Theoretical Studies Of The Interactions Of Zn²⁺ With Water And N-methyl Acetamide

Almost half of the proteomes of living organisms are metalloproteins, of which includingzinc proteins occupies a large proportion. Therefore, using the theoretical studies on theinteraction between zinc cation’ protein and water molecules are of great significance. In thisdissertation, the interactions of Zn2+with water, Zn2+with water and N-methyl acetamide(NMA) were studied by quantum chemistry (QM) and the atom-bond electronegativityequalization fluctuating charge model (ABEEM/MM).First, the gas-phase hydrated clustes of Zn2+(H2O)n=1~12were optimized by threequantum chemistry methods, B3LYP/6-311++G(2d,2p), M062X/6-311+G(d,p) andMP2/6-311++G(2d,2p), then the energies were calculated at the MP2/6-311++G(2d,2p) level.The stable structures with different coordination number (CN) of Zn2+were obtained, as wellas the binding energies and charge distributions. Results show that when n=10~12, the CN ofZn2+can be4,5and6, and those of the most stable structure are five or six. The numbers ofhydrogen bonding, the distances between Zn2+and the oxygen atoms of the inner shell watermolecules (RZn-O) increase with the increasing number of water molecules. In the spirit ofABEEM/MM, the ABEEM parameters of Zn2+were parameterized by fitting the chargedistributions from ab inito HF/STO-3G method. An accurate ABEEM/MM interactionpotential function for Zn2+with H2O was constructed to calculate the structures andbinding energies of Zn2+(H2O)n=1~12clusters, and the results are consistent with the QM results.For the structure, the average absolute deviation (AAD) and root-mean-square deviation(RMSD) of the RZn-Oare0.003and0.001, respectively. For the binding energy, the biggestAADs of the total binding energy and successive binding energy are2.6and1.7kcal·mol-1,respectively, and the RMSD are3.1and0.7kcal·mol-1, respectively. The linear correlationcoefficient of the comparison of charges from ABEEM/MM and QM methods is beyond0.99,the corresponding linear intercept is close to zero, and the maximum deviation is0.058e.Further construction of the ABEEM/MM interaction potential function for Zn2+-NMAwas performed, and the parameters were determined by fitting the structures, chargedistributions and binding energies from ab inito calculations. Calculating the characters ofZn2+(NMA)n=1~6and Zn2+·NMA·(H2O)n=1~12by using the potential function. The results ofQM show that when n=1~4, the RZn-Oof system is lengthened gradually; when n>4, it begin toappear more coordination layers, and the RZn-Odid not change obviously, which indicate thatthe first coordination layer of Zn2+is saturated and the CN of Zn2+is4. The RZn-Oof the most stable structure is the smallest when both n and CN are the same; the RZn-Odid not changeobviously in the structures with the same n and different CN. The positive charge of Zn2+gradually reduces with the increase of n. For Zn2+·NMA·(H2O)n=1~12, the linear correlationcoefficient of the comparison of charges from ABEEM/MM and QM methods is beyond0.98,and the corresponding linear intercept is close to zero. The biggest AADs of the total bindingenergy and successive binding energy are0.1and1.5kcal·mol-1, respectively.