Abstract
The coordinated metal ions in metal complex of DNA bases play a significant role in the biological action of nucleic acids. Especially, metal cations interact with DNA bases, destroying the hydrogen bonding between the base pairs. The structure of DNA is changed as the result. Therefore, the metal cations affect syntheses, replication and cleavage of DNA. A number of experimental and theoretical studies have been reported for the metal cation interactions with DNA bases. Cerda and Wesdemiotis have reported the interaction of alkali metal ions (Li, Na and K) with DNA bases. However the binding sites were not suggested as the suitable to receive the metal cations. Del Ben have reported the results of a study for the Li complexes of the DNA bases by ab initio calculations to determine the optimized structures and stabilization energies. Burda et al. have studied on the interaction of guanine and adenine with Zn at the HF and MP2 level. In the present paper, as a continuation of study on the binding of metal cations with DNA bases we report a DFT investigation on the interaction of Cu with DNA bases. DFT calculations are carried out at B3LYP level of theory with the 6-31G(d,p) basis sets using the Gaussian03 series of program. The metal binding sites for Cu complexes were taken from the previous theoretical data for the protonation sites of DNA bases proposed by Del Bene. The geometries of all structures are fully optimized without any constraint. The vibration frequencies of the optimized structures are also calculated at same level to determine the nature of the stationary points. All the conformers are found to be local minima, with all real harmonic frequencies and all positive Hessian eigenvalues. Zero point corrections are included in association energies. To obtain accurate association energies, basis set superposition errors(BSSE) are also subtracted from the calculated association energies in the full counterpoise(CP) approximation. The copper(II) cation association energies(∆E) are calculated as the difference of the optimized energy of the base-Cu complex [E(B-Cu)] and the sum of the energies of the base [E(B)] and cupric cation monomer [E(Cu)] for the reaction
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