| The selectivity of the active sites of biomacromolecules— nucleic acid with metal cations were studied by using the density functional theory with a hybrid B3LYP exchange-correlation functional and 6-31G** basis set in the first part of this paper, the structures and properties of complexes were systemically investigated, and the function of metal cations in organism was testified or forecasted. The interaction of adenine with Mg2+, Ca2+, Mn2+, Co2+, Zn2+, Ni2+, Cu2+ and Cd2+ cations were calculated with DFT/B3LYP method by using the standard 6-31G(d,p) basis set. Effective core potential (ECP) was used for Cd2+. The calculations of stabilities of the complexes in a polar medium have been performed with Onsager solvation model. All geometries were optimized without symmetry restrictions. The interaction energies and interaction Gibbs energies of complexes provide a comparatively reliable quantification of the selectivity of adenine for the studied metal ions not only in gas but also in the polar medium (water ε = 78.39), and relative interaction Gibbs energies of the isomer of the complexes have shown the selectivity of different metal-binding sites of the ligands, as to N7, the order is Co2+ > Mg2+ >Cd2+ > Ca2+ >Zn2+ > Mn2+ > Ni2+ > Cu2+.The interactions of guanine-cytosine pair with Li+,Na+,K+,Cu+,Mg2+,Ca2+,Cu2+,Zn2+,Cd2+,Ba2+, Hg2+ cations were computed with DFT/B3LYP method using the standard 6-31G(d,p) basis set. Effective core potentials (ECP) were used for Cd2+,Ba2+,Hg2+. All geometries were fully optimized without symmetry restrictions as well, while the calculations of the single point energy of the complexes in a polar medium have been performed using Onsager solvation model. Interaction energies of complexes provide an comparatively reliable order of the complexes' stability, and the mechanism of interaction of complexes is shown by the analysis of the energies—the interaction between the metal ions of subgroup A and bases is mainly composed of electrostatic attraction, while the covalent bonds play an important role in the complexes of metal ions of subgroup B and bases, which may be the cause of the differences between various complexes and is in reasonable agreement with the analysis of the charges and the orbital of the complexes too. The interactions of dimethyl phosphate anion (DMPï¼) with Mg2+, Ca2+, Mn2+, Co2+, Ni2+, Cu2+ and Zn2+ cations were calculated with DFT/B3LYP method by using the standard 6-31G(d,p) basis set too, while the remaining coordination bonds are saturated with water molecules ((H2O)4). All geometries were optimized without symmetry restrictions. The interaction energies of complexes provide a comparatively reliable quantification of the selectivity of dimethyl phosphate anion for the studied metal ions, which is in reasonable agreement with the Irving-Williams list. Moreover, the cations with an unfilled state of d-electrons may be sensitive to the changing of ligands. In addition, the population of changes of the complexes and the significant donor-acceptor natural bond orbital interaction were analyzed with the method of Natural Bond Orbital analysis. The interactive system of bases groups representing the single chain of DNA with Mg2+, Mn2+, Ni2+, Cu2+, Zn2+ cations were computed with the same method. All geometries were optimized without symmetry restrictions. Interaction energies of complexes provide a comparatively reliable quantification of the selectivity of dimethyl phosphate anion for the studied metal ions, which is in reasonable agreement with the experiment, as to guanine: aCu2+>aNi2+>aZn2+>bCu2+> aMg2+>bZn2+>bNi2+>aMn2+; as to cytosine: aCu2+>aNi2+>aZn2+>aMg2+>bCu2+>aMn2+>bZn2+>bNi2+. In addition, interplay between the structure of the complexes and coordinator number and their stability, measured by the values of interaction energies, has been discussed. A total of 16 hydrogen bonded complexes between the lowest energy tautomers of L-leucine and each of bases of RNA have been characterized at the density functional level of theory... |
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