Short but Weak: The Z-DNA Lone-Pair⋅⋅⋅π Conundrum Challenges Standard Carbon Van der Waals Radii

Angew Chem Int Ed Engl. 2020 Sep 14;59(38):16553-16560. doi: 10.1002/anie.202004201. Epub 2020 Jul 15.

Abstract

Current interest in lone-pair⋅⋅⋅π (lp⋅⋅⋅π) interactions is gaining momentum in biochemistry and (supramolecular) chemistry. However, the physicochemical origin of the exceptionally short (ca. 2.8 Å) oxygen-to-nucleobase plane distances observed in prototypical Z-DNA CpG steps remains unclear. High-level quantum mechanical calculations, including SAPT2+3 interaction energy decompositions, demonstrate that lp⋅⋅⋅π contacts do not result from n→π* orbital overlaps but from weak dispersion and electrostatic interactions combined with stereochemical effects imposed by the locally strained structural context. They also suggest that the carbon van der Waals (vdW) radii, originally derived for sp3 carbons, should not be used for smaller sp2 carbons attached to electron-withdrawing groups. Using a more adapted carbon vdW radius results in these lp⋅⋅⋅π contacts being no longer of the sub-vdW type. These findings challenge the whole lp⋅⋅⋅π concept that refers to elusive orbital interactions that fail to explain short interatomic contact distances.

Keywords: Z-DNA; lp⋅⋅⋅π interactions; molecular recognition; non-covalent interactions; van der Waals radii.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Carbon / chemistry*
  • DNA, Z-Form / chemistry*
  • Hydrophobic and Hydrophilic Interactions
  • Quantum Theory*

Substances

  • DNA, Z-Form
  • Carbon