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Crystal structure of pimecrolimus Form B, C43H68ClNO11

Published online by Cambridge University Press:  15 February 2021

Shivang Bhaskar ,
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]
Shivang Bhaskar
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: [email protected]
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Abstract

The crystal structure of pimecrolimus Form B has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional techniques. Pimecrolimus crystallizes in the space group P21 (#4) with a = 15.28864(7), b = 13.31111(4), c = 10.95529(5) Å, β = 96.1542(3)°, V = 2216.649(9) Å3, and Z = 2. Although there are an intramolecular six-ring hydrogen bond and some larger chain and ring patterns, the crystal structure is dominated by van der Waals interactions. There is a significant difference between the conformation of the Rietveld-refined and the DFT-optimized structures in one portion of the macrocyclic ring. Although weak, intermolecular interactions are apparently important in determining the solid-state conformation. The powder pattern is included in the Powder Diffraction File™ (PDF®) as entry 00-066-1619. This study provides the atomic coordinates to be added to the PDF entry.

Keywords

pimecrolimusElidelpowder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 36 , Issue 1 , March 2021 , pp. 35 - 42
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Copyright
Copyright © The Author(s), 2021. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

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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.CrossRefGoogle Scholar
Baumann, K. (1990). “Heteroatoms-containing tricyclic compounds,” European Patent Application EP0427680.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.CrossRefGoogle ScholarPubMed
Dassault Systèmes (2018). Materials Studio 2019 (BIOVIA, San Diego, CA).Google Scholar
David, W. I. F., Shankland, K., van de Streek, J., Pidcock, E., Motherwell, W. D. S., and Cole, J. C. (2006). “DASH: a program for crystal structure determination from powder diffraction data,” J. Appl. Crystallogr. 39, 910–915.CrossRefGoogle Scholar
Donnay, J. D. H. and Harker, D. (1937). “A new law of crystal morphology extending the law of Bravais,” Am. Mineral. 22, 446–447.Google Scholar
Dosenbach, C., Grassberger, M., Hartmann, O., Horvath, A., Mutz, J.-P., Penn, G., Pfeiffer, S., and Wieckhusen, D. (2002). “Crystalline macrolides and process for their preparation,” U.S. Patent 6,423,722B1.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
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,” Powd. Diffr. 39(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,” Powd. Diffr. 29(3), 269–273.CrossRefGoogle Scholar
Kovacsne-Mezei, A., Racz, C. N., Aronhime, J., Gyollai, V., Molnar, S., and Pinchasov, M. (2009). “Non-hygroscopic and powdery amorphous pimecrolimus,” U.S. Patent 7,589,100B2.Google Scholar
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, 15–50.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. Radiat. 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
Materials Design (2016). MedeA 2.20.4 (Materials Design Inc., Angel Fire, NM).Google Scholar
MDI (2014). Jade 9.5 (Materials Data Inc., Livermore, CA).Google Scholar
MDI (2019). JADE Pro Version 7.7 (Computer Software) (Materials Data, 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 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
Rammohan, A. and Kaduk, J. A. (2018). “Crystal structures of alkali metal (Group 1) citrate salts,” Acta Crystallogr. Sect. B: Crystallogr. Eng. Mater. 74, 239–252. doi:10.1107/S2052520618002330.CrossRefGoogle ScholarPubMed
Silk Scientific (2013). UN-SCAN-IT 7.0 (Silk Scientific Corporation, Orem, UT).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. Crystallogr. 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