A density functional investigation of the interaction between calcium and magnesium divalent cations and nucleic acid bases was performed to determine coordination geometries, electronic features, absolute metal ion affinities, entropies, and free energies for all possible complexation stable products. Cations were allowed to interact with the canonical and noncanonical tautomers of free bases after a careful selection of several attachment sites. Magnesium ion shows a greater affinity for nucleic acid bases than calcium. All complexes are characterized by a ionic interaction between ligand and metal ions that appears slightly more pronounced for magnesium.