{"title":"Reaction Space Projector (ReSPer) for Visualizing Dynamic Reaction Routes Based on Reduced-Dimension Space","authors":"Takuro Tsutsumi, Yuriko Ono, Tetsuya Taketsugu","doi":"10.1007/s41061-022-00377-7","DOIUrl":null,"url":null,"abstract":"<div><p>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<sub>5</sub> 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.</p></div>","PeriodicalId":54344,"journal":{"name":"Topics in Current Chemistry","volume":"380 3","pages":""},"PeriodicalIF":7.1000,"publicationDate":"2022-03-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://link.springer.com/content/pdf/10.1007/s41061-022-00377-7.pdf","citationCount":"3","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Topics in Current Chemistry","FirstCategoryId":"92","ListUrlMain":"https://link.springer.com/article/10.1007/s41061-022-00377-7","RegionNum":2,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q1","JCRName":"CHEMISTRY, MULTIDISCIPLINARY","Score":null,"Total":0}
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.
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.