Extended Weak Bonding Interactions in DNA: π-Stacking (Base−Base), Base−Backbone, and Backbone−Backbone Interactions† Export

@article{citeulike:6045477, abstract = {We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (basebackbone) and (ii) interactions among atoms within the backbone itself (backbonebackbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogenhydrogen bonding, and several other weak closed-shell XY interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.53 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title.}, author = {Matta, Cherif F. and Castillo, Norberto and Boyd, Russell J.}, citeulike-article-id = {6045477}, citeulike-linkout-0 = {http://dx.doi.org/10.1021/jp054986g}, citeulike-linkout-1 = {http://pubs.acs.org/doi/abs/10.1021/jp054986g}, day = {1}, doi = {10.1021/jp054986g}, journal = {The Journal of Physical Chemistry B}, keywords = {ab-initio, dft, dna}, month = {January}, number = {1}, pages = {563--578}, posted-at = {2009-10-30 23:50:42}, priority = {2}, title = {Extended Weak Bonding Interactions in DNA: π-Stacking (Base−Base), Base−Backbone, and Backbone−Backbone Interactions{\dag}}, url = {http://dx.doi.org/10.1021/jp054986g}, volume = {110}, year = {2006} }

TY - JOUR ID - citeulike:6045477 L3 - citeulike-article-id:6045477 N2 - We report on several weak interactions in nucleic acids, which, collectively, can make a nonnegligible contribution to the structure and stability of these molecules. Fragments of DNA were obtained from previously determined accurate experimental geometries and their electron density distributions calculated using density functional theory (DFT). The electron densities were analyzed topologically according to the quantum theory of atoms in molecules (AIM). A web of closed-shell bonding interactions is shown to connect neighboring base pairs in base-pair duplexes and in dinuleotide steps. This bonding underlies the well-known pi-stacking interaction between adjacent nucleic acid bases and is characterized topologically for the first time. Two less widely appreciated modes of weak closed-shell interactions in nucleic acids are also described: (i) interactions between atoms in the bases and atoms belonging to the backbone (basebackbone) and (ii) interactions among atoms within the backbone itself (backbonebackbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogenhydrogen bonding, and several other weak closed-shell XY interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.53 kcal/mol, the sum total of these interactions is postulated to play a role in stabilizing the structure of nucleic acids. The Watson-and-Crick hydrogen bonding is also characterized in detail at the experimental geometries as a prelude to the discussion of the modes of interactions listed in the title. IS - 1 JF - The Journal of Physical Chemistry B EP - 578 TI - Extended Weak Bonding Interactions in DNA: π-Stacking (Base−Base), Base−Backbone, and Backbone−Backbone Interactions† VL - 110 SP - 563 KW - ab-initio KW - dft KW - dna AU - Matta, Cherif AU - Castillo, Norberto AU - Boyd, Russell PY - 2006/01/01/ UR - http://dx.doi.org/10.1021/jp054986g ER -