Towards a complete description of the reaction mechanisms between nitrenium ions and water

IF 2.5 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-10-23 DOI:10.1007/s00894-024-06169-8
Sara Gómez, Natalia Rojas-Valencia, Chiara Cappelli, Frank Weinhold, Albeiro Restrepo
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Abstract

Context

Nitrenium ions are intermediates in the metabolic routes producing the highly carcinogenic nitrosamines and binding to DNA molecules. The reaction mechanism of nitrenium molecules with explicit water molecules is sensibly dependent on the number of waters: when a second molecule is involved, it acts as a catalyst for the reaction, lowering intrinsic activation barriers regardless of the substituent. For all cases, the reaction force constants and reaction electron flux indicate highly synchronous reactions for \({n=1}\). Conversely, for \({n=2}\) highly non-synchronous reactions are obtained, involving two separate proton transfers happening early and late in the reaction path. As a test case, for the simplest \([\text {N}\text {H}_{2}]^{+} + 2 \text {H}_{2}\text {O}\) reactions, orbital interactions within the NBO paradigm, bond orders, and their derivatives indicate that each individual proton transfer is highly synchronous.

Methods

Molecular geometries were optimized and characterized at the B3LYP/6–311++G(d, p) level. Intrinsic reaction coordinates were calculated. CCSD(T) single point energies with the same basis were computed on all stationary points. The reaction force, reaction force constant, and reaction electron flux are used to study the evolution of the reacting systems. Natural bond orbitals are used to understand the primitive changes driving the reaction.

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全面描述锑离子与水的反应机理。
背景:在产生高致癌物亚硝胺和与 DNA 分子结合的代谢过程中,钌离子是中间体。腈分子与显式水分子的反应机理与水的数量有关:当有第二个分子参与时,它就会成为反应的催化剂,从而降低内在活化障碍,而与取代基无关。在所有情况下,反应力常数和反应电子通量都表明 n = 1 时反应高度同步。相反,当 n = 2 时,反应高度非同步,涉及反应路径早期和晚期发生的两次质子转移。作为一个测试案例,对于最简单的 [ NH 2 ] + + 2 H 2 O 反应,NBO 范式中的轨道相互作用、键阶及其衍生物表明,每个单独的质子转移都是高度同步的:方法:在 B3LYP/6-311++G(d, p) 水平上对分子几何结构进行了优化和表征。计算了本征反应坐标。计算了所有静止点上具有相同基础的 CCSD(T) 单点能量。反应力、反应力常数和反应电子通量用于研究反应体系的演化。自然键轨道用于理解驱动反应的原始变化。
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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