Journal of Molecular Modeling

, Volume 13, Issue 2, pp 291–296

Halogen bonding: the σ-hole

Proceedings of “Modeling interactions in biomolecules II”, Prague, September 5th–9th, 2005
  • Timothy Clark
  • Matthias Hennemann
  • Jane S. Murray
  • Peter Politzer
Original Paper

DOI: 10.1007/s00894-006-0130-2

Cite this article as:
Clark, T., Hennemann, M., Murray, J.S. et al. J Mol Model (2007) 13: 291. doi:10.1007/s00894-006-0130-2

Abstract

Halogen bonding refers to the non-covalent interactions of halogen atoms X in some molecules, RX, with negative sites on others. It can be explained by the presence of a region of positive electrostatic potential, the σ-hole, on the outermost portion of the halogen’s surface, centered on the R–X axis. We have carried out a natural bond order B3LYP analysis of the molecules CF3X, with X = F, Cl, Br and I. It shows that the Cl, Br and I atoms in these molecules closely approximate the \(s^{2} p^{2}_{x} p^{2}_{y} p^{1}_{z} \) configuration, where the z-axis is along the R–X bond. The three unshared pairs of electrons produce a belt of negative electrostatic potential around the central part of X, leaving the outermost region positive, the σ-hole. This is not found in the case of fluorine, for which the combination of its high electronegativity plus significant sp-hybridization causes an influx of electronic charge that neutralizes the σ-hole. These factors become progressively less important in proceeding to Cl, Br and I, and their effects are also counteracted by the presence of electron-withdrawing substituents in the remainder of the molecule. Thus a σ-hole is observed for the Cl in CF3Cl, but not in CH3Cl.

Figure

Schematic representation of the atomic charge generation. The molecular electrostatic potential (MEP) is calculated using the AM1* Hamiltonian. The semiempirical MEP is then scaled to DFT or ab initio level and atomic charges are generated from it by the restrained electrostatic potential (RESP) fit method.

Keywords

Halogen bonding Sigma-hole Electrostatic potential DFT 

Copyright information

© Springer-Verlag 2006

Authors and Affiliations

  • Timothy Clark
    • 1
  • Matthias Hennemann
    • 1
  • Jane S. Murray
    • 2
  • Peter Politzer
    • 2
  1. 1.Computer-Chemie-CentrumFriedrich-Alexander-Universität Erlangen-NürnbergErlangenGermany
  2. 2.Department of ChemistryUniversity of New OrleansNew OrleansUSA

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