Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid

Abstract

The behavior of the reaction rate of an isomerizing diatomic molecule solvated in a Lennard-Jones fluid is studied by molecular dynamics simulations. A comprehensive study of solvation effects on the rate constant, using the reactive flux absorbing boundary approximation of Straub and Berne, is presented. We provide simulation data over three orders of magnitude in solvent density for four systems differing in the mass of the solvent atoms and frequencies of the internal potential. Rate constants are also calculated for the model system using both Langevin Dynamics with exponential memory and impulsive collision dynamics of the BGK model. A simple method for calculating the average energy transfer and collision frequency is used to determine the collision efficiency for systems in which the mass of the solvent atoms is lighter than, equal to, or heavier than that of the atoms composing the isomerizing diatomic. We find that for solvents of equal and heavy mass compared to the solute the impulsive collision model provides the best description of the dynamics. Finally, we employ a method recently introduced by us to calculate the spatial dependence of the dynamic friction; we compare the reaction coordinate friction at the transition state separation with an approximation based on the single particle friction. This directly calculated reaction coordinate friction, when combined with the Grote–Hynes theory for barrier crossing, gives good agreement with the simulation data at high density.