Selenium chalcogen bonds are involved in protein–carbohydrate recognition: a combined PDB and theoretical study

Abstract

In this manuscript the ability of Selenium carbohydrates to undergo Chalcogen bonding (ChB) interactions with protein residues has been studied at the RI-MP2/def2-TZVP level of theory. An inspection of the...

Pd and Pt metal atoms as electron donors in σ-hole bonded complexes

“…[33][34][35][36][37][38][39] Over the years, the investigations of these interactions have moved beyond halogen atoms, hence the development of analogous chalcogen or pnicogen bonds which engender robust study. 36,[40][41][42][43][44] The bulk of bonds of this type utilize either a lone pair of the nucleophile as the source of charge to be transferred, or a p-electron system, either localized as in ethylene, or aromatic. A new wrinkle in this bonding is the finding that there are occasions where metal atoms can serve as the electron source, despite their low electronegativity.…”

“…33–39 Over the years, the investigations of these interactions have moved beyond halogen atoms, hence the development of analogous chalcogen or pnicogen bonds which engender robust study. 36,40–44…”

Various Sorts of Chalcogen Bonds Formed by an Aromatic System

“…Although not commonly considered in the older literature, there were instances of this interaction occurring, even if not formally recognized under this rubric at the time . Its presence and influence is currently being demonstrated in a startling number of different sorts of systems. − In its typical divalent bonding pattern, a chalcogen (Y) atom is connected to two R substituents and also carries two lone electron pairs in an overall tetrahedral arrangement, as in the simple example of SMe 2 . Each substituent would generate a σ-hole along the extension of the R-Y axis, which could engage in a ChB with an approaching nucleophile, but the position and strength of each such σ-hole would be mediated by its neighboring Y lone pairs.…”

Adjusting the balance between hydrogen and chalcogen bonds

“…41 An intramolecular ChB influences cis/trans isomerization involved in photoswitching. 42 An interested reader is referred to several quality reviews of this phenomenon, [43][44][45][46][47][48] including their participation in biological phenomena [49][50][51][52] such as proteins and nucleic acids.…”