应用ABEEMσπ/GB-SA方法估算4个带电二肽的溶剂化自由能  

Estimation of solvation free energy of four charged dipeptides by ABEEMσπ/GB-SA method

作　　者：赵东霞[1] 张超[1] 孟祥娜[1] ZHAO Dongxia;ZHANG Chao;MENG Xiangna(School of Chemistry and Chemical Engineering,Liaoning Normal University,Dalian 116029,China)

机构地区：[1]辽宁师范大学化学化工学院

出　　处：《辽宁师范大学学报（自然科学版）》2019年第4期471-476,共6页Journal of Liaoning Normal University:Natural Science Edition

基　　金：国家自然科学基金资助项目（21133005;21473083）

摘　　要：采用B3LYP/6-311++G(d,p)理论水平优化获得体系的稳定几何结构.在相同的理论水平下,使用SMD溶剂模型,计算这些分子在水溶剂中的溶剂化自由能,并以其作为标准值.将各分子的稳定结构作为初始结构,在298 K、NVT系综下,应用ABEEMσπ可极化分子力场,对氨基酸侧链分子的水溶液进行分子动力学模拟,模拟的时间为1ns.平衡后的结构作为训练集,以调节和确定ABEEMσπ的相关参数,最终得到与从头计算相一致的溶剂化自由能.使用相同的参数,计算带电氨基酸二肽的溶剂化自由能,ABEEMσπ的计算结果与从头计算结果具有良好的一致性,表明该参数具有可转移性,这为研究多肽和蛋白质分子的溶剂化自由能奠定了基础.B3LYP/6-311++G(d,p)level of theory was used to optimize and obtain the geometries of the molecules.The same level of theory was used to calculate their solvation free energies(G sol),and these energies were set as standard.Setting each stable structure as the initial structure,the MD simulation is launched at 298 K in a canonical ensemble NVT by ABEEMσπpolarizable force field.Each MD simulation time is 1 ns.The equilibrium structures of side chains were selected as the training set.After calibrating the parameters of ABEEMσπ,the solvation free energies showed a good agreement with the results of B3LYP.Then,these parameters were applied to calculate the solvation free energies of dipeptides with charged side chains.It can be found that the parameters are suitable and transferable.Thus,ABEEMσπ/GB-SA method will play an important role in the fields of estimating the solvation free energy of peptide and protein systems.

关 键 词：氨基酸侧链 带电二肽分子 原子电荷 ABEEMσπ可极化分子力场 溶剂化自由能 

分 类 号：O641[理学—物理化学]