Synthesis of novel keto-bromothymol blue in different media using oxidation–reduction reactions: combined experimental and DFT-TDDFT computational studies

Study of the structural characteristics, optical properties, and electrical conductivity of doped [P(An-MMa)/ZrO2]TF nanofiber composite using experimental data and TD-DFT/DMol3 computations

The powder form of the new nanofiber composite of poly(acrylonitrile-co-methylmethacrylate) (P(An-MMa)) with zirconium dioxide (ZrO2) was synthesized using the sol-gel method and subsequently converted to a thin film [P(An-MMa)/ZrO2]TF via the physical vapor deposition (PVD) technique. Numerous characterization techniques, including Raman spectroscopy, X-ray diffraction (XRD), thermogravimetric analysis (TGA), scanning electron microscopy (SEM), and ultraviolet-visible (UV-Vis) optical spectroscopy, were used to characterize [P(An-MMa)/ZrO2]TF. Additionally, using density functional theory (DFT), optimization via time-dependent density functional theory (TD-DFT/DMol3) and Cambridge Serial Total Energy Bundle (TD-DFT/CASTEP) was developed. The TD-DFT calculations accurately matched the observed XRD and Raman spectra and validated the molecular structure of the examined materials. The average crystallite size of [P(An-MMa)/ZrO2]TF, as determined by XRD calculations, is 171.04 nm. The SEM image depicts a one-dimensional morphological structure made up of tightly packed fibrous nanowires or brushes. The optical properties of the films were determined using optical absorbance spectrophotometric results in the 200-850-nm wavelength range. The optical energy bandgaps computed using Tauc's equation for [P(An-MMa)/ZrO2]TF are 2.352 and 2.253 eV, respectively, whereas the isolated molecule of the composite [P(An-MMa)/ZrO2]Iso has a bandgap of 2.415 eV as determined by TD-DFT/DMol3. The optical characteristics predicted by CASTEP in TD-DFT are in good agreement with the experimental values. The investigated large optical energy bandgap nanofiber composite is advantageous for some energy storage applications.

Computational drug design of novel COVID-19 inhibitor

BACKGROUND

In 2003, the first case of severe acute respiratory syndrome coronavirus (SARS-CoV) was recorded. Coronaviruses (CoVs) have caused a major outbreak of human fatal pneumonia. Currently, there is no specific drug or treatment for diseases caused by SARS CoV 2. Computational approach that adopts dynamic models is widely accepted as indispensable tool in drug design but yet to be exploited in covid-19 in Zaria, Nigeria. In this study, steps were taken to advance on the successful achievements in the field of covid-19 drug, with the aid of in silico drug design technique, to create novel inhibitor drug candidates with better activity. In this study, one thousand human immunodeficiency virus (HIV1) antiviral chemical compounds from www.bindingBD.org were docked on the SARS CoV 2 main protease protein data bank identification number 6XBH (PDB ID: 6XBH) and the molecular docking score were ranked in order to identify the compounds with the highest inhibitory effects, and easy selection for future studies.

RESULTS

The docking studies showed some interesting results. Inhibitors with Index numbers 331, 741, and 819 had the highest binding affinity. Similarly, inhibitors with Index number 441, 847, and 46 had the lowest hydrogen bond energy. Inhibitor with index number 331 was reported with the lowest value (- 48.38kCal/mol). Five new compounds were designed from the selected six (6) compounds with the best binding score giving a total of thirty (30) novel compounds. The low binding energy of inhibitor with index no. 847b is unique, as most of the interaction energies are of H-bond type with amino acids (Thr26, Gly143, Ser144, Cys145, Glu166, Gln189, Hie164, Met49, Thr26, Thr25, Thr190, Asn142, Met165) resulting in an overall negative value (-16.31 kCal/mol) making it the best of all the newly designed inhibitors.

CONCLUSIONS

The novel inhibitor is 2-(2-(5-amino-2-((((3-aminobenzyl)oxy)carbonyl)amino)-5-oxopentanamido)-4-(2-(tert-butyl)-4-oxo-4-(pentan-3-ylamino) butanamido)-3-hydroxybutyl) benzoic acid. The improvement it has over the parent inhibitor is from the primary amine group attached to meta position of first benzene ring and the carboxyl group attached to the ortho position of the second benzene ring. The molecular dynamics studies also show that the novel inhibitor remains stable after the study. This result makes it a better drug candidate against SARS CoV 2 main protease when compared with the co-crystallized inhibitor or any of the 1000 docked inhibitors.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1186/s42269-022-00892-z.

Kinetics and Mechanism Studies of Oxidation of Dibromothymolsulfonphthalein Toxic Dye by Potassium Permanganate in Neutral Media with the Synthesis of 2-Bromo-6-isopropyl-3-methyl-cyclohexa-2,5-dienone

The oxidation of 3',3″-dibromothymolsulfonphthalein (DBTS) in neutral medium by potassium permanganate multi-equivalent oxidant has been studied spectrophotometrically. Pseudo-first-order plots showed inverted S-shape throughout the entire course of the reaction. The initial rates were found to be relatively fast in the early stages, followed by a decrease in the oxidation rates over longer time periods in the slow stage. Under pseudo-first-order conditions where [DBTS] ≫ 10 [MnO₄ ^-], the experimental results showed a first-order dependence in [MnO₄ ^-] and fractional-first-order kinetics in the [DBTS] concentration. The formation of 1:1 coordination intermediate complex prior to the rate-determining step was revealed kinetically. In addition, the intermediate species involving complexes of Mn(V) coordination has been detected. The oxidation product of DBTS was identified by Fourier transform infrared spectroscopy, ultraviolet-visible spectrophotometry, and gas chromatography-mass analysis. The obtained results indicated the formation of 2-bromo-6-isopropyl-3-methyl-cyclohexa-2,5-dienone as a derivative oxidation of DBTS.

Novel synthesis of antibacterial pyrone derivatives using kinetics and mechanism of oxidation of azithromycin by alkaline permanganate

Dimethylamino-2H-5-dihydropyrane-6-methyl-4-one (DADHP) is a novel antibacterial pyrones derivatives and potential pharmaceutical that was quantitatively synthesized by oxidizing azithromycin (AZ) antibiotic with potassium permanganate in an alkaline medium (pH > 12). The oxidation reaction was kinetically studied using spectrophotometric technique at ionic strength equal to 0.02 mol dm^-3. The redox reaction was discovered to have two separate stages that could be measured. The first stage was relatively fast and corresponding to the formation of coordination intermediate complexes involving blue hypomanganate (V) and/or green manganate (VI) transient species. Variable parameters like as the concentration of permanganate ion and AZ substrate, as well as pH and ionic strength, have been studied to see how they affect oxidation rates. The experimental results showed a first-order dependency in [MnO₄^-] and fractional first-order kinetics in each of [AZ] and alkali concentration under pseudo-first-order reaction conditions of [AZ] ≫ 10 [MnO₄^-]. The oxidation process was base-catalyzed, and the oxidation rates increased as the alkali concentration increased. The product was confirmed by Fourier Transform Infrared spectroscopy (FTIR), elemental analysis, condensation tests with 2,4-dinitrophenyl haydrazine and hydroxyl amine, and GC-Mass. The oxidation product obtained can be employed as interesting class of organic compounds with diverse chemical and pharmacological applications.