Hostname: page-component-78c5997874-fbnjt Total loading time: 0 Render date: 2024-11-17T20:12:16.909Z Has data issue: false hasContentIssue false
  • English
  • Français

Crystal structure of merimepodib, C23H24N4O6

Published online by Cambridge University Press:  19 May 2022

James A. Kaduk Open the ORCID record for James A. Kaduk [Opens in a new window] ,
Stacy Gates-Rector Open the ORCID record for Stacy Gates-Rector [Opens in a new window] ,
Amy M. Gindhart Open the ORCID record for Amy M. Gindhart [Opens in a new window]  and
Thomas N. Blanton Open the ORCID record for Thomas N. Blanton [Opens in a new window]
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
Amy M. Gindhart
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: [email protected]
Get access Rights & Permissions [Opens in a new window]

Abstract

The crystal structure of merimepodib has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Merimepodib crystallizes in space group P212121 (#19) with a = 4.60827(3), b = 12.30400(14), c = 37.9583(4) Å, V = 2152.241(20) Å3, and Z = 4. The crystal structure is dominated by two chains of N–H⋯O hydrogen bonds along the a-axis. The solid-state conformation has a similar general shape to the minimum-energy conformation, but different orientations of several of the rings. The differences indicate that intermolecular interactions are important in determining the solid-state conformation. The powder pattern has been submitted to ICDD for inclusion in the Powder Diffraction File™ (PDF®).

Keywords

merimepodibVX-497powder diffractionRietveld refinementdensity functional theory
Type
New Diffraction Data
Information
Powder Diffraction , Volume 37 , Issue 3 , September 2022 , pp. 143 - 149
Check for updates
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, 1231–1235.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, 1501–1509.CrossRefGoogle Scholar
Armistead, D. M., Badia, M. C., Bemis, G. W., Bethiel, R. S., Fank, C. A., Novak, P. M., Ronkin, S. M., and Saunders, J. O. (1997). “Urea derivatives as inhibitors of IMPDH enzyme,” International Patent Application WO 97/40028.Google Scholar
Armistead, D. M., Badia, M. C., Bemis, G. W., Bethiel, R. S., Fank, C. A., Novak, P. M., Ronkin, S. M., and Saunders, J. O. (1998). “Inhibitors of IMPDH enzyme,” US Patent 5,807,876.Google Scholar
Armistead, D. M., Badia, M. C., Bemis, G. W., Bethiel, R. S., Fank, C. A., Novak, P. M., Ronkin, S. M., and Saunders, J. O. (2000). “Inhibitors of IMPDH enzyme,” US Patent 6,054,472.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,” Angew. Chem., Int. Ed. Engl. 34(15), 1555–1573.CrossRefGoogle Scholar
BioSig (2020). https://ir.biosig.com/press-releases/detail/234/viralclear-halts-its-phase-2-hospitalized-covid-19-trial (accessed January 20, 2020).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, 2133–2144.CrossRefGoogle ScholarPubMed
Crystal Impact - Dr. H. Putz & Dr. K. Brandenburg (2021). Diamond - Crystal and Molecular Structure Visualization (Kreuzherrenstr. 102, 53227 Bonn, Germany). Available at: https://www.crystalimpact.de/diamond.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, 446–447.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,” Wiley Interdiscip. Rev.: Comput. Mol. Sci. 8, e1360.Google Scholar
Etter, M. C. (1990). “Encoding and decoding hydrogen-bond patterns of organic compounds,” Acc. Chem. Res. 23(4), 120–126.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,” Powder 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. Chim. Acta 44, 129–138.CrossRefGoogle Scholar
Jain, J., Almquist, S. J., Shlyakhter, D., and Harding, M. W. (2001). “VX-497: a novel, selective IMPDH inhibitor and immunosuppressive agent,” J. Pharm. Sci. 90, 625–637.3.0.CO;2-1>CrossRefGoogle ScholarPubMed
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
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), D1102–D1109. 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, 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. Synchrotron Radiat. 15(5), 427–432.CrossRefGoogle ScholarPubMed
Looker, A. R., Littler, B. J., Blythe, T. A., Snoonian, J. R., Ansell, G. K., Jones, A. D., Nyce, P., Chen, M., and Neubert, B. J. (2008). “Development and manufacture of the inosine monophosphate dehydrogenase inhibitor merimepodib, VX-497,” Org. Process Res. Dev. 12, 666–673.CrossRefGoogle Scholar
Louër, D., and Boultif, A. (2014). “Some further considerations in powder diffraction pattern indexing with the dichotomy method,” Powder Diffr. 29, S7–S12.CrossRefGoogle Scholar
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, 226–235.CrossRefGoogle ScholarPubMed
Materials Design (2016). MedeA 2.20.4 (Materials Design Inc., Angel Fire, NM).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. Cheminformatics 3, 33. doi:10.1186/1758-2946-3-33.CrossRefGoogle ScholarPubMed
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 Crystallogr. Sect. B: Struct. Sci., Cryst. Eng. Mater. 56(3), 455–465.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, 882–886.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, 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. (2020). Spartan ‘18 Version 1.4.5 (Wavefunction Inc., 18401 Von Karman Ave., Suite 370, Irvine, CA 92612).Google Scholar
Wheatley, A. M., and Kaduk, J. A. (2019). “Crystal structures of ammonium citrates,” Powder Diffr. 34, 35–43.CrossRefGoogle Scholar