Skip to main content

Parallel Genetic Algorithms for Crystal Structure Prediction: Successes and Failures in Predicting Bicalutamide Polymorphs

  • Conference paper
Book cover Emerging Intelligent Computing Technology and Applications (ICIC 2009)

Part of the book series: Lecture Notes in Computer Science ((LNTCS,volume 5754))

Included in the following conference series:

Abstract

This paper describes the application of our distributed computing framework for crystal structure prediction, Modified Genetic Algorithms for Crystal and Cluster Prediction (MGAC), to predict the crystal structure of the two known polymorphs of bicalutamide. The paper describes our success in finding the lower energy polymorph and the difficulties encountered in finding the second one. The results show that genetic algorithms are very effective in finding low energy crystal conformations, but unfortunately many of them are not plausible due to spurious effects introduced by the energy potential function used in the selection process. We propose to solve this by using a multi objective optimization GA approach, adding the unit cell volume as a second optimization target.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 129.00
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 169.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Schellhammer, P.F.: An Evaluation of Bicalutamide in the Treatment of Prostate Cancer. Expert Opinion on Pharmacotherapy 3, 1313–1328 (2002)

    Article  Google Scholar 

  2. Muderris, I., Bayram, F., Ozçelik, B., Güven, M.: New Alternative Treatment in Hirsutism: Bicalutamide 25 mg/day. Gynecological Endocrinology 16, 63–66 (2002)

    Google Scholar 

  3. Vega, D.R., Polla, G., Martinez, A., Mendioroz, E., Reinoso, M.: Conformational Polymorphism in Bicalutamide. International Journal of Pharmaceutics 328, 112–118 (2007)

    Article  Google Scholar 

  4. Hu, X.R., Gu, J.M.: N-[4-Cyano-3-(trifluoromethyl)phenyl]-3-(4-fluorophenylsulfonyl)-2-hydroxy-2-methylpropionamide. Acta Crystallographica Section E 61, 3897–3898 (2005)

    Article  Google Scholar 

  5. Dunitz, J.D., Bernstein, J.: Disappearing Polymorphs. Acc. Chem. Res. 28, 193–200 (1995)

    Article  Google Scholar 

  6. Threlfall, T.L.: Analysis of Organic Polymorphs. A Review. Analyst (Cambridge, United Kingdom) 120, 2435–2460 (1995)

    Google Scholar 

  7. Erk, P., Hengelsberg, H., Haddow, M.F., Gelder, R.V.: The Innovative Momentum of Crystal Engineering. CrstEngComm 6, 474 (2004)

    Article  Google Scholar 

  8. Day, G.M., et al.: A Third Blind Test of Crystal Structure Prediction. Acta Crystallogr., Sect. B: Struct. Sci. 61, 511–527 (2005)

    Article  Google Scholar 

  9. Lommerse, J.P.M., Motherwell, W.D.S., Ammon, H.L., Dunitz, J.D., Gavezzotti, A., Hofmann, D.W.M., Leusen, F.J.J., Mooij, W.T.M., Price, S.L., Schweizer, B., Schmidt, M.U., Eijck, B.P.V., Verwer, P., Williams, D.E.: A Test of Crystal Structure Prediction of Small Organic Molecules. Acta Cryst. B 56, 697 (2000)

    Article  Google Scholar 

  10. Day, G.M., Motherwell, W.D.S., Ammon, H.L., Boerrigter, S.X.M., Della Valle, R.G., Venuti, E., Dzyabchenko, A., Dunitz, J.D., Schweizer, B., van Eijck, B.P., Erk, P., Facelli, J.C., Bazterra, V.E., Ferraro, M.B., Hofmann, D.W.M., Leusen, F.J.J., Liang, C., Pantelides, C.C., Karamertzanis, P.G., Price, S.L., Lewis, T.C., Nowell, H., Torrisi, A., Scheraga, H.A., Arnautova, Y.A., Schmidt, M.U., Verwer, P.: CSP workshop at Cambridge UK. Acta Cryst. B-STRUCTURAL SCIENCE 65, 107–125 (2009)

    Article  Google Scholar 

  11. Goldberg, D.E.: Genetic Algorithms in Search, Optimization and Machine Learning. Addison-Wesley, New York (1989)

    MATH  Google Scholar 

  12. Man, K.F., Tang, K.S., Kwong, S.: Genetic Algorithms. Springer, Berlin (1999)

    MATH  Google Scholar 

  13. Niesse, J.A., Mayne, H.R.: Global Optimization of Atomic and Molecular Clusters Using the Space-fixed Modified Genetic Algorithm Method. J. Comput. Chem. 18, 1233 (1997)

    Article  Google Scholar 

  14. Bazterra, V.E., Ferraro, M.B., Facelli, J.C.: Modified Genetic Algorithm to Model Crystal Structures. I. Benzene, Naphthalene and Nnthracene. J. Chem. Phys. 116, 5984–5991 (2002)

    Article  Google Scholar 

  15. Bazterra, V.E., Ferraro, M.B., Facelli, J.C.: Modified Genetic Algorithm to Model Crystal Structures. II. Determination of a Polymorphic Structure of Benzene Using Enthalpy Minimization. J. Chem. Phys. 116, 5992–5995 (2002)

    Google Scholar 

  16. Bazterra, V.E., Ferraro, M.B., Facelli, J.C.: Modified Genetic Algorithm to Model Crystal Structures. III. Determination of Crystal Structures Allowing Simultaneous Molecular Geometry Relaxation. Int. J. Quantum Chem. 96, 312–320 (2004)

    Article  Google Scholar 

  17. Bazterra, V.E., Thorley, M., Ferraro, M.B., Facelli, J.C.: A Distributed Computing Method for Crystal Structure Prediction of Flexible Molecules: An Application to N-(2-Dimethyl-4-5-dinitrophenyl) Acetamide. J. Chem. Theory and Comp. 3, 201–209 (2007)

    Article  Google Scholar 

  18. Kim, S., Orendt, A.M., Ferraro, M.B., Facelli, J.C.: Crystal Structure Orediction of Flexible Molecules Using Parallel Geneic Algorithms with Standard Force Field. J. Comp. Chem. (in press, 2009)

    Google Scholar 

  19. Axel, D.B.: Density-functional Thermochemistry. III. The Role of Exact Exchange. The Journal of Chemical Physics 98, 5648–5652 (1993)

    Article  Google Scholar 

  20. Kohn, W., Sham, L.J.: Self-Consistent Equations Including Exchange and Correlation Effects. Physical Review 140, A1133 (1965)

    Article  MathSciNet  Google Scholar 

  21. Lee, C., Yang, W., Parr, R.G.: Development of the Colle-Salvetti Correlation-energy Formula into a Functional of the Electron Density. Physical Review B: Condensed Matter and Materials Physics 37, 785–789 (1988)

    Google Scholar 

  22. Stephens, P.J., Devlin, F.J., Chabalowski, C.F., Frisch, M.J.: Ab Initio Calculation of Vibrational Absorption and Circular Dichroism Spectra Using Density Functional Force Fields. J. Phys. Chem. 98, 11623–11627 (1994)

    Article  Google Scholar 

  23. Ziegler, T.: Approximate Density Functional Theory as a Practical Tool in Molecular Energetics and Dynamics. Chem. Rev. 91, 651–667 (1991)

    Article  Google Scholar 

  24. Besler, B.H., Merz, K.M., Kollman, P.A.: Atomic Charges Derived from Semiempirical Methods. Journal of Computational Chemistry 11, 431–439 (1990)

    Article  Google Scholar 

  25. Coombes, D.S., Price, S.L., Willock, D.J., Leslie, M.: Role of Electrostatic Interactions in Determining the Crystal Structures of Polar Organic Molecules. A Distributed Multipole Study. J. Phys. Chem. 100, 7352–7360 (1996)

    Google Scholar 

  26. Stone, A.J., Alderton, M.: Distributed Multipole Analysis. Molecular Physics 56, 1047–1064 (1985)

    Article  Google Scholar 

  27. Williams, D.E.: Representation of the Molecular Electrostatic Potential by Atomic multipole and Bond Dipole Models. Journal of Computational Chemistry 9, 745–763 (1988)

    Article  Google Scholar 

  28. Brodersen, S., Wilke, S., Leusen, F.J.J., Engel, G.: A Study of Different Approaches to the Electrostatic Interaction in Force Field Methods for Organic Crystals. Physical Chemistry Chemical Physics 5, 4923–4931 (2003)

    Article  Google Scholar 

  29. Neumann, M.A., Perrin, M.A.: Energy Ranking of Molecular Crystals Using Density Functional Theory Calculations and an Empirical van der Waals Correction. J. Phys. Chem. B 109, 15531–15541 (2005)

    Article  Google Scholar 

  30. Neumann, M.A.: Crystal Structures of Moderately Complex Organic Molecules are Predictable. In: 24th European Christallographic Meeting, Micro Symposium 14, Advanced computational methods in structural chemistry, Marrakech, Morocco, pp. 11H00–11H20 (2007)

    Google Scholar 

  31. Neumann, M.A., Leusen, F.J.J., Kendrick, J.: A Major Advance in Crystal Structure Prediction. Angew. Chem. Int. Ed. 47, 2427–2430 (2008)

    Article  Google Scholar 

  32. Misquitta, A.J., Welch, G.W.A., Stone, A.J., Price, S.L.: A First Principles Prediction of the Crystal Structure of C6Br2ClFH2. Chem. Phys. Lett. 456, 105–109 (2008)

    Article  Google Scholar 

  33. Price, S.L.: Quantifying Intermolecular Interactions and Their Use in Computational Crystal Structure Prediction. Cryst. Eng. Comm. 6, 344–353 (2004)

    Google Scholar 

  34. Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A.: Development and Testing of a General Amber Force Field. J. Comput. Chem. 25, 1157 (2004)

    Article  Google Scholar 

  35. Brooks, B.R., Bruccoleri, R.E., Olafson, B.D., States, D.J., Swaminathan, S., Karplus, M.: CHARMM: A Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comp. Chem. 4, 187–217 (1983)

    Article  Google Scholar 

  36. MacKerell, A.D., Brooks, J.B., Brooks III, C.L., Nilsson, L., Roux, B., Won, Y., Karplus, M.: CHARMM: The Energy Function and Its Parameterization with an Overview of the Program. In: Schleyer (ed.) The Encyclopedia of Computational Chemistry, pp. 271–277. John Wiley & Sons, Chichester (1998)

    Google Scholar 

  37. Bayly, C.I., Cieplak, P., Cornell, W., Kollman, P.A.: A Well-behaved Electrostatic Potential Based Method Using Charge Restraints for Deriving Atomic Charges: the RESP Model. J. Phys. Chem. 97, 10269–10280 (1993)

    Article  Google Scholar 

  38. Cornell, W.D., Cieplak, P., Bayly, C.I., Kollman, P.A.: Application of RESP Charges to Calculate Conformational Energies, Hydrogen Bond Energies, and Free Energies of Solvation. J. Am. Chem. Soc. 115, 9620–9631 (1993)

    Article  Google Scholar 

  39. Chisholm, J.A., Motherwell, S.: COMPACK: a Program for Identifying Crystal Structure Similarity Using Distances. Journal of Applied Crystallography 38, 228–231 (2005)

    Article  Google Scholar 

  40. Ammon, H.L.: Updated Atom/Functional Group and Atom_Code Volume Additivity Parameters for the Calculation of Crystal Densities of Single Molecules, Organic Salts, and Multi-Fragment Materials Containing H, C, B, N, O, F, S, P, Cl, Br, and I. Propellants, Explosives, Pyrotechnics 33, 92–102 (2008)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2009 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Ferraro, M.B., Orendt, A.M., Facelli, J.C. (2009). Parallel Genetic Algorithms for Crystal Structure Prediction: Successes and Failures in Predicting Bicalutamide Polymorphs. In: Huang, DS., Jo, KH., Lee, HH., Kang, HJ., Bevilacqua, V. (eds) Emerging Intelligent Computing Technology and Applications. ICIC 2009. Lecture Notes in Computer Science, vol 5754. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-04070-2_14

Download citation

  • DOI: https://doi.org/10.1007/978-3-642-04070-2_14

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-04069-6

  • Online ISBN: 978-3-642-04070-2

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics