Significant structural deformation of nucleic acid bases in stacked base pairs: an ab initio study beyond Hartree–Fock

Stacked structures of the uracil, thiouracil and cytosine dimers, adenine–uracil and uracil–cytosine pairs were investigated by gradient optimization at the ab initio second-order Møller–Plesset correlated level. The aromatic rings of bases and exocyclic groups were significantly distorted from planarity upon complexation. Nevertheless, the stabilization energies were similar to those obtained previously with rigid monomers, because the non-negligible improvement in intermolecular stabilization energy is compensated for by the deformation energies of the bases. The largest distortions were found for uracil. Deformation of uracil rings leads to the formation of intermolecular H-bonds and improves the stabilization energy.