Parallel genetic algorithms for crystal structure prediction: Successes and failures in predicting bicalutamide polymorphs

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 findin...

Descripción completa

Detalles Bibliográficos
Autor principal: Ferraro, Marta Beatriz
Otros Autores: Orendt, A.M, Facelli, J.C
Formato: Acta de conferencia Capítulo de libro
Lenguaje:Inglés
Publicado: 2009
Acceso en línea:Registro en Scopus
DOI
Handle
Registro en la Biblioteca Digital
Aporte de:Registro referencial: Solicitar el recurso aquí
Descripción
Sumario: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. © 2009 Springer Berlin Heidelberg.
Bibliografía:Schellhammer, P.F., An Evaluation of Bicalutamide in the Treatment of Prostate Cancer (2002) Expert Opinion on Pharmacotherapy, 3, pp. 1313-1328
Muderris, I., Bayram, F., Ozçelik, B., Güven, M., New Alternative Treatment in Hirsutism: Bicalutamide 25 mg/day (2002) Gynecological Endocrinology, 16, pp. 63-66
Vega, D.R., Polla, G., Martinez, A., Mendioroz, E., Reinoso, M., Conformational Polymorphism in Bicalutamide (2007) International Journal of Pharmaceutics, 328, pp. 112-118
Hu, X.R., Gu, J.M., N-[4-Cyano-3-(trifluoromethyl)phenyl]-3-(4- fluorophenylsulfonyl)-2-hydroxy-2-methylpropionamide (2005) Acta Crystallographica Section E, 61, pp. 3897-3898
Dunitz, J.D., Bernstein, J., Disappearing Polymorphs (1995) Acc. Chem. Res, 28, pp. 193-200
Threlfall, T.L.: Analysis of Organic Polymorphs. A Review. Analyst (Cambridge, United Kingdom) 120, 2435-2460 (1995); Erk, P., Hengelsberg, H., Haddow, M.F., Gelder, R.V., The Innovative Momentum of Crystal Engineering (2004) CrstEngComm, 6, p. 474
Day, G.M., A Third Blind Test of Crystal Structure Prediction (2005) Acta Crystallogr., Sect. B: Struct. Sci, 61, pp. 511-527
Lommerse, J.P.M., Motherwell, W.D.S., Ammon, H.L., Dunitz, J.D., Gavezzotti, A., Hofmann, D.W.M., Leusen, F.J.J., Williams, D.E., A Test of Crystal Structure Prediction of Small Organic Molecules (2000) Acta Cryst. B, 56, p. 697
Day, G.M., Motherwell, W.D.S., Ammon, H.L., Boerrigter, S.X.M., Della Valle, R.G., Venuti, E., Dzyabchenko, A., Verwer, P., CSP workshop at Cambridge UK. Acta Cryst. B-STRUCTURAL (2009) SCIENCE, 65, pp. 107-125
Goldberg, D.E., (1989) Genetic Algorithms in Search, Optimization and Machine Learning, , Addison- Wesley, New York
Man, K.F., Tang, K.S., Kwong, S., (1999) Genetic Algorithms, , Springer, Berlin
Niesse, J.A., Mayne, H.R., Global Optimization of Atomic and Molecular Clusters Using the Space-fixed Modified Genetic Algorithm Method (1997) J. Comput. Chem, 18, p. 1233
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); 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 (2002) J. Chem. Phys, 116, pp. 5992-5995
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 (2004) Int. J. Quantum Chem, 96, pp. 312-320
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 (2007) J. Chem. Theory and Comp, 3, pp. 201-209
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 (2009) J. Comp. Chem, , in press
Axel, D.B., Density-functional Thermochemistry. III. The Role of Exact Exchange (1993) The Journal of Chemical Physics, 98, pp. 5648-5652
Kohn, W., Sham, L.J., Self-Consistent Equations Including Exchange and Correlation Effects (1965) Physical Review, 140, pp. A1133
Lee, C., Yang, W., Parr, R.G., Development of the Colle-Salvetti Correlation-energy Formula into a Functional of the Electron Density (1988) Physical Review B: Condensed Matter and Materials Physics, 37, pp. 785-789
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 (1994) J. Phys. Chem, 98, pp. 11623-11627
Ziegler, T., Approximate Density Functional Theory as a Practical Tool in Molecular Energetics and Dynamics (1991) Chem. Rev, 91, pp. 651-667
Besler, B.H., Merz, K.M., Kollman, P.A., Atomic Charges Derived from Semiempirical Methods (1990) Journal of Computational Chemistry, 11, pp. 431-439
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 (1996) J. Phys. Chem, 100, pp. 7352-7360
Stone, A.J., Alderton, M., Distributed Multipole Analysis (1985) Molecular Physics, 56, pp. 1047-1064
Williams, D.E., Representation of the Molecular Electrostatic Potential by Atomic multipole and Bond Dipole Models (1988) Journal of Computational Chemistry, 9, pp. 745-763
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 (2003) Physical Chemistry Chemical Physics, 5, pp. 4923-4931
Neumann, M.A., Perrin, M.A., Energy Ranking of Molecular Crystals Using Density Functional Theory Calculations and an Empirical van der Waals Correction (2005) J. Phys. Chem. B, 109, pp. 15531-15541
Neumann, M.A., Crystal Structures of Moderately Complex Organic Molecules are Predictable (2007) 24th European Christallographic Meeting, Micro Symposium 14, Advanced computational methods in structural chemistry, Marrakech, Morocco, pp. 11H00-11H20
Neumann, M.A., Leusen, F.J.J., Kendrick, J., A Major Advance in Crystal Structure Prediction (2008) Angew. Chem. Int. Ed, 47, pp. 2427-2430
Misquitta, A.J., Welch, G.W.A., Stone, A.J., Price, S.L., A First Principles Prediction of the Crystal Structure of C6Br2ClFH2 (2008) Chem. Phys. Lett, 456, pp. 105-109
Price, S.L., Quantifying Intermolecular Interactions and Their Use in Computational Crystal Structure Prediction (2004) Cryst. Eng. Comm, 6, pp. 344-353
Wang, J., Wolf, R.M., Caldwell, J.W., Kollman, P.A., Case, D.A., Development and Testing of a General Amber Force Field (2004) J. Comput. Chem, 25, p. 1157
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 (1983) J. Comp. Chem, 4, pp. 187-217
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 (1998) The Encyclopedia of Computational Chemistry, pp. 271-277. , Schleyer ed, John Wiley & Sons, Chichester
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 (1993) J. Phys. Chem, 97, pp. 10269-10280
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 (1993) J. Am. Chem. Soc, 115, pp. 9620-9631
Chisholm, J.A., Motherwell, S., COMPACK: A Program for Identifying Crystal Structure Similarity Using Distances (2005) Journal of Applied Crystallography, 38, pp. 228-231
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 (2008) Propellants, Explosives, Pyrotechnics, 33, pp. 92-102
ISBN:3642040691
9783642040696
ISSN:03029743
DOI:10.1007/978-3-642-04070-2_14