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We develop a broadly-applicable computational method for the automaticexploration of the bimolecular multi-reaction mechanism. The currentmethodology mainly involves the high-energy Born-Oppenheimer molecular dynamics(BOMD) simulation and the successive reaction pathway construction. Severalcomputational tricks are introduced, which include the selection of thereactive regions based on the electronic-structure calculations and theemployment of the virtual collision-dynamics simulations with monitoring atomicdistance before BOMD. These prescreening steps largely reduce the number oftrajectories in the BOMD simulations and significantly save computational cost.The hidden Markov model combined with modified atomic connectivity matrix istaken for the detection of reaction events in each BOMD trajectory. Startingfrom several geometries close to reaction events, the further intermediateoptimization and transition-state searches are conducted. The proposed methodallows us to build the complicated multi-reaction mechanism of medium-sizedbimolecular systems automatically. Here we examine the feasibility andefficiency of the current method by its performance in searching the mechanismsof two prototype reactions in environmental science, which are the penicillin Ganion + H2O and the penicillin G anion + OH radical reactions. The resultindicates that the proposed theoretical method is a powerful protocol for theautomatic searching of the bimolecular reaction mechanisms for medium-sizedcompounds.

An automatic approach to explore multi-reaction mechanism for  medium-sized bimolecular reactions via collision dynamics simulations and  transition state searches