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

IF 7.1 2区 化学 Q1 CHEMISTRY, MULTIDISCIPLINARY
Takuro Tsutsumi, Yuriko Ono, Tetsuya Taketsugu
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引用次数: 3

Abstract

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 Au5 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.

基于降维空间的动态反应路径可视化反应空间投影(ReSPer)
为了分析基于反应路径网络的化学反应动力学,我们借助降维方法开发了“反应空间投影”(ReSPer)方法。该程序具有两个功能:从分子结构数据集构建降维反应空间,以及将动态轨迹投影到低维反应空间中。本文将ReSPer应用于Au5簇的异构化和分岔反应,成功地分析了多个基本反应过程中涉及的动态反应路线,构建了核置换-反演(NPI)异构化反应的复杂网络(称为“闭岛”),并参考轨迹束阐明了分岔反应的动态行为。有趣的是,在第二个应用中,我们发现可视化能力的贡献率与封闭岛屿形态的对称性之间存在对应关系。此外,第三个应用表明,在分岔反应中存在决定选择性的边界,这在相空间中进行了讨论。ReSPer程序是一个多功能和强大的工具,用于阐明基于降维反应空间的动态反应机制,而无需预先了解目标反应。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
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来源期刊
Topics in Current Chemistry
Topics in Current Chemistry Chemistry-General Chemistry
CiteScore
13.70
自引率
1.20%
发文量
48
期刊介绍: Topics in Current Chemistry is a journal that presents critical reviews of present and future trends in modern chemical research. It covers all areas of chemical science, including interactions with related disciplines like biology, medicine, physics, and materials science. The articles in this journal are organized into thematic collections, offering a comprehensive perspective on emerging research to non-specialist readers in academia or industry. Each review article focuses on one aspect of the topic and provides a critical survey, placing it in the context of the collection. Selected examples highlight significant developments from the past 5 to 10 years. Instead of providing an exhaustive summary or extensive data, the articles concentrate on methodological thinking. This approach allows non-specialist readers to understand the information fully and presents the potential prospects for future developments.
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