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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.丙氨酸二肽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.
The structure and hydrogen bonding of alanine dipeptide molecules in aqueous solution were investigated by using all-atom molecular dynamics simulations.The radial distribution function and hydrogen bond statistics were used to analyze molecular dynamics simulations.From the radial distribution function (RDF) It is found that different types of strong hydrogen bonds show different formative ability, while the CH ... O weak interaction in the system is obvious and can not be neglected.The results of hydrogen bond statistical analysis also confirm this point.The intramolecular distance, radius of gyration and The dihedral angle of the skeleton is used to characterize the conformational change of the alanine dipeptide molecule in aqueous solution.The alanine dipeptide molecule has good flexibility in aqueous solution and the conformational transition between folding and stretching.