Ab initio and Density Functional Studies of Substituted Effects of an A-U Base Pair on Stability of Hydrogen Bonding

The substituent effects on the stability of the hydrogen bonding between 9-methyladenine (A) and l-methyluracil derivatives (U^X) having various substituents groups were systematically studied. The hydrogen bond stability of mismatched base pairs between 9-methylguanine (G) and the tautomeric enol structures (U^X,) of U^X was also examined. Geometry optimization of these bases and their base pairs using the 6-31G^* basis set was carried out by Hartree-Fock (HF) self-consistent field (SCF) and the density functional theory (DFT) using Becke's three-parameter hybrid method with Perdew/Wang 91 expression (B3PW91). The strength of hydrogen bonding was evaluated at the HF level and the second-order Moller-Plesset correlation energy correction (MP2) level in some cases. The values for the hydrogen bonding strength calculated using DFT procedure were situated between those obtained by HF and MP2 levels but closer to the latter than the former. Introduction of an electron-withdrawing group (EWG) into the uracil ring resulted in the formation of more stable hydrogen bonding. These indicate that the hydrogen bond between ³H of U and N¹ of A is crucial for the A-U base pairing.