Molecular Dynamics of Complex Gas-Phase Reactive Systems by Time-Dependent Groups

Abstract

A novel way of assembling the total potential for performing molecular dynamical studies of complex gas-phase reactive chemical systems is introduced. The method breaks the calculation of the total potential and gradients of the potential into time-dependent groups that are governed by spatial cutoffs. These groups evolve during the course of the simulation and their number may increase or diminish as the dynamics of the system determine. In an effort to extend the simulation time of these complex reactive processes and to use high levels of theory when necessary, multiple levels of theory may be used over the groups for the calculation of both the intragroup and intergroup interactions. Representative simulations are performed to illustrate the method and a computationally facile method of obtaining the groups of a simulation are also discussed.

Adaptive Partitioning in Combined Quantum Mechanical and Molecular Mechanical Calculations of Potential Energy Functions for Multiscale Simulations

“…In the present article, we are interested in systems with nonlocalized active regions, such as processes in solution, [25][26][27][28][29][30] diffusion, reaction, and island evolution studies on catalytic surfaces or nanoparticles or in membranes, [31][32][33][34][35] defect propagation in materials, 36 and complex gas-phase reactive systems. 37 The method presented here can be used to combine multilevel methods with sampling schemes for systems with atoms or groups of atoms entering or leaving the active zone (the QM region) during the simulation. Since an atom should be treated at a high level of theory when it is in the active zone (for accuracy) and at a lower level of theory otherwise (for efficiency) the level of theory used to describe an atom changing zones changes during the simulation.…”

“…In the present article, we are interested in systems with nonlocalized active regions, such as processes in solution, − diffusion, reaction, and island evolution studies on catalytic surfaces or nanoparticles or in membranes, − defect propagation in materials, and complex gas-phase reactive systems …”

Properties of a Method for Performing Adaptive, Multilevel QM Simulations of Complex Chemical Reactions in the Gas-Phase

“…Most often QM/MM methodology is formulated in a static manner, where the defined QM region (that may involve as little as a few atoms to multiples of tens of atoms or molecules) is connected to a defined MM region (typically involving orders of magnitude more atoms/molecules as that found in the QM region), and these regions remain fixed during the course of the simulation. Recently, however, time-dependent (or adaptive) partitioning between the QM and MM regions has provided a means of atomic exchange between regions, where the QM and MM regions are free to change as a function of the simulation time. − This feature is particularly important when studying chemical systems where the phenomena change significantly in time, such as complex reactive systems, solution dynamics, diffusion, and reactions on surfaces. Perhaps the primary difficulty in these dynamically defined QM/MM methods is the significant discontinuties in the total potential (and, perhaps, the atomic force field) and the result that the total energy is not a conserved quantity. ,− The recent adaptive partitioning method of Heyden and Truhlar , has been uniquely formulated in a manner that is able to make the connection between dynamically resolved QM and MM regions in a way that does not induce discontinuities in the potential energy and forces, which ensures microcanonical (NVE) ensemble simulations that conserve energy, angular, and linear momentum.…”

“…Recently, however, time-dependent (or adaptive) partitioning between the QM and MM regions has provided a means of atomic exchange between regions, where the QM and MM regions are free to change as a function of the simulation time. − This feature is particularly important when studying chemical systems where the phenomena change significantly in time, such as complex reactive systems, solution dynamics, diffusion, and reactions on surfaces. Perhaps the primary difficulty in these dynamically defined QM/MM methods is the significant discontinuties in the total potential (and, perhaps, the atomic force field) and the result that the total energy is not a conserved quantity. ,− The recent adaptive partitioning method of Heyden and Truhlar , has been uniquely formulated in a manner that is able to make the connection between dynamically resolved QM and MM regions in a way that does not induce discontinuities in the potential energy and forces, which ensures microcanonical (NVE) ensemble simulations that conserve energy, angular, and linear momentum. The method connects the QM and MM zones through a buffer zone that ensures a smooth transition in the potential and atomic forces for atomic passage by means of 2 N or N additional multilevel calculations of the buffer zone, where N is the number of groups in the buffer zone.…”

“…However, the significant discontinuities resulting in the total potential from time-dependent QM/MM methods has been shown not to induce deviations in the simulations themselves. ,, The reason for this is that the motions of the atoms in the simulation depend on the gradient of the potential (which yields the force field) and not on the potential itself. Thus, in order to have accurate and smooth simulations, the gradients must be continuous between time steps, not the potential.…”