On Analogies in Proton-Transfers for Pyrimidine Bases in the Gas Phase (Apolar Environment)—Cytosine Versus Isocytosine

Abstract

Inter- and intra-molecular proton-transfers between functional groups in nucleobases play a principal role in their interactions (pairing) in nucleic acids. Although prototropic rearrangements (intramolecular proton-transfers) for neutral pyrimidine bases are well documented, they have not always been considered for their protonated and deprotonated forms. The complete isomeric mixtures in acid-base equilibria and in acidity–basicity parameters have not yet been examined. Taking into account the lack of literature and data, research into the question of prototropy for the ionic (protonated and deprotonated) forms has been undertaken in this work. For the purposes of this investigation, two isomeric pyrimidine bases (C—cytosine and iC—isocytosine) were chosen. They exhibit analogous (symmetrical) general acid-base equilibria (intermolecular proton-transfers). Being similar polyfunctional tautomeric systems, C and iC possess two labile protons and five conjugated tautomeric sites. However, positions of exo groups are different. Consequently, structural conversions such as prototropy, rotational, and geometrical isomerism of exo groups (=O/−OH and =NH/−NH2) and their intramolecular interactions with endo groups (=N−/>NH) possible in neutral C and iC and in their ionic forms lead to some differences in compositions of isomeric mixtures. By application of quantum–chemical methods to the isolated (in vacuo) species, stability of all possible neutral and ionic isomers has been examined and the candidate isomers selected. The complete isomeric mixtures have been considered for the first time for di-deprotonated, mono-deprotonated, mono-protonated, and di-protonated forms. Protonation–deprotonation reactions have been analyzed in the gas phase that models non-polar environment. The gas-phase microscopic (kinetic) and macroscopic (thermodynamic) acidity–basicity parameters have been estimated for each step of acid-base equilibria. When proceeding from di-anion to di-cation in four steps of protonation–deprotonation reaction, the macroscopic proton affinities for C and iC differ by less than 10 kcal mol−1. Their DFT-calculated values are as follows: 451 and 457, 340 and 339, 228 and 224, and 100 and 104 kcal mol−1, respectively. Differences between the microscopic proton affinities for analogous isomers of C and iC seem to be larger for the exo than endo groups. Owing to variations of relative stabilities for neutral and ionic isomers, in some cases they are even larger than 10 kcal mol−1.