Koda Shin-Ichi, Saito Shinji
Department of Theoretical and Computational Molecular Science, Institute for Molecular Science, Myodaiji, Okazaki, Aichi 444-8585, Japan.
School of Physical Sciences, The Graduate University for Advanced Studies, Myodaiji, Okazaki, Aichi 444-8585, Japan.
J Chem Theory Comput. 2024 Aug 16. doi: 10.1021/acs.jctc.4c00792.
Rapid generation of a plausible reaction path connecting a given reactant and product in advance is crucial for the efficient computation of precise reaction paths or transition states. We propose a computationally efficient potential energy based on the molecular structure to generate such paths. This potential energy has a flat bottom consisting of structures without atomic collisions while preserving nonreactive chemical bonds, bond angles, and partial planar structures. By combining this potential energy with the direct MaxFlux method, a recently developed reaction-path/transition-state search method, we can find the shortest plausible path passing within the bottom. Numerical results show that this combination yields lower energy paths compared to the paths obtained by the well-known image-dependent pair potential. We also theoretically investigate the differences between these two potential energies. The proposed potential energy and path generation routine are implemented in our Python version of the direct MaxFlux method, available on GitHub.
预先快速生成连接给定反应物和产物的合理反应路径对于精确反应路径或过渡态的高效计算至关重要。我们基于分子结构提出了一种计算效率高的势能来生成此类路径。这种势能具有一个平底，由没有原子碰撞的结构组成，同时保留非反应性化学键、键角和部分平面结构。通过将这种势能与最近开发的反应路径/过渡态搜索方法——直接最大通量方法相结合，我们可以找到在平底内通过的最短合理路径。数值结果表明，与通过著名的图像相关对势获得的路径相比，这种组合产生的能量路径更低。我们还从理论上研究了这两种势能之间的差异。所提出的势能和路径生成程序在我们的直接最大通量方法的Python版本中实现，可在GitHub上获取。
