Synthesis, crystal structure, Hirshfeld surface analysis and theoretical studies of an oxime-based ligand: DNA binding and docking studies of its novel Pd(II) complex

Abstract

A novel mononuclear orange palladium(II) complex, [PdCl(L)] (1), has been synthesized from an oxime-based Schiff base ligand, 3-[(2‑hydroxy-5‑methoxy-benzylidene)-hydrazono]-butan-2-one oxime (HL). The newly synthesized ligand has been comprehensively characterized by CHN microanalyses, 1H and 13C NMR, ESI-MS, FT-IR and UV–Vis spectroscopic methods. 1 has also been characterized by elemental analyses (CHN), FAB-MS, FT-IR, UV–Vis spectra and molar electrical conductivity measurements. Single crystal X-ray structural elucidation reveals that HL crystallizes in the monoclinic space group (P21/c). Powder X-ray diffraction (PXRD) on HL has also been performed to check the bulk purity of it. Hirshfeld Surface (HS) analysis on HL has also been undertaken to delve into the type, nature and relative contributions of various interactions leading to the stability of HL in its crystalline form. Geometry optimization through DFT based calculations shows that the Pd(II) centre in 1 is nested in a square-planar ‘NNOCl’ coordination chromophore. TD-DFT computations were also executed to augment the electronic spectra of both HL and 1. Photophysical studies have been carried out to decipher the DNA binding aspects of both HL and 1. The calculated binding constants as determined from Benesi-Hildebrand plots, employing the fluorescence spectral analyses for HL and 1, were found to be 2.0 × 103 and 1.8 × 103 M−1 respectively. The binding aspects of both HL and 1 have also been corroborated through circular dichroism (CD) spectroscopy. To have an insight into the mode of binding of both HL and 1 with CT-DNA, molecular docking analysis was also undertaken. A groove binding efficacy has been revealed both for HL and 1.