Experimental FTIR and FT-Raman and theoretical studies on the molecular structures of monomer and dimer of 3-thiopheneacrylic acid

Investigation of the molecular structure of CHBP, biological activities and SARS-CoV-2 protein binding interaction by molecular and biomolecular spectroscopy approaches

The objective of this investigation is to learn more about the structural, electrical, spectroscopic, and physiochemical characteristics of biologically active cyano-4'-hydroxybiphenyl (CHBP). The title molecule's optimized conformational analysis was computed using the DFT/B3LYP/6-311++G (d, p) level of theory. The observed wavenumbers were compared with theoretical FT-IR and FT-Raman spectra. 1H and 13C NMR experimental spectra in CDCl3 solution (solvent phase) were recorded and the chemical shift was calculated. NBO analysis was used to examine the transfer of charge as well as the intermolecular and intramolecular bonding of orbitals. The TD-DFT (time-dependent DFT) approach was used to estimate theoretical values for both the gas and solvent (ethanol) in the corresponding transitional research, which was conducted using UV-Vis's spectra. Energy gap (Eg = 0.26764 eV) implies that the strong potential for charge transfer, and the stability of the CHBP compound. CHBP compound's has bioactive nature, its drug-likeness and biological properties were evaluated. The predicted topological polar surface area of 44.02 \AA2 for the molecule falls within the permissible range of < 140 \AA2. Based on the docking results, the most stable docking score value is -6.84 kcal/mol. In that interaction, MET 165 affects both phenyl rings in a pi-sulphur fashion and a single bond hydrogen with protein moieties GLN 192. This suggests that the pi-alkyl in PRO 168 is a hydroxyl substitutional ring. Our findings demonstrate the CHBP compound is a good inhibitor against the SAR COVID-19 viral protein.

Investigation on molecular and biomolecular spectroscopy of the novel 2BCA molecule to analyse its biological activities and binding interaction with nipah viral protein

The molecule of 2-Biphenyl Carboxylic Acid (2BCA), which contains peculiar features, was explored making use of density functional theory (DFT) and experimental approaches in the area of quantum computational research. The optimised structure, atomic charges, vibrational frequencies, electrical properties, electrostatic potential surface (ESP), natural bond orbital analysis and potential energy surface (PES) were obtained applying the B3LYP approach with the 6-311++ G (d,p) basis set.. The 2BCA molecule was examined for possible conformers using a PES scan. The methods applied for spectral analyses included FT-IR, FT-RAMAN, NMR, and UV-Vis results. Vibrational frequencies for all typical modes of vibration were found using the Potential Energy Distribution (PED) data. The UV-Vis spectrum was simulated using the TD-DFT technique, which is also seen empirically. The Gauge-Invariant Atomic Orbital (GIAO) approach was employed to model and study the 13C and 1H NMR spectra of the 2BCA molecule in a CDCL3 solution. The spectra were then exploited experimentally to establish their chemical shifts. To predict the donor and acceptor interaction, the NBO analysis was used. The electrostatic potential surface was employed to anticipate the locations of nucleophilic and electrophilic sites. Hirshfeld surfaces and their related fingerprint plots are exploited for the investigation of intermolecular interactions. Reduced Density Gradient (RDG) helps to measure and illustrate electron correlation effects, offering precise insights into chemical bonding, reactivity, and the electronic structure of 2BCA. According to Lipinski and Veber's drug similarity criteria, 2BCA exhibits the typical physicochemical and pharmacokinetic properties that make it a potential oral pharmaceutical candidate. According to the findings of a molecular docking study, the 2BCA molecule has promise as a treatment agent for the Nipah virus (PDB ID: 6 EB9), which causes severe respiratory and neurological symptoms in humans.

Ternary Mixture of Pentanamide in Solvent Analogy with Halogenated Phenol: Experimental, Theoretical, and In Silico Biological Studies

This research describes the preparation of mixtures of new halogen-substituted phenol derivatives and their effects due to linkages with a fatty amide (pentanamide). The molecules were optimized using DFT, and the vibrational and electronic analysis was done subsequently. The energies of frontier molecular orbitals (FMOs) were used to estimate the global chemical reactivity parameters as we suggest that hydrogen-bonded networks may have contributed to the stability and reactivity of the compound. In addition to the experimental investigation, dielectric parameters were calculated. Fukui functions were analyzed to study the chemical reactivity. To get insight into interactions of σ → π* orbitals, natural bond orbital calculations were done. Additionally, surface analysis of the MEP and Hirshfeld charges were performed at the equivalent DFT levels. The research also indicated that both (interaction region indicator) IRI and (electron delocalize range) EDR would proficiently identify chemical-bonding and weak interaction regions, providing a significant advantage in exploring diverse chemical systems and reactions. This indicated that compounds could diffuse through noncovalent interactions, including intramolecular hydrogen bonding. Dielectric relaxation studies taken at five distinct molar ratios identified significant dielectric properties such as ε', ε″, ε0, and ε∞. The PA with FP, CP, BP, and IP molecules has potential antiviral and antioxidant benefits for carbonic anhydrase, with favorable drug-like features and diverse biological benefits. Pharmacological effects were forecasted using the PASS server, and these molecules exhibited favorable pharmacokinetic properties.

Structural Studies of Monounsaturated and ω-3 Polyunsaturated Free Fatty Acids in Solution with the Combined Use οf NMR and DFT Calculations-Comparison with the Liquid State

Molecular structures, in chloroform and DMSO solution, of the free fatty acids (FFAs) caproleic acid, oleic acid, α-linolenic acid, eicosapentanoic acid (EPA) and docosahexaenoic acid (DHA) are reported with the combined use of NMR and DFT calculations. Variable temperature and concentration chemical shifts of the COOH protons, transient 1D NOE experiments and DFT calculations demonstrate the major contribution of low molecular weight aggregates of dimerized fatty acids through intermolecular hydrogen bond interactions of the carboxylic groups, with parallel and antiparallel interdigitated structures even at the low concentration of 20 mM in CDCl3. For the dimeric DHA, a structural model of an intermolecular hydrogen bond through carboxylic groups and an intermolecular hydrogen bond between the carboxylic group of one molecule and the ω-3 double bond of a second molecule is shown to play a role. In DMSO-d6 solution, NMR and DFT studies show that the carboxylic groups form strong intermolecular hydrogen bond interactions with a single discrete solvation molecule of DMSO. These solvation species form parallel and antiparallel interdigitated structures of low molecular weight, as in chloroform solution. This structural motif, therefore, is an intrinsic property of the FFAs, which is not strongly affected by the length and degree of unsaturation of the chain and the hydrogen bond ability of the solvent.

Molecular Structure, Electronic Properties, Reactivity (ELF, LOL, and Fukui), and NCI-RDG Studies of the Binary Mixture of Water and Essential Oil of Phlomis bruguieri

Essential oils are volatile oil-like liquids with a characteristic strong smell and taste. They are formed in plants and are then extracted. Essential oils have extremely strong physiological and pharmacological properties, which are used in the medicine, cosmetics, and food industries. In this study, the molecules caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene, which are the molecules with the highest contents in the essential oil of the plant mentioned in the title, were selected and theoretical calculations describing their interactions with water were performed. Because oil–water mixtures are very important in biology and industry and are ubiquitous in nature, quantum chemical calculations for binary mixtures of water with caryophyllene oxide, β-pinene, 1,8-cineol, α-cubebene, and β-caryophyllene were performed using the density functional theory (DFT)/B3LYP method with a basis of 6–31 G (d, p). Molecular structures, HOMO–LUMO energies, electronic properties, reactivity (ELF, LOL, and Fukui), and NCI-RDG and molecular electrostatic potential (MEP) on surfaces of the main components of Phlomis bruguieri Desf. essential oil were calculated and described.

Vibrational Spectroscopies, Global Reactivity, Molecular Docking, Thermodynamic Properties and Linear and Nonlinear Optical Parameters of Monohydrate Arsonate Salt of 4-Aminopyridine

In this work, a structural and electronic properties of a novel organic arsenate template by 4-aminopyridine, with the general formula (C₅H₇N₂)(C₅H₈N₂)[AsO₄]·H₂O ((4-APH)(4-APH₂)[AsO₄]·H₂O) have been presented. The density functional theory (DFT) along with B3LYP hybrid functional is employed. The optimized structure was found to be in well consistent with the X-ray diffraction geometry. The examination of the vibrational spectrum was correlated by DFT calculation using the unit cell parameters obtained from the experiment data. Besides, the thermodynamic functions (heat capacity, entropy, enthalpy) from spectroscopic data by statistical methods were obtained for the range of temperature 100–1000 K. In addition, the molecular orbital calculations such as Natural Bond Orbitals (NBOs), AIM approach, HOMO–LUMO energy gap, NLO characteristic and Hirshfeld surface analysis were also performed with the same level of DFT. Electronic stability of the compound arising from hyper conjugative interactions and charge delocalization were also investigated based on the natural bond orbital (NBO) analysis. Molecular docking studies were also conducted as part of this study. The theoretical results showed an excellent agreement with the experimental values.

Design, molecular docking analysis of an anti-inflammatory drug, computational analysis and intermolecular interactions energy studies of 1-benzothiophene-2-carboxylic acid

In this paper, theoretical study on molecular geometry, vibrational, pharmaceutical and electronic properties of the monomeric and dimeric structures of 1-benzothiophene-2-carboxylic acid (2BT) were carried out using B3LYP hybrid functional with 6-311++G(d,p) as basis set. The structural study show that the stability of 2BT crystalline structure arising from O-H…O, C-H…O as well as S-H…O hydrogen bonding interactions. Vibrational analysis, for monomer and dimer species, show a good compatibility between experimental and theoretical frequencies. Then, the 1H and 13C NMR chemical shifts were calculated using Gauge Independent Atomic Orbital (GIAO) technical. In addition, the UV-Vis spectrum was simulated in gas phase and in water throughout TD-DFT calculation. The electronic transitions were identified based on HOM-LUMO energies. However, donor-acceptor interactions and charge delocalization has been studied via natural bond orbital (NBO). The nucleophilic and electrophilic site localization is identified by molecular electrostatic potential. Hirshfeld surface analysis has been discussed based on color code demonstrating the various non covalent interactions. Besides, molecular docking analysis was reported to evince the pharmaceutical properties of the studied molecule.

A microscopic and macroscopic investigation of the adsorption of N719 dye on ZnO nanopowders (ZNP) and ZnO nanorods (ZNR) for dye sensitized solar cells using statistical physics treatment and DFT simulation

In this paper, three adsorption isotherms of N719 dye on two different adsorbents, ZnO nanopowder and ZnO nanorods, at three different thicknesses have been fitted using a monolayer model with three types of receptor sites treated by statistical physics. The model involved parameters are: three coefficients (n 1, n 2 and n 3) indicating the numbers of adsorbed dye molecules per site, three parameters (N m1, N m2 and N m3) indicating the receptor site densities and three adsorption energies ((-ε 1), (-ε 2) and (-ε 3)). The evolution of these parameters in relation with thickness of ZnO was discussed. The pore size distribution (PSD) of ZnO nanopowder and ZnO nanorods as a function of the thickness has been studied using the chosen adequate model. The molecular electrostatic potential (MEP) has been investigated to optimize the different adsorbed geometries of the complex N719 dye@ZnO. The intermolecular interactions between the N719 dye and the ZnO surface have been studied by using the quantum theory of atoms in molecules (AIM) and reduced density gradient RDG. The results of the MEP, topological AIM and RDG are in agreement with the results of statistical physics.

Computational study of 3-thiophene acetic acid: Molecular docking, electronic and intermolecular interactions investigations

The present work undertakes the structural and electronic properties of 3-thiophene acetic acid (abbreviated as 3-TAA) monomer and dimer. DFT calculations were performed using B3LYP functional in combination with the aug-cc-pVTZ basis set. The optimized structural parameters were found to be in a good agreement with experimental molecular geometry. The stability of the crystal packing was ensured by OH⋯O, C-H⋯O and CH⋯S intermolecular interactions. All the Non covalent interactions were deeply studied in terms of their topological parameters, Hirshfeld surface (HS) analysis and reduced density gradient (RDG) analysis. The electronic properties of the investigated compound have been performed using time dependent density functional theory (TD-DFT) and discussed through its correspondant HOMO, LUMO and excitation energy values. Likewise, the reactivity of 3-TAA was discussed in terms of several thermodynamic parameters. In addition, the molecular electrostatic potential (MEP) surface has been performed and discussed in terms of color distribution. In addition, the natural bond orbital (NBO) analysis was used to investigate the electronic charge transfer into the molecule. Harmine, Clorgyline, Isatin, zonisamide and our title compound including are known with their competitive inhibitory activity on Human monoamine oxidase, commonly named MAO A and B. This enzyme is a critical enzyme in the degradative deamination of biogenic amines throughout the body. Thus, molecular docking behaviors of 3-TAA are computed and compared to the results found for Harmine, Clorgyline, Isatin, zonisamide ligands.

S(-) and R(+) species derived from antihistaminic promethazine agent: structural and vibrational studies

Structural and vibrational properties of free base, cationic and hydrochloride species derived from both S(-) and R(+) enantiomers of antihistaminic promethazine (PTZ) agent have been theoretically evaluated in gas phase and in aqueous solution by using the hybrid B3LYP/6-31G* calculations. The initial structures of S(-) and R(+) enantiomers of hydrochloride PTZ were those polymorphic forms 1 and 2 experimentally determined by X-ray diffraction. Here, all structures in aqueous solution were optimized at the same level of theory by using the polarized continuum (PCM) and the universal solvation model. As was experimentally reported, variations in the unit cell lead to slight energy, density, and melting point differences between the two forms but, this behavior is not carried through in isotropic condition, like in solution with non-chiral solvents. Hence, the N-C distances, Mulliken, atomic natural population (NPA) and Merz-Kollman (MK) charges, bond orders, stabilization and solvation energies, frontier orbitals, some descriptors and their topological properties were compared with the antihistaminic cyclizine agent. The frontier orbitals studies show that the free base species of both forms in solution are more reactive than cyclizine. Higher electrophilicity indexes are observed in the cationic and hydrochloride species of PTZ than cyclizine while the cationic species of cyclizine have higher nucleophilicity index than both species of PTZ. The presences of bands attributed to cationic species of both enantiomers are clearly supported by the infrared and Raman spectra in the solid phase. The expected 114, 117 and 120 vibration normal modes for the free base, cationic and hydrochloride species of both forms were completely assigned and the force constants reported. Reasonable concordances among the predicted infrared, Raman, UV-Vis and Electronic Circular Dichroism (ECD) with the corresponding experimental ones were found.