Automatic Approach to Explore the Multireaction Mechanism for Medium-Sized Bimolecular Reactions via Collision Dynamics Simulations and Transition State Searches

We develop a broadly applicable computational method for the automatic exploration of the bimolecular multireaction mechanism. The current methodology mainly involves the high-energy Born-Oppenheimer molecular dynamics (BOMD) simulation and the successive reaction pathway construction. Several computational tricks are introduced, which include the selection of the reactive regions based on the electronic structure calculations and the employment of the virtual collision dynamics simulations with the monitoring of the atomic distance before the BOMD simulation. These prescreening steps largely reduce the number of trajectories in the BOMD simulations and significantly save the computational cost. The hidden Markov model combined with the modified atomic connectivity matrix is used for the detection of reaction events in each BOMD trajectory. Starting from several geometries close to the reaction events, the further intermediate optimization and transition state searches are conducted. The proposed method allows us to build the complicated multireaction mechanism of medium-sized bimolecular systems automatically. Here, we examine the feasibility and efficiency of the current method by its performance in searching the mechanisms of two prototype reactions in environmental science, which are the penicillin G anion + H2O and penicillin G anion + OH radical reactions. The result indicates that the proposed theoretical method is a powerful protocol for the automatic search of the bimolecular reaction mechanisms for medium-sized compounds.

Automated summary

The study introduces a computational method for automatic exploration of bimolecular multireaction mechanism, which significantly reduces trajectory numbers and computational costs in BOMD simulations through pre-screening steps and simulation tricks. Experimental results demonstrate that the method shows great potential in searching for reaction mechanisms of medium-sized bimolecular compounds.