Hydration of Uracil and Thymine

The purine and pyrimidine bases found in nucleic acids are planar heterocyclic molecules which contain both proton acceptor and proton donor substituents and hydrogen-bonding interactions between them facilitates molecular recognition during biological information processing. The polar (hydrogen-bonding) groups are situated around the rim of the aromatic rings. The pi-electron clouds are very nonpolar.

The two following models are based on quantum mechanics calculations. In both models, the state of lowest energy is a cooperative hydrogen-bonded configuration. The equilibria do not reveal a rigid hydration shell or cage which encapsulates the base. In aqueous solution, the surfaces of all solutes are indeed fully coated by water molecules, but in this case those states are higher in energy and more labile. It's important to remember that water molecules in the hydration shell of any solute, whether it's an ion, charged molecule, or a nonpolar solute such as methane, exchange with waters in the "regular" (bulk) water at high rates.