Hostname: page-component-7c8c6479df-995ml Total loading time: 0 Render date: 2024-03-28T21:26:01.524Z Has data issue: false hasContentIssue false

Crystal structure solution of an elusive polymorph of Dibenzylsquaramide

Published online by Cambridge University Press:  14 November 2013

Anna Portell
Affiliation:
Unitat de Polimorfisme i Calorimetria, CCiTUB
Xavier Alcobé
Affiliation:
Unitat de Difracció de Raigs X, CCiTUB
Latévi M. Lawson Daku
Affiliation:
Laboratory of Crystallography, University of Geneva, Quai Ernest-Ansermet 24, CH-1211 Geneva 4
Radovan Černý
Affiliation:
Dpt. Physical Chemistry, University of Geneva, Quai Ernest-Ansermet 30, CH-1211 Geneva 4
Rafel Prohens*
Affiliation:
Scientific and Technological Centers of the University of Barcelona, C/ Baldiri i Reixac 10, 08028 Barcelona, Spain
*
*To whom correspondence should be addressed. Tel. + 34 93 4034656. Fax. + 34 93 4037206. E.mail: rafel@ccit.ub.edu

Abstract

The crystal structure of the third polymorph of dibenzylsquaramide (Portell, A. et al., 2009), (fig. 1) has been determined from laboratory X-ray powder diffraction data by means of direct space methods using the computing program FOX. (Favre-Nicolin and Černý, 2002) The structure resolution has not been straightforward due to several difficulties on the indexing process and in the space group assignment. The asymmetric unit contains two different conformers, which has implied an additional difficulty during the Rietveld (Rietveld, 1969) refinement. All these issues together with particular structural features of disquaramides are discussed.

Type
Technical Articles
Copyright
Copyright © International Centre for Diffraction Data 2013 

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

Barone, V., Casarin, M., Forrer, D., Pavone, M., Sambi, M. and Vittadini, A., (2009). “Role and effective treatment of dispersive forces in materials: Polyethylene and graphite crystals as test cases,” J. Comput. Chem. 30, 934939.CrossRefGoogle ScholarPubMed
Boultif, A. and Louër, D. (2004). “Powder pattern indexing with the dichotomy method,” J. Appl. Crystallogr. 37, 724731.CrossRefGoogle Scholar
Bruker AXS. (2003). TOPAS V2.1: General Profile and Structure Analysis Software for Powder Diffraction Data. User's Manual (Bruker AXS, Karlsruhe, Germany).Google 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, 734743.CrossRefGoogle Scholar
Giannozzi, P., Baroni, S., Bonini, N., Calandra, M., Car, R., Cavazzoni, C., Ceresoli, D., Chiarotti, G. L., Cococcioni, M., Dabo, I., Dal Corso, A., de Gironcoli, S., Fabris, S., Fratesi, G., Gebauer, R., Gerstmann, U., Gougoussis, C., Kokalj, A., Lazzeri, M., Martin-Samos, L., Marzari, N., Mauri, F., Mazzarello, R., Paolini, S., Pasquarello, A., Paulatto, L., Sbraccia, C., Scandolo, S., Sclauzero, G., Seitsonen, A. P, Smogunov, A., Umari, P. and Wentzcovitch, R. M. (2009). “QUANTUM ESPRESSO: a modular and open-source software project for quantum simulations of materials,” J. Phys. Condens. Matter, 21, 395502.CrossRefGoogle ScholarPubMed
Glaser, R., Knotts, N. and Wu, H. (2003). “Polar Order in Crystalline Molecular Organic Materials by Rational Design,” Chemtracts Org. Chem. 16, 643652.Google Scholar
Grimme, S. (2006). “Semiempirical GGA-type density functional constructed with a long-range dispersion correction,” J. Comput. Chem. 27, 17871799.CrossRefGoogle ScholarPubMed
Hohenberg, P. and Kohn, W. (1964). “Inhomogeneous Electron Gas,” Phys. Rev., 136, B864B871.CrossRefGoogle Scholar
Hunter, A. C., Lawson, K. R., Perkins, J and Urch, C. J. (2001). “Aromatic interactions,” J. Chem. Soc., Perkin Trans. 2, 651669.CrossRefGoogle Scholar
Kohn, W. and Sham, L. J. (1965) “Self-Consistent Equations Including Exchange and Correlation Effects,” Phys. Rev. 140, A1133A1138.CrossRefGoogle Scholar
McKinnon, J. J., Spackman M. A., Mitchell, A. S. (2004). “Novel tools for visualizing and exploring intermolecular interactions in molecular crystals,” Acta Crystallogr., Sect. B : Struct. Sci. 60, 627668.CrossRefGoogle ScholarPubMed
Monkhorst, H. J. and Pack, J. D. (1976). “Special points for Brillouin-zone integrations,” Phys. Rev. B 13, 51885192.CrossRefGoogle Scholar
Perdew, J. P., Burke, K. and Ernzerhof, M. (1997). “Generalized Gradient Approximation Made Simple,” Phys. Rev. Lett. 78, 38653868.Google Scholar
Portell, A., Barbas, R., Braga, D., Polito, M., Puigjaner, C. and Prohens, R. (2009). “New polymorphic hydrogen bonding donor–acceptor system with two temperature coincident solid–solid transitions,” CrystEngComm 11, 5254.CrossRefGoogle Scholar
Prohens, R.; Portell, A. and Alcobé, X. (2012). “Effect of Preorganization on the Polymorphism and Cocrystallization of a Squaramide Compound,” Cryst. Growth Des. 12, 45484553.CrossRefGoogle Scholar
Prohens, R., Portell, A., Puigjaner, C., Barbas, R., Alcobe, X., Font-Bardia, M. and Tomas, S. (2012). “Cooperative induction in double H-bonding donor/acceptor compounds: Chains vs. ribbons,” CrystEngComm 14, 57455748.CrossRefGoogle Scholar
Prohens, R., Portell, A., Puigjaner, C., Tomas, S, Fujii, K., Harris, K. D. M., Alcobe, X., Font-Bardia, M. and Barbas, R. (2011). “Cooperativity in Solid-State Squaramides,” Cryst. Growth Des. 11(9), 37253730.CrossRefGoogle Scholar
Rietveld, H. M. (1969). “A profile refinement method for nuclear and magnetic structures,” J. Appl. Crystallogr. 2 (2), 6571.CrossRefGoogle Scholar
Rodríguez-Carvajal, J. (1993). “Recent advances in magnetic structure determination by neutron powder diffraction,” Physica B, 192, 5569.CrossRefGoogle Scholar
Spackman, M. A. and McKinnon, J. J. (2002). “Fingerprinting intermolecular interactions in molecular crystals,” CrystEngComm 4 (66), 378392.CrossRefGoogle Scholar
Vanderbilt, D. (1990). “Soft Self-Consistent Pseudopotentials in a Generalized Eigenvalue Formalism,” Phys. Rev. B 41, 78927895.CrossRefGoogle Scholar
Wolff, S. K., Grimwood, D. J., McKinnon, J. J., Jayatilaka, D. and Spackman, M. A. (2007). Illustrations with computer package CrystalExplorer v2.1. (Computer Software), University of Western Australia, Perth, Australia.Google Scholar
Xu, X. and Goddard, W. A. (2004). “The extended Perdew-Burke-Ernzerhof functional with improved accuracy for thermodynamic and electronic properties of molecular systems,” J. Chem. Phys. 121, 4068.CrossRefGoogle ScholarPubMed