Synthesis, Spectroscopic and Crystal Structures, Hirshfeld Surface Analysis, and DNA Interaction Properties with Modelling Studies of a Novel Hydrazone–Oxime Ligand

Abstract

The title compound, a novel hydrazone-oxime ligand, was synthesized through the condensation of p-methoxyisonitrosophenylhydrazine and 5-acetyl-1,3-dimethylbarbituric acid. Spectroscopic techniques and single crystal X-ray crystallography confirmed its (─C─NH) tautomeric form and monoclinic structure with a P21/n space group. Centrosymmetric dimers stabilized by C─H⋯O and O─H⋯O hydrogen bonds formed a 3D supramolecular architecture. Hirshfeld surface analysis identified H⋯H and H⋯O/O⋯H interactions as key contributors to crystal packing, emphasizing hydrogen bonding and van der Waals forces. The ligand showed strong DNA-binding affinity, primarily through groove binding, as evidenced by hypochromic shifts in UV–vis spectroscopy upon interaction with CT-DNA. Competitive binding experiments with groove binders DAPI and methyl green confirmed preferential binding to the DNA minor groove. Molecular docking studies supported these findings, revealing the ligand's minor groove binding stabilized by hydrogen bonds, with a calculated binding energy of −8.343 kcal/mol. DNA cleavage assays showed efficient cleavage under oxidative and hydrolytic conditions, analyzed through agarose gel electrophoresis. Radical scavenging studies highlighted the involvement of oxidative radicals and hydroxyl species in the cleavage mechanism. These findings suggest the ligand's potential for applications in DNA-targeted therapeutic and diagnostic research.