JOURNAL OF CHEMICAL CRYSTALLOGRAPHY

Synthesis, Structure, Hirshfeld Surface Analysis, Non-Covalent Interaction, and In Silico Studies of 4-Hydroxy-1-[(4-Nitrophenyl)Sulfonyl]Pyrrolidine-2-Carboxyllic Acid
Ugwu DI, Eze FU, Ezeorah CJ, Rhyman L, Ramasami P, Tania G, Eze CC, Uzoewulu CP, Ogboo BC and Okpareke OC
The new compound 4-hydroxy-1-[(4-nitrophenyl)sulfonyl]pyrrolidine-2-carboxyllic acid was obtained by the reaction of 4-hydroxyproline with 4-nitrobenzenesulfonyl chloride. The compound was characterized using single crystal X-ray diffraction studies. Spectroscopic methods including NMR, FTIR, ES-MS, and UV were employed for further structural analysis of the synthesized compound. The title compound was found to have crystallized in an orthorhombic crystal system with space group P222. The S1-N1 bond length of 1.628 (2) Å was a strong indication of the formation of the title compound. The absence of characteristic downfield H NMR peak of pyrrolidine ring and the presence of S-N stretching vibration at 857.82 cm on the FTIR are strong indications for the formation of the sulfonamide. The experimental study was complemented with computations at the B3LYP/6-311G +  + (d,p) level of theory to gain more understanding of interactions in the compound at the molecular level. Noncovalent interaction, Hirsfeld surface analysis and interaction energy calculations were employed in the analysis of the supramolecular architecture of the compound. Predicted ADMET parameters, awarded suitable bioavailability credentials, while the molecular docking study indicated that the compound enchants promising inhibition prospects against dihydropteroate synthase, DNA topoisomerase, and SARS-CoV-2 spike.
Crystal Structure Analysis of 4-Oxo, 4-hydroxy- and 4-alkyl-7-bromopyrazolo[5,1-][1,2,4]triazines
Ivanov SM and Koltun DS
The crystal structures of 8-R-7-bromo-3--butyl-1-R-pyrazolo[5,1-][1,2,4]triazin-4(1)-ones (R = CN, COEt, NO, R = H, 1:1 and 3:1 solvates with DMSO; R = CN, COEt, R = CHBoc), 8-R-7-bromo-3--butyl-1-R-1,4-dihydropyrazolo[5,1-][1,2,4]triazin-4-ols (R = CN, R = -Bu; R = Br, R = CHBoc), 1,4-dihydro- and aromatic 7-R-3--butyl-4-R-8-methylpyrazolo[5,1-][1,2,4]triazines (R = H, R = -Pr; R = Br, R = -Bu) were investigated by X-ray diffraction analysis. The structural preferences and different packing modes based on the intermolecular interactions were analyzed by the Hirshfeld surface and energy framework analysis.
Identification of seven-coordinate Ln ions in a Ln[15-MC -5](OAc)Cl species crystallized from methanol and pyridine
Biros ES, Ward CL, Allen MJ and Lutter JC
The title metallacrown (MC) complexes Ln[15-MC-5](OAc)CI(CHN) (), where OAc is acetate, shi is salicylhydroximate, and Ln = Gd and Dy, were synthesized via a self-assembly reaction in methanol and pyridine. Single crystals were grown using slow evaporation and characterized using X-ray diffraction. Seven-coordinate capped octahedron geometries were observed for the lanthanide ion in both complexes, which is uncommon for trivalent lanthanide species. The 15-MC-5 is a ruffled metallacrown archetype similar to previously reported mixed-valent manganese metallacrowns.
Synthesis and crystal structure of a phenazine N-oxide
Ding K, Dibrov SM and Hermann T
The preparation and crystal structure of 8-chloro-1H-pyrrolo[2,3-b]phenazine 5-oxide () are described. Compound formed dark purple crystals from deeply colored solution in methanol. Crystal plates were in the triclinic system, P-1 space group with unit cell parameters = 6.9514(8), = 9.1568(10), = 10.2067(11), α = 84.509(2), = 82.936(2), γ = 72.357(2) and a cell volume of 613.25(12) A. The title compound which contains the first example of the extensively conjugated pyrrolo-phenazine N-oxide system exhibits strong light absorption in the green to cyan wavelength range which disappears upon protonation.
Crystal structure of a benzimidazole hepatitis C virus inhibitor free and in complex with the viral RNA target
Dibrov SM, Parker MA, Bergdahl BM and Hermann T
The crystal structure of 8-((dimethylamino)methyl)-1-(3-(dimethylamino)propyl)-1,7,8,9-tetrahydrochromeno[5,6-d]imidazol-2-amine (), an inhibitor of the hepatitis C virus internal ribosome entry site, is described and compared to the structure of the compound in complex with the viral RNA target. Compound crystallized by pentane vapor diffusion into dichloroethane solution. It crystallized in the monoclinic system, P2/c space group with unit cell parameters = 15.7950(5) Å, = 14.0128(4) Å, = 8.8147(3) Å, = 94.357(2)° and a cell volume of 1945.34(11) A. Packing interactions in the small molecule crystal lattice correspond to key interactions of the compound with the viral RNA target.
Structural and Spectral Analyses of 2-[(2-Benzothiazolylmethyl)thio]-benzenamine and 2-[(2-Benzothiazolylmethyl)thio]-benzenamine hydrobromide
Demoin DW, Barnes CL, Hoffman TJ and Jurisson SS
2-[2-benzothiazoylmethyl)thio]-benzenamine, which was first reported in 1898, was isolated from the reaction of bromoacetyl bromide and 2-aminothiophenol [1]. The product crystallized from an aqueous methanol solution of the reaction mixture to which nickel(II) acetate had been added. 2-[(2-benzothiazolylmethyl)thio]-benzenamine crystallized in the monoclinic system, in space group C2/c, with cell dimensions of a = 27.392 (19) Å, b = 4.730 (3) Å, and c = 23.686 (16) Å, β = 122.465 (6)°, V = 2589(3) Å(3), Z = 8 and refined to R = 0.0343 and R(w) = 0.0844. Crystallization from methanol yielded the product as the hydrobromide salt in the monoclinic space group Cc, with cell dimensions of a = 10.488 (3) Å, b = 33.404 (9) Å, c = 5.2578 (14) Å, β = 116.769(2)°, V = 1644.7(8) Å(3), Z = 4 and refined to R = 0.0296 and R(w) = 0.0600. Mass spectral and NMR analyses confirmed that the bulk and crystalline compound were all 2-[(2-benzothiazolylmethyl)thio]-benzenamine.
Synthesis and Crystal Structure of the Azoxydichinyl Helicene, Pyrido[3,2-f]quinolino[6,5-c]cinnoline 5-Oxide Monohydrate
Rajapakse A, Barnes CL and Gates KS
The helicene, pyrido[3,2-f]quinolino[6,5-c]cinnoline 5-oxide, was prepared by treatment of 6-hydroxylaminoquinoline with xanthine oxidase or treatment of 6-nitroquinoline with glucose in 30% NaOH and the product characterized using NMR, high resolution mass spectrometry, and X-ray crystallography. The hydrogens on carbons 7 and 12 of the terminal aromatic rings are separated by 2.495 Å creating an angle of 25.0° between the planes of the two quinoline ring systems. In the crystal, water molecules serve to link the helicenes into a one dimensional chain structure forming a hydrogen bonded bridge between N2 of one molecule and N4 of another. The molecule (C(18)H(10)N(4)O•H(2)O) crystallized in the monoclinic P2(1)/n space group. Unit cell parameters for pyrido[3,2-f]quinolino[6,5-c]cinnoline 5-oxide monohydrate: a = 7.0829(12), b = 18.559(3), c = 11.0985(19) Å, β = 107.736(2)°, and Z = 4.
Synthesis and Crystallographic Study of '-(1-benzylpiperidin-4-yl)acetohydrazide
Nichol GS, Vardanyan R and Hruby VJ
As part of a study into new Fentanyl-derived opioid compounds with potent analgesic activity and reduced side effects the starting material title compound, CHNO (), was synthesized and characterized by NMR spectroscopy and single-crystal X-ray diffraction. The crystal structure is monoclinic with unit cell parameters = 14.1480(3) Å, = 14.1720(4) Å, = 27.6701(7) Å, = 96.956(1)°, = = 90°. The compound has crystallized with four crystallographically unique molecules in the asymmetric unit; each molecule has a very similar conformation and an analysis of the structure shows that although all four unique molecules overlay very well there is no evidence of -symmetry which would relate the molecules in the higher symmetry space group 2/. The crystal packing consists of two separate hydrogen bonded chains which are linked together to form a thick 2D structure in the plane.
Synthesis, Crystal Structure, and Rotational Energy Profile of 3-Cyclopropyl-1,2,4-benzotriazine 1,4-Di-N-oxide
Sarkar U, Glaser R, Parsons ZD, Barnes CL and Gates KS
1,2,4-Benzotriazine 1,4-di-N-oxides are potent antitumor drug candidates that undergo in vivo bioreduction leading to selective DNA damage in the low oxygen (hypoxic) cells found in tumors. Tirapazamine (TPZ) is the lead compound in this family. Here we report on the synthesis, crystal structure, and conformational analysis of a new analog, 3-cyclopropyl-1,2,4-benzotriazine 1,4-di-N-oxide (3). Compound 3 (C(10)H(10)N(3)O(2)) crystallized in the monoclinic space group C2/c. Unit cell parameters for 3: a = 16.6306 (12), b = 7.799 (5), c = 16.0113 (11) Å, α = 90, β = 119.0440 (10), γ = 90, and z = 8.
Ethynyl and Propynylpyrene Inhibitors of Cytochrome P450
Zhu N, Lightsey D, Liu J, Foroozesh M, Morgan KM, Stevens ED and Klein Stevens CL
The single-crystal X-ray structures and in vivo activities of three aryl acetylenic inhibitors of cytochromes P450 1A1, 1A2, 2A6, and 2B1 have been determined and are reported herein. These are 1-ethynylpyrene, 1-propy-nylpyrene, and 4-propynylpyrene. To investigate electronic influences on the mechanism of enzyme inhibition, the experimental electron density distribution of 1-ethynylpy-rene has been determined using low-temperature X-ray diffraction measurements, and the resulting net atomic charges compared with various theoretical calculations. A total of 82,390 reflections were measured with Mo Kα radiation to a (sinθ/λ)(max) = 0.985 Å(-1). Averaging symmetry equivalent reflections yielded 8,889 unique reflections. A least squares refinement procedure was used in which multipole parameters were added to describe the distortions of the atomic electron distributions from spherical symmetry. A map of the model electron density distribution of 1-ethynylpyrene was obtained. Net atomic charges calculated from refined monopole population parameters yielded charges that showed that the terminal acetylenic carbon atom (C18) is more negative than the internal carbon (C17). Net atomic charges calculated by ab initio, density functional theory, and semi-empirical methods are consistent with this trend suggesting that the terminal acetylenic carbon atom is more likely to be the site of oxidation. This is consistent with the inhibition mechanism pathway that results in the formation of a reactive ketene intermediate. This is also consistent with assay results that determined that 1-ethynylpyrene acts as a mechanism-based inhibitor of P450s 1A1 and 1A2 and as a reversible inhibitor of P450 2B1. Crystallographic data: 1-ethynylpyrene, C(18)H(10), P2(1)/c, a = 14.571(2) Å, b = 3.9094(5) Å, c = 20.242(3) Å, β = 105.042(2)°, V = 1,113.5(2) Å(3); 1-propynylpyrene, C(19)H(12), P2(1)/n, a = 8.970(2) Å, b = 10.136(1) Å, c = 14.080(3) Å, β = 99.77(2)°, V = 1,261.5(4) Å(3); 4-propynylpyrene, C(19)H(12), Pbca, a = 9.904(1) Å, b = 13.174(2) Å, c = 19.401(1) Å, V = 2,531.4(5) Å(3).
Crystal Structures and Thermal Properties of Two Transition-Metal Compounds {[Ni(DNI)(2)(H(2)O)(3)][Ni(DNI)(2) (H(2)O)(4)]}.6H(2)O and Pb(DNI)(2)(H(2)O)(4) (DNI = 2,4-Dinitroimidazolate)
Zhang GF, Cai MY, Jing P, He C, Li P, Zhao FQ, Li JZ, Fan XZ and Ng SW
Two transition-metal compounds derived from 2,4-dinitroimidazole, {[Ni(DNI)(2)(H(2)O)(3)][Ni(DNI)(2) (H(2)O)(4)]}.6H(2)O, 1, and Pb(DNI)(2)(H(2)O)(4), 2, were characterized by elemental analysis, FT-IR, TG-DSC and X-ray single-crystal diffraction analysis. Crystal data for 1: monoclinic, space group C2/c, a = 26.826(3), b = 7.7199(10), c = 18.579(2) A, beta = 111.241(2) degrees and Z = 4; 2: monoclinic, space group C2/c, a = 6.5347(6), b = 17.1727(17), c = 14.1011(14) A, beta = 97.7248(10) and Z = 4. Compound 1 contains two isolated nickel centers in its structure, one being six-coordinate and another five-coordinate. The structure of 2 contains a lead (II) center surrounded by two chelating DNI ligands and four water molecules in distorted square-antiprism geometry. The abundant hydrogen bonds in two compounds link the molecules into three-dimensional network and stabilize the molecules. The TG-DSC analysis reveals that the first step is the loss of water molecules and the final residue is the corresponding metal oxides and carbon.
Syntheses, Structural Characterization and Thermoanalysis of Transition-Metal Compounds Derived from 3,5-Dinitropyridone
Fan R, Zhou QP, Zhang GF, Cai MY, Li P, Gan LH, Zhao FQ, Li JZ, Fan XZ and Ng SW
Nine metal compounds of Mn(II), Zn(II) and Cd(II) derived from dinitropyridone ligands (3,5-dinitro-pyrid-2-one, 2HDNP; 3,5-dinitropyrid-4-one, 4HDNP and 3,5-dinitropyrid-4-one-N- hydroxide, 4HDNPO) were characterized by elemental analysis, FT-IR and partly by TG-DSC. Three of which were further structurally characterized by X-ray single-crystal diffraction analysis. The structures of the three compounds, Mn(4DNP)(2)(H(2)O)(4), 4, Zn(4DNPO)(2)(H(2)O)(4), 8, and Cd(4DNPO)(2)(H(2)O)(4), 9, crystallize in the monoclinic space group P2(1)/n and Z = 2, with a = 8.9281(9), b = 9.1053(9), c = 10.6881(11) A, beta = 97.9840(10) degrees for 4; a = 8.4154(7), b = 9.9806(8), c = 10.5695(8) A, beta = 97.3500(10) degrees for 8; a = 8.5072(7), b = 10.2254(8), c = 10.5075(8) A, beta 96.6500(10) degrees for 9. All three complexes are octahedral consisting of four equatorial water molecules, and two nitrogen or oxygen donor ligands (DNP or DNPO). The abundant hydrogen-bonding and pi-pi stacking interactions seem to contribute to stabilization of the crystal structures of the compounds. The TG-DTG results revealed that the complexes showed a weight loss sequence corresponding to all coordinated water molecules, nitro groups, the breaking of the pyridine rings and finally the formation of metal oxides.
Crystal and Molecular Structure of Dichloro(ethylenediamine)gold(III) Nitrate: [Au(NHCHCHNH)Cl]NO
Motley DM, Walmsley JA, Zukerman-Schpector J and Tiekink ER
The gold(III) atom in [Au(NHCHCHNH) Cl]NO is chelated by the ethylenediamine (en) ligand and the approximately square planar geometry is completed by two chloride atoms. Weak Au⋯O and Au⋯Cl contacts are noted above and below the square plane leading to a tetragonally distorted octahedron for the gold(III) center. Extensive charge-assisted hydrogen bonding of the type N-H⋯O leads to the formation of a 2-D array and layers are consolidated into a 3-D network via C-H⋯O and C-H⋯Cl contacts. The compound crystallizes in the orthorhombic space group with = 10.3380(11) Å, = 8.2105(7) Å, = 19.625(2) Å, and = 8.
Heterometallic Copper-Vanadium Compounds: Crystal Structures of Polymers [Cu()(VO())] and [Cu()(VO(()-))] ·2HO ( = imidazole,  = mandelato)
Šimuneková M, Schwendt P, Gyepes R and Krivosudský L
Two new 1D polymeric heterometallic copper-vanadium compounds were prepared. The polymers are constructed from [Cu()] cations that are coordinated to two terminal oxido ligands of [VO()] anions. The stronger coordination in [Cu()VO()] () that contains the racemic mandelato ligand is manifested by a shorter Cu‒O bond distance 2.4095(12) Å, while the weaker interaction in [Cu()(VO(()-))] ·2HO () is exhibited by Cu‒O bond distances 2.4547(16) Å and 2.5413(16) Å. The vanadate anion in compound carries only the ()-enantiomer of the initial mandelic acid and differs from the anion in in parallel orientation of the phenyl groups of the mandelato ligand. FT-IR spectroscopy was used for the confirmation of the coordination mode of mandelato ligand. Strong bands corresponding to the vibrations of carboxyl groups can be observed around 1650 and at 1344 cm. The stretching vibration of deprotonated hydroxyl group in the mandelato ligand occurs at 1045 and 1065 cm for and , respectively. In addition, the very strong, characteristic band corresponding to (V=O) vibration can be observed at 931 cm for and 925 cm for , as well as in Raman spectrum.
A Dual Approach on Experimental, Theoretical Insight of Structural Elucidation, Hirshfeld Surface Analysis, Optical and Electrochemical Properties of Acyl Thiourea-Ethynyl Hybrid Derivatives
Daud AI, Khairul WM, Arshad S, Razak IA, González DLN and Erben MF
Hybrid moieties of ethynylated-thiourea, Th1 and Th2 have been synthesised via the addition reaction between ethynyl derivatives and 4--butylbenzoyl isothiocyanate in acetone, and were characterised by selected spectroscopic methods (i.e., H and C NMR, UV-visible, FT-IR) and elemental analysis. Thermogravimetric analysis indicated that Th1 and Th2 were relatively stable up to 210 °C. Single-crystal X-ray diffraction was used to identify the crystal structure of Th2 in which the centre of 1-acyl thiourea moiety (-C(O)NHC(S)NH) exhibits conformation. The Hirshfeld surface analysis has allowed visualizing the crystal packing, which is characterised by the prolonged intermolecular N-H⋯O = C and N-H⋯S = C hydrogen-bonding interactions within Th2 molecule. Electrochemical data of both compounds correspondingly exhibit irreversible redox potential processes. Besides, frontier molecular orbitals and Natural Bond Orbital population analysis were computed at the B3LYP/6-31G (d, p) level of approximation, suggesting strong delocalization of the electronic density through a conjugated π-system involving the ethynyl-phenyl and thiourea groups.