The applicability of resonance theory to explain the protonation of pyrimidinic bases was analyzed within the framework of the atoms in molecules (AIM) theory using B3LYP/6-31++G**//B3LYP/6-31G** charge densities of the neutral and diverse protonated forms of uracil and cytosine. The present study demonstrates that AIM atomic properties and delocalization indexes do not follow the trends that should be expected according to the resonance model. The resonance model is only able to predict the stability sequence of protonated forms and explain the changes exhibited by most of the bond properties upon protonations. Both the O-and N-protonated forms are found to be better described by RO-H + and RN-H + forms than by the classical RO + -H and RN + -H structures. According to the AIM analysis the electron charge gained by the proton is mainly provided by the other hydrogens of the molecule.
The stability and electron density topology of quinhydrone complex was studied using multiple computational levels, including MPW1B95 Truhlar's density functional. The QTAIM analysis demonstrates that an electron population transfer from hydroquinone to quinone monomer accompanies the complex formation. The variations undergone by atomic populations indicate that the electron transfer through HOMO LUMO overlap is combined with a reorganization of the electron density within each monomer. Variations of two- and six-center delocalization indices show a small reduction of electron delocalization in the hydroquinone ring upon complex formation.
The atomic properties of neutral and protonated forms of uracil and some model compounds, computed from B3LYP/6-31++G//B3LYP/6-31G charge densities with the QTAIM theory, indicate that sigma electron reorganization plays a significant role in the protonation processes. This reorganization is substantially different for O=C-C=C and O=C-C-X (X = N, O) units, involving transfers of electron population between all atoms in the first case but not across the C-X bond in the second unit. O-Protonation is basically favored over the N-protonation because of the lower electron population transferred to the proton. The stability sequence of N-protonated forms can be rationalized in terms of the closer position of the proton, when attached to N3, to regions of larger electron population (carbonyl groups).
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