Density, Diffusion, and Site-Dipole Field of Solvent around Four Types of Flavonoid Studid by Molecular Dynamics

IF 0.4 Q4 BIOCHEMISTRY & MOLECULAR BIOLOGY
丸山 慶一朗, 成敏 神谷, 永淑 尹, 彰 功刀, 剛 横溝, 順一 肥後
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引用次数: 1

Abstract

We studied hydration of four types of small nonpeptidic molecule, flavonoid, by molecular dynamics simulations at 300 K with focusing on three physical quantities: solvent density, solvent site-dipole field, and solvent diffusion. The solvent site-dipole field is a quantity recently introduced by us to study directional ordering of water molecules around solute. The spatial patterns of these quantities showed strong site-dependency around the flavonoids. Common to the four flavonoids, high solvent-density sites around hydrophilic solute atoms were characterized by strong directional ordering of water molecule and by depressed solvent diffusive motions. Contrarily, high solvent-density sites around hydrophobic solute surface were characterized by weak directional ordering. The solvent site-dipole field showed specific ordering patterns of water molecules not only in the first solvent layer but also in the second solvent layer. The spatial patterns of the three quantities were conservative among the four flavonoids whether the intra-flavonoid flexibility was large or not. Thus, an adiabatic approximation, which has been assumed in various theoretical hydration studies, was satisfied well. The hydration at a site in the vicinity of solute was determined mainly by the physico-chemical property of the solute atom group nearest to the solvent site, which supports a phenomenological theorem that the solvent accessible surface area of a solute is proportional to the solvation free energy.
分子动力学研究了四类黄酮类化合物周围溶剂的密度、扩散和位偶极子场
在300 K条件下,通过分子动力学模拟研究了四种非肽小分子类黄酮的水合作用,重点研究了溶剂密度、溶剂位偶极子场和溶剂扩散三个物理量。溶剂位偶极子场是我们最近引入的用于研究水分子围绕溶质定向排序的一个量。这些数量的空间格局在黄酮类化合物周围表现出强烈的位点依赖性。与四种类黄酮一样,亲水溶质原子周围的高溶剂密度位点以水分子的强定向有序和溶剂扩散运动抑制为特征。相反,疏水溶质表面周围的高溶剂密度位点具有弱定向有序的特征。溶剂位偶极子场不仅在第一溶剂层中,而且在第二溶剂层中也表现出特定的水分子有序模式。无论类黄酮内弹性是否大,这3个量在4种黄酮类化合物中的空间格局都是保守的。因此,在各种理论水化研究中所假定的绝热近似得到了很好的满足。溶质附近位置的水化作用主要由最靠近溶质位置的溶质原子群的物理化学性质决定,这支持了一个现象学定理,即溶质的溶剂可达表面积与溶剂化自由能成正比。
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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来源期刊
Chem-Bio Informatics Journal
Chem-Bio Informatics Journal BIOCHEMISTRY & MOLECULAR BIOLOGY-
CiteScore
0.60
自引率
0.00%
发文量
8
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