Cation-pi and amino-acceptor interactions between hydrated metal cations and DNA bases. A quantum-chemical view

Cation-pi interactions between cytosine and hexahydrated cations have been characterized using ab initio method with inclusion of electron correlation effects, assuming idealized and crystal geometries of the interacting species. Hydrated metal cations can interact with nucleobases in a cation-pi manner. The stabilization energy of such complexes would be large and comparable to the one for cation-pi complex with benzene. Further, polarized water molecules belonging to the hydration shell of the cation are capable to form a strong hydrogen bond interaction with the nitrogen lone electron pair of the amino groups of bases and enforce a pronounced sp3 pyramidalization of the nucleobase amino groups. However, in contrast to the benzene-cation complexes, the cation-pi configurations are highly unstable for a nucleobase since the conventional in plane binding of hydrated cations to the acceptor sites on the nucleobase is strongly preferred. Thus, a cation-pi interaction with a nucleobase can occur only if the position of the cation is locked above the nucleobase plane by another strong interaction. This indeed can occur in biopolymers and may have an effect on the local DNA architecture. Nevertheless, nucleobases have no intrinsic propensity to form cation-pi interactions.