香农熵变化作为化学反应中原子间电子密度收缩的总体指标。

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
César Barrales-Martínez, Rocío Durán, Julio Caballero
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引用次数: 0

摘要

背景:香农熵导数的负数是为了解释化学反应过程中化学键断裂和形成时的电子密度收缩而提出的。我们将这一特性称为电子密度收缩指数(EDC),它可以识别反应中电子收缩或膨胀占主导地位的阶段。我们分析了四种不同的反应,以展示 EDC 指数如何沿反应坐标变化。结果表明,香农熵的变化率与分子体系中所有原子对之间键临界点的电子密度变化率直接相关。预计 EDC 将补充利用现有理论工具对反应机理进行的详细分析:方法:使用高斯 16 在 B3LYP/6-31G(d,p) 理论水平上进行了密度泛函理论计算,以分析所研究的四个反应的反应机理。通过本征反应坐标法获得了反应路径,并以此为反应坐标获得了每种情况下的反应力和 EDC 曲线。使用 Multiwfn 3.7 软件包计算了键临界点的香农熵和电子密度。
本文章由计算机程序翻译,如有差异,请以英文原文为准。
Shannon entropy variation as a global indicator of electron density contraction at interatomic regions in chemical reactions

Context

The negative of the Shannon entropy derivative is proposed to account for electron density contraction as the chemical bonds are breaking and forming during a chemical reaction. We called this property the electron density contraction index, EDC, which allows identifying stages in a reaction that are dominated by electron contraction or expansion. Four different reactions were analyzed to show how the EDC index changes along the reaction coordinate. The results indicate that the rate of change of Shannon entropy is directly related to the rate of change of the electron density at the bond critical points between all the atomic pairs in the molecular systems. It is expected that EDC will complement the detailed analysis of reaction mechanisms that can be performed with the theoretical tools available to date.

Methods

Density functional theory calculations at the B3LYP/6-31G(d,p) level of theory were carried out using Gaussian 16 to analyze the reaction mechanisms of the four reactions studied. The reaction paths were obtained via the intrinsic reaction coordinate method, which served as the reaction coordinate to obtain the reaction force and the EDC profiles in each case. Shannon entropy and electron density at the bond critical points were calculated using the Multiwfn 3.7 package.

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来源期刊
Journal of Molecular Modeling
Journal of Molecular Modeling 化学-化学综合
CiteScore
3.50
自引率
4.50%
发文量
362
审稿时长
2.9 months
期刊介绍: The Journal of Molecular Modeling focuses on "hardcore" modeling, publishing high-quality research and reports. Founded in 1995 as a purely electronic journal, it has adapted its format to include a full-color print edition, and adjusted its aims and scope fit the fast-changing field of molecular modeling, with a particular focus on three-dimensional modeling. Today, the journal covers all aspects of molecular modeling including life science modeling; materials modeling; new methods; and computational chemistry. Topics include computer-aided molecular design; rational drug design, de novo ligand design, receptor modeling and docking; cheminformatics, data analysis, visualization and mining; computational medicinal chemistry; homology modeling; simulation of peptides, DNA and other biopolymers; quantitative structure-activity relationships (QSAR) and ADME-modeling; modeling of biological reaction mechanisms; and combined experimental and computational studies in which calculations play a major role.
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