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

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J. Chem. Theory Comput. 16-7_4029–4037.pdf3.7 MBPDFView/Open
Please use this identifier to cite or link to this item:http://hdl.handle.net/2115/81801

Title: Visualization of the Dynamics Effect : Projection of on-the-Fly Trajectories to the Subspace Spanned by the Static Reaction Path Network
Authors: Tsutsumi, Takuro Browse this author
Ono, Yuriko Browse this author
Arai, Zin Browse this author
Taketsugu, Tetsuya Browse this author →KAKEN DB
Issue Date: 14-Jul-2020
Publisher: American Chemical Society
Journal Title: Journal of chemical theory and computation
Volume: 16
Issue: 7
Start Page: 4029
End Page: 4037
Publisher DOI: 10.1021/acs.jctc.0c00018
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.
Rights: 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.
Type: article (author version)
URI: http://hdl.handle.net/2115/81801
Appears in Collections:理学院・理学研究院 (Graduate School of Science / Faculty of Science) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 武次 徹也

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