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) Å3, 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, ß = 95.095 (6)°, V = 2007.4 (5)Å3 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.

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.

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.

trans-2,5-Di-methyl-piperazine-1,4-diium bis(perchlorate) dihydrate: crystal structure and Hirshfeld surface analysis.

The asymmetric unit of the title hydrated mol-ecular salt, C6H16N2 (2+)·2ClO4 (-)·2H2O, contains a half dication (completed by inversion symmetry), a perchlorate anion and a water mol-ecule. The extended structure consists of infinite chains of formula [(ClO4)H2O] n (n) (-) ions extending along the b axis linked by Ow-H⋯O (w = water) hydrogen bonds. These chains are cross-linked by the dications via N-H⋯Ow and weak C-H⋯O hydrogen bonds, thus forming a three-dimensional supra-molecular network. Three-dimensional Hirshfeld surface analysis and two-dimensional fingerprint maps reveal that the structure is dominated by H⋯O/O⋯H and H⋯H contacts.

m-Xylylenediaminium sulfate: crystal structure and Hirshfeld surface analysis.

The crystal structure of the title salt {systematic name: [1,3-phenyl-enebis(methyl-ene)]bis-(aza-nium) sulfate}, C8H14N2 (2+)·SO4 (2-), 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 inter-action 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.

Bis(4-amino-pyridinium) dichromate(VI).

The asymmetric unit of the title salt, (C5H7N2)2[Cr2O7], contains four independent cations and two independent dichromate anions. The crystal structure consists of discrete dichromate anions with an eclipsed conformation stacked in layers parallel to (010) at y = 1/4 and y = 3/4. These layers are linked via 4-amino-pyridinium cations by N-H⋯O and weak C-H⋯O hydrogen bonds, forming a three-dimensional supra-molecular network. In addition, π-π inter-actions are present in this structure; the shortest distance separating mean planes through 4-amino-pyridinium cations is 3.679 (6) Å.

Bis(1-methyl-piperazine-1,4-diium) di-µ-bromido-bis-[tetra-bromido-bismuthate(III)] dihydrate.

In the title hydrated salt, (C5H14N2)2[Bi2Br10]·2H2O, the com-plete [Bi2Br10](4-) biocta-hedron is generated by crystallographic inversion symmetry. The diprotonated piperazine ring adopts a chair conformation, with the methyl group occupying an equatorial position. In the crystal, the tetra-anions and water mol-ecules are linked by O-H⋯Br and O-H⋯(Br,Br) hydrogen bonds to generate [100] chains. The chains are crosslinked by N-H⋯Br, N-H⋯O and C-H⋯Br hydrogen bonds originating from the piperazinediium dications, thereby forming a three-dimensional network.

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

In the structure of the title salt, C6H16N2 (2+)·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, C9H26N3 (3+)·3NO3 (-), the triprotonated 1,1,4,7,7-penta-methyl-diethylenetri-amine mol-ecules 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)°.

Propane-1,2-di-ammonium chromate(VI).

In the title mol-ecular salt, (C3H12N2)[CrO4], each chromate anion accepts six N-H⋯O and C-H⋯O hydrogen bonds from nearby propane-1,2-di-ammonium cations. Three of the four O atoms of the chromate anion accept these bonds; the remaining Cr-O bond length is notably shorter than the others. In the crystal, the anions and cations stack in layers lying parallel to (100): the hydrogen-bonding pattern leads to a three-dimensional network.

1-Methyl-piperazine-1,4-dium bis-(hydrogen oxalate).

In the crystal structure of the title compound, C5H14N2 (2+)·2HC2O4 (-), the two crystallographically independent hydrogen oxalate anions are linked by strong inter-molecular O-H⋯O hydrogen bonds, forming two independent corrugated chains parallel to the b axis. These chains are further connected by N-H⋯O and C-H⋯O hydrogen bonds originating from the organic cations, forming a three-dimensional network. The diprotonated piperazine ring adopts a chair conformation, with the methyl group occupying an equatorial position.

N'-(2,4-Di-nitro-phen-yl)acetohydrazide monohydrate.

In the crystal structure of the title compound, C8H8N4O5·H2O, the organic and lattice water mol-ecules are linked together via N-H⋯O and O-H⋯O hydrogen bonds. A C-H⋯O inter-action is also observed between the organic mol-ecules. These hydrogen bonds and inter-actions lead to the formation of a three-dimensional network. An intra-molecular N-H⋯O hydrogen bond also occurs. The dihedral angle between the acetyl group and the almost planar hydrazide moiety [maximum deviation from the least-squares plane is 0.209 (2) Šfor one of the nitro O atoms] is 88.5 (3)°.

5-Amino-1H-1,2,4-triazol-4-ium hydrogen oxalate.

In the title salt, C2H5N4 (+)·C2HO4 (-), the hydrogen oxalate anions form corrugated chains parallel to the c axis, linked by inter-molecular O-H⋯O hydrogen bonds. The 5-amino-1H-1,2,4-triazol-4-ium cations are connected into centrosymmetric clusters via weak C-H⋯N hydrogen bonds forming nine-membered rings with an R 3 (3)(9) motif. These clusters are inter-connected via anions through N-H⋯O hydrogen bonds, building a three-dimensional network.

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) Šfrom 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.

2,3-Xylidinium nitrate.

In the crystal structure of the title compound, C8H12N(+)·NO3 (-), the 2,3-xylidinium (2,3-di-methyl-anilinium) cations are connected to the nitrate anions through bifurcated N-H⋯(O,O) and weak C-H⋯O hydrogen bonds, generating corrugated layers parallel to (001) at z = 0.25 and 0.75. These layers are connected via C-H⋯O inter-actions, giving rise to a three-dimensional network.

Propane-1,3-diammonium dichromate(VI).

The title compound, (C(3)H(12)N(2))[Cr(2)O(7)], consists of a discrete dichromate anion with an eclipsed conformation and a propane-1,3-diammonium cation. Both kinds of ions have a mirror plane passing through the bridging O atom and the central methyl-ene C atom of the Cr(2)O(7) (2-) and C(3)H(12)N(2) (2+) moieties, respectively. Anions and cations are alternately stacked to form columns parallel to the b axis. Ions are linked by intra- and inter-column hydrogen bonds of types N-H⋯O and C-H⋯O, involving O atoms of the dichromate anions as acceptors, and ammonium or methyl-ene groups as donors.

2-Amino-pyrimidinium dihydrogen phosphate monohydrate.

In the title compound, C(4)H(6)N(3) (+)·H(2)O(4)P(-)·H(2)O, the pyrimidin-ium ring is essentially planar, with an r.m.s. deviation of 0.0016 Å. In the structure, pairs of symmetry-related anions are connected into centrosymmetric clusters via strong O-H⋯O hydrogen bonds forming six-membered rings with an R(2) (2)(6) motif. These clusters are inter-connected via water mol-ecules through OW-H⋯O hydrogen bonds, building an infinite layer parallel to the ab plane. Moreover, infinite chains of 2-amino-pyrimidinium cations spread along the a-axis direction. These chains are connected to the inorganic layer through N-H⋯O, C-H⋯O and C-H⋯N hydrogen bonds, which, together with electrostatic and van der Waals inter-actions, contribute to the cohesion and stability of the network in the crystal structure.