Study On Solvation Free Energy Of Peptide Containing Charged Amino Acid Residue Based On ABEEM??/GB-SA Model

As an important parameter and a powerful tool for understanding the dissolution process,solvation free energy has become one of the topics of science.In the thesis,the sidechains,dipeptides,tripeptides,tetrapeptides of charged amino acids(Arg,Asp,Glu,Lys)were studied,and the solvation free energies were calculated.The detailed contents as follows:1.The B3LYP/6-311++G(d,p)level of theory was used to optimize the molecular structure,and obtain the stable structures of the molecules.The SMD solvent model has been used to calculate the solvation free energies of charged amino acid sidechains and dipeptides at the B3LYP/6-311++G(d,p),M052X/6-31G(d),MP2/aug-cc-pvdz,M062X/6-31+G(d,p)levels of theory.It can be found that the solvation free energies of these molecules are less than zero,and the solvation free energies of these systems at various levels of theory are different.The absolute values of the solvation energy calculated by the MP2 method are the smallest.2.Using the ab initio HF/STO-3G charges and the solvation free energies obtained from B3LYP/6-311++G(d,p)as the standard,least squares method and linear regression have been applied to fit the charge parameters and dihedral parameters in the ABEEM??/GB-SA model.Using these parameters,our dipeptides of Arginine,Lysine,Aspartate and Glutamate were calculated by using our ABEEM??/GB-SA solvation model.The results are in good agreement with those obtained by B3LYP/6-311++G(d,p)method.Using these parameters and our model,the solvation free energy of the tripeptides and tetrapeptides were calculated,and suitable.3.By using the parameters and new added parameters of ABEEM?? polarizable force field and the ABEEM??/GB-SA solvation model,we have calculated the solvation energies of charged and uncharged dipeptides.the polar uncharged dipeptides of Aspartic acide,Cysteine,Serine and the non-polar uncharged dipeptides of Valine,Isoleucine,Glycine.Our results are in good agreement with those obtained by B3LYP/6-311++G(d,p)level of theory.It can be found that our parameters of ABEEM??/GB-SA model can be applied to study the solvation free energies of the polypeptides and protein.