Combined Experimental and Computational Insight into the Role of Substrate in the Synthesis of Two-Dimensional WSe2

Synthesis of large-area transition-metal dichalcogenides (TMDs) with controlled orientation is a significant challenge to their industrial applications. Substrate plays a vital role in determining the final quality of monolayer materials grown via the chemical vapor deposition process by controlling their orientation, crystal structure, and grain boundary. This study determined the binding energy and equilibrium distance for tungsten diselenide (WSe2) monolayers on crystalline and amorphous silicon dioxide and aluminum dioxide substrates. Differently oriented WSe2 monolayers are considered to investigate the role of the substrate in the orientation, binding strength, and equilibrium distance. This study can pave the way to synthesizing high-quality two-dimensional (2D) materials for electronic and chemical applications.

Effects of Nanoparticle Size on the Thermal Decomposition Mechanisms of 3,5-Diamino-6-hydroxy-2-oxide-4-nitropyrimidone through ReaxFF Large-Scale Molecular Dynamics Simulations

ReaxFF-lg molecular dynamics method was employed to simulate the decomposition processes of IHEM-1 nanoparticles at high temperatures. The findings indicate that the initial decomposition paths of the nanoparticles with different sizes at varying temperatures are similar, where the bimolecular polymerization reaction occurred first. Particle size has little effect on the initial decomposition pathway, whereas there are differences in the numbers of the species during the decomposition and their evolution trends. The formation of the hydroxyl radicals is the dominant decomposition mechanism with the highest reaction frequency. The degradation rate of the IHEM-1 molecules gradually increases with the increasing temperature. The IHEM-1 nanoparticles with smaller sizes exhibit greater decomposition rate constants. The activation energies for the decomposition are lower than the reported experimental values of bulk explosives, which suggests a higher sensitivity.

Reactive Molecular Dynamics Simulations of Polystyrene Pyrolysis

Polymers' controlled pyrolysis is an economical and environmentally friendly solution to prepare activated carbon. However, due to the experimental difficulty in measuring the dependence between microstructure and pyrolysis parameters at high temperatures, the unknown pyrolysis mechanism hinders access to the target products with desirable morphologies and performances. In this study, we investigate the pyrolysis process of polystyrene (PS) under different heating rates and temperatures employing reactive molecular dynamics (ReaxFF-MD) simulations. A clear profile of the generation of pyrolysis products determined by the temperature and heating rate is constructed. It is found that the heating rate affects the type and amount of pyrolysis intermediates and their timing, and that low-rate heating helps yield more diverse pyrolysis intermediates. While the temperature affects the pyrolytic structure of the final equilibrium products, either too low or too high a target temperature is detrimental to generating large areas of the graphitized structure. The reduced time plots (RTPs) with simulation results predict a PS pyrolytic activation energy of 159.74 kJ/mol. The established theoretical evolution process matches experiments well, thus, contributing to preparing target activated carbons by referring to the regulatory mechanism of pyrolytic microstructure.

Atomistic Insights into Interfacial Optimization Mechanism for Achieving Ultralow-Friction Amorphous Carbon Films under Solid-Liquid Composite Conditions

The combination of fluid lubricants and textured amorphous carbon (a-C) can provide an ultralow friction state, which can improve the reliability and service life of dynamic machinery. However, the coupling effects of the contact pressure and oil content on the friction-reducing efficiency is still lack of study, and the corresponding friction mechanism is also not fully understood, which cannot be achieved by experiment due to the limitation of in situ characterization. In this study, using the reactive molecular dynamics simulation, the insight into the evolution of interfacial structures induced by both contact pressures and oil contents on a-C surface was systematically investigated to explore the fundamental mechanism. In particular, the friction difference between textured and untextured a-C films was evaluated comparatively. Results indicate that the tribological performance strongly depends on the interfacial lubrication state, which is jointly determined by the oil content and contact pressure; the best operating condition to achieve ultralow friction coefficient (0.002) is obtained, and the evolution of friction coefficient with oil content and contact pressure is highly dominated by the lubricant mobility, cross-linking between mating a-C surfaces, or competition/synergy of the H stress state from the lubricant with interfacial passivation. Furthermore, the difference in friction reduction between textured and untextured systems is unveiled; with the increase of contact pressure, the role of texturing a-C surface in antifriction changes from positive to negative effect, which is related to the transformation of interfacial hybridized structure and anomalous flow of lubricant. These results can significantly enhance the understanding of composite lubrication systems through computation and also provide a roadmap for the R&D of the advanced lubrication system according to the working conditions.

Atomic-Scale Understanding on the Tribological Behavior of Amorphous Carbon Films under Different Contact Pressures and Surface Textured Shapes

The textured design of amorphous carbon (a-C) film can significantly improve the tribological performance and service life of moving mechanical components. However, its friction dependence on different texture shapes, especially under different load conditions, remains unclear. In particular, due to the lack of information regarding the friction interface, the underlying friction mechanism has still not been unveiled. Therefore, the effects of contact pressure and textured shapes on the tribological behavior of a-C films under dry friction conditions were comparatively studied in this work by reactive molecular dynamics simulation. The results show that under low contact pressure, the tribological property of a-C film is sensitive to the textured shape, and the system with a circular textured surface exhibits a lower friction coefficient than that with a rectangular textured surface, which is attributed to the small fraction of unsaturated bonds. However, the increase of contact pressure results in the serious reconstruction and passivation of the friction interface. On the one hand, this induces a growth rate of friction force that is much smaller than that of the normal load, which is followed by a significant decrease in the friction coefficient with contact pressure. On the other hand, the destruction or even disappearance of the textured structure occurs, weakening the difference in the friction coefficient caused by different textured shapes of the a-C surface. These results reveal the friction mechanism of textured a-C film and provide a new way to functionalize the a-C as a protective film for applications in hard disks, MEMS, and NEMS.

Molecular Dynamics Simulation of Cracking Process of Bisphenol F Epoxy Resin under High-Energy Particle Impact

The current lead insulation of high-temperature superconductivity equipment is under the combined action of large temperature gradient field and strong electric field. Compared with a uniform temperature field, its electric field distortion is more serious, and it is easy to induce surface discharge to generate high-energy particles, destroy the insulation surface structure and accelerate insulation degradation. In this paper, the degradation reaction process of bisphenol F epoxy resin under the impact of high-energy particles, such as O₃⁻, HO^–, H₃O⁺ and NO⁺, is calculated based on ReaxFF simulation. According to the different types of high-energy particles under different voltage polarities, the micro-degradation mechanism, pyrolysis degree and pyrolysis products of epoxy resin are analyzed. The results show that in addition to the chemical reaction of high-energy particles with epoxy resin, their kinetic energy will also destroy the molecular structure of the material, causing the cross-linked epoxy resin to pyrolyze, and the impact of positive particles has a more obvious impact on the pyrolysis of epoxy resin.

A quantitative paradigm for water-assisted proton transport through proteins and other confined spaces

Water-assisted proton transport through confined spaces influences many phenomena in biomolecular and nanomaterial systems. In such cases, the water molecules that fluctuate in the confined pathways provide the environment and the medium for the hydrated excess proton migration via Grotthuss shuttling. However, a definitive collective variable (CV) that accurately couples the hydration and the connectivity of the proton wire with the proton translocation has remained elusive. To address this important challenge-and thus to define a quantitative paradigm for facile proton transport in confined spaces-a CV is derived in this work from graph theory, which is verified to accurately describe water wire formation and breakage coupled to the proton translocation in carbon nanotubes and the Cl^-/H⁺ antiporter protein, ClC-ec1. Significant alterations in the conformations and thermodynamics of water wires are uncovered after introducing an excess proton into them. Large barriers in the proton translocation free-energy profiles are found when water wires are defined to be disconnected according to the new CV, even though the pertinent confined space is still reasonably well hydrated and-by the simple measure of the mere existence of a water structure-the proton transport would have been predicted to be facile via that oversimplified measure. In this paradigm, however, the simple presence of water is not sufficient for inferring proton translocation, since an excess proton itself is able to drive hydration, and additionally, the water molecules themselves must be adequately connected to facilitate any successful proton transport.

The role of electric field on decomposition of CL-20/HMX cocrystal: A reactive molecular dynamics study

Electric field can initiate decomposition or detonation of explosives, but underlying mechanism is unclear. Here, we performed ReaxFF molecular dynamics simulation for decomposition of a cocrystal, formed by 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazaisowurtzitane (CL-20) and 1,3,5,7-tetranitro-1,3,5,7-tetrazacyclooctane (HMX), solely induced by electric field. A new analytical method was proposed to obtain detailed decomposition mechanism. Results show that electric fields play important roles in decomposition of CL-20/HMX cocrystal, such as heating the system and causing the explosive to decompose. Strong constant field makes CL-20 molecules in the cocrystal decompose at significantly lower temperature, which greatly increases sensitivity. This is ascribed to the distinct decomposition mechanism that CN bond rupture dominates the initial step of CL-20's decomposition. Contrarily, oscillating field has a stronger heating effect but weaker influence on sensitivity. Moreover, HMX exhibits desensitizing effect in CL-20/HMX cocrystal under electric field. These results enhance our understanding of sensitivity mechanism beyond mechanical stimuli in explosives.

Atomistic Mechanics of Torn Back Folded Edges of Triangular Voids in Monolayer WS2

Triangular nanovoids in 2D materials transition metal dichalcogenides have vertex points that cause stress concentration and lead to sharp crack propagation and failure. Here, the atomistic mechanics of back folding around triangular nanovoids in monolayer WS2 sheets is examined. Combining atomic-resolution images from annular dark-field scanning transmission electron microscopy with reactive molecular modelling, it is revealed that the folding edge formation has statistical preferences under geometric conditions based on the orientation mismatch. It is further investigated how loading directions and strong interlayer friction, interplay with WS2 lattice's crack preference, govern the deformation and fracture pattern around folding edges. These results provide fundamental insights into the combination of fracture and folding in flexible monolayer crystals and the resultant Moiré lattices.

Insights into Superlow Friction and Instability of Hydrogenated Amorphous Carbon/Fluid Nanocomposite Interface

Hydrogenated amorphous carbon (a-C:H) film exhibits the superlubricity phenomena as rubbed against dry sliding contacts. However, its antifriction stability strongly depends on the working environment. By composting with the fluid lubricant, the friction response and fundamental mechanisms governing the low-friction performance and instability of a-C:H remain unclear, while they are not accessible by experiment due to the complicated interfacial structure and the lack of advanced characterization technique in situ. Here, we addressed this puzzle with respect to the physicochemical interactions of a-C:H/oil/graphene nanocomposite interface at atomic scale. Results reveal that although the friction capacity and stability of system are highly sensitive to the hydrogenated degrees of mated a-C:H surfaces, the optimized H contents of mated a-C:H surfaces are suggested in order to reach the superlow friction or even superlubricity. Interfacial structure analysis indicates that the fundamental friction mechanism attributes to the hydrogenation-induced passivation of friction interface and squeezing effect to fluid lubricant. Most importantly, the opposite diffusion of fluid oil molecules to the sliding direction is observed, resulting in the transformation of the real friction interface from a-C:H/oil interface to oil/oil interface. These outcomes enable an effective manipulation of the superlow friction of carbon-based films and the development of customized solid-fluid lubrication systems for applications.

Self-Stable Precipitation Polymerization Molecular Entanglement Effect and Molecular Weight Simulations and Experiments

In this paper, we developed a reactive molecular dynamics (RMD) scheme to simulate the Self-Stable Precipitation (SP) polymerization of 1-pentene and cyclopentene (C5) with maleic anhydride (MAn) in an all-atom resolution. We studied the chain propagation mechanism by tracking the changes in molecular conformation and analyzing end-to-end distance and radius of gyration. The results show that the main reason of chain termination in the reaction process was due to intramolecular cyclic entanglement, which made the active center wrapped in the center of the globular chain. After conducting the experiment in the same condition with the simulation, we found that the distribution trend and peak value of the molecular-weight-distribution curve in the simulation were consistent with experimental results. The simulated number average molecular weight (Mn) and weight average molecular weight (Mw) were in good agreement with the experiment. Moreover, the simulated molecular polydispersity index (PDI) for cyclopentene reaction with maleic anhydride was accurate, differing by 0.04 from the experimental value. These show that this model is suitable for C5–maleic anhydride self-stable precipitation polymerization and is expected to be used as a molecular weight prediction tool for other maleic anhydride self-stable precipitation polymerization system.

How Small Molecules Affect the Thermo-Oxidative Aging Mechanism of Polypropylene: A Reactive Molecular Dynamics Study

Understanding the aging mechanism of polypropylene (PP) is fundamental for the fabrication and application of PP-based materials. In this paper, we present our study in which we first used reactive molecular dynamics (RMD) simulations to explore the thermo-oxidative aging of PP in the presence of acetic acid or acetone. We studied the effects of temperature and oxygen on the aging process and discussed the formation pathways of typical small molecule products (H₂, CO, CO₂, CH₄, C₂H₄, and C₂H₆). The effect of two infection agents, acetic acid and acetone, on the aging reaction was analyzed emphatically. The simulation results showed that acetone has a weak impact on accelerating the aging process, while acetic acid has a significant effect, consistent with previous experimental studies. By tracking the simulation trajectories, both acetic acid and acetone produced small active free radicals to further react with other fragment products, thus accelerating the aging process. The first reaction step of acetic acid is often the shedding of the H atom on the hydroxyl group, while the reaction of acetone is often the shedding of the H atom or the methyl. The latter requires higher energy at lower temperatures. This is why the acceleration effect of acetone for the thermo-oxidative aging of PP was not so significant compared to acetic acid in the experimental temperature (383.15 K).

On the Mechanical Properties of Popgraphene-Based Nanotubes: a Reactive Molecular Dynamics Study

Carbon-based tubular materials have sparked a great interest in future electronics and optoelectronics device applications. In this work, we computationally studied the mechanical properties of nanotubes generated from popgraphene (PopNTs). Popgraphene is a 2D carbon allotrope composed of 5-8-5 rings. We carried out fully atomistic reactive (ReaxFF) molecular dynamics for PopNTs of different chiralities ( n , 0 and 0 , n ) and/or diameters and at different temperatures (from 300 up to 1200 K). Results showed that the tubes are thermally stable (at least up to 1200 K). All tubes presented stress/strain curves with a quasi-linear behavior followed by an abrupt drop of stress values. Interestingly, armchair-like PopNTs ( 0 , n ) can stand a higher strain load before fracturing when contrasted to the zigzag-like ones ( n , 0 ). Moreover, it was obtained that Young's modulus (Y_Mod ) (750-900 GPa) and ultimate strength (σ_US ) (120-150 GPa) values are similar to the ones reported for conventional armchair and zigzag carbon nanotubes. Y_Mod values obtained for PopNTs are not significantly temperature-dependent. While the σ_US values for the 0 , n showed a quasi-linear dependence with the temperature, the n , 0 exhibited no clear trends.

Strain-Induced Growth of Twisted Bilayers during the Coalescence of Monolayer MoS2 Crystals

Tailoring the grain boundaries (GBs) and twist angles between two-dimensional (2D) crystals are two crucial synthetic challenges to deterministically enable envisioned applications such as moiré excitons, emerging magnetism, or single-photon emission. Here, we reveal how twisted 2D bilayers can be synthesized from the collision and coalescence of two growing monolayer MoS₂ crystals during chemical vapor deposition. The twisted bilayer (TB) moiré angles are found to preserve the misorientation angle (θ) of the colliding crystals. The shapes of the TB regions are rationalized by a kink propagation model that predicts the GB formed by the coalescing crystals. Optical spectroscopy measurements reveal a θ-dependent long-range strain in crystals with stitched grain boundaries and a sharp (θ > 20°) threshold for the appearance of TBs, which relieves this strain. Reactive molecular dynamics simulations explain this strain from the continued growth of the crystals during coalescence due to the insertion of atoms at unsaturated defects along the GB, a process that self-terminates when the defects become saturated. The simulations also reproduce atomic-resolution electron microscopy observations of faceting along the GB, which is shown to arise from the growth-induced long-range strain. These facets align with the axes of the colliding crystals to provide favorable nucleation sites for second-layer growth of a TB with twist angles that preserve the misorientation angle θ. This interplay between strain generation and aligned nucleation provides a synthetic pathway for the growth of TBs with deterministic angles.

Tailoring the Nanostructure of Graphene as an Oil-Based Additive: toward Synergistic Lubrication with an Amorphous Carbon Film

Graphene exhibits great potential as a lubricant additive to enhance the antifriction capacity of moving mechanical components in synergism with amorphous carbon (a-C) as a solid lubricant. However, it is particularly challenging for experiments to accurately examine the friction dependence on the physical nanostructure of the graphene additive and the corresponding interfacial reactions because of the inevitable complexity of the graphene structure fabricated in experiments. Here, we address this puzzle regarding the coeffect of the size and content of the graphene additive at the a-C interface using reactive molecular dynamics simulations. Results reveal that the friction-reducing behavior is more sensitive to graphene size than content. For each graphene structure, with increasing content, the friction coefficient always decreases first and then increases, while the friction behavior exhibits significant dependence on the graphene size when the graphene content is fixed. In particular, the optimized size and content of the graphene additive are suggested, in which an excellent antifriction behavior or even superlubricity can be achieved. Analysis of the friction interface indicates that with increasing graphene size, the dominated low-friction mechanism transforms from the high mobilities of the base oil and graphene additive in synergism to the passivation and graphene-induced smoothing of the friction interface. These outcomes disclose the roadmap for developing a robust solid-liquid synergy lubricating system.

Identifying Physical and Chemical Contributions to Friction: A Comparative Study of Chemically Inert and Active Graphene Step Edges

Friction has both physical and chemical origins. To differentiate these origins and understand their combined effects, we study friction at graphene step edges with the same height and different terminating chemical moieties using atomic force microscopy (AFM) and reactive molecular dynamics (MD) simulations. A step edge produced by physical exfoliation of graphite layers in ambient air is terminated with hydroxyl (OH) groups. Measurements with a silica countersurface at this exposed step edge in dry nitrogen provide a reference where both physical topography effects and chemical hydrogen-bonding (H-bonding) interactions are significant. H-bonding is then suppressed in AFM experiments performed in alcohol vapor environments, where the OH groups at the step edge are covered with physisorbed alcohol molecules. Finally, a step edge buried under another graphene layer provides a chemically inert topographic feature with the same height. These systems are modeled by reactive MD simulations of sliding on an OH-terminated step edge, a step edge with alkoxide group termination, or a buried step edge. Results from AFM experiments and MD simulations demonstrate hysteresis in friction measured during the step-up versus step-down processes in all cases except the buried step edge. The origin of this hysteresis is shown to be the anisotropic deflection of terminal groups at the exposed step edge, which varies depending on their chemical functionality. The findings explain why friction is high on atomically corrugated and chemically active surfaces, which provides the insight needed to achieve superlubricity more broadly.

Effect of Domain Size, Boundary, and Loading Conditions on Mechanical Properties of Amorphous Silica: A Reactive Molecular Dynamics Study

Mechanical properties are very important when choosing a material for a specific application. They help to determine the range of usefulness of a material, establish the service life, and classify and identify materials. The size effect on mechanical properties has been well established numerically and experimentally. However, the role of the size effect combined with boundary and loading conditions on mechanical properties remains unknown. In this paper, by using molecular dynamics (MD) simulations with the state-of-the-art ReaxFF force field, we study mechanical properties of amorphous silica (e.g., Young's modulus, Poisson's ratio) as a function of domain size, full-/semi-periodic boundary condition, and tensile/compressive loading. We found that the domain-size effect on Young's modulus and Poisson's ratio is much more significant in semi-periodic domains compared to full-periodic domains. The results, for the first time, revealed the bimodular and anisotropic nature of amorphous silica at the atomic level. We also defined a "safe zone" regarding the domain size, where the bulk properties of amorphous silica can be reproducible, while the computational cost and accuracy are in balance.

Mechanisms of Iodide⁻Triiodide Exchange Reactions in Ionic Liquids: A Reactive Molecular-Dynamics Exploration

Efficient charge transport has been observed in iodine-doped, iodide-based room-temperature ionic liquids, yielding high ionic conductivity. To elucidate preferred mechanistic pathways for the iodide ( I - )-to-triiodide ( I 3 - ) exchange reactions, we have performed 10 ns reactive molecular-dynamics calculations in the liquid state for 1-butyl-3-methylimidazolium iodide ([BMIM][I]) at 450 to 750 K. Energy-barrier distributions for the iodine-swapping process were determined as a function of temperature, employing a charge-reassignment scheme drawn in part from electronic-structure calculations. Bond-exchange events were observed with rate-determining energy barriers ranging from ~0.19 to 0.23 ± 0.06 eV at 750 and 450 K, respectively, with an approximately Arrhenius temperature dependence for iodine self-diffusivity and reaction kinetics, although diffusion dominates/limits the bond-exchange events. This charge transfer is not dissimilar in energetics to those in solid-state superionic conductors.

Faceting, Grain Growth, and Crack Healing in Alumina

Reactive molecular dynamics simulations are performed to study self-healing of cracks in Al₂O₃ containing core/shell SiC/SiO₂ nanoparticles. These simulations are carried out in a precracked Al₂O₃ under mode 1 strain at 1426 °C. The nanoparticles are embedded ahead of the precrack in the Al₂O₃ matrix. When the crack begins to propagate at a strain of 2%, the nanoparticles closest to the advancing crack distort to create nanochannels through which silica flows toward the crack and stops its growth. At this strain, the Al₂O₃ matrix at the interface of SiC/SiO₂ nanoparticles forms facets along the prismatic (A) ⟨2̅110⟩ and prismatic (M) ⟨1̅010⟩ planes. These facets act as nucleation sites for the growth of multiple secondary amorphous grains in the Al₂O₃ matrix. These grains grow with an increase in the applied strain. Voids and nanocracks form in the grain boundaries but are again healed by diffusion of silica from the nanoparticles.

First-principles-based reaction kinetics from reactive molecular dynamics simulations: Application to hydrogen peroxide decomposition

This paper presents our vision of how to use in silico approaches to extract the reaction mechanisms and kinetic parameters for complex condensed-phase chemical processes that underlie important technologies ranging from combustion to chemical vapor deposition. The goal is to provide an analytic description of the detailed evolution of a complex chemical system from reactants through various intermediates to products, so that one could optimize the efficiency of the reactive processes to produce the desired products and avoid unwanted side products. We could start with quantum mechanics (QM) to ensure an accurate description; however, to obtain useful kinetics we need to average over ∼10-nm spatial scales for ∼1 ns, which is prohibitively impractical with QM. Instead, we use the reactive force field (ReaxFF) trained to fit QM to carry out the reactive molecular dynamics (RMD). We focus here on showing that it is practical to extract from such RMD the reaction mechanisms and kinetics information needed to describe the reactions analytically. This analytic description can then be used to incorporate the correct reaction chemistry from the QM/ReaxFF atomistic description into larger-scale simulations of ∼10 nm to micrometers to millimeters to meters using analytic approaches of computational fluid dynamics and/or continuum chemical dynamics. In the paper we lay out the strategy to extract the mechanisms and rate parameters automatically without the necessity of knowing any details of the chemistry. We consider this to be a proof of concept. We refer to the process as RMD2Kin (reactive molecular dynamics to kinetics) for the general approach and as ReaxMD2Kin (ReaxFF molecular dynamics to kinetics) for QM-ReaxFF-based reaction kinetics.

Molecular Dynamics Simulations on the Thermal Decomposition of Meta-Aramid Fibers

The thermal decomposition mechanism of a meta-aramid fiber was simulated at the atomic level using the ReaxFF reactive force field. The simulation results indicated that the main initial decomposition positions of the meta-aramid fiber elements were Caromatic ring⁻N and C=O, which could be used as targets for the modification of meta-aramid fibers. The meta-aramid fiber elements first decomposed into C6⁻C13 and then into smaller segments and micromolecular gases. The temperature was shown to be the key factor affecting the thermal decomposition of the meta-aramid fibers. More complex compositions and stable gases were produced at high temperatures than at lower temperatures. HCN was a decomposition product at high temperature, suggesting that its presence could be used for detecting thermal faults in meta-aramid fibers. Generation path tracing of the thermal decomposition products NH₃ and H₂O was also performed. NH₃ was produced when the NH₂ group captured an H atom adjacent to the system. H₂O was formed after a carbonyl group captured an H atom, became a hydroxyl group, with subsequent intramolecular dehydration or intermolecular hydrogen abstraction.

Kinetic Analysis and Structural Interpretation of Competitive Ligand Binding for NO Dioxygenation in Truncated Hemoglobin N

The conversion of nitric oxide (NO) into nitrate (NO₃^- ) by dioxygenation protects cells from lethal NO. Starting from NO-bound heme, the first step in converting NO into benign NO₃^- is the ligand exchange reaction FeNO+O₂ →FeO₂ +NO, which is still poorly understood at a molecular level. For wild-type (WT) truncated hemoglobin N (trHbN) and its Y33A mutant, the calculated barriers for the exchange reaction differ by 1.5 kcal mol^-1 , compared with 1.7 kcal mol^-1 from experiment. It is directly confirmed that the ligand exchange reaction is rate-limiting in trHbN and that entropic contributions account for 75 % of the difference between the WT and the mutant. Residues Tyr 33, Phe 46, Val 80, His 81, and Gln 82 surrounding the active site are expected to control the reaction path. By comparison with electronic structure calculations, the transition state separating the two ligand-bound states was assigned to a ² A state.

Driving Chemical Reactions in Plasmonic Nanogaps with Electrohydrodynamic Flow

Nanoparticles from colloidal solution-with controlled composition, size, and shape-serve as excellent building blocks for plasmonic devices and metasurfaces. However, understanding hierarchical driving forces affecting the geometry of oligomers and interparticle gap spacings is still needed to fabricate high-density architectures over large areas. Here, electrohydrodynamic (EHD) flow is used as a long-range driving force to enable carbodiimide cross-linking between nanospheres and produces oligomers exhibiting sub-nanometer gap spacing over mm² areas. Anhydride linkers between nanospheres are observed via surface-enhanced Raman scattering (SERS) spectroscopy. The anhydride linkers are cleavable via nucleophilic substitution and enable placement of nucleophilic molecules in electromagnetic hotspots. Atomistic simulations elucidate that the transient attractive force provided by EHD flow is needed to provide a sufficient residence time for anhydride cross-linking to overcome slow reaction kinetics. This synergistic analysis shows assembly involves an interplay between long-range driving forces increasing nanoparticle-nanoparticle interactions and probability that ligands are in proximity to overcome activation energy barriers associated with short-range chemical reactions. Absorption spectroscopy and electromagnetic full-wave simulations show that variations in nanogap spacing have a greater influence on optical response than variations in close-packed oligomer geometry. The EHD flow-anhydride cross-linking assembly method enables close-packed oligomers with uniform gap spacings that produce uniform SERS enhancement factors. These results demonstrate the efficacy of colloidal driving forces to selectively enable chemical reactions leading to future assembly platforms for large-area nanodevices.

Atomistic Insights into Nucleation and Formation of Hexagonal Boron Nitride on Nickel from First-Principles-Based Reactive Molecular Dynamics Simulations

Atomistic-scale insights into the growth of a continuous, atomically thin hexagonal boron nitride (hBN) lattice from elemental boron and nitrogen on Ni substrates were obtained from multiscale modeling combining density functional theory (DFT) and reactive molecular dynamics. The quantum mechanical calculations focused on the adsorption and reaction energetics for the hBN building-block species, i.e., atomic B, N, B_xN_y (x, y = 1, 2), on Ni(111) and Ni(211), and the diffusion pathways of elemental B and N on these slab model surfaces and in the sublayer. B can diffuse competitively on both the surface and in the sublayer, while N diffuses strictly on the substrate surface. The DFT data were then used to generate a classical description of the Ni-B and Ni-N pair interactions within the formulation of the reactive force field, ReaxFF. Using the potential developed from this work, the elementary nucleation and growth process of an hBN monolayer structure from elemental B and N is shown at the atomistic scale. The nucleation initiates from the growth of linear BN chains, which evolve into branched and then hexagonal lattices. Subsequent DFT calculations confirmed the structure evolution energetically and validate the self-consistency of this multiscale modeling framework. On the basis of this framework, the fundamental aspects regarding crystal quality and the role of temperature and substrates used during hBN growth can also be understood.

Multiscale simulations reveal key features of the proton-pumping mechanism in cytochrome c oxidase

Cytochrome c oxidase (CcO) reduces oxygen to water and uses the released free energy to pump protons across the membrane. We have used multiscale reactive molecular dynamics simulations to explicitly characterize (with free-energy profiles and calculated rates) the internal proton transport events that enable proton pumping during first steps of oxidation of the fully reduced enzyme. Our results show that proton transport from amino acid residue E286 to both the pump loading site (PLS) and to the binuclear center (BNC) are thermodynamically driven by electron transfer from heme a to the BNC, but that the former (i.e., pumping) is kinetically favored whereas the latter (i.e., transfer of the chemical proton) is rate-limiting. The calculated rates agree with experimental measurements. The backflow of the pumped proton from the PLS to E286 and from E286 to the inside of the membrane is prevented by large free-energy barriers for the backflow reactions. Proton transport from E286 to the PLS through the hydrophobic cavity and from D132 to E286 through the D-channel are found to be strongly coupled to dynamical hydration changes in the corresponding pathways and, importantly, vice versa.

ReaxFF Reactive Force-Field Modeling of the Triple-Phase Boundary in a Solid Oxide Fuel Cell

In our study, the Ni/YSZ ReaxFF reactive force field was developed by combining the YSZ and Ni/C/H descriptions. ReaxFF reactive molecular dynamics (RMD) were applied to model chemical reactions, diffusion, and other physicochemical processes at the fuel/Ni/YSZ interface. The ReaxFF RMD simulations were performed on the H2/Ni/YSZ and C4H10/Ni/YSZ triple-phase boundary (TPB) systems at 1250 and 2000 K, respectively. The simulations indicate amorphization of the Ni surface, partial decohesion (delamination) at the interface, and coking, which have indeed all been observed experimentally. They also allowed us to derive the mechanism of the butane conversion at the Ni/YSZ interface. Many steps of this mechanism are similar to the pyrolysis of butane. The products obtained in our simulations are the same as those in experiment, which indicates that the developed ReaxFF potential properly describes complex physicochemical processes, such as the oxide-ion diffusion, fuel conversion, water formation reaction, coking, and delamination, occurring at the TPB and can be recommended for further computational studies of the fuel/electrode/electrolyte interfaces in a SOFC.

Exploding Nitromethane in Silico, in Real Time

Nitromethane (NM) is widely applied in chemical technology as a solvent for extraction, cleaning, and chemical synthesis. NM was considered safe for a long time, until a railroad tanker car exploded in 1958. We investigate the detonation kinetics and explosion reaction mechanisms in a variety of systems consisting of NM, molecular oxygen, and water vapor. Reactive molecular dynamics allows us to simulate reactions in time-domain, as they occur in real life. High polarity of the NM molecule is shown to play a key role, driving the first exothermic step of the reaction. Rapid temperature and pressure growth stimulate the subsequent reaction steps. Oxygen is important for faster oxidation, whereas its optimal concentration is in agreement with the proposed reaction mechanism. Addition of water (50 mol %) inhibits detonation; however, water does not prevent detonation entirely. The reported results provide important insights for improving applications of NM and preserving the safety of industrial processes.

Computationally Efficient Multiconfigurational Reactive Molecular Dynamics

It is a computationally demanding task to explicitly simulate the electronic degrees of freedom in a system to observe the chemical transformations of interest, while at the same time sampling the time and length scales required to converge statistical properties and thus reduce artifacts due to initial conditions, finite-size effects, and limited sampling. One solution that significantly reduces the computational expense consists of molecular models in which effective interactions between particles govern the dynamics of the system. If the interaction potentials in these models are developed to reproduce calculated properties from electronic structure calculations and/or ab initio molecular dynamics simulations, then one can calculate accurate properties at a fraction of the computational cost. Multiconfigurational algorithms model the system as a linear combination of several chemical bonding topologies to simulate chemical reactions, also sometimes referred to as "multistate". These algorithms typically utilize energy and force calculations already found in popular molecular dynamics software packages, thus facilitating their implementation without significant changes to the structure of the code. However, the evaluation of energies and forces for several bonding topologies per simulation step can lead to poor computational efficiency if redundancy is not efficiently removed, particularly with respect to the calculation of long-ranged Coulombic interactions. This paper presents accurate approximations (effective long-range interaction and resulting hybrid methods) and multiple-program parallelization strategies for the efficient calculation of electrostatic interactions in reactive molecular simulations.