School of Chemistry, University of Leeds, Leeds LS2 9JT, UK.
J Phys Chem A. 2012 Sep 27;116(38):9545-60. doi: 10.1021/jp3051033. Epub 2012 Sep 12.
The most commonly used theoretical models for describing chemical kinetics are accurate in two limits. When relaxation is fast with respect to reaction time scales, thermal transition state theory (TST) is the theoretical tool of choice. In the limit of slow relaxation, an energy resolved description like RRKM theory is more appropriate. For intermediate relaxation regimes, where much of the chemistry in nature occurs, theoretical approaches are somewhat less well established. However, in recent years master equation approaches have been successfully used to analyze and predict nonequilibrium chemical kinetics across a range of intermediate relaxation regimes spanning atmospheric, combustion, and (very recently) solution phase organic chemistry. In this article, we describe a Master Equation Solver for Multi-Energy Well Reactions (MESMER), a user-friendly, object-oriented, open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where energy transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user options specified via keywords and also includes some unique statistical mechanics approaches like contracted basis set methods and nonadiabatic RRKM theory for modeling spin-hopping. It is our hope that the design principles implemented in MESMER will facilitate its development and usage by workers across a range of fields concerned with chemical kinetics. As accurate thermodynamics data become more widely available, electronic structure theory is increasingly reliable, and as our fundamental understanding of energy transfer improves, we envision that tools like MESMER will eventually enable routine and reliable prediction of nonequilibrium kinetics in arbitrary systems.
描述化学反应动力学最常用的理论模型在两个极限中是准确的。当弛豫相对于反应时间尺度较快时，热过渡态理论（TST）是首选的理论工具。在弛豫缓慢的极限下，像 RRKM 理论这样的能量分辨描述更为合适。对于中间弛豫区，自然界中发生的大部分化学反应都处于这个区域，理论方法的建立就不那么完善了。然而，近年来，主方程方法已成功地用于分析和预测跨越一系列中间弛豫区的非平衡化学反应动力学，涵盖了大气、燃烧和（最近）溶液相有机化学等领域。在本文中，我们描述了一个用于多势阱反应的主方程求解器（MESMER），这是一个用户友好、面向对象、开源的代码，旨在促进具有外部浴能影响现象学动力学的多势阱分子能量拓扑结构上的动力学模拟。MESMER 为用户提供了一系列通过关键字指定的用户选项，还包括一些独特的统计力学方法，如收缩基组方法和非绝热 RRKM 理论，用于模拟自旋跳跃。我们希望在 MESMER 中实现的设计原则将促进其在关注化学反应动力学的各个领域的工作者中的开发和使用。随着更广泛地获得准确的热力学数据，电子结构理论越来越可靠，并且随着我们对能量转移的基本理解的提高，我们设想像 MESMER 这样的工具最终将能够在任意系统中常规且可靠地预测非平衡动力学。
