The Applications Of ABEEM/MM On The Interactions Of Na⁺with N-methylacetamide,H₂O And Ethanol

Metal ions play an irreplaceable role in many biological processes and life activities.Na⁺is an indispensable ion in organisms,so it is significant to simulate the structures and properties of the electrolyte aqueous solution and biomolecular system containing Na⁺.In this thesis,the interaction potential energy function of Na⁺-NMA/H₂O were constructed in terms of the atom-bond electronegativity equalization fluctuating charge force field?ABEEM/MM?.By a large number of ab initio calculations,the stable structures of[Na?NMA?_n]⁺?n=4-8?,[Na?H₂O?_n]⁺?n=4-8?were optimized.The parameters were optimized and determined,and used to study the[Na?NMA?_n?H₂O?_m]⁺?n+m=4,6?system.The geometries,energies and charge distributions of the above clusters were calculated by the ABEEM/MM,and the results are in good agreement with those from quantum chemical method?QM?.The average absolute deviations?AADs?of the distances between Na⁺-ligand are in range of 0.04-0.07?,and the relative root mean square deviations?RRMSDs?are in range of 3.1-4.4%.The AADs of the average binding energies are in range of 0.91-1.49kcal/mol,and the RRMSDs are in range of 4.9-9.6%.The linear correlation coefficients of the charge distributions obtained by ABEEM/MM and QM are above 0.98.The results of ABEEM/MM are significantly better than those of OPLS-AA,of which the AADs and RRMSDs of the distances between Na⁺-ligand are in range of 0.14-0.18?and 6.9-10.3%,respectively.The AADs and RRMSDs of the average binding energies are in range of1.00-13.46 kcal/mol and 6.4-62.8%,respectively.Preliminary molecular dynamic simulations on a series of different concentrations of NMA-NaCl aqueous solutions were carried out by using ABEEM/MM.The results show that the coordination number of NMA of first hydration shell increases and H₂O decreases gradually,with the increases of NMA concentration.The coordination numbers of Na⁺in the system with NMA concentration of 4 mol/L,6 mol/L and 8 mol/L are 5.41,5.86 and 5.96,respectively.Similarly,the ABEEM/MM potential energy function of Na⁺-ETOH was constructed,and it was used to calculate the structures,energies and charge distributions of[Na?ETOH?_n]⁺?n=4-8?.The results are also in good agreement with those of QM.The AAD of the distances between Na⁺-ligand is about 0.09?,and the RRMSD is about 5.6%.The AAD of the binding energies is about 6.14 kcal/mol,and the RRMSD is about 6.5%.The linear correlation coefficients of the charge distributions obtained by ABEEM/MM and QM are above 0.97.The results of ABEEM/MM are also significantly better than those of OPLS-AA.The ABEEM/MM fluctuating charge field of Na⁺-NMA/H₂O/ETOH system constructed in this paper can reasonably represent the interactions between Na⁺and N-methylacetamide,water and ethanol,and the overall results are better than those of the OPLS-AA force field.