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

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 (base-backbone) and (ii) interactions among atoms within the backbone itself (backbone-backbone). These interactions include hydrogen bonding, dihydrogen bonding, hydrogen-hydrogen bonding, and several other weak closed-shell X-Y interactions (X, Y = O, N, C). While each individual interaction is very weak and typically accompanied by perhaps 0.5-3 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.

Packing of Helices: Is Chirality the Highest Crystallographic Symmetry?

“…Thus, Λ-stacking occurs between the 2,2'-bipyridyne ligands of the helicates. Such interactions are common in organometallic or DNA helices [23][24][25]. The handedness of the helices is induced by the intrinsic character of helicates: the enantiomer leads to the 31 helices while the Δ enantiomer leads to the 32 helices.…”

Synthesis, structure and photophysical properties of binuclear methylplatinum complexes containing cyclometalating 2-phenylpyridine or benzo{h}quinoline ligands: a comparison of intramolecular Pt–Pt and π–π interactions

“…A cumulative effect of several such interactions leads to a non-negligible stabilization energy. 13 However when the sum of the r(r) of all the p-p interactions BCPs is considered, the total value is about 2.2 ¥ 10 -2 au (between ppy rings in 1a) and 3.5 ¥ 10 -2 au (between bhq rings in 1b). It seems that there is a competition between Pt-Pt and p-p interactions in these two complexes, such that twisting of the flexible ppy ligands in 1a promotes a decrease in the p-p interaction between ppy ligands and an increase in the Pt-Pt interaction.…”

An Introduction to the Quantum Theory of Atoms in Molecules

“…For example, the electron density at the BCP, r b , has been shown on several occasions to be strongly correlated with the bond energies, and hence provide a measure of bond order (Eq. 8) [1,30]; the potential energy density at the BCP has been shown to be highly correlated with hydrogen bond energies [32]; full interaction potentials in hydrogen bonds were recovered from the potential energy density at the BCP [63]; p-p stacking interactions in benzene dimers and in stacked DNA bases and base-pairs have been found to be highly correlated to BCP and cage critical point data between p-stacked monomers [64][65][66].…”