A cartography of the van der Waals territories

Abstract

The distribution of distances from atoms of a particular element E to a probe atom X (oxygen in most cases), both bonded and intermolecular non-bonded contacts, has been analyzed. In general, the distribution is characterized by a maximum at short E···X distances corresponding to chemical bonds, followed by a range of unpopulated distances--the van der Waals gap--and a second maximum at longer distances--the van der Waals peak--superimposed on a random distribution function that roughly follows a d(3) dependence. The analysis of more than five million interatomic "non-bonded" distances has led to the proposal of a consistent set of van der Waals radii for most naturally occurring elements, and its applicability to other element pairs has been tested for a set of more than three million data, all of them compared to over one million bond distances.

Non-covalent interactions of N-phenyl-1,5-dimethyl-1H-imidazole-4-carboxamide 3-oxide derivatives—a case of intramolecular N-oxide hydrogen bonds

“…In all cases, this interatomic N…O distance is evidently shorter than the sum of their van der Waals radii, reported as 3.16 Å [43]. The shortest hydrogen bonds, with N…O distances around 2.60 Å, are observed in structures III, IV, and V. In turn, the longest, with a corresponding distance of 2.655(2) Å, is observed for the unsubstituted derivative I. D-H…A angles of hydrogen bridges vary from 145(2)°for IA to 158(2)°for III.…”

Neutral organoantimony(III) and organobismuth(III) ligands as acceptors in transition metal complexes – Role of substituents and co-ligands

“…Less well explored is their Lewis acidic character, which, while weak, allows the formation of long intra-or inter-molecular contacts, often referred to as 'hypervalent' interactions,  van der Waals radii for Sb and Bi are 2.47 and 2.54 Å, respectively. 4 with a range of donor atoms. A significant amount of work in recent years has focused on organostibines with pendant-arm substituents bearing heteroatoms (usually N or O), many of which display intramolecular 'hypervalent' behaviour of this kind, and have been recently reviewed.…”

Pyridine, thiophosphine, and selenophosphine complexes of the phenylphosphine dication

“…All P---O interactions are outside the sum of the P-O covalent radii (Σ r,cov = 1.74 Å), [11] but some are inside the sum of the van der Waals radii (Σ r,vdW = 3.32 Å). [12] The N-P bond van der Waals radii for sulfur or phosphorus. The terminal P-S bonds (S1-P2 2.0815(7) Å and S2-P3 2.0785(7) Å, respectively) are significantly longer than in SPCy 3 (1.966(5) Å), [13] but are shorter than the central bonds (S1-P1…”