open access

https://hdl.handle.net/2115/81801

Visualization of the Dynamics Effect : Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network

英語

2020-07-14

American Chemical Society

Journal of chemical theory and computation

16(7)

4029-4037

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- + CH3F, 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.

学術雑誌論文

Accepted Manuscript

This document is the Accepted Manuscript version of a Published Work that appeared in final form in Journal of chemical theory and computation, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://doi.org/10.1021/acs.jctc.0c00018.

1549-9618