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EXPO2011: A new package for powder crystallography

Published online by Cambridge University Press:  06 March 2012

Angela Altomare ,
Corrado Cuocci ,
Carmelo Giacovazzo ,
Anna Moliterni  and
Rosanna Rizzi
Angela Altomare
Affiliation:
Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
Corrado Cuocci
Affiliation:
Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
Carmelo Giacovazzo*
Affiliation:
Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
Anna Moliterni
Affiliation:
Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
Rosanna Rizzi
Affiliation:
Istituto di Cristallografia, Sede di Bari, Via G. Amendola 122/o, 70126 Bari, Italy
*
a)Author to whom correspondence should be addressed. Electronic mai: [email protected]
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Abstract

EXPO2011 is a new package for phasing crystal structures from powder diffraction diagrams. It is able to carry out all the steps necessary for crystal structure solution, from pattern indexation up to Rietveld method for structure refinement: for each step, the basic algorithm is described. Phasing is performed via ab initio (e.g., Direct Methods, integrated by real space refinement) and non ab initio techniques (e.g., simulated annealing algorithm, when molecular geometry is a priori known). Some emphasis is given to running procedures: the main commands and directives are described, to allow the user to run default and non-default phasing attempts.

Keywords

structure solutionpowder diffractioncomputing program
Type
Powder Diffraction Software
Information
Powder Diffraction , Volume 26 , Supplement S1 , December 2011 , pp. S2 - S12
Copyright
Copyright © Cambridge University Press 2011

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References

Altomare, A., Burla, M. C., Cascarano, G., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., and Polidori, G. (1995). “EXTRA: a program for extracting structure-factor amplitudes from powder diffraction data,” J. Appl. Crystallogr. 28, 842–846.10.1107/S0021889895005619 CrossRefGoogle Scholar
Altomare, A., Caliandro, R., Camalli, M., Cuocci, C., da Silva, I., Giacovazzo, C., Moliterni, A. G. G., and Spagna, R. (2004a). “Space-group determination from powder diffraction data: a probabilistic approach,” J. Appl. Crystallogr. 37, 957–966.10.1107/S0021889804023982 CrossRefGoogle Scholar
Altomare, A., Caliandro, R., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2003). “A systematic procedure for the decomposition of a powder diffraction pattern,” J. Appl. Crystallogr. 36, 906–913.10.1107/S0021889803004655 CrossRefGoogle Scholar
Altomare, A., Caliandro, R., Cuocci, C., da Silva, I., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2004b). “The use of error-correcting codes for the decomposition of a powder diffraction pattern,” J. Appl. Crystallogr. 37, 204–209.10.1107/S002188980302908X CrossRefGoogle Scholar
Altomare, A., Camalli, M., Cuocci, C., da Silva, I., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2005). “Space group determination: improvements in EXPO2004,” J. Appl. Crystallogr. 38, 760–767.10.1107/S0021889805020820 CrossRefGoogle Scholar
Altomare, A., Camalli, M., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2007a). “Direct methods and the solution of organic structures from powder data,” J. Appl. Crystallogr. 40, 344–348.10.1107/S0021889807006358 CrossRefGoogle Scholar
Altomare, A., Camalli, M., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2007b). “Advances in space-group determination from powder diffraction data,” J. Appl. Crystallogr. 40, 743–748.10.1107/S0021889807027501 CrossRefGoogle Scholar
Altomare, A., Camalli, M., Cuocci, C., Giacovazzo, C., Moliterni, A., and Rizzi, R. (2009a). “EXPO2009: structure solution by powder data in direct and reciprocal space,” J. Appl. Crystallogr. 42, 1197–1202.10.1107/S0021889809042915 CrossRefGoogle Scholar
Altomare, A., Campi, G., Cuocci, C., Eriksson, L., Giacovazzo, C., Moliterni, A., Rizzi, R., and Werner, P.-E. (2009b). “Advances in powder diffraction pattern indexing: N-TREOR09,” J. Appl. Crystallogr. 42, 768–775.10.1107/S0021889809025503/ce5059sup1.pdf CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A. G. G., and Rizzi, R. (2006). “Powder diffraction: the new automatic least-squares Fourier recycling procedure in EXPO2005,” J. Appl. Crystallogr. 39, 558–562.10.1107/S0021889806017912 CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Kamel, G. S., Moliterni, A., and Rizzi, R. (2008a). “Minimally resolution biased electron-density maps,” Acta Crystallogr., Sect. A: Found. Crystallogr. 64, 326–336.10.1107/S0108767308004303 CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., and Rizzi, R. (2008c). “Correcting resolution bias in electron density maps of organic molecules derived by direct methods from powder data,” J. Appl. Crystallogr. 41, 592–599.10.1107/S0021889808011527 CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Maggi, S., Moliterni, A., and Rizzi, R. (2009c). “Correcting electron-density resolution bias in reciprocal space,” Acta Crystallogr., Sect. A: Found. Crystallogr. 65, 183–189.10.1107/S0108767309003687 CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., and Rizzi, R. (2010). “The dual-space resolution bias correction algorithm: applications to powder data,” J. Appl. Crystallogr. 43, 798–804.10.1107/S0021889810015499 CrossRefGoogle Scholar
Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., and Rizzi, R. (2011). “Advances in the EXPO2009 systematic decomposition procedure: an atom-matching-based figure of merit,” J. Appl. Crystallogr. 44, 448–453.10.1107/S0021889811010727 CrossRefGoogle Scholar
Altomare, A., Giacovazzo, C., Guagliardi, A., Moliterni, A. G. G., Rizzi, R., and Werner, P.-E. (2000). “New techniques for indexing: N-TREOR in EXPO,” J. Appl. Crystallogr. 33, 1180–1186.10.1107/S0021889800006427 CrossRefGoogle Scholar
Altomare, A., Giacovazzo, C., and Moliterni, A. (2008c). “Indexing and Space Group Determination,” in Powder Diffraction Theory and Practice, edited by Dinnebier, R. E. and Billinge, S. J. L. (RCS Publishing, Cambridge), pp. 206–226.CrossRefGoogle Scholar
Cascarano, G., Giacovazzo, C., Camalli, M., Spagna, R., Burla, M. C., Nunzi, A., and Polidori, G. (1984). “The method of representations of structure seminvariants. The strengthening of triplet relationships,” Acta Crystallogr., Sect. A: Found. Crystallogr. 40, 278–283.10.1107/S0108767384000556CrossRefGoogle Scholar
Cascarano, G., Giacovazzo, C., and Guagliardi, A. (1992). “Improved figures of merit for direct methods,” Acta Crystallogr., Sect. A: Found. Crystallogr. 48, 859–865.10.1107/S0108767392004240CrossRefGoogle Scholar
de Wolff, P. M. (1968). “A simplified criterion for the reliability of a powder pattern indexing,” J. Appl. Crystallogr. 1, 108–113.10.1107/S002188986800508XCrossRefGoogle Scholar
Favre-Nicolin, V. and Cerny, R. (2002). “FOX, ‘free objects for crystallography’: a modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. 35, 734–743.10.1107/S0021889802015236CrossRefGoogle Scholar
Florence, A. J., Shankland, N., Shankland, K., David, W. I. F., Pidcock, E., Xu, X., Johnston, A., Kennedy, A. R., Cox, P. J., Evans, J. S. O., Steele, G., Cosgrove, S. D., and Frampton, C. S. (2005). “Solving molecular crystal structures from laboratory X-ray powder diffraction data with DASH: the state of the art and challenges,” J. Appl. Crystallogr. 38, 249–259.10.1107/S0021889804032662CrossRefGoogle Scholar
Giacovazzo, C., (1998). Direct Phasing in Crystallography (IUCr, Oxford University Press, Oxford).CrossRefGoogle Scholar
Karle, J. and Hauptman, H. (1956). “A theory of phase determination for the four types of non-centrosymmetric space groups 1P222, 2P22, 3P 12, 3P 22,” Acta Cryst. 9, 635–651.10.1107/S0365110X56001741CrossRefGoogle Scholar
Kirkpatrick, S., Gelatt, C. D., and Vecchi, M. P. (1983). “Optimization by simulated annealing,” Science 220, 671–680.10.1126/science.220.4598.671CrossRefGoogle ScholarPubMed
Hodgson, D. J. and Asplund, R. O. (1991). “Phenylacetic acid,” Acta Crystallogr., Sect. C: Cryst. Struct. Commun. 47, 1986–1987.10.1107/S0108270191002275CrossRefGoogle Scholar
Le Bail, A., Duroy, H., and Fourquet, J. L. (1988). “Ab initio structure determination of LiSbWO6 by X-ray powder diffraction,” Mater. Res. Bull. 23, 447–452.10.1016/0025-5408(88)90019-0CrossRefGoogle Scholar
Norby, P., Christensen, A. N., Fjellvag, H., and Nielsen, M. (1991). “The crystal structure of Cr8O21 determined from powder diffraction data: thermal transformation and magnetic properties of a chromium-cromate-tetrachromate,” J. Solid State Chem. 94, 281–293.10.1016/0022-4596(91)90193-LCrossRefGoogle Scholar
Nishibori, E., Ogura, T., Aoyagi, S., and Sakata, M. (2008). “Ab initio structure determination of a pharmaceutical compound, prednisolone succinate, from synchrotron powder data by combination of a genetic algorithm and the maximum entropy method,” J. Appl. Crystallogr. 41, 292–301.10.1107/S0021889808001520/db5036sup1.cifCrossRefGoogle Scholar
Rietveld, H. M. (1969). “A profile refinement method for nuclear and magnetic structures,” J. Appl. Crystallogr. 2, 65–71.10.1107/S0021889869006558CrossRefGoogle Scholar
Shankland, K., David, W.I.F., Csoka, T., and McBride, L. (1998). “Structure solution of Ibuprofen from powder diffraction data by the application of a genetic algorithm combined with prior conformational analysis,” Int. J. Pharm. 165, 117–126.10.1016/S0378-5173(98)00009-XCrossRefGoogle Scholar
Werner, P.-E., Eriksson, L., and Westdahl, M. (1985). “TREOR, a semi-exhaustive trial-and-error powder indexing program for all symmetries,” J. Appl. Crystallogr. 18, 367–370.10.1107/S0021889885010512CrossRefGoogle Scholar
Wilson, A. J. C. (1942). “Determination of absolute from relative x-ray intensity data,” Nature 150, 151–152.CrossRefGoogle Scholar