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水中羟基氨基酸的分子性质

Molecular Properties of Hydroxyamino Acids in Water.

作者信息

Boča Roman, Rádiková Žofia, Štofko Juraj, Vranovičová Beata, Rajnák Cyril

机构信息

Faculty of Health Sciences, University of SS Cyril and Methodius, Trnava 91701, Slovakia.

Faculty of Natural Sciences, University of Ss Cyril and Methodius, Trnava 91701, Slovakia.

出版信息

J Phys Chem A. 2025 Mar 27;129(12):2903-2911. doi: 10.1021/acs.jpca.5c00701. Epub 2025 Mar 19.

DOI:10.1021/acs.jpca.5c00701
PMID:40103526
Abstract

Aliphatic hydroxyamino acids, namely, α-hydroxyglycine, α-hydroxyalanine, serine, threonine, and homoserine, were studied by quantum chemical calculations using two methods in water as a solvent. A hybrid variant of DFT-B3LYP was applied to optimize the geometry of neutral molecules, molecular cations, and anions for the canonical and zwitterionic form of amino acids. In the energy minimum, vibrational analysis was applied, enabling the evaluation of thermodynamic functions (internal energy, enthalpy, entropy, and Gibbs energy) of individual species and absolute oxidation and reduction potentials for redox couples. In the B3LYP preoptimized geometry, the advanced DLPNO-CCSD(T) method was applied to include the major part of the interelectron correlation energy. Calculated molecular descriptors were compared with previously studied molecules by the same method, and the whole set for 17 amino acids was processed by advanced statistical methods such as cluster analysis and principal component analysis. Calculated oxidation potentials correlate with the adiabatic ionization energies along a straight line, and analogously, the calculated reduction potential correlates with the electrophilicity index. The ionization energy in α-amino acids is systematically influenced (reduced) by the functional groups such as hydroxyl, methyl, ethyl, and -propyl; it decreases along a series of α-, β-, γ-, and δ-amino acids.

摘要

采用两种方法在水作为溶剂的条件下,通过量子化学计算对脂肪族羟基氨基酸,即α-羟基甘氨酸、α-羟基丙氨酸、丝氨酸、苏氨酸和高丝氨酸进行了研究。运用密度泛函理论(DFT)-B3LYP的混合变体来优化氨基酸的中性分子、分子阳离子和阴离子在标准形式及两性离子形式下的几何结构。在能量最小值处,进行振动分析,从而能够评估各个物种的热力学函数(内能、焓、熵和吉布斯自由能)以及氧化还原电对的绝对氧化和还原电位。在B3LYP预优化几何结构中,应用先进的密度拟合局部二阶微扰耦合簇理论(DLPNO-CCSD(T))方法来包含电子间相关能的主要部分。将计算得到的分子描述符与之前用相同方法研究的分子进行比较,并通过聚类分析和主成分分析等先进统计方法对17种氨基酸的整个数据集进行处理。计算得到的氧化电位与绝热电离能呈直线相关,类似地,计算得到的还原电位与亲电性指数相关。α-氨基酸中的电离能受到羟基、甲基、乙基和丙基等官能团的系统性影响(降低);它沿着α-、β-、γ-和δ-氨基酸系列递减。

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