Visualization of the Dynamics Effect: Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network
Takuro Tsutsumi, Y. Ôno, Zin Arai, Tetsuya Taketsugu
Abstract
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 SN2 reaction, OH– + CH3F, in which trajectories show a bifurcating nature around the highly curved region of the IRC path, and to the structural transformation of Au5 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.