Prediction of the crystal structures of axitinib, a polymorphic pharmaceutical molecule

Chemical Engineering Science

Volumn 121, Issue , 2015, Pages 60-76

  Vasileiadis, Manolis ^a   Pantelides, Constantinos C ^a   Adjiman, Claire S ^a  

^a IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

CrystalOptimizer; CrystalPredictor; Lattice energy; Local approximate models; Polymorph

Indexed keywords

FORECASTING; MECHANICAL PROPERTIES; MOLECULES; POLYMORPHISM;

COMPUTATIONAL ASPECTS; CONFORMATIONAL FLEXIBILITY; CRYSTAL STRUCTURE PREDICTION; CRYSTALOPTIMIZER; CRYSTALPREDICTOR; LATTICE ENERGIES; LOCAL APPROXIMATE MODELS; PHYSICAL AND MECHANICAL PROPERTIES;

CRYSTAL STRUCTURE;

EID: 84921895064     PISSN: 00092509     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.ces.2014.08.058     Document Type: Article

References (99)

1. Aaltonen J., Allesø M., Mirza S., Koradia V., Gordon K.C., Rantanen J. Solid form screening - a review. Eur. J. Pharm. Biopharm. 2009, 71:23-37.
2. Abramov Y.A. QTAIM application in drug development: prediction of relative stability of drug polymorphs from experimental crystal structures. J. Phys. Chem. A 2011, 115:12809-12817.
3. Abramov Y.A. Current computational approaches to support pharmaceutical solid form selection. Org. Process. Res. Dev. 2013, 17:472-485.
4. Admiraal G., Eikelenboom J.C., Vos A. Structures of the triclinic and monoclinic modifications of (2-Oxo-1-pyrrolidinyl)acetamide. Acta Crystallogr. Sect. B 1982, 38:2600-2605.
5. Allan D.R., Clark S.J., Dawson A., McGregor P.A., Parsons S. Pressure-induced polymorphism in phenol. Acta Crystallogr. Sect. B 2002, 58:1018-1024.
6. Allen F.H. The Cambridge structural database: a quarter of a million crystal structures and rising. Acta Crystallogr. Sect. B 2002, 58:380-388.
7. Arlin J.-B., Price L.S., Price S.L., Florence A.J. A strategy for producing predicted polymorphs: catemeric carbamazepine form V. Chem. Commun, vol. 345. 2011, 47:7074-7076.
8. Atahan-Evrenk S., Aspuru-Guzik A.(Eds.) Prediction and calculation of crystal structures. Topics in Current Chemistry, vol. 345 2014, Springer International Publishing, Switzerland.
9. 1H NMR spectroscopy. Phys. Chem. Chem. Phys. 2013, 15:8069-8080.
10. Bardwell D.A., Adjiman C.S., Arnautova Y.A., Bartashevich E., Boerrigter S.X.M., Braun D.E., Cruz-Cabeza A.J., Day G.M., Della Valle R.G., Desiraju G.R., van Eijck B.P., Facelli J.C., Ferraro M.B., Grillo D., Habgood M., Hofmann D.W.M., Hofmann F., Jose K.V.J., Karamertzanis P.G., Kazantsev A.V., Kendrick J., Kuleshova L.N., Leusen F.J.J., Maleev A.V., Misquitta A.J., Mohamed S., Needs R.J., Neumann M.A., Nikylov D., Orendt A.M., Pal R., Pantelides C.C., Pickard C.J., Price L.S., Price S.L., Scheraga H.A., van de Streek J., Thakur T.S., Tiwari S., Venuti E., Zhitkov I.K Towards crystal structure prediction of complex organic compounds - a report on the fifth blind test. Acta Crystallogr. Sect. B 2011, 67:535-551.
11. Bauer J., Spanton S., Henry R., Quick J., Dziki W., Porter W., Morris J. Ritonavir: an extraordinary example of conformational polymorphism. Pharm. Res. 2001, 18:859-866.
12. Bernstein J. Polymorphism in Molecular Crystals 2002, Clarendon Press, Oxford.
13. Bhardwaj R.M., Price L.S., Price S.L., Reutzel-Edens S.M., Miller G.J., Oswald I.D.H., Johnston B.F., Florence A.J. Exploring the experimental and computed crystal energy landscape of olanzapine. Cryst. Growth Des. 2013, 13:1602-1617.
14. Braun D.E., Ardid-Candel M., D'Oria E., Karamertzanis P.G., Arlin J.-B., Florence A.J., Jones A.G., Price S.L. Racemic naproxen: a multidisciplinary structural and thermodynamic comparison with the enantiopure form. Cryst. Growth Des. 2011, 11:5659-5669.
15. Breneman C.M., Wiberg K.B. Determining atom-centered monopoles from molecular electrostatic potentials. The need for high sampling density in formamide conformational analysis. J. Comput. Chem. 1990, 11:361-373.
16. Brog J.-P., Chanez C.-L., Crochet A., Fromm K.M. Polymorphism, what it is and how to identify it: a systematic review. RSC Adv. 2013, 3:16905-16931.
17. Bruno I.J., Cole J.C., Kessler M., Luo J., Motherwell W.D.S., Purkis L.H., Smith B.R., Taylor R., Cooper R.I., Harris S.E., Orpen A.G. Retrieval of crystallographically-derived molecular geometry information. J. Chem. Inf. Comput. Sci. 2004, 44:2133-2144.
18. Burger A., Ramberger R. On the polymorphism of pharmaceuticals and other molecular crystals. I Theory of thermodynamic rules. Microchim. Acta 1979, 72:259-271.
19. Cabri W., Ghetti P., Pozzi G., Alpegiani M. Polymorphisms and patent, market, and legal battles:Cefdinir case study. Org. Process. Res. Dev. 2007, 11:64-72.
20. Campeta A.M., Chekal B.P., Abramov Y.A., Meenan P.A., Henson M.J., Shi B., Singer R.A., Horspool K.R. Development of a targeted polymorph screening approach for a complex polymorphic and highly solvating API. J. Pharm. Sci. 2010, 99:3874-3886.
21. Chekal B.P., Campeta A.M., Abramov Y.A., Feeder N., Glynn P.P., McLaughlin R.W., Meenan P.A., Singer R.A. The challenges of developing an API crystallization process for a complex polymorphic and highly solvating system. Part I. Org. Process. Res. Dev. 2009, 13:1327-1337.
22. Chisholm J.A., Motherwell W.D.S. COMPACK: a program for identifying crystal structure similarity using distances. J. Appl. Crystallogr. 2005, 38:228-231.
23. 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. 1996, 100:7352-7360.
24. Cooper T.G., Hejczyk K.E., Jones W., Day G.M. Molecular polarization effects on the relative energies of the real and putative crystal structures of valine. J. Chem. Theory Comput. 2008, 4:1795-1805.
25. COSMOLogic, G., COSMOTherm Version C21_0108.
26. Cox S.R., Hsu L.Y., Williams D.E. Nonbonded potential function models for the crystalline oxohydrocarbons. Acta Crystallogr. Sect. A 1981, 37:293-301.
27. Cruz-Cabeza A.J., Bernstein J. Conformational polymorphism. Chem. Rev. 2014, 114:2170-2191.
28. Day G.M. Computational crystal structure prediction: towards in silico solid form screening. Organic Crystal Engineering: Frontiers in Crystal Engineering 2010, 43-66. Wiley, Chichester, UK. E.R.T. Tiekink, J. Vittal, M. Zaworotko (Eds.).
29. Day G.M. Current approaches to predicting molecular organic crystal structures. Crystallogr. Rev. 2011, 17:3-52.
30. Day G.M. Crystal structure prediction. Supramolecular Chemistry: From Molecules to Nanomaterials 2012, 2905-2926. John Wiley & Sons, Ltd, Chichester, UK. J.W. Steed, P.A. Gale (Eds.).
31. Day G.M., Cooper T.G., Cruz-Cabeza A.J., Hejczyk K.E., Ammon H.L., Boerrigter S.X.M., Tan J.S., Della Valle R.G., Venuti E., Jose J., Gadre S.R., Desiraju G.R., Thakur T.S., van Eijck B.P., Facelli J.C., Bazterra V.E., Ferraro M.B., Hofmann D.W.M., Neumann M.A., Leusen F.J.J., Kendrick J., Price S.L., Misquitta A.J., Karamertzanis P.G., Welch G.W.A., Scheraga H.A., Arnautova Y.A., Schmidt M.U., van de Streek J., Wolf A.K., Schweizer B. Significant progress in predicting the crystal structures of small organic molecules - a report on the fourth blind test. Acta Crystallogr. Sect. B 2009, 65:107-125.
32. 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. A third blind test of crystal structure prediction. Acta Crystallogr. Sect. B 2005, 61:511-527.
33. Day G.M., Price S.L., Leslie M. Atomistic calculations of phonon frequencies and thermodynamic quantities for crystals of rigid organic molecules. J. Phys. Chem. B 2003, 107:10919-10933.
34. Ewald P.P. Die Berenchnung optischer und elektrostatischer Gitteropotentiale. Ann. Phys. 1921, 64:253-287.
35. Frenkel D., Smit B. Understanding Molecular Simulation: From Algorithms to Applications 2002, Academic Press, San Diego, California.
36. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Scalmani, G., Barone, V., Mennucci, B., Petersson, G.A., Nakatsuji, H., Caricato, M., Li, X., Hratchian, H.P., Izmaylov, A.F., Bloino, J., Zheng, G., Sonnenberg, J.L., Hada, M., Ehara, M., Toyota, K., Fukuda, R., Hasegawa, J., Ishida, M., Nakajima, T., Honda, Y., Kitao, O., Nakai, H., Vreven, T., Montgomery, J.A., Peralta, J.E., Ogliaro, F., Bearpark, M., Heyd, J.J., Brothers, E., Kudin, K.N., Staroverov, V.N., Kobayashi, R., Normand, J., Raghavachari, K., Rendell, A., Burant, J.C., Iyengar, S.S., Tomasi, J., Cossi, M., Rega, N., Millam, J.M., Klene, M., Knox, J.E., Cross, J.B., Bakken, V., Adamo, C., Jaramillo, J., Gomperts, R., Stratmann, R.E., Yazyev, O., Austin, A.J., Cammi, R., Pomelli, C., Ochterski, J.W., Martin, R.L., Morokuma, K., Zakrzewski, V.G., Voth, G.A., Salvador, P., Dannenberg, J.J., Dapprich, S., Daniels, A.D., Farkas, Foresman, J.B., Ortiz, J.V., Cioslowski, J., Fox, D.J., 2009. Gaussian 09, Revision D.01, Wallingford CT.
37. Friščić T., Lancaster R.W., Fábián L., Karamertzanis P.G. Tunable recognition of the steroid a-face by adjacent p-electron density. Proc. Natl. Acad. Sci. 2010, 107:13216-13221.
38. Gavezzotti A. Are crystal structures predictable?. Acc. Chem. Res. 1994, 27:309-314.
39. Gavezzotti A., Filippini G. Polymorphic forms of organic crystals at room conditions: thermodynamic and structural implications. J. Am. Chem. Soc. 1995, 117:12299-12305.
40. Grimme S. Semiempirical GGA-type density functional constructed with a long-range dispersion correction. J. Comput. Chem. 2006, 27:1787-1799.
41. Habgood M. Analysis of enantiospecific and diastereomeric cocrystal systems by crystal structure prediction. Cryst. Growth Des. 2013, 13:4549-4558.
42. Hilfiker R. Polymorphism in the Pharmaceutical Industry 2006, Wiley-VCH, Weinheim, Germany.
43. Ismail S.Z., Anderton C.L., Copley R.C.B., Price L.S., Price S.L. Evaluating a crystal energy landscape in the context of industrial polymorph screening. Cryst. Growth Des. 2013, 13:2396-2406.
44. Karamertzanis P.G., Kazantsev A.V., Issa N., Welch G.W.A., Adjiman C.S., Pantelides C.C., Price S.L. Can the formation of pharmaceutical cocrystals be computationally predicted? 2. Crystal structure prediction. J. Chem. Theory Comput. 2009, 5:1432-1448.
45. Karamertzanis P.G., Pantelides C.C. Optimal site charge models for molecular electrostatic potentials. Mol. Simul. 2004, 30:413-436.
46. Karamertzanis P.G., Pantelides C.C. Ab initio crystal structure prediction - I. Rigid molecules. J. Comput. Chem. 2005, 26:304-324.
47. Karamertzanis P.G., Pantelides C.C. Ab initio crystal structure prediction. II. Flexible molecules. Mol. Phys. 2007, 105:273-291.
48. Karamertzanis P.G., Raiteri P., Parrinello M., Leslie M., Price S.L. The thermal stability of lattice-energy minima of 5-fluorouracil: metadynamics as an aid to polymorph prediction. J. Phys. Chem. B 2008, 112:4298-4308.
49. Kazantsev A.V. Molecular Flexibility in Crystal Structure Prediction 2011, Imperial College London, London, U.K.
50. Kazantsev A.V., Karamertzanis P.G., Adjiman C.S., Pantelides C.C. Efficient handling of molecular flexibility in lattice energy minimization of organic crystals. J. Chem. Theory Comput. 2011, 7:1998-2016.
51. Kazantsev A.V., Karamertzanis P.G., Adjiman C.S., Pantelides C.C., Price S.L., Galek P.T.A., Day G.M., Cruz-Cabeza A.J. Successful prediction of a model pharmaceutical in the fifth blind test of crystal structure prediction. Int. J. Pharm. 2011, 418:168-178.
52. Kendrick J., Leusen F.J.J., Neumann M.A., van de Streek J. Progress in crystal structure prediction. Chem. - Eur. J. 2011, 17:10736-10744.
53. Kendrick J., Stephenson G.A., Neumann M.A., Leusen F.J.J. Crystal structure prediction of a flexible molecule of pharmaceutical interest with unusual polymorphic behavior. Cryst. Growth Des. 2013, 13:581-589.
54. Kim K.-H., Jung D.H., Kim D., Lee A., Choi K., Kim Y., Choi S.-H. Crystal structure prediction of organic materials: tests on the 1,4-diketo-3,6-diphenylpyrrolo(3,4-c)pyrrole and 1,4-diketo-3,6-bis(4'-dipyridyl)-pyrrolo-[3,4-c]pyrrole. Dye. Pigment. 2011, 89:37-43.
55. Klamt A. COSMO-RS from Quantum Chemistry to Fluid Phase Thermodynamics and Drug Design 2005, Elsevier, Amsterdam.
56. Kofke D.A., Cummings P.T. Quantitative comparison and optimization of methods for evaluating the chemical potential by molecular simulation. Mol. Phys. 1997, 92:973-996.
57. Kofke D.A., Cummings P.T. Precision and accuracy of staged free-energy perturbation methods for computing the chemical potential by molecular simulation. Fluid Phase Equil. 1998, 150-151:41-49.
58. Kolossváry I., Guida W.C. Low mode search. An efficient, automated computational method for conformational analysis: application to cyclic and acyclic alkanes and cyclic peptides. J. Am. Chem. Soc. 1996, 118:5011-5019.
59. 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., van Eijck B.P., Verwer P., Williams D.E. A test of crystal structure prediction of small organic molecules. Acta Crystallogr. Sect. B 2000, 56:697-714.
60. Lupyan D., Abramov Y., Sherman W. Close intramolecular sulfur-oxygen contacts: modified force field parameters for improved conformation generation. J. Comput.-Aided Mol. Des. 2012, 26:1195-1205.
61. Macrae C.F., Bruno I.J., Chisholm J.A., Edgington P.R., McCabe P., Pidcock E., Rodriguez-Monge L., Taylor R., van de Streek J., Wood P.A. Mercury CSD 2.0 - new features for the visualization and investigation of crystal structures. J. Appl. Crystallogr. 2008, 41:466-470.
62. McQuaid M.J., Sun H., Rigby D. Development and validation of COMPASS force field parameters for molecules with aliphatic azide chains. J. Comput. Chem. 2004, 25:61-71.
63. 2. Chem. Phys. Lett. 2008, 456:105-109.
64. Mooij W.T.M., Leusen F.J.J. Multipoles versus charges in the 1999 crystal structure prediction test. Phys. Chem. Chem. Phys. 2001, 3:5063-5066.
65. Mooij W.T.M., van Duijneveldt F.B., van Duijneveldt-van de Rijdt J.G.C.M., van Eijck B.P. Transferable ab initio intermolecular potentials. 1. Derivation from methanol dimer and trimer calculations. J. Phys. Chem. A 1999, 103:9872-9882.
66. Mooij W.T.M., van Eijck B.P., Price S.L., Verwer P., Kroon J. Crystal structure predictions for acetic acid. J. Comput. Chem. 1998, 19:459-474.
67. Morissette S.L., Soukasene S., Levinson D., Cima M.J., Almarsson Ö. Elucidation of crystal form diversity of the HIV protease inhibitor ritonavir by high-throughput crystallization. Proc. Natl. Acad. Sci. 2003, 100:2180-2184.
68. Motherwell W.D.S., Ammon H.L., Dunitz J.D., Dzyabchenko A., Erk P., Gavezzotti A., Hofmann D.W.M., Leusen F.J.J., Lommerse J.P.M., Mooij W.T.M., Price S.L., Scheraga H., Schweizer B., Schmidt M.U., van Eijck B.P., Verwer P., Williams D.E. Crystal structure prediction of small organic molecules: a second blind test. Acta Crystallogr. Sect. B 2002, 58:647-661.
69. Mukhopadhyay R., Chaplot S.L., Rao K.R. Phase transition in tetracyanoethylene. Physica Status Solidi (a) 1985, 92:467-474.
70. 14N nuclear quadrupole resonance and the observation of the phase transition in cubic tetracyanoethylene. J. Chem. Phys. 1975, 62:92-93.
71. 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 2005, 109:15531-15541.
72. Newman A. Specialized solid form screening techniques. Org. Process. Res. Dev. 2013, 17:457-471.
73. Nocedal J., Wright S.J. Numerical Optimization 2006, Springer, New York. second ed.
74. Noya E.G., Conde M.M., Vega C. Computing the free energy of molecular solids by the Einstein molecule approach: ICES XIII and XIV, hard-dumbbells and a patchy model of proteins. J. Chem. Phys. 2008, 129. , 104704.
75. Paliwoda D., Dziubek K.F., Katrusiak A. Imidazole hidden polar phase. Cryst. Growth Des. 2012, 12:4302-4305.
76. Pantelides C.C., Adjiman C.S., Kazantsev A.V. General computational algorithms for ab initio crystal structure prediction for organic molecules. Topics in Current Chemistry 2014, 25-58. Springer International Publishing, Switzerland. S. Atahan-Evrenk, S. Aspuru-Guzik (Eds.).
77. Perdew J.P., Burke K., Ernzerhof M. Generalized gradient approximation made simple. Phys. Rev. Lett. 1996, 77:3865-3868.
78. Pillardy J., Wawak R.J., Arnautova Y.A., Czaplewski C., Scheraga H.A. Crystal structure prediction by global optimization as a tool for evaluating potentials: role of the dipole moment correction term in successful predictions. J. Am. Chem. Soc. 2000, 122:907-921.
79. Price, L.S., McMahon, J.A., Lingireddy, S.R., Lau, S.-F., Diseroad, B.A., Price, S.L., Reutzel-Edens, S.M. A molecular picture of the problems in ensuring structural purity of tazofelone.J. Mol. Struct, in press. http://dx.doi.org/10.1016/j.molstruc.2014.01.014.
80. Price S. Why don't we find more polymorphs?. Acta Crystallogr. Sect. B 2013, 69:313-328.
81. Price S.L. Computational prediction of organic crystal structures and polymorphism. Int. Rev. Phys. Chem. 2008, 27:541-568.
82. Price S.L. From crystal structure prediction to polymorph prediction: interpreting the crystal energy landscape. Phys. Chem. Chem. Phys. 2008, 10:1996-2009.
83. Price S.L. Predicting crystal structures of organic compounds. Chem. Soc. Rev. 2014, 43:2098-2111.
84. Price S.L., Leslie M., Welch G.W.A., Habgood M., Price L.S., Karamertzanis P.G., Day G.M. Modeling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials. Phys. Chem. Chem. Phys. 2010, 12:8478-8490.
85. Shivakumar D., Williams J., Wu Y., Damm W., Shelley J., Sherman W. Prediction of absolute solvation free energies using molecular dynamics free energy perturbation and the OPLS force field. J. Chem. Theory Comput. 2010, 6:1509-1519.
86. Sobol' I.M. On the distribution of points in a cube and the approximate evaluation of integrals. USSR Comput. Math. Math. Phys. 1967, 7:86-112.
87. Stone A.J., Alderton M. Distributed multipole analysis - methods and applications. Mol. Phys. 1985, 56:1047-1064.
88. Storey R.A., Ymén I. Solid State Characterization of Pharmaceuticals 2011, Wiley, Chichester, U.K.
89. Uzoh O.G., Cruz-Cabeza A.J., Price S.L. Is the fenamate group a polymorphophore? Contrasting the crystal energy landscapes of fenamic and tolfenamic acids. Cryst. Growth Des. 2012, 12:4230-4239.
90. van Eijck B.P. Ab initio crystal structure predictions for flexible hydrogen-bonded molecules. Part III. Effect of lattice vibrations. J. Comput. Chem. 2001, 22:816-826.
91. Vasileiadis M. Calculation of the Free Energy of Crystalline Solids 2013, Imperial College London, London, U.K.
92. Vasileiadis M., Kazantsev A.V., Karamertzanis P.G., Adjiman C.S., Pantelides C.C. The polymorphs of ROY: application of a systematic crystal structure prediction technique. Acta Crystallogr. Sect. B 2012, 68:677-685.
93. Williams D.E. Improved intermolecular force field for crystalline hydrocarbons containing four- or three-coordinated carbon. J. Mol. Struct. 1999, 485-486:321-347.
94. Williams D.E. Improved intermolecular force field for molecules containing H, C, N, and O atoms, with application to nucleoside and peptide crystals. J. Comput. Chem. 2001, 22:1154-1166.
95. Williams D.E., Cox S.R. Nonbonded potentials for azahydrocarbons: the importance of the Coulombic interaction. Acta Crystallogr. Sect. B 1984, 40:404-417.
96. Wu H., Habgood M., Parker J.E., Reeves-McLaren N., Cockcroft J.K., Vickers M., West A.R., Jones A.G. Crystal structure determination by combined synchrotron powder X-ray diffraction and crystal structure prediction: 1: 1 l-ephedrine d-tartrate. CrystEngComm 2013, 15:1853-1859.
97. Yao J.W., Cole J.C., Pidcock E., Allen F.H., Howard J.A.K., Motherwell W.D.S. CSDSymmetry: the definitive database of point-group and space-group symmetry relationships in small-molecule crystal structures. Acta Crystallogr. Sect. B 2002, 58:640-646.
98. Zhao Y., Truhlar D. The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theor. Chem. Acc. 2008, 120:215-241.
99. Zykova-Timan T., Raiteri P., Parrinello M. Investigating the polymorphism in PR179: a combined crystal structure prediction and metadynamics study. J. Phys. Chem. B 2008, 112:13231-13237.