Monoclinic Space Group Research Articles

Crystal structure of the monocupin ring-cleaving dioxygenase 5-nitrosalicylate 1,2-dioxygenase from Bradyrhizobium sp.

5-Nitrosalicylate 1,2-dioxygenase (5NSDO) is an iron(II)-dependent dioxygenase involved in the aerobic degradation of 5-nitroanthranilic acid by the bacterium Bradyrhizobium sp. It catalyzes the opening of the 5-nitrosalicylate aromatic ring, a key step in the degradation pathway. Besides 5-nitrosalicylate, the enzyme is also active towards 5-chlorosalicylate. The X-ray crystallographic structure of the enzyme was solved at 2.1 Å resolution by molecular replacement using a model from the AI program AlphaFold. The enzyme crystallized in the monoclinic space group P21, with unit-cell parameters a=50.42, b = 143.17, c = 60.07 Å, β = 107.3°. 5NSDO belongs to the third class of ring-cleaving dioxygenases. Members of this family convert para-diols or hydroxylated aromatic carboxylic acids and belong to the cupin superfamily, which is one of the most functionally diverse protein classes and is named on the basis of a conserved β-barrel fold. 5NSDO is a tetramer composed of four identical subunits, each folded as a monocupin domain. The iron(II) ion in the enzyme active site is coordinated by His96, His98 and His136 and three water molecules with a distorted octahedral geometry. The residues in the active site are poorly conserved compared with other dioxygenases of the third class, such as gentisate 1,2-dioxygenase and salicylate 1,2-dioxygenase. Comparison with these other representatives of the same class and docking of the substrate into the active site of 5NSDO allowed the identification of residues which are crucial for the catalytic mechanism and enzyme selectivity.

Crystal structures and Hirshfeld surface analyses of (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-phenyl-diazene, (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(4-methyl-phen-yl)diazene, (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(4-meth-oxy-phen-yl)diazene and (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(3-methyl-phen-yl)diazene.

The crystal structures and Hirshfeld surface analyses of four similar azo compounds are reported. (E)-1-[1-(4-tert-Butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-phenyl-diazene, C18H18Cl2N2, (I), and (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(4-methyl-phen-yl)diazene, C19H20Cl2N2, (II), crystallize in the monoclinic space group C2/c with Z = 8, and (E)-1-[1-(4-tert-butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(4-meth-oxy-phen-yl)diazene, C19H20Cl2N2O, (III), in the monoclinic space group P21/c with Z = 4. (E)-1-[1-(4-tert-Butyl-phen-yl)-2,2-di-chloro-ethen-yl]-2-(3-methyl-phen-yl)diazene, C19H20Cl2N2, (IV), crystallizes in the triclinic space group P with Z = 4 and comprises two mol-ecules (A and B) in the asymmetric unit. In the crystal structures of (I) and (II), mol-ecules are linked by C-H⋯π and C-Cl⋯π inter-actions, forming layers parallel to (02), while mol-ecules of (III) are linked by C-H⋯O contacts, C-H⋯π and C-Cl⋯π inter-actions forming layers parallel to (02). The stability of the mol-ecular packing is ensured by van der Waals forces between these layers. In the crystal structure of (IV), mol-ecules are linked by C-H⋯π and C-Cl⋯π inter-actions, forming a tri-periodic network.

Crystal structure of 1-(4-bromo-phen-yl)but-3-yn-1-one.

The title compound, 1-(4-bromo-phen-yl)but-3-yn-1-one, C10H7BrO, crystallizes in the monoclinic space group P21/n with one mol-ecule in the asymmetric unit. The structure displays a planar geometry. The crystal structure is consolidated by C-H⋯O hydrogen bonding and a short C=O⋯C≡C (acetyl-ene) contacts. Hirshfeld surface analysis indicates that H⋯H, C⋯H/H⋯C and H⋯Br/Br⋯H inter-actions play a more important role in consolidating the crystal structure compared to H⋯O/O⋯H and C⋯C contacts.

Structural analysis and molecular docking study of pachypodostyflavone: A potent anti-onchocerca

In order to get a better insight into the intermolecular interactions in the solid state of the naturally occurring flavone derivative, pachypodostyflavone, its single crystal X-ray diffraction was performed and analysed. Structural analysis revealed that the compound crystallises in the monoclinic space group P21/c with a = 23.910(1), b = 13.256(1), c = 8.044(1) Å, β = 94.96(1), Z = 4. An experimental and theoretical investigation of pachypodostyflavone is presented, combining the use of vibrational spectroscopies (IR, NMR and UV–visible) with density functional theory (DFT) that employs hybrid B3LYP exchange correlation functional with 6–311++G(d,p) as basis set. HOMO-LUMO, MEP, and NBO analysis was investigated and reactivity descriptors were calculated. Analysis of chemical reactivity indicates that the compound is more reactive in water, which is a good indicator for clinical preparations. Thermodynamic properties viz., heat capacity, entropy, and enthalpy change of title molecule at various temperatures are presented. Additionally, molecular docking results revealed that pachypodostyflavone structure strongly binds to the parasitic worm Onchocerca volvulus by relative binding affinity of –7.00 kcal mol–1.

High-humidity Sensor of a New Trinuclear Ti3-Oxo Cluster

Crystalline polyoxo-titanium clusters (PTCs), as a molecular model of TiO2 nanomaterials, have attracted unprecedented attention due to their designable structure, tunable band gap, catalysis, and photochromic properties. A new trinuclear Ti3-oxo cluster, [Ti3(µ2-O)(µ3-O)(abz)6(OiPr)2] CH3CNH2O (Ti3), was synthesized by solvothermal method with a yield of 60% by using 4-aminobenzoic acid as ligand. Single-crystal X-ray diffraction shows that it has a [Ti3(µ2-O)(µ3-O)(abz)6(OiPr)2] trinuclear cluster structure. Ti3 crystallizes in monoclinic space group P21/c with a = 11.091(1), b = 22.837(2), c = 22.754(1) Å, ß = 90.580(6)°, V = 5763.0(6) Å3, Z = 4, Dc = 1.345 g·cm−3, F(000) = 2412, µ = 2.743 mm−1, R = 0.0796, and wR = 0.2260 (I >2σ(I)).Ti3 shows typical semiconductive behavior determined by temperature-dependent conductivity test. The chemiresistive humidity sensor fabricated by Ti3 showed good performance, including high response (four orders of magnitude current change from 0 to 100% RH) and fast response time (160 s) and recovery time (26 s).

Investigation of Photoelectrocatalytic and Magnetic Properties of Sr2YbRu1-xTaxO6 (x = 0, 0.25, 0.5, 0.75, and 1).

We report the effect of substitution of Ru by Ta in Sr2YbRuO6 on its magnetic and photoelectrocatalytic properties. The powder X-ray diffraction data, was satisfactorily refined in the monoclinic space group, P21/n. The DC magnetization studies indicated that Sr2YbRuO6 shows antiferromagnetic interaction through Yb-O-Ru orbital ordering, with the highest Weiss temperature, among Sr2YbRu1-xTaxO6 (x = 0, 0.25, 0.5, and 0.75) which have values of -148, -125, -118, and -102 K, respectively. The difference in observed and theoretical magnetic moments was found to increase as x increases. It was also observed that with the increase of Ta concentration in Sr2YbRu1-xTaxO6, the band gap increased almost linearly, from 1.78(1) eV (x = 0) to 2.08(1) (x = 0.75), and thereafter a sharp increase 2.65(1) eV (x = 1) was observed, with the lowering of energy level of valence band, along with disruption in orbital ordering as x increases. The photoelectrocatalytic oxygen evolution reaction (OER) studies carried out on the series yield a maximum photocurrent density of 17 μA/cm2 and photoresponse current of 5.5 μA/cm2 at 0.8 V at an onset potential at 0.29 V vs Ag/AgCl for Sr2YbRuO6. The XPS analysis showed Ta and Ru to be in +5/+4 oxidation states, with the highest concentration of Ru4+ ion observed for Sr2YbRuO6. The presence of oxygen vacancies was confirmed by XPS as well as EPR studies.

Synthesis, crystal structure, Hirshfeld surface analysis and DFT study of the 1,1'-(buta-1,3-diyne-1,4-di-yl)bis-(cyclo-hexan-1-ol).

The title compound, C16H22O2, was synthesized in order to obtain its guest-free form because 'wheel-and-axle'-shaped mol-ecules tend to crystallize from solutions as solvates or host-guest mol-ecules. It crystallizes in the monoclinic space group P2/c with two crystallographically non-equivalent mol-ecules, one situated on an inversion center and the other on a twofold axis. The rod-like 1,3-diyne fragments have the usual linear geometry. In the crystal, O-H ⋯ O bonds form eight-membered rings of the R 4 4(8) type, linking mol-ecules into layers. The Hirshfeld surface analysis indicates that the largest con-tributions are from inter-molecular H⋯H (ca 71%) and H⋯C/C⋯H (ca 19%) contacts. The energies of the frontier mol-ecular orbitals were determined by DFT calculations at the B3LYP/def2-TZVP level of theory.

Crystal structure of 9,10-bis-((perchloro-phenyl)-ethynyl)anthracene determined from three-dimensional electron diffraction data

Abstract The crystal structure of the title compound was determined using electron diffraction data collected in continuous rotation mode. The structure was successfully solved and refined kinematically in the monoclinic space group P21/c, with a Z value of 2 and Z′ value of 0.5. Within the crystal structure, the entire molecule is predominantly flat. The molecular packing exhibits a herringbone pattern, distinct from that of the unchlorinated analogue molecule. The largest facet of the crystals, which faces the supporting carbon film, is designated as (0 1 ‾ 1 ‾ $\bar{1}\bar{1}$ ).

Synthesis, spectral, single crystal XRD structure, Hirshfeld surface, molecular docking and in silico ADMET studies of symmetrical azine: 1,2-bis(4 (methylthio) benzylidene)hydrazine

FT-IR, 1H NMR and 13C NMR spectrum approaches were used to characterise 1,2-bis(4 (methylthio)benzylidene)hydrazine (MTBHD), which was synthesized under microwave irradiation. A study using single crystal- XRD analysis, the molecule MTBHD with the empirical formula C16H16N2S2 crystallises in the monoclinic space group P121/n1. To identify the lead chemical, symmetrical azine ADME properties and interactions with the estrogen receptor were anticipated using a molecular docking experiment (2IOK). Frontier molecular orbitals, specifically HOMO-LUMO, were calculated and the maximum values were recorded in order to investigate the forbidden energy gap.

Synthesized and characterization of a new Cd(II)-based coordination polymer: Sensing activity and photocatalytic activity against antibiotic

A new coordination polymer (CP) with formula [Cd4(2.2′-bipy)4(HL)2·H2O] (1) [H5L = 2,5ʹ-di(3,5-dicarboylphenoxy)benzoic acid, 2.2ʹ-bipy = 2.2ʹ-bipyridine] has been synthesized. 1 is characterized by single X-ray diffraction, FT-IR, UV–visible spectroscopy and TGA. X-ray crystallography exposes that 1 crystallized in monoclinic space group with C2/c point group. (1) has intramolecular hydrogen bonding and 2D pillared-layer hydrogen-bonded organic frameworks (HOFs). 1 exhibits sensitive and selective detection for nitrofurazone (NFZ) (Ksv = 1.08 × 103 M−1 and LOD = 1.38 ppm). Moreover, the photocatalytic degradation properties of 1 are also investigated against NFZ. In addition, the plausible mechanism displayed by 1 for the catalytic degradation toward NFZ was proposed using the LC-MS studies. The Hirshfeld surfaces analysis revealed that the different types of intermolecular interactions (C···C, H···C, H···H, and O···H) are presented.

Hg3(SeO3)2(SO4): A UV Nonlinear Optical Mercury Selenite Sulfate Constructed by Neat [Hg6O8(SeO3)4]∞ Layers and SO4 Tetrahedra.

A novel mercury selenite sulfate named Hg3(SeO3)2(SO4) has been successfully synthesized under a mild hydrothermal method. Hg3(SeO3)2(SO4) crystallizes in a monoclinic space group P21 and features a unique three-dimensional (3D) frame structure formed by [Hg6O8(SeO3)4]∞ layers and SO4 tetrahedra, which enables it to exhibit a comprehensive performance of a moderate second-harmonic generation (SHG) response of approximately 1.3 times that of baseline KH2PO4 (KDP), a moderate birefringence (0.118@546 nm), and a wide band gap (4.70 eV), which indicates that it has potential for application as an ultraviolet (UV) nonlinear optical material. Detailed theoretical calculations show that the Hg2+-based polyhedra with large polarizability and deformability and the SeO3 groups with stereochemically active lone pair (SCALP) electrons are the main contributors to moderate optical properties.

Two New Aluminoborates with 3D Porous-Layered Frameworks.

Two new aluminoborates, NaKCs[AlB7O13(OH)]·H2O (1) and K4Na5[AlB7O13(OH)]3·5H2O (2), have been hydro(solvo)thermally made with mixed alkali metal cationic templates. Both 1 and 2 crystallize in the monoclinic space group P21/n and contain similar units of [B7O13(OH)]6- cluster and AlO4 tetrahedra. The [B7O13(OH)]6- cluster is composed of three classical B3O3 rings by vertex sharing, of which two of them connect with AlO4 tetrahedra to constitute monolayers, and one provides an O atom as a bridging unit to link two oppositely orientated monolayers by Al-O bonds to form 3D porous-layered frameworks with 8-MR channels. UV-Vis diffuse reflectance spectra indicate that both 1 and 2 exhibit short deep-UV cutoff edges below 190 nm, revealing that they have potential applications in deep-UV regions.

High‐pressure Synthesis, Structure, IR Spectroscopy, and Theoretical Calculations of the New Silver Tetraborate Ag2B4O7 with a Unique Crystal Structure

AbstractAg2B4O7 is synthesized at high‐pressure/high‐temperature conditions of 11 GPa and 1073 K in a multianvil device. It crystallizes in the monoclinic centrosymmetric space group P21/c (no. 14) with four formula units per unit cell (Z=4). The cell parameters are a=787.53(3), b=651.63(2), c=943.88(3) pm, β=107.911(2)°, and V=460.90(3) Å3. Ag2B4O7 crystallizes in a unique crystal structure that consists of complex anionic borate layers with Ag+ ions in between. Additionally, the silver cations show argentophilic interactions. The compound was analysed via single‐crystal and powder diffraction as well as infrared spectroscopy. Furthermore, theoretical calculations at HSEsol level were conducted.

Syntheses and characterizations of 2-nitrobenzaldehyde amino acid Schiff base reductive amination compounds

Condensation of 2-nitrobenzaldehyde with five amino acid compounds (valine, glycine, leucine, aspartic acid, and glutamic acid) gives the corresponding Schiff bases, which upon treatment with sodium borohydride afford the reductive amination products 1−5. Compounds 1−5 have been well characterized by FT-IR and 1H NMR spectroscopic techniques, in addition to X-ray crystallography, from which the structure of compound 2 has been established. Compound 2 crystallizes in monoclinic space group P21/c, with a = 12.215(8), b = 8.096(5), c = 10.608(7) Å, β = 115.324(7), and Z = 4.

Insights into Synthesis, Crystal Structure, Bioactivity and Computational Studies of Cu(II) and Zn(II) Carboxylates Containing Aminopyridine

Abstract[Cu2(μ‐2‐chlorobenzoato‐O,O’)4Cl2].2(4‐DMAPH) (1) and [Zn2(μ‐2‐chlorobenzoato‐O,O’)4(4‐DMAP)2] (2) (4‐DMAP=4‐Dimethylaminopyridine) were synthesized from CuCl2/Zn(NO)3)2 . 6H2O, 2‐chlorobenzoic acid and 4‐dimethylaminopyridine in methanol under reflux. Compounds were comprehensively characterized by elemental analyses, conductance measurement, spectroscopic and X‐ray diffraction studies. Complexes crystallized in the monoclinic space group P21/n having dinuclear paddle‐wheel structure. DFT studies along with NCI plot, QTAIM analysis indicate presence of N−H⋯Cl, C−H⋯O, C−H⋯π interactions in 1 and CH3⋯π, π⋯π and C−H⋯Cl in 2. The charge distribution in the complexes was shown via MEP analysis. Complexes interact with CT‐DNA in moderately strong non‐intercalative mode of binding. Antimicrobial study against Shigella flexneri (B), Streptococcus pneumoniae (K), Klebsiella pneumoniae (P) and Shigella boydii (Q) shows appreciable activity of 1 whereas compound 2 is comparatively less active. In vitro cytotoxicity study against cell lines (L‐132) exhibits moderate activity by the complexes, but compound 2 shows significant cell inhibition activity against cell lines K‐562. The complexes are emissive in nature.

Tb2Co(B2O5)2 and Tb2Cu(B2O5)2 – two new borates with gadolinite-type structures

Abstract Using high-pressure/high-temperature synthesis methods, it was possible to increase the number of known borates with a crystal structure derived from gadolinite. Syntheses of Tb2Co(B2O5)2 (8 GPa, 1000 °C) and Tb2Cu(B2O5)2 (11 GPa, 650 °C) were carried out in a Walker-type multianvil device. The crystal structures were determined by single-crystal X-ray diffraction methods and Rietveld refinements of the powder patterns. The new compounds were further characterized by their infrared spectra. The lanthanoid cobalt and copper borates Tb2Co(B2O5)2 and Tb2Cu(B2O5)2 crystallize in the monoclinic space group P21/c (no. 14) with the unit cell parameters a = 4.5630(1), b = 7.2991(2), c = 9.4161(2) Å, and β = 91.14(1)° for the cobalt and a = 4.5757(1), b = 7.3078(2), c = 9.3771(3) Å, β = 90.73(1)° for the copper compound.

Synthesis of <I>N</I>'-(2,3-dihydroxybenzylidene)-4-methylbenzohydrazide: Spectroscopic Characterization and X-ray Structure Determination

p-Toluic hydrazide was used for synthetizing a new Schiff base <I>N</I>'-(2,3-dihydroxybenzylidene)-4-methylbenzohydrazide (I). The prepared compound was characterized by elemental analysis, infrared and ¹H and ¹³C NMR spectroscopy techniques, and the structure of compound (I) was determined by single-crystal X-ray diffraction study. The compound (C₁₅H₁₄N₂O₃) crystallises in the monoclinic space group <I>P</I>2₁/<i>n</i> with the following unit cell parameters: <i>a</i> = 11.7820 (6) Å, <i>b</i> = 8.5278 (4) Å, <i>c</i> = 13.6054 (7) Å, <i>β</i> = 109.346 (5)°, <I>V </I>= 1289.81 (12) ų, <I>Z</I> = 4, <I>R</I>₁ = 0.071 and <i>wR</i>₂ = 0.197. The X-ray structure shows that the compound (I) adopts an <I>E</I> configuration with respect to the double bond C7=N1. The carbonyl oxygen atom O3 and the nitrogen atom N1 of the hydrazide moiety are in a <i>syn</i> conformation with respect to C8—N2 bond. The crystal packing of compound (I) is stabilized by intramolecular O(phenol)–H•••N(carbohydrazide) which results in an <I>S</I>(6) ring motif and intermolecular O(phenol)–H•••O(carbohydrazide) hydrogen bonds which form chains. The carbonohydrazide moiety C=N–N–C(O)–N–N=C fragment is almost coplanar with the two benzene rings with dihedral angles of their mean planes of 10.35° [C1—C6] and 7.99° [C9—C14], respectively. The dihedral angle between the mean planes of the phenyl rings is 2.46°.

Synthesis, spectroscopic findings, SEM/EDX, DFT, and single-crystal structure of Hg/Pb/Cu–SCN complexes: In silico ADME/T profiling and promising antibacterial activities

This work contemplates synthesizing M-SCN crystal compounds (M = Hg/Pb/Cu) in the presence of respective metal salts and exogenous ancillary SCN− ion by slowly evaporating the mixed solvent (CH3OH + ACN). The complexes were characterized by spectroscopy, SEM/EDX, and X-ray crystallography. The Hg-Complex, Pb-Complex, and Cu-Complex crystallize in the monoclinic space group (Z = 2/4). The crystal packing fascinatingly consists of weak covalent bonding and Pb⋯S contacts of tetrel type bond. Here are the incredible supramolecular topographies delineated by the Hirshfeld surface and 2D fingerprint plot. The B3LYP/6–311++G (d, p) level calculations in the gas phase optimized the compound's geometry. The energy difference (Δ) between HOMO-LUMO and global reactivity parameters investigates the complex's energetic activity. MESP highlights the electrophilic/nucleophilic sites and H-bonding interactions. Molecular docking was conceded with the Gram- + ve bacterium Bacillus Subtilis (PDB ID: 6UF6) and the Gram-ve bacterium Proteus Vulgaris (PDB ID: 5HXW) to authenticate the bactericidal activity. ADME/T explains the various pharmacological properties. In addition, we studied the antibacterial activity with MIC (μg/mL) values and time-kill kinetics against Staphylococcus aureus (ATCC 25923) and Bacillus subtilis (ATCC 6635) as Gram-positive, Pseudomonas aeruginosa (ATCC 27853) and Escherichia coli (ATCC 25922) as Gram-negative bacteria.

New organic (Dye) Sensitized Solar Cells with ferric iron III oxide doped barium chromite (Fe2O3-BaCrO4)

A new organic Dye has been successfully synthesized by a slow evaporation method. A single crystal x-ray diffraction study confirms the crystal system and lattice parameters of E-2HM4N. Powder XRD and NMR data were used to determine the crystal structure. The crystal system is a monoclinic Pc space group. Thus, the PXRD analysis confirms the good crystallinity nature and purity. UV–Vis spectral analysis has been used to measure the optical absorption of E-2HM4N its confirmed by a semiconducting material and the band gap energy is 2.1 eV. The nano dimension morphology of the particle was confirmed by FESEM. The characterization is (I -V) relationships between Maximum Voltage (518 mV) and Maximum Current (1.6 mA) is calculated by efficiency 0.8%. According to a survey of the literature, binary metal oxide Fe2BaCrO7 with organic dye E-2HM4N is newly reported. A flexible DSSCs was successfully fabricated.

Synthesis of the first remdesivir cocrystal: design, characterization, and therapeutic potential for pulmonary delivery

While cocrystal engineering is an emerging formulation strategy to overcome drug delivery challenges, its therapeutic potential in non-oral applications remains not thoroughly explored. We herein report for the first time the successful synthesis of a cocrystal for remdesivir (RDV), an antiviral drug with broad-spectrum activities against RNA viruses. The RDV cocrystal was prepared with salicylic acid (SA) via combined liquid-assisted grinding (LAG) and thermal annealing. Formation of RDV-SA was found to be a thermally activated process, where annealing at high temperature after grinding was a prerequisite to facilitate the cocrystal growth from an amorphous intermediate, rendering it elusive under ambient preparing conditions. Through powder X-ray analysis with Rietveld refinement, the three-dimensional molecular structure of RDV-SA was resolved. The thermally annealed RDV-SA produced by LAG crystalized in a non-centrosymmetric monoclinic space group P21 with a unit cell volume of 1826.53(17) Å3, accommodating one pair of RDV and SA molecules in the asymmetric unit. The cocrystal formation was also characterized by differential scanning calorimetry, solid-state nuclear magnetic resonance, and Fourier-transform infrared spectroscopy. RDV-SA was further developed as inhaled dry powders by spray drying for potential COVID-19 therapy. The optimized RDV-SA dry powders exhibited a mass median aerodynamic diameter of 4.33 ± 0.2 μm and fine particle fraction of 41.39 ± 4.25 %, indicating the suitability for pulmonary delivery. Compared with the raw RDV, RDV-SA displayed a 15.43-fold higher fraction of release in simulated lung fluid at 120 min (p = 0.0003). RDV-SA was safe in A549 cells without any in vitro cytotoxicity observed in the RDV concentration from 0.05 to 10 µM.