Synthesis, computational, spectroscopic, hirshfeld surface, electronic state and molecular docking studies on diethyl-5-amino-3-methylthiophene-2,4-dicarboxylate

Evaluation of experimental, computational, molecular docking and dynamic simulation of flucytosine

Flucytosine (5-fluorocytosine), a fluorine derivative of pyrimidine, has been studied both experimentally and quantum chemically. To obtain the optimized structure, vibrational frequencies and other various parameters, the B3LYP method with a 6-311++G(d,p) basis set was used. Atom-in-molecule theory was used to calculate the binding energies, ellipticity and isosurface projection by electron localization of the molecule (AIM). In addition, the computational results from IR and Raman were compared with the experimental spectra. NBO analysis was used to analyze the donor and acceptor interactions. To know the reactive region of the molecule, the molecular electrostatic potential (MEP) and Fukui functions were determined. The UV-Vis spectrum calculated by the TD-DFT/PCM method was also compared with the experimentally determined spectrum. The HOMO-LUMO energy outcomes proved that there was a good charge exchange occurring within the molecule. With DMSO and MeOH as the solvents, maps of the hole and electron density distribution (EDD and HDD) were produced in an excited state. An electrophilicity index parameter was looked at to theoretically test the bioactivity of the compound. To find the best ligand-protein interactions, molecular docking was also carried out with various receptor proteins. In order to verify the inhibitory potency for the receptor protein complex predicted by docking and molecular dynamic simulation studies, the binding free energy of the receptor protein complex was calculated. Using the MM/GBSA technique, we determined the docked complex's binding free energy. To confirm the molecule's drug similarity, a biological drug similarity investigation was also executed.Communicated by Ramaswamy H. Sarma.

A boronate-affinity magnetic molecularly imprinted polymer for luteolin recognition

In this study, 3-carboxyphenylboronic acid (CP)-functionalized amino-modified Fe₃O₄ (Fe₃O₄@NH₂-CP, FNC) magnetic molecularly imprinted polymers (FNC@MIPs) were synthesized and applied for the quick identification and selective separation of luteolin (LTL). The structure and morphology were characterized in detail by Fourier transform-infrared spectroscopy (FT-IR), scanning electron microscopy (SEM), dynamic light scattering (DLS), X-ray photoelectron spectroscopy (XPS), X-ray diffraction (XRD), thermogravimetric analysis (TGA), and vibrating specimen magnetometry (VSM) methods. The FNC@MIPs had a homogeneous shape, excellent magnetic characteristics, quick binding kinetics, a high adsorption capacity, acceptable selectivity, and stable reusability. The solid-phase extraction parameters and preparation conditions were both optimized. Under optimized conditions, the maximal adsorption capacity was 14.26 mg g^-1 and the imprinting factor was 3.62. Furthermore, the experimental kinetics data were best fitted with the pseudo-first-order model (R² = 0.9877), and the Langmuir model could describe the adsorption process (R² = 0.9979), suggesting a monolayer covering. The practical application of the sorbent for LTL detection in Lonicera japonica Thunb samples showed recoveries in the range of 84.5-108.7%. Therefore, the strategy offers a fresh avenue for the extraction and purification of LTL.

Identification of 4-acrylamido-N-(pyridazin-3-yl)benzamide as anti-COVID-19 compound: a DFTB, molecular docking, and molecular dynamics study

Omicron is one of the variants of COVID-19 and continuing member of a pandemic. There are several types of vaccines that were developed around the globe to fight against the virus. However, the world is suffering to find suitable drug candidates for the virus. The main protease (Mpro) enzyme of the virus is the best target for finding drug molecules because of its involvement in viral infection and protein synthesis. ZINC-15 is a database of 750 million commercially available compounds. We find 125 compounds having two aromatic rings and amide groups for non-covalent interactions with active site amino acids and functional groups with the capability to bind -SH group of C145 of Mpro through covalent bonding by a nucleophilic addition reaction. The lead compound (Z144) was identified using molecular docking. The non-covalent interactions (NCI) calculations show the interactions between amino acids present in the active site of the protein and the lead molecules are attractive in nature. The density functional-based tight-binding (DFTB) study of the lead compound with amino acids in the active site indicates that Q190 and Q193 play a very critical role in stabilization. The Michael addition of the acrylamide group of the lead molecule at β-position is facile because the low energy lowest unoccupied molecular orbital (LUMO) is concentrated on the group. From molecular dynamics during 100 ns, it has come to light that strong non-covalent interactions are key for the stability of the lead inside the protein and such binding can fold the protein. The free energy for this interaction is -42.72 kcal mol-1 which was obtained from MM-GB/SA calculations.

Vibrational Spectroscopy, Quantum Computational and Molecular Docking Studies on 2-[(1H-Benzimidazol-1-yl)-methyl]benzoic Acid

Experimental and theoretical investigations on the optimized geometrical structure, electronic and vibrational features of 2-[(1H-benzimidazol-1-yl)-methyl]benzoic acid are provided using the B3LYP/6-311++G(d,p) basis set. The Vibrational Energy Distribution Analysis (VEDA) program was used to perform the vibrational assignments and calculate the Potential Energy Distribution (PED). The acquired FT-IR and FT Raman data were used to complete the vibrational assignment and characterization of the compound fundamental modes. Theoretical and actual NMR chemical shifts were found to be quite similar. The UV-vis spectrum of 21HBMBA, as well as effects of solvents, have been investigated. The calculated HOMO and LUMO energies reveal that charge transfer happens within the molecule and MEP surface to be a chemically reactive area appropriate for drug action. Furthermore, a thorough examination of Non-Bonding Orbitals, excitation energies, AIM charges, Fukui functions and the Electron Localization Function (ELF) is carried out. The research is also expanded to compute first-order hyperpolarizability and forecast NLO characteristics. The details of the docking studies aided in the prediction of protein binding.