Sigma-holes from iso-molecular electrostatic potential surfaces. Academic Article uri icon


  • Visualization of the halobenzene -hole region of molecules (PhX, X = Cl, Br, I) was conducted to investigate the nature of the -hole present between covalently bonded elements of groups IVB-VIIB (known as halogen bonding for group VIIB) and corresponding negative sites, such as Lewis base lone electron pairs, -electrons, or anions. The -hole consists of a region of poor electron density and often relatively positive electrostatic potential surrounding the outermost portion of the halogen atom along the A-X bond axis. In this work, molecular electrostatic potential (MEP) isosurfaces for PhX obtained from ab initio calculations are examined to determine the -hole in 3D, showing the surfaces of corresponding positive and negative regions. Surfaces were mapped for isopotentials of PhX molecules as low as 0.003V and scaled up by factors of 10 up to 3V. The -hole is revealed as a positive region exposed underneath a predominantly negative MEP isosurface. As isopotential values move away from zero, this hole grows in radius; conversely, its presence completely fades as potential approaches zero with increasing distance from the molecule. This technique can also be used to compare behaviors of neutral molecules and their ionic counterparts like the case of neutral PF6 (not observed experimentally) and the hexafluorophosphate anion, PF6-, a typical counter-ion in commercial Li-ion batteries. The pnictogen halide PF5 features similar MEP trends as the neutral PF6, which features reactive sites, shown as negative potential caps, at specific points in the molecule, similar to those of PF5. The portrayal of MEP behavior in iso-surfaces at specific and practical values of chemical interest is crucial when defining lump parameter sets for Coulombic force fields for molecular dynamics simulations to be used in systems that go from biological macromolecules to crystal engineering to devices to final products. Active chemical sites can be described by the MEP function, V(r), more proficiently than just wavefunctions or electron densities that intrinsically contain the same information, and this is fully enhanced when color-coding electron densities on isopotential surfaces are shown. Graphical abstract The hidden features of orbital holes depicted by iso-potentials.

published proceedings

  • J Mol Model

author list (cited authors)

  • Alaminsky, R. J., & Seminario, J. M.

citation count

  • 6

complete list of authors

  • Alaminsky, Ryan J||Seminario, Jorge M

publication date

  • May 2019