Reactive Molecular Dynamics

Phys., 122, 054502 (2005). Thermal Decomposition of RDX from Reactive Molecular Dynamics. 

In this work, we have approaehed the understanding of proton transport with two tasks. In the first task, deseribed above, we have sought to identify the moleeular-level stmeture of PFSA membranes and their relevant interfaees as a funetion of water content and polymer architecture. In the second task, described in this Section, we explain our efforts to model and quantify proton transport in these membranes and interfaces and their dependence on water content and polymer architecture. As in the task I, the tool employed is molecular dynamics (MD) simulation. A non-reactive algorithm is sufficient to generate the morphology of the membrane and its interfaces. It is also capable of providing some information about transport in the system such as diffusivities of water and the vehicular component of the proton diffusivity. Moreover, analysis of the hydration of hydronium ion provides indirect information about the structural component of proton diffusion, but a direct measure of the total proton diffusivity is beyond the capabilities of a non-reactive MD simulation. Therefore, in the task II, we develop and implement a reactive molecular dynamics algorithm that will lead to direct measurement of the total proton diffusivity. As the work is an active field, we report the work to date. 

Coarse-Grained Reactive Molecular Dynamics Algorithm... 

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... 

Meuwly, M. Becker, O. M. Stote, R. Karplus, M., NO rebinding to myoglobin A reactive molecular dynamics study. Biophys. Chem. 2002, 98,183-207. 

Yue D-C, Ma T-B, Hu Y-Z, Yeon J, van Duin ACT, Wang H, Luo J (2013) Tribochemistry of phosphoric acid sheared between quartz surfaces a reactive molecular dynamics study. J Phys Chem C 117 25604-25614... 

Assowe, O. PoUtano, O. gntil, V. Amoux, R Diawara, B. Vemers, O. van Duin, A. C. T., Reactive Molecular Dynamics of the Initial Oxidation Stages of Niflll) in Pure Water Effect of an Applied Electric Field. J. Phys. Chem. A 2012,116,11796-11805. 

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]...

In addition to QC studies, reactive molecular dynamics (RMD) simulations using the reactive force field ReaxFF have been used to gain insight into reactions of singly reduced EC in the condensed (solution) phase [31]. In this study the reaction of Li /o-EC with both LiVo-EC and LiVc-EC has been studied in a solution of EC molecules. A snapshot of the system is shown in Fig. 7.5. RMD simulations were used to determine the free energy as a function of reaction coordinate (see below) and to examine the propensity of various radical combination reactions to occur in the condensed phase of an EC solvent. 

Keywords Multiscale modeling, Nanotube growth, Non-adiabatic molecular dynamics, Organometallic structures. Protein structure prediction. Reactive molecular dynamics... 

Strachan A et al (2005) Thermal decomposition of RDX from reactive molecular dynamics. J Chem Phys 122(5) 054502... 

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

Reactive molecular dynamics (ReaxMD) is based on the Reax force field (ReaxFF) parameterized by fitting to a training set of QM data. Compared to first-principles simulations, with the ReaxFF model it is possible to speed up the calculation by several orders of magnitude. However, due to the enormous complexity of the underlying mathematical expressions, ReaxFF is -10 to 100 times more expensive computationally than simple (nonreactive) FFs. 

Other popular atomic reactive FFs include the reactive molecular dynamics (RMD) modef and the Reax force field (ReaxFF). The potential importance of ReaxFF in advancing realistic MD simulations merits a short discussion. 

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. 

For calculation of the equilibrium compositions of the liquid phase either the equilibrium constants of the dissociation and polycondensation reactions have to be known or they can be computed by methods which use the approach of minimizing Gibbs free energy [200-202]. In addition, ab initio modeling techniques such as density functional theory (DFT) in combination with reactive molecular dynamic (MD) simulations could be used. Once the liquid phase system is modeled, there are in principle two options to describe the vapor-liquid equilibrium. Either equations of state (EOS) or excess Gibbs free energy models (g -models) may be used to describe the thermodynamics of the liquid... 

Neyts EC, Van Duin ACT, Bogaerts A (2011) Changing chirality during single-walled carbon nanotube growth a reactive molecular dynamics/Monte Carlo study. J Am Chem Soc 133(43) 17225-17231... 

M.C. Classical reactive molecular dynamics implementations state of the art. (2012) Chem. Phys. Chem., doi 10.1002/cphc.201100681. 

Abolfath, R.M., van Duin, A.C.T., Biswas, P., and Brabec, T. Reactive molecular dynamic smdy on the first steps of DNA damage by free hydroxyl radicals. Journal of Physical Chemistry A, 115,11045-11049, 2011. 

Reactive molecular dynamics may be viewed as a microscopic computer experiment inasmuch as all relevant particle processes can be included to some degree. In particular the method treats elastic as well as inelastic or reactive collisions between particles and, indeed, requires that the latter be relatively rare events in order to simulation actual chemical kinetics in a realistic way. When large enough systems are considered (e.g., thousands of particles) it should be possible to "measure" temporal and spatial correlation functions, for example, and to make quantitative the notion of critical size and amplitude of fluctuations necessary to nucleate a macroscopic transition. A first step in the latter direction will be reported here. 

Applications to date of reactive molecular dynamics methods demonstrate feasibility for the study of hundreds or thousands of particles involved in chemical reactions for which reactive probabilities do not vary too widely. The latter condition is essential if statistically significant numbers of all possible events are to occur within a practical computation period. Even if the requirement for a large excess of elastic collisions is relaxed, however, reaction rates typical of experimental chemical systems demand simulation run times which approach the feasible limit except for quite small numbers of particles. Turning therefore to a higher level method for this type of system, one may treat numbers of particles in a small cell or volume element rather than individual particles, and invoke a Monte Carlo procedure for determining which reactive event will occur, how much time will elapse between events, and in which "cell" of the system the... 

Microscopic Chemical Simulations Reactive Molecular Dynamics... 

Reactive Molecular Dynamics. A microscopic computer model of a chemically reacting mixture is constructed with the following... 

A Discrete Model of Cooperative Isomerization. The algorithm which implements the method of reactive molecular dynamics (RMD) is understood best in the context of a specific application. Therefore let us specialize now to the simple isomerization reaction (Eq. 2) to address the questions of "chemical nucleation" raised in that context. Only the main ideas are stressed here. 

Reactive Molecular Dynamics Force Field for the Dissociation of Light Hydrocarbons on Ni(111)... 

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