Status of the neutron time-of-flight single-crystal diffraction data-processing software STARGazer

Yano, Naomine*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*

Acta Crystallographica Section D; Structural Biology (Internet), 74(11), p.1041 - 1052, 2018/11

https://doi.org/10.1107/S2059798318012081

Application of profile fitting method to neutron time-of-flight protein single crystal diffraction data collected at the iBIX

Yano, Naomine*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi; Tanaka, Ichiro*; Kusaka, Katsuhiro*

Scientific Reports (Internet), 6, p.36628_1 - 36628_9, 2016/12

https://doi.org/10.1038/srep36628

Accurate structure analyses of polymer crystals on the basis of wide-angle X-ray and neutron diffractions

Tashiro, Koji*; Hanesaka, Makoto*; Yamamoto, Hiroko*; Wasanasuk, K.*; Jayaratri, P.*; Yoshizawa, Yoshinori*; Tanaka, Ichiro*; Niimura, Nobuo*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; et al.

Kobunshi Rombunshu, 71(11), p.508 - 526, 2014/11

https://doi.org/10.1295/koron.71.508

The crystal structure analysis of various polymer substances has been reviewed on the basis of wide-angle high-energy X-ray and neutron diffraction data. The progress in structural analytical techniques of polymer crystals have been reviewed at first. The structural models proposed so far were reinvestigated and new models have been proposed for various kinds of polymer crystals including polyethylene, poly(vinyl alcohol), poly(lactic acid) and its stereocomplex etc. The hydrogen atomic positions were also clarified by the quantitative analysis of wide-angle neutron diffraction data, from which the physical properties of polymer crystals have been evaluated theoretically. The bonded electron density distribution has been estimated for a polydiacetylene single crystal on the basis of the so-called X-N method or by the combination of structural information derived from X-ray and neutron diffraction data analysis. Some comments have been added about future developments in the field of structure-property relationship determination.

Evaluation of performance for IBARAKI biological crystal diffractometer iBIX with new detectors

Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Tomoyori, Katsuaki; Ohara, Takashi; Katagiri, Masaki*; Kurihara, Kazuo; Tanaka, Ichiro*; Niimura, Nobuo*

Journal of Synchrotron Radiation, 20(6), p.994 - 998, 2013/11

https://doi.org/10.1107/S0909049513021845

The IBARAKI biological crystal diffractometer, iBIX, is a high-performance time-of-flight neutron single-crystal diffractometer for elucidating mainly the hydrogen, protonation and hydration structures of biological macromolecules in various life processes. Since the end of 2008, iBIX has been available to user's experiments supported by Ibaraki University. Since August 2012, an upgrade of the 14-existing detectors has begun and 16 new detectors have been installed for iBIX. The total measurement efficiency of the present diffractometer has been impoved by one order of magnitude from the previous one with the increasing of accelerator power. In December 2012, commissioning of the new detectors was successful, and collection of the diffraction dataset of ribonucrease A as a standard protein was attempted in order to estimate the performance of the upgraded iBIX in comparison with previous results. The resolution of diffraction data, equivalence among intensities of symmetry-related reflections and reliability of the refined structure have been improved dramatically. iBIX is expected to be one of the highest-performance neutron single-crystal diffractometers for biological macromolecules in the world.

Structure of morpholinium tribromoplumbate CHONHPbBr studied using single-crystal neutron diffraction

Kawasaki, Takuro; Takahashi, Miwako*; Ohara, Takashi*; Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Yamada, Taro*; Kurihara, Kazuo

Journal of the Physical Society of Japan, 81(9), p.094602_1 - 094602_6, 2012/09

https://doi.org/10.1143/JPSJ.81.094602

Hydrogen-bond network and pH sensitivity in transthyretin; Neutron crystal structure of human transthyretin

Yokoyama, Takeshi*; Mizuguchi, Mineyuki*; Nabeshima, Yuko*; Kusaka, Katsuhiro*; Yamada, Taro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Tomoyori, Katsuaki*; Tanaka, Ichiro*; et al.

Journal of Structural Biology, 177(2), p.283 - 290, 2012/02

https://doi.org/10.1016/j.jsb.2011.12.022

Beginning of open use of a New Biological Neutron Diffractometer (iBIX) in J-PARC

Tanaka, Ichiro*; Kusaka, Katsuhiro*; Hosoya, Takaaki*; Ohara, Takashi*; Kurihara, Kazuo; Niimura, Nobuo*

Yakugaku Zasshi, 130(5), p.665 - 670, 2010/05

https://doi.org/10.1248/yakushi.130.665

Ibaraki Prefectural Government together with Ibaraki University and Japan Atomic Energy Agency (JAEA) has almost finished constructing a time-of-flight (TOF) neutron diffractometer for biological macromolecules for industrial use at J-PARC, IBARAKI Biological Crystal Diffractometer (iBIX). Since 2009, Ibaraki University has been asked to operate this machine in order for users to do experiments by Ibaraki Prefecture. The diffractometer is designed to cover sample crystals which have their cell edges up to around 150 . It is expected to measure more than 100 samples per year if they have 2 mm in crystal volume, and to measure even around 0.1 mm in crystal volume of biological samples. The efficiency of iBIX is also expected about 100 times larger than those of the present high performance diffractometers at JRR-3 in JAEA when 1MW power realizes in J-PARC. Since December 2008, iBIX has been open to users and several proteins and organic compounds were tested under 20 kW proton power of J-PARC. It was found that one of their proteins was diffracted up to 1.4 in d-spacing, which was nearly comparable resolution to that of BIX-3 in JRR-3 when used the same crystal as at iBIX for reasonable exposure time. In May 2009, 14 detector units were set up. By the end of fiscal year 2009, the basic part of data reduction software will be finished and an equipment blowing low temperature gas to the sample will be installed with the cooperation of JAEA.

Development of two-dimensional scintillator neutron detector using wavelength-shifting fibres; Development of a compact detector for iBIX instrument in J-PARC/MLF

Nakamura, Tatsuya; Katagiri, Masaki; Hosoya, Takaaki*; Birumachi, Atsushi; Ebine, Masumi; Soyama, Kazuhiko; Schooneveld, E.*; Rhodes, N.*

JAEA-Research 2008-115, 33 Pages, 2009/03

JAEA-Research-2008-115.pdf:3.77MB

A compact two-dimensional neutron detector was developed for iBIX instrument in the J-PARC/MLF. The specifications required for the detector were a spatial resolution of less than 1 mm, a detector efficiency of more than 50% for thermal neutrons, a sensitivity of less than 10, detector coverage of around 1515 cm with least dead area, compactness, modularity, and a pulse pair resolution of less than 2 s. The detector components were studied in detail and optimized for the purpose. The compact prototype detector that has a neutron sensitive area of 13.313.3 cm was made and feasibility of the detector was demonstrated successfully in the experiments at the ISIS pulsed neutron source.

Performance test of the Japanese ENGIN-X type linear scintillation neutron detector

Nakamura, Tatsuya; Sakasai, Kaoru; Katagiri, Masaki; Birumachi, Atsushi; Hosoya, Takaaki; Soyama, Kazuhiko; Sato, Setsuo*; Shooneveld, E.*; Rhodes, N.*

JAEA-Research 2007-014, 14 Pages, 2007/03

JAEA-Research-2007-014.pdf:1.9MB

The ENGIN-X type linear scintillation neutron detector was manufactured in Japan and the detector performances were evaluated. The ENGIN-X type linear scintillation neutron detector was originally developed by the detector group in Rutherford Appleton Laboratory and the Japanese prototype detector was identical to that which is one of the detector modules installed in the ENGIN-X diffractometer at ISIS pulsed neutron source. The prototype detector can install 240 elements of neutron-sensitive scintillator, where each element has 3 mm in width and 196 mm in length. The prototype detector exhibited a spatial resolution of 3 mm, detection efficiency of 64% for neutrons with wave-lengths of 1.8, count uniformity of 67%, Co sensitivity of 510. Technological transfer to the Japanese manufacturer was done successfully and the mass production of these detectors for the J-PARC project is feasible.

Neutron diffraction analysis of deuterium transfer in chiral -thiolactam formation in the crystalline state

Hosoya, Takaaki*; Uekusa, Hidehiro*; Ohashi, Yuji*; Ohara, Takashi; Tanaka, Ichiro*; Niimura, Nobuo*

Acta Crystallographica Section B; Structural Science, Crystal Engineering and Materials (Internet), 62(1), p.153 - 160, 2006/02

https://doi.org/10.1107/S0108768105038656

Since N,N-dibenzyl-1-cyclohexenecarbothioamide is photoisomerized to the optically active -thiolactam with the retention of the single-crystal form, the mechanism of chirality induction was identified by X-ray crystal structure analyses during the process of the reaction. In order to clarify the mechanism of hydrogen transfer in the reaction, the H atomsof the benzyl groups were replaced with deuterium atoms. The crystal structure after photoisomerization was analyzed by neutron diffraction. One of four deuterium atoms of the two benzyl groups is transferred to the C atom of the cyclohexene ring. The absolute configuration of the -CHD- group(chiral methylene) in the photoproduct r-thiolactam revealed that the deuterium atom occupies the equatorial position. This suggests that the deuterium atom is not transferred from the benzyl group of a neighbouring molecule, but from one of the benzyl groups within the molecule.