Peters Baron
Department of Chemical Engineering, University of California, Santa Barbara, California 93106; email:
Annu Rev Phys Chem. 2016 May 27;67:669-90. doi: 10.1146/annurev-physchem-040215-112215. Epub 2016 Apr 18.
Reaction coordinates are integral to several classic rate theories that can (a) predict kinetic trends across conditions and homologous reactions, (b) extract activation parameters with a clear physical interpretation from experimental rates, and (c) enable efficient calculations of free energy barriers and rates. New trajectory-based rare events methods can provide rates directly from dynamical trajectories without a reaction coordinate. Trajectory-based frameworks can also generate ideal (but abstract) reaction coordinates such as committors and eigenfunctions of the master equation. However, rates and mechanistic insights obtained from trajectory-based methods and abstract coordinates are not readily generalized across simulation conditions or reaction families. We discuss methods for identifying physically meaningful reaction coordinates, including committor analysis, variational transition state theory, Kramers-Langer-Berezhkovskii-Szabo theory, and statistical inference methods that can use path sampling data to screen, mix, and optimize thousands of trial coordinates. Special focus is given to likelihood maximization and inertial likelihood maximization approaches.
反应坐标对于几种经典速率理论至关重要，这些理论能够：(a) 预测不同条件下和同源反应的动力学趋势；(b) 从实验速率中提取具有清晰物理解释的活化参数；(c) 实现对自由能垒和速率的高效计算。新的基于轨迹的稀有事件方法可以直接从动力学轨迹中提供速率，而无需反应坐标。基于轨迹的框架还可以生成理想的（但抽象的）反应坐标，如主方程的反应几率和本征函数。然而，从基于轨迹的方法和抽象坐标获得的速率和机理见解不易在不同的模拟条件或反应族中推广。我们讨论了识别具有物理意义的反应坐标的方法，包括反应几率分析、变分过渡态理论、克拉默斯 - 兰格 - 贝雷日科夫斯基 - 萨博理论以及可以使用路径采样数据来筛选、混合和优化数千个试验坐标的统计推断方法。特别关注似然最大化和惯性似然最大化方法。
