Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network
Takuro Tsutsumi, Yuriko Ono, Zin Arai, Tetsuya Taketsugu · Journal of Chemical Theory and Computation · 2020
Following our recent work to reduce a dimension of a set of reference structures along the intrinsic reaction coordinate (IRC) by a classical multidimensional scaling (CMDS) approach ( J. Chem. Theory Comput. 2018, 14, 4263–4270), we propose the method to project on-the-fly trajectories into a reduced-dimension subspace determined by the IRC network, using the out-of-sample extension of CMDS. The method was applied to the S N 2 reaction, OH – + CH 3 F, in which trajectories show a bifurcating nature around the highly curved region of the IRC path, and to the structural transformation of Au 5 cluster in which the global reaction path network consists of five equilibrium structures and 14 IRCs. It was demonstrated that the present analysis can visualize the dynamics effect by showing a dynamic reaction route on the basis of the static reaction paths.