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Structure solution and refinement from powder or single-crystal diffraction data? Pros and cons: An example of the high-pressure β′-polymorph of glycine

Published online by Cambridge University Press:  29 February 2012

Nickolay A. Tumanov ,
Elena V. Boldyreva  and
Hans Ahsbahs
Nickolay A. Tumanov
Affiliation:
Novosibirsk State University, Novosibirsk, Russian Federation and Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russian Federation
Elena V. Boldyreva
Affiliation:
Novosibirsk State University, Novosibirsk, Russian Federation and Institute of Solid State Chemistry and Mechanochemistry, Siberian Branch of the Russian Academy of Sciences (SB RAS), Novosibirsk, Russian Federation
Hans Ahsbahs
Affiliation:
Philipps-Universität Marburg, Marburg, Germany
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Abstract

The structure of a high-pressure polymorph of glycine (the β′-polymorph formed reversibly at 0.8 GPa from the β-polymorph) was determined from high-resolution X-ray powder diffraction data collected in situ in a diamond anvil cell at nine pressure points up to 2.6 GPa. X-ray powder diffraction study gave a structural model of at least the same quality as that obtained from a single-crystal diffraction experiment. The difference between the powder-diffraction and the single-crystal models is related to the orientation of the NH3-tails and the structure of the hydrogen-bonds network. The phase transition between the β- and β′-polymorphs is reversible and preserves a single crystal intact. No transformations were observed between the β-, α-, and β′-polymorphs on compression and decompression, although the α- and β′-polymorphs belong to the same space group (P21/c). The instability of the β- and γ-forms with pressure can be predicted easily when considering the densities of their structures versus pressure. The direction of the transformation (i.e., which of the high-pressure polymorphs is formed) is determined by structural filiation between the parent and the high-pressure phases because of the kinetic control of the transformations.

Keywords

amino acidhigh pressurepolymorphstructure solution from powder diffraction datagrid search techniquesimulated annealing
Type
Technical Articles
Information
Powder Diffraction , Volume 23 , Issue 4 , December 2008 , pp. 307 - 316
Copyright
Copyright © Cambridge University Press 2008

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References

Ahsbahs, H. (1996). “Einige experimentelle Aspekte bei der Rцntgenbeugung an Einkristallen bei hohem Druck,” Z. Kristallogr.ZEKRDZ 11, 30.Google Scholar
Ahsbahs, H. (2004). “New pressure cell for single-crystal X-ray investigations on diffractometers with area detectors,” Z. Kristallogr.ZEKRDZ10.1524/zkri.219.6.305.34643 219, 305–308.CrossRefGoogle Scholar
Angel, R. J., Bujak, M., Zhao, J., Gatta, G. D., and Jacobsen, S. D. (2007). “Effective hydrostatic limits of pressure media for high-pressure crystallographic studies,” J. Appl. Crystallogr.JACGAR10.1107/S0021889806045523 40, 26–32.CrossRefGoogle Scholar
Boldyreva, E. V. (2007a). “High-pressure polymorphs of molecular solids: When are they formed, and when are they not? Some examples of the role of kinetic control,” Cryst. Growth Des.CGDEFU 7, 1662–1668.CrossRefGoogle Scholar
Boldyreva, E. V. (2007b). “Crystalline amino acids—A link between chemistry, materials science and biology,” in Models, Mysteries, and Magic of Molecules, edited by Boeyens, J. C. A. and Ogilvie, J. F. (Springer, New York), pp. 169–194.Google Scholar
Boldyreva, E. V. (2008). “High-pressure diffraction studies of molecular organic solids. A personal view,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ 64, 218–231.CrossRefGoogle ScholarPubMed
Boldyreva, E. V., Ahsbahs, H., and Weber, H.-P. (2003a). “A comparative study of pressure-induced lattice strain of α- and γ-polymorphs of glycine,” Z. Kristallogr.ZEKRDZ 218, 231–236.CrossRefGoogle Scholar
Boldyreva, E. V., Drebushchak, V. A., Drebushchak, T. N., Paukov, I. E., Kovalevskaya, Yu. A., and Shutova, E. S. (2003b). “Polymorphism of glycine: thermodynamic aspects. 1. Relative stability of the polymorphs,” J. Therm Anal. Calorim.JTACF7 73, 409–418.CrossRefGoogle Scholar
Boldyreva, E. V., Drebushchak, V. A., Drebushchak, T. N., Paukov, I. E., Kovalevskaya, Yu. A., and Shutova, E. S. (2003c). “Polymorphism of glycine: thermodynamic aspects. 2. Polymorphic transformations,” J. Therm Anal. Calorim.JTACF7 73, 419–428.Google Scholar
Boldyreva, E. V., Ivashevskaya, S. N., Sowa, H., Ahsbahs, H., and Weber, H.-P. (2004). “Effect of high pressure on the crystalline glycine: formation of a new polymorph,” Dokl. Akad. NaukDAKNEQ 396, 358–361.Google Scholar
Boldyreva, E. V., Ivashevskaya, S. N., Sowa, H., Ahsbahs, H., and Weber, H.-P. (2005). “Effect of hydrostatic pressure on the γ-polymorph of glycine. 1. A polymorphic transition into a new δ-form,” Z. Kristallogr.ZEKRDZ 220, 50–57.CrossRefGoogle Scholar
Boldyreva, E. V., Ahsbahs, H., Chernyshev, V. V., Ivashevskaya, S. N., and Oganov, A. R. (2006a). “Effect of hydrostatic pressure on the crystal structure of sodium oxalate: X-ray diffraction study and ab initio simulations,” Z. Kristallogr.ZEKRDZ10.1524/zkri.2006.221.3.186 221, 186–197.CrossRefGoogle Scholar
Boldyreva, E. V., Sowa, H., Seryotkin, Yu. V., Drebushchak, T. N., Ahsbhas, H., Chernyshev, V., and Dmitriev, V. (2006b). “Pressure-induced phase transitions in crystalline L-serine studied by single-crystal and high-resolution powder X-ray diffraction,” Chem. Phys. Lett.CHPLBC 429, 474–478.CrossRefGoogle Scholar
Boultif, A. and Louër, D. (2004). “Powder pattern indexing with the dichotomy method,” J. Appl. Crystallogr.JACGAR10.1107/S0021889804014876 37, 724–731.CrossRefGoogle Scholar
David, W. I. F. and Shankland, K. (2008). “Structure determination from powder diffraction data,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ 64, 52–64.CrossRefGoogle ScholarPubMed
David, W. I. F., Shankland, K., and Shankland, N. (1998). “Routine determination of molecular crystal structures from powder diffraction data,” Chem. Commun. (Cambridge)CHCOFS 1998, 931–932.CrossRefGoogle 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.JACGAR 39, 910–915.CrossRefGoogle Scholar
Dawson, A., Allan, D. R., Belmonte, S. A., Clark, S. J., David, W. I. F., McGregor, P. A., Parsons, S., Pulham, C. R., and Sawyer, L. (2005). “Effect of high pressure on crystal structures of polymorphs of glycine,” Cryst. Growth Des.CGDEFU 5, 1415–1427.CrossRefGoogle Scholar
Dollase, W. A. (1986). “Correction of intensities for preferred orientation in powder diffractometry: Application of the March model,” J. Appl. Crystallogr.JACGAR10.1107/S0021889886089458 19, 267–272.CrossRefGoogle Scholar
Drebushchak, V. A., Boldyreva, E. V., Drebushchak, T. N., and Shutova, E. S. (2002a). “Synthesis and calorimetric investigation of unstable β-glycine,” J. Cryst. GrowthJCRGAE 241, 266–268.CrossRefGoogle Scholar
Drebushchak, T. N., Boldyreva, E. V., and Shutova, E. S. (2002b). “β-Glycine,” Acta Crystallogr., Sect. E: Struct. Rep. OnlineACSEBH 58, o634–o636.CrossRefGoogle Scholar
Forman, R. A., Piermarini, G. J., Barnett, J. D., and Block, S. (1972). “Pressure measurement made by the utilization of ruby sharp-line luminescence,” ScienceSCIEAS10.1126/science.176.4032.284 176, 284–285.CrossRefGoogle ScholarPubMed
Goryainov, S. V., Kolesnik, E. N., and Boldyreva, E. V. (2005) “”A reversible pressure-induced phase transition in β-glycine at 0.76 GPa,” Physica BPHYBE3 357, 340–347.CrossRefGoogle Scholar
Hammersley, A. P., Svensson, S. O., Hanfland, M., Fitch, A. N., and Hausermann, D. (1996). “Two-dimensional detector software: From real detector to idealised image or two-theta scan,” High Press. Res.HPRSEL10.1080/08957959608201408 14, 235–248.CrossRefGoogle Scholar
Hinrichsen, B., Dinnebier, R. E., and Jansen, M. (2006). “Powder3D: An easy to use program for data reduction and graphical presentation of large numbers of powder diffraction patterns,” Z. Kristallogr.ZEKRDZ 2006, 231–236.CrossRefGoogle Scholar
Howard, C. J. (1982). “The approximation of asymmetric neutron powder diffraction peaks by sums of Gaussians,” J. Appl. Crystallogr.JACGAR10.1107/S0021889882012783 15, 615–620.Google Scholar
Katrusiak, A. (2008). “High-pressure crystallography,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ 64, 135–148.CrossRefGoogle ScholarPubMed
Larson, A. C., and Von Dreele, R. B. (2000). “General Structure Analysis System (GSAS),” (Report LAUR 86-748). Los Alamos National Laboratory, Los Alamos, New Mexico.Google Scholar
Loveday, J. S., McMahon, M. I., and Nelmes, R. J. (1990). “The effect of diffraction by the diamonds of a diamond-anvil cell on single-crystal sample intensities,” J. Appl. Crystallogr.JACGAR10.1107/S0021889890005635 23, 392–396.CrossRefGoogle Scholar
Macrae, C. F., Edgington, P. R., McCabe, P., Pidcock, E., Shields, G. P., Taylor, R., Towler, M., and van de Streek, J. (2006). “Mercury: Visualization and analysis of crystal structures,” J. Appl. Crystallogr.JACGAR10.1107/S002188980600731X 39, 453–457.CrossRefGoogle Scholar
Moggach, S. A., Allan, D. R, Morrison, C. A., Parsons, S., and Sawyer, L. (2005). “Effect of pressure on the crystal structure of L-serine-I and the crystal structure of L-serine-II at 5.4 GPa,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 61, 58–68.CrossRefGoogle ScholarPubMed
Moggach, S. A., Allan, D. R., Clark, S. J., Gutmann, M. J., Parsons, S., Pulham, C. R., and Sawyer, L. (2006a). “High-pressure polymorphism in L-cysteine: the crystal structures of L-cysteine-III and L-cysteine-IV,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 62, 296–309.CrossRefGoogle ScholarPubMed
Moggach, S. A., Allan, D. R., Parsons, S., and Sawyer, L. (2006b). “Effect of pressure on the crystal structure of α-glycilglycine to 4.7 GPa; application of Hirshfeld surfaces to analyse contacts on increasing pressure,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 62, 310–320.CrossRefGoogle ScholarPubMed
Piermarini, G. J., Block, S., and Barnett, J. D. (1973). “Hydrostatic limits in liquids and solids to 100 kbar,” J. Appl. Phys.JAPIAU10.1063/1.1662159 44, 5377–5382.CrossRefGoogle Scholar
Piermarini, G. J., Block, S., Barnett, J. D., and Forman, R. A. (1975). “Calibration of the pressure dependence of the R 1 ruby fluorescence line to 195 kbar,” J. Appl. Phys.JAPIAU10.1063/1.321957 46, 2774–2780.CrossRefGoogle Scholar
Sowa, H. and Ahsbahs, H. J. (2006). “High-pressure X-ray investigation of zincite ZnO single crystals using diamond anvils with an improved shape,” J. Appl. Crystallogr.JACGAR10.1107/S0021889805042457 39, 169–175.CrossRefGoogle Scholar
Spek, A. L. (2003). “Single-crystal structure validation with the program PLATON,” J. Appl. Crystallogr.JACGAR10.1107/S0021889802022112 36, 7–13.CrossRefGoogle Scholar
Thompson, P., Cox, D. E., and Hastings, J. B. (1987). “Rietveld refinement of Debye-Scherrer synchrotron X-ray data from Al2O3,” J. Appl. Crystallogr.JACGAR10.1107/S0021889887087090 20, 79–83.CrossRefGoogle Scholar
Toby, B. H. (2001). “EXPGUI, a graphical user interface for GSAS,” J. Appl. Crystallogr.JACGAR10.1107/S0021889801002242 34, 210–213.CrossRefGoogle Scholar
Toraya, H. (1986). “Whole-powder-pattern fitting without reference to a structural model: Application to X-ray powder diffraction data,” J. Appl. Crystallogr.JACGAR10.1107/S0021889886088982 19, 440–447.CrossRefGoogle Scholar
Werner, P.-E., Eriksson, L., and Westdahl, M. (1985). “TREOR, a semi-exhaustive trial-and-error powder indexing program for all symmetries,” J. Appl. Crystallogr.JACGAR10.1107/S0021889885010512 18, 367–370.CrossRefGoogle Scholar
Wright, J. (2002). Perl Angles and Bonds 〈http://www.ccp14.ac.uk/solution/gsas/jon_wright_restraints_script.html〉.Google Scholar
Zlokazov, V. B. (2003). “DELPHI-based visual object-oriented programming for the analysis of experimental data in low-energy physics,” Nucl. Instrum. Methods Phys. Res. ANIMAER 502, 723–724.CrossRefGoogle Scholar
Zlokazov, V. B. and Chernyshev, V. V. (1992). “MRIA—a program for a full profile analysis of powder multiphase neutron-diffraction time-of-flight (direct and Fourier) spectra,” J. Appl. Crystallogr.JACGAR10.1107/S0021889891013122 25, 447–451.CrossRefGoogle Scholar