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Crystal structure of pantoprazole sodium sesquihydrate Form I, C16H14F2N3O4SNa(H2O)1.5

Published online by Cambridge University Press:  20 January 2020

Diana Gonzalez ,
Joseph T. Golab ,
James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Amy M. Gindhart  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
Diana Gonzalez
Affiliation:
Illinois Mathematics and Science Academy, 1500 Sullivan Rd., Aurora, Illinois60506-1000, USA
Joseph T. Golab
Affiliation:
Illinois Mathematics and Science Academy, 1500 Sullivan Rd., Aurora, Illinois60506-1000, USA
James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, Illinois60616, USA North Central College, 131 S. Loomis St., Naperville, Illinois60540, USA
Amy M. Gindhart
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, Pennsylvania19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, Pennsylvania19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: kaduk@polycrystallography.com
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Abstract

The crystal structure of pantoprazole sodium sesquihydrate has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pantoprazole sodium sesquihydrate crystallizes in space group Pbca (#61) with a = 33.4862(6), b = 17.29311(10), c = 13.55953(10) Å, V = 7852.06(14) Å3, and Z = 16. The crystal structure is characterized by layers parallel to the bc-plane. One layer contains the Na coordination spheres. The two independent sodium ions are trigonal bipyramidal and octahedral. The NaO3N2 and NaO4N2 coordination spheres share an edge to form pairs. The sodium bond valence sums are 1.17 and 1.15. The difluoromethyl groups are probably disordered. Two water molecules act as hydrogen bond donors to pyridine nitrogen atoms and sulfoxide oxygen atoms. The third water molecule participates in bifurcated hydrogen bonds, but one of its hydrogen atoms does not participate in hydrogen bonds. The powder pattern is included in the Powder Diffraction File™ as entry 00-065-1424.

Keywords

pantoprazole sodium sesquihydrateProtonixpowder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 35 , Issue 1 , March 2020 , pp. 53 - 60
Copyright
Copyright © International Centre for Diffraction Data 2020

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References

Allegrini, P., Ventimiglia, G., Sommei, A., and Castaldi, G. (2005). “Polymorphs of pantoprazole sodium salt and process for the preparation thereof,” U. S. Patent Application 2005/024578 A1.Google Scholar
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.CrossRefGoogle Scholar
Badwan, A., Nabulsi, L., Al Omari, M., Daraghmeh, N., Ashour, M., Abdoh, A., and Jaber, A. (2002). “Pantoprazole sodium,” Anal. Profiles Drug Subst. Excipients. 29, 213–259.CrossRefGoogle 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.CrossRefGoogle ScholarPubMed
Dassault Systèmes (2018). Materials Studio 2019 (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,” Am. Min. 22, 446–447.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., and Kirtman, B. (2014). “CRYSTAL14: a program for the ab initio investigation of crystalline solids,” Int. J. Quantum Chem. 114, 1287–1317.CrossRefGoogle 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.CrossRefGoogle Scholar
Finkelstein, N., Krochmal, B., Wizel, S., and Braude, V. (2009). “Solid states of pantoprazole sodium, processes for preparing them and processes for preparing known pantoprazole sodium hydrates,” U.S. Patent 7,507,829 B2.Google Scholar
Friedel, G. (1907). “Etudes sur la loi de Bravais,” Bull. Soc. Fr. Mineral. 30, 326–455.Google Scholar
Gates-Rector, S., and Blanton, T. (2019). “The powder diffraction file: a quality materials characterization database,” Powder Diffr. 34(4), 352–360.CrossRefGoogle Scholar
Gatti, C., Saunders, V. R., and Roetti, C. (1994). “Crystal-field effects on the topological properties of the electron-density in molecular crystals – the case of urea,” J. Chem. Phys. 101, 10686–10696.CrossRefGoogle 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.CrossRefGoogle ScholarPubMed
Hirshfeld, F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chem. Acta. 44, 129–138.CrossRefGoogle 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.CrossRefGoogle 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.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
MDI (2018). Jade 9.8 (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.Google ScholarPubMed
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.CrossRefGoogle ScholarPubMed
Petricek, V., Dusek, M., and Palatinus, L. (2014). “Crystallographic computing system JANA2006: general features,” Z. Kristallogr. 229, 345–352.Google Scholar
Rammohan, A., and Kaduk, J. A. (2018). “Crystal structures of alkali metal (Group 1) citrate salts,” Acta Crystallogr. Sect. B: Cryst. Eng. Mater. 74, 239–252.CrossRefGoogle ScholarPubMed
Reddy, M., Eswaraiah, S., Mathad, V., Anilkumar, P., Chandrashekar, E., and Shanmugam, G. (2005). “Process for preparation of crystalline form-I of pantoprazole sodium sesquihydrate,” U.S. Patent 6,933,389 B2.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.CrossRefGoogle ScholarPubMed
Toby, B. H., and Von Dreele, R. B. (2013). “GSAS II: the genesis of a modern open source all purpose crystallography software package,” J. Appl. Crystallogr. 46, 544–549.CrossRefGoogle Scholar
Turner, M. J., McKinnon, J. J., Wolff, S. K., Grimwood, D. J., Spackman, P. R., Jayatilaka, D., and Spackman, M. A. (2017). CrystalExplorer17 (University of Western Australia). Available at: http://hirshfeldsurface.net.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 Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater. 70(6), 1020–1032.CrossRefGoogle 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. Instrum. 79, 085105.CrossRefGoogle ScholarPubMed
Wavefunction, Inc. (2018). Spartan‘18 Version 1.2.0 (Wavefunction Inc., Irvine, CA).Google Scholar