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Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space

期刊

TOPICS IN CURRENT CHEMISTRY
卷 380, 期 3, 页码 -

出版社

SPRINGER INT PUBL AG
DOI: 10.1007/s41061-022-00377-7

关键词

Reaction space projector; Dimensionality reduction; Reaction path network; On-the-fly molecular dynamics

资金

  1. Wakeshima Makoto Research Fellowship
  2. Elements Strategy Initiative of MEXT [JPMXP0112101003]
  3. Photo-excitonix Project in Hokkaido University
  4. JST CREST, Japan [JPMJCR1902]

向作者/读者索取更多资源

A method based on a reaction path network analysis is developed and applied to isomerization and bifurcation reactions of the Au-5 cluster. The method can construct a reduced-dimensionality reaction space, analyze dynamic reaction routes, and elucidate dynamic behaviors in reactions. It is a versatile tool with wide application value.
To analyze chemical reaction dynamics based on a reaction path network, we have developed the Reaction Space Projector (ReSPer) method with the aid of the dimensionality reduction method. This program has two functions: the construction of a reduced-dimensionality reaction space from a molecular structure dataset, and the projection of dynamic trajectories into the low-dimensional reaction space. In this paper, we apply ReSPer to isomerization and bifurcation reactions of the Au-5 cluster and succeed in analyzing dynamic reaction routes involved in multiple elementary reaction processes, constructing complicated networks (called closed islands) of nuclear permutation-inversion (NPI) isomerization reactions, and elucidating dynamic behaviors in bifurcation reactions with reference to bundles of trajectories. Interestingly, in the second application, we find a correspondence between the contribution ratios in the ability to visualize and the symmetry of the morphology of closed islands. In addition, the third application suggests the existence of boundaries that determine the selectivity in bifurcation reactions, which was discussed in the phase space. The ReSPer program is a versatile and robust tool to clarify dynamic reaction mechanisms based on the reduced-dimensionality reaction space without prior knowledge of target reactions.

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