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X-ray diffractometry for the structure determination of a submicrometre single powder grain.

ABSTRACT: A high-precision diffractometer has been developed for the structure analysis of a submicrometre-scale single grain of a powder sample at the SPring-8 BL40XU undulator beamline. The key design concept is the combination of a stable focused synchrotron radiation beam and the precise axis control of the diffractometer, which allows accurate diffraction intensity data of a submicrometre-scale single powder grain to be measured. The phase zone plate was designed to create a high-flux focused synchrotron radiation beam. A low-eccentric goniometer and high-precision sample positioning stages were adopted to ensure the alignment of a micrometre-scale focused synchrotron radiation beam onto the submicrometre-scale single powder grain. In order to verify the diffractometer performance, the diffraction pattern data of several powder grains of BaTiO(3), of dimensions approximately 600 x 600 x 300 nm, were measured. By identifying the diffraction data set of one single powder grain, the crystal structure was successfully determined with a reliable factor of 5.24%.

SUBMITTER: Yasuda N

PROVIDER: S-EPMC2678016 | biostudies-literature | 2009 May

REPOSITORIES: biostudies-literature

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X-ray diffractometry for the structure determination of a submicrometre single powder grain.

Yasuda Nobuhiro N Murayama Haruno H Fukuyama Yoshimitsu Y Kim Jungeun J Kimura Shigeru S Toriumi Koshiro K Tanaka Yoshihito Y Moritomo Yutaka Y Kuroiwa Yoshihiro Y Kato Kenichi K Tanaka Hitoshi H Takata Masaki M

Journal of synchrotron radiation 20090401 Pt 3

A high-precision diffractometer has been developed for the structure analysis of a submicrometre-scale single grain of a powder sample at the SPring-8 BL40XU undulator beamline. The key design concept is the combination of a stable focused synchrotron radiation beam and the precise axis control of the diffractometer, which allows accurate diffraction intensity data of a submicrometre-scale single powder grain to be measured. The phase zone plate was designed to create a high-flux focused synchro ...[more]

PMID: 19395798

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Project description:Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-difluoroquinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. All models are chemically sensible, but differ in their lattice parameters, space groups, Z, Z′, molecular packing and hydrogen bond patterns, and were investigated by fit to the pair-distribution function, solid-state NMR and lattice-energy minimizations. Four different structural models, which all fit the same X-ray powder pattern, were obtained in the structure determination of 4,11-difluoroquinacridone (C20H10N2O2F2) from unindexed X-ray powder data by a global fit. The models differ in their lattice parameters, space groups, Z, Z′, molecular packing and hydrogen bond patterns. The molecules form a criss-cross pattern in models A and B, a layer structure built from chains in model C and a criss-cross arrangement of dimers in model D. Nevertheless, all models give a good Rietveld fit to the experimental powder pattern with acceptable R-values. All molecular geometries are reliable, except for model D, which is slightly distorted. All structures are crystallochemically plausible, concerning density, hydrogen bonds, intermolecular distances etc. All models passed the checkCIF test without major problems; only in model A a missed symmetry was detected. All structures could have probably been published, although 3 of the 4 structures were wrong. The investigation, which of the four structures is actually the correct one, was challenging. Six methods were used: (1) Rietveld refinements, (2) fit of the crystal structures to the pair distribution function (PDF) including the refinement of lattice parameters and atomic coordinates, (3) evaluation of the colour, (4) lattice-energy minimizations with force fields, (5) lattice-energy minimizations by two dispersion-corrected density functional theory methods, and (6) multinuclear CPMAS solid-state NMR spectroscopy (1H, 13C, 19F) including the comparison of calculated and experimental chemical shifts. All in all, model B (perhaps with some disorder) can probably be considered to be the correct one. This work shows that a structure determination from limited-quality powder data may result in totally different structural models, which all may be correct or wrong, even if they are chemically sensible and give a good Rietveld refinement. Additionally, the work is an excellent example that the refinement of an organic crystal structure can be successfully performed by a fit to the PDF, and the combination of computed and experimental solid-state NMR chemical shifts can provide further information for the selection of the most reliable structure among several possibilities.

Dataset Information

X-ray diffractometry for the structure determination of a submicrometre single powder grain.

Publications

X-ray diffractometry for the structure determination of a submicrometre single powder grain.

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