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).

Impact of non-covalent interactions on FT-IR spectrum and properties of 4-methylbenzylammonium nitrate. A DFT and molecular docking study

In this research, the impact of non-covalent interactions on the FT-IR spectrum and structural, electronic, topological and vibrational properties of hybrid 4-methylbenzylammonium nitrate (4MBN) have been studied combining B3LYP/CC-PVTZ calculations with molecular docking. 4MBN was synthesized and characterized by using the FT-IR spectrum while the optimized structures in gas phase and in ethanol and aqueous solutions have evidenced monodentate coordination between the nitrate and methylbenzylammonium groups, in agreement with that experimental determined for this species by X-ray diffraction. Here, non-covalent interactions were deeply analyzed in terms of topological parameters (AIM), electron localization function (ELF), localized orbital locator (LOL), Hirshfeld surface and reduced density gradient (RDG) method. Weak interactions such as H-bonds, VDW and steric effect in 4MBN were visualized and quantified by the independent gradient density (IGM) based on the promolecular density. The hyper-conjugative and the delocalization of charge in 4MBN have been elucidated by natural bonding orbital (NBO) while its chemical reactivity was studied and discussed by using molecular electrostatic potential surface (MESP), frontier molecular orbital (FMOs), density of state (DOS) and partial density of state (PDOS). The complete vibrational assignments of 69 vibration modes expected for 4MBN are reported together with the scaled force constants while the electronic transitions were evaluated by TD-DFT calculations in ethanol solution. Thermal analysis (DTA and DSC) was also determined. Molecular docking calculations have suggested that 4MBN presents biological activity and could act as a good inhibitor against schizophrenia disease.

m-Xylylenediaminium sulfate: crystal structure and Hirshfeld surface analysis

The crystal structure of the title salt consists of infinite (100) sheets of alternating organic and inorganic entities The m-xylylenediaminium cations are linked to the sulfate anions by N—H⋯O and asymmetric bifurcated N—H⋯(O,O) hydrogen bonds, generating a three-dimensional network. The Hirshfeld surface analysis and the two-dimensional fingerprint maps indicate that the packing is dominated by H⋯O/O⋯H and H⋯H contacts.

The crystal structure of the title salt {systematic name: [1,3-phenyl­enebis(methyl­ene)]bis­(aza­nium) sulfate}, C₈H₁₄N₂²⁺·SO₄²⁻, consists of infinite (100) sheets of alternating organic and inorganic entities The m-xylylenediaminium cations are linked to the sulfate anions by N—H⋯O and asymmetric bifurcated N—H⋯(O,O) hydrogen bonds, generating a three-dimensional network. A weak C—H⋯O inter­action also occurs. The Hirshfeld surface analysis and the two-dimensional fingerprint maps indicate that the packing is dominated by H⋯O/O⋯H and H⋯H contacts.

trans-2,5-Di-methyl-piperazine-1,4-diium dinitrate

In the structure of the title salt, C₆H₁₆N₂²⁺·2NO₃⁻, the cations are connected to the anions through bifurcated N—H⋯(O,O) and weak C—H⋯O hydrogen bonds, generating corrugated layers parallel to the (100) plane. The organic cation is centrosymmetric and the diprotonated piperazine ring adopts a chair conformation, with the methyl groups occupying equatorial positions.

Dopaminium nitrate

THE ASYMMETRIC UNIT OF THE TITLE SALT [SYSTEMATIC NAME: 2-(3,4-di-hydroxy-phen-yl)ethanaminium nitrate], C8H12NO2 (+)·NO3 (-), contains two independent cations and two independent nitrate anions. The crystal structure consists of discrete nitrate ions stacked in layers parallel to (010). These layers are linked via the dopaminium cations by O-H⋯O, N-H⋯O and weak C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular network.

m-Xylylenediaminium dinitrate

The asymmetric unit of the title salt, C8H14N2 (2+)·2NO3 (-), contains two independent dications and four independent nitrate anions. The crystal structure consists of discrete nitrate ions, three of which stack in layers parallel to (001) at z = 0 and 0.5. These layers are connected via m-xylylenediaminium dications. The fourth anion is sandwiched by the two independent organic cations in the asymmetric unit. In the crystal, the ions are connected by a large number of bifurcated and non-bifurcated N-H⋯O(O) hydrogen bonds, forming sheets parallel to (100). These sheets are connected by C-H⋯O hydrogen bonds, forming a three-dimensional network.

1,1,4,7,7-Penta-methyl-diethylenetri-ammonium trinitrate

In the title compound, C₉H₂₆N₃³⁺·3NO₃⁻, the triprotonated 1,1,4,7,7-penta­methyl­diethylenetri­amine mol­ecules are linked to the nitrate anions by multiple bifurcated N—H⋯(O,O) and weak C—H⋯O hydrogen bonds. The organic cation is characterized by N—C—C—N torsion angles of −176.2 (2) and 176.6 (2)°.

4-Methyl-benzyl-ammonium nitrate

In the title salt, C8H12N(+)·NO3 (-), the N atom of the 4-methyl-benzyl-ammonium cation is displaced by 1.366 (2) Å from the mean plane of the other atoms. In the crystal, the cations are connected to the anions by N-H⋯O and N-H⋯(O,O) hydrogen bonds, generating a layered network parallel to (100). A weak C-H⋯O inter-action also occurs.