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  • Title: Red-shifted hydrogen bonds and blue-shifted van der Waals contact in the standard Watson-Crick adenine-thymine base pair.
    Author: Zhou PP, Qiu WY.
    Journal: J Phys Chem A; 2009 Sep 24; 113(38):10306-20. PubMed ID: 19715282.
    Abstract:
    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 rho 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) sigma bonding orbital with that in the sigma* 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.
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