Molecular Dynamics Simulations Of Reactions Research Articles

Molecular dynamics simulations of isothermal reactions in Al/Ni nanolaminates.

Molecular dynamics simulations of reactions in Al/Ni layered systems have been carried out under isothermal conditions for a wide range of temperatures and several system sizes. An embedded atom method potential, known to reasonably reproduce the phase behavior of Al/Ni, was employed. Simulations revealed reaction mechanisms involving an initial fast process and much slower more complex longer-time reactions. The initial reaction process consists of diffusion of Ni from the pure solid Ni phase into the molten Al phase, resulting in the formation of an Al-rich Al/Ni liquid. The initial reaction ends when the Al/Ni liquid becomes saturated in Ni and solid Al/Ni phases begin to form at the interfaces between the pure solid Ni phase and the Al/Ni liquid. The growth of these solid phases is intrinsically slow compared to the formation of the liquid and is further slowed by the need for Ni to diffuse through the growing interfacial Al/Ni solid phases. Analysis of the initial Al/Ni liquid forming process indicates Fickian behavior with the Ni diffusion coefficient exhibiting Arrhenius temperature dependence. The longer-time slow reaction process(es) resulting in the growth of Al/Ni solid phases do not lend themselves to detailed numerical analysis because of the complex dependence of the Ni transport on the detailed nature of the interfacial layers.

General application of Tolman’s concept of activation energy

We present a generalization of Tolman's concept of activation energy applicable to thermal and non-thermal reactions in molecular dynamics simulations of reactions in bulk gases. To illustrate the applicability of the method, molecular dynamics calculations were carried out for the NVT ensemble to determine the activation energies of O2 + H2 → H + HO2 and 2O2 + H2 → 2HO2 from MD simulation results for [H2]/[O2] = 1 at 3000 K using the reactive force field, ReaxFF. Assuming local thermodynamic equilibrium, we define the reaction cluster local energy, the energy of the atoms participating in an individual reaction, which is conserved. The generalized Tolman activation energy (GTEa) approach is applicable to reactions of any molecularity. Although we have applied GTEa for thermal conditions, it is applicable to chemistry occurring under non-thermal conditions because it rests upon local rather than global equilibrium. We have defined the transition configurations, unique points that define a seam separating reactants and products at which the local energies of the reactants and products become equal.

Combined model of the material excitation and relaxation in swift heavy ion tracks

A multiscale approach describing material excitation in the nanometric track of a swift heavy ion (SHI) decelerated in a solid in the electronic stopping regime is presented. This model consists of a combination of three different methods: (a) Monte Carlo simulations of excitation of the electron subsystem of a solid at the femtosecond scale due to scatterings of a SHI and generated fast electrons; (b) a molecular-kinetic approach describing the spatial spreading of electrons after finishing of ionization cascades up to timescales of a hundred femtoseconds; and (c) molecular dynamics simulations of reaction of the lattice on the excess energy transferred from the relaxing electron subsystem at the picosecond time scale. The dynamic structure factor (DSF) formalism links together all these methods. It takes into account effects of spatial and temporal correlations in the atomic system of a target during its interaction with excited electrons in an ion track. For LiF crystals a good agreement is demonstrated between track heating estimated from the experimental data and that predicted by the model.

Temporal quantum mechanics/molecular mechanics: Extending the time scales accessible in molecular dynamics simulations of reactions

An approach termed temporal quantum mechanics/molecular mechanics is presented to extend the time scales accessible in molecular dynamics simulations of reactions. This approach employs a hierarchy of methods: force-fields (FFs) to simulate the system near potential energy minima, semi-empirical (SE) molecular orbital methods to assess the likelihood of trajectories overcoming reaction barriers, and quantum chemical (QC) methods to model changes in bonding and electronic structure during reactions. This method relies primarily on FFs and SE methods, providing access to much longer time scales than those accessible using QC methods alone, with the targeted use of QC methods ensuring reactive events are described properly.

Molecular dynamics simulations of reactions on metal surfaces: rate constants for selected diatomic dissociation reactions

We have employed our normalized bond index (NBI) potential energy function in molecular dynamics simulations of the dissociation of various isotopes of (a) O 2 on Ag(111), Au(111), Pt(111) and Ni(111), (b) S 2 on Ni(111), and (c) C 2 on Ni(111) surfaces for the purpose of computing the zero coverage limit Arrhenius reaction rate constants. For 16O 2 on Pt(111) we repeated the rate constant calculations at a simulated coverage of 0.4, in order to compare our result with an experimental value that corresponds to a low but otherwise unknown coverage. Our computed rate constants for 16O 2 dissociation on Pt(111) are: (a) for the zero coverage limit, k=5.42×10 12 s −1 exp{−1.1 kcal/mol/RT}, (b) for moderate coverage, k=7.43×10 11 s −1 exp{−5.8 kcal/mol/RT}. The experimentally determined rate constant 9×10 11 s −1 exp{−2.5 kcal/mol/RT} is bracketed by our calculated values. Our computed rate constants possess the general trend that the Arrhenius pre-exponentials decrease with increasing vibrational mass of the dissociating bond. Also, the Arrhenius pre-exponentials tend to decrease with decreasing atomic heat of adsorption. We emphasize that the Arrhenius activation barrier is an effective barrier that depends on several aspects of the system, and may not closely correspond with any single feature of the potential energy surface.

Molecular Dynamics Simulations of Reactions of Hyperthermal Fluorine Atoms with Fluorosilyl Adsorbates on the Si{100}-(2 × 1) Surface

Molecular dynamics simulations of the reactions between gaseous fluorine atoms and (SiFx)n adsorbates on the Si{100}-(2 × 1) surface are performed using the SW potential with the WWC reparameterization. The objective of the simulations is to determine how the chemical composition and energy distribution of the etched gas-phase products depend on the identity of the reacting adsorbate. Reactions of normal incident fluorine atoms with SiF3, SiF2−SiF3, and SiF2−SiF2−SiF3 adsorbates are simulated at incident kinetic energies from 3.0 to 9.0 eV. SiF4 is the major product in nearly all cases. An SN2-like mechanism is responsible for the formation of SiF4, Si2F6, and Si3F8. In addition, at 7.0 and 9.0 eV, the simulations have discovered a previously unknown mechanism for the formation of SiF4, which involves an insertion between a silicon−silicon bond. The simulations predict that radical species are formed predominantly from fragmentation of the higher mass etched products with only a few being formed directly from the reaction between the incoming fluorine atom and the adsorbate. Comparisons are made to experimental data on silicon−fluorine etching with both thermal and hyperthermal fluorine atoms.

Molecular Dynamics Simulations of Reactions between Molecules: High-Energy Particle Bombardment of Organic Films

High energy bombardment mass spectrometric techniques are becoming ever more important for organic and biological samples. Before the molecule can be detected, though, it must first be ejected. The authors have developed a molecular dynamics prescription for examining the fundamental processes important for the ejection of organic molecules during the particle bombardment event. The major advance here over previous simulations is the use of an empirical many-body potential energy function constructed for studying reactive dynamics. Specifically, bonds can be broken and reformed. For the first time, one can examine the possibility of reactions among the organic molecules. As an initial test system, the authors have investigated the 500 eV Ar bombardment of ethylidyne, C{sub 2}H{sub 3}, on Pt (111). This specific system has been studied experimentally by White and co-workers using SIMS. The authors have modeled both 0.25 and 0.50 monolayer ethylidyne coverage in order to test density effects. They find that approximately 80% of the ejected hydrocarbon species originate from a single C{sub 2}H{sub 3} adsorbate, while the others result from reactions between two C{sub 2}H{sub 3} adsorbates. A study of the internal energies of all of the ejected hydrocarbon aggregates reveals that those originating from a single C{submore » 2}H{sub 3} adsorbate are generally stable to any further fragmentation or rearrangement. Examples of common ejection mechanisms for species which originate from a single adsorbate, such as CH{sub 3}, C{sub 2}H{sub 3}, HCCH, and those which originate from more than one adsorbate, such as CH{sub 4} and H{sub 2} will be discussed.« less

Molecular dynamics simulations of reactions on metal surfaces

We present a molecular dynamics method for the simulation of reactions on metal surfaces. The method employs reactive potentials obtained from our modified version of the bond order conservation method of Shustorovich. Although we have used these potentials in solving classical equations of motion, quantum mechanical calculations could also employ them. Example calculations in four and six dimensions are given for the dissociation of H2 over Ni(111) and H–SCH3 over Au(111). It is demonstrated that the calculated quantities representing reaction rate constants show the correct Arrhenius behavior. We show that the coupling of the reaction coordinate to ‘‘rotational’’ degrees of freedom contains important effects in agreement with existing work in the literature.

Solvent dynamical effects in electron transfer: molecular dynamics simulations of reactions in methanol

Molecular-dynamics simulations of solvation dynamics accompanying activated electron-transfer (ET) reactions in methanol have been undertaken in order to explore the physical nature of the solvent dynamics coupled to ET barrier crossing, and to probe some underlying reasons for the facile kinetics observed in this solvent. The reactant is modeled by a pair of Lennard-Jones (LJ) spheres in contact, of varying diameter (4 or 5 Å), and containing a univalent charge (cation or anion) on one site so to probe possible effects of the ionic charge sign. Following equilibration, the collective solvent response to a sudden charge transfer between the spherical sites is followed, and described in terms of the response function C( t), describing the difference in the solvent-induced electrostatic potential between the initial and final solute states. In all cases, the C( t) curves exhibit a very rapid (50–100 fs) initial decay component associated with hydroxyl inertial motion, followed by components arising from hydrogen-bond librational and diffusive motions. Interestingly, the dynamics and relative importance of these relaxation modes are dependent on the charge sign as well as size of the solute pair. The molecular-level origins of these sensitivities are explored by examining time-dependent radial distribution functions, which implicate the dominance of short-range solvation in the rapid relaxation dynamics. In particular, the initial very rapid C( t) component for the smaller anion-neutral reactant pair is seen to arise chiefly from dissipation of the hydroxyl solvent polarization around the newly formed neutral site following ET, being accompanied by a slower build up of solvent structuring around the adjacent anionic site. The simulated ET reorganization energies are also shown to be dependent upon the reactant size and charge type. Some more general implications of these and other MD simulation results to the elucidation of dynamical solvent effects in activated ET processes are also noted.

Molecular dynamics simulations of reactions in solids: Photodissociation of Cl2 in crystalline Xe

The photodissociation of isolated Cl2 impurities in a Xe crystal was investigated by molecular dynamics simulations. The calculations were carried out for a photodissociation energy of 3.775 eV, and for several temperatures in the range from 10 to 150 K (the melting point is 162 K). The focus was on the physical mechanisms whereby the product atoms exit from the cage, on the properties of the final sites occupied by the Cl atom, and on the temperature dependence of the processs. The main findings were: (1) exit of a Cl atom from the original reagent cage, when it occurs, is always direct upon photodissociation, and does not involve multiple collisions with the surrounding cage walls. This is in qualitative contrast with the dynamics of cage exit in the case of HI photodissociation in Xe at very low temperatures, found in a previous study. (2) The occurrence of product exit from the cage depends entirely on whether the reagent molecule has been oriented at the direction of a transition state for the exit at the instant of photodissociation. (3) The temperature threshold of Cl exit from the cage is 95 K, and essentially coincides with onset of free rotation for the reagent molecules in the host crystal. (4) The temperature dependence of the probability for cage exit is strongly nonmonotonic: The probability increases as T increases from 95 to 110 K, falls off to 0 around 125 K, then increases again as T approaches melting. (5) At the photodissociation energy used, the only site that the Cl atoms occupy in the new cage is the octahedral interstitial site. Various aspects of reaction dynamics in crystalline solids are discussed in the light of the above results and by their comparison with findings of a previous study on photodissociation of HI in Xe.