A proton transfer compound template phenylethylamine: Synthesis, a collective experimental and theoretical investigations

Structural, electronic, intermolecular interaction, reactivity, vibrational spectroscopy, charge transfer, Hirshfeld surface analysis, pharmacological and hydropathy plot on 5-Bromo nicotinic acid - Antiviral study (Hepatitis A, B, and C)

The therapeutic properties of 5-Bromonicotinatic acid (5BNA) were studied for antiviral illnesses like Hepatitis A, Hepatitis B and Hepatitis C and the influence of electron-donating and electron-withdrawing properties of functional groups on the nicotinic acid was evaluated and represented in this study using the DFT approach. The molecular parameters were determined for both gases as well as for various solvent phases. The reactive areas in the compound are examined utilising Fukui analysis. The molecular interactions are accomplished by recognising the different types of bonding found in the compound using the AIM, ELF, LOL, RDG and IRI. Solvation investigations were demonstrated to have an influence on molecular orbital energy, ESP, UV-Vis and NLO analyses. Electron-hole, NBO and Hirshfeld investigations are used to investigate the transfer of charges and interactions inside the molecule. The method of vibrational spectroscopy (IR and Raman) is used to differentiate and identify the various types of vibrations displayed by the compound. The hydropathy plots for the proteins 2A4O, 6CWD and 2OC8 associated with Hepatitis A, Hepatitis B and Hepatitis C illustrate the disquiet and attraction of the amino acids towards the water.

Synthesis, characterization and identification of inhibitory activity on the main protease of COVID-19 by molecular docking strategy of (4-oxo-piperidinium ethylene acetal) trioxonitrate

In this investigation a single crystal of (4-oxo-piperidinium ethylene acetal) trioxonitrate (4-OPEAN) was synthesized by modifying the mechanism of gradual evaporation at ambient temperature. The operational groupings are found in the complex material in the elaborate substance, according to the infrared spectrum. Single crystal X-ray diffraction suggests, (4-OPEAN) with the chemical formula (C₇H₁₂NO₂)NO₃ belongs to the orthorhombic space group Pnma and is centrosymmetric in three dimensions with the aforementioned network configurations, a = 11.7185(8) Å, b = 7.2729(6) Å, c = 11.0163(8) Å, Z = 4, V = 938.89(12) ų, R = 0.0725 and wR = 0.1762. Many N-H…O and C-H…O hydrogen bridges, both bifurcated and non-bifurcated, link the 4-oxo-piperidinium ethylene acetal cations to the trigonal (NO₃^-) anions. Molecular geometry and optimal parameters of (4-OPEAN) have been determined via DFT computations at the theory-level B3LYP/6-311 ++ G(d, p), these have been contrasted with the X-ray data already available. Hirshfeld surface analysis has made it possible for the visualization and quantification of relationships between molecules in the crystal composition. Quantum theory atoms in molecules, electron location function, decreased density gradient, and localized orbital locator research have all been used to explore non-covalent interactions in crystal structure. In order to pinpoint both the nucleophilic and electrophilic locations that support hydrogen bond formation, the molecule electrostatic potential was determined. The greatest and lowest energies of occupied and unfilled molecular orbitals, together with additional derived atomic characteristics, show the material to be extremely stable and hard. According to a molecular docking study, 4-OPEAN may exhibit inhibiting effects on the 6Y84 and 7EJY virus proteins from corona (COVID-19).

Synthesis, Empirical and Theoretical Investigations on New Histaminium Bis(Trioxonitrate) Compound

In this paper, a novel hybrid material, entitled histaminium bis(trioxonitrate), with the general chemical formula (C₅H₁₁N₃)(NO₃)₂, denoted by HTN was presented. Single-crystal X-ray diffraction was used to determine the structural characteristics of this compound after it was made using a slow evaporation method at room temperature. This compound was elaborated and crystallized to the monoclinic system with space group P2₁/c, and the lattice parameters obtained were: a = 10.4807 (16)Å, b = 11.8747 (15)Å, c = 16.194 (2)Å, β = 95.095 (6)°, V = 2007.4 (5)ų and Z = 8. The title compound's atomic structure couldbe modeled as a three-dimensional network. Organic cations and nitrate anions were connected via N-H...O and C-H...O hydrogen bonds in the HTN structure. The intermolecular interactions responsible for the formation of crystal packing were evaluated using Hirshfeld surfaces and two-dimensional fingerprint plots. The compound's infrared spectrum, which ranged from 4000 to 400 cm^-1, confirmed the presence of the principal bands attributed to the internal modes of the organic cation and nitrate anions. Additionally, spectrofluorimetry and the ultraviolet-visible spectrum was used to investigate this compound. DFT calculations were used to evaluate the composition and properties of HTN. The energy gap, chemical reactivity and crystal stability of HTN were quantified by performing HOMO-LUMO frontier orbitals analysis. Topological analysis (AIM), Reduced Density Gradient (RDG), molecular electrostatic potential surface (MEPS) and Mulliken population were processed to determine the types of non-covalent interactions, atomic charges and molecular polarity in detail.

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.

Comparative antibacterial analysis of the anthraquinone compounds based on the AIM theory, molecular docking, and dynamics simulation analysis

BACKGROUND

Hydroxyanthraquinones and anthraquinone glucoside derivatives are always considered as the active antibacterial components.

METHODS

Comparison of structure characteristics and antibacterial effect of these compounds was performed by applying quantum chemical calculations, atoms in molecules theory, molecular docking, and dynamics simulation procedure. Density functional theory calculation with B3LYP using 6-31G (d, p) basis set has been used to determine ground state molecular geometries.

RESULTS

The molecular geometric stability, electrostatic potential, frontier orbital energies, and topological properties were analyzed at the active site. Once glucose ring is introduced into the hydroxyanthraquinone rings, almost all of the positive molecular potentials are distributed among the hydroxyl hydrogen atoms of the glucose rings. In addition, low electron density ρ (r) and positive Laplacian value of the O-H bond of the anthraquinone glucoside are the evidences of the highly polarized and covalently decreased bonding interactions. The anthraquinone glucoside compounds have generally higher intermolecular binding energies than the corresponding aglycones due to the strong interaction between the glucose rings and the surrounding amino acids. Molecular dynamics simulations further explored the stability and dynamic behavior of the anthraquinone compound and protein complexes through RMSD, RMSF, SASA, and Rg.

CONCLUSION

The type of carboxyl, hydroxyl, and hydroxymethyl groups on phenyl ring and the substituent glucose rings is important to the interactions with the topoisomerase type II enzyme DNA gyrase B.

Sulfation of Diethylaminoethyl-Cellulose: QTAIM Topological Analysis and Experimental and DFT Studies of the Properties

Sulfated cellulose derivatives are biologically active substances with anticoagulant properties. In this study, a new sulfated diethylaminoethyl (DEAE)-cellulose derivative has been obtained. The effect of a solvent on the sulfation process has been investigated. It is shown that 1,4-dioxane is the most effective solvent, which ensures the highest sulfur content in DEAE-cellulose sulfate under sulfamic acid sulfation. The processes of sulfamic acid sulfation in the presence of urea in 1,4-dioxane and in a deep eutectic solvent representing a mixture of sulfamic acid and urea have been compared. It is demonstrated that the use of 1,4-dioxane yields the sulfated product with a higher sulfur content. The obtained sulfated DEAE-cellulose derivatives have been analyzed by Fourier transform infrared spectroscopy, X-ray diffractometry, and scanning electron and atomic force microscopy, and the degree of their polymerization has been determined. The introduction of a sulfate group has been confirmed by the Fourier transform infrared spectroscopy data; the absorption bands corresponding to sulfate groups have been observed in the ranges of 1247-1256 and 809-816 cm-1. It is shown that the use of a deep eutectic solvent leads to the side carbamation reactions. Amorphization of DEAE-cellulose during sulfation has been demonstrated using X-ray diffractometry. The geometric structure of a molecule in the ground state has been calculated using the density functional theory with the B3LYP/6-31G(d, p) basis set. The reactive areas of DEAE-cellulose and its sulfated derivatives have been analyzed using molecular electrostatic potential maps. The thermodynamic parameters (heat capacity, entropy, and enthalpy) of the target sulfation products have been determined. The HOMO-LUMO energy gap, Mulliken atomic charges, and electron density topology of the title compound have been calculated within the atoms in molecule theory.

5-((1H-imidazol-1-yl)methyl)quinolin-8-ol as potential antiviral SARS-CoV-2 candidate: Synthesis, crystal structure, Hirshfeld surface analysis, DFT and molecular docking studies

A potential new drug to treat SARS-CoV-2 infections and chloroquine analogue, 5-((1H-imidazol-1-yl)methyl)quinolin-8-ol (DD1) has been here synthesized and characterized by FT-IR, 1H-NMR, 13C-NMR, ultraviolet-visible, ESI-MS and single-crystal X-ray diffraction. DD1 was optimized in gas phase, aqueous and DMSO solutions using hybrid B3LYP/6-311++G(d,p) method. Comparisons between experimental and theoretical infrared spectra, 1H and 13C NMR chemical shifts and electronic spectrum in DMSO solution evidence good concordances. Higher solvation energy was observed in aqueous solution than in DMSO, showing in aqueous solution a higher value than antiviral brincidofovir and chloroquine. on Bond orders, atomic charges and topological studies suggest that imidazole ring play a very important role in the properties of DD1. NBO and AIM analyses support the intra-molecular O15-H16•••N17 bonds of DD1 in the three media. Low gap value supports the higher reactivity of DD1 than chloroquine justified by the higher electrophilicity and low nucleophilicity. Complete vibrational assignments of DD1 in gas phase and aqueous solution are reported together with the scaled force constants. In addition, better intermolecular interactions were observed by Hirshfeld surface analysis. Finally, the molecular docking mechanism between DD1 ligand and COVID-19/6WCF and COVID-19/6Y84 receptors were studied to explore the binding modes of these compounds at the active sites. Molecular docking results have shown that the DD1 molecule can be considered as a potential agent against COVID-19/6Y84-6WCF receptors.

Quantum chemical studies on molecular structure, AIM, ELF, RDG and antiviral activities of hybrid hydroxychloroquine in the treatment of COVID-19: Molecular docking and DFT calculations

Structure-activity relationships for hydroxychloroquine compound and its derivatives resulted in a potent antiviral activity. Where hydroxychloroquine derivatives showed an apparent efficacy against coronavirus related pneumonia. For this reason, the current study is focused on the structural properties of hydroxychloroquine and hydroxychloroquine sulfate. Optimized structures of these molecules have been reported by using DFT method at B3LYP/6-31G* level of theory. The geometric were determined and compared with the experimental crystal structure. The intra and intermolecular interactions which exist within these compounds are analyzed by different methods namely the topological analysis AIM, ELF and the reduced gradient of the density. These approaches make it possible in particular to study the properties of hydrogen bonds. The highest occupied molecular orbital and the lowest unoccupied molecular orbital energy levels are constructed and the corresponding frontier energy gaps are determined to realize the charge transfer within the molecule. The densities of state diagrams were determined to calculate contributions to the molecular orbitals. The molecular electrostatic potential surfaces are determined to give a visual representation of charge distribution of these ligands and to provide information linked to electrophilic and nucleophilic sites localization. Finally, these derivatives were evaluated for the inhibition of COVID-19 activity by using the molecular docking method.

Theoretical and experimental study of guar gum sulfation

The synthesis of guar gum sulfates by a complex of sulfur trioxide with 1,4-dioxane was studied. The influence of temperature, process duration, and the volume of chlorosulfonic acid on the degree of substitution of guar gum sulfates was studied. The sulfation process has been optimized using the Box-Behnken design. It was shown that the optimal conditions for sulfation of guar gum with a complex of sulfur trioxide-1.4-dioxane: temperature 60 °C, duration 2.9 h, and a volume of chlorosulfonic acid of 3.1 ml. Sulfate groups embedding into the structure of guar gum was confirmed by elemental analysis and FTIR. The initial and sulfated guar gum were also characterized by methods: X-ray diffraction, scanning electron microscopy, and gel permeation chromatography. Using X-ray diffraction, it was shown that amorphization of guar gum occurs during sulfation. Using scanning electron microscopy, it was shown that the morphology of guar gum changes in the process of sulfation. Using gel permeation chromatography, it was shown in the process of guar gum sulfation by a complex of sulfur trioxide with 1,4-dioxane, the molecular weight decreases from 600 to 176 kDa. The geometric parameters of all complexes were carried out by using the DFT/B3PW91 method with a 6-31 + G (d,p) basis set. These structures are optimized to predict the important properties of a theme. MEP with contour map has been performed to obtain the electronic properties. Frontier molecular orbital HOMO-LUMO orbital diagram has been obtained for different energy levels and their band gap energies have been computed.

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.

Study on the shift of ultraviolet spectra in aqueous solution with variations of the solution concentration

In this study, we mainly focused on predictable regularities of the red shift of ultraviolet spectra for β-phenylethylamine (PEA), NaCl and NaOH in aqueous solution. The absorption peaks of the UV spectra near 191 nm of NaCl, NaOH and PEA in aqueous solution moved in the direction of a red shift while the molar absorption coefficient at the peak increased regularly with the increasing solution concentration. These shifts were obtained for solutions with concentrations ranging from 3.68 to 1000 mmol/L for NaCl, from 0.762 to 2000 mmol/L for NaOH, and from 0.0515 to 8.91 mmol/L for PEA. The plots of the logarithm of the solution concentration for NaCl and PEA versus the absorbance at 191 nm and at the peak were linear, and the plots of the logarithm of the solution concentration for NaCl and PEA versus the wavelength at the peak (shifted from 191 nm) were also linear. In addition, the plots of the logarithm of the solution concentration for NaOH that ranged from 0.762 to 1.96 mmol/L versus the absorbance at 191 nm and at the peak were linear as well as the plots of the logarithm of the solution concentration for NaOH that ranged from 1.96 to 2000 mmol/L versus the wavelength at the peak. The slopes of the absorbance at 191 nm of PEA, NaCl and NaOH were somewhat similar to the absorbance at the peak separately, whereas the slopes of the wavelengths at the peak were different from them. Finally, in order to obtain the predictable regularity of the red shift of the UV spectrum for the mixture, 22 ternary mixtures were prepared. The results indicate that the inhibiting effect of hydroxide ions (OH-) caused the wavelength near 206 nm to remain unchanged when the solution concentration of NaOH in the mixture was more than 0.762 mmol/L.

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.

Predicting the redshift on the ultraviolet spectrum using the peak area method

The ultraviolet (UV) absorption peaks of NaCl, NaOH, and $\beta $β-phenylethylamine (PEA) in an aqueous solution move toward redshift. We proposed the peak area method for the quantitative analysis of PEA, NaCl, and NaOH. First, we obtained the predictable regularities of the redshift of the single component sample. Then, we obtained the regularities of the redshift of the UV spectrum for the mixture by the peak height and peak area methods. Finally, the BP-ANN algorithm was applied to determine the concentration of the mixture using the peak height and peak area method. The results of the testing set showed that correlation coefficients (${{\rm R}^2}$R²) of 0.992, 0.993, and 0.992 were obtained by peak height method and 0.997, 0.998, and 0.998 were obtained by peak area method for NaCl, NaOH, and PEA, respectively. Meanwhile, the relative errors of the prediction of NaCl, NaOH, and PEA obtained by peak area method were less than 3%, whereas the REP of NaCl, NaOH, and PEA obtained by peak height method were more than 5%. Compared with the results of the peak height method, the results showed that the peak area was more accurate than the peak height in predicting the redshift of the UV spectrum.