σ-Hole interactions in small-molecule compounds containing divalent sulfur groupsR₁—S—R₂

Abstract

Hydrogen bonds, aromatic stacking contacts and σ-hole interactions are all noncovalent interactions commonly observed in biological systems. Structural data derived from the Protein Data Bank showed that methionine residues can interact with oxygen atoms through directional S...O contacts in the protein core. In the present work, the Cambridge Structural Database (CSD) was used in conjunction with ab initio calculations to explore the σ-hole interaction properties of small-molecule compounds containing divalent sulfur. CSD surveys showed that 7095 structures contained R 1—S—R 2 groups that interact with electronegative atoms like N, O, S and Cl. Frequencies of occurrence and geometries of the interaction were dependent on the nature of R 1 and R 2, and the hybridization of carbon atoms in C,C—S, and C,S—S fragments. The most common interactions in terms of frequency of occurrence were C,C—S...O, C,C—S...N and C,C—S...S with predominance of Csp 2. The strength of the chalcogen interaction increased when enhancing the electron-withdrawing character of the substituents. The most positive electrostatic potentials (V S,max; illustrating positive σ-holes) calculated on R 1—S—R 2 groups were located on the S atom, in the S—R 1 and S—R 2 extensions, and increased with electron-withdrawing R 1 and R 2 substituents like the interaction strength did. As with geometric data derived from the CSD, interaction geometries calculated for some model systems and representative CSD compounds suggested that the interactions were directed in the extensions of S—R 1 and S—R 2 bonds. The values of complexation energies supported attractive interactions between σ-hole bond donors and acceptors, enhanced by dispersion. The interactions of R 1—S—R 2 with large V S,max and nucleophiles with large negative V S,min coherently provided more negative energies. According to NBO analysis, chalcogen interactions consisted of charge transfer from a nucleophile lone pair to an S—R 1 or S—R 2 antibonding orbital. The directional σ-hole interactions at R 1—S—R 2 can be useful in crystal engineering and the area of supramolecular biochemistry.

Chalcogen Bonds in Small-Organic Molecule Compounds Derived from the Cambridge Structural Database (CSD)

“…Interestingly, the lowest unoccupied molecular orbital also lies along extension of the covalent bond X-R like MEP does. Thus, both MEP and LUMO of chalcogen-bond donor predict directional bonding of nucleophiles at divalent chalcogen atoms as previously reported (Pal et al 2001 [1]; Lundemba et al 2020 [27]).…”

“…We use Equations ( 1) and ( 2) (Murray et al, 2011 [26]; Lundemba S. et al, 2020 [27]) to perform electrostatic potential (V) in the space around a chalcogen-bond donor, written in atomic units (au), and interaction energy (E int ) between a chalcogen donor and an acceptor, respectively. Energies E int are energy minima at 0 K. Large basis sets are used to minimize the problem of correction for the basis set superposition error (Grimme S., 2006 [28]; Politzer P. et al, 2013 [7]).…”

Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons

“…As examples, understanding the forces behind crystal engineering and supramolecular chemistry benefits from a knowledge of σ-hole interactions due to their directionality, strength, and selforganization properties which promote formation of adducts in the solid state [34][35][36][37][38][39][40][41][42][43][44][45][46][47][48][49][50][51][52]. The importance of σ-hole bonding has also been verified in the context of anion recognition processes [53][54][55][56][57][58][59][60][61], materials chemistry [62][63][64][65][66][67][68][69][70][71][72], or biochemistry [73][74][75][76][77][78][79][80][81]. An early work connecti...…”

“…The full range of these sorts of bonds, along with their designations, is summarized in Figure 1. processes [53][54][55][56][57][58][59][60][61], materials chemistry [62][63][64][65][66][67][68][69][70][71][72], or biochemistry [73][74][75][76][77][78][79][80][81]. An early work connecting σ-hole bonds with crucial concepts in chemistry occurred when Grabowski recognized that tetrel bonds can be thought of as a preliminary stage of the very important SN2 reaction [82].…”

Experimental and Theoretical Studies of Dimers Stabilized by Two Chalcogen Bonds in the Presence of a N···N Pnicogen Bond

“…Due to its high directionality, chalcogen bonding is particularly important in crystal engineering and self-assembly of supramolecular structures. Evidence of chalcogen bond-like motifs in crystalline structures is frequently seen in the literature. ,,− An often repeated example is the structure of Ebselen, an essential biological compound, which is stabilized by short Se···O noncovalent contacts . Selenocyanate crystals have recently come under intense investigation ,, as the substitution of the cyano group strongly enhances one of the σ-holes over the other on the Se atom .…”