Skip to main content Accessibility help
×
Home

Crystal structures of cefdinir, C14H13N5O5S2, and cefdinir sesquihydrate C14H13N5O5S2(H2O)1.5

  • Austin M. Wheatley (a1), James A. Kaduk (a1) (a2), Amy M. Gindhart (a3) and Thomas N. Blanton (a3)

Abstract

The crystal structures of cefdinir and cefdinir sesquihydrate have been solved and refined using synchrotron X-ray powder diffraction data, and optimized using density functional techniques. Cefdinir crystallizes in space group P21 (#4) with a = 5.35652(4), b = 19.85676(10), c = 7.57928(5) Å, β = 97.050(1) °, V = 800.061(6) Å3, and Z = 2. Cefdinir sesquihydrate crystallizes in space group C2 (#5) with a = 23.98775(20), b = 5.01646(3), c = 15.92016(12) Å, β = 109.4470(8) °, V = 1806.438(16) Å3, and Z = 4. The cefdinir molecules in the anhydrous crystal structure and sesquihydrate have very different conformations. The two conformations are similar in energy. The hydrogen bonding patterns are very different in the two structures, and the sesquihydrate is more stable than expected from the sum of the energies of cefdinir and cefdinir sesquihydrate, the result of additional hydrogen bonding. The powder patterns are included in the Powder Diffraction File™ as entries 00-066-1604 (cefdinir) and 00-066-1605 (cefdinir sesquihydrate).

Copyright

Corresponding author

a)Author to whom correspondence should be addressed. Electronic mail: kaduk@polycrystallography.com

References

Hide All
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, 12311235.
Bernstein, J., Davis, R. E., Shimoni, L. and Chang, N. L. (1995). “Patterns in hydrogen bonding: functionality and graph set analysis in crystals,” Angew. Chem. Int. Ed. Eng. 34(15), 15551573.
Bravais, A. (1866). Etudes Cristallographiques (Gauthier Villars, Paris).
Bredow, T., Heitjans, P. and Wilkening, M. (2004). “Electric field gradient calculations for Li x Ti S 2 and comparison with Li 7 NMR results,” Phys. Rev. B 70, 115111.
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, 21332144.
Cabri, W., Ghetti, P., Pozzi, G. and Alpegiani, M. (2007). “Polymorphisms and patent, market, and legal battles: cefdinir case study,” Org. Process Res. Dev. 11, 6472.
Chandrasekaran, R., Senthilkumar, K., Murugan, S., Siviah Sangaraju, V. R. and Reddy, O. M. (2005). “Novel Polymorph of Cefdinir,” World Patent Application WO2005/090360.
Daemon, O., Hartmann, K. and Raneburger, J. (2006). “Crystalline cefdinir,” U.S. Patent Application 11/294,116.
Dandala, R. and Sivakumaran, M. (2005). “Novel Crystalline Form of Cefdinir,” US Patent Application 2005/0137182.
Dassault Systèmes (2018). Materials Studio 2018 (BIOVIA, San Diego, CA).
Donnay, J. D. H and Harker, D. (1937). “A new law of crystal morphology extending the law of Bravais,” Am. Mineral. 22, 446447.
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, 12871317.
Duerst, R. W., Law, D. and Lou, X. (2005). “Polymorph of a Pharmaceutical,” US Patent Application 2005/0059818.
Etter, M. C. (1990). “Encoding and decoding hydrogen-bond patterns of organic compounds,” Acc. Chem. Res. 23(4), 120126.
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, 734743.
Fawcett, T. G., Kabekkodu, S. N., Blanton, J. R. and Blanton, T. N. (2017). “Chemical analysis by diffraction: the Powder Diffraction File™,” Powder Diffr. 32(2), 6371.
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), 892900.
Friedel, G. (1907). “Etudes sur la loi de Bravais,” Bull. Soc. Fr. Mineral. 30, 326455.
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, 1068610696.
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, 171179.
Hirshfeld, F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chem. Acta 44, 129138.
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), 269273.
Kresse, G. and Furthmüller, J. (1996). “Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane-wave basis set,” Comput. Mater. Sci. 6, 1550.
Kumar, Y., Prasad, M. and Prasad, A. (2004). “Crystalline Form of Cefdinir,” World Patent Application WO2004/104010.
Larson, A. C. and Von Dreele, R. B. (2004). General Structure Analysis System, (GSAS), (Los Alamos National Laboratory Report LAUR 86-784).
Law, D., Henry, R. F. and Lou, X. (2005). “Trihemihydrate, Anhydrate and Hydrate Forms of Cefdinir,” World Patent Application WO2005/090361.
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), 427432.
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, 466470.
Manca, S., Sala, B. and Monguzzi, R. (2003). “Crystalline Form of Cefdinir,” US Patent Application 2003/0204082.
MDI (2017). Jade 9.8 (Materials Data Inc., Livermore, CA).
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.
Ohnishi, N., Deguchi, S. and Kitamura, S. (2008). “Oral Pharmaceutical Suspension of Cefdinir Crystal,” US Patent 7,351,419.
Rammohan, A. and Kaduk, J. A. (2018). “Crystal structures of alkali metal (Group 1) citrate salts,” Acta Cryst. B: Struct. Sci. Cryst. Eng. Mater. 74, 239252.
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), 455465.
Silk Scientific (2013). UN-SCAN-IT 7.0 (Silk Scientific Corporation, Orem, UT).
Singh, G. P., Sen, H., Srivastava, D., Godbole, H. M., Singh, G. P., Mahajan, P. R., Rananaware, U. B., Nehate, S. P. and Wagh, S. C. (2005). “Stable Bioavailable Crystalline Form of Cefdinir and a Process for the Preparation Thereof,” US Patent Application 2005/0245738.
Stephens, P. W. (1999). “Phenomenological model of anisotropic peak broadening in powder diffraction,” J. Appl. Crystallogr. 32, 281289.
Sun, S., Liu, W. and Feng, C. (2015). “A new crystal form and preparation method Cefdinir,” Chinese patent application CN 103467494 B.
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, 882886.
Takaya, T., Takasugi, H., Magugi, T., Yamanaka, H. and Kawabata, K. (1985). “7-substituted-3-vinyl-3-cephem Compounds and Processes for Production of the Same,” US Patent 4,559,334.
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), 7983.
Toby, B. H. (2001). “EXPGUI, a graphical user interface for GSAS,” J. Appl. Crystallogr. 34, 210213.
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): http://hirshfeldsurface.net.
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), 10201032.
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.
Wavefunction, Inc. (2017). Spartan ‘16 Version 2.0.1, Wavefunction Inc., 18401 Von Karman Ave., Suite 370, Irvine CA 92612.
Wheatley, A. M. and Kaduk, J. A. (2018). “Crystal structures of ammonium citrates,” Powder Diffr. 34, 3543.

Keywords

Type Description Title
UNKNOWN
Supplementary materials

Wheatley et al. supplementary material
Wheatley et al. supplementary material

 Unknown (761 KB)
761 KB

Crystal structures of cefdinir, C14H13N5O5S2, and cefdinir sesquihydrate C14H13N5O5S2(H2O)1.5

  • Austin M. Wheatley (a1), James A. Kaduk (a1) (a2), Amy M. Gindhart (a3) and Thomas N. Blanton (a3)

Metrics

Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed