New pyridyl-functionalized phosphor-/thiophosphor-amides with the same [(5-CH ₃ )- ² Py-NH]P(X) (X = O and S) segment: X-ray crystallography investigation, Hirshfeld surface analysis and molecular docking study

Abstract Three novel phosphor/thiophosphor-amides, [(5-CH 3 )- 2 Py-NH] 2 [C 6 H 11 (CH 3 )N]P(X) (X = O ( 1 ) and S ( 2 )) and [(5-CH 3 )- 2 Py-NH]P(O)[OCH 2 C(CH 3 ) 2 CH 2 O] ( 3 ), were synthesized and characterized by FT-IR and 1 H/ 13 C/ 31 P-NMR spectroscopy. The structures of 1 and 3 were determined by using single-crystal X-ray diffraction (SC-XRD) crystallography which reveals both compounds to crystallize in monoclinic space groups ( P 2 1 / c and P 2 1 / n , respectively). A crystal packing analysis shows that neighbouring molecules are connected together via N–H⋯O═P hydrogen bonds forming one-dimensional chains. A Hirshfeld surface analysis indicates that crystal packing is dominated by H⋯H, H⋯O/O⋯H, H⋯C/C⋯H, and H⋯N/N⋯H contacts, with O⋯H/H⋯O interactions including the classical N–H⋯O═P hydrogen bonds being particularly favored. Phosphor/thiophosphor-amide derivatives are emerging as promising scaffolds for targeting key enzymes of acetylcholinesterase (1EEA, 5FPP) and urease (2UBP, 4GY7). Molecular docking revealed favorable binding affinities (up to −10.3 kcal/mol for 1 with 1EEA), with compounds 1 and 2 generally exhibiting stronger predicted interactions than compound 3 . Key stabilizing interactions involve phosphoryl/thiophosphoryl groups and pyridine rings. Redocking of co-crystallized ligands with RMSD assessment confirmed the reliability of the docking protocol. While these results do not provide definitive evidence of inhibitory potency, they support further computational refinement and experimental evaluation, highlighting the potential of these derivatives as enzyme-interacting agents with biomedical relevance.