Molecular Dynamics Simulation of the Hydration of the Alanine Dipeptide
Molecular Dynamics Simulation of the Hydration of the Alanine Dipeptide
复制标题
丙氨酸二肽水合的分子动力学模拟
DOI：
10.1021/jp984001d
复制
发表时间：
1999
影响因子：
3.3
通讯作者：
J. Padró
中科院分区：
文献类型：
--
作者：
S. Kalko;E. Guàrdia;J. Padró
已经对水溶液中的丙氨酸二肽分子进行了分子动力学计算机模拟。考虑了三种不同的分子构象（α、β 和 C7ax）。对于围绕这种二肽的不同原子或原子团（即两个羰基氧、三个甲基和两个酰胺氢）的溶剂分子，分别计算了水合水分子的结构和动力学性质。比较了三种构象的结果可能存在的差异。该研究包括分子位点、水径向分布函数和配位数以及水分子在水化壳中的停留时间、氢键和重新取向时间。极性和非极性原子团周围水的性质之间的微小差异已经被仔细分析。不同构象的水合水性质之间的差异并不显着。
Molecular dynamics computer simulations of an alanine dipeptide molecule in aqueous solutions have been carried out. Three different molecular conformations (α, β, and C7ax) have been considered. Structural and dynamical properties of the hydration water molecules have been calculated separately for solvent molecules surrounding different atoms or atomic groups of such dipeptide, i.e., two carbonyl oxygens, three methyls, and two amide hydrogens. The results for the three conformations have been compared for possible differences. The study includes molecule siteswater radial distribution functions and coordination numbers as well as residence times, hydrogen bonding, and reorientational times of water molecules in the hydration shells. The little differences between the properties of water around the polar and nonpolar atomic groups have been carefully analyzed. The discrepancies between the hydration water properties on the different conformations are not significant.