Online ISSN : 1884-4111
Print ISSN : 0033-8303
ISSN-L : 0033-8303
Volume 59 , Issue 4
Showing 1-6 articles out of 6 articles from the selected issue
  • Susumu MINATO
    2010 Volume 59 Issue 4 Pages 257-262
    Published: 2010
    Released: April 28, 2010
    Air absorbed dose rate data taken at 36 sites have been analyzed in order to understand lithologic characteristics of dose rate levels measured on soils in dacitic and rhyolitic terrains. The dose rate increased with increasing K2O content of rock. The following three models were tested to interpret this trend, i.e., crystallization-differentiation of mafic or felsic magma, partial melting of mafic or felsic material, and mixing of mafic and felsic magmas. Semi-empirical formulas expressing the dose rate as a function of K2O content were derived based on the above models.
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Serial Lectures
Fundamentals and Applications of Neutron Diffraction(Fundamentals5)
    2010 Volume 59 Issue 4 Pages 263-277
    Published: 2010
    Released: April 28, 2010
    Crystallographic analysis using neutron diffraction allows identification and position determination of light atoms like hydrogen. This method has been used for three-dimensional structure determination of low molecular mass organic compounds as well as large macromolecules like protein. Hydrogen atoms in proteins, as well as those in solvent molecules, play significant roles in many naturally occurring processes, such as catalytic function and molecular recognition. In the field of neutron crystallography, the development of novel diffractometers and techniques for preparation and crystallization of target samples has been developed to complement the low flux of neutron sources to permit higher measurement performance. In Japan, single-crystal diffractometers named BIX-3 and BIX-4 were constructed with Neutron Imaging Plates as a detector. These diffractometers have contributed to the investigation of hydrogen-related molecular structures; for example, determination of hydrogen atom positions which are difficult to predict based on X-ray structure data, precise configuration of hydrogen bonds, and the orientation degree of freedom of hydration water molecules. On the other hand, a complementary application of neutron diffraction data with X-ray diffraction has also been developed. Using a joint structure refinement method with X-ray diffraction data, elucidation of an enzymatic reaction mechanism and observation of a particular atomic configuration including hydrogen atoms were successfully achieved in neutron crystallographic studies of drug-discovery-target proteins. The information obtained from these neutron analyses has been consolidated into a database called Hydrogen and Hydration Database for Biomolecules, which permits the analysis of key statistical information. In Japan as well as overseas, efforts to acquire higher measurement performance are now in progress to further investigate mechanisms involving hydrogen atoms, and to increase the application of neutron crystallographic studies.
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Fundamentals and Applications of Neutron Diffraction(Applications10)
  • Takaaki HOSOYA, Takashi OHHARA
    2010 Volume 59 Issue 4 Pages 279-287
    Published: 2010
    Released: April 28, 2010
    Single-crystal neutron diffraction technique is a powerful method to analyze the reaction mechanism whose hydrogen atom or proton has a key role in the reaction. Especially hydrogen atom or proton transfer(HT/PT) is one of the most elemental phenomena and often observed in many organic, inorganic, enzymatic and catalytic reactions. We describe several applications in chemistry. At first, hydrogen atom in metal hydride complexes, which is quite difficult to do using X-ray diffraction because of the great cloud of electrons of central metal atom. Secondary, hydrogen atom in hydrogen-bonding network, e.g., low-barrier hydrogen bond(LBHB) system. Neutron diffraction can refine the thermal motion of hydrogen atom. Finally, our results, photo-induced HT/PTs using “deuterium atom labeling” technique and “crystalline-state reaction” technique, which are currently developing applications. Despite the success illustrated by the many studies presented here or many other studies, we have many problems in using single-crystal neutron diffraction technique. For example, extremely limited flux and the requirement for mm-size sample crystals. Now, these limitations are being solved by the operation of powerful instruments at a new generation of pulsed neutron sources, including iBIX diffractometer running at Japan Proton Accelerator Research Complex(J-PARC) in Japan.
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Fundamentals and Applications of Neutron Diffraction(Applications11)
  • Hironari KAMIKUBO, Shigeo YAMAGUCHI, Mikio KATAOKA
    2010 Volume 59 Issue 4 Pages 289-297
    Published: 2010
    Released: April 28, 2010
    The hydrogen bond network were studied by high-resolution neutron crystallography. Two short hydrogen bonds are involved in the hydrogen bond network as well as the ordinary hydrogen bonds. A fairly large crystal of photoactive yellow protein(PYP)(2.89×0.85×0.79mm3)required for the neutron crystallography was successfully prepared and the obtained crystal diffracts X-rays and neutrons to 0.125 nm and 0.15 nm, respectively. A new refinement method with the combination of X-ray diffraction and neutron diffraction revealed the presence of 819 hydrogen atoms among total 942 hydrogen atoms. The short hydrogen bond between the chromophore and E46 was identified as the low barrier hydrogen bond, while the short hydrogen bond between the chromophore and Y42 was the short ionic hydrogen bond. The expected counter ion, R52, is revealed to be in electrically neutral. The observation leads to the proposal of the novel mechanism of charge stabilization. The role of low barrier hydrogen bond in the photoreaction of PYP is also discussed.
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Fundamentals and Applications of Neutron Diffraction(Applications12)
  • Taro TAMADA, Motoyasu ADACHI
    2010 Volume 59 Issue 4 Pages 299-308
    Published: 2010
    Released: April 28, 2010
    High resolution X-ray crystallography provides information for most of the atoms comprising the proteins, with the exception of hydrogen atoms. Whereas, neutron crystallography, which is a powerful technique for locating hydrogen atoms, enables us to obtain accurate atomic positions within proteins. Neutron diffraction data can provide information of the location of hydrogen atoms to the structural information determined by X-ray crystallography. Here, we show the recent results of the structural determination of drug-target proteins, porcine pancreatic elastase and human immuno-deficiency virus type-1 protease by both X-ray and neutron diffraction. The structure of porcine pancreatic elastase with its potent inhibitor was determined to 0.094nm resolution by X-ray diffraction and 0.165nm resolution by neutron diffraction. The structure of HIV-PR with its potent inhibitor was also determined to 0.093nm resolution by X-ray diffraction and 0.19nm resolution by neutron diffraction. The ionization state and the location of hydrogen atoms of the catalytic residue in these enzymes were determined by neutron diffraction. Furthermore, collaborative use of both X-ray and neutron crystallography to identify the location of ambiguous hydrogen atoms will be shown.
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