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Total-Scattering Pair-Distribution Function of Organic Material from Powder Electron Diffraction Data

  • Tatiana E. Gorelik (a1), Martin U. Schmidt (a2), Ute Kolb (a1) (a3) and Simon J. L. Billinge (a4) (a5)


This paper shows that pair-distribution function (PDF) analyses can be carried out on organic and organometallic compounds from powder electron diffraction data. Different experimental setups are demonstrated, including selected area electron diffraction and nanodiffraction in transmission electron microscopy or nanodiffraction in scanning transmission electron microscopy modes. The methods were demonstrated on organometallic complexes (chlorinated and unchlorinated copper phthalocyanine) and on purely organic compounds (quinacridone). The PDF curves from powder electron diffraction data, called ePDF, are in good agreement with PDF curves determined from X-ray powder data demonstrating that the problems of obtaining kinematical scattering data and avoiding beam damage of the sample are possible to resolve.


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Abeykoon, M., Malliakas, C.D., Juhás, P., Božin, E.S., Kanatzidis, M.G. & Billinge, S.J.L. (2012). Quantitative nanostructure characterization using atomic pair distribution functions obtained from laboratory electron microscopes. Z Krist 227, 248256.
Ankele, J.E., Mayer, J., Lamparter, P. & Steeb, S. (2005). Quantitative electron diffraction data of amorphous materials. Z Naturforsch 60a, 459468.
Anstis, G.R., Liu, Z. & Lake, M. (1988). Investigation of amorphous materials by electron diffraction—The effects of multiple scattering. Ultramicroscopy 26, 6570.
Barnes, A.C., Fischer, H.E. & Salmon, P.S. (2003). Neutron and X-ray diffractions for the structural study of liquids and glasses. Journal de Physique IV 103, 359390. (in French).
Bates, S., Zografi, G., Engers, D., Morris, K., Crowley, K. & Newman, A. (2006). Analysis of amorphous and nanocrystalline solids from their X-ray diffraction patterns. Pharm Res 23, 23332349.
Billinge, S.J.L. (2008 a). Nanoscale structural order from the atomic pair distribution function (PDF): There’s plenty of room in the middle. J Solid State Chem 181, 16981703.
Billinge, S.J.L. (2008 b). Local structure from total scattering and atomic pair distribution function (PDF) analysis. In Powder Diffraction: Theory and Practice, Dinnebier, R.E. & Billinge, S.J.L. (Eds.), pp. 464493. London, England: Royal Society of Chemistry.
Billinge, S.J.J., Dykhne, T., Juhás, P., Božin, E., Taylor, R., Florence, A.J. & Shankland, K. (2010). Characterisation of amorphous and nanocrystalline molecular materials by total scattering. CrystEngComm 12, 13661368.
Billinge, S.J.L. & Kanatzidis, M.G. (2004). Beyond crystallography: the study of disorder nanocrystallinity and crystallographically challenged materials. Chem Commun 2004, 749760.
Billinge, S.J.L. & Levin, I. (2007). The problem with determining atomic structure at the nanoscale. Science 316, 561565.
Brown, C.J. (1968). Crystal structure of β-copper phthalocyanine. J Chem Soc A 1968, 24882493.
Capitani, G.C., Oleynikov, P., Hovmöller, S. & Mellini, M. (2006). A practical method to detect and correct for lens distortion in the TEM. Ultramicroscopy 106, 6674.
Chupas, P.J., Qiu, X., Hanson, J.C., Lee, P.L., Grey, C.P. & Billinge, S.J.L. (2003). Rapid-acquisition pair distribution function (RA-PDF) analysis. J Appl Cryst 36, 13421347.
Cockayne, D.J.H. (2007). The study of nanovolumes of amorphous materials using electron scattering. Annu Rev Mater Res 37, 159187.
Coltman, J.W. (1955). Electron diffraction camera, United States Patent 2727153.
Dorset, D.L. (1995). Structural Electron Crystallography. New York: Plenum Publishing Corporation.
Dubochet, J., Adrian, M., Chang, J.J., Homo, J.C., Lepault, J., McDowall, A.W. & Schultz, P. (1988). Cryo-electron microscopy of vitrified specimens. Q Rev Biophys 21(2), 129228.
Dykhne, T., Taylor, R., Florence, A. & Billinge, S.J.L. (2011). Data requirements for the reliable use of atomic pair distribution functions in amorphous pharmaceutical fingerprinting. Pharm Res 28, 10411048.
Egami, T. & Billinge, S.J.L. (2012). Underneath the Bragg Peaks: Structural Analysis of Complex Materials. Oxford: Pergamon Press Elsevier.
Elschner, C., Levin, A.A., Wilde, L., Grenzer, J., Schroer, C., Leo, K. & Riede, M. (2011). Determining the C60 molecular arrangement in thin films by means of X-ray diffraction. J Appl Cryst 44, 983990.
Farrow, C.L. & Billinge, S.J.L. (2009). Relationship between the atomic pair distribution function and small angle scattering: Implications for modeling of nanoparticles. Acta Cryst A 65, 232239.
Farrow, C.L., Juhás, P., Liu, J., Bryndin, D., Bozin, E.S., Bloch, J., Proffen, T. & Billinge, S.J.L. (2007). PDFfit2 and PDFgui: Computer programs for studying nanostructure in crystals. J Phys Condens Mat 19, 335219.
Farrow, C.L., Ruan, C.-Y. & Billinge, S.J.L. (2010). Quantitative nanoparticle structures from electron crystallography data. Phys Rev B81, 124104.
Faruqi, A.R. & McMullan, G. (2011). Electronic detectors for electron microscopy. Q Rev Biophys 44, 357390.
Gemmi, M. & Nicolopoulos, S. (2007). Structure solution with three-dimensional sets of precessed electron diffraction intensities. Ultramicroscopy 107, 483494.
Gemmi, M., Voltolini, M., Ferretti, A.M. & Ponti, A. (2011). Quantitative texture analysis from powder-like electron diffraction data. J Appl Cryst 44, 454461.
Gemmi, M., Zou, X., Hovmoller, S., Migliori, A., Vennstrom, M. & Andersson, Y. (2003). Structure of Ti2P solved by three-dimensional electron diffraction data collected with the precession technique and high-resolution electron microscopy. Acta Cryst A 59, 117126.
Gorelik, T., Matveeva, G., Kolb, U., Schleuss, T., Kilbinger, A.F.M., van de Streek, J., Bohle, A. & Brunklaus, G. (2010). H-bonding schemes of di- and tri-p-benzamides assessed by a combination of electron diffraction, X-ray powder diffraction and solid-state NMR. CrystEngComm 12, 18241832.
Gorelik, T., Schmidt, M.U., Brüning, J., Bekoe, S. & Kolb, U. (2009). Using electron diffraction to solve the crystal structure of a laked azo pigment. Cryst Growth Des 9, 38983903.
Gorelik, T.E., van de Streek, J., Kilbinger, A.F.M., Brunklaus, G. & Kolb, U. (2012). Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data. Acta Cryst B 68, 171181.
Herbst, W. & Hunger, K. (2004). Industrial Organic Pigments, 3rd ed. Weinheim: Wiley-VCh.
Hirata, A., Hirotsu, Y., Ohkubo, T., Hanada, T. & Bengus, V.Z. (2006). Compositional dependence of local atomic structures in amorphous Fe100−xBx (x=14, 17, 20) alloys studied by electron diffraction and high-resolution electron microscopy. Phys Rev B 74, 214206-1214206-9.
Hirata, A., Morino, T., Hirotsu, Y., Itoh, K. & Fukunaga, T. (2007). Local atomic structure analysis of Zr-Ni and Zr-Cu metallic glasses using electron diffraction. Mater Trans 48, 12991303.
Hirotsu, Y., Ohkubo, T., Bae, I.-T. & Ishimaru, M. (2003). Electron diffraction structure analysis for amorphous materials. Mater Chem Phys 81, 360363.
Juhás, P., Cherba, D.M., Duxbury, P.M., Punch, W.F. & Billinge, S.J.L. (2006). Ab initio determination of solid-state nanostructure. Nature 440, 655658.
Juhás, P., Granlund, L., Gujarathi, S.R., Duxbury, P.M. & Billinge, S.J.L. (2010). Crystal structure solution from experimentally determined atomic pair distribution functions. J Appl Cryst 42, 623629.
Klug, H.P. & Alexander, L.E. (1974). X-ray Diffraction Procedures, 2nd ed. New York: Wiley.
Kolb, U., Gorelik, T. & Otten, M.T. (2008). Towards automated diffraction tomography. Part II—Cell parameter determination. Ultramicroscopy 108, 763772.
Kolb, U., Mugnaioli, E. & Gorelik, T.E. (2011). Automated electron diffraction tomography—A new tool for nano crystal structure analysis. Cryst Res Technol 46, 542554.
Kolb, U., Gorelik, T.E., Mugnailoi, E. & Stewart, A. (2010). Structural characterization of organics using manual and automated electron diffraction. Polym Rev 50, 385409.
Kolb, U., Gorelik, T., Kübel, C., Otten, M.T. & Hubert, D. (2007). Towards automated diffraction tomography: Part I—Data acquisition. Ultramicroscopy 107, 507513.
Kim, J.-S., Kim, M.-S., Park, H.J., Jin, S.-J., Lee, S. & Hwang, S.-J. (2008). Physicochemical properties and oral bioavailability of amorphous atorvastatin hemi-calcium using spray-drying and SAS process. Int J Pharm 359, 211219.
Kim, J.G., Seo, J.W., Cheon, J. & Kim, Y.J. (2009). Rietveld analysis of nano-crystalline MnFe2O4 with electron powder diffraction. Bull Korean Chem Soc 30, 183187.
Làbàr, J.L. (2004). Phase identification by combining local composition from EDX with information from diffraction database. In Electron Crystallography: Novel Approaches for Structure Determination of Nanosized Materials, Weirich, T.E., Lábár, J.L. & Zuo, X.D. (Eds.), pp. 207218. Dordrecht, The Netherlands: Springer. (Proceedings of the NATO Advances Study Institute on Electron Crystallography, Erice, Italy, June 10–14, 2004).
Lábár, J. (2008). Electron diffraction based analysis of phase fractions and texture in nanocrystalline thin films, Part I: Principles. Microsc Microanal 14, 287295.
Lábár, J.L. (2009). Electron diffraction based analysis of phase fractions and texture in nanocrystalline thin films, Part II: Implementation. Microsc Microanal 15, 2029.
Lotsch, B.V., Döblinger, M., Sehnert, J., Seyfarth, L., Senker, J., Oeckler, O. & Schnick, W. (2007). Unmasking melon by a complementary approach employing electron diffraction, solid-state NMR spectroscopy, and theoretical calculations—Structural characterization of a carbon nitride polymer. Chem Eur J 13, 49694980.
Luo, Z., Vasquez, Y., Bondi, J.F. & Schaak, R.E. (2011). Pawley and rietveld refinements using electron diffraction from L12-type intermetallic Au3Fe1−x nanocrystals during their in-situ order–disorder transition. Ultramicroscopy 111, 12951304.
Marijnissen, J.C.M., Yurteri, C.U., van Erven, J. & Ciach, T. (2010). Medicine nanoparticle production by EHDA. In Nanoparticles in Medicine and Environment Inhalation and Health Effects. Springer, Dordrecht, The Netherlands, 3958.
McCulloch, D.G., McKenzie, D.R., Goringe, C.M., Cockayne, D.J.H., McBride, W. & Green, D.C. (1999). Experimental and theoretical characterisation of structure in thin disordered films. Acta Cryst A 55, 178187.
Mizuguchi, J., Sasaki, T. & Tojo, K. (2002). Refinement of the crystal structure of 5,7,12,14-tetrahydro[2,3-b]-quinolinoacridine (gamma-form), C20H12N2O2, at 223 K. Z Krist 217, 249250.
Moeck, P. & Rouvimov, S. (2009). Structural Fingerprinting of Nanocrystals in the Transmission Electron Microscope: Utilizing Information on Projected Reciprocal Lattice Geometry, 2D Symmetry, and Structure Factors, in Drug Delivery Nanoparticles Formulation and Characterization. USA, New York: Informa Healthcare.
Moore, M.D., Steinbach, A.M., Buckner, I.S. & Wildfong, P.L.D. (2009). A structural investigation into the compaction behavior of pharmaceutical composites using powder X-ray diffraction and total scattering analysis. Pharm Res 26, 24292437.
Moss, S.C. & Graczyk, J.F. (1969). Evidence of voids within the as-deposited structure of glassy silicon. Phys RevLett 23, 11671171.
Mugnaioli, E., Capitani, G., Nieto, F. & Mellini, M. (2009). Accurate and precise lattice parameters by selected-area electron diffraction in the transmission electron microscope. Am Mineral 94, 793800.
Neder, R.B. & Proffen, T. (2009). Diffuse Scattering and Defect Structure Simulations: A Cook Book Using the Program DISCUS. New York: Oxford University Press.
Noerenberg, H., Saeverin, R., Hoppe, U. & Holzhueter, G. (1999). Estimation of radial distribution functions in electron diffraction experiments: Physical, mathematical and numerical aspects. J Appl Cryst 32, 911916.
Paulus, E.F., Leusen, F.J.J. & Schmidt, M.U. (2007). Crystal structures of quinacridones. CrystEngComm 9, 131143.
Petkov, V. & Billinge, S.J.L. (2002). From crystals to nanocrystals: Semiconductors and beyond, In Proceedings of the Workshop From Semiconductors to Proteins: Beyond the Average Structure, July 28–August 1, 2001, Traverse City, MI, Billinge, S. J. L. & Thorpe, M. F. (Eds.). Plenum, New York, 153168.
Petkov, V., Parvanov, V., Trikalitis, P., Malliakas, C., Vogt, T. & Kanatzidis, M. (2005 a). Three-dimensional structure of nanocomposites from atomic pair distribution function analysis: Study of polyaniline and polyaniline 0.5V2O5×1.0 H2O. J Am Chem Soc 127, 88058812.
Petkov, V., Parvanov, V., Tomalia, D., Swanson, D., Bergstrom, D. & Vogt, T. (2005 b). 3D structure of dendritic and hyper-branched macromolecules by X-ray diffraction. Solid State Commun 134, 671675.
Prasad, R.S., Yandrapu, S.K. & Manavalan, R. (2010). Preparation and characterization of itraconazole solid dispersions for improved oral bioavailability. Int J ChemTech Res 2, 133142.
Rademacher, N., Daemen, L.L., Chronister, E.L. & Proffen, T. (2012). Pair distribution function analysis of molecular compounds: Significance and modeling approach discussed using the example of p-terphenyl. J Appl Cryst 45, 482488.
Schmidt, M.U. (2010). PDF investigations on quinacridone polymorphs. 12th European Powder Diffraction Conference EPDIC-12, Darmstadt, Germany, August 27–30, 2010.
Schmidt, M.U., Brühne, S., Wolf, A.K., Rech, A., Brüning, J., Alig, E., Fink, L., Buchsbaum, C., Glinnemann, J., van de Streek, J., Gozzo, F., Brunelli, M., Stowasser, F., Gorelik, T., Mugnaioli, E. & Kolb, U. (2009). Electron diffraction, X-ray powder diffraction and pair distribution function analyses to determine the crystal structures of pigment yellow 213, C23H21N5O9 . Acta Cryst B 65, 189199.
Sproul, A., McKenzie, D.R. & Cockayne, D.J.H. (1986). Structural study of hydrogenated amorphous silicon–carbon alloys. Phil Mag B 54, 113131.
Tucker, M.G., Keen, D.A., Dove, M.T., Goodwin, A.L. & Hui, Q. (2007). RMCProfile: Reverse Monte Carlo for polycrystalline material. J Phys Condensed Matter 19, 335218/1335218/16.
Vainshtein, B.K. (1964). Structure Analysis by Electron Diffraction. New York: Pergamon Press.
Vincent, R. & Midgley, P.A. (1994). Double conical beam-rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy 53, 271282.
Voigt-Martin, I.G., Yan, D.H., Yakimansky, A., Schollmeyer, D., Gilmore, C.J. & Bricogne, G. (1995). Structure determination by electron crystallography using both maximum-entropy and simulation approaches. Acta Cryst A 51, 849868.
Wagner, C.N.J. (1978). Direct methods for the determination of atomic-scale structure of amorphous solids (X-ray, electron, and neutron scattering). J Non-Cryst Solids 31, 140.
Warren, B.E. (1969). X-ray Diffraction. New York: Addison-Wesley.
Waseda, Y. (1980). The Structure of Non-Crystalline Materials. New York: McGraw-Hill.
Weirich, T.E., Portillo, J., Cox, G., Hibst, H. & Nicolopoulos, S. (2006). Ab initio determination of the framework structure of the heavy-metal oxide CsxNb2.54W2.46O14 from 100 kV precession electron diffraction data. Ultramicroscopy 106, 164175.
Weirich, T.E., Winterer, M., Seifried, S., Hahn, H. & Fuess, H. (2000). Rietveld analysis of electron powder diffraction data from nanocrystalline anatase, TiO2 . Ultramicroscopy 81, 263270.
Wolf, A.K., Brühne, S., Glinnemann, J., Hu, C., Kirchner, M.T. & Schmidt, M.U. (2012). Local atomic order in sodium p-chlorobenzenesulfonate monohydrate studied by pair distribution function analyses and lattice-energy minimisations. Z Krist 127, 113121.
Wright, A.C. (1985). Scientific opportunities for the study of amorphous solids using pulsed neutron sources. J Non-Cryst Solids 76, 187.
Young, C.A. & Goodwin, A.L. (2011). Applications of pair distribution function methods to contemporary problems in materials chemistry. J Mater Chem 21, 64646476.
Yu, L. (2001). Amorphous pharmaceutical solids: Preparation, characterization and stabilization. Adv Drug Deliv Rev 48, 2742.
Zewail, A.H. (2006). 4D Ultrafast electron diffraction, crystallography, and microscopy. Annu Rev Phys Chem 57, 65103.
Zhang, P., Borgnia, M., Mooney, P., Shi, D., Pan, M., O’Herron, P., Mao, A., Brogan, D., Milne, J.L.S. & Subramaniam, S. (2003). Automated image acquisition and processing using a new generation of 4 K x 4 K CCD cameras for cryo electron microscopic studies of macromolecular assemblies. J Struct Biol 143(2), 135144.


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Total-Scattering Pair-Distribution Function of Organic Material from Powder Electron Diffraction Data

  • Tatiana E. Gorelik (a1), Martin U. Schmidt (a2), Ute Kolb (a1) (a3) and Simon J. L. Billinge (a4) (a5)


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