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New complexes of Ni(II) and Pd(II) with Schiff base ligand derived from 5-nitro isatin with 4-phenyl-3-thiosemicarbazide have been synthesized in absolute ethanol. The isolated solid compounds have been characterized by elemental analyses and spectral (FT-IR, ¹H NMR and UV-Vis) measurements. The Schiff base ligand has been further characterized by single-crystal XRD. It has been found that the Schiff base ligand behaves as a tridentate ligand forming chelates with 1:2 (metal:ligand) in the case of Ni-complex and 1:1 (metal:ligand) in the case of Pd-complex. Octahedral geometry has been suggested for the Ni(II) chelate while square-planar geometry has been suggested for the Pd(II) chelate. The supramolecular structure of the thiosemicarbazide is controlled by large number of short intermolecular contacts such as O...H, H...H, C...C, S...C, S...H, S...N, H...C, N...O and C...O interactions where the most dominant contacts are H...H, H...C, C...C, O...H and S...H interactions. The optimized molecular geometry calculated at B3LYP/6-31G(d,p) level agreed very well with the reported X-ray structure. The two bands observed at 434 and 250 nm in the UV-Vis spectrum of the compound in DMSO as solvent have been calculated using TD-DFT method at 430.9 nm (f = 0.1178) and 257.2 nm (f = 0.387), respectively. These bands have been assigned to HOMO→LUMO (96%) and HOMO→LUMO+2 (90%) excitations which belong to n-π* and π-π* transitions, respectively. All the synthesized compounds have been tested against supercoiled pBR322 DNA. These compounds have been found to promote the cleavage of plasmid DNA in the presence of H2O2. The molecular docking of the ligand and its metal complexes refer to groove binding toward the DNA with high docking score of Ni(II) complex rather than the corresponding ligand and Pd(II) complex. [ABSTRACT FROM AUTHOR]