Study Of Interaction Between DNA Based And Mg²⁺/Ca²⁺ By Quantum Chemistry Method And ABEEM/MM Model

At the physiology, nucleic acids are polyanionic polymers hence they need cations to neutralize this charge. However, metal ion coordination to nucleic acids is not only required for charge neutralization, it is also essential for their biologic function. The interaction between different metal cations and DNA bases depend on the charge, size and electronical structure of canons. In this work, the binding sites, geometries, charge transformation and binding energies of metal cation (Mg2+ICa2+) interacting with different DNA bases and Watson-Crick bases pairs were systemically studied by quantum chemistry method and ABEEMIMM model.The geometries of MZ+-bases (MZ+=Mgt+ICa2+) complexes were determined at the B3LYPI6-311++G(d,p) and MP216-311++G(2d,2p) level of theory, respectively. Energy calculations were performed at MP216-311++G(2d,2p) and CCSD(T)16-311++G{2d,2p) level with BSSE corrections, respectively. The ABEEMIMM (atom-bond electronegativity equalization method), which is based on the density functional theory and electronegativity equalization principle, was applied to study the properties of Mz+-bases (M2+-Mgt+ICa2+) complexes. A large number of quantum chemistry calculations were performed to determine the ABEEM parameters of metal cations, with the original parameters of DNA bases and a separated program of our own. The ABEEMIMM model gives reasonable geometries and energies compared with the present quantum chemistry methods.The complexes for the M2+-base pairs(MZ+--Mgt+ICa2+) were optimized within the Hartree-Fock approximation applying the 6-31 l++g(d,p) basis set of orbital, while relativistic pseudopotentials were used for the cations, and the energy calculations were performed at the MP216-311++G{d,p) level with BSSE corrections. Furthermore, structure and energy of system based on the MZ+-bases (Mz+=Mg2+/Ca2+) complexes were analyzed.At last, the absorption interactions between alkali metals canons and the mercury interface were studied by a quantum chemical method. Three typical sites of mercury interface, i.e. the hollow, bridge and top sites were chosen to calculate the adsorption energy with MP2 method. It is revealed that the hollow site has the largest adsorption energy, followed by the bridge and top sites. Moreover, as the ionic radius increases from Li+ to Na+ and K+,the distance between the canon and the mercury interface increases, while the absorption energy gradually decreases, as well as the charge transfer between the cation and the mercury.