Hostname: page-component-78c5997874-94fs2 Total loading time: 0 Render date: 2024-11-05T12:48:47.024Z Has data issue: false hasContentIssue false

Ab initio structure determination of the low-temperature phase of succinonitrile from laboratory X-ray powder diffraction data—Coping with potential poor powder quality using DFT ab initio methods

Published online by Cambridge University Press:  29 February 2012

P. S. Whitfield
Affiliation:
Institute for Chemical Process and Environmental Technology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
Y. Le Page
Affiliation:
Institute for Chemical Process and Environmental Technology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
A. Abouimrane
Affiliation:
Institute for Chemical Process and Environmental Technology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada
I. J. Davidson
Affiliation:
Institute for Chemical Process and Environmental Technology, National Research Council Canada, 1200 Montreal Road, Ottawa, Ontario K1A 0R6, Canada

Abstract

Without experimental or predicted literature crystal structures for succinonitrile at low temperature, structure solution was attempted from powder diffraction data taken at 173 and 90 K from a solid sample. Its room-temperature plastic-crystal state makes production of a sample with good particle statistics and random orientation almost impossible. Combining constrained models, simulated annealing, and careful application of second-order spherical harmonic corrections nevertheless produced viable-looking structures at 90 and 173 K, yielding two distinct structure models with the same projection down c. VASP optimization of atom coordinates in the experimental cell agreed well with the 90 K model but poorly with the model derived from the 173 K data. The refined 90 K structure changed little on optimization and fitted all datasets from 85 to 225 K. Plots of cell data, torsion angles, and isotropic displacement parameters against temperature suggest possible phase transitions around 100, 120, and 180 K. Cell data at 90 K: monoclinic P21/a, a=9.0851(5) Å, b=8.5617(5) Å, c=5.8343(3) Å, β=79.295(2)°, and Z=4. Succinonitrile has gauche conformation, in agreement with literature spectroscopy data.

Type
Technical Articles
Copyright
Copyright © Cambridge University Press 2008

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

Abouimrane, A., Whitfield, P. S., Niketic, S., and Davidson, I. J. (2007). “Investigation of Li salt doped succinonitrile as potential solid electrolytes for lithium batteries,” J. Power SourcesJPSODZ 174, 883888.Google Scholar
Alarco, P.-J., Abu-Lebdeh, Y., Abouimrane, A., and Armand, M. (2004). “The plastic-crystalline phase of succinonitrile as a universal matrix for solid-state ionic conductors,” Nature Mater.NMAACR10.1038/nmat1158 3, 476481.CrossRefGoogle ScholarPubMed
Badea, E., Blanco, I., and Gatta, G. D. (2007). “Fusion and solid-to-solid transitions of a homologous series of alkane-α, ω-dinitriles,” J. Chem. Thermodyn.JCTDAF 39, 13921398.CrossRefGoogle Scholar
Baikie, T., Mercier, P. H. J., Elcombe, M. M., Kim, J. Y., Le Page, Y., Mitchell, L. D., White, T. J., and Whitfield, P. S. (2007). “Triclinic apatites,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 63, 251256.Google Scholar
Carlucci, L., Ciani, G., Proserpio, D. M., and Rizzato, S. (2002). “Coordination networks from the self-assembly of silver salts and the linear chain dinitriles NC(CH2)nCN (n=2 to 7): A systematic investigation of the role of counterions and of the increasing length of the spacers,” Cryst. Eng. Commun. 4, 413425.CrossRefGoogle Scholar
Coelho, A. A. (2003). “Indexing of powder diffraction patterns by iterative use of singular value decomposition,” J. Appl. Crystallogr.JACGAR10.1107/S0021889802019878 36, 8695.CrossRefGoogle Scholar
Davidson, E. R. (1983). “Matrix eigenvector methods,” in Methods in Computational Molecular Physics, edited by Diercksen, G. H. F. and Wilson, S. (Plenum, New York), pp. 95113.CrossRefGoogle Scholar
Derollez, P., Lefebvre, J., Descamps, M., Press, W., and Fontaine, H. (1990). “Structure of succinonitrile in its plastic phase,” J. Phys.: Condens. MatterJCOMEL10.1088/0953-8984/2/33/002 2, 68936903.Google Scholar
Dinnebier, R. E., Ding, L., Ma, K., Neumann, M. A., Tanpipat, N., Leusen, F. J. J., Stephens, P. W., and Wagner, M. (2001). “Crystal structure of a rigid ferrocene-based macrocycle from high-resolution X-ray powder diffraction,” OrganometallicsORGND7 20, 56425647.Google 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, 267272.Google Scholar
Efron, B. and Tibshirani, (1986). “Bootstrap methods for standard errors, confidence intervals, and other measures of statistical accuracy,” Stat. Sci.STSCEP 1, 5477.Google Scholar
Fedorov, O. P., Shpak, A. P., Zhivolub, E. L., and Shuleshova, O. V. (2005). “The influence of crystalline anisotropy on the evolution of the crystallization front during directional solidification,” Crystallogr. Rep.CYSTE310.1134/1.2132413 50, 10271033.CrossRefGoogle Scholar
Fengler, O. I. and Ruoff, A. (2001). “Vibrational spectra of succinonitrile and its [1,4-13C2]-, [2,2,3,3-2H4]- and [1,4-13C2-2,2,3,3-2H4]-isotopomers and a force field of succinonitrile,” Spectrochim. Acta, Part ASAMCAS 57, 105117.Google Scholar
Glicksman, M. E., Scaefer, R. J., and Ayers, J. D. (1976). “Dendritic growth—a test of theory,” Metall. Trans. AMTTABN 7A, 17471759.Google Scholar
Hore, S., Dinnebier, R., Wen, W., Hanson, J., Belabbas, I., Carlsson, J. M., Scheffler, M., and Maier, J. (2008). “High resolution in situ powder diffraction of highly disordered plastic crystal, namely succinonitrile,” Z. Anorg. Allg. Chem. ZAACAB (in press).Google Scholar
Janz, G. J. and Fitzgerald, W. E. (1955). “Infrared spectrum and molecular structure of succinonitrile,” J. Chem. Phys.JCPSA6 23, 19731974.Google Scholar
Kresse, G. (1993). Ab initio Molekular Dynamik für flüssige Metalle, Ph.D. Thesis, Technische Universität Wein, Vienna, Austria.Google Scholar
Kresse, G. and Hafner, J. (1993). “Ab initio molecular dynamics for open-shell transition metals,” Phys. Rev. B: Condens. Matter 48, 1311513118.CrossRefGoogle ScholarPubMed
Kresse, G. and Hafner, J. (1994). “Ab initio molecular-dynamics simulation of the liquid-metal-amorphous-semiconductor transition in germanium,” Phys. Rev. B: Condens. Matter 49, 1425114269.CrossRefGoogle ScholarPubMed
Kresse, G. and Joubert, D. (1999). “From ultrasoft pseudopotentials to the projector augmented-wave method,” Phys. Rev. B: Condens. Matter 59, 17581775.Google Scholar
Larson, A. C. and Von Dreele, R. B. (1994). General Structure Analysis System (GSAS) (Report LAUR 86–748). Los Alamos National Laboratory, Los Alamos, New Mexico.Google Scholar
Le Page, Y. and Rodgers, J. R. (2005). “Quantum software interfaced with crystal-structure databases: Tools, results and perspectives,” J. Appl. Crystallogr.JACGAR10.1107/S0021889805017358 38, 697705.CrossRefGoogle Scholar
Lide, D. R. (Ed.) (2007). CRC Handbook of Chemistry and Physics, 88th ed. (CRC, Cleveland).Google Scholar
Long, S., MacFarlane, D. R., and Forsyth, M. (2003). “Fast ion conduction in molecular plastic crystals,” Solid State IonicsSSIOD310.1016/S0167-2738(03)00208-X 161, 105112.CrossRefGoogle Scholar
Looijenga-Vos, A. and Buerger, M. J. (2006). “Space-group determination and diffraction symbols,” in International Tables for Crystallography, edited by Hahn, Th. (IUCr, Chester), Vol. A, pp. 4454.CrossRefGoogle Scholar
Madsen, I. C. and Hill, R. J. (1994). “Collection and analysis of powder diffraction data with near-constant counting statistics,” J. Appl. Crystallogr.JACGAR 27, 385392.Google Scholar
Markvardsen, A. J., David, W. I. F., Johnston, J. C., and Shankland, K. (2001). “A probabilistic approach to space-group determination from powder diffraction data,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ10.1107/S0108767300012174 57, 4754.Google Scholar
Mercier, P. H. J., Dong, Z., Baikie, T., Le Page, Y., White, T. J., Whitfield, P. S., and Mitchell, L. D. (2007). “Ab initio constrained crystal-chemical Rietveld refinement of Ca10(VxP1−xO4)F2 apatites,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 63, 3748.CrossRefGoogle Scholar
Methfessel, M. and Paxton, A. T. (1989). “High-precision sampling for Brillouin-zone integration in metals,” Phys. Rev. B: Condens. Matter 40, 36163621.Google Scholar
Monkhorst, H. J. and Pack, J. D. (1976). “Special points for Brillouin-zone integrations,” Phys. Rev. B: Condens. Matter 13, 51885192.CrossRefGoogle Scholar
Neumann, M. A., Tedesco, C., Destri, S., Ferro, D. R., and Porzio, W. (2002). “Bridging the gap—structure determination of the red polymorph of tetrahexylsexithiophene by Monte Carlo simulated annealing, first-principles DFT calculations and Rietveld refinement,” J. Appl. Crystallogr.JACGAR 35, 296303.CrossRefGoogle Scholar
Oszlányi, G. and Süto, A. (2004). “Ab initio structure solution by charge flipping,” Acta Crystallogr., Sect. A: Found. Crystallogr.ACACEQ10.1107/S0108767303027569 60, 134141.CrossRefGoogle ScholarPubMed
Pawley, G. S. (1981). “Unit-cell refinement from powder diffraction scans,” J. Appl. Crystallogr.JACGAR10.1107/S0021889881009618 14, 357361.Google Scholar
Sherwood, J. N. (1979). The Plastically Crystalline State (Wiley, London).Google Scholar
Smith, D. K. (2001). “Particle statistics and whole-pattern methods in quantitative X-ray powder diffraction analysis,” Powder Diffr.PODIE210.1154/1.1423285 16, 186191.CrossRefGoogle Scholar
Smrčok, Ĺ., Jorík, V., Scholtzová, E., and Milata, V. (2007). “Ab initio structure determination of 5-anilino-methylene-2,2-dimethyl-1,3-dioxane-4,6-dione from laboratory powder data—a combined use of X-ray, molecular and solid-state DFT study,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 63, 477484.Google Scholar
Von Dreele, R. B. (1997). “Quantitative texture analysis by Rietveld refinement,” J. Appl. Crystallogr.JACGAR10.1107/S0021889897005918 30, 517525.CrossRefGoogle Scholar
Whitfield, P. S., Abouimrane, A., and Davidson, I. J. (2007a). “Structure determination from powder diffraction data of some moisture-sensitive network coordination compounds,” Adv. X-Ray Anal.AXRAAA 50, 139144.Google Scholar
Whitfield, P. S., Le Page, Y., Grice, J. D., Stanley, C. J., Jones, G. C., Rumsey, M. S., Blake, C., Roberts, A. C., Stirling, J. A. R., and Carpenter, G. J. C. (2007b). “LiNaSiB3O7(OH)—novel structure of the new borosilicate mineral jadarite determined from laboratory powder diffraction data,” Acta Crystallogr., Sect. B: Struct. Sci.ASBSDK 63, 396401.Google Scholar