Theoretical and experimental studies of newly synthesized (Z)-4-(2-(3,5-dibromo-2-hydroxy-4-methoxybenzylidene)hydrazinyl)benzonitrile compound

Design, synthesis and spectroscopic and structural characterization of novel N-(2-hydroxy-5-methylphenyl)-2,3-dimethoxybenzamide: DFT, Hirshfeld surface analysis, antimicrobial activity, molecular docking and toxicology

The novel compound N-(2-hydroxy-5-methylphenyl)-2,3-dimethoxybenzamide, C16H17NO4, I, was prepared by a two-step reaction and then characterized by elemental analysis and X-ray diffraction (XRD) methods. Moreover, its spectroscopic properties were investigated by FT–IR and 1H and 13C NMR. Compound I crystallized in the monoclinic space group P21/c and the molecular geometry is not planar, being divided into three planar regions. Supramolecular structures are formed by connecting units via hydrogen bonds. The ground-state molecular structure of I was optimized by the DFT-B3LYP/6-31G(d,p) method and the theoretical structure was compared with that obtained by X-ray diffraction. Intermolecular interactions in the crystal network were studied by two-dimensional (2D) and three-dimensional (3D) Hirshfeld analyses. The calculated electronic transition results were examined and the molecular electrostatic potentials (MEPs) were also determined. The in vitro antimicrobial activities of I against three Gram-positive bacteria, three Gram-negative bacteria and two fungi were determined. The compound was compared with several control drugs and showed better activity than the amoxicillin standard against Gram-positive bacteria B. subtilis, S. aureus and E. faecalis, and Gram-negative bacteria E. coli, K. pneumoniae and P. aeruginosa. The density functional theory (DFT)-optimized structure of the small molecule was used to perform molecular docking studies with proteins from experimentally studied bacterial and fungal organisms using AutoDock to determine the most preferred binding mode of the ligand within the protein cavity. A druglikeness assay and ADME (absorption, distribution, metabolism and excretion) and toxicology studies were carried out and predict a good drug-like character.

Vibrational spectroscopy and DFT analysis of 4-cyanophenylhydrazine: A potential SERS probe

4-Cyanophenylhydrazine (4-CPH) is an organic synthesis intermediate. To date, several products derived from 4-CPH have been well studied; however, 4-CPH itself has not been extensively investigated. Herein, we performed vibrational and theoretical analyses of 4-CPH. Density functional theory (DFT) calculations were applied to predict the IR and Raman spectra of 4-CPH, which were compared with the experimental spectra. The calculated and experimental spectral results were in good agreement, except for an abnormal transformation of the protonated 4-CPH cyano group (C≡N), which was observed in the theoretical IR spectrum. Several wavefunction analyses revealed that this transformation was due to the protonation-induced depolarization of the molecule. Moreover, we verified the applicability of 4-CPH as a probe for surface-enhanced Raman spectroscopy (SERS). We observed a pH-dependent shift in the cyano bond frequency within the silent region and determined, as a novel discovery, that this shift was induced by 4-CPH protonation. Our results provide considerable, fundamental information that confirms the potential of 4-CPH as a SERS probe.

Synthesis, structural, spectral and antimicrobial activity studies of copper-nalidixic acid complex with 1,10-phenanthroline: DFT and molecular docking

The mix-ligand coordination compound, [Cu(Nal)(Phen)(H₂O)].(Phen).ClO₄.(H₂O)₂ (Nal= Monoanion of nalidixic acid and Phen = 1,10- Phenanthroline), was investigated by focusing on its supramolecular architecture. Structural properties of the complex were characterized by XRD, spectroscopic methods and elemental analysis. The complex has crystallized in the triclinic crystal system and P-1 space group. In the structure where the Cu (II) ion is in the center of symmetry, nalidixate anion and water molecule coordinated to Cu (II) metal through oxygen atoms while phen coordinated through nitrogen atoms. The monomer units are connected by hydrogen bonds to form supramolecular structures. The ground state molecular structure of the complex was optimized using DFT/B3LYP/LANL2DZ method, and compared with experimental X-ray geometry. The FT-IR study of the complex was carried out in the middle IR region focusing on the characteristic vibrations of the free ligands and the complex. Scaled calculated vibrational frequencies are compared with experimental values. The magnetic properties of the complex were investigated by electron paramagnetic resonance (EPR) spectroscopy. Further ultra-violet (UV)-visible spectral analysis was also performed to understand optical properties. The experimental UV-Vis data were associated with the calculated frontier molecular orbitals HOMO/LUMO and, molecular electrostatic potentials (MEP) are also investigated. Biological study of the complex against Bacillus subtilis, Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Klebsiella pneumoniae, and Candida albicans showed very strong antibacterial activity with MIC values ranging from 128 μg/ml to 1 μg/ml concentration. The optimized complex is docked to the DNA Gyrase (3LPX) and gyrase tip IIA topoisomerase (3UC1).