分子模拟在黑土胡敏酸三维结构模型构建中的应用
Applications of molecular simulation technology in construction of three-dimensional model about black soil humic acid
吕贻忠 1郑殷恬 1赵楠1
作者信息
- 1. 中国农业大学资源与环境学院,北京,100193
- 折叠
摘要
选取吉林省公主岭市黑土胡敏酸为研究对象,使用元素分析,红外光谱分析,13C核磁共振分析3种化学分析手段对胡敏酸样品进行结构解析,利用ChemBioOffice软件搭建了土壤胡敏酸分子二维结构单体,通过将模拟光谱与实际光谱比较验证了构建的二维结构有很大的可适性,同时借助Hyperchem软件,在MM+、AMBER、OPLS,3种力场下对三维单体结构进行分子力学结构优化,优化前后键能、键角能、二面角能、范德华能、静电能及总势能皆发生变化,变化的大小及趋势没有固定规律;同时进行分子动力学模拟,黑土胡敏酸的三维结构单体在AMBER力场下的生成热最小,等于-358.72 Kcal/mol,所以其构象最为稳定.
Abstract
The humic acid of black soil from Gongzhuling city, Jilin province was chosen as the study object and the elemental analysis, IR and 13C-NMR methods were used to analyse the molecular structural characteristics of humic acid. ChemBioOffice was applied to build two dimensional molecular structure of soil humic acid monomers. Comparing actual spectrum with simulating spectrum, the results show that the two-dimensional structure of soil humic acid molecular model has a better suitability. This study also uses Hyperchem to simulate three-dimensional monomer molecular structure models, which are optimized by molecular mechanics in the MM+, AMBER and OPLS force fields. After the optimization, bond energy, bond angle energy, dihedral angle energy, Van der Waals energy, electrostatic energy and total potential energy are all changed, which show no rules during the variation. At the same time, the molecular dynamics simulation is also used. In the AMBER force field, the three-dimensional structure of soil humic acid monomers has the least heat of formation -358.72 Kcal/mol, which indicates it is the most stable in all of the three fields.
关键词
黑土/胡敏酸/分子模拟/三维结构/AMBER力场Key words
black soil/humic acid/molecular simulation/there-dimensional structure/AMBER force field引用本文复制引用
基金项目
国家自然科学基金(40771099)
十一·五国家科技支撑课题(2006BAD15B01)
出版年
2011
NETL
NSTL
维普
万方数据