CARNOT: a Fragment-Based Direct Molecular Dynamics and Virtual–Reality Simulation Package for Reactive Systems

作者：Xin Chen, Meiyi Liu, Jiali Gao · 发表于：Journal of Chemical Theory and Computation · 年份：2022 · DOI：10.1021/acs.jctc.1c01032 · 被引用次数：16 · 研究领域：Advanced Chemical Physics Studies、Spectroscopy and Quantum Chemical Studies、Synthesis and Properties of Aromatic Compounds

Traditionally, the study of reaction mechanisms of complex reaction systems such as combustion has been performed on an individual basis by optimizations of transition structure and minimum energy path or by reaction dynamics trajectory calculations for one elementary reaction at a time. It is effective, but time-consuming, whereas important and unexpected processes could have been missed. In this article, we present a direct molecular dynamics (DMD) approach and a virtual-reality simulation program, CARNOT, in which plausible chemical reactions are simulated simultaneously at finite temperature and pressure conditions. A key concept of the present ab initio molecular dynamics method is to partition a large, chemically reactive system into molecular fragments that can be adjusted on the fly of a DMD simulation. The theory represents an extension of the explicit polarization method to reactive events, called ReX-Pol. We propose a highest-and-lowest adapted-spin approximation to define the local spins of individual fragments, rather than treating the entire system by a delocalized wave function. Consequently, the present ab initio DMD can be applied to reactive systems consisting of an arbitrarily varying number of closed and open-shell fragments such as free radicals, zwitterions, and separate ions found in combustion and other reactions. A graph-data structure algorithm was incorporated in CARNOT for the analysis of reaction networks, suitable for reaction mechanism reduction...