An Electron Density Study of the Characterization of Extended Weak Bonding in DNA: B-Stacking (Base-Base), Base-Backbone, and Backbone-Backbone Interactions

摘要

We have recently undertaken a detailed study of several weak interactions in nucleic acids, many of which have been overlooked so far, and which can, cooperatively, have a non-negligible contribution to the structure and stability of these molecules. While the B-stacking interaction is well documented as being a major contributor to the structure and stability of nucleic acids, not much has been published on the nature of the bonding giving rise to this stabilization, with the exception of a recent report about the closed-shell bonding in benzene dimers. In contrast, two broad classes of interaction that, we conjecture, may well be of significance in determining the structure of DNA have been largely left out in the literature: The weak interactions between the bases and the backbone and the interactions between the backbone and itself.rnFragments of DNA were extracted from previously determined accurate experimental geometries and the electron densities of these fragments were calculated at the B3LYP/6-311++G(d,p) density functional theory level of theory. All electronic structure calculations were conducted using Gaussian 03. The electron densities were analyzed according to the quantum theory of atoms in molecules (AIM) to obtain the topological feature of the density distribution using the AIM 2000 software.