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肌酐互变异构机理的量子化学计算与化学动力学研究

Quantum chemistry calculations and chemical kinetic studies on the tautomeric mechanism of creatinine.

作者信息

Sun Yiqing, Jiang Xiankai, Xiong Zhenhai, Miao Junjian

机构信息

College of Oceanography and Ecological Science, Shanghai Ocean University, Shanghai, 201306, China.

School of Sciences, Changzhou Institute of Technology, Changzhou, 213032, China.

出版信息

J Mol Model. 2025 Sep 13;31(10):267. doi: 10.1007/s00894-025-06501-w.

Abstract

CONTEXT

Thermal processing of meat typically leads to the formation of heterocyclic aromatic amines (HAAs), a class of highly toxic compounds. Although extensive research has been conducted on HAAs, the precise formation mechanisms of individual HAAs remain incompletely understood, with many critical details yet to be elucidated. Several unresolved aspects concern the number of tautomers of creatinine-the key precursor in HAA formation, the interconversion pathways among these tautomers and the time scales involved, and the equilibrium distribution ratios among the tautomeric forms. Addressing these questions is essential for achieving an accurate understanding of the mechanistic pathways underlying the formation of HAAs.

METHODS

All possible tautomers were manually deduced and verified by RDkit, a chemoinformatics toolkit. Geometry optimizations and frequency analyses were performed using density functional theory (DFT). The distribution of various tautomers was evaluated under three different environments-gas phase, ethanol, and water-to simulate real conditions. Calculations were carried out at the B3LYP/def2QZVPP//6-31G(d,p) level of theory, with the polarizable continuum model (PCM) applied for ethanol and water. A similar computational approach to the calculations on distribution was employed to investigate tautomerization mechanisms. Tautomerization kinetics were analyzed within the framework of transition state theory (TST) to determine rate constants for each tautomeric interconversion. Tunneling correction factors (κ) were then calculated to account for quantum mechanical tunneling effects. Subsequently, the corresponding system of differential equations was solved to obtain the time-dependent concentration profiles of each tautomeric species.

摘要

背景

肉类的热处理通常会导致杂环芳香胺(HAAs)的形成,这是一类剧毒化合物。尽管对HAAs已经进行了广泛的研究,但单个HAAs的确切形成机制仍未完全理解,许多关键细节尚待阐明。几个未解决的方面涉及肌酸酐(HAA形成中的关键前体)的互变异构体数量、这些互变异构体之间的相互转化途径和所涉及的时间尺度,以及互变异构形式之间的平衡分布比。解决这些问题对于准确理解HAAs形成的机制途径至关重要。

方法

所有可能的互变异构体均通过化学信息学工具包RDkit手动推导并验证。使用密度泛函理论(DFT)进行几何优化和频率分析。在气相、乙醇和水三种不同环境下评估各种互变异构体的分布,以模拟实际条件。计算在理论水平B3LYP/def2QZVPP//6 - 31G(d,p)下进行,对乙醇和水应用极化连续介质模型(PCM)。采用与分布计算类似的计算方法来研究互变异构机制。在过渡态理论(TST)框架内分析互变异构动力学,以确定每个互变异构体相互转化的速率常数。然后计算隧道校正因子(κ)以考虑量子力学隧道效应。随后,求解相应的微分方程组以获得每个互变异构体物种随时间变化的浓度分布。

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