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

• Published in: arXiv.org
• Main Authors: Cui, Qinghai, Peng, Jiawei, Xu, Chao, Lan, Zhenggang
• Format: Paper Journal Article
• Language: English
• Published: Ithaca Cornell University Library, arXiv.org 23.12.2021
• Subjects: Anions; Collision dynamics; Computational efficiency; Computing costs; Electronic structure; Markov chains; Molecular dynamics; Optimization; Penicillin; Physics - Chemical Physics; Reaction mechanisms; Searching; Simulation
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.2108.03104

We develop a broadly-applicable computational method for the automatic exploration of the bimolecular multi-reaction 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 monitoring atomic distance before BOMD. These prescreening steps largely reduce the number of trajectories in the BOMD simulations and significantly save computational cost. The hidden Markov model combined with modified atomic connectivity matrix is taken for the detection of reaction events in each BOMD trajectory. Starting from several geometries close to reaction events, the further intermediate optimization and transition-state searches are conducted. The proposed method allows us to build the complicated multi-reaction 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 the penicillin G anion + OH radical reactions. The result indicates that the proposed theoretical method is a powerful protocol for the automatic searching of the bimolecular reaction mechanisms for medium-sized compounds.