Crystal structure analysis, hirshfield surface study, quantum chemical studies, and molecular docking investigations of a novel Cu(II) complex of 4-amino-6-methoxypyrimidine-based ligand

Abstract

At ambient temperature, a novel copper complex with the bridge bidentate ligand 4-amino-6-methoxypyrimidine of formula [Cu(C₅H₇N₃O)(H₂O)₃](ClO₄)₂.H₂O (pipClO) has been synthesized and described using elemental analysis, FT-IR spectroscopy, and single crystal X-ray diffraction. Density functional theory (DFT) at the B3LYP-D3(BJ)/Def2-SVP method and in-silico molecular docking approach were utilized to gain insight into the electronic properties and the biological potential of the synthesized compound respectively. Two nitrogen atoms from the organic ligand’s pyrimidine ring and three oxygen atoms from water molecules pentacoordinate the Cu(II) cations in a deformed square pyramid pattern. The 4-amino-6-methoxylpyrimidine ligands and the Cu atom centers connect to form a 1-D corrugated chain that runs along the c-axis direction in the atomic arrangement. Through O–H–O hydrogen bonds, the compound’s various chemical units are joined to form an infinite three-dimensional network. Intermolecular interactions were investigated by Hirshfeld surfaces. Analysis of binding interactions reveals binding affinity of − 4.2 kcal/mol for the best pose of the binding interaction between pipCIO and Pseudomonas aeruginosa Hemagglutinin protein (Hemagglutinin PA–HA) and − 4.6 kcal/mol between pipClO and Fucose-binding lectin (PA-IIL) which very comparable to the interactions between gentamicin and the proteins (− 4.9 kcal/mol and − -4.3 kcal respectively).