Does the Hydrated Cytosine Molecule Retain the Canonical Structure? A DFT Study

The molecular geometry of complex of cytosine with 14 water molecules was calculated within the density functional theory using the B3LYP functional. The standard 6-31G(d) basis set has been employed. It was found that the interaction with water molecules forming a locked chain around cytosine results in a significant change of its gas-phase geometry. The structure of the hydrated nucleobase cannot be described by canonical chemical formula, and it is best approximated as a superposition of the oxoamino and zwitterionic hydroxoimino resonance structures. The unique features of the interaction of water with cytosine are also revealed: the formation of three hydrogen bonds with the participation of the oxygen atom of the carbonyl group and the presence of weak C H···O hydrogen bonds between the water molecules and the hydrophobic part of cytosine.