Structures and energetics of complexes between the adenine-thymine Watson-Crick (AT WC) and adenine-adenine reverse-Hoogsteen (AA rH) DNA base pairs and hydrated (five water molecules) Mg2+, Ca2+, Sr2+, Ba2+, Zn2+, Cd2+, and Hg2+ metal cations were studied using high-level quantum chemical techniques. Binding of the cations to N7 of adenine does not enhance the strength of the base pairing through polarization effects. This is in stark contrast with the results obtained for the GG and GC base pairs. This finding and other recently published data indicate a qualitative difference between adenine-containing (AA,AT) and guanine-containing (GC,GG) base pairs. There are significant changes in the electronic structure of the guanine aromatic system upon cation binding to N7 which propagate toward the H-bonded partner. No such effect has been observed for any adenine-containing pair. The interaction between hydrated cations and adenine is much weaker than that between hydrated cations and guanine due to the low dipole moment of adenine. Furthermore, the cation and its surrounding polarized water molecules interact with the nitrogen atom of the adenine amino group which then acts as an H-bond acceptor. This can lead to destabilization of the base pairing. The zinc and magnesium groups of divalent cations have a different balance of the water-cation and base-cation interactions. Binding of the zinc-group elements to nucleobases is more efficient. Interaction of large IIa group divalent cations (Ca2+, Sr2+, and mainly Ba2+) with the N7 site of adenine is not likely unless the amino group nitrogen atom serves as a coordination center which may disrupt the base pairing. The complexes were optimized within the Hartree-Fock approximation with the 6-31 G* basis set of atomic orbitals and relativistic pseudopotentials for the cations. All atoms of the base pairs were kept coplanar. No other constraints were applied. The interaction energies have been calculated with inclusion of the electron correlation by means of the full second-order Moeller-Plesset perturbational theory.