The study of the interaction between isolated DNA bases and metallic surface can be considered as a useful source of information in atomic scale to understand the nature of interaction of DNA with metallic surfaces and its geometry relative to the surface. The structures of four bases of DNA were optimized on the Cu(111) surface using ONIOM method so that the first layer of the surface interacting with the bases was considered in quantum mechanical (QM) region and the second layer in the molecular mechanical (MM) region. The DFT method employing wB97XD functional and universal force field (UFF) was selected for the QM and MM parts, respectively. For the QM region, the 6-31+G(d) basis set was used for the DNA bases and LANL2DZ for the Cu atoms of the first layer. The valence electrons of Cu atoms in the first layer were described by DZ basis set. A two layer of Cu(111) surface containing 77 atoms which 38 and 39 atoms form the first and second layers of the surface, respectively were considered for the calculations. The tilted angle between the plane of the molecule and the surface (a) in the optimized orientation of the DNA bases on the Cu(111) surface for AD, CY, GU and TY are 1.8, 15.1, 6.5 and 0.7°, respectively. It is seen that using a DFT functional such as wB97XD which considers the vdW interactions predicts more parallel geometry for the DNA bases on the Cu(111) surface especially for CY compared to the result reported in literature. Also interaction, adsorptio and deformation energies were calculated for the DNA bases on the Cu(111) surface. The calculated interaction energies were corrected by basis set superposition error (E). The calculated values of E int,corr for AD, TY, CY and GU are -0.881, -0.753, -0.849 and -1.073 eV, respectively. The calculated values of E ad for AD, TY, CY and GU are -1.351, -1.204, -1.277 and -1.567 eV, respectively. It was found that the using of the van der Waals corrected DFT functional such as wB97XD functional increases the adsorption energies of the DNA bases on the Cu(111) surface. The calculated values of deformation energies for the DNA bases on the Cu(111) surface are small and for GU AD CY TY are 0.078, 0.049, 0.045 and 0.011 eV, respectively. The electronic structure of DNA bases on the Cu(111) surface was investigated and observed a strong hybridization between the base and metal states. So, there is some portion of the charge density on the base, as well as a significant portion distributed over the cu surface. It was observed overlap between the molecular orbitals of DNA bases with the d atomic orbitals of Cu atoms, especially for CY and GU which is very important in the charge transfer between molecules and surface.
