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Crystal structure of pemetrexed disodium heptahydrate, C20H33N5Na2O13 (Alimta)

Published online by Cambridge University Press:  27 February 2018

James A. Kaduk ,
Amy M. Gindhart  and
Thomas N. Blanton
James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago IL 60616, and North Central College, 30 N. Brainard St., Naperville IL 60540
Amy M. Gindhart
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square PA, 19073-3273
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square PA, 19073-3273
*
a)Author to whom correspondence should be addressed. Electronic mail: [email protected]
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Abstract

The crystal structure of pemetrexed disodium heptahydrate has been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Pemetrexed disodium heptahydrate crystallizes in space group P21 (#4) with a = 11.732 697(27), b = 5.244 195(14), c = 21.689 00(6) Å, β = 92.663 90(20)°, V = 1333.051(6) Å3, and Z = 2. Each of the two ionized carboxylate groups acts as a unidentate ligand to a Na cation. The remaining five positions of the octahedral coordination spheres are occupied by water molecules. The Na octahedra share an edge to form pairs. These pairs share corners to form chains along the b-axis. All of the water molecule hydrogen atoms act as hydrogen bond donors. In addition the hydrogen atoms associated with the nitrogen atoms and amino groups of the pemetrexed anion were also observed to act as hydrogen bond donors. The powder pattern has been submitted to the International Centre for Diffraction Data (ICDD) for inclusion in the Powder Diffraction File™.

Keywords

pemetrexed disodium heptahydratepowder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 33 , Issue 2 , June 2018 , pp. 166 - 171
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Copyright
Copyright © International Centre for Diffraction Data 2018 

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References

Altomare, A., Cuocci, C., Giacovazzo, C., Moliterni, A., Rizzi, R., Corriero, N., and Falcicchio, A. (2013). “EXPO2013: a kit of tools for phasing crystal structures from powder data,” J. Appl. Crystallogr. 46, 1231–1235.Google Scholar
Bernstein, J., Davis, R. E., Shimoni, L., and Chang, N. L. (1995). “Patterns in hydrogen bonding: functionality and graph set analysis in crystals,” Angewandte Chem. Int. Ed. Eng. 34(15), 1555–1573.Google Scholar
Bravais, A. (1866). Etudes Cristallographiques (Gauthier Villars, Paris).Google Scholar
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., and Orpen, A. G. (2004). “Retrieval of crystallographically-derived molecular geometry information,” J. Chem. Inf. Sci. 44, 2133–2144.Google Scholar
Chelius, E. C., Reutzel-Eden, S. M., and Snorek, S. V. (2003). “Novel Crystalline of N-[4-[2-(amino-4,7-dihydro-4-oxo-3H-pyrrolo[2,3-D]pyrimidin-5-yl)ethyl]-benzoyl]-L-glutamic acid and Process Therefore,” US Patent Application 2003/0216416.Google Scholar
Dassault Systèmes (2014). Materials Studio 8.0 (BIOVIA, San Diego, CA).Google Scholar
Donnay, J. D. H., and Harker, D. (1937). “A new law of crystal morphology extending the law of Bravais,” Amer. Mineral. 22, 446–467.Google Scholar
Dovesi, R., Orlando, R., Erba, A., Zicovich-Wilson, C. M., Civalleri, B., Casassa, S., Maschio, L., Ferrabone, M., De La Pierre, M., D-Arco, P., Noël, Y., Causà, M., Kirtman, B. (2014). “CRYSTAL14: a program for the ab initio investigation of crystalline solids,” Int. J. Quantum Chem. 114, 1287–1317.Google Scholar
Etter, M. C. (1990). “Encoding and decoding hydrogen-bond patterns of organic compounds,” Acc. Chem. Res. 23(4), 120–126.Google Scholar
Favre-Nicolin, V., and Černý, R. (2002). FOX, “free objects for crystallography: a modular approach to ab initio structure determination from powder diffraction,” J. Appl. Crystallogr. 35, 734–743.Google Scholar
Finger, L. W., Cox, D. E., and Jephcoat, A. P. (1994). “A correction for powder diffraction peak asymmetry due to axial divergence,” J. Appl. Crystallogr. 27(6), 892–900.Google Scholar
Friedel, G. (1907). “Etudes sur la loi de Bravais,” Bull. Soc. Fr. Mineral. 30, 326–455.Google Scholar
Groom, C. R., Bruno, I. J., Lightfoot, M. P., and Ward, S. C. (2016). “The cambridge structural database,” Acta Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater. 72, 171–179.Google Scholar
Hirshfeld, F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chem. Acta 44, 129–138.Google Scholar
ICDD (2016). PDF-4+ 2016 (Database), edited by Dr. Soorya Kabekkodu, International Centre for Diffraction Data, Newtown Square, PA, USA.Google Scholar
Kaduk, J. A., Crowder, C. E., Zhong, K., Fawcett, T. G., and Suchomel, M. R. (2014). “Crystal structure of atomoxetine hydrochloride (Strattera), C17H22NOCl,” Powder Diffr. 29(3), 269–273.Google Scholar
Larson, A. C., and Von Dreele, R. B. (2004). General Structure Analysis System, (GSAS) (Report LAUR 86-784). Los Alamos National Laboratory.Google Scholar
Lee, P. L., Shu, D., Ramanathan, M., Preissner, C., Wang, J., Beno, M. A., Von Dreele, R. B., Ribaud, L., Kurtz, C., Antao, S. M., Jiao, X., and Toby, B. H. (2008). “A twelve-analyzer detector system for high-resolution powder diffraction,” J. Synch. Rad. 15(5), 427–432.Google Scholar
Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J., and Wood, P. A. (2008). “Mercury CSD 2.0 – new features for the visualization and investigation of crystal structures,” J. Appl. Crystallogr. 41, 466–470.Google Scholar
McKinnon, J. J., Spackman, M. A., and Mitchell, A. S. (2004). “Novel tools for visualizing and exploring intermolecular interactions in molecular crystals,” Acta Cryst. Sect. B 60, 627–668.Google Scholar
MDI (2016). Jade 9.7 (Materials Data. Inc., Livermore, CA).Google Scholar
O'Boyle, N., Banck, M., James, C. A., Morley, C., Vandermeersch, T., and Hutchison, G. R. (2011). “Open Babel: an open chemical toolbox,” J. Chem. Informatics 3, 33. doi: 10.1186/1758-2946-3-33.Google Scholar
Peintinger, M. F., Vilela Oliveira, D., and Bredow, T. (2013). “Consistent Gaussian basis sets of triple-zeta valence with polarization quality for solid-state calculations,” J. Comput. Chem. 34, 451–459.Google Scholar
Rammohan, A., and Kaduk, J. A. (2017). “Crystal structures of alkali metal (group 1) citrate salts,” Acta Cryst. Sect. B: Cryst. Eng. Mater. hw5048.Google Scholar
Shields, G. P., Raithby, P. R., Allen, F. H., and Motherwell, W. S. (2000). “The assignment and validation of metal oxidation states in the cambridge structural database,” Acta Cryst. Sec. B: Struct. Sci. 56(3), 455–465.Google Scholar
Silk Scientific (2013). UN-SCAN-IT 7.0 (Silk Scientific Corporation, Orem, UT).Google Scholar
Spackman, M. A., and Jayatilaka, D. (2009). “Hirshfeld surface analysis,” CrystEngComm 11, 19–32.Google Scholar
Stephens, P. W. (1999). “Phenomenological model of anisotropic peak broadening in powder diffraction,” J. Appl. Crystallogr. 32, 281–289.Google Scholar
Sykes, R. A., McCabe, P., Allen, F. H., Battle, G. M., Bruno, I. J., and Wood, P. A. (2011). “New software for statistical analysis of cambridge structural database data,” J. Appl. Crystallogr. 44, 882–886.Google Scholar
Thompson, P., Cox, D. E., and Hastings, J. B. (1987). “Rietveld refinement of Debye-Scherrer synchrotron X-ray data from Al2O3,” J. Appl. Crystallogr. 20(2), 79–83.Google Scholar
Toby, B. H. (2001). “EXPGUI, a graphical user interface for GSAS,” J. Appl. Crystallogr. 34, 210–213.Google Scholar
van de Streek, J., and Neumann, M. A. (2014). “Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D),” Acta Cryst. Sect. B: Struct. Sci., Cryst. Eng. Mater. 70(6), 1020–1032.Google Scholar
Wang, J., Toby, B. H., Lee, P. L., Ribaud, L., Antao, S. M., Kurtz, C., Ramanathan, M., Von Dreele, R. B., and Beno, M. A. (2008). “A dedicated powder diffraction beamline at the advanced photon source: commissioning and early operational results,” Rev. Sci. Inst. 79, 085105.Google Scholar
Wavefunction, Inc. (2017). Spartan ‘16 Version 2.0.3 (Wavefunction Inc., Irvine, CA).Google Scholar
Wolff, S. K., Grimwood, D. J., McKinnon, M. J., Turner, M. J., Jayatilaka, D., and Spackman, M. A. (2012). CrystalExplorer Version 3.1 (Perth, Western Australia: University of Western Australia).Google Scholar
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