利用 Dreiding 力场中的具体原子电荷分配,探索水、醇类及其二元混合物的结构特征。

IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Journal of molecular graphics & modelling Pub Date : 2024-09-20 DOI:10.1016/j.jmgm.2024.108863
Chen Zhuang , Haoli Ji , Antian Xu , Muyuan Chai
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引用次数: 0

摘要

水、醇类及其二元混合物被广泛用于分子模拟。然而,Dreiding 力场在模拟过程中缺乏一种普遍接受的为这些溶剂分配原子电荷的方法。在本研究中,我们提出了 Dreiding 力场中水和八种水溶性醇的通用电荷赋值方法。通过大量的分子模拟,我们证明了我们的电荷分配在显示这些溶剂及其混合物的特征(包括液体密度和结构)方面具有良好的准确性。此外,我们还研究了平衡快照、径向分布函数、配位数和氢键,所有这些都证实了醇类与水或乙醇的混溶性。值得注意的是,我们发现不同混合物的结构多样性可归因于醇类的独特特征,包括分子体积以及羟基的数量和位置。
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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Exploring the structural feature of water, alcohols, and their binary mixtures with concrete atomic charge assignments in Dreiding forcefield
The water, alcohols, and their binary mixtures are widely used in molecular simulations. However, the Dreiding force field lacks a generally accepted method for assigning atomic charges to these solvents during simulations. In this study, we propose a universal charge assignment for water and eight water-miscible alcohols in Dreiding. Through extensive molecular simulations, we demonstrate the good accuracy of our charge assignments in displaying characteristic of these solvents and their mixtures, including liquid density and structure. Moreover, we investigate equilibrium snapshot, radial distribution function, coordination number and hydrogen bonding, all of which confirm the miscibility of alcohols with water or ethanol. Notably, we reveal that the structure diversity among different mixtures can be attributed to distinctive characteristic of alcohols, including molecular volume, as well as the number and position of hydroxyls.
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来源期刊
Journal of molecular graphics & modelling
Journal of molecular graphics & modelling 生物-计算机:跨学科应用
CiteScore
5.50
自引率
6.90%
发文量
216
审稿时长
35 days
期刊介绍: The Journal of Molecular Graphics and Modelling is devoted to the publication of papers on the uses of computers in theoretical investigations of molecular structure, function, interaction, and design. The scope of the journal includes all aspects of molecular modeling and computational chemistry, including, for instance, the study of molecular shape and properties, molecular simulations, protein and polymer engineering, drug design, materials design, structure-activity and structure-property relationships, database mining, and compound library design. As a primary research journal, JMGM seeks to bring new knowledge to the attention of our readers. As such, submissions to the journal need to not only report results, but must draw conclusions and explore implications of the work presented. Authors are strongly encouraged to bear this in mind when preparing manuscripts. Routine applications of standard modelling approaches, providing only very limited new scientific insight, will not meet our criteria for publication. Reproducibility of reported calculations is an important issue. Wherever possible, we urge authors to enhance their papers with Supplementary Data, for example, in QSAR studies machine-readable versions of molecular datasets or in the development of new force-field parameters versions of the topology and force field parameter files. Routine applications of existing methods that do not lead to genuinely new insight will not be considered.
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