Theoretical Study On The Interaction Between Na~+/K~+ And The Base And Water

Metal ions,biological macromolecules and water exist in organism.This thesis studies the interaction between Na+/K+and five nucleic acid bases and water by ABEEM??/MM and high-level ab initio methods.The structures of base-M+and base-M+-(H2O)n(base=A/T/G/C/U,M=Na/K,n=0-3)are optimized by a high-level quantum chemistry(QM)method,MP2/6-311+G(d,p),then frequency and binding energy of stable conformations are calculated at the same level with BSSE correction.The charge distributions of the base-M-(H2O)n(M=Li+/Na+/K+/Be2+/Mg2+/Ca2+,n=1?3)are studied by HF/STO-3G method.The results show that with the gradual increase in the number of ligand molecules,the charge of metal ions decrease gradually,and the distance between metal ionsA and coordination atoms increases gradually.According to the least square method and referring to the results of QM Mulliken charge distribution,the ABEEM??/MM parameters,valence electro negativity x*and valence hardness ?*,of Na+/K+ were fitted.The parameters of the hydrogen bonding between metal ions and the base or water molecules are determined by the results of binding energies obtained by QM calculations.At last,the ABEEM ??/MM potentials constructed here were applied to calculate the properties of M+-(H2O)n(n=1?6)and base-M+-(H2O)n(n=0?3),including structure,energy and charge distribution.Compared with the QM results,the RMSD of metal ion charge are 0.076 and 0.072 a.u.,the RRMSD of metal ion charge are 10.8%and 11.6%,the RMSD of binding energy are 1.652 and 1.487 kcal/mol,the RRMSD of binding energy are 16.7%and 6.1%,the RSMD of the distance between M+and coordinative atoms are 0.052 and 0.062 A,the RRMSD of structures are 0.026%and 0.016%.It can be seen that the results from ABEEM??/MM model have good consistency with those of QM.Further the above parameters are applied to study the dynamic properties of T-Na+aqueous solution which contains 500 water molecules.Compared with the initial structure,the RMSD of the bond length,bond angles and dihedral angles are 0.033 A?2.320� and 4.460�respectively.Analysis on the radial distribution function shows that the sodium ion is surrounded by thymine and water molecules,and the interaction between Na+with the base is stronger than that of with the water molecule,which is in agreement with the ab initio calculation.