• Title/Summary/Keyword: NMR spectra

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NMR peak assignment for the elucidation of the solution structure of T4 Endonuclease V

  • Im, Hoo-Kang;Hyungmi Lihm;Yu, Jun-Suk;Lee, Bong-Jin
    • Proceedings of the Korean Society of Applied Pharmacology
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    • 1996.04a
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    • pp.183-183
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    • 1996
  • Bacteriophage T4 endonuclease V initiates the repair of ultraviolet (UV)-induced pyrimidine dimer photoproducts in duplex DNA. The mechanism of DNA strand cleavage involves four sequential stens: linear diffusion along dsDNA, pyrimidine dimer-specific binding,l pyrimidine dimer-DNA glycosylase activity, and Af lyase activity. Although crystal structure is known for this enzyme, solution structure has not been yet known. In order to elucidate the solution structure of this enzyme NMR spectroscopy was used. As a basis for the NMR peak assignment of the protein, HSQC spectrum was obtained on the uniformly $\^$15/N-labeled T4 endonuclease V. Each amide peak of the spectrum were classified according to amino acid spin systems by interpreting the spectrum of $\^$15/N amino acid-specific labeled T4 endonuclease V. The assignment was mainly obtained from three-dimensional NMR spectra such as 3D NOESY-HMQC, 3D TOCSY-HMQC. These experiments were carried out will uniformly $\^$15/N-labeled sample. In order to assign tile resonance of backbon atom, triple-resonance theree-dimensional NMR experiments were also performed using double labeled($\^$15/N$\^$13/C) sample. 3D HNCA, HN(CO)CA, HNCO, HN(CA)HA spectra were recorded for this purpose. The results of assignments were used to interpret the interaction of this enzyme with DNA. HSQC spectrum was obtained for T4 endonuclease V with specific $\^$15/N-labeled amino acids that have been known for important residue in catalysis. By comparing the spectrum of enzyme*DNA complex with that of the enzyme, we could confirm the important role of some residues of Thr, Arg, Tyr in activity. The results of assignments were also used to predict the secondary structure by chemical shift index (CSI).

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Single Crystal 133Cs NMR Study of Cs+(15-Crown-5)2I-

  • Lee, Kang-Yeol;Kim, Tae-Ho;Shin, Yong-Woon;Kim, Jin-Eun
    • Bulletin of the Korean Chemical Society
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    • v.25 no.4
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    • pp.529-532
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    • 2004
  • Cesium-133 NMR spectra of a single crystal of tetragonal $Cs^+ (15-crown-5)_2I^-$ were obtained as a function of crystal orientation in an applied magnetic field of 9.40T and analyzed to provide the magnitudes and orientations of the $^{133}Cs$ chemical shift and quadrupolar tensors for two magnetically nonequivalent and symmetry related sites. Chemical shift tensor components and parameters of quadrupolar interactions are obtained as ${\delta}_{11}=46(1),\;{\delta}_{22}=60(1),\;{\delta}_{33}=-30(1)$ ppm, quadrupole coupling constant QCC = 581(1) kHz, and asymmetry parameter ${\eta}$ = 0.481(1), respectively. The nonaxially symmetric NMR parameters imply that the local environment of the cesium nuclei is nonaxially symmetric. The DANTE experiment burned holes in the $^{133}Cs$ NMR line of the title compound. The hole burning of the single crystal and powder $^{133}Cs$ NMR lines showed that the NMR lines are not homogeneously broadened.

Heteronuclear NMR studies on 44 kDa dimer, syndesmos

  • Kim, Heeyoun;Lee, Inhwan;Han, Jeongmin;Cheong, Hae-kap;Kim, Eunhee;Lee, Weontae
    • Journal of the Korean Magnetic Resonance Society
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    • v.19 no.2
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    • pp.83-87
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    • 2015
  • Syndesmos, which is co-localized with syndecan-4 cytoplasmic domain ($Syn4^{cyto}$) in focal contacts, interacts with various cell adhesion adaptor proteins including $Syn4^{cyto}$ to control cell signaling. Syndesmos consists of 211 amino acids and it exists as a dimer (44kDa) in solution. Recently, we have determined the structure of syndesmos by x-ray crystallography, however, dynamics related to syndecan binding still remain elusive. In this report, we performed NMR experiments to acquire biochemical and structural information of syndesmos. Based on a series of three-dimensional triple resonance experiments on a $^{13}C/^{15}N/^2H$ labeled protein, NMR spectra were obtained with well dispersed and homogeneous NMR data. We present the sequence specific backbone assignment of syndesmos and assigned NMR data with combination structural information can be directly used for the studies on interaction with $Syn4^{cyto}$ and other binding molecules.

Structural Studies on Conjugated Oximes (I). The Syntheses of 2-Butenedialdioximes, and the Conformational Study of their cis-Isomer by NMR (Conjugated Oxime의 立體構造에 關한 硏究 (第1報). 2-Butenedialdioxime의 合成 및 NMR에 依한 cis-Isomer의 Conformation 決定)

  • Hong Young-Suek;Lee Hak-Ki;Park Byung Kack
    • Journal of the Korean Chemical Society
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    • v.19 no.1
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    • pp.21-33
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    • 1975
  • cis-and trans-2-butenedialdioximes are synthesized via 2-butenedials, very unstable precursors, and the conformation of the cis-isomer of those compounds is determined by the NMR spectra of 1,4-dideutero-and 1-deutero-cis-2-butenedialdioximes; it is certain that the conformation has an unsymmetrical structure as shown below.

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Dehydrodivanillin: Multi-dimensional NMR Spectral Studies, Surface Morphology and Electrical Characteristics of Thin Films

  • Gaur, Manoj;Lohani, Jaya;Balakrishnan, V.R.;Raghunathan, P.;Eswaran, S.V.
    • Bulletin of the Korean Chemical Society
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    • v.30 no.12
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    • pp.2895-2898
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    • 2009
  • The complete structural characterization of dehydrodivanillin, an important natural product of interest to the food, cosmetics and aroma industries, has been carried out using multi-dimensional NMR spectroscopic techniques, and its previously $reported^{13}$C-NMR values have been reassigned. Dense and granular thin films of dehydrodivanillin have been grown by sublimation under high vacuum and studied using Scanning Electron Microscopy (SEM), electrical and optical techniques. The transmittance spectra of the films indicate a wide optical band gap of more than 3 eV. Typical J-V characteristics of Glass/ITO/dehydrodivanillin/Al structure exhibited moderate current densities ${\sim}10^{-4}\;A/cm^2$ at voltages > 25 V with an appreciable SCLC mobility of the order of $10^{-6}\;cm^2$/V-s.

High-resolution 1H NMR Spectroscopy of Green and Black Teas

  • Jeong, Ji-Ho;Jang, Hyun-Jun;Kim, Yongae
    • Journal of the Korean Chemical Society
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    • v.63 no.2
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    • pp.78-84
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    • 2019
  • High-resolution $^1H$ NMR spectroscopic technique has been widely used as one of the most powerful analytical tools in food chemistry as well as to define molecular structure. The $^1H$ NMR spectra-based metabolomics has focused on classification and chemometric analysis of complex mixtures. The principal component analysis (PCA), an unsupervised clustering method and used to reduce the dimensionality of multivariate data, facilitates direct peak quantitation and pattern recognition. Using a combination of these techniques, the various green teas and black teas brewed were investigated via metabolite profiling. These teas were characterized based on the leaf size and country of cultivation, respectively.

Synthesis and Spectroscopic Studies of Metal Complexes Formed in the Reaction of Metal Ions with Urea at High Temperature (높은 온도에서 Urea와 금속이온과의 반응으로 얻어진 금속 Complexes의 합성과 분광학적 연구)

  • Gaballa, Akmal S.;Teleb, Said M.;Nour, El-Metwally
    • Journal of the Korean Chemical Society
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    • v.51 no.4
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    • pp.339-345
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    • 2007
  • Urea reacts with PtCl2, H2[PtCl6]·6H2O, H2[IrCl6] and Ni(CH3CO2)2 in aqueous solution at high temperature (60-80 °C) yielding [PtCl2(Urea)]·2H2O (1), (NH4)2[PtCl6] (2), (NH4)2[IrCl6]·H2O (3) and [Ni2(OH)2(NCO)2(H2O)2] (4) complexes, respectively. In complex 1, urea coordinates to Pt(II) as a neutral bidentate ligand via amido nitrogen atoms. In complexes 2, 3 and 4 it seems that the coordinated urea molecules decompose during the reaction at high temperature and a variety of reaction products are obtained. All complexes were isolated in moderate yields as dark green (1), yellow (2), pale brown (3) and faint green (4) precipitates, respectively. The reaction products were characterized by their microanalysis, IR, 1H and 13C NMR spectra as well as thermal analysis. General mechanisms describing the formation of these complexes were suggested.

Investigation of $xV_2O_5-B_2O_3$ and $xV_2O_5-B_2O_3-yNa_3O$ Glasses by $^{11}B MAS$ NMR

  • Kim, Sun-ha;Han, Oc-Hee;Kang, Jae-Pil
    • Journal of the Korean Magnetic Resonance Society
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    • v.9 no.1
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    • pp.61-66
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    • 2005
  • $^{11}B MAS NMR$ spectra of binary glass system $xV_2O5-B_2O_3$ and ternary glass system $xV_2O5-B_2O_3-yNa_2O$ (x = $V_2O_5 mol%/$B_2O_3$ mol%, y = $Na_2O$ mol$/$B_2O_3$ mol%) were acquired. $BO_3$ units are dominant components in the spectra of $xV_2O_5-B_2O_3$glass systems while both $BO_3$ and $BO_4$ unit appear in comparable amounts in the spectra of $xV_2O_5-B_2O_3-yNa_2O$ glass systems. More $BO_3$ units were monitored for higher $V_2O_5$ contents while more $BO_4$ unit for higher $Na_2O$ contents. Quadrupole parameters such as $e^2qQ$ and $\eta$ obtained form spectral simulation indicate that $e^2qQ$ has a maximum value at x = y 1 and $\eta$ decreases and increases as x or y grows, respectively. Our results suggest that $V_2O_5$ and $Na_2O$ play opposite roles in the ternary glasses.

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New Cryptand Complexes of Lanthanides(Ⅲ) and Dioxouranium(Ⅵ) Nitrates

  • Oh-Jin Jung;Chil-Nam Choi;Hak-Jin Jung
    • Bulletin of the Korean Chemical Society
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    • v.12 no.2
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    • pp.130-137
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    • 1991
  • The following new cryptand 221 complexes of lanthanides(Ⅲ) and dioxouranium(Ⅵ) nitrate have been synthesized: $(Ln(C_{16}H_{32}N_2O_5)(H_2O)_2(NO_3)_3\ and \((UO_2)_2(C_{16}H_{32}N_2O_5)(H_2O)_4(NO_3)_4$. These complexes have been identified by elemental analysis, moisture titration, conductivity measurements and various spectroscopic techniques. The proton and carbon-13 NMR as well as calorimetric measurements were used to study the interaction of cryptand 221 with La(Ⅲ), Pr(Ⅲ ), Ho(Ⅲ) and $UO_2(Ⅱ)$ ions in nonaqueous solvents. The bands of metal-oxygen atoms, metal-nitrogen atoms and O-U-O in the IR spectra shift upon complexation to lower frequencies, and the vibrational spectra ({\delta}NMN$) of metal-amide complexes in the crystalline state exhibit lattice vibrations below 300 $cm^{-1}$. The NMR spectra of the lanthanides(Ⅲ) and dioxouranium(Ⅵ) nitrate complexes in nonaqueous solvents are quite different, indicating that the ligand exists in different conformation, and also the $^1H$ and $^{13}C-NMR$ studies indicated that the nitrogen atom of the ring has greater affinity to metal ions than does the oxygen atom, and the planalities of the ring are lost by complexation with metal ions. Calorimetric measurements show that cryptand 221 forms more stable complexes with $La^{3+}$ and $Pr^{3+}$ ions than with $UO^{22+}$ ion, and $La^{3+}/Pr^{3+}$ and $UO^{22+}/Pr^{3+}$ selectivity depends on the solvents. These changes on the stabilities are dependent on the basicity of the ligand and the size of the metal ions. The absorption band (230-260 nm) of the complex which arises from the direct interaction of macrocyclic donor atoms with the metal ion is due to n-{\delta}*$ transition and also that (640-675 nm) of $UO^{22+}$-cryptand 221 complex, which arises from interaction between two-dioxouranium(Ⅵ) ions in being out of cavity of the ligand ring is due to d-d* transition.