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Journal Articles

Journal Articles

Fine structural analysis using single crystal neutron diffraction

Kaneko, Koji

Nihon Kessho Gakkai-Shi, 61(4), p.237 - 242, 2019/12

Journal Articles

What can we do with the high-pressure neutron diffractometer PLANET?

Hattori, Takanori; Sano, Asami; Machida, Shinichi*; Abe, Jun*; Funakoshi, Kenichi*; Okazaki, Nobuo*

Nihon Kessho Gakkai-Shi, 59(6), p.301 - 308, 2017/12

PLANET is a neutron beamline dedicated to high-pressure experiments. Combining the intense neutron source of J-PARC and high-pressure devices designed for time-of-flight powder neutron diffraction enables precise structure analysis of crystal, liquid and amorphous solids over wide pressure and temperature region of 0-20 GPa and 77-2000K. This beamline is effective for various studies in geophysics, planetary science, physics and chemistry. This paper overviews the beamline and introduces recent results obtained at PLANET.

Journal Articles

Two protonation states and structural features of a bilin reductase PcyA revealed by neutron crystallography

Unno, Masayoshi*; Sugishima, Masakazu*; Wada, Kei*; Hagiwara, Yoshinori*; Kusaka, Katsuhiro*; Tamada, Taro; Fukuyama, Keiichi*

Nihon Kessho Gakkai-Shi, 57(5), p.297 - 303, 2015/10

Bilin compounds are fundamentally important for oxygenic photosynthetic organisms, because they are utilized as pigments for photosynthesis (phycobilins) and photoreceptors (phytochromobilin). Phycocyanobilin (PCB), a phycobilin, comprises the chromophore of algal phytochromes and the core phycobiliprotein antennae of cyanobacteria and red algae. PCB is biosynthesized by a member of the ferredoxin-dependent bilin reductase family, phycocyanobilin:ferredoxin oxidoreductase (PcyA). In the present study, we determined the neutron crystal structure of PcyA in complex with its substrate biliverdin (BV). This neutron structure revealed the protonation state of BV and the surrounding residues. We found that two forms of BV, neutral BV and protonated BVH$$^{+}$$, were coupled with the two conformation/protonation states of the essential residue Asp105. Further, His88 and His74 near BV were singly protonated and were connected with an intervening hydronium ion. Neutron analysis also revealed how X-ray irradiation of the PcyA-BV crystal altered the structure of the PcyA-BV complex.

Journal Articles

Strain analysis of III-V epitaxial growth by ${{it in situ}}$ synchrotron X-ray diffraction

Sasaki, Takuo; Takahashi, Masamitsu

Nihon Kessho Seicho Gakkai-Shi, 42(3), p.210 - 217, 2015/10


Journal Articles

Journal Articles

Journal Articles

Structural study on hydrogen-metal systems using X-rays and neutrons

Machida, Akihiko

Nihon Kessho Gakkai-Shi, 57(1), p.34 - 40, 2015/02

This article reports the recent structural studies on hydrogen-metal systems using X-rays and neutrons. We have focused on the interactions between interstitial hydrogen atoms and their surrounding metal atoms. The hydrogen-metal interactions provide the important knowledge to develop the high performance hydrogen absorbing alloys. The X-ray and neutron diffraction are complementary methods to investigate the structural changes of metals induced by the absorbing hydrogen atoms. As a typical example, pressure-induced phase separation of lanthanum di-hydride are described.

Journal Articles

Recent advance of the neutron crystal chemistry by using high intensity neutron beam at J-PARC

Ohara, Takashi

Nihon Kessho Gakkai-Shi, 56(5), p.301 - 306, 2014/10

no abstracts in English

Journal Articles

Seven cysteine-deficient mutants depict interplay between thermal and chemical stabilities of individual cysteine residues in MAP kinase JNK1

Nakaniwa, Tetsuko*; Kuroki, Ryota; Kinoshita, Takayoshi*

Nihon Kessho Gakkai-Shi, 55(3), p.197 - 202, 2013/06

To characterize the role of cysteine residues on the structure, function and stability of JNK1, we prepared and evaluated the wild-type JNK1 and seven cysteine-deficient JNK1 proteins. The solvent exposed cysteine residues did not influence biological function and mutating these residues raised the thermal stability because of newly formed hydrogen bonds and of higher hydration as speculated by the mutant structures. The surface cysteine involved in the molecular surface hydrophobic pocket did not affect biological function; although a moderate thermal destabilization was observed. Cysteines in the loosely-assembled hydrophobic environment moderately contributed to thermal stability and the mutations of these cysteines had negligible effect on enzyme activity. The other cysteines are involved in the tightly-filled hydrophobic core and mutation of these residues conferred the adverse effects on the thermal stability and enzyme activity.

Journal Articles

Electronic nematic transition and orthorhombic distortion in iron-based superconductors

Shibauchi, Takasada*; Kasahara, Shigeru*; Matsuda, Yuji*; Fukuda, Tatsuo; Sugimoto, Kunihisa*

Nihon Kessho Gakkai-Shi, 55(2), p.128 - 134, 2013/04

no abstracts in English

Journal Articles

Structure of enzyme-inhibitor complex determined by neutron crystallography

Tamada, Taro; Adachi, Motoyasu; Kurihara, Kazuo; Kuroki, Ryota

Nihon Kessho Gakkai-Shi, 55(1), p.47 - 51, 2013/02

Neutron crystallography enables us to identify the accurate hydrogen positions in proteins, which play important roles in many chemical reactions in living system. Here we show our results of neutron structure determination of enzymes in complex with its inhibitors which corresponds to transition state analogues. Neutron structure analysis elucidated the detail catalytic reaction of each enzyme by direct observation of hydrogen atoms. Furthermore we would like to introduce a new neutron beam line for neutron structural biology planned at MLF in J-PARC.

Journal Articles

Atomic Pair Distribution Function (PDF) analysis of ferroelectric materials

Yoneda, Yasuhiro

Nihon Kessho Gakkai-Shi, 54(3), p.155 - 158, 2012/06

PDF is a function meaning the establishment which finds out another atom in the position which only the distance r separated from arbitrary atoms. Domain structure exists in a ferroelectric. Since lattice distortion piles up a domain boundary, a crystal face "deviation" arises, and coherent nature is lost. PDF analysis of a ferroelectric crystal with such domain structure is effective. The influence of a domain showed using BaTiO$$_3$$ whether what kind of "deviation" would arise between average structure and partial structure, and also the example of application of the PDF analysis from the latest research to this BiMg$$_{0.5}$$Ti$$_{0.5}$$O$$_3$$ whose it "shifts" it is a very big system was shown.

Journal Articles

Effects of randomness and frustration on the relaxor nature in Pb(In$$_{1/2}$$Nb$$_{1/2}$$)O$$_{3}$$

Owada, Kenji

Nihon Kessho Gakkai-Shi, 54(3), p.147 - 154, 2012/06

It is well known that B-site randomness contributes to the appearance of relaxor phenomena in the lead-based complex perovskite Pb(B'B'')O$$_{3}$$. But the microscopic mechanism of the effect of B-site randomness on the systems has not been understood yet. Among the Pb(B'B'')O$$_{3}$$ systems, Pb(In$$_{1/2}$$Nb$$_{1/2}$$)O$$_{3}$$ (PIN) has drawn much attention because it can be in the antiferroelectric (AFE), ferroelectric (FE), or relaxor state depending on B-site randomness. We review the recent progress in our understanding of the effect of B-site randomness on PIN from the experimental viewpoint. As a conclusion of the arguments, we also introduce the frustration mechanism in Pb(B'B'')O$$_{3}$$.

Journal Articles

Investigation of reactions at high pressures and temperatures by ${it in situ}$ synchrotron radiation X-ray diffraction measurement; ${it In situ}$ X-ray diffraction measurements of hydrogenation reactions of aluminum

Saito, Hiroyuki; Machida, Akihiko; Katayama, Yoshinori; Aoki, Katsutoshi

Nihon Kessho Seicho Gakkai-Shi, 38(1), p.55 - 61, 2011/05

Structural information of specimens can be obtained ${it in situ}$ at high pressures and temperatures using a cubic-type multi-anvil press and synchrotron radiation X-ray diffraction measurements. This system enables us to clarify reaction mechanism at high pressures. In the present paper, energy dispersive and angle dispersive ${it in situ}$ X-ray diffraction measurement systems are explained. Hydrogenation reaction of aluminum has been investigated via these methods, and the results are described. These methods are expected to be useful for crystal growth studies at high pressures and temperatures.

Journal Articles

The Existence of ferroelectric ice on icy bodies in space; A Neutron diffraction study

Fukazawa, Hiroshi

Nihon Kessho Gakkai-Shi, 52(4), p.219 - 225, 2010/08

The complex behavior of water and the unusual properties of ferroelectric ice XI continue to attract much interest. Whether ice in the space exists as ice XI, is an important question, because long range electrostatic forces caused by the ferroelectricity might be an important factor for planet formation. From neutron diffraction experiments, we found the temperature and pressure conditions for the transformation of the largest fraction of ice into ferroelectric ice. It suggests that myriad big icy-bodies, which exist as dwarf planets and Kuiper Belt Object, consist of thick ferroelectric-ice surface. Furthermore, we report spectral and vibrational properties of ferroelectric ice investigated by inelastic neutron scattering and infrared absorption measurements. Because the spectral properties of ferroelectric ice are clearly different from those of ordinary ice, the distinct ferroelectric ice in the universe is detectable using infrared telescopes and planetary exploration.

Journal Articles

Elucidation of advanced function by combined high-resolution neutron and X-ray analysis

Tamada, Taro; Kinoshita, Takayoshi*; Tada, Toshiji*; Kuroki, Ryota

Nihon Kessho Gakkai-Shi, 52(2), p.133 - 138, 2010/04

To help resolve long-standing questions regarding the catalytic activity of the serine proteases the structure of porcine pancreatic elastase has been analyzed by high-resolution neutron (1.65 ${AA}$ resolution) and X-ray (0.94 ${AA}$ resolution) crystallography. In order to mimic the tetrahedral transition intermediate, a peptidic inhibitor was used. The neutron and X-ray data show that the hydrogen bond between His57 and Asp102 is not consistent with a low-barrier hydrogen which is predicted to have the hydrogen midway between the donor and acceptor atom. The neutron analysis also shows that the oxygen of the oxopropyl group of the inhibitor is present as an oxygen anion rather than a hydroxyl group, supporting the role of the "oxyanion hole" in stabilizing the tetrahedral intermediate in catalysis.

Journal Articles

Pressure-induced structural transition and long-period structures of rare-earth metal hydrides

Machida, Akihiko; Watanuki, Tetsu; Aoki, Katsutoshi

Nihon Kessho Gakkai-Shi, 51(6), p.320 - 326, 2009/12

Pressure-induced structural transition of rare-earth metal hydride, YH$$_3$$, has been investigated by synchrotron radiation X-ray diffraction experiments. We observed the pressure-induced structural transformation from the hexagonal metal lattice into an fcc one through an intermediate state, which appears in the wide pressure span of 12$$sim$$22 Gather obtained X-ray diffraction patterns in the intermediate state are represented by long-period structures, e.g. 27$$R$$, of the yttrium metal lattice. These long-period structures are interpreted in terms of the periodic arrangements of hexagonal-type and fcc-type stacking layers of the yttrium metals. Such structural transition is considered to be characteristic for rare-earth metal hydride.

Journal Articles

Ferroelectricity from ordering of Fe valences in the rare-earth iron oxides RFe$$_{2}$$O$$_{4}$$(R=Y, Ho-Lu)

Yoshii, Kenji; Ikeda, Naoshi*; Matsuo, Yoji*; Mori, Shigeo*

Nihon Kessho Gakkai-Shi, 51(2), p.162 - 168, 2009/04

The rare-earth iron oxides RFe$$_{2}$$O$$_{4}$$ (R=Y, Ho-Lu) have a rhombohedral crystal structure, consisting of an alternating stacking of triangular lattices of R, Fe and O ions. Recently, we have proposed that this system shows a new mechanism of ferroelectricity; the ferroelectric state originates from a polar charge-ordered structure of Fe$$^{2+}$$ and Fe$$^{3+}$$ on a triangular lattice. In this article, a review is given on the details of this ferroelectricity, which were revealed by measurements of synchrotron X-ray diffraction and dielectric properties of one of the RFe$$_{2}$$O$$_{4}$$ oxides, LuFe$$_{2}$$O$$_{4}$$.

Journal Articles

High pressure and high temperature EXAFS and diffraction study of AgI (MS35)

Yoshiasa, Akira*; Arima, Hiroshi; Fukui, Hiroshi*; Okube, Maki*; Katayama, Yoshinori; Otaka, Osamu*

Nihon Kessho Gakkai-Shi, 51(1), p.66 - 69, 2009/02

We have determined a precise P-T phase diagram of AgI by high-temperature high-pressure synchrotron experiments. X-ray diffraction and X-ray absorption measurements were performed using a multi-anvil high pressure apparatus at SPring-8 synchrotron radiation facility. In a disordered rock-salt phase, Ag ions occupy both octahedral and tetrahedral sites. The occupancy of tetrahedral site has a maximum value, 20%, at 2 GPa. A change from rock-salt structure to disordered rock-salt structure is gradual in the X-ray diffraction measurements while it is clearly observed in the X-ray absorption measurements. Analysis of EXAFS Debye-Waller factor is useful because the force constant can be decided directly even at high pressure and high temperature. Pressure influences greatly the effective potential and anharmonicity decreases with increasing pressure.

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