-field molecular dynamics study
Flexible woven SiC ceramics are prone to accelerated fiber embrittlement under high temperature oxidation in dynamic oxygen environments. The nanocrystalline structure of the constituent fibers impacts the reaction kinetics and phase transformations during active oxidation. However, fundamental understanding and quantification of grain boundary effects on oxidation behavior in nanocrystalline SiC remain elusive when temperatures exceed 1500 K. This study deploys large-scale molecular dynamics simulations with a reactive force-field to elucidate the complex roles of atomic oxygen reservoir conditions and grain size on oxidation kinetics and the nature of oxides produced in both monocrystalline and nanocrystalline 3C-SiC between 1100 K and 2000 K. The simulations with dynamically replenished oxygen provide good agreement with oxidation kinetics and activation energies for the monocrystalline Si(100) and C(100) orientations published in the available literature. This study reveals that, by contrast, nanocrystalline SiC samples exhibit two distinct oxidation kinetics with a transition point at 1500 K due to surface melting, which is supported by experimental evidence. The introduction of a grain-boundary network produces a two-fold decrease in oxidation activation energies compared to monocrystalline SiC below 1500 K. Above 1500 K, however, the activation energies rise substantially due to the formation of a liquid Si phase at the SiC/Si oxide interface. Further, it is shown that the stability of the interfacial liquid phase is promoted by incoherent grain boundaries in the crystalline SiC. These findings are important for the deployment of nanocrystalline SiC fibers in advanced thermal protection systems for high-temperature applications.
The Role of Dimer Formation in the Nucleation of Superlattice Transformations and Its Impact on Disorder
The formation of defect-free two-dimensional nanocrystal (NC) superstructures remains a challenge as persistent defects hinder charge delocalization and related device performance. Understanding defect formation is an important step toward developing strategies to mitigate their formation. However, specific mechanisms of defect formation are difficult to determine, as superlattice phase transformations that occur during fabrication are quite complex and there are a variety of factors influencing the disorder in the final structure. Here, we use Molecular Dynamics (MD) and electron microscopy in concert to investigate the nucleation of the epitaxial attachment of lead chalcogenide (PbX, where X = S, Se) NC assemblies. We use an updated implementation of an existing reactive force field in an MD framework to investigate how initial orientational (mis)alignment of the constituent building blocks impacts the final structure of the epitaxially connected superlattice. This Simple Molecular Reactive Force Field (SMRFF) captures both short-range covalent forces and long-range electrostatic forces and allows us to follow orientational and translational changes of NCs during superlattice transformation. Our simulations reveal how robust the oriented attachment is with regard to the initial configuration of the NCs, measuring its sensitivity to both in-plane and out-of-plane misorientation. We show that oriented attachment nucleates through the initial formation of dimers, which corroborate experimentally observed structures. We present high-resolution structural analysis of dimers at early stages of the superlattice transformation and rationalize their contribution to the formation of defects in the final superlattice. Collectively, the simulations and experiments presented in this paper provide insights into the nucleation of NC oriented attachment, the impact of the initial configuration of NCs on the structural fidelity of the final epitaxially connected superlattice, and the propensity to form commonly observed defects, such as missing bridges and atomic misalignment in the superlattice due to the formation of dimers. Here, we present potential strategies to mitigate the formation of superlattice defects.