全原子分子动力学模拟研究丙氨酸二肽水溶液的结构和氢键作用

摘要

All-atom molecular dynamics (MD) simulations are used to investigate the structure and hydrogen bonds of alanine dipeptide aqueous solution. The strong hydrogen bonds and weak C-H···O contacts are found existing in the mixtures from the information of radial distribution function (RDF). And different types of hydrogen bonds exhibit different capabilities. The statistical results of the hydrogen bonds alanalysis also show the same results. The intramolecular distance, the radius of gyration (Rg) and dihedral angel are used to study the conformation of the alanine dipeptide. The alanine dipeptide does not exist as a unique native state, and it can convert quickly from "extended" to "folded" conformations.%采用全原子分子动力学模拟研究了丙氨酸二肽分子在水溶液中的结构和氢键作用.径向分布函数和氢键统计用于分子动力学模拟的分析.从径向分布函数( RDF)发现不同类型的强氢键显示出不同的形成能力,而体系中的C- H…O弱相互作用较为明显,也不能忽略.氢键统计分析的结果也证实了这一点.分子内距离、回转半径和骨架二面角用于表征丙氨酸二肽分子在水溶液中的构象变化.丙氨酸二肤分子在水溶液中的柔顺性较好,构象在折叠和伸展之间相互转换.