DFT calculations, spectroscopy and antioxidant activity studies on (E)-2-nitro-4-[(phenylimino)methyl]phenol

Synthesis, DFT study, theoretical and experimental spectroscopy of fatty amides based on extra-virgin olive oil and their antibacterial activity

Medication products from natural materials are preferred due to their minimal side effects. Extra-virgin olive oil (EVOO) is a highly acclaimed Mediterranean diet and a common source of lipids that lowers morbidity and disease severity. This study synthesised two fatty amides from EVOO: hydroxamic fatty acids (FHA) and fatty hydrazide hydrate (FHH). The Density Functional Theory (DFT) was applied to quantum mechanics computation. Nuclear magnetic resonance (NMR), Fourier transforms infrared (FTIR), and element analysis were used to characterise fatty amides. Likewise, the minimum inhibitory concentration (MIC) and timing kill assay were determined. The results revealed that 82 % for FHA and 80 % for FHH conversion were achieved. The amidation reagent/EVOO ratio (mmol: mmol) was 7:1, using the reaction time of 12 h and hexane as an organic solvent. The results further revealed that fatty amides have high antibacterial activity with low concentration at 0.04 μg/mL during eight h of FHA and 0.3 μg/mL during ten h of FHH. This research inferred that FHA and FHH could provide an alternative and effective therapeutic strategy for bacterial diseases. Current findings could provide the basis for the modernisation/introduction of novel and more effective antibacterial drugs derived from natural products.

Molecular structure determination, spectroscopic, quantum computational studies and molecular docking of 4-(E)-[2-(benzylamino)phenylimino) methyl-2]ethoxy phenol

A Schiff base compound 4-(E)-[2-(benzylamino)phenylimino)methyl-2]ethoxy phenol (4BPM2EP) was synthesized and spectroscopic characterization was performed using experimental methods such as FT-IR, FT-Raman and UV-Vis spectroscopy. Density functional theory (DFT/B3LYP/6-311++G(d,p)) computation was used to investigate the optimized molecular geometry, harmonic vibrational wavenumber, NMR chemical shifts, natural bond orbital (NBO) analysis, non-linear optical (NLO) properties, molecular electrostatic potential (MEP) map and Mulliken atomic charges of 4BPM2EP molecule. TD-DFT calculations have been carried out on the optimized geometry at gaseous phase, DMSO and ethanol to further understand the electronic transitions and solvents effect on the UV-Vis spectra of the compound. The assignments of vibrational modes were performed on the basis of total energy distribution (TED) using VEDA 4 program and were compared with experimental data. Molecular docking study was performed using Glide program to establish the information about the interactions between the topoisomerase DNA gyrase enzymes and the novel compound in order to explore the biological behaviour of the examined compound. The compound screened against four pathogens two gram positive, two gram negative and two fungal strains had shown good anti-bacterial and antifungal behaviour. Furthermore the compound was subjected to in-silico ADMET studies.Communicated by Ramaswamy H. Sarma.

Density functional theory studies of the antioxidants-a review

The following review article attempts to compare the antioxidant activity of the compounds. For this purpose, density functional theory/Becke three-parameter Lee-Yang-Parr (DFT/B3LYP) methodology was carried out instead of using pharmacological methodologies because of economic benefits and high accuracy. This methodology filtrates the compounds with the lowest antioxidant activity. At first, the Koopmans' theorem was carried out to calculate some descriptors to compare antioxidants. The energy of the highest occupied molecular orbitals (HOMO) was accepted as the best indicator, and then some studies confirmed that the highest occupied molecular orbital/lowest unoccupied molecular orbital (HOMO-LUMO) energy gap is the more precise descriptor. Although it would be better to compare spin density distribution (SDD) on the oxygen of the corresponding radical in the polarizable continuum model (PCM) to evaluate their capability to chain reaction inhibition. Next, it was mentioned that in the multi-target directed ligands (MTDLs), the antioxidant is connected to other moieties in para positions to create better antioxidants or novel hybrid compounds. Indeed, SDD was introduced as a descriptor for MTDL antioxidant effectiveness. Then, the relation between antioxidants and aromaticity was investigated. The more the aromaticity of an antioxidant, the more stable the corresponding radical is. Subsequently, in preferred antioxidant activity, it was defined that the hydrogen atom transfer (HAT) mechanism is more favored in metabolism phase I. It has been seen that the solvent model can change the antioxidant mechanism. Therefore, the solvent model is more important than the chemical structure of antioxidants, and an ideal antioxidant should be evaluated in PCM for pharmacological evaluations.

Synthesis, antioxidant activity, and density functional theory study of some novel 4-[(benzo[d]thiazol-2-ylimino)methyl]phenol derivatives: a comparative approach for the explanation of their radical scavenging activities

Background and purpose:

Radicals produced by Fenton and Haber-Weiss reactions play detrimental roles in our body. Some oxidized proteins as toxic configurations are identified in amyloid-β deposits. These deposits mostly occur in conditions, such as Alzheimer’s disease. Here, we report the synthesis, evaluation of the antioxidant activity, and implementation of density functional theory (DFT) calculations of some4- [(benzo[d]thiazol-2-ylimino) methyl]phenol derivatives. The aim of this study was to provide a comparative theoretical-experimental approach to explain the antioxidant activities of the compounds.

Experimental approach:

Compounds were synthesized by the reaction between para hydroxybenzaldehyde and aminobenzothiazole derivatives. The scavenging activity of the compounds was evaluated. Various electronic and energetic descriptors such as high occupied molecular orbital and low unoccupied molecular orbital energy gaps, bonding dissociation enthalpy of OH bond, ionization potential, electron affinity, hardness, softness, and spin density of the radical and neutral species were calculated. DFT calculations with B3LYP hybrid functional and 6-311++ G** basis set in the polarizable continuum model were utilized to obtain these descriptors.

Findings/Results:

Ascorbic acid showed the best DPPH scavenging activity. However, 4d and 4c showed promising antioxidant activity. The values of EHOMO for 4c and 4d were closer to zero, thus, they showed the best scavenging activities. The computational results were in accordance with the experimental ones. The energetic descriptors indicated that the sequential proton loss-electron transfer mechanism is preferred over other mechanisms.

Conclusion and implication:

Antioxidant activity of 4-[(Benzo[d]thiazol-2-ylimino) methyl]phenol derivatives confirmed by experimental and theoretical documents proves them as novel antioxidants against amyloid-β based disease.

Crystal, spectroscopic and quantum mechanics studies of Schiff bases derived from 4-nitrocinnamaldehyde

Two Schiff bases, (E)-1-(4-methoxyphenyl)-N-((E)-3-(4-nitrophenyl)allylidene)methanamine (compound 1) and (E)-N-((E)-3-(4-nitrophenyl)allylidene)-2-phenylethanamine (compound 2) have been synthesized and characterized using spectroscopic methods; time of flight MS, ¹H and ¹³C NMR, FT-IR, UV-VIS, photoluminescence and crystallographic methods. The structural and electronic properties of compounds 1 and 2 in the ground state were also examined using the DFT/B3LYP functional and 6-31 + G(d,p) basis set, while the electronic transitions for excited state calculations were carried out using the TD-DFT/6-31 + G(d,p) method. The Schiff base compounds, 1 and 2 crystallized in a monoclinic crystal system and the P2₁/c space group. The emission spectra of the compounds are attributed to conjugated π-bond interaction while the influence of the intra-ligand charge transfer resulted in a broad shoulder for 1 and a double emission peak for 2. The calculated transitions at 450 and 369 nm for 1 and 2 respectively are in reasonable agreement with the experimental results. The higher values of dipole moment, linear polarizability and first hyperpolarizability of 1, suggest a better optical property and better candidate for the development of nonlinear optical (NLO) materials.

Synthesis, structural, spectral, antioxidant, bioactivity and molecular docking investigations of a novel triazole derivative

The structural, spectroscopic and electronic properties of 4-(4-nitrophenyl)-5-(pyridin-3-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione have been analyzed by using single crystal X-ray diffraction (SCXRD), ¹H and ¹³C NMR chemical shifts and FT-IR spectroscopic methods both theoretically and experimentally. The tautomeric (thiol and thione) energetic analysis results, structural optimization parameters (bond lengths and angles), vibrational wavenumbers, proton and carbon NMR chemical shifts, UV-Vis. parameters, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) analyses and Molecular Electrostatic Potential (MEP) surface have been calculated by using DFT/B3LYP quantum chemical method with 6-311++G(2d,2p) basis set to compare with the experimental results. The computed geometry parameters, vibrational wavenumbers, and NMR chemical shifts have been in good agreement with the experimental results. It should be noted that the radical scavenging activities of the title compound have been evaluated by using different test methods i.e. 2,2-Diphenyl-1-picrylhydrazyl (DPPH), N,N-dimethyl-p-phenylenediamine (DMPD) and 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS). According to obtained results, the title compound displayed DPPH (SC₅₀ 19.42 ± 0.11 μg/mL), DMPD (SC₅₀ 21.13 ± 0.08 μg/mL) and ABTS (SC₅₀ 38.17 ± 0.25 μg/mL) scavenging activities. Also, these results have been compared with Butylated hydroxyanisole (BHA), Rutin (RUT) and Trolox (TRO) used as standard compounds. The physicochemical, pharmacokinetic, and toxicity features of the compound have been determined by using drug-likeness and in silico ADMET investigations. The interaction results with SARS-CoV-2 main protease (M^pro) of the title ligand compound have been analyzed via the help of molecular docking study.Communicated by Ramaswamy H. Sarma.

Experimental (FT-IR, Laser-Raman and NMR) and theoretical comparative study on 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile, a potential bioactive agent

In this paper, the experimental and theoretical vibrational frequencies of a potential bioactive pyrimidine derivative molecule named 2-benzylsulfanyl-4-pentyl-6-(phenylsulfanyl)pyrimidine-5-carbonitrile has been investigated. The experimental FT-IR and Laser-Raman spectra of the studied molecule are in the region (4000–400[Formula: see text]cm[Formula: see text] and (4000–100[Formula: see text]cm[Formula: see text], respectively, in gas phase. The vibrational modes and optimized ideal structure parameters(bond lengths, bond angles and selected dihedral angles) were calculated by using DFT/B3LYP, DFT/BHandHLYP and DFT/PBE1PBE methods with 6-311[Formula: see text]G(d,p) basis set. The theoretical mode assignments have been obtained by using potential energy distribution (PED) with the VEDA4 software program. Additionally, infrared and Raman intensities, the highest occupied molecular orbital (HOMO), the lowest unoccupied molecular orbital (LUMO) energies and their clouds, and other related molecular properties were calculated and evaluated. The proton (1H) and carbon-13 ([Formula: see text]C) nuclear magnetic resonance (NMR) chemical shifts have been investigated for the title molecule, both experimentally (in DMSO-d[Formula: see text] and theoretically (in vacuum and DMSO). The thermodynamic properties of the tile compound have been investigated using the mentioned theoretical computational methods. The results revealed that there isgood agreement between experimental and theoretical results and these results have supported the related literature.

A comparison of the antioxidant activities and biomonitoring of heavy metals by pollen in the urban environments

Pollen is one of the most valuable nutrients due to its content and antioxidant activity. In this study, its botanic origin, total phenol content (TPC), total flavonoid content (TFC), the hydrogen peroxide scavenging activity (HPSA) (in terms of SC₅₀), ferric reducing antioxidant power capacity (FRAP), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity (in terms of SC₅₀), metal-chelating activity (MCA) (%), and heavy metal content were examined to determine the quality of pollen that has been collected from seven different cities of Turkey. According to the melissopalynological analysis, the botanic origin of samples is six uni-flora and one multiflora. The TPC, TFC, HPSA, FRAP, DPPH, and MCA were found between 1360.70-2981.34 mg GAE/100 g, 74.23-111.74 mg CAE/100 g, 25.56-30.28 μg/mL, 71.92-73.86%, 52.26-53.27 μg/mL, and 43.97-65.21%, respectively. When obtained results compared to the standards (Butylated Hydroxy Anisole (BHA), Butylated Hydroxy Toluene (BHT) and α-Tocopherol (TOC)), pollen samples showed the effective antioxidant properties with respect to HPSA, FRAP, and DPPH radical scavenging activity. In addition, it was observed that honey samples were being contaminated with most of the metals to some extent (Al, Cr, Mn, Fe, Ni, Cu, Zn, B, As, Te, U), while some heavy metals (Co, Cd, V, Ga, and Ag) were never determined in all samples. However, Pb was determined only in sample 2 and sample 4, Mo in sample 1 and sample 2. According to meteorological parameters, samples 3, 4, and 5 were distinguished from the other samples. Finally, the data indicate that pollen could be affected by environmental pollutions.

Protective effect of gigantol against hydrogen peroxide‑induced apoptosis in rat bone marrow mesenchymal stem cells through the PI3K/Akt pathway

Bone marrow mesenchymal stem cell (BMSC) transplants are promising for the treatment of certain central nervous system diseases. However, oxidative stress is one of the major factors that may limit the survival of the transplanted BMSCs. The present study investigated the effect of pretreatment with gigantol on hydrogen peroxide (H2O2)‑induced apoptosis in rat BMSCs (rBMSCs) and the potential underlying mechanisms. The results demonstrated that gigantol pretreatment significantly inhibited H2O2‑induced apoptosis of rBMSCs. rBMSCs were incubated with 600 µM H2O2 in the absence or presence of different doses of gigantol (1‑100 µM). Cell viability and apoptosis ratios were assessed by MTT assays and flow cytometry, respectively. Morphological alterations and reactive oxygen species were measured by the fluorescent‑based methods of Hoechst staining and dichlorodihydrofluorescein diacetate, respectively. Furthermore, the protein levels of phosphorylated‑protein kinase B (Akt), B‑cell lymphoma‑2 (Bcl‑2), Bcl‑2‑associated X (Bax), caspase‑3 and caspase‑9 were investigated by western blotting. Following incubation with H2O2 for 2 h, gigantol significantly inhibited the H2O2‑induced reductions in the cell viability of rBMSCs in a dose‑dependent manner. Furthermore, gigantol upregulated Akt phosphorylation and Bcl‑2 expression, downregulated Bax expression, and reduced the expression of caspase‑3 and caspase‑9 in H2O2‑treated rBMSCs, whereas an opposite effect was detected when LY294002, an inhibitor of phosphatidylinositol 3‑kinase, was administered in combination with gigantol. These results indicate that gigantol may be developed as a promising neuroprotective agent for successful MSC transplantation in ischemic diseases.

Experimental (FT-IR, Laser-Raman and NMR) and theoretical spectroscopic analysis of 3-[(N-methylanilino)methyl]-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3H)-thione

The structure of a potential bioactive agent namely, 3-[([Formula: see text]-methylanilino)methyl]-5-(thiophen-2-yl)-1,3,4-oxadiazole-2(3[Formula: see text]-thione was characterized by proton and carbon-13 nuclear magnetic resonance (NMR) chemical shifts, Fourier transform infrared (FT-IR) and Laser-Raman spectroscopic techniques. The quantum chemical computations of molecular structures (disorder I and disorder II forms), vibrational wavenumbers, carbon-13 and proton chemical shifts and UV-Vis spectroscopic parameters have been performed with DFT/B3LYP method at 6-311[Formula: see text]G(d,p) basis set. The highest occupied molecular orbital (HOMO), lowest unoccupied molecular orbital (LUMO), nonlinear optical (NLO) properties and natural bond orbital (NBO) analyses have been theoretically examined with the mentioned calculation level. The calculated values have been compared with the recorded experimental data. The computed molecular geometric parameters, vibrational wavenumbers, NMR chemical shifts, and UV-Vis wavelengths have been found to be in a good harmony with the experimental values and spectral results of similar structures in the literature. We believe that the work will be of considerable interest to anyone working in the area of theoretical chemistry, whether in industry or academics.

Optimization of Supercritical Fluid Extraction of Total Alkaloids, Peimisine, Peimine and Peiminine from the Bulb of Fritillaria thunbergii Miq, and Evaluation of Antioxidant Activities of the Extracts

Supercritical fluid extraction (SFE) was used to extract total alkaloids, peimisine, peimine and peiminine from the bulb of Fritillaria thunbergii Miq. The antioxidant capacity of the extracts was evaluated by DPPH radical scavenging activity (DPPH-RSA), ABTS radical scavenging activity (ABTS-RSA) and ferric reducing capacity (FRAP) assay. A central composite design (CCD) with four variables and five levels was employed for optimization of process parameters, and response surface plots were constructed in accordance with a second order polynomial model. Under optimal conditions of 3.0 h, 60.4 °C, 26.5 MPa and 89.3% ethanol, the highest yields were predicted to be 3.8 mg/g for total alkaloids, 0.5 mg/g for peimisine, 1.3 mg/g for peimine and 1.3 mg/g for peiminine, and the antioxidant capacity of extracts displayed EC_{50, DPPH} value of 5.5 mg/mL, EC_{50, ABTS} value of 0.3 mg/mL and FRAP value of 118.2 mg ascorbic acid equivalent (AAE)/100 g.