The basis of a sigma hole interaction is an energetically stabilizing interaction between a positively charged site (sigma hole) and a negatively charged site (lone pair) on different atoms. The positive site is produced by a covalent sigma bond between the atom hosting the sigma hole and a neighboring atom. The presence of the bond results in the distortion of the electron density around the host atom, with the density increasing equatorially (with respect to the bond) about the atom but decreasing along the extension of the bond. Through this mechanism, a region of positive electrostatic potential, termed a sigma hole, can be localized onto the surface of an atom bearing a sigma bond. This sigma hole could then engage in electrostatic interactions with a lone pair associated with a negative electrostatic potential.
In addition to the electrostatic interaction described above, dispersive forces are also thought to play a role in the overall interaction. Studies have found electrostatic and dispersive contributions to be roughly comparable in magnitude, and for the dominant contributor to vary from system to system.
Alternatively, sigma hole pair interactions can be conceptualized in terms of the mixing of molecular orbitals. The occupied sigma bonding orbital associated with the bond would give rise to a corresponding unoccupied sigma antibonding orbital lying on the opposite face of the atom. Mixing between the antibonding orbital and the occupied orbital associated with a lone pair would be expected to result in energetic stabilization.
Several atoms, including those which are relatively electronegative (such as Chlorine, Oxygen, and even Fluorine) can act as positive sites in sigma hole pair interactions. Counterintuitively, this can occur even when the atom acting as the positive site has an overall negative partial charge. The solution to this apparent contradiction lies in the anisotropy in the electron cloud introduced by the presence of the sigma bond. If the electronic charge is not evenly distributed around the nucleus, it remains possible for a positive partial charge to develop opposite the sigma bond in the region of electron depletion. This partial positive charge coexists with a partial negative charge of larger magnitude associated with the more electron-rich regions of the atomic surface, which results in an overall negative partial charge.