Computational Study on Hydrogen Bonding and Stacking Interactions Between Nucleic Acid Bases,

Hydrogen bonding in DNA bases was investigated using reliable nonempirical ab initio computational methods. Gradient optimization was carried out on 30 DNA base pairs using the Hartree Fock HF approximation and the 6-31G basis set. The optimizations were performed within the Cs symmetry. However, the harmonic vibrational analysis indicates that 13 of the studied base pairs are intrinsically somewhat nonplanar. The interaction energies of the base pairs were then evaluated at the optimized planar geometries with inclusion of the electron correlation energy at the MP2 level. The stabilization energies of the studied base pairs range from 24 kcalmol to 9 kcalmol, and the calculated gas phase interaction enthalpies agree well within 2 kcalmol with the available experimental values. The binding energies and molecular structures of the base pairs are not determined solely by the hydrogen bonds, but are also strongly influenced by the polarity of the monomers and by a wide variety of secondary long range electrostatic interactions involving the hydrogen atoms bonded to ring carbon atoms. The stabilization of the base pairs is dominated by the Hartree-Fock interaction energy. This result confirms that the stability of the base pairs originates in the electrostatic interactions. For weakly bonded base pairs, the correlation interaction energy amounts to as much as 30-40 of the stabilization. For some other base pairs, however, a repulsive correlation interaction energy was found. This fact is explained as a result of a reduction of the electrostatic attraction upon inclusion of the electron correlation. The empirical London dispersion energy does not correctly reproduce the correlation interaction energy.