Density functional theory and molecular dynamics simulation of water molecules confined between two-dimensional graphene oxide surfaces

IF 2.7 4区 生物学 Q2 BIOCHEMICAL RESEARCH METHODS Journal of molecular graphics & modelling Pub Date : 2024-09-12 DOI:10.1016/j.jmgm.2024.108862
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Abstract

In this work, the interaction potentials of water molecule with the two-dimensional graphene oxide (GO) surfaces containing epoxy groups have been determined using the M06–2X/6-31g (d,p) level of theory at different orientations and separations and fitted to the Born-Huggins-Meyer (BHM) potential. Good agreements were found between the computed and the well-known OPLS-AA and Dreiding potentials. We have also used some calculated potentials and the well-known models in the molecular dynamics (MD) simulations. Our results showed that some of the calculated force fields for both 2D GO structures almost represent similar results of average number of hydrogen bonds (<HB>), radial distribution functions (RDF), self-diffusion coefficient, and angle distribution function (ADF) with the OPLS-AA and Dreiding models which are due to their agreements of the interaction potentials. However, some models in both GO systems represent different results because of their shifted potentials to the larger distances. Our results also showed that the confined water molecules tend to orient toward the epoxy groups on the GO surfaces and the distributions at the angles of θ = 0o (or θ = 180o) is more than the other distributions. The water molecules confined between the bent GO surfaces showed less diffusion coefficients than the flat structure.

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封闭在二维氧化石墨烯表面之间的水分子的密度泛函理论和分子动力学模拟
本研究采用 M06-2X/6-31g (d,p)理论水平测定了水分子与含有环氧基团的二维氧化石墨烯(GO)表面在不同取向和分离条件下的相互作用势,并与 Born-Huggins-Meyer (BHM) 势进行了拟合。我们发现计算结果与著名的 OPLS-AA 和 Dreiding 电位有很好的一致性。我们还在分子动力学(MD)模拟中使用了一些计算电位和知名模型。我们的结果表明,两种二维 GO 结构的一些计算力场在氢键平均数量(<HB>)、径向分布函数(RDF)、自扩散系数和角度分布函数(ADF)方面的结果几乎与 OPLS-AA 和 Dreiding 模型相似,这是因为它们的相互作用位势一致。然而,这两个 GO 系统中的某些模型由于将相互作用位移到了更大的距离上,结果有所不同。我们的研究结果还表明,封闭的水分子倾向于朝向 GO 表面的环氧基团,θ = 0o(或 θ = 180o)角处的分布比其他分布多。封闭在弯曲 GO 表面之间的水分子的扩散系数小于平面结构。
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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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