Spectroscopic investigation, vibrational assignments, Fukui functions, HOMO-LUMO, MEP and molecular docking evaluation of 4 – [(3, 4 – dichlorophenyl) amino] 2 – methylidene 4 – oxo butanoic acid by DFT method

Discovery of potential anti- Staphylococcus aureus natural products and their mechanistic studies using machine learning and molecular dynamic simulations

The structure-activity analysis (SAR) and machine learning were used to investigate potential anti-S. aureus agents in a faster method. In this study, 24 oxygenated benzene ring components with S. aureus inhibition capacity were confirmed by literature exploring and in-house experiments, and the SAR analysis suggested that the hydroxyl group position may affect the anti-S. aureus activity. The 2D-MLR-QSAR model with 9 descriptors was further evaluated as the best model among the 21 models. After that, hesperetic acid and 2-HTPA were further explored and evaluated as the potential anti-S. aureus agents screening in the natural product clustering library through the best QSAR model calculation. The antibacterial capacities of hesperetic acid and 2-HTPA had been investigated and proved the similar predictive pMIC value resulting from the QSAR model. Besides, the two novel components were able to inhibit the growth of S. aureus by disrupting the cell membrane through the molecular dynamics simulation (MD), which further evidenced by scanning electron microscopy (SEM) test and PI dye results. Overall, these results are highly suggested that QSAR can be used to predict the antibacterial agents targeting S. aureus, which provides a new paradigm to research the molecular structure-antibacterial capacity relationship.

3-(5-(1H-imidazol-1-yl) pent-1-en-1-yl)-9-ethyl-9H-carbazole: synthesis, characterization (IR, NMR), DFT, antimicrobial-antioxidant activities and docking study

3-(5-(1H-imidazol-1-yl) pent-1-en-1-yl)-9-ethyl-9H-carbazole called as compound 1 was synthesized and characterized by proton and carbon-13 nuclear magnetic resonance (¹H- and ¹³C- NMR) and Fourier transform infrared (FTIR) spectroscopic methods. Density Functional Theory/Becke, 3-parameter (DFT/B3LYP), for compound 1 were performed with 6-311++G(d,p) method. Optimized geometry, frontier molecular orbitals (HOMO; highest occupied molecular orbital; LUMO: lowest unoccupied molecular orbital), IR and NMR parameters of compound 1 were obtained. The evaluations reveal that the calculation results support the experimental results. In addition, the antimicrobial (a microwell dilution method) and antioxidant activities (2,2-Diphenyl-1-picrylhydrazyl (DPPH), 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (ABTS) ferric ion reducing antioxidant power (FRAP) of compound 1 were evaluated. According to the results obtained, it showed higher antimicrobial activity (Minimal inhibition concentration (MIC): 78.12 µg/mL) against B. subtilis subsp. Spizizenii. Morever, molecular docking studies were carried out to investigate the interactions of an antimicrobial agent on some important enzymes played important roles in nucleic acid (Deoxyribo nucleic acid (DNA) synthesis, cell wall synthesis, protein synthesis, and metabolism etc. The compound 1 was strongly bound to tyrosyl-tRNA synthetase enzyme (binding energy: -11.18 and K_i: 6.37 nM) and Beta-Ketoacyl-Acp Synthase III enzyme (binding energy: -10.29 and K_i: 28.47 nM).Communicated by Ramaswamy H. Sarma.

Organically surface engineered mesoporous silica nanoparticles control the release of quercetin by pH stimuli

Controlling the premature release of hydrophobic drugs like quercetin over physiological conditions remains a challenge motivating the development of smart and responsive drug carriers in recent years. This present work reported a surface modification of mesoporous silica nanoparticles (MSN) by a functional compound having both amines (as a positively charged group) and carboxylic (negatively charged group), namely 4-((2-aminoethyl)amino)-4-oxobut-2-enoic acid (AmEA) prepared via simple mechanochemistry approach. The impact of MSN surface modification on physical, textural, and morphological features was evaluated by TGA, N₂ adsorption-desorption, PSA-zeta, SEM, and TEM. The BET surface area of AmEA-modified MSN (MSN-AmEA) was found to be 858.41 m² g^-1 with a pore size of 2.69 nm which could accommodate a high concentration of quercetin 118% higher than MSN. In addition, the colloidal stability of MSN-AmEA was greatly improved as indicated by high zeta potential especially at pH 4 compared to MSN. In contrast to MSN, MSN-AmEA has better in controlling quercetin release triggered by pH, thanks to the presence of the functional groups that have a pose-sensitive interaction hence it may fully control the quercetin release, as elaborated by the DFT study. Therefore, the controlled release of quercetin over MSN-AmEA verified its capability of acting as a smart drug delivery system.

New benzyltriethylammonium/urea deep eutectic solvent: Quantum calculation and application to hyrdoxylethylcellulose modification

In this paper, a new deep eutectic solvent (DES) has been successfully synthesized that is based on benzyltriethylammonium bromide as a hydrogen bond acceptor (HBA) and urea as a hydrogen bond donor (HBD). However, its usability in modifying cellulose derivatives, especially acylating hydroxyethylcellulose (HEC) was investigated. The chemical modification (acetylation) of HEC was carried out in BTEAB/urea DES system without any additional conventional solvent or catalyst. However, the proposed structure of acetylated HEC (HECA) was confirmed according to the structural spectra analyses FTIR-ATR, ¹H, ¹³C, and APT-NMR. The crystalline behavior of acetylated and unmodified HEC in the DES system has been evaluated using XRD patterns, where the thermal stability was evaluated basing on the TD-TGA thermograms. Hence, SEM images and EDX spectra were recorded to prove the changes that are expected at the morphological level and elemental profile. Yet, the nanometric sheets aspect was observed. The Functional Density Theory (DFT) was investigated as a useful computational tool to understand mechanism and donor-acceptor interactions. The topological parameters (electron density Laplacian, kinetic energy density, potential energy density, and energy density) at the bond critical points (BCP), between TBEAB and urea, are deducted according to Quantum Bader's theory, and Atoms-in-molecules (AIM). The non-covalent interactions and steric effect in the DES system were studied using the reduced density gradient isosurface (RDG). Theoretical and computational calculations revealed that the H-bonds and the electrostatic coexist, as predominant interactions in the BTEAB-based DES resulting chemical structure, and mechanism formation. The physical interactions between the component entities of DES lead to a new equilibrium that is more stable than that of HBA and HBD in their separate states.

Quantum chemical calculation, performance of selective antimicrobial activity using molecular docking analysis, RDG and experimental (FT-IR, FT-Raman) investigation of 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile

The research received a great deal of worldwide attention due to the nature of interpretation before the experimental process. Based on the systematic process the structure of thiazole -pyrazole compound 4-[{2-[3-(4-chlorophenyl)-5-(4-propan-2-yl) phenyl)-4, 5-dihydro- 1H- pyrazol-1-yl]-4-oxo-1, 3- thiazol-5(4H)-ylidene} methyl] benzonitrile [CPTBN] was investigated. In the first level, the spectral statistics on experimental FT-IR and FT- Raman was reported. At the next level, geometrical parameters was theoretically acquired from density functional theory (DFT) using B3LPY/6-31G and 6-311G basis set. The computed Wavenumber were collected and compared with the experimental data. The vibrational modes were interpreted in terms of potential energy distribution (PED) results. The FMO, MEP, and NBO analysis further validated the electrophilic and nucleophilic interaction in the molecular systems. Two grams-positive bacteria: staphylococcus aureus, Bacillus subtilis and two gram-negative bacteria: Esherichia coli, Pseudomonas aeruginosa was performed for antibacterial activity. Two fungal strain Candida albicans and Aspergillus Niger was carried out against a ligand using anti-fungal activity. The molecular docking analysis explores the antimicrobial and selective potential inhibitory nature of the binding molecule. Besides, RDG and ELF analysis were also performed to show the nature of interactions between the molecule.

Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers

Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP–MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.