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

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.

Carbon-Oxygen Hydrogen Bonding in Biological Structure and Function

“…However, this structure does not address many common RNA secondary and tertiary structural elements. Although the formation of CH⅐⅐⅐O hydrogen bonds in A-T base pairs, both in Watson-Crick and Hoogsteen conformation, has been debated in the literature (37)(38)(39)(40), experiments have yet to definitively resolve whether these interactions represent true hydrogen bonds that stabilize DNA and RNA structure. Corollary studies to those in proteins aimed at directly probing CH⅐⅐⅐O hydrogen bond formation in base pairs, backbone interactions, and tertiary structure represent a promising area of future research.…”

Copigmentation of malvidin-3-O-glucoside with five hydroxybenzoic acids in red wine model solutions: Experimental and theoretical investigations

“…When the electron density q was about 10 À3 a.u. and its 5 2 q value was smaller than 0.024 a.u., the interaction between two atoms was usually classified as vdW interaction (Zhou & Qiu, 2009). When one of the three eigenvalues was negative and the other two were positive, it was denoted as (3,+1) and was named as the ring critical point (RCP) which indicated the existence of a ring structure.…”

Vibrational solvatochromism. II. A first-principle theory of solvation-induced vibrational frequency shift based on effective fragment potential method

“…Additionally, it was observed that repulsive potential, appearing due to the shortening of intermolecular distances, may be associated with blueshifting patterns. [50][51][52] Neverthe-less, to our knowledge, no first-principles study of the nonelectrostatic vibrational solvatochromism was undertaken up to date. In particular, it is not clear under what circumstances the electrostatic interaction is the dominant contribution 9,42 to experimentally observed vibrational frequency shift.…”