摘要
使用B3LYP/6-311++G(d,p)方法优化了极性的Gly、Ser、Cys、Asn、Gln和Thr二肽以及非极性的Ala、Pro、Val、Met、Leu、Ile、Phe和Trp二肽的结构,然后使用MP2/aug-cc-pvdz/PCM方法分别计算了这些二肽在水、四氢呋喃、氯仿和四氯化碳溶剂中的溶剂化自由能.应用ABEEMσπ浮动电荷极化分子力场,在298K、NVT系综下分别对这些二肽的水溶液进行分子动力学模拟.模拟了1ns后,计算骨架原子坐标与初始结构相比的均方根偏差.使用ABEEM/GBr4-SA模型计算这些二肽的溶剂可及表面积和溶剂化自由能.获得其溶剂可及表面积与自身原子数成正比.比较了ABEEM/GBr4-SA模型所计算的氨基酸二肽分子的溶剂化自由能与从头算所获得的结果,两者有很好的线性关系.说明该模型和力场参数是合理的,可应用到这些氨基酸多肽的溶剂化自由能的研究中.
The B3LYP/6-311＋＋G（d,p）method was used to optimize the geometries of polar Gly,Ser,Cys,Asn,Gln,Thr,as well as nonpolar Ala,Pro,Val,Met,Leu,Ile,Phe and Trp dipeptides.The solvation free energies of these dipeptides were calculated in water,THF,CHCl3 and CCl4.by using the MP2/aug-cc-pvdz/PCM method.ABEEMσπfluctuating charge force field was employed to carry out the molecular dynamic simulations of these amino acid dipeptides in aqueous solution at 298 Kand NVT ensemble.With 1ns simulation,we calculated the root mean square deviations（RMSD）of the backbone atoms between the simulated coordinates and the corresponding initial structures.ABEEMσπ/GBr4-SA was used to calculate the solvent-accessible surface areas（SASA）and the solvation free energies.We obtain that the amino acid dipeptide SASAs are proportional to their respective atomic numbers.Finally,for amino acids dipeptides,their solvation free energies obtained from ABEEM/GBr4-SA are in agreement with those by using quantum chemistry method,which indicates that the model and force field parameters are transferable and reasonable.This model can be applied to the study of the solvation free energy of these amino acid polypeptides.
出处
《辽宁师范大学学报（自然科学版）》
CAS
2015年第3期344-348,共5页
Journal of Liaoning Normal University:Natural Science Edition
基金
国家自然科学基金项目(21133005
21473083)
