Department of Physics, NGM College, Pollachi 642 001, India.
J Mol Graph Model. 2012 May;35:11-20. doi: 10.1016/j.jmgm.2012.02.002. Epub 2012 Feb 20.
Molecular dynamics (MD) simulations were carried out to study the conformational characteristics of Glycine Dipeptide (GD) in the presence of explicit water molecules for over 10 ns with a MD time step of 2 fs. The density functional theory (DFT) methods with 6-311G** basis set have been employed to study the effects of microsolvation on the conformations of GD with 5-10 water molecules. The interaction energy with BSSE corrections and the strength of the intermolecular hydrogen bond interactions have been analyzed. The Bader's Atoms in Molecules (AIM) theory has been employed to investigate H-bonding patterns in water interacting complexes. The natural bond orbital (NBO) analysis has been carried out to analyze the charge transfer between proton acceptor to the antibonding orbital of the XH bond in the hydrated complexes. NMR calculations have been carried out at B3LYP/6-311G (2d, 2p) level of theory to analyse the changes in structure and hydrogen bonding environment that occur upon solvation.
采用分子动力学（MD）模拟方法，在 MD 时间步长为 2 fs 的情况下，使用显式水分子对甘氨酸二肽（GD）进行了超过 10 ns 的构象特征研究。采用密度泛函理论（DFT）方法和 6-311G**基组研究了微溶剂化对 GD 与 5-10 个水分子的构象的影响。分析了与 BSSE 校正的相互作用能和分子间氢键相互作用的强度。采用分子中原子（AIM）理论的 Bader 方法研究了与水相互作用的复合物中的氢键模式。进行了自然键轨道（NBO）分析，以分析水合配合物中质子受体与 XH 键的反键轨道之间的电荷转移。在 B3LYP/6-311G（2d，2p）理论水平上进行了 NMR 计算，以分析溶剂化时结构和氢键环境的变化。
