Molecular dynamics simulation study of post-transition state bifurcation: A case study on the ambimodal transition state of dipolar/Diels–Alder cycloaddition

IF 1.9 4区 化学 Q2 CHEMISTRY, ORGANIC
Tatsuhiro Murakami, Yuya Kikuma, Daiki Hayashi, Shunichi Ibuki, Shoto Nakagawa, Hinami Ueno, Toshiyuki Takayanagi
{"title":"Molecular dynamics simulation study of post-transition state bifurcation: A case study on the ambimodal transition state of dipolar/Diels–Alder cycloaddition","authors":"Tatsuhiro Murakami,&nbsp;Yuya Kikuma,&nbsp;Daiki Hayashi,&nbsp;Shunichi Ibuki,&nbsp;Shoto Nakagawa,&nbsp;Hinami Ueno,&nbsp;Toshiyuki Takayanagi","doi":"10.1002/poc.4611","DOIUrl":null,"url":null,"abstract":"<p>The potential energy surfaces for the reactions of 1,3-butadiene with 2-hydroxythioacrolein and 2-aminoacrolein exhibit ambimodal transition states leading to both dipolar (4 + 3) and Diels–Alder (4 + 2) cycloaddition products, thereby demonstrating a post transition state bifurcation feature. We have investigated the bifurcation dynamics of these reactions using three molecular dynamics (MD) methods: quasi-classical trajectory, classical MD, and ring-polymer MD simulations. The trajectory calculations were performed with the semiempirical GFN2-xTB method with the element-specific parameters optimized to reproduce the density-functional theory calculations. The effect of water solvation was examined using an implicit solvation model, revealing significant differences in bifurcation dynamic between gas-phase and solution-phase reactions. Nuclear quantum effects were found to play a crucial role in the proton-transfer process from the (4 + 3) intermediate to the (4 + 3) product in the case of the 2-aminoacrolein reaction.</p>","PeriodicalId":16829,"journal":{"name":"Journal of Physical Organic Chemistry","volume":null,"pages":null},"PeriodicalIF":1.9000,"publicationDate":"2024-05-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1002/poc.4611","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of Physical Organic Chemistry","FirstCategoryId":"92","ListUrlMain":"https://onlinelibrary.wiley.com/doi/10.1002/poc.4611","RegionNum":4,"RegionCategory":"化学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q2","JCRName":"CHEMISTRY, ORGANIC","Score":null,"Total":0}
引用次数: 0

Abstract

The potential energy surfaces for the reactions of 1,3-butadiene with 2-hydroxythioacrolein and 2-aminoacrolein exhibit ambimodal transition states leading to both dipolar (4 + 3) and Diels–Alder (4 + 2) cycloaddition products, thereby demonstrating a post transition state bifurcation feature. We have investigated the bifurcation dynamics of these reactions using three molecular dynamics (MD) methods: quasi-classical trajectory, classical MD, and ring-polymer MD simulations. The trajectory calculations were performed with the semiempirical GFN2-xTB method with the element-specific parameters optimized to reproduce the density-functional theory calculations. The effect of water solvation was examined using an implicit solvation model, revealing significant differences in bifurcation dynamic between gas-phase and solution-phase reactions. Nuclear quantum effects were found to play a crucial role in the proton-transfer process from the (4 + 3) intermediate to the (4 + 3) product in the case of the 2-aminoacrolein reaction.

Abstract Image

后过渡态分岔的分子动力学模拟研究:双极性/Diels-Alder 环加成的伏过渡态案例研究
1,3 丁二烯与 2-hydroxythioacrolein 和 2-aminoacrolein 反应的势能面显示了导致双极(4 + 3)和 Diels-Alder (4 + 2)环加成产物的非模态过渡态,从而显示了过渡态后分岔特征。我们使用三种分子动力学(MD)方法研究了这些反应的分岔动力学:准经典轨迹、经典 MD 和环状聚合物 MD 模拟。轨迹计算采用半经验 GFN2-xTB 方法,并对特定元素参数进行了优化,以重现密度泛函理论计算结果。利用隐式溶解模型研究了水溶的影响,发现气相反应和溶液相反应的分岔动态存在显著差异。研究发现,在 2-氨基丙烯醛反应中,核量子效应在质子从 (4 + 3) 中间体转移到 (4 + 3) 产物的过程中发挥了关键作用。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
求助全文
约1分钟内获得全文 求助全文
来源期刊
CiteScore
3.60
自引率
11.10%
发文量
161
审稿时长
2.3 months
期刊介绍: The Journal of Physical Organic Chemistry is the foremost international journal devoted to the relationship between molecular structure and chemical reactivity in organic systems. It publishes Research Articles, Reviews and Mini Reviews based on research striving to understand the principles governing chemical structures in relation to activity and transformation with physical and mathematical rigor, using results derived from experimental and computational methods. Physical Organic Chemistry is a central and fundamental field with multiple applications in fields such as molecular recognition, supramolecular chemistry, catalysis, photochemistry, biological and material sciences, nanotechnology and surface science.
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
确定
请完成安全验证×
copy
已复制链接
快去分享给好友吧!
我知道了
右上角分享
点击右上角分享
0
联系我们:info@booksci.cn Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号:481959085
Book学术官方微信