Red-Shifted Hydrogen Bonds and Blue-Shifted van der Waals Contact in the Standard Watson−Crick Adenine−Thymine Base Pair.

Standard Watson−Crick adenine−thymine (AT) base pair has been investigated by using the B3LYP functional with 6-31G(d, p) basis set, at which level of theory the geometrical characteristics of the AT base pair are the best in agreement with the experiment. It exhibits simultaneously red-shifted N−H···O and N−H···N hydrogen bonds as well as a blue-shifted C−H···O contact. AIM analysis suggests that the blue-shifted C−H···O contact exists as van der Waals interaction, and the electron density ρ that reflects the strength of a bond has been used to explain the red- and blue-shifted. By means of NBO analysis, we report a method to estimate the effect of hyperconjugation quantitatively, which combines the electron density in the X−H (X = N, C) σ bonding orbital with that in the σ* antibonding orbital. The effect of structural reorganization on the origins of the red- and blue-shifted has been considered by the partial optimization, its behavior on the X−H (X = N, C) bond is quite different. Rehybridization and repolarization models are employed, and they act as bond-shortening effects. The competition between the electrostatic attractions and Pauli/nucleus repulsions is present in the two typical red-shifted N−H···O and N−H···N hydrogen bonds as well as in the blue-shifted C−H···O van der Waals contact. Electrostatic attraction between H and Y atoms (Y = O, N) is an important reason for the red shift, while the nucleus−nucleus repulsion between H and O atoms may be a factor leading to the C−H bond contraction and its blue shift. The electric field effect induced by the acceptor O atom on the C−H bond is also discussed. [ABSTRACT FROM AUTHOR]