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A study is conducted to analyze the binding of first-row transition metal monocations (Sc-Cu) to N7 of guanine and N7 to N3 of adenine nucleobases. The result from analysis show that differences between guanine and adenine arise from Pauli repulsion and deformation terms.

The effects of oxidation, protonation and metal cationization with Cu(super +) and Cu(super 2+) on the strength of the N-glycosidic bond in 2'-deoxyguanosine are studied by using quantum chemical calculations. The analysis has shown that these changes might not only influence the hydrolysis mechanism of the N-glycosidic bond but also affect other properties such as N9-C1' chemical shielding tensors.

This paper analyses the behavior of different density functionals in the description of the most stable structures of Cu(2+)-(H(2)O)(n) complexes (n = 1-6). From n = 3 to n = 6, different coordination numbers of the metal cation were considered. The structures and energies of the complexes were theoretically determined by means of density functional methods that include different amounts of exact exchange: the BLYP functional (0% of exact exchange), the B3LYP functional (20% of exact exchange), the MPWB1K functional (44% of exact exchange), and BHLYP functional (50% of exact exchange). In addition, CCSD(T) calculations with a large basis set were carried out. It has been found that the functionals with lesser amount of exact exchange, especially BLYP, fail to describe the relative energies between the different structures of each cluster because these functionals tend to overestimate the stability of low-coordinated structures. The inclusion of the exact exchange into the functional improves the results, those obtained with MPWB1K and BHLYP being in very good agreement with the CCSD(T) ones. This behavior is related to the poor description of the second ionization energy of Cu by pure functionals, which leads to a too delocalized spin density in the complex with GGA functionals.

The influence of N7 protonation on the mechanism of the N-glycosidic bond hydrolysis in 2'-deoxyguanosine has been studied using density functional theory (DFT) methods. For the neutral system, two different pathways (with retention and inversion of configuration at the C1' anomeric carbon) have been found, both of them consisting of two steps and involving the formation of a dihydrofurane-like intermediate. The Gibbs free energy barrier for the first step is very high in both cases (53 and 46 kcal/mol for the process with inversion and with retention, respectively). However, the N7-protonated system shows a very different mechanism which consists of two steps. The first one leads to the formation of an oxacarbenium ion intermediate, with a Gibbs free energy barrier of 27 kcal/mol, and the second one corresponds to the nucleophilic attack of the water molecule to the oxacarbenium ion and takes place with a barrier of 1.3 kcal/mol. Thus, these results agree with a stepwise SN1 mechanism (DN*AN), with a discrete intermediate formed between the leaving group and the nucleophile approach, and show that N7 protonation strongly catalyzes the hydrolysis of the N-glycosidic bond, making the guanine a better leaving group. Finally, kinetic isotope effects have been calculated for the protonated system, and the results obtained are in very good agreement with experimental data for analogous systems.