A comparative study on the interaction of M3+(H2O)5–6 ions (M = Fe, Ru, and Os) with the hydroxy group

IF 2.1 4区 化学 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY Journal of Molecular Modeling Pub Date : 2024-10-29 DOI:10.1007/s00894-024-06185-8
Dang T. Nguyen, Hai V. Mai, Han H. La, Anh D. Nguyen, Anh H. Nguyen
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Abstract

Context

The heavy metal ions are the typical carcinogenic agents. Up to now, the interaction mechanism of toxic metal ions with the biomolecules such as carbohyrate have not been elucidated and reported in the detail. In this research work, the adjacent dissociation Gibbs energy (EAB) of M3+(H2O)5(R-OH) complexes depended significantly on the molecular volume of primary alcohols and the inductive effects of substituent R in primary alcohols (R = CH3, CH3CH2, CH3CH2CH2, CH3CH2CH2CH2, Cl-CH2, F-CH2) as well as the length of linear cellulose. The affinity of M3+(H2O)5 ions with the sixth water molecule in gas phase reduced in the order as follows: Fe3+  > Ru3+  > Os3+, which were determined by the EAB values and bond lengths of M–O. The water solvent made the EAB values of Fe3+(H2O)6 ions and Fe3+(H2O)5(CH3OH) ions changed completely in the case of the polarizable continuum model, while the Onsager model gave the good agreement with the gas phase model.

Methods

The nature of interaction between hydrated Fe3+(H2O)5 ion and the hydroxy groups of primary alcohols were investigated using density functional theory method at the B3LYP/6–311 + G** level, the PBEPBE/6–311 + G** level. The influence of water solvent was evaluated using the Onsager model and the polarizable continuum model. The two-layer ONIOM approach and the local softness analysis were employed for the hydroxy groups of linear cellulose at the B3LYP/6–311 + G**:HF/6-31G* level. The affinity of M3+(H2O)5 ions (M = Fe, Ru, and Os) with the sixth water molecule were probed at the B3LYP/QZVPP/6–311 + G** level (QZVPP basis set for the metal atoms).

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M3+(H2O)5-6 离子(M = Fe、Ru 和 Os)与羟基相互作用的比较研究
背景重金属离子是典型的致癌物质。迄今为止,有毒金属离子与羧酸盐等生物大分子的相互作用机制尚未得到详细阐明和报道。在这项研究工作中,M3+(H2O)5(R-OH)配合物的相邻解离吉布斯能(EAB)明显取决于伯醇的分子体积和伯醇中取代基 R(R = CH3、CH3CH2、CH3CH2CH2、CH3CH2CH2CH2、Cl-CH2、F-CH2)的感应效应以及线性纤维素的长度。在气相中,M3+(H2O)5 离子与第六个水分子的亲和力依次降低,具体顺序如下Fe3+ > Ru3+ > Os3+,这是由 EAB 值和 M-O 的键长决定的。方法采用密度泛函理论方法在 B3LYP/6-311 + G** 和 PBEPBE/6-311 + G** 水平研究了水合 Fe3+(H2O)5 离子与伯醇羟基的相互作用性质。使用 Onsager 模型和可极化连续体模型评估了水溶剂的影响。在 B3LYP/6-311 + G**:HF/6-31G* 水平上,对线性纤维素的羟基采用了双层 ONIOM 方法和局部软度分析。在 B3LYP/QZVPP/6-311 + G** 水平(金属原子的 QZVPP 基集)上探测了 M3+(H2O)5 离子(M = Fe、Ru 和 Os)与第六个水分子的亲和力。
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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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