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The Monte Carlo method for finding missing atoms in solving crystal structures from powder diffraction data without applying a rigid-body approximation

Published online by Cambridge University Press:  05 March 2012

Hisayoshi Nakamura ,
Satoru Yamazaki ,
Tomohiko Ohnishi ,
Takashi Ida  and
Hideo Toraya
Hisayoshi Nakamura
Affiliation:
Ceramics Research Laboratory, Nagoya Institute of Technology, Asahigaoka, Tajimi 507-0071, Japan
Satoru Yamazaki
Affiliation:
Ceramics Research Laboratory, Nagoya Institute of Technology, Asahigaoka, Tajimi 507-0071, Japan
Tomohiko Ohnishi
Affiliation:
Ceramics Research Laboratory, Nagoya Institute of Technology, Asahigaoka, Tajimi 507-0071, Japan
Takashi Ida
Affiliation:
Ceramics Research Laboratory, Nagoya Institute of Technology, Asahigaoka, Tajimi 507-0071, Japan
Hideo Toraya*
Affiliation:
Ceramics Research Laboratory, Nagoya Institute of Technology, Asahigaoka, Tajimi 507-0071, Japan
*
a)Electronic mail: [email protected]
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Abstract

The Monte Carlo method is applied to finding missing atoms in solving inorganic crystal structures without applying a rigid-body approximation. Whole powder patterns of α-SiO2 and Mg2SiO4 were used for testing a procedure. Four atoms among the six in the asymmetric unit of Mg2SiO4 could be found in the present analysis. The use of well-refined profile parameters enhanced the frequency of correct structure configurations in the Monte Carlo search. Utilizing structural information available for constructing a trial configuration is also considered to be important for efficiently searching the structure solution. A procedure for assignment of equivalent positions to respective atoms is presented. The method can be used as a powerful tool for finding missing atoms in a partially solved structure. A histogram of weighted reliability index in Monte Carlo calculations is very informative for evaluating the performance of the method. ©

Type
Technical Articles
Information
Powder Diffraction , Volume 16 , Issue 2 , June 2001 , pp. 65 - 70
Copyright
Copyright © Cambridge University Press 2001

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References

Altomare, A., Cascarano, G., Giacovazzo, C., Guagliardi, A., Burla, M. C., Polidori, G., and Camalli, M. (1994). “SIRPOW.92—a Program for Automatic Solution of Crystal Structures by Direct Methods Optimized for Powder Data,” J. Appl. Crystallogr. JACGAR 27, 435–436. acr, JACGAR Google Scholar
Caglioti, G., Paoletti, A., and Ricci, F. P. (1958). “Choice of Collimators for a Crystal Spectrometer for Neutron Diffraction,” Nucl. Instrum. NUINAO 3, 223–228. nun, NUINAO CrossRefGoogle Scholar
Giacovazzo, C. (1996). “Direct Methods and Powder Data: State of the Arts and Perspectives,” Acta Crystallogr., Sect. A: Found. Crystallogr. ACACEQ 52, 331–339. acf, ACACEQ CrossRefGoogle Scholar
Harris, K. D. M., and Tremayne, M. (1996). “Crystal Structure Determination from Powder Diffraction Data,” Chem. Mater. CMATEX 8, 2554–2570. cma, CMATEXCrossRefGoogle Scholar
Harris, K. D. M., Tremayne, M., Lightfoot, P., and Bruce, P. (1994). “Crystal Structure Determination from Powder Diffraction Data by Monte Carlo Methods,” J. Am. Chem. Soc. JACSAT 116, 3543–3547. acs, JACSAT CrossRefGoogle Scholar
International Tables for X-ray Crystallography (1974). Vol. IV (Kynock, Birmingham) (present distributor Kluwer Academic, Dordrecht).Google Scholar
International Tables for Crystallography (1983). Vol. A (Reidel, Dordrecht).Google Scholar
Kihara, K. (1990). “An X-ray Study of the Temperature Dependence of the Quartz Structure,” Eur. J. Mineral. EJMIER 2, 63–77. eum, EJMIER CrossRefGoogle Scholar
Lager, G. A., Ross, F. K., Rotella, F. J., and Jorgensen, J. D. (1981). “Neutron Powder Diffraction of Forsterite, Mg2SiO4: a Comparison with Single-Crystal Investigations,” J. Appl. Crystallogr. JACGAR 14, 137–139. acr, JACGAR CrossRefGoogle Scholar
Merlino, S., Bonaccorsi, E., and Armbruster, T. (1999). “Tobermorites: Their Real Structure and Order-Disorder (OD) Character,” Am. Mineral. AMMIAY 84, 1613–1621. amn, AMMIAY CrossRefGoogle Scholar
Metropolis, N., Rosenbluth, A. W., Rosenbluth, M. N., and Teller, A. H. (1953). “Equation of State Calculations by Fast Computing Machines,” J. Chem. Phys. JCPSA6 21, 1087–1092. jcp, JCPSA6 CrossRefGoogle Scholar
Miura, Y., and Kikuchi, T. (1999). “Crystal Structure Model-Assembly Program Using the Monte Carlo and R-Factor Methods,” J. Chem. Software CHSFEC 5, 163–171., CHSFEC CrossRefGoogle Scholar
Pawley, G. S. (1981). “Unit-Cell Refinement from Powder Diffraction Scans,” J. Appl. Crystallogr. JACGAR 14, 357–361. acr, JACGAR CrossRefGoogle Scholar
Putz, H., Schön, J. C., and Jansen, M. (1999). “Combined Method for ab initio Structure Solution from Powder Diffraction Data,” J. Appl. Crystallogr. JACGAR 32, 864–870. acr, JACGAR CrossRefGoogle Scholar
Rietveld, H. M. (1969). “A Profile Refinement Method for Nuclear and Magnetic Structures,” J. Appl. Crystallogr. JACGAR 2, 65–71. acr, JACGAR CrossRefGoogle Scholar
Schmidt, M. U., and Dinnebier, R. E. (1999). “Combination of Energy Minimizations and Rigid-Body Rietveld Refinement: the Structure of 2,5-dihydroxybenzo[de] benzo[4,5]imidazo[2,1-a]isoquinolin-7-one.” J. Appl. Crystallogr. JACGAR 2, 178–186. acr, JACGAR CrossRefGoogle Scholar
Tanahashi, Y., Nakamura, H., Yamazaki, S., Kojima, Y., Saito, H., Ida, T., and Toraya, H. (2001). “Ab initio Structure Determination of Monoclinic 2,2-dihydroxy-methylbutanoic Acid from Synchrotron Radiation Powder Diffraction Data: a Combined Use of the Direct Method and the Monte Carlo Method,” Acta Cryst. B (accepted for publication).Google Scholar
Toraya, H. (1986). “Whole-Powder-Pattern Fitting without Reference to a Structural Model: Application to X-ray Powder Diffractometer Data” J. Appl. Crystallogr. JACGAR 19, 440–447. acr, JACGAR CrossRefGoogle Scholar
Toraya, H. (1998). “Weighting Scheme for the Minimization Function in Rietveld Refinement,” J. Appl. Crystallogr. JACGAR 31, 333–343. acr, JACGAR CrossRefGoogle Scholar
Toraya, H., Hibino, H., and Ohsumi, K. (1996). “A New Powder Diffractometer for Synchrotron Radiation with a Multiple-Detector System,” J. Synchrotron Radiat. JSYRES 3, 75–83. jsy, JSYRES CrossRefGoogle ScholarPubMed
Tremayne, M., MacLean, E. J., Tang, C. C., and Glidewell, C. (1999). “2,4,6-Triisopropylbenzensulfonamide: Monte Carlo Structure Solution from X-ray Powder Diffraction Data for a Molecular System Containing Four Independent Asymmetric Rotors,” J. Appl. Crystallogr. JACGAR 29, 211–214. acr, JACGAR CrossRefGoogle Scholar
Yamazaki, S., and Toraya, H. (2001). J. Am. Ceram. Soc. (submitted).Google Scholar
Yamamoto, H. (2000). Bc. thesis, Nagoya Institute of Technology, Japan.Google Scholar