Direct space methods of structure determination from powder diffraction: Principles, guidelines and perspectives

Zeitschrift fur Kristallographie

Volumn 222, Issue 3-4, 2007, Pages 105-113

  Černý, Radovan ^a   Favre Nicolin, Vincent ^b  

^a UNIVERSITY OF GENEVA   (Switzerland)

^b UNIV GRENOBLE ALPES   (France)

Author keywords

Crystal structure solution; Direct space methods; Powder diffraction

Indexed keywords

EID: 33947576586     PISSN: 00442968     EISSN: None     Source Type: Journal    
DOI: 10.1524/zkri.2007.222.3-4.105     Document Type: Review

References (69)

1. Altomare, A.; Cascarano, G.; Giacovazzo, C.; Guagliardi, A.: Early finding of preferred orientation: a new method. J. Appl. Cryst. 27 (1994) 1045-1050.
2. 2. J. Appl. Cryst. 30 (1997) 294-305.
3. Baerlocher, Ch.; McCusker, L. B.; Palatinus, L.: Ab initio structure solution from powder diffraction data using charge flipping. Acta Cryst. A62 (2006) s231.
4. Baerlocher, Ch.; McCusker, L. B.; Prokic, S.; Wessels, T.: Exploiting texture to estimate the relative intensities of overlapping reflections. Z. Kristallogr. 219 (2004) 803-819.
5. Bergmann, J.; Le Bail, A.; Shirley, R.; Zlokazov, V.: Renewed interest in powder diffraction data indexing. Z. Kristallogr. 219 (2004) 783-790.
6. Beyer, T.; Lewis, T.; Price, S. L.: Which organic crystal structures are predictable by lattice energy minimisation? Cryst. Eng. Comm 3(44) (2001) 178-212.
7. Bianchi, R.; Gramaccioli, C. M.; Pilati, T.; Simonetta, M.: Solving Crystal Structures by Constrained Least-Squares Refinement. Acta Cryst. A37 (1981) 65-71.
8. Brenner, S.; McCusker, L. B.; Baerlocher, C.: The application of structure envelopes in structure determination from powder diffraction data. J. Appl. Cryst. 35 (2002) 243-252.
9. Brodski, V.; Peschar, R.; Schenk, H.: Organa - a program package for structure determination from powder diffraction data by direct-space methods. J. Appl. Cryst. 38 (2005) 688-693.
10. Brünger, A. T.: Free R value: a novel statistical quantity for assessing the accuracy of crystal structures. Nature 355 (1992) 472.
11. Coelho, A. A.: Whole-profile structure solution from powder diffraction data using simulated annealing. J. Appl. Cryst. 33 (2000) 899-908.
12. 6S) solved from synchrotron-radiation X-ray powder diffraction data. J. Appl. Cryst. 24 (1991) 222-226.
13. Černý, R.; Favre-Nicolin, V.: FOX: A friendly tool to solve non-molecular structures from powder diffraction. Powder Diffraction 20 (2005) 359-365.
14. Chang, G.; Lewis, M.: Using Genetic Algorithms for Solving Heavy-Atom Sites. Acta Cryst. D50 (1994) 667-674.
15. David, W. I. F.: On the equivalence of the Rietveld method and the correlated integrated intensities method in powder diffraction. J. Appl. Cryst. 37 (2004) 621-628.
16. David, W. I. F.; Shankland, K.; McCusker, L. B.; Baerlocher, Ch.: Structure Determination from Powder Diffraction Data. IUCr. Monographs on Crystallography 13., Oxford University Press, 2002.
17. David, W. I. F.; Shankland, K.; Shankland, N.: Routine determination of molecular crystal structures from powder diffraction data. Chem. Commun. (1998) 931-932.
18. Dollase, W. A.: Correction of Intensities for Preferred Orientation in Powder Diffractometry: Application of the March Model. J. Appl. Cryst. 19 (1986) 267-272.
19. Dovesi, R.; Saunders, V. R.; Roetti, C.; Causa, M.; Harrison, N. M.; Orlando, R.; Apra, E.: CRYSTAL95. University of Torino 1996.
20. Edgar, M.; Carter, V. J.; Tunstall, D. P.; Grewal, P.; Favre-Nicolin, V.; Cox, P. A.; Lightfoot, P.; Wright, P. A.: Structure solution of a novel aluminium methylphosphonate using a new simulated annealing program and powder X-ray diffraction data. Chem. Commun. 8 (2002) 808-809.
21. Egami, T.; Billinge, S. J. L.: Underneath the Bragg-Peaks: Structural Analysis of Complex Materials. Pergamon Press, Oxford 2003.
22. Engel, G. E.; Wilke, S.; König, O.; Harris, K. D. M.; Leusen, F. J. J.: PowderSolve - a complete package for crystal structure solution from powder diffraction patterns. J. Appl. Cryst. 32 (1999) 1169-1179.
23. Falcioni, M.; Deem, M. W.: A biased Monte Carlo scheme for zeolite structure solution. J. Chem. Phys. 110 (1999) 1754-1766.
24. Favre-Nicolin, V.; Černý, R.: FOX, "Free Objects for Crystallography": a modular approach to ab initio structure determination from powder diffraction. J. Appl. Crystallography 35 (2002) 734-743.
25. Favre-Nicolin, V.; Černý, R.: A better FOX: using flexible modelling and maximum likelihood to improve direct-space ab initio structure determination from powder diffraction. Z. Kristallogr. 219 (2004) 847-856.
26. Ferraris, G.; Makovicky, E.; Merlino, S.: Crystallography of modular materials. Oxford University Press 2004.
27. Floudas, C. A.; Pardalos, P. M.: Optimization in Computational Chemistry and Molecular Biology. Kluwer Academic Publisher, Dordrecht 2000.
28. Geyer, G. J.: Practical Markov Chain Monte Carlo. Stat. Sci. 7 (1992) 437-483.
29. Goldberg, D. E.: Genetic algorithms in search, optimization and machine learning. Addison-Wesley, Reading 1989.
30. Grosse-Kunstleve, R. W.; McCusker, L. B.; Baerlocher, Ch.: Powder Diffraction Data and Crystal Chemical Information Combined in an Automated Structure Determination Procedure for Zeolites. J. Appl. Cryst. 30 (1997) 985-995.
31. Harris, K. D. M.; Tremyane, M.; Lightfoot, P.; Bruce, P. G.: Crystal Structure Determination from Powder Diffraction Data by Monte Carlo Methods. J. Am. Chem. Soc. 116 (1994) 3543-3547.
32. Harris, K. D. M.; Habershon, S.; Cheung, E. Y.; Johnston, R. L.: Developments in genetic algorithm techniques for structure solution from powder diffraction data. Z. Kristallogr. 219 (2004) 838-846.
33. Hodeau, J. L.; Bordet, P.; Anne, M.; Prat, A.; Fitch, A. N.; Dooryhée, E.; Vaughan, G.; Freund, A.: in Part of the SPIE Conference on Crystal and Multilayer Optics. San Diego 1998, SPIE Vol. 3448.
34. Holland, J. H.: Adaptation in natural and artificial systems. The University of Michigan Press, Ann Arbor 1975.
35. Hukushima, K.; Nemoto, K.: Exchange Monte Carlo Method and Applications to Spin Glass Simulations. J. Phys. Soc. Jap. 65 (1996) 1604-1608.
36. Kariuki, B. M.; Serrano-González, H.; Johnston, R. L.; Harris, K. D. M.: The application of a genetic algorithm for solving crystal structures from powder diffraction data. Chem. Phys. Lett. 280 (1997) 189-195.
37. Johnston, J. C.; David, W. I. F.; Markvardsen, A. J.; Shankland, K.: A hybrid Monte Carlo method for crystal structure determination from powder diffraction data. Acta Cryst. A58 (2002) 441-447.
38. Juháš, P.; Cherba, D. M.; Duxbury, P. M.; Punch, W. F.; Billinge, S. J. L.: Ab-initio determination of solid-state nanostructure. Nature 440 (2006) 655-658.
39. 6 by X-ray powder diffraction. Mat. Res. Bull. 23 (1988) 447-452.
40. Le Bail, A.: ESPOIR: A program for solving structures by monte Carlo analysis of powder diffraction data. Materials Science Forum 378-381 (2001) 65-70.
41. Le Bail, A.: Inorganic structure prediction with GRINSP. J. Appl. Cryst. 38 (2005) 389-395.
42. Mahfoud, S. W.; Goldberg, D. E.: Parallel recombinative simulated annealing: A genetic algorithm. Parallel Computing 21 (1995) 1-28.
43. Markvardsen, A. J.; David, W. I. F.; Shankland, K.: A maximum-likelihood method for global-optimization-based structure determination from powder diffraction data. Acta Cryst. A58 (2002) 316-326.
44. Markvardsen A. J.; Shankland K.; David W. I. F.; Didlick G.: Characterization of a hybrid Monte Carlo search algorithm for structure determination. J. Appl. Cryst. 38 (2005) 107-111.
45. Masciocchi, N.; Bianchi, R.; Cairati, P.; Mezza, G.; Pilati, T.; Sironi, A.: P-RISCON: a real-space scavenger for crystal structure determination from powder diffraction data. J. Appl. Cryst. 27 (1994) 426-429.
46. McCusker, L. B.; Von Dreele, R. B.; Cox, D. E.; Louër, D.; Scardi, P.: Rietveld refinement guidelines. J. Appl. Cryst. 32 (1999) 36-50.
47. McGreevy, R. L.; Pusztai, L.: Reverse Monte Carlo simulation: a new technique for the determination of disordered structures. Molec. Simul. 1 (1988) 359-367.
48. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E.: Equation of State Calculations by Fast Computing Machines. J. Chem. Phys. 21 (1953) 1087-1092.
49. Murshudov, G. N.; Vagin, A. A.; Dodson, E. J.: Refinement of Macromolecular Structures by the Maximum-Likelihood Method. Acta Cryst. D53 (1997) 240-255.
50. Neumaier, A.: Complete Search in Continuous Global Optimization and Constraint Satisfaction. Acta Numerica, Ed. Iserles, A. Cambridge University Press 2004.
51. Newman, M. E. J.; Barkema, G. T.: Monte Carlo Methods in Statistical Physics. Claredon Press, Oxford 1999.
52. Newsam, J. W.; Deem, M. W.; Freeman, C. M.: Direct Space Methods of Structure Solution From Powder Diffraction Data. Accuracy in Powder Diffraction II, NIST Special Publication 846 (1992) 80-91.
53. Pannetier, J.; Bassas-Alsina, J.; Rodriguez-Carvajal, J.; Caignaert, V.: Prediction of crystal structures from crystal chemistry rules by simulated annealing. Nature 346 (1990) 343-345.
54. Pannu, N. S.; Read, R. J.: Improved Structure Refinement Through Maximum Likelihood. Acta Cryst. A52 (1996) 659-668.
55. Pawley, G. S.: Unit-cell refinement from powder diffraction scans. J. Appl. Cryst. 14 (1981) 357-361.
56. Peschar, R.; Pop, M. M.; De Ridder, D. J. A.; van Mechelen, J. B.; Driessen, R. A. J.; Schenk, H.: Crystal Structures of 1,3-Distearoyl-2- oleoylglycerol and Cocoa Butter in the (V) Phase Reveal the Driving Force Behind the Occurrence of Fat Bloom on Chocolate. J. Phys. Chem. B108 (2004) 15450-15453.
57. Putz, H.; Schön, J. C.; Jansen, M.: Combined method for ab-initio structure solution from powder diffraction data. J. Appl. Crystallogr. 32 (1999) 864-870.
58. Read, R. J.: Structure-Factor Probabilities for Related Structures. Acta Cryst. A46 (1990) 900-912.
59. Read, R. J.: Pushing the boundaries of molecular replacement with maximum likelihood. Acta Cryst. D57 (2001) 1373.
60. Schmitt, B.; Brönnimann, Ch.; Eikenberry, E. F.; Gozzo, F.; Hörmann, C.; Horisberger, R.; Patterson, B.: Mythen detector system. Nucl. Instr. Meth. Phys. Res. A501 (2003) 267-272.
61. Schön, J. C.; Jansen, M.: Determination, prediction, and understanding of structures, using the energy landscape of chemical systems. Z. Kristallogr. 216 (2001) 307-325, 361-383.
62. Seaton, C. C.; Tremayne, M.: Differential evolution: Crystal structure determination of a triclinic polymorph of adipamide from powder diffraction data. Chem. Commun. (2002) 880.
63. Shankland, K.: Whole molecule constraints - the Z-matrix unravelled. Newsletter of the Commission on Crystallographic Computing of the International Union of Crystallography, no. 4, (2004) 46-51. See also: http://www.iucr.org/ iucrtop/comm/ccom/newsletters/2004aug/index.html
64. Shankland, K.; David, W. I. F.; Csoka, T.: Crystal structure determination from powder diffraction data by the application of a genetic algorithm. Z. Kristallogr. 212 (1997) 550-552.
65. Shirley, R.: The Crysfire 2002 system for automatic powder indexing: user's manual. Lattice Press: Guildford 2002. (Similarly the Crysfire 2003 user's manual).
66. Sivia, D. S.: Data Analysis: A Bayesian Tutorial. Oxford University Press 1996.
67. Toby, B.: R factors in Rietveld analysis: How good is good enough? Powder Diffraction 21 (2006) 67-70.
68. Tremayne, M.; Kariuki, B. M.; Harris, K. D. M.: Structure determination of a complex organic solid from X-ray powder diffraction data by a generalized Monte Carlo method: The crystal structure of red fluorescein. Angew. Chemie - Int. Ed. Engl. 36 (1997) 770.
69. 30. J. Appl. Cryst. 36 (2003) 1182-1189.