Synthesis, crystal structure, DFT calculations, and Hirshfeld surface analysis of an NNN pincer type compound

Abstract

The novel benzamide derivative NNN pincer type, N,N'-(azanediylbis(2,1-phenylene))bis(3-chlorobenzamide) (H3L), was synthesized from bis(2-nitrophenyl)amine starting material. The pincer ligand was characterized by 1H NMR, 13C NMR, COSY, HMQC, and FT-IR techniques. The geometry of pincer ligand was also confirmed by a single-crystal X-ray diffraction analysis. Structural analysis demonstrate that H3L is monoclinic and space group P21/n with Z = 4. It was find out the molecular conformation of the structure is promoted by intramolecular (NH⋅⋅⋅O, NH⋅⋅⋅N, and CH⋅⋅⋅O) and intermolecular (N(2)-H(2)⋅⋅⋅O(2)i, symmetry code (i) = 1/2 + x, 3/2-y, 1/2 + z) hydrogen bonds. The theoretical study of H3L was performed in the gaseous phase by B3LYP/6-311G(d,p) method to determine the structural properties of the title molecule, as a consequence the obtained data showed that the considerable agreement between the experimental and theoretical results. The reactivity and stability of the molecule were evaluated by calculating the HOMO–LUMO energy gap which was found as 6.5163 eV. In addition, FMO, NBO, NLO, DOS, RDG, MEP surface, and Mulliken atomic charge analyses were carried out. Hirshfeld surface analysis and two-dimensional fingerprint plots were investigated and the obtained data exposed that the most significant contributions to the crystal packing are from C···H/H···C (33.2%), H···H (31.5%), and H···Cl/Cl··H (18.9%) contacts. Furthermore, the molecular docking studies were performed to reveal the binding affinity between the title compound and the main protease (6LU7) of COVID-19 coronavirus.