Development of the reaction time accelerating molecular dynamics method for simulation of chemical reaction

We present a novel and efficient method to integrate chemical reactions into molecular dynamics to simulate chemical reaction systems. We have dubbed this method RTAMD, an acronym for reaction time accelerating molecular dynamics. The methodology we propose here requires no more than the knowledge of the empirical intermolecular potentials for the species at play as well as the elementary reaction path among them. Bond formation during the simulation is performed by changing the inter-atomic potentials from those of the non-bonded species to those of the bonded ones, and a reaction is deemed to occur by the distance separating the bond forming atoms. In this way the energy barrier for a reaction is no longer considered; the estimation of the reaction rate, however, is possible by introducing the principles of the transition state theory. The simplicity of the present scheme to simulate chemical reactions enables it to be used in large-scale MD simulations involving a large number of simultaneous chemical reactions and to evaluate kinetic parameters. In this paper, the basic theory of the method is presented and application to simple equiatomic reaction system where the reaction rates were estimated was illustrated.