On the Anisotropy of van der Waals Atomic Radii of O, S, Se, F, Cl, Br, and I

Abstract

The Cambridge Structural Database (CSD) was used to obtain flattening factors to describe the overall anisotropy of nonbonding van der Waals (vdW) contacts between several main group elements. The method for obtaining the flattening factors is based on a novel minimization process. Results show that the vdW contact distances are significantly dependent on the environment and the orientations of the surrounding covalently bonded atoms: head-on vdW contacts are generally shorter than sideways contacts in overall agreement with earlier results by Nyburg and Faerman (Acta Crystallogr., Sect. B: Struct. Sci. 1985, 41, 274-279). With the exception of Se, we find flattening factors that are somewhat smaller than those found earlier. High-level ab initio quantum chemical calculations using Ar and Ne as a probe also confirm the flattening effect and its dependency on the environment. A dozen popular long-range corrected and dispersion supplemented density functionals are compared with the CCSD(T) data. While several of them perform quite poorly, four DFT-D methods, especially B3LYP-GD3BJ, provided vdW flattening similar to those found by the CCSD(T) theory and experiment.

Stable N‐Heterocyclic Germylenes of the Type [Fe{(η5‐C5H4)NR}2Ge] and Their Oxidation Reactions with Sulfur, Selenium, and Diphenyl Diselenide

“…The two shortest ones respectively involve a 2‐adamantyl (H ··· S 2.67 Å, C–H–S 130°) and a cyclopentadienyl CH group (H ··· S 2.77 Å, C–H–S 123°). Note that the van der Waals radii of S and Se differ only by 0.07 Å , . In view of the fact that trigonal‐planar N atoms are the exception rather than the rule for tertiary amines,, it remains highly speculative, whether the CH ··· E contacts discussed above exhibit a significant distortive influence.…”

σ-Hole Interactions: Perspectives and Misconceptions

“…One is that van der Waals radii are typically based upon the assumption that the atoms, despite being covalently bonded, are spherical. It is well known that this is not true [12,[35][36][37][38][39][40]; σ-holes are in fact a manifestation of the asymmetry of covalently-bonded atoms, which can be quite substantial. From analyses of crystal data, Nyburg and Faerman estimated the radii of chlorines bonded to carbons to be, on the average, 0.2 Å shorter along the extensions of the bonds than perpendicular to them [36]; for sulfurs doubly-bonded to carbons, they found a difference of 0.4 Å. Eramian et al predict somewhat smaller but still significant asymmetries [40].…”

“…It is not only covalently-bonded halogens that have lower electronic densities (σ-holes) on the extensions of their bonds; this is true as well of covalently-bonded atoms in other Groups of the periodic table [12,[35][36][37][38]40]. In the years 2007-2009, positive σ-hole potentials were found for atoms in Groups VI [41], V [42], and IV [43].…”

“…However, they were not What is the origin of such positive potentials on electronegative atoms? It has been known for quite some time that atoms involved in covalent single (and sometimes double) bonds have lesser electronic densities (and shorter radii) on the extensions of the bonds than on their lateral sides [12,26,27,[35][36][37][38][39][40]. This has sometimes been called "polar flattening".…”

The volume of cavities in proteins and virus capsids

“…and Dean, the concept of a vdW radius is intrinsically approximate because atoms in molecules are not spherical and the radii cannot be equated precisely to a distance that could be uniquely defined in terms of potential energy surfaces for any specific system. The anisotropic character of vdW shapes of bonded atoms was noticed long ago and revisited with useful theoretical analyses but only for a selected sample of electronegative elements. Still, the simplified spherically‐symmetric vdW radii are very useful in modeling within the approximations of classical molecular dynamics.…”