Evolutionary Algorithms in Crystallographic Applications

Evolutionary Algorithms in Molecular Design

Volumn 8, Issue , 2008, Pages 159-194

  Harris, Kenneth D M ^a   Johnston, Roy L ^a   Kariuki, Benson M ^a  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

Author keywords

Chemistry; Compounds; Mathematical methods; Molecules; Valence bond

Indexed keywords

MOLECULES;

COMPOUNDS; MATHEMATICAL METHOD; VALENCE BONDS;

CHEMISTRY;

EID: 84956781302     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527613168.ch9     Document Type: Chapter

References (82)

1. J. D. Dunitz, X-ray Analysis and the Structures of Organic Molecules, Verlag Helvetica Chimica Acta, Basel, 1995.
2. J. P. Glusker, K. N. Trueblood, Crystal Structure Analysis - A Primer, Oxford University Press, Oxford, 1985.
3. J. Holland, Adaptation in Natural and Artificial Systems, University of Michigan Press, Ann Arbor, Michigan, 1975.
4. D. E. Goldberg, Genetic Algorithms in Search, Optimization and Machine Learning, Addison-Wesley, Reading, Massachusetts, 1989.
5. H. M. Cartwright, Applications of Artificial Intelligence in Chemistry, Oxford University Press, Oxford, 1993.
6. H. M. Rietveld, A Profile Refinement Method for Nuclear and Magnetic Structures, J. Appl. Crystallogr. 1969, 2, 65-71.
7. R. A. Young (Ed.), The Rietveld Method, International Union of Crystallography and Oxford University Press, Oxford, 1993.
8. A. N. Christensen, M. S. Lehmann, M. Nielsen, Solving Crystal Structures from Powder Diffraction Data, Aust. J. Phys. 1985, 38, 497-505.
9. A. K. Cheetham, A. P. Wilkinson, Structure Determination and Refinement with Synchrotron X-ray Powder Diffraction Data, J. Phys. Chem. Solids 1991, 52, 1199-1208.
10. L. B. McCusker, Zeolite Crystallography - Structure Determination in the Absence of Conven-tional Single-crystal Data, Acta Crystallogr. 1991, A47, 297-313.
11. A. K. Cheetham, A. P. Wilkinson, Synchrotron X-ray and Neutron Diffraction Studies in Solid State Chemistry, Angew. Chemie, Int. Ed. Engl. 1992,37, 1557-1570.
12. P. R. Rudolf, Techniques for Ab Initio Structure Determination from X-ray Powder Diffraction Data, Mater. Chem. Phys. 1993, 35, 267-272.
13. K. D. M. Harris, M. Tremayne, Crystal Structure Determination from Powder Diffraction Data, Chem. Mater. 1996, 8, 2554-2570.
14. J. I. Langford, D. Louer, Powder Diffraction, Rep. Progr. Phys. 1996, 59, 131-234.
15. D. M. Poojary, A. Clearfield, Application of X-ray Powder Diffraction Techniques to the Solu-tion of Unknown Crystal Structures, Ace. Chem. Res. 1997, 30, 414-422.
16. W. I. F. David, The Probabilistic Determination of Intensities of Completely Overlapping Re-flections in Powder Diffraction Patterns, J. Appl. Crystallogr. 1987, 20, 316-319.
17. W. I. F. David, Extending the Power of Powder Diffraction for Structure Determination, Nature 1990,346, 731-734.
18. J. Jansen, R. Peschar, H. Schenk, On the Determination of Accurate Intensities from Powder Diffraction Data - Estimation of Intensities of Overlapping Reflections, J. Appl. Crystallogr. 1992,25, 237-243.
19. M. A. Estermann, L. B. McCusker, C. Baerlocher, Ab Initio Structure Determination from Se-verely Overlapping Powder Diffraction Data, /. Appl. Crystallogr. 1992, 25, 539-543.
20. M. A. Estermann, V. Gramlich, Improved Treatment of Severely or Exactly Overlapping Bragg Reflections for the Application of Direct-methods to Powder Data, /. Appl. Crystallogr. 1993, 26, 396-404.
21. C. J. Gilmore, K. Shankland, G. Bricogne, Applications of the Maximum Entropy Method to Powder Diffraction and Electron Crystallography, Proc. Royal Soc. (London) 1993, A442, 97-111.
22. D. S. Sivia, W. I. F. David, A Bayesian Approach to Extracting Structure Factor Amplitudes from Powder Diffraction Data, Acta Crystallogr. 1994, A50, 703-714.
23. C. J. Gilmore, Maximum Entropy and Bayesian Statistics in Crystallography: A Review of Prac-tical Applications, Acta Crystallogr. 1996, A52, 561-589.
24. W. I. F. David, On the Number of Independent Reflections in a Powder Diffraction Pattern, / Appl. Crystallogr. 1999, 32, 654-663.
25. K. D. M. Harris, M. Tremayne, P. Lightfoot, P. G. Bruce, Crystal Structure Determination from Powder Diffraction Data by Monte Carlo Methods, J. Amer. Chem. Soc. 1994, 116, 3543-3547.
26. B. M. Kariuki, D. M. S. Zin, M. Tremayne, K. D. M. Harris, Crystal Structure Solution from Powder X-ray Diffraction Data: The Development of Monte Carlo Methods to Solve the Crystal Structure of the y Phase of 3-Chloro-frans-cinnamic acid, Chem. Mater. 1996, 8, 565-569.
27. M. Tremayne, B. M. Kariuki, K. D. M. Harris, The Development of Monte Carlo Methods for Crystal Structure Solution from Powder Diffraction Data: Simultaneous Translation and Rotation of a Structural Fragment within the Unit Cell, J. Appl. Crystallogr. 1996, 29, 211-214.
28. M. Tremayne, B. M. Kariuki, K. D. M. Harris, Solution of an Organic Crystal Structure from X-ray Powder Diffraction Data by a Generalized Monte Carlo Method: Crystal Structure Determi-nation of 1-Methylfluorene, J. Mat. Chem. 1996, 6, 1601-1604.
29. M. Tremayne, B. M. Kariuki, K. D. M. Harris, 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. 1997, 36, 770-772.
30. L. Elizabe, B. M. Kariuki, K. D. M. Harris, M. Tremayne, M. Epple, J. M. Thomas, Topochemical Rationalization of the Solid State Polymerization Reaction of Sodium Chloroacetate: Crystal Structure Determination from Powder Diffraction Data by the Monte Carlo Method, J. Phys. Chem. 1997, B101, 8827-8831.
31. M. Tremayne, B. M. Kariuki, K. D. M. Harris, K. Shankland, K. S. Knight, Crystal Structure So-lution from Neutron Powder Diffraction Data by a New Monte Carlo Approach Incorporating Restrained Relaxation of the Molecular Geometry, J. Appl. Crystallogr. 1997, 30, 968-974.
32. K. D. M. Harris, B. M. Kariuki, M. Tremayne, Crystal Structure Solution from Powder Diffrac-tion Data by the Monte Carlo Method, Mat. Sci. Forum 1998, 278-291, 32-37.
33. J. M. Newsam, M. W. Deem, C. M. Freeman, Accuracy in Powder Diffraction II: NIST Special Publ. No. 846, pp. 80-91, 1992.
34. D. Ramprasad, G. B. Pez, B. H. Toby, T. J. Markley, R. M. Pearlstein, Solid-state Lithium Cyano-cobaltates with a High-capacity for Reversible Dioxygen Binding - Synthesis, Reactivity and Structures, J. Amer. Chem. Soc. 1995,117, 10694-10701.
35. Y. G. Andreev, P. Lightfoot, P. G. Bruce, Structure of the Polymer Electrolyte Poly(ethylene oxi-de)2:LiN(S02CF3)2 Determined by Powder Diffraction using a Powerful Monte Carlo Approach, Chem. Commun. 1996, 2169-2170.
36. Y. G. Andreev, G. S. MacGlashan, P. G. Bruce, Ab Initio Solution of a Complex Crystal Struc-ture from Powder Diffraction Data using Simulated Annealing Method and a High Degree of Molecular Flexibility, Phys. Rev. B 1997, 55, 12011-12017.
37. C. M. Freeman, A. M. Gorman, J. M. Newsam, Simulated Annealing and Structure Solution, in C. R. A. Catlow (Ed.), Computer Modelling in Inorganic Crystallography, Academic Press, San Diego, pp. 117-150, 1997.
38. W. I. F. David, K. Shankland, N. Shankland, Routine Determination of Molecular Crystal Struc-tures from Powder Diffraction Data, Chem. Commun. 1998, 931-932.
39. G. E. Engel, S. Wilke, O. Konig, K. D. M. Harris, F. J. J. Leusen, Powder Solve - A Complete Package for Crystal Structure Solution from Powder Diffraction Patterns, J. Appl. Crystallogr. 1999,32, 1169-1179.
40. A. M. T. Bell, J. N. B. Smith, J. P. Attfield, J. M. Rawson, K. Shankland, W. I. F. David, A Syn-chrotron X-ray Powder Diffraction Study of 4-(2,3,4-Trifluorophenyl)-l,2,3,5-dithiadiazolyl -Crystal Structure Determination using a Global Optimisation Method, New J. Chem. 1999. 23, 565-567.
41. G. Reck, R.-G. Kretschmer, L. Kutschabsky, W. Pritzkow, POSIT: A Method for Structure Determination of Small Partially Known Molecules from Powder Diffraction Data - Structureof 6-Methyl-l,2,3,4-tetrahydropyrimidine-2,4-dione (6-methyluracil), Acta Crystallogr. 1988, A44, 417-421.
42. J. Cirujeda, L. E. Ochando, J. M. Amigo, G Rovira, J. Rius, J. Veciana, Structure Determination from Powder X-ray Diffraction Data of a Hydrogen-bonded Molecular Solid with Competing Ferromagnetic and Antiferromagnetic Interactions - The 2-(3,4-Dihydroxyphenyl)-ot-nitronyl Nitroxide Radical, Angew. Chemie, Int. Ed. Engl. 1995, 34, 55-57.
43. 2, J- Appl. Crystallogr. 1995, 28, 327-334.
44. R. B. Hammond, K. J. Roberts, R. Docherty, M. Edmondson, Computationally Assisted Structure Determination for Molecular Materials from X-ray Powder Diffraction Data, /. Phys. Chem. 1997, B101, 6532-6356.
45. B. M. Kariuki, H. Serrano-Gonzalez, R. L. Johnston, K. D. M. Harris, The Application of a Ge-netic Algorithm for Solving Crystal Structures from Powder Diffraction Data, Chem. Phys. Lett. 1997, 280, 189-195.
46. K. D. M. Harris, R. L. Johnston, B. M. Kariuki, M. Tremayne, A Genetic Algorithm for Crystal Structure Solution from Powder Diffraction Data, J. Chem. Res. (S) 1998, 390-391.
47. K. D. M. Harris, R. L. Johnston, B. M. Kariuki, The Genetic Algorithm: Foundations and Applications in Structure Solution from Powder Diffraction Data, Acta Crystallogr. 1998, A54, 632-645.
48. K. Shankland, W. I. F. David, T. Csoka, Crystal Structure Determination from Powder Diffrac-tion Data by the Application of a Genetic Algorithm, Z. Kristallogr. 1997, 212, 550-552.
49. K. Shankland, W. I. F. David, T. Csoka, L. McBride, Structure Solution of Ibuprofen from Pow-der Diffraction Data by the Application of a Genetic Algorithm Combined with Prior Confor-mational Analysis, Int. J. Pharm. 1998, 165, 117-126.
50. T. Csoka, W. I. F. David, K. Shankland, Crystal Structure Determination from Powder Diffrac-tion Data by the Application of a Genetic Algorithm, Mat. Sci. Forum 1998, 278-281, 294-299.
51. B. M. Kariuki, P. Calcagno, K. D. M. Harris, D. Philp, R. L. Johnston, Evolving Opportunities in Structure Solution from Powder Diffraction Data - Crystal Structure Determination of a Mole-cular System with 12 Variable Torsion Angles, Angew. Chemie, Int. Ed. Engl. 1999, 38, 831-835.
52. B. M. Kariuki, K. Psallidas, K. D. M. Harris, R. L. Johnston, R. W. Lancaster, S. E. Staniforth, S. M. Cooper, Structure Determination of a Steroid Directly from Powder Diffraction Data, Chem. Commun. 1999, 1677-1678.
53. K. D. M. Harris, R. L. Johnston, B. M. Kariuki, An Evolving Technique for Powder Structure Solution - Fundamentals and Applications of the Genetic Algorithm, Anales de Qulmica, Int. Ed. 1998, 94, 410-416.
54. R. L. Johnston, B. M. Kariuki, K. D. M. Harris, GAPSS: Genetic Algorithm for Powder Structure Solution, University of Birmingham, 1997.
55. G. S. Pawley, Unit-cell Refinement from Powder Diffraction Scans, / Appl. Crystallogr. 1981, 14, 357-361.
56. H. Toraya, Position Constrained and Unconstrained Powder Pattern Decomposition Methods, in R. A. Young (Ed.), The Rietveld Method, International Union of Crystallography and Oxford University Press, Oxford, pp. 254-275, 1993.
57. M. S. Lehman, T. F. Koetzle, W. C. Hamilton, Precision Neutron Diffraction Structure Determi-nation of Protein and Nucleic Acid Components VIII: The Crystal and Molecular Structure of the p Form of the Amino Acid L-Glutamic Acid, J. Cryst. Mol. Struct. 1972, 2, 225-233.
58. M. S. Lehman, A. C. Nunes, A Short Hydrogen Bond Between Near Identical Carboxyl Groups in the a Modification of L-Glutamic Acid, Acta Crystallogr. 1980, B36, 1621-1625.
59. J. W. Visser, A Fully Automatic Program for Finding the Unit Cell from Powder Data, J. Appl. Crystallogr. 1969, 2, 89-95.
60. F. H. Allen, O. Kennard, D. G. Watson, L. Brammer, A. G. Orpen, R. Taylor, Tables of Bond Lengths Determined by X-ray and Neutron Diffraction - Bond Lengths in Organic Compounds, J. Chem. Soc, Perkin Trans. 2 1987, S1-S19.
61. O. J. Lanning, S. Habershon, K. D. M. Harris, R. L. Johnston, B. M. Kariuki, E. Tedesco, G. W. Turner, Definition of a "Guiding Function" in Global Optimization: a Hybrid Approach Com-bining Energy and R-factor in Structure Solution from Powder Diffraction Data, Chem. Phys. Lett., 2000, 317, 296-303.
62. T. S. Bush, C. R. A. Catlow, P. D. Battle, Evolutionary Programming Techniques for Predicting Inorganic Crystal Structures, J. Mater. Chem. 1995, 5. 1269-1272.
63. S. M. Woodley, P. D. Battle, J. D. Gale, C. R. A. Catlow, The Prediction of Inorganic Crystal Structures using a Genetic Algorithm and Energy Minimisation, Phys. Chem. Chem. Phys. 1999, /, 2535-2542.
64. J. D. Gale, GULP: A Computer Program for the Symmetry Adapted Simulation of Solids, J. Chem. Soc, Faraday Trans. 1997, 93, 629-637.
65. B. M. Kariuki, S. A. Belmonte, M. I. McMahon, R. L. Johnston, K. D. M. Harris, R. J. Nelmes, A New Approach for Indexing Powder Diffraction Data Based on Whole-profile Fitting and Global Optimization using a Genetic Algorithm, J. Synchrotron Radiation 1999, 6, 87-92.
66. P.-E. Werner, L. Eriksson, M. Westdahl, TREOR: A Semi-exhaustive Trial-and-error Powder In-dexing Program for All Symmetries, J. Appl. Crystallogr. 1985, 18, 367-370.
67. A. Boultif, D. Louer, Indexing of Powder Diffraction Patterns for Low-symmetry Lattices by the Successive Dichotomy Method, J. Appl. Crystallogr. 1991, 24, 987-993.
68. R. Shirley, Data Accuracy for Powder Indexing, Natl. Bur. Stand. (US) Spec. Publ. No. 567361, 1980.
69. D. Louer, Accuracy in Powder Diffraction II: NIST Special Publ. No. 846 (E. Prince, J. K. Sta-lick, Eds.), pp. 92-104, 1992.
70. W. Paszkowicz, Application of the Smooth Genetic Algorithm for Indexing Powder Patterns -Tests for the Orthorhombic System, Mat. Sci. Forum 1996, 228-231, 19-24.
71. A. Le Bail, H. Duroy, J. L. Fourquet, Ab Initio Structure Determination of LiSbW06 by X-ray Powder Diffraction, Mater. Res. Bull. 1988, 23, 447-452.
72. M. I. McMahon, R. J. Nelmes, D. R. Allan, S. A. Belmonte, T. Bovornratanaraks, Observation of a Simple Cubic Phase of GaAs with a 16-Atom Basis (SC16), Phys. Rev. Lett. 1998, 80, 5564-5567.
73. J. P. Glusker, M. Lewis, M. Rossi, Crystal Structure Analysis for Chemists and Biologists, Wiley-VCH, New York, 1994.
74. S. T. Miller, J. M. Hogle, D. J. Filman, A Genetic Algorithm for the Ab Initio Phasing of Icosa-hedral Viruses, Acta Crystallogr. 1996, D52, 235-251.
75. G. Chang, M. Lewis, Molecular Replacement using Genetic Algorithms, Acta Crystallogr. 1997, D53, 279-289.
76. C. R. Kissinger, D. K. Gehlhaar, D. B. Fogel, Rapid Automated Molecular Replacement by Evo-lutionary Search, Acta Crystallogr. 1999, D55, 484-491.
77. G. Chang, M. Lewis, Using Genetic Algorithms for Solving Heavy Atom Sites, Acta Crystallogr. 1994, D50, 667-674.
78. P. Chacon, F. Moran, J. F. Diaz, E. Pantos, J. M. Andreu, Low-resolution Structures of Proteins in Solution Retrieved from X-ray Scattering with a Genetic Algorithm, Biophys. J. 1998, 74, 2760-2775.
79. E. Landree, C. Collazo-Davila, L. D. Marks, Multi-solution Genetic Algorithm Approach to Sur-face Structure Determination using Direct Methods, Acta Crystallogr. 1997, B53, 916-922.
80. K. Y Tam, R. G. Compton, GAMATCH - A Genetic Algorithm Based Program for Indexing Crystal Faces, J. Appl. Crystallogr. 1995, 28, 640-645.
81. K. Knorr, F. Madler, The Application of Evolution Strategies to Disordered Structures, J. Appl. Crystallogr. 1999, 32, 902-910.
82. K. Knorr, F. Madler, R. J. Papoular, Model-free Density Reconstruction of Host/guest Com-pounds from High-resolution Powder Diffraction Data, Micropor. Mesopor. Mater. 1998, 21, 353-363.