Nature of Nucleic Acid−Base Stacking: Nonempirical ab Initio and Empirical Potential Characterization of 10 Stacked Base Dimers. Comparison of Stacked and H-Bonded Base Pairs

Ab initio (MP2/6-31G*(0.25)) interaction energies were calculated for almost 240 geometries of 10 stacked nucleic acid−base pairs: A···A, C···C, G···G, U···U, A···C, G···A, A···U, G···C, C···U, and G···U; in some cases uracil was replaced by thymine. The most stable stacked pair is the G···G dimer (−11.3 kcal/mol), and the least stable is the uracil dimer (−6.5 kcal/mol). The interaction energies of H-bonded base pairs range from −25.8 kcal/mol (G···C) to −10.6 kcal/mol (T···T). The stability of stacked pairs originates in the electron correlation, while all the H-bonded pairs are dominated by the HF energy. The mutual orientation of the stacked bases is, however, primarily determined by the HF interaction energy. The ab initio base stacking energies are well reproduced by the empirical potential calculations, provided the atomic charges are derived by the same method as used in the ab initio calculations. Some contributions previously postulated to significantly influence base stacking (induction interac...