• Title/Summary/Keyword: X-ray structure analysis

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The Crystal Structure of Cinmetacin ($C_{21}H_{19}NO_4$), A Non-steroidal Antiinflammatory Agent

  • Kim, Yang-Bae;Park, Il-Yeong;Park, Yang-Hwan
    • Archives of Pharmacal Research
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    • v.12 no.1
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    • pp.52-57
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    • 1989
  • The structure of cinmetacin was determined by single crystal X-ray diffraction analysis. The compound was recrystallized from a mixture of acetone and water in orthorhombic, space group $P2_12_12_1$, with Z=4, a=35.681(8), b=9.482(2), c:5.071(1) ${\AA}$, $D_x=1.352 g/cm^3$, and $D_m=1.35g/cm^3$. The structure was solved by direct method and refined by least-squares procedure to the final R value of 0.036 for 1441 observed reflections ($F{\geq}3{\sigma}(F)$). The carboxyl group of the molecule is nearly perpendicular to the indole ring. The dihedral angle between indole ring and phenyl group is $64.5^{\circ}$. The molecules are linked together via O(1)-H ----O(3) hydrogen bonds, and arranged along 2-fold screw axis in the crystal. The intermolecular contacts are the normal van der Waals' forces.

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Spatial Pattern of Copper Phosphate Precipitation Involves in Copper Accumulation and Resistance of Unsaturated Pseudomonas putida CZ1 Biofilm

  • Chen, Guangcun;Lin, Huirong;Chen, Xincai
    • Journal of Microbiology and Biotechnology
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    • v.26 no.12
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    • pp.2116-2126
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    • 2016
  • Bacterial biofilms are spatially structured communities that contain bacterial cells with a wide range of physiological states. The spatial distribution and speciation of copper in unsaturated Pseudomonas putida CZ1 biofilms that accumulated 147.0 mg copper per g dry weight were determined by transmission electron microscopy coupled with energy dispersive X-ray analysis, and micro-X-ray fluorescence microscopy coupled with micro-X-ray absorption near edge structure (micro-XANES) analysis. It was found that copper was mainly precipitated in a $75{\mu}m$ thick layer as copper phosphate in the middle of the biofilm, while there were two living cell layers in the air-biofilm and biofilm-medium interfaces, respectively, distinguished from the copper precipitation layer by two interfaces. The X-ray absorption fine structure analysis of biofilm revealed that species resembling $Cu_3(PO_4)_2$ predominated in biofilm, followed by Cu-Citrate- and Cu-Glutathione-like species. Further analysis by micro-XANES revealed that 94.4% of copper were $Cu_3(PO_4)_2$-like species in the layer next to the air interface, whereas the copper species of the layer next to the medium interface were composed by 75.4% $Cu_3(PO_4)_2$, 10.9% Cu-Citrate-like species, and 11.2% Cu-Glutathione-like species. Thereby, it was suggested that copper was initially acquired by cells in the biofilm-air interface as a citrate complex, and then transported out and bound by out membranes of cells, released from the copper-bound membranes, and finally precipitated with phosphate in the extracellular matrix of the biofilm. These results revealed a clear spatial pattern of copper precipitation in unsaturated biofilm, which was responsible for the high copper tolerance and accumulation of the biofilm.

Distribution of Co Ions in Ferromagnetic Zn (1-x) Co (x)O Films

  • Park, Chang-In;Seo, Su-Yeong;Kim, Jeong-Ran;Han, Sang-Uk
    • Proceedings of the Korean Vacuum Society Conference
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    • 2012.08a
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    • pp.166-166
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    • 2012
  • We examined the distribution of Co ions of ferromagnetic n-type Zn(1-x)Co(x)O semiconducting films with the Co concentrations of 0.03~0.07 using x-ray absorption fine structure (XAFS) measurements at the Co and Zn K edges. Extended XAFS (EXAFS) revealed that Co ions mainly occupied the zinc sites of the films. X-ray absorption near edge structure (XANES) spectra demonstrated that the pre-edge peak of the Co K edge was substantially affected by the second neighboring Co ions at the zinc sites due to hybridizing of the Co 4p conduction electrons with the Co 3d bounded electrons. From XANES and EXAFS analysis using ab initio calculations, we found that Co ions uniformly occupied the zinc sites of the Zn (0.93) Co (0.07)O film, whereas the Co ions of the Zn (0.97) Co (0.03)O and Zn (0.95) Co (0.05)O films were substituted at localized zinc sites. The ferromagnetic properties of the Zn (0.93) Co(0.07)O film could be induced by direct interaction between the magnetic dipoles of the Co ions with a mean distance of 4.3 A or by Co 4p electron mediation.

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Analysis of the Changes of composition of Hardened Cement at High Temperature by X-Ray Diffraction (X-선 회절 분석을 통한 고온 피해 시멘트 경화체의 성분 변화 분석)

  • Ji, Woo-Ram;Park, Ji-Woong;Shin, Ki-Don;Lee, Gun-Cheol;Heo, Young-Sun
    • Proceedings of the Korean Institute of Building Construction Conference
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    • 2017.11a
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    • pp.113-114
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    • 2017
  • In this study, the change of composition of cement hardened at high temperature through XRD was observed. The specimen was made of cement paste and the heating rate condition was applied at rapid thermal annealing (10.0℃ / min). The decrease of calcium hydroxide was not confirmed, but the calcium carbonate tended to be impossible or decreased after 800℃. Calcium silicate and larnite were observed to increase with increasing temperature. It is considered that silicic acid, which is a stable structure due to the decomposition of calcium silicate, is changed into a phase such as lime.

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1D-Coordination Polymer Formed by Structural Conversion of an Oxazolidine Ligand in Reaction with the Copper(II) Halides

  • Mardani, Zahra;Golsanamlou, Vali;Jabbarzadeh, Zahra;Moeini, Keyvan;Carpenter-Warren, Cameron;Slawin, Alexandra M.Z.;Woollins, J. Derek
    • Journal of the Korean Chemical Society
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    • v.62 no.5
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    • pp.372-376
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    • 2018
  • A 1D-coordination polymer of $1D-\{Cu({\mu}-picolinato)_2\}$ $\{Hakimi,\;2012\;\sharp73\}_n$ (1), was prepared by the reactions between 2-(2-(pyridin-2-yl)oxazolidin-3-yl)ethanol (AEPC) ligand and $CuCl_2$ or $CuBr_2$. The product was characterized by elemental analysis, UV-Vis, FT-IR spectroscopy and single-crystal X-ray diffraction. The X-ray analysis results revealed that the AEPC ligand, after reactions with the copper(II) chloride or bromide, gives the same product - $1D-\{Cu({\mu}-picolinato)_2\}_n$ (1). The coordination modes for various picolinate-based ligands were extracted from the Cambridge Structural Database (CSD). In the crystal structure of 1, the copper atom has a $CuN_2O_4$ environment and octahedral geometry, which is distorted by elongation of the axial bond lengths due to the Jahn-Teller effect.

Analysis of 3D Geometry and Compressive Behavior of Aluminum Open Cell Foam Using X-ray Micro CT (마이크로 X-ray CT를 활용한 알루미늄 개방형 폼의 형상 및 압축 거동 분석)

  • Kim, Y.I.;Kim, J.H.;Lee, J.K.;Kim, D.
    • Transactions of Materials Processing
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    • v.20 no.7
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    • pp.518-523
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    • 2011
  • The three dimensional geometries of an aluminum open cell foam before and after uniaxial compressive loading were investigated using the X-ray micro CT(computed tomography). Aluminum 6101-T6 open cell foams of 10, 20, 40 ppi (pore per inch) were considered in this work. After the serial sectioning CT images of aluminum foams were obtained from non-destructive X-ray images, the exact 3D structure were reproduced and visualized with commercial image processing program. The relative density ratio was around the 7.0 to 9.0 range, the unit cells showed anisotropic shapes having the different dimensional ratios of 1.1 to 1.3 between the rise and the transverse directions. The yield stress increased with the relative density ratio and the volumetric strain increased proportionally with compressive strain. The plateau stress in the compressive stress-strain curve was caused by the buckling of ligaments.

Crystal Structure Analysis of 6-Ethoxy-3-phenyl-5a,9a-dihydro-3H-chromen[4,3-c][1,2]oxazole-3a(4H)-carbonitrile

  • Malathy, P.;Sharmila, P.;Srinivasan, J.;Manickam, Bakthadoss;Aravindhan, S.
    • Journal of Integrative Natural Science
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    • v.9 no.2
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    • pp.94-102
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    • 2016
  • The crystal structure of the potential active 6-ethoxy-3-phenyl-5a,9a-dihydro-3H-chromen[4,3-c][1,2]oxazole-3a(4H)-carbonitrile ($C_{19}H_{15}N_2O_3$) has been determined from single crystal X-ray diffraction technique. The title compound crystallizes in the monoclinic space group C2/c with unit cell dimension a= 29.3026(9) ${\AA}$, b= 6.7695(2) ${\AA}$ and c= 19.7597(6) ${\AA}$ [${\alpha}= 90^{\circ}$, ${\beta}= 125.709(10)^{\circ}$ and ${\gamma}= 90^{\circ}$]. Single crystals suitable for X-ray diffraction were obtained by slow evaporation method, the isoxazole and six membered pyran rings adopts envelope conformation. The crystal packing of the molecules is stabilized by the weak $C-H{\ldots}N$ hydrogen bond interaction.

Crystal Structure Analysis of Methyl 8-bromo-3-phenyl-5a,9a-dihydro-3H-chromen [4,3-c][1,2] isoxazole-3a(4H)-carboxylate

  • Malathy, P.;Sharmila, P.;Srinivasan, J.;Manickam, Bakthadoss;Aravindhan, S.
    • Journal of Integrative Natural Science
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    • v.9 no.2
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    • pp.103-112
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    • 2016
  • The crystal structure of the potential active Methyl 8-bromo-3-phenyl-5a,9a-dihydro-3H-chromen [4,3-c][1,2] isoxazole-3a(4H)-carboxylate ($C_{18}H_{15}BrNO_4$) has been determined from single crystal X-ray diffraction technique. The title compound crystallizes in the triclinic space group Pī with unit cell dimension a=8.3129 (3) ${\AA}$, b=9.5847 (4) ${\AA}$ and c=11.1463(4) ${\AA}$ [${\alpha}=98.457(3)^{\circ}$, ${\beta}=102.806(2)^{\circ}$ and ${\gamma}=105.033(5)^{\circ}$]. Single crystals suitable for X-ray diffraction were obtained by slow evaporation method, the isoxazole and six membered pyran rings adopts envelope conformation. In the crystal, molecules are linked via pairs of inter molecular $C-H{\ldots}O$ hydrogen bonds to form dimmers.

Synthesis and Structural Analysis of 2-Amino-4-(4-hydroxy-3-methoxyphenyl)-7,9-dimethyl-5-oxo-4, 5, 6, 7-tetrahydropyrano [2, 3-d] pyrazolo [3, 4-b] pyridine-3-carbonitrile through X-ray Crystallography

  • Ganapathy, Jagadeesan;Jayarajan, R.;Vasuki, G.;Sanmargam, Aravindhan
    • Journal of Integrative Natural Science
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    • v.8 no.1
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    • pp.30-39
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    • 2015
  • The crystal structure of the potential active 2-amino-4-(4-hydroxy-3-methoxyphenyl)-7, 9-dimethyl-5-oxo-4, 5, 6, 7-tetrahydropyrano [2, 3-d] pyrazolo [3, 4-b] pyridine-3-carbonitrile ($C_{21}H_{22}N_5O_6S$) has been determined from single crystal X-ray diffraction data. In the title compound crystallizes in the monoclinic space group P-1 with unit cell dimension a=8.1201(9)${\AA}$, b=12.2684(4)${\AA}$ and c=12.387(2)${\AA}$ [${\alpha}=69.573^{\circ}$, ${\beta}=12.168^{\circ}$ and ${\gamma}=76.060^{\circ}$]. In the structure the pyrazole, pyridine and pyran are almost coplanar each other. The crystal packing is stabilized by intermolecular C-H...O and N-H... O hydrogen bond interaction.