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

• Tsutsumi, Takuro

• Ono, Yuriko

• Arai, Zin

• Taketsugu, Tetsuya

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 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.

Journal

• Journal of chemical theory and computation

  Journal of chemical theory and computation 16 (7), 4029-4037, 2020-07-14

  American Chemical Society

Keywords

• Physical and Theoretical Chemistry
• Computer Science Applications

Details

• CRID: 1050006895483814784
• NII Article ID: 120007044513
• DOI: 10.1021/acs.jctc.0c00018
• ISSN: 15499626
• ISSN: 15499618
• HANDLE: 2115/81801
• Web Site: https://pubs.acs.org/doi/pdf/10.1021/acs.jctc.0c00018
• Text Lang: en
• Article Type: journal article
• Data Source:
  • IRDB
  • Crossref
  • CiNii Articles
  • KAKEN