【摘要】 提出了用于分子动力学模拟后处理氢键网络图的感知算法。对从头算分子动力学(CPMD)模拟的轨迹文件进行统计分析,得到了水溶液中醋酸单分子水合体系的局域结构特征信息。由径向分布函数得到定义氢键的上限,运用图论方法分析了溶液结构中水合团簇大小和简单氢键环结构及头环分布,其中六元环的突出含量与从头算稳定性分析一致。更多还原

【Abstract】 We present a perception algorithm for hydrogen bonded network based on chemical graphics. The upper limit of hydrogen bond 2. 3 A is defined from radial distribution functions. An adjacency matrix and an incidence matrix are obtained from one of configurations in the CPMD trajectory file. The circuit matrix is deduced from the incidence matrix and its spanning tree. This post-simulation method has been applied to the analysis of the hydrogen bond angle, complex, and hydrogen bond rings in the local structure of a dilute acetic acid monomer-water system. The hydrogen bonded angles (C = )O...H-Ow, ( C-) O( H)...H-Ow and (C-) O-H...Ow are favorable around 165°, 158°and 167°, respectively. The interesting distribution of hydrogen bonded acetic acid monomer-water complexes are obtained. The most stable structure is six-membered head-on planar ring, which is consistent with the previous ab initio quantum chemistry calculations.更多还原