A novel silver(I) two-dimensional coordination polymer of thiophosphoric triamide ligand with two different coordination modes: Experimental, theoretical and molecular docking study

Abstract

Novel thiophosphoric triamide (S)P[NC₄H₈O]₃ (PS, compound 1) and silver(I) two-dimensional coordination polymer derived from it ([Ag^(I)₃(PS)₂(NO₃)₃]_n, 2) as the first coordination polymer derived form a S-donor mono-dentate thiophosphoric triamide ligand were synthesized and structurally studied. The structures crystallize in the monoclinic system with space group P2₁/n for PS and C2/c for Ag^(I) complex. The asymmetric unit consists of one complete molecule for 1 and of two Ag^(I) ion, one PS ligand, one nitrate anion as well as one-half of a nitrate anion for 2. The infinite array of [Ag^(I)₃(PS)₂(NO₃)₃]_n is composed of the two different coordination modes of two- and five-coordinate Ag^(I) with metal center environment of a near linear of Ag(S)₂ and a highly distorted square pyramidal of Ag(O)₄(S). Intermolecular interactions are addressed by Hirshfeld surface (HS) analysis showing C—H…O hydrogen bonds (in 1 and 2) and Ag…O contacts (in 2) as dominant interactions to form the crystal packing cohesion. A molecular docking simulation was performed to study interactions and binding modes between 1 and 2 with target proteins of SARS-CoV-2 and Monkeypox showing an acceptable interaction tendency with maximum binding affinities of around −6 (for CoV-2) and −8 (for Mpox) kcal/mol for Ag^(I) coordination polymer 2. For a further investigation of the Ag^(I)—O/S contacts, theoretical QTAIM and NBO calculations were run suggesting that these contacts are closed-shell (mainly ionic) in nature.