改进反应路径中键重排的相关平底弹性网络模型

IF 5.5 1区 化学 Q2 CHEMISTRY, PHYSICAL
Shin-ichi Koda*,  and , Shinji Saito*, 
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引用次数: 0

摘要

本文引入了相关平底弹性网络模型(CFB-ENM),这是我们最近开发的平底弹性网络模型(FB-ENM)的扩展,用于生成合理的反应路径,即保留非反应部分的无碰撞路径。虽然FB-ENM通过解决非预期的结构扭曲和键断裂,改进了广泛使用的图像依赖对电位(IDPP),但它仍然难以调节一系列键断裂和形成的时间。CFB-ENM通过结合基于结构的相关项克服了这一限制。这些条件对原子对施加约束,确保在现有键断裂后立即形成新键。使用直接MaxFlux方法,我们生成了121个涉及主族元素的反应路径和35个涉及过渡金属的反应路径。我们发现,与FB-ENM相比,CFB-ENM显著改善了反应路径。在大多数反应中,CFB-ENM路径的最大DFT能量较低,其中近一半的反应能量显著降低了几十千卡/摩尔。在少数情况下,CFB-ENM产生更高的能量路径,大多数增加低于10千卡/摩尔。我们还证实,与FB-ENM相比,CFB-ENM减少了后续精确反应路径或过渡态搜索的计算成本。在GitHub上有一个基于原子模拟环境的CFB-ENM的实现,用于计算化学研究。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Correlated Flat-Bottom Elastic Network Model for Improved Bond Rearrangement in Reaction Paths

This study introduces correlated flat-bottom elastic network model (CFB-ENM), an extension of our recently developed flat-bottom elastic network model (FB-ENM) for generating plausible reaction paths, i.e., collision-free paths preserving nonreactive parts. While FB-ENM improved upon the widely used image-dependent pair potential (IDPP) by addressing unintended structural distortion and bond breaking, it still struggled with regulating the timing of series of bond breaking and formation. CFB-ENM overcomes this limitation by incorporating structure-based correlation terms. These terms impose constraints on pairs of atom pairs, ensuring immediate formation of new bonds after breaking of existing bonds. Using the direct MaxFlux method, we generated paths for 121 reactions involving main group elements and 35 reactions involving transition metals. We found that CFB-ENM significantly improves reaction paths compared to FB-ENM. CFB-ENM paths exhibited lower maximum DFT energies along the paths in most reactions, with nearly half showing significant energy reductions of several tens of kcal/mol. In the few cases where CFB-ENM yielded higher energy paths, most increases were below 10 kcal/mol. We also confirmed that CFB-ENM reduces computational costs in subsequent precise reaction path or transition state searches compared to FB-ENM. An implementation of CFB-ENM based on the Atomic Simulation Environment is available on GitHub for use in computational chemistry research.

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来源期刊
Journal of Chemical Theory and Computation
Journal of Chemical Theory and Computation 化学-物理:原子、分子和化学物理
CiteScore
9.90
自引率
16.40%
发文量
568
审稿时长
1 months
期刊介绍: The Journal of Chemical Theory and Computation invites new and original contributions with the understanding that, if accepted, they will not be published elsewhere. Papers reporting new theories, methodology, and/or important applications in quantum electronic structure, molecular dynamics, and statistical mechanics are appropriate for submission to this Journal. Specific topics include advances in or applications of ab initio quantum mechanics, density functional theory, design and properties of new materials, surface science, Monte Carlo simulations, solvation models, QM/MM calculations, biomolecular structure prediction, and molecular dynamics in the broadest sense including gas-phase dynamics, ab initio dynamics, biomolecular dynamics, and protein folding. The Journal does not consider papers that are straightforward applications of known methods including DFT and molecular dynamics. The Journal favors submissions that include advances in theory or methodology with applications to compelling problems.
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