A focus on penetration index – a new descriptor of chemical bonding

Abstract

Electron clouds surrounding atoms interpenetrate in a molecule, due to weak van der Waals interactions or formation of a genuine chemical bond. Now, Alvarez and Echeverría have suggested a simple descriptor of how deep this interpenetration is, and called it a penetration index, i.

Comprehensive analysis of C–H⋯π(alkyne) interactions in the crystal packing of diastereomers of 1,2-di(7′-methoxynaphth-1′-yl)-3,6-di(4′′-n-propylphenylethynyl)benzene

“…To quantitatively identify short contacts, Echeverria and Alvarez recently proposed the van der Waals crust based on the modified Lennard-Jones potential. 20,21 Considering the overlap of the electronic clouds of the two neighboring atoms, the nascent method simply quantifies the chemical bond by the penetration depth of the van der Waals spheres from the sum of the van der Waals radii (Fig. 7).…”

“…This study extensively analyzed the C–H⋯π contacts using a new diagnostic method based on the modified Lennard-Jones potential, referred to as the van der Waals crust. 20,21 The findings were further corroborated by the quantum theory of atoms-in-molecules (QTAIM) method as a well-established quantum mechanical formalism. 22–24…”

A further focus on penetration indices of misfit van der Waals crusts

“…Simultaneously to the appearance of that paper, W. Grochala published a commentary warning about the problems that might arise when using such a penetration index for pairs of atoms with dissimilar sizes and different van der Waals crust widths. 3 Although we had pinpointed such a possible problem in the text and given a simplied preliminary analysis in an Appendix, we think that the concern expressed by Grochala deserves a more detailed analysis that we present here.…”