Insights into the variations of kinetic and potential energies in a multi-bond reaction: the reaction electronic flux perspective.

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-07-11 DOI:10.1007/s00894-024-06024-w
Nery Villegas-Escobar
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Abstract

Context: The debate over whether kinetic energy (KE) or potential energy (PE) are the fundamental energy components that contribute to forming covalent bonds has been enduring and stimulating over time. However, the supremacy of these energy components in reactions where multiple bonds are simultaneously formed or broken has yet to be explored. In this study, we use the reaction electronic flux (REF), an effective tool for investigating changes in driving electronic activity when bond formation or dissociation occurs in a chemical reaction, to examine the fluctuations in the KE and PE in a multi-bond reaction. To that end, the activation of CO 2 by low-valent group 14 catalysts through a concerted σ -bond metathesis mechanism is analyzed. The findings of this preliminary study suggest that the REF can be utilized as a tool to rationalize alterations in the KE and PE in a multi-bond reaction. Specifically, analyses across the reaction coordinate reveal that changes in the KE and PE precede activation in the REF, stimulating the electronic activity where bond formation or dissociation processes dominate.

Methods: The activation of CO 2 by the low-valent LEH catalysts (L = N,N'-bis(2,6-diisopropyl phenyl)- β -diketiminate; E = Si, Ge, Sn, and Pb) was studied along the reaction coordinate at the M06-2X/6-31 G(d,p)-LANL2DZ(E) level of theory. The respective minimum energy path calculations were obtained using the intrinsic reaction coordinate (IRC) procedure. The reaction electronic flux (REF) was calculated through the computation of the electronic chemical potential using the frontier molecular orbital approximation. Mayer bond orders along the reaction coordinate have been determined using the NBO 3.1 program in Gaussian16. Most of the reaction coordinate quantities reported in this study (REF, KE, PE, among others) have been determined using the Kudi program and custom Python scripts.

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洞察多键反应中的动能和势能变化:反应电子通量视角。
背景:关于形成共价键的基本能量成分是动能(KE)还是势能(PE)的争论,历来经久不衰,引人深思。然而,在同时形成或断裂多个键的反应中,这些能量成分的优越性还有待探讨。在本研究中,我们利用反应电子通量(REF)--一种研究化学反应中键形成或解离时驱动电子活动变化的有效工具--来研究多键反应中 KE 和 PE 的波动。为此,我们分析了低价 14 族催化剂通过协同 σ 键元合成机制活化 CO 2 的过程。这项初步研究的结果表明,在多键反应中,REF 可用作合理改变 KE 和 PE 的工具。具体来说,对整个反应坐标的分析表明,KE 和 PE 的变化先于 REF 中的活化,从而刺激了电子活动,其中键的形成或解离过程占主导地位:在 M06-2X/6-31 G(d,p)-LANL2DZ(E) 理论水平上,沿着反应坐标研究了低价 LEH 催化剂(L = N,N'-bis(2,6-disopropyl phenyl)-β -diketiminate;E = Si、Ge、Sn 和 Pb)对 CO 2 的活化。利用本征反应坐标(IRC)程序获得了各自的最小能量路径计算结果。反应电子通量(REF)是通过使用前沿分子轨道近似计算电子化学势计算得出的。沿反应坐标的梅耶键阶数是使用高斯16 中的 NBO 3.1 程序确定的。本研究中报告的大部分反应坐标量(REF、KE、PE 等)都是通过 Kudi 程序和自定义 Python 脚本确定的。
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
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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