Synthesis, spectroscopic, computational (DFT/B3LYP), AChE inhibition and antioxidant studies of imidazole derivative

Sturgeon (Acipenser schrenckii) spinal cord peptides: Antioxidative and acetylcholinesterase inhibitory efficacy and mechanisms

Providing antioxidants and targeting acetylcholinesterase (AChE) are key strategies in treating neurocognitive dysfunction. In this study, bioactive sturgeon (Acipenser schrenckii) spinal cord peptides (SSCPs) with antioxidant and AChE inhibitory potency were extracted and separated from sturgeon spinal cord by enzymatic hydrolysis and ultrafiltration, and targeted peptide PGGW was screened via computer simulated molecular docking. Further, the molecular dynamic interactions of the PGGW with superoxide dismutase (SOD) and AChE were analyzed, and the protective effect of PGGW on glutamate-induced PC12 cells in vitro was evaluated. The <3 kDa fraction of SSCPs displays the most potent antioxidative efficacy (1 mg/mL, DPPH•: 89.07%, ABTS+: 76.35%). Molecular dynamics simulation showed that PGGW was stable within AChE and tightly bound to residues SER203, PHE295, ILE294 and TRP236. When combined with SOD, the indole group of PGGW was stuck inside SOD, but the tail chain PGG fluctuated greatly outside. Surface plasmon resonance demonstrated that PGGW has a high binding affinity for AChE (KD = 1.4 mM) and 0.01 mg/mL PGGW provided good protection against glutamate-induced apoptosis. The findings suggest a promising strategy for drug research on neurodegenerative diseases.

Exploration of electronic and vibrational properties of sulfanilic acid through periodic and non-periodic DFT calculations

CONTEXT

The electronic, discrete water solvation, and vibrational properties of zwitterionic sulfanilic acid were thoroughly investigated using periodic and non-periodic DFT approaches. The periodic-DFT results, obtained by employing the PBE-TS functional (Perdew-Burke-Ernzerhof (PBE) functional with the Tkatchenko and Scheffler (TS) dispersion correction) were first presented in order to analyze the band structures of the studied crystal. An attentive reading of the predicted band structures has shown three lowest gap energies calculated at 4.23, 4.24, and 4.29 eV arising from the Γ→Γ, Γ→Z, and Γ→S transitions, respectively. Then, non-periodic calculations were carried out, at the B3LYP-D3 level of theory (B3LYP functional with the D3 Grimme dispersion correction) in order to optimize the sulfanilic acid-(H2O)10 complex. Starting from the optimized structure, non-covalent interaction calculations were performed and the H-bonding, van der Waals, and steric effect interactions were identified. Finally, the PBE-TS calculations were strengthened by conducting anharmonic B3LYP-D3 calculations in order to achieve a complete decryption of the experimental IR spectrum of sulfanilic acid. The spectral analysis is not limited only to the interpretation of both the NH/CH stretching and fingerprint regions but also extended to the 1800-2600 cm-1 region, which is characterized by a strong anharmonic effect. In the latter wavenumber region, the large experimental IR band centered at 1937 cm-1 is reproduced theoretically employing the anharmonic B3LYP-D3 calculations. The similarity of this band with those usually considered as a fingerprint of zwitterionic amino acids is observed, and its origin is elucidated theoretically. In the vibrational spectroscopy field, the calculations presented in this study are probably the most appropriate for achieving vast analysis and accurate assignments of vibrational spectra of hydrogen bonding compounds recorded in the solid state.

METHOD

The periodic and non-periodic calculations were conducted within the Density Functional Theory (DFT) using the Generalized Gradient Approximation (GGA) at the PBE-TS level of theory and B3LYP-D3 functional with the 6-311++G(d,p) basis set, respectively. The PBE-TS and B3LYP-D3/6-311++G(d,p) calculations were performed using the CASTEP and Gaussian 09 programs, respectively. In addition, The non-covalent interactions were calculated by the Multiwfn 3.8 software. The obtained results for different calculations were visualized by employing the visualization tools in Materials Studio, GaussView, VMD, and Gnuplot programs.

Inhibitory potential of nitrogen, oxygen and sulfur containing heterocyclic scaffolds against acetylcholinesterase and butyrylcholinesterase

Heterocycles are the key structures in organic chemistry owing to their immense applications in the biological, chemical, and pharmaceutical fields. Heterocyclic compounds perform various noteworthy functions in nature, medication, innovation etc. Most frequently, pure nitrogen heterocycles or various positional combinations of nitrogen, oxygen, and sulfur atoms in five or six-membered rings can be found. Inhibition of acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) enzymes is a popular strategy for the management of numerous mental diseases. In this context, cholinesterase inhibitors are utilized to relieve the symptoms of neurological illnesses like dementia and Alzheimer's disease (AD). The present review focuses on various heterocyclic scaffolds and their role in designing and developing new potential AChE and BChE inhibitors to treat AD. Moreover, a detailed structure-activity relationship (SAR) has been established for the future discovery of novel drugs for the treatment of AD. Most of the heterocyclic motifs have been used in the design of new potent cholinesterase inhibitors. In this regard, this review is an endeavor to summarize the biological and chemical studies over the past decade (2010-2022) describing the pursuit of new N, O and S containing heterocycles which can offer a rich supply of promising AChE and BChE inhibitory activities.

Aminothiazole-Linked Metal Chelates: Synthesis, Density Functional Theory, and Antimicrobial Studies with Antioxidant Correlations

During the current study, the new aminothiazole Schiff base ligands (S1 ) and (S2 ) were designed by reacting 1,3-thiazol-2-amine and 6-ethoxy-1,3-benzothiazole-2-amine separately with 3-methoxy-2-hydroxybenzaldehyde in good yields (68-73%). The ligands were characterized through various analytical, physical, and spectroscopic (FT-IR, UV-Vis, 1H and 13C NMR, and MS) methods. The ligands were exploited in lieu of chelation with bivalent metal (cobalt, nickel, copper, and zinc) chlorides in a 1:2 (M:L) ratio. The spectral (UV-Vis, FT-IR, and MS), as well as magnetic, results suggested their octahedral geometry. The theoretically optimized geometrical structures were examined using the M06/6-311G+(d,p) function of density function theory. Their bioactive nature was designated by global reactivity parameters containing a high hardness (η) value of 1.34 eV and a lower softness (σ) value of 0.37 eV. Different microbial species were verified for their potency (in vitro), revealing a strong action. The Gram-positive Micrococcus luteus and Gram-negative Escherichia coli gave the highest activities of 20 and 21 mm for compounds (8) and (7), respectively. The antifungal activity against the Aspergillus niger and Aspergillus terreus species gave the highest activities of 20 and 18 mm for compounds (7) and (6), respectively. The antioxidant activity, evaluated as DPPH and ferric reducing power, gave the highest inhibition (%) as 72.0 ± 0.11% (IC50 = 144 ± 0.11 μL) and 66.3% (IC50 = 132 ± 0.11 μL) for compounds (3) and (8), respectively. All metal complexes were found to be more biocompatible than free ligands due to their chelation phenomenon. The energies of LUMOs had a link with their activities.

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.

PEPPSI complexes as potential prodrugs: enzyme inhibition, antioxidant activity, electrochemical characterization, molecular docking analysis

In this study, enzyme inhibition and antioxidant activity analyzes of previously characterized pyridine-enhanced precatalyst preparation stabilization and initiation (PEPPSI)-type Palladium(II) complexes with benzimidazole-type ligands {dichloro[L]pyridine palladium(II), L1: 1-(2-methyl-2-propenyl)-3-[benzylbenzimidazole]-2-ylidene, L2: 1-(2-methyl-2-propenyl)-3-[4-chloro benzylbenzimidazole]-2-ylidene, L3: 1-(2-methyl-2-propenyl)-3-[3-methylbenzylbenzimidazole]-2-ylidene, L4: 1-(2-methyl-2-propenyl)-3-[3,4,5-thrimethoxybenzylbenzimidazole]-2-ylidene, L5: 1-(2-methyl-2-propenyl)-3-[3-naphthylbenzylbenzimidazole]-2-ylidene, L6: 1-(2-methyl-2-propenyl)-3-[anthracen-9-ylmethylbenzimidazole]-2-ylidene} were performed and evaluated as potential drugs for neurodegenerative disorders such as Alzheimer disease and Parkinson disease. Inhibition of tyrosinase enzyme of N-heterocyclic carbenes (NHC) complexes was determined for the first time in literature. Chelating activities of the complexes were determined and compared with EDTA. Electrochemical characterization was performed using cyclic voltammetry method. Moreover, global reactivity descriptors and electronic transitions were evaluated by DFT/TDDFT methods and molecular docking interactions with human acetylcholine esterase, human butyrylcholine esterase and oxidoreductase were studied.

Molecular docking studies, structural and spectroscopic properties of monomeric and dimeric species of benzofuran-carboxylic acids derivatives: DFT calculations and biological activities

Structural optimization, molecular docking analysis, electronic and vibrational properties have been investigated for the 1-benzofuran-2-carboxylic acid (2BF) and 1-benzofuran-3-carboxylic acid (3BF) using DFT/B3LYP/6-311++G(d,p) level of theory. The theoretical parameters have a very good consistency with the experimental ones. The weak intermolecular interactions were analyzed by different tool such as: Hirshfeld surfaces, topological analysis and natural bond orbital studies. The nonlinear optical properties have been investigated. Molecular electrostatic potential and frontier molecular orbitals (FMOs) analysis have been carried out to understand the reactivity of the molecule. In addition, TD-DFT calculation is initiated to simulate the UV-vis absorption spectrum and to determine several important electronic properties like HOMO-LUMO gap energy and electronic transitions. The complete vibrational assignments and the force constants were reported for monomer and dimers of both acids. The biological activities of the tow acids have been studied via molecular docking analysis. The later calculations prove that the studied acids have an inhibitor effect against cancer and microbial diseases.

Electronic structure and second-order nonlinear optical properties of lemniscular [16]cycloparaphenylene compounds

Chiral organic compounds are excellent second-order nonlinear optical (NLO) materials due to their inherent non-symmetric electronic structures combined with the advantages of organic compounds. At present, density functional theory (DFT) has become a powerful tool for predicting the properties of novel materials. In this paper, based on chiral lemniscular [16]cycloparaphenylene, three novel compounds are designed by introduction of donor/acceptor units and their combinations. The geometrical/electronic structure, electronic absorption, and the second-order NLO properties of these compounds have been systematically investigated by DFT/TDDFT theory. The simulated UV-Vis/CD spectra of compound 1 are in good agreement with the experimental ones, enabling us to assign their electronic transition characteristics and absolute configuration with high confidence. The investigations show that energy gaps, absorption wavelength and second-order NLO response may be effectively tuned by the introduction of the donor or acceptor units or their combinations. For instance, the second-order NLO value of compound 4 is about 207 times as large as the average second-order polarizability of the organic molecule urea. Thus, the studied compounds are expected to be potential large second-order NLO materials.

Electronic structure and second-order nonlinear optical properties of linear [3]spirobifluorenylene compounds

The nonlinear optical property of the studied compounds were studied with the aid of the DFT calculations.

Theoretical study on functionalized acrylonitrile compounds with a large second-order nonlinear optical response

The nonlinear optical properties of the studied compounds were studied with the help of DFT calculations.

Improved Description of a Coordinate Bond in the ReaxFF Reactive Force Field

To improve the description of a coordinate bond of the reactive force field (ReaxFF), we have developed ReaxFF_coord by explicitly incorporating the coordinate bond contribution, E_coord, into the original ReaxFF ( Chenoweth et al. J. Phys. Chem. A 2008 , 112 , 1040 - 1053 ), in which the auxiliary functions are newly suggested to describe the plug-in behavior of lone-pair electrons from a donor atom to a vacant orbital of an acceptor atom. To validate the developed ReaxFF_coord, we tested it in various systems, including a representative coordinate bond-containing molecule, namely, carbon monoxide or ammonia borane. Although the fitting abilities of the ReaxFF_coord and original ReaxFF are similar, their molecular dynamics (MD) simulations are significantly different, where MD simulations employing ReaxFF_coord provide more realistic dynamic behaviors of atoms. It is expected that the ReaxFF_coord will significantly help ReaxFF to successfully extend its applicability to the material and biological systems, including coordinate bonds in organometallic systems.

Microwave-assisted expeditious approach towards benzimidazole acrylonitrile derivatives exploring a new silica supported SBPTS catalyst

An efficient and eco-friendly synthesis of benzimidazole-acrylonitrile derivatives.