First X-ray diffraction and quantum chemical study of proton-acceptor and proton-donor forms of 5-carboxylcytosine, the last-discovered nucleobase

Abstract

The recently-discovered nucleobase 5-carboxylcytosine (caC) is the final product of oxidative attack on the 5 position of cytosine. It can exist in solution in an equilibrium of different protonated and unprotonated forms within a range of pH, although only the zwitterionic caC± and the anionic caC− species have been detected in the liquid phase. In this work, four proton-transfer compounds of caC have been prepared by varying chemical reagents to ensure different pH during crystallization, and then determined by X-ray crystallography: 5-carboxylcytosinium chloride, bromide and nitrate and 5-carboxylcytosinate phenylbiguanidium. Both cationic and anionic species of caC exist in the solid state as canonical aminooxo tautomers. In caCH+-containing compounds, site protonation always occurs at N3 imino atom. Structural changes in the heterocyclic ring of cationic and anionic forms of caC can be interpreted, in terms of valence bond theory, as an increase in the contribution of different polar canonical forms. Quantum chemical calculations on unionized 5-carboxylcytosine, as well as on the zwitterionic and the anionic species, are also reported in order to estimate the relative energies of the possible tautomeric forms. Theoretical calculations confirm the existence in the isolated molecules of the strong intramolecular hydrogen bond found in the crystal between the adjacent amino and carboxyl groups.