Theoretical Study of the Effects of Different Coordination Atoms (O/S/N) on Crystal Structure, Stability, and Protein/DNA Binding of Ni(II) Complexes with Pyridoxal-Semi, Thiosemi, and Isothiosemicarbazone Ligand Systems

• Published in: Inorganics 2024-09, Vol.12 (9), p.251
• Main Authors: Jevtovic, Violeta, Rakić, Aleksandra, Alshammari, Odeh A. O., Alhar, Munirah Sulaiman, Alenezi, Tahani, Rakic, Violeta, Dimić, Dušan
• Format: Article
• Language: English
• Subjects: Binding; Biological activity; Biomolecules; Cations; Chemical bonds; Coordination compounds; Crystal structure; DFT; DNA; DNA structure; Geometry; HSA; Human serum albumin; Hydrogen bonds; Ligands; Molecular docking; Nickel; nickel(II) complexes; Nitrates; Nitrogen; Protein structure; Proteins; QTAIM; Quantum theory; Serum albumin; Structural stability; Sulfur; Surface analysis (chemical); Transition metal compounds
• ISSN: 2304-6740; 2304-6740
• DOI: 10.3390/inorganics12090251

Nickel transition metal complexes have shown various biological activities that depend on the ligands and geometry. In this contribution, six Ni(II) nitrate complexes with pyridoxal-semi, thiosemi, and isothiosemicarbazone ligands were examined using theoretical chemistry methods. The structures of three previously reported complexes ([Ni(PLSC)(H2O)3]∙2NO3−, [Ni(PLTSC)2] ∙2NO3−∙H2O, and [Ni(PLITSC)(H2O)3]∙2NO3−) were investigated based on Hirshfeld surface analysis, and the most important stabilization interactions in the crystal structures were outlined. These structures were optimized at the B3LYP/6-311++G(d,p)(H,C,N,O,(S))/LanL2DZ(Ni) level of theory, and the applicability was checked by comparing theoretical and experimental bond lengths and angles. The same level of theory was applied for the optimization of three additional structures, ([Ni(PLSC)2]2+, [Ni(PLTSC)(H2O)3]2+, and [Ni(PLITSC)2]2+). The interactions between selected ligands and Ni(II) were examined using the Natural Bond Orbital (NBO) and Quantum Theory of Atoms in Molecules (QTAIM) approaches. Particular emphasis was placed on interactions between oxygen, sulfur, and nitrogen donor atoms and Ni(II). Human Serum Albumin (HSA) and the DNA-binding properties of these complex cations were assessed using molecular docking simulations. The presence of water molecules and various substituents in the thermodynamics of the processes was demonstrated. The results showed significant effects of structural parameters on the stability and reactivity towards important biomolecules.