• Title/Summary/Keyword: X-ray crystallography

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Structure of Hydroxy-bisbenzoyloxy-allyloxycalix[4]arene (Hydroxy-bisbenzoyloxy-allyloxycalix[4]arene의 구조)

  • Lee, Bo-Hyeong;Jo, Seon-Hui;Park, Yeong-Ja
    • Korean Journal of Crystallography
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    • v.8 no.2
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    • pp.111-118
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    • 1997
  • The structrue of hydroxy-bisbenzoyloxy-allyloxycalix[4]arene (C45H36O6) has been determined by X-ray crystallography. The crystals are monoclinic, space group P21, unit cell constants a=11.045(3), b=33.545(2) c=10.319(4)Å, β=113.86(2)˚, Z=4, V=3496.0(1.8) Å3, DC=1.28 gcm-3. The intensity data were collected on an Enraf-Noninus CAD-4 Diffractometer with a graphite monochromated Mo-Kα radiation. The structure was solved by direct method and refined by full-matrix least-squares calculations to a final R value of 0.076 for 2945 observed reflections. Two independent enantiomeric molecules are crystallized in a 1:1 racemate mixture. They have the flattened cone conformation with the flattening hydroxy1 pheny1 rings. There is an intramolecular hydrogen bond in both molecules.

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Three-dimensional Structure Analysis of $SmZn_{0.67}Sb_2$ by Transmission Electron Microscopy (투과전자현미경을 이용한 $SmZn_{0.67}Sb_2$의 3차원적 구조 분석)

  • Kim, Jin-Gyu;Kang, Sung-Kwon;Kim, Wan-Cheol;Kim, Youn-Joong
    • Applied Microscopy
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    • v.34 no.4
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    • pp.255-264
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    • 2004
  • The three-dimensional (3D) structure of an inorganic crystal, $SmZn_{0.67}Sb_2$ (space group P4/nmm, $a=4.26{\AA}\;and\;c=10.37{\AA}$) was solved by electron crystallography. High resolution electron microscopy (HREM) images from 3 different major zone axes and selected-area electron diffraction patterns from 16 different zone axes were combined to obtain a 3D information. A crystallographic image processing (CIP) of HREM images was used for more accurate determination of the crystal structure. As a result of this electron crystallography, average phase errors (${\Phi}_{res}$) of [001], [100] and [110] HREM images are $17.0^{\circ},\;8.3^{\circ}\;and\;21.9^{\circ}$, respectively. Xray crystallography of $SmZn_{0.67}Sb_2$ has attempted to compare accuracy of the structure determination by electron crystallography, which resulted in the cell parameters of $a=4.2976(6){\AA}\;and\;c=10.287(2){\AA}$, and the R-factor ($R_{sym}$) of 4.16%.

Crystal Structure of $KD_2PO_4$: Neutron and X-ray Diffraction Studies ($KD_2PO_4$의 결정구조: 중성자와 X-선 회절에 의한 연구)

  • 김신애;심해섭;이창희
    • Korean Journal of Crystallography
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    • v.11 no.3
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    • pp.162-166
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    • 2000
  • KD₂PO₄ single crystals were grown from D₂O with reagent KH₂PO₄ and the crystal structure was determined by X-ray and neutron diffraction methods. The crystals are tetragonal at room temperature, I42d, with lattice parameters of a=7.4633(7), c=6.9785(5) Å and Z=4. Intensity data were collected on an Enraf-nonius CAD4 diffractometer with a graphite monochromated MoK/sub α/ radiation (λ=0.7107Å) and on the neutron four circle single crystal diffractometer with Ge(331) monochromated neutron beam (λ=0.997Å). The structure was refined by full-matrix least-square to final R and wR values of 0.030 and 0.072, respectively, for 204 observed reflections with I>2σ(I) by X-ray diffraction and to final R=0.041 and wR=0.096 for 144 observed relfecdtions by neutron diffraction. The O…O distance of 2.516(4)Å obtained by X-ray diffraction is the same as that of 2.515(4)Å by neutron diffraction. On the other hand, the O-D/H distance of 0.84(4)Å by X-ray diffraction is considerably shorter than 1.029(7) Åby neutron diffraction. Hydrogen and deuterium can be readily distinguished by neutrons. In this crystal 66% of H-positions were substituted by D and the rest 34% occupied by H. The phase transition temperature of DKDP obtained with deuteration levels is f193K. This value agrees fairly well with the result of DSC measurement. The nuclear density distribution by neutron diffraction provides an observation of the disordered state of D/H in KD₂PO₄ at room temperature.

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X-Ray Triple Crystal Diffraction Spectrometer and Its Applications (X-Ray Triple Crystal Diffraction Spectrometer의 제작과 그 응용)

  • Park Young-Han;Yeom Byo-Young;Yoon Hyng-Guen;Min Suk-ki;Park Young Joo
    • Korean Journal of Crystallography
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    • v.8 no.1
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    • pp.20-25
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    • 1997
  • Two experimental methods have been developed for high resolution measurement of x-ray scattering. The methods used were (1) an x-ray double crystal diffraction (DCD) spectrometer set-up and (2) an x-ray triple crystal diffraction (TCD) spectrometer set-up. With the DCD arrangement of Si(511)-sample(hkl), rocking curves have been plotted for Si (333), Si(004) and GaAs(004). Also, with the TCD arrangement of Si(111)-Si(111)-Si(511)-sample(hkl) including monolithic monocro-collimator and $K_{\alpha1}$ selector, rocking curves have been plotted for Si(333), Si(004) and GaAs(004). The results of FWHM by DCD and TCD set-up have been compared each other and discussed. The reflection topographs (004) and (115) in an $In_{0.037}Ga_{0.0963}As/GaAs$ sample have been obtained by DCD set-up.

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Docking Studies on Formylchromone Derivatives as Protein Tyrosine Phosphatase 1B (PTP1B) Inhibitors

  • Kim, Chan-Kyung;Lee, Kyung-A;Zhang, Hui;Cho, Hyeong-Jin;Lee, Bon-Su
    • Bulletin of the Korean Chemical Society
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    • v.28 no.7
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    • pp.1141-1150
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    • 2007
  • Molecular modeling study has been performed to assist in the design of PTP1B inhibitors using FlexX. FlexX dockings with 19 test ligands, whose structures have been determined by X-ray crystallography, were successful in reproducing the experimental conformations within the protein. An increase in biological activity is observed as hydrophobic character of formylchromone derivatives increases. Most ligands bind to the activesite regions of the protein successfully in two different score runs. The Drug score run gave better results than the FlexX score run based on the score, rank, binding modes and bond distance of docked structures. Consensus values from the CScore scoring function are between 3 and 5, suggesting that the scoring scheme is reliable. All formylchromone inhibitors considered in this work show unidirectional binding modes in the active site pocket, which is contrary to the bidirectional X-ray results by Malamas et al. and amino acid residues responsible for such orientation are identified to help further development of the inhibitors.

A Macrocyclization of (2R)-2-(N,N-Ditosylimido) -3-butenyl methyl malonate by Using Palladium Catalyst (팔라듐 촉매를 이용한 (2R)-2-(N,N-Ditosylimido)-3-butenyl methyl malonate의 거대고리화 반응)

  • Kim, Gyu-Soon;Rhee, Hak-June
    • Journal of the Korean Chemical Society
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    • v.44 no.1
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    • pp.30-36
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    • 2000
  • Upon Pd(0)-catalyzed coupling reaction of (2R)-2-(N,N-ditosylimido)-3-butenyl methyl malonate (4) which was selected for the total synthesis of A-factor, (3R)-2-(6-methylheptanoyl)-3-hydroxy methyl-4-buttinolide (1), an unexpected 14-membered cyclic compound, bis(2-methoxycabonyl-(4E)-hexenolide) (15) was obtained. The structure of this compound was conformed by X-ray crystallography. This result implies that this method can be applied the synthesis of various size of symmetrical macrocyclic compounds.

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Crystal Structure Analysis of 3-(4-ethylphenyl)-3H-chromeno[4,3-c]isoxazole-3a(4H)-carbonitrile

  • Malathy, P.;Ganapathy, Jagadeesan;Srinivasan, J.;Manickam, Bakthadoss
    • Journal of Integrative Natural Science
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    • v.8 no.4
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    • pp.250-257
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    • 2015
  • The crystal structure of the potential active 3-(4-ethylphenyl)-3H-chromeno[4,3-c]isoxazole-3a(4H)-carbonitrile ($C_{19}H_{16}N_2O_2$) has been determined from single crystal X-ray diffraction data. In the title compound crystallizes in the monoclinic space group $P2_1/c$ with unit cell dimension a=6.6869 (8) ${\AA}$, b=15.8326 (19) ${\AA}$ and c= 15.237 (2) ${\AA}$ [${\alpha}=90^{\circ}$, ${\beta}=100.663^{\circ}$ and ${\gamma}=90^{\circ}$]. In the structure chromene, isoxazole and carboxylate are almost coplanar each other. All geometrical parameters revelled that chromene ring of pyran ring adopt sofa conformation. The crystal packing is stabilized by intermolecular C-H...N and C-H...O hydrogen bond interaction.

Isolation and Structure of $[Ph_3P(OH)]^+[ $N_3$]^-$ ($[Ph_3P(OH)]^+[ $N_3$^-$의 분리 및 구조)

  • Beom Jun Lee;Won Seok Han;Soon Won Lee
    • Korean Journal of Crystallography
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    • v.12 no.3
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    • pp.141-144
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    • 2001
  • From the reaction of Na[Ga(N₃)₄] with PPh₃, an ionic compound [Ph₃P(OH)]/sup +/[N₃]/sup -/ (1) was isolated. Compound 1 was characterized by spectroscopy (¹H-NMR, /sup 13C{¹H}-NMR, and IR) and X-ray diffraction. Crystallographic data for 1 : orthorhombic space group P2₁2₁2₁, a = 10.491 (4) Å, b=11.603(5)Å, c=13.149(5)Å, Z=4, R(wR₂)=0.0547(0.0978).

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Bis(morpholine)-substituted 1,3,5-Triazines Derivatives: Synthesis and Structural Study

  • Lee, Jong-Dae
    • Journal of Integrative Natural Science
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    • v.11 no.2
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    • pp.61-68
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    • 2018
  • New 4,4'-[6-(o-carboranylalkoxy)-1,3,5-triazine-2,4-diyl]dimorpholine derivatives have been prepared by reacting 4,4'-[6-(alkynyloxy)-1,3,5-triazine-2,4-diyl]dimorpholines with decaborane and N,N-dimethylaniline as base. The intermediate compounds, 4,4'-[6-(alkynyloxy)-1,3,5-triazine-2,4-diyl]dimorpholines, have been prepared by reacting 4,4'-[6-chloro-1,3,5-triazine-2,4-diyl]dimorpholines with prop-2-yn-1-ol, but-3-yn-1-ol, and pet-4-yn-1-ol, and potassium tert-butoxide (t-BuOK) as base. The structure of these compounds has been confirmed by IR, $^1H$, $^{11}B$, and $^{13}C$ NMR and X-ray crystallographic studies.