Reactive molecular dynamics simulations

To date, our reactive molecular dynamics simulations of proton transport have been limited to bulk water. However, the extension of Ae RMD algorithm to proton transport in PFSA membranes is analogous to what has been done in bulk water and simi-... 

F. Zipoli, M. Bernasconi, and R. Martohak (2004) Constant pressure reactive molecular dynamics simulations of phase transitions under pressure The graphite to diamond conversion revisited. Eur. Phys. J. B 39, p. 41... 

FIGURE 7.10 Side view models showing the system and protocol adopted for the reactive molecular dynamics simulation of the interaction of chloride ions with passivated copper surfaces. Left Cu(l 11) slab covered by CU2O thin films with O-deficient (top) and O-enriched (bottom) terminations after thermal relaxation at 300 K. Middle filling the gap with 20 M Cl" aqueous solution (pH 7). Right complete system after relaxation for 250 ps at 300 K showing preferential interaction of the chlorides ions with the O-deficient surface. Periodic boundary conditions apply along the x-, y-, and z-directions.Adapted from Jeon et al. [135], 1229, with permission from the Ameriean Chemical Society. 

Fig. 7.5 Snapshot of a reactive molecular dynamics simulation (ReaxEF) of singly reduced EC species in a solution of EC molecules [31]...

Bhattacharya S, Kieffer J (2005) Fractal dimensions of silica gels generated using reactive molecular dynamics simulations. J Chem Phys 122 094715. 

Huang LL, Gubbins KE, Li LC, Lu XH Water on titanium dioxide surface a revisiting by reactive molecular dynamics simulations, Langmuir 30 14832—14840, 2014. 

Barone M E and Graves D B 1995 Molecular dynamics simulations of direct reactive ion etching of silicon by fluorine and chlorine J. Appi. Phys. 78 6604-15... 

Hanson D E, Voter A F and Kress J D 1997 Molecular dynamics simulation of reactive Ion etching of SI by energetic Cl Ions J. Appl. Phys. 82 3552-9... 

For the 1,3-dithiane-1-oxide (R=H) case molecular dynamics simulations at the experimental temperature revealed that the R-hydroxysulfoniiun cation was considerably more stable than the more weakly adsorbed 1,3-dithiane molecule We consider that the hydroxydithiane cation may act as a proton transfer agent and this may account for the enhanced reactivity of this system. 

Andre, S. Pei, Z. Siebert, H.-C. Ramstrom, O. Cabins, H.-J. Glycosyl-disulfides from dynamic combinatorial libraries as O-glycoside mimetics for plant and endogenous lectins Their reactivities in solid-phase and cell assays and conformational analysis by molecular dynamics simulations. Bioorg. Med. Chem. 2006,14, 6314-6326. 

Various theoretical methods and approaches have been used to model properties and reactivities of metalloporphyrins. They range from the early use of qualitative molecular orbital diagrams (24,25), linear combination of atomic orbitals to yield molecular orbitals (LCAO-MO) calculations (26-30), molecular mechanics (31,32) and semi-empirical methods (33-35), and self-consistent field method (SCF) calculations (36-43) to the methods commonly used nowadays (molecular dynamic simulations (31,44,45), density functional theory (DFT) (35,46-49), Moller-Plesset perturbation theory ( ) (50-53), configuration interaction (Cl) (35,42,54-56), coupled cluster (CC) (57,58), and CASSCF/CASPT2 (59-63)). 

Ray Kapral came to Toronto from the United States in 1969. His research interests center on theories of rate processes both in systems close to equilibrium, where the goal is the development of a microscopic theory of condensed phase reaction rates,89 and in systems far from chemical equilibrium, where descriptions of the complex spatial and temporal reactive dynamics that these systems exhibit have been developed.90 He and his collaborators have carried out research on the dynamics of phase transitions and critical phenomena, the dynamics of colloidal suspensions, the kinetic theory of chemical reactions in liquids, nonequilibrium statistical mechanics of liquids and mode coupling theory, mechanisms for the onset of chaos in nonlinear dynamical systems, the stochastic theory of chemical rate processes, studies of pattern formation in chemically reacting systems, and the development of molecular dynamics simulation methods for activated chemical rate processes. His recent research activities center on the theory of quantum and classical rate processes in the condensed phase91 and in clusters, and studies of chemical waves and patterns in reacting systems at both the macroscopic and mesoscopic levels. 

The development of multiscale simulation techniques that involve the atomistic modeling of various structures and processes still remains at its early stage. There are many problems to be solved associated with more accurate and detailed description of these structures and processes. These problems include the development of efficient and fast methods for quantum calculations at the atomistic level, the development of transferable interatomic potentials (especially, reactive potentials) for molecular dynamic simulations, and the development of strategies for the application of multiscale simulation methods to other important processes and materials (optical, magnetic, sensing, etc.). 

Describe the main approaches to the construction of empirical force fields for molecular dynamic simulations. Describe the difference between ordinary and reactive force fields. 

The main advantage of the MFA is that it permits one to dramatically reduce the computational requisites associated with the study of solvent effects. This allows one to focus attention on the solute description, and it consequently becomes possible to use calculation levels similar to those usually employed in the study of systems and processes in the gas phase. Furthermore, in the case of ASEP/MD this high level description of the solute is combined with a detailed description of the solvent structure obtained from molecular dynamics simulations. Thanks to these features ASEP/MD [8] enables the study of systems and processes where it is necessary to have simultaneously a good description of the electron correlation of the solute and the explicit consideration of specific solute-solvent interactions, such as for VIS-UV spectra [9] or chemical reactivity [10]. 

A description of the method of molecular dynamics simulations and its applications to energetic materials research is provided. We present an overview of the development of both reactive and non-reactive interaction potentials used to describe the energetic materials in different phases. Limitations as well as performances of the current models are indicated, including recent advances in reactive model development. Applications of the method to both gas and condensed phases of energetic materials are given to illustrate current capabilities. 

In the early 1990s, Brenner and coworkers [163] developed interaction potentials for model explosives that include realistic chemical reaction steps (i.e., endothermic bond rupture and exothermic product formation) and many-body effects. This potential, called the Reactive Empirical Bond Order (REBO) potential, has been used in molecular dynamics simulations by numerous groups to explore atomic-level details of self-sustained reaction waves propagating through a crystal [163-171], The potential is based on ideas first proposed by Abell [172] and implemented for covalent solids by Tersoff [173]. It introduces many-body effects through modification of the pair-additive attractive term by an empirical bond-order function whose value is dependent on the local atomic environment. The form that has been used in the detonation simulations assumes that the total energy of a system of N atoms is ... 

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