KinBot: Automated stationary point search on potential energy surfaces

KinBot is a Python code that automatically characterizes kinetically important stationary points on reactive potential energy surfaces and arranges the results into a form that lends itself easily to master equation calculations. This version of KinBot tackles C, H, O and S atom containing species and unimolecular (isomerization or dissociation) reactions. KinBot iteratively changes the geometry of the reactant to obtain initial guesses for reactive saddle points defined by KinBot’s reaction types, which are then optimized by a third-party quantum chemistry package. KinBot verifies the connectivity of the saddle points with the reactant and identifies the products through intrinsic reaction coordinate calculations. New calculations can be automatically spawned from the products to obtain complete potential energy surfaces. The utilities of KinBot include conformer searches, projected frequency and hindered rotor calculations, and the automatic determination of the rotational symmetry numbers. Input files for popular RRKM master equation codes are automatically built, enabling an automated workflow all the way to the calculation of pressure and temperature dependent rate coefficients. Four examples are included. (i) [1,3]-sigmatropic H-migration reactions of unsaturated hydrocarbons and oxygenates are calculated to assess the relative importance of suprafacial and antrafacial reactions. (ii) Saddle points on three products of gamma-valerolactone thermal decomposition are studied and compared to literature potential energy surfaces. (iii) The previously published propene+OH reaction is reproduced to show the capability of building an entire potential energy surface. (iv) All species up to C4 in the Aramco Mech 2.0 are subjected to a KinBot search.

KinBot是一款Python代码，可自动表征反应势能面上具备动力学重要性的驻点，并将结果整理为便于主方程（master equation）求解的格式。本版本的KinBot可处理含碳、氢、氧与硫原子的化学物种，以及单分子反应（包括异构化与解离过程）。KinBot通过迭代调整反应物的几何结构，为基于其预设反应类型定义的反应鞍点生成初始猜测结构，随后交由第三方量子化学软件完成结构优化。KinBot会验证鞍点与反应物的连接性，并通过内禀反应坐标（intrinsic reaction coordinate, IRC）计算识别反应产物；新的计算任务可自动从产物出发生成，进而得到完整的反应势能面。KinBot的功能涵盖构象搜索、投影频率计算、受阻转子计算，以及旋转对称数的自动测定。它可自动为主流RRKM主方程代码生成输入文件，从而实现从计算流程到压力与温度依赖的速率系数计算的全自动化工作流。本文附带四个示例：
(i) 针对不饱和烃与含氧化合物的[1,3]-σ迁移氢迁移反应开展计算，以评估同面（suprafacial）反应与异面（antrafacial）反应的相对重要性；
(ii) 研究γ-戊内酯热分解三种产物对应的鞍点，并与已发表文献中的势能面对比；
(iii) 复现此前已发表的丙烯+OH反应，以展示构建完整反应势能面的能力；
(iv) 对Aramco Mech 2.0机制中所有碳原子数不超过4的化学物种执行KinBot搜索。