如何寻找和揭示隐藏的中间体?定向外电场下双质子转移反应非同步性的 ELF 拓扑描述。

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
Vanessa Labet, Antoine Geoffroy-Neveux, Mohammad Esmaïl Alikhani
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引用次数: 0

摘要

背景:在定向外电场下,利用 ELF 拓扑方法研究了两个模型二聚体(甲酸同二聚体和 1,2,3 三唑-胍杂二聚体)分子间双质子转移的性质。研究表明,根据外电场的强度和方向,这两种二聚体中的每一种都可以有一步反应路径(一种过渡态结构)或两步反应路径(两种过渡态结构)。由于反应具有很强的异步性,因此在正式过渡态结构周围会出现一个奇异的宽肩(同二聚体为高原,异二聚体为类似高原的结构)。通过对反应路径上的质子、氢化物(定位)质子或漫游质子(非定位)质子的性质进行仔细的 ELF 拓扑分析,我们可以明确地将双质子转移反应的一步机制分为三个不同的类别:(1) 协作-同步,即两个事件(质子漫游区)完全重叠;(2) 协作-非同步,即两个事件(质子漫游区)部分重叠;(3) 两阶段一步法非确认,即两个质子漫游区被一个 "隐藏中间区 "分开。属于该分离矩阵区域的所有结构都是齐聚物形式:方法:使用密度泛函理论-wB97XD 函数,结合所有原子的 6-311+ +G(2d, 2p) 基集,对势能面上的静止点进行了几何优化。所有第一原理计算都是使用高斯 09 量子化学软件包进行的。我们还利用电子定位函数(ELF)揭示了质子在反应路径上的性质:结合质子(氢化物)变成了漫游质子(携带微小负电荷 ≈ 0.3 e),通过两个吸引子(具有 (3, - 3) 特征的拓扑临界点)与两个相邻原子交换。ELF 分析使用 TopMod 软件包进行。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

How to search for and reveal a hidden intermediate? The ELF topological description of non-synchronicity in double proton transfer reactions under oriented external electric field

How to search for and reveal a hidden intermediate? The ELF topological description of non-synchronicity in double proton transfer reactions under oriented external electric field

Context

The nature of double intermolecular proton transfer was studied with the ELF topological approach in two model dimers (the formic acid homodimer and the 1,2,3-triazole–guanidine heterodimer) under an oriented external electric field. It has been shown that each of the two dimers can have either a one-step (one transition state structure) or two-step (two transition state structures) reaction path, depending on the intensity and orientation of the external electric field. The presence of a singularly broad shoulder (plateau in the case of homodimer and plateau-like for heterodimer) around the formal transition state structure results from the strong asynchronicity of the reaction. A careful ELF topological analysis of the nature of protons, hydride (localized) or roaming (delocalized) proton, along the reaction path allowed us to unambiguously classify the one-step mechanisms governing the double-proton transfer reactions into three distinct classes: (1) concerted-synchronous, when two events (roaming proton regions) completely overlap, (2) concerted-asynchronous, when two events (roaming proton regions) partially overlap, and (3) two-stage one-step non-concerted, when two roaming proton regions are separated by a “hidden intermediate region”. All the structures belonging to this separatrix region are of the zwitterion form.

Methods

Geometry optimization of the stationary points on the potential energy surface was performed using density functional theory—wB97XD functional—in combination with the 6–311+ +G(2d, 2p) basis set for all the atoms. All first-principles calculations were performed using the Gaussian 09 quantum chemical packages. We also used the electron localization function (ELF) to reveal the nature of the proton along the reaction path: a bound proton (hydride) becomes a roaming proton (carrying a tiny negative charge ≈ 0.3 e) exchanging with two adjacent atoms via two attractors (topological critical points with (3, − 3) signature). The ELF analyses were performed using the TopMod 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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