Hostname: page-component-cd9895bd7-q99xh Total loading time: 0 Render date: 2024-12-26T08:02:48.980Z Has data issue: false hasContentIssue false

Crystal structure of a second polymorph of germacrone, C15H22O

Published online by Cambridge University Press:  07 April 2022

James A. Kaduk*
Affiliation:
Illinois Institute of Technology, 3101 S. Dearborn St., Chicago, IL 60616, USA North Central College, 131 S. Loomis St., Naperville, IL 60540, USA
Stacy Gates-Rector
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
Thomas N. Blanton
Affiliation:
ICDD, 12 Campus Blvd., Newtown Square, PA 19073-3273, USA
*
a)Author to whom correspondence should be addressed. Electronic mail: kaduk@polycrystallography.com

Abstract

The crystal structure of a new polymorph of germacrone has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. This polymorph (Form II) crystallizes in space group C2/c (#15) with a = 26.0073(4), b = 9.84383(10), c = 10.53713(13) Å, β = 95.7547(11)°, V = 2684.04(3) Å3, and Z = 8. The crystal structure is dominated by van der Waals interactions, but four C–H⋯O hydrogen bonds are present. The structure exhibits many similarities to the previously reported Form I polymorph FIQLOG, but is clearly different. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF).

Type
New Diffraction Data
Copyright
Copyright © The Author(s), 2022. Published by Cambridge University Press on behalf of International Centre for Diffraction Data

Access options

Get access to the full version of this content by using one of the access options below. (Log in options will check for institutional or personal access. Content may require purchase if you do not have access.)

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, 12311235.CrossRefGoogle Scholar
Antao, S. M., Hassan, I., Wang, J., Lee, P. L., and Toby, B. H. (2008). “State-of-the-art high-resolution powder X-ray diffraction (HRPXRD) illustrated with Rietveld refinement of quartz, sodalite, tremolite, and meionite,” Can. Mineral. 46, 15011509.CrossRefGoogle Scholar
Barrero, A. F., Mar Herrador, M., Arteaga, P., and Catalán, J. V. (2008). “Germacrone: occurrence, synthesis, chemical transformations and biological properties,” Nat. Prod. Commun. 3, 567576.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. Comput. Sci. 44, 21332144.10.1021/ci049780bCrossRefGoogle ScholarPubMed
Clardy, J. C. and Lobkovsky, E. (1998). “Germacra-1(10),4,7(11)-trien-8-one,” CSD Communication; Refcode FIQLOG.Google Scholar
Dassault Systèmes (2021). Materials Studio 2021 (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. Mineral. 22, 446447.Google Scholar
Dovesi, R., Erba, A., Orlando, R., Zicovich-Wilson, C. M., Civalleri, B., Maschio, L., Rerat, M., Casassa, S., Baima, J., Salustro, S., and Kirtman, B. (2018). “Quantum-mechanical condensed matter simulations with CRYSTAL,” WIREs Comput. Mol. Sci. 8, e1360.10.1002/wcms.1360CrossRefGoogle Scholar
Friedel, G. (1907). “Etudes sur la loi de Bravais,” Bull. Soc. Fr. Mineral. 30, 326455.Google Scholar
Gates-Rector, S. and Blanton, T. (2019). “The Powder Diffraction File: a quality materials characterization database,” Powd. Diffr. 39(4), 352360.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, 1068610696.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, 171179.CrossRefGoogle ScholarPubMed
Hirshfeld, F. L. (1977). “Bonded-atom fragments for describing molecular charge densities,” Theor. Chem. Acta 44, 129138.10.1007/BF00549096CrossRefGoogle Scholar
Jacobsson, U., Norin, T., Weber, M., and Tsankova, E. (1985). “The configuration and conformation of isogermacrone. The significance of crossed conformations in olefinic cyclisations,” Tetrahedron 41, 20332036. doi:10.1016/S0040-4020(01)96572-X.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), 269273.CrossRefGoogle Scholar
Kim, S., Chen, J., Cheng, T., Gindulyte, A., He, J., He, S., Li, Q., Shoemaker, B. A., Thiessen, P. A., Yu, B., Zaslavsky, L., Zhang, J., and Bolton, E. E. (2019). “PubChem 2019 update: improved access to chemical data,” Nucleic Acids Res. 47(D1), D1102D1109. doi:10.1093/nar/gky1033.CrossRefGoogle ScholarPubMed
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.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. Synchrotron Radiat. 15(5), 427432.CrossRefGoogle ScholarPubMed
Macrae, C. F., Sovago, I., Cottrell, S. J., Galek, P. T. A., McCabe, P., Pidcock, E., Platings, M., Shields, G. P., Stevens, J. S., Towler, M., and Wood, P. A. (2020). “Mercury 4.0: from visualization to design and prediction,” J. Appl. Crystallogr. 53, 226235.CrossRefGoogle ScholarPubMed
Materials Design (2016). MedeA 2.20.4 (Materials Design Inc., Angel Fire, NM).Google Scholar
MDI (2021). JADE Pro Version 8.1 (Computer Software) (Materials Data, Livermore, CA, USA).Google Scholar
Rovesti, P. (1927). “Researches on the ethereal oil of Geranium macrorrhizum L. of Bulgaria,” Notiz. chim. - ind. 2, 438439.Google Scholar
Spek, A. L. (2009). “Structure validation in chemical crystallography,” Acta Crystallogr. D 65, 148155.CrossRefGoogle ScholarPubMed
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.CrossRefGoogle Scholar
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, 544549.10.1107/S0021889813003531CrossRefGoogle 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), 10201032.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. (2020). Spartan ‘18 Version 1.4.5, Wavefunction Inc., 18401 Von Karman Ave., Suite 370, Irvine, CA 92612.Google Scholar