Study On Amino Acid Dipeptides In Aqueous Solution By Using ABEEMσπ Polarizable Force Field And Ab Initio Method

Amino acids are the building blocks of proteins which serve crucial functions in essentially all biological processes.Many biological and chemical reactions processes are carried out in a solvent,especially in aqueous solution.Therefore,it is significant to study the structure and properties of the amino acids dipeptide in aqueous solution.In the thesis,ABEEMσπfluctuating charge force field was employed to investigate the molecular dynamic simulation for amino acid dipeptide in aqueous solution at 298K and NVT ensemble.After simulation time 1ns,the dynamics properties of these dipeptides are investigated,including the root-mean-square deviations（RMSD）of several kinds of non-hydrogen atoms[C_αatoms,backbone atoms（C,C_α,N,O）and heavy atoms]and their respective initial structure.ABEEMσπ/GB/SA was used to calculate the solvation free energies,non-polar solvation free energies,polarsolvationfree energies,the solvent-accessible surface areas,hydrophilic surface areas,and hydrophobic surface areas.Their solvation free energies are smaller than zero.They dissolve in water.We obtain that the solvent-accessible surface areas of the amino acid dipeptide is proportional to their respective atomic number.The hydrophilicities of Arg,Glu,Lys,Asp,His,Gly,Thr,Cys,Asn,Ser,Gln,Tyr dipeptides are stronger,whereas Leu,Met,Phe,Pro,Trp,Val,Ala,Ile dipeptides are much more hydrophobic.That is to say,polar dipeptides are much more hydrophilic.Our results are consistent with the experimental ones.In addition,MP2/aug-cc-pvdz method altogether with the polarizable continuum model（PCM）in Gaussian was employed to calculate the solvation free energies of some amino acid dipeptides.The solvents include water,THF,CHCl₃ and CCl₄.We obtain that polar dipeptides are much easier to dissolve in water and THF solution,compared with nopolar dipeptides.Finally,for neutral amino acids,their solvation free energies by using ABEEM/GB/SA are in agreement with those by using ab initio PCM model.Therefore,ABEEMσπfluctuating charge force field is able to study the amino acid dipeptides in aqueous solution and to rightly calculate their solvation free energies.It provides us a suitable tool for investigating the polypeptides and proteins in aqueous solution.