Acceleration of Reaction Space Projector Analysis Using Combinatorial Optimization: Application to Organic Chemical Reactions
Lihao Qu, Takuro Tsutsumi, Yuriko Ono, Tetsuya Taketsugu · Journal of Chemical Theory and Computation · 2024
In recent years, automated reaction path search methods have established the concept of a reaction route network. The Reaction Space Projector (ReSPer) visualizes the potential energy hypersurface into a lower-dimensional subspace using principal coordinates. The main time-consuming process in ReSPer is calculating the structural distance matrix, making it impractical for complex organic reaction route networks. We implemented the Alternate Optimization (AO) algorithm, one of the combinatorial optimizations, in ReSPer to reduce computational costs. Evaluations using gold clusters and the Au 5 several reaction route networks showed that ReSPer-AO accurately computes distances with lower computational costs. Applying ReSPer-AO to the C 5 H 8 O reaction route network clarified dynamic conformation changes in its potential energy landscape. The ReSPer-AO method enables analysis of chemical reactions and dynamic conformations in a low-dimensional reaction space that accurately represents hydrocarbon reaction route networks.