Visualization of static reaction pathway and embedding of dynamic reaction pathways based on principal coordinate analysis

Abstract

The intrinsic reaction coordinate (IRC), which is defined as a minimum energy pathway connecting two equilibrium structures via a transition state structure on the potential energy surface, are useful tool to describe an elementary reaction mechanism. Recently, the global reaction route mapping strategy has been developed, and it enables us to construct a global reaction route network which is composed of all IRC pathways for a given molecular system. However, the overall positional relationship of each molecular structure in the network is difficult to reproduce in a lower-dimensional space because of the multidimensionality of molecular structures. Very recently, to visualize the static reaction coordinate onto a 2- and 3-dimensional space, we applied the principal coordinate (PCo) analysis, one of the dimensionality reduction techniques, to IRC pathways and a global reaction route network. In this study, we embed classical trajectories given by the on-the-fly molecular dynamics method into a PCo-subspace obtained by projecting an IRC pathway, and we also discuss dynamical reaction pathways based on the visualized static reaction pathway.