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(E)-4-((4-Bromobenzylidene) Amino)-N-(Pyrimidin-2-yl) Benzenesulfonamide from 4-Bromobenzaldehyde and Sulfadiazine, Synthesis, Spectral (FTIR, UV–Vis), Computational (DFT, HOMO–LUMO, MEP, NBO, NPA, ELF, LOL, RDG) and Molecular Docking Studies
Abstract
(E)-4-((4-bromobenzylidene) amino)-N-(pyrimidin-2-yl) benzenesulfonamide were synthesized with condensation of 4-bromobenzaldehyde and sulfadiazine (4BRDA). This compound characterized with FTIR and Electronic spectra in experimental part. The calculated part used for DFT mode and B3LYP with 6311++G(d,p) basic set. IR designed with B3LYP/6311++G(d,p) basic set, and UV–Vis spectra computed with TD-DFT (time-dependent density functional theory) mode with same basic set level, with IEFPCM solvation model and dimethyl sulfoxide used for solvent. ADME properties considered with Swiss ADME online tools. Molecular docking calculation calculated with patch-dock online server. The Multiwfn software used for compute the ELF, RDG and LOL.
In this research, a new Ag(I) complex, namely, [Ag(5‐chloro‐1H‐benzimidazole)2(NO3)], has been synthesized using the benzimidazole‐based ligand 5‐chloro‐1H‐benzimidazole (5ClBZ). Ag(I) complexes were characterized by elemental analysis, UV‐Vis, FT‐IR, and ¹H NMR spectroscopy, and DFT analysis was used. The free ligand and its Ag(I) complexes were tried for their biochemical properties, including antioxidant and antidiabetic properties. To study the molecular structures of the title compounds, in silico ADME/Tox research was performed on the newly made complex and free ligand. The empirical guidelines relating to ADME were utilized to conduct molecular docking simulations and in‐depth drug‐likeness profiling. This was carried out to validate the conclusions and identify exact binding interactions. Based on the study's findings, it has been determined that these new compounds have significant potential as powerful therapeutic agents for controlling antioxidant and antidiabetic activities.
The compound (E)‐1‐(4‐chlorophenyl)‐N‐(nitrophenyl)methanimine was synthesised and characterised using techniques FTIR, UV‐Vis, NMR and it was compared with the experimental and simulated methods. The compound prepared was optimized using the DFT method employing the basis set B3LYP / cc‐pVDZ. The simulated spectra appeared to be in accordance with the experimental one. The HOMO‐LUMO orbitals and MEP are calculated with the same basis set; the study is chiefly forcasted to the biological activity of the synthesized compound. The wave function regards like localized orbital locator, electron localized function, average localized ionization energy and non‐covalent interaction are also examined as a means of theoretical evidence of the titled compound. The NBO calculations probe the intermolecular and intramolecular movement of charges, and additionally the molecule's stability. The ADMET properties are also considered for the compound with the assistance of Swiss ADMET online tool. The molecular docking analysis was accomplished against the protein (3RW9) of Spermidine dehydrogenase inhibitor employing the software Auto‐dock.
Pyrroles are an exciting class of organic compounds with immense medicinal activities. This manuscript presents the structural and quantum mechanical studies of 1-(2-aminophenyl) pyrrole using X-Ray diffraction and various spectroscopic methods like Infra-Red, Raman, Ultra-violet and Fluorescence spectroscopy and its comparison with theoretical simulations. The single-crystal X-ray diffraction values and optimized geometry parameters also were within the agreeable range. A fully relaxed potential energy scan revealed the stability of the possible conformers of this molecule. We present the density functional theory results and assignment of the vibrational modes in the infrared spectrum. The experimental and scaled simulated vibrations matched when density functional theory simulations (B3LYP functional with 6–311++G∗∗). The electronic spectrum was simulated using time-dependent density functional theory with CAM-B3LYP functional in dimethylsulphoxide solvent. The fluorescence spectrum of the compound was studied at different excitation wavelengths in the dimethylsulphoxide solvent. The stability of the molecule by intramolecular electron transfer by hyperconjugation was studied with the natural bond orbital analysis. Frontier molecular orbitals and molecular electrostatic potentials of the compound gave an idea about the reactive behaviour of the compounds. Prediction of activity spectral studies followed by docking analysis indicated that the molecule is active against arylacetonitrilase inhibitor.
Two new Zn (II)‐dicyanamide (dca) 1‐D chain coordination polymers (CPs), [Zn (LOMe)(μ1‐dca)(μ1,5‐dca)]n(1) and [Zn (LOEt)(μ1‐dca)(μ1,5‐dca)]n(2) have been successfully synthesized from bicompartmental Schiff base ligands N,N′‐Bis(3‐methoxysalicylidenimino)‐1,3‐diaminopropane (H2LOMe), N,N′‐Bis(3‐ethoxysalicylidenimino)‐1,3‐diaminoproane (H2LOEt) respectively and structurally characterized using various spectroscopic protocols like ¹H NMR, IR, Raman, UV–Vis, fluorescence as well as elemental analysis, TGA, PXRD and SCXRD studies. X‐ray single crystal study revealed that both the complexes have two different geometrical arrangement of Zn metal centres with distorted square pyramidal Zn(2) and trigonal prismatic geometry Zn(1). Ab‐initio DFT (Density functional theory) has been executed at B3LYP (Becke, 3‐parameter, Lee‐Yang‐Parr) using DGDVP (Diffuse gradient double valence polarised) basis set to explain FMO (Frontier molecular orbital), TD‐DFT (Time‐dependent density functional theory) and photovoltaic efficiency in Dye Sensitized Solar Cell (DSSC). Hirshfeld surface (HS) and 2D fingerprint plot analyses are shed more light on the non‐covalent supramolecular interactions. The steady state and time‐resolved fluorescence measurements have been conducted in DMSO and solid‐state. CPs exhibited bi‐exponential decay in DMSO as well as solid‐state where fluorescence behaviors are mainly intra‐ligand (π → π*) in nature with lifetimes in the range (1.11–1.06 ns). In particular, in vitro cytotoxic activities were evaluated towards MCF7 (breast cancer) cell line, MDA‐MB‐231 (breast carcinoma) cell line and MCF10A (breast epithelial) cell line using MTT assay. CP1 had lower cytotoxic effect against MCF7 (20 μM), MDA‐MB‐231 (15 μM) cell lines in comparison with cisplatin (42.2 ± 8, 128.2 ± 7 μM). CP1 induced classical cell death apoptosis, autophagy and necrosis. Lower IC50 value of CP1 against MDA‐MB‐231 cell line provide new insights in the development of cancer therapeutics.
Highlights
• Two new Zn(II)‐dicyanamide CPs were synthesized and characterized
• X‐ray Crystal structures of Zn(II)‐CPs were determined
• DFT, TD‐DFT and luminescence behaviors have been explored
• Zn(II)‐CPs show noteworthy cytotoxic activity against breast cancer cell lines
• Apoptosis, autophagy and necrosis type classical cell death phenomenon was explained
A fluoro-based Schiff base (E)-2-fluoro-N′-(1-(4-nitrophenyl)ethylidene)benzohydrazide (FNEB) has been synthesized from condensation of 2-fluorobenzohydrazide and 4′-nitroacetophenone catalyzed by glacial acetic acid with ethanol as the solvent. The dipole moment of FNEB in both the electronic states were found using different solvatochromic approaches such as Lippert-Mataga, Bakhshiev, Kawski-Chamma-Viallet, Reichardt and Bilot-Kawski. The experimental ground state dipole moment of FNEB was calculated using Guggenheim-Debye method and theoretical ground state dipole moment using Bilot-Kawski solvatochromic approach. The solvatochromic behavior of the Schiff base in different solvents was studied using absorption and emission spectra. Catalan and Kamlet-Abboud-Taft parameters were used from the multiple linear regression (MLR) analysis in order to study the solute-solvent interaction. The dipole moments were also calculated using Time Dependent-Density Functional Theory (TD-DFT). The chemical stability of FNEB was determined using computational and Cyclic Voltammetry by the use of obtained energy gap between the frontier orbitals. Using the frontier orbitals energy gap, global reactivity parameters were computed. Further, Light Harvesting efficiency was determined to comprehend the photovoltaic property of the Schiff base.
1,1-Dimethyl-3-phenylurea (known as fenuron) which is a phenyl urea-based widely used herbicide exhibits interesting structural and conformational properties and a notable biological activity. A detailed analysis on the vibrational, molecular and electronic characteristics of fenuron has been carried out. Potential energy scans (PESs) performed at the B3LYP/6-311++G(d,p) level of theory predicted two possible minima corresponding to the optimized anti and synforms resulting from the internal rotation about the N-C bond. The presence of an auxochrome together with the interaction with DMSO solvent exhibited a blue shift corresponding to the C=O orbitals. Delocalization of HOMO and LUMO orbital facilitated the charge transfer effect in the molecule. The calculated HOMO-LUMO energies, chemical potential, energy gap and global hardness suggested a low softness value for the compound while its biological activity was described by the value of electrophilicity. Chlorine substitution in the phenyl ring influenced the orbital delocalization for ortho and para substitutions but that of meta remained unaffected. NLO properties were noticed to increase due to chlorine substitution in the parent molecule. The docking results suggested that the compound exhibits an inhibitory activity against mitochondrial ubiquinol-cytochrome-c reductase and can be developed as a potential anticancer agent. Keywords: Organic chemistry, Pharmaceutical chemistry, Theoretical chemistry, DFT, Fenuron, Molecular docking, NBO, NLO
The quantum chemical calculation of 9-methylanthracene and 2,3-dimethylanthracene molecules were carried out (9MA and 23DMA). The Density Functional Theory (DFT) by the method RB3LYP with the basis set of 6-311 + G(d) were performed. The Fourier Transform Infra Red (FTIR) spectrum and FT-Raman spectrum of the compounds were recorded in the region 4000–400 cm⁻¹ and 4000–50 cm⁻¹, respectively. The theoretical frequencies were scaled down and compared with experimental FT-IR and FT-Raman spectral values and they agree well. The Natural Bond analysis is performed to gauge the Lewis structure of the molecule. The first order hyperpolarizability values were calculated from the Non-Linear Optical (NLO) studies of the title molecules and compared with standard reference value of Urea. The molecular electrostatic potential surface is obtained and used to get the nucleophilic and electrophilic sites. The molecular docking study for title compound indicates anti cancer properties. Molecules show excellent Light Harvesting Efficiency, hence can be used in DSSC’s.
In the drug development process, the selection of potential drug candidate molecules, by virtual screening, often depend on computation intensive methods. The processing objectives mainly focus on the classification, structure analysis and segregation of molecules using numerical data. In this direction, a screening strategy is designed which makes use of the numerical data derived from the geometry of the molecular structures and with a data mining algorithm called Support Vector Machine (SVM).For implementing the algorithm, Radial basis function and Neural kernels are used to predict the possibility of drug like characteristics in the test molecules. The results of the prediction experiment have been compared with the predictions made by Drug Mint, a web server tool
Three cocrystals of pyrazinamide (PYZ) with 2,4-dihydroxy benzoic acid (2,4HBA-PYZ), 2,6-dihydroxybenzoic acid (2,6HBA-PYZ) and 3,5-dihydroxybenzoic acid (3,5HBA-PYZ) are investigated by computational simulations. DFT calculations have been performed in order to understand the reactive properties of molecules that constitute the cocrystals. These calculations were followed by symmetry-adapted perturbation theory (SAPT) simulations to understand the interactions between molecules of the studied cocrystals. Molecular Dynamics (MD) simulations helped us to identify possible excipient substances. The ring vibrational modes have small variations during the cocrystal formation, while changes were observed in the peaks of the associated functional groups. Most reactive sites are identified by MEP maps. From the DFT analysis, we found that N–H⋯N intra molecular hydrogen between the N atom of pyrazine and H–N of amide produces conformational rigidity in the pyrazine ring in the co-crystal assembly of 2,4HBA-PYZ and 2,6HBA-PYZ but not for 3,5HBA-PYZ. The polarization nature of the functional groups was predicted by VCD spectra. Molecular docking results imply that the cocrystals might exhibit inhibitory activity against mycobacterium tuberculosis type II and against methylenetetrahydrofolate reductase and can be formulated as new anti-TB drug. The system showed fairly good light harvesting efficiency (LHE); hence, could be used in photovoltaic systems for energy conversion. Among the three cocrystal systems 2,4HBA-PYZ is a better candidate to be used in DSSC’s.
Quantum chemical density functional theory approach (DFT) and vibrational spectroscopy investigation were done on one of the benzimidazole derivatives called 6-Aminobenzimidazole (6ABM). The B3LYP method and 6–311++G (d,p) basis set were used to get the optimized structure, vibrational frequencies, and other various parameters. Atoms in molecules theory were employed to find the binding energies, ellipticity and isosurface projection by electron localization function. The various functional groups are identified using FT-IR, FT-Raman and NMR spectra and compared with the scaled value of simulated spectra. The donor and acceptor interactions are studied by NBO analysis. The reactive areas of the molecule are obtained by molecular electrostatic potential (MEP) and Fukui functions. By using the UV–Vis spectrum the maximum absorption wavelength was obtained and compared with TD-DFT/PCM method with different solvents. The biological studies like drug-likeness and molecular docking are carried out on the molecule.
Theoretical calculations were done using density functional theory in order to determine vibrational frequencies, infrared and Raman intensities, MEP, NLO and NBO properties of the Hydrochlorothiazide-isoniazid (HCTA-IN) and Hydrochlorothiazide-malonamide (HCTA-MA) cocrystals. Electron donor-acceptor due to charge transfer mechanism has been scrutinized by the NBO investigation. First order hyperpolarizability of HCTA-IN and HCTA-MA are 19.86 and 7.80 times that of urea. The downshift of NH2, NH and CO modes are due to strong hyper conjugative interactions are indicated in NBO analysis. TD-DFT analysis was used to generate the theoretical electronic spectra, which shows a charge transfer process between the thiazide and isoniazid in HCTA-IN complex. Light harvesting efficiency studies reveal efficient photosensitization potential and photochemical modeling proves the efficiency of the cocrystal to be used in dye sensitized solar cells. Title compounds are docked with glucocorticoid receptor (1NHZ) and peroxidase manganese-dependent I (1YYD).