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Automated Electron Diffraction Tomography

  • Ute Kolb
Conference paper
Part of the NATO Science for Peace and Security Series B: Physics and Biophysics book series (NAPSB)

Abstract

Ab-initio structure analysis by electron diffraction is hampered by two major problems: insufficient number of reflections sampled and an intensity alteration by dynamical scattering contribution or beam damage. Thus, in recent years the principles of automated diffraction tomography (ADT) allowing systematic reciprocal space sampling and automated data analysis were developed. Here the basic ideas of ADT and its general applicability will be discussed along with some examples of solved structures.

Keywords

Structure Solution Reciprocal Space Electron Diffraction Data Electron Crystallography Ewald Sphere 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

References

  1. 1.
    Vainshtein BK (1964) Structure analysis by electron diffraction. Pergamon Press, New YorkGoogle Scholar
  2. 2.
    Kolb U, Gorelik T, Kübel C, Otten MT, Hubert D (2007) Towards automated diffraction tomography: part I – data acquisition. Ultramicroscopy 107:507–513. doi: 10.1016/j.ultramic.2006.10.007 CrossRefGoogle Scholar
  3. 3.
    Peng LM, Dudarev SL, Whelan MJ (2004) High-energy electron diffraction and microscopy. Oxford University Press, New YorkGoogle Scholar
  4. 4.
    Fultz B, Howe JM (2008) Transmission electron microscopy and diffractometry of materials. Springer, BerlinGoogle Scholar
  5. 5.
    Van Dyck D, Coene W (1984) The real space method for dynamical electron diffraction calculations in high resolution electron microscopy: I. Principles of the method. Ultramicroscopy 15:29–40. doi: 10.1016/0304-3991(84)90072-X CrossRefGoogle Scholar
  6. 6.
    Tanaka M, Terauchi M, Kaneyama T, Tsuda M, Saitoh K (1985) Convergent beam electron diffraction, vol I–IV. JEOL, TokyoGoogle Scholar
  7. 7.
    Sung CM, Williams DB (1991) A bibliography of CBED papers from 1939–1990. J Electron Micro Tech 17:95–118CrossRefGoogle Scholar
  8. 8.
    Gorelik TE, Stewart AA, Kolb U (2011) Structure solution with automated electron diffraction tomography data: different instrumental approaches. J Microsc 244:325–331CrossRefGoogle Scholar
  9. 9.
    Palatinus L, Klementová M, Dřínek V, Jarošová M, Petříček V (2011) An incommensurately modulated structure of η’-phase of Cu3+xSi determined by quantitative electron diffraction tomography. Inorg Chem 50:3743–3751CrossRefGoogle Scholar
  10. 10.
    Dorset DL (1995) Structural electron crystallography. Plenum Press, New YorkGoogle Scholar
  11. 11.
    Williams DB, Carter CB (1996) Transmission electron microscopy, vol II. Plenum Press, New YorkGoogle Scholar
  12. 12.
    Vincent R, Midgley PA (1994) Double conical beam-rocking system for measurement of integrated electron diffraction intensities. Ultramicroscopy 53:271–282CrossRefGoogle Scholar
  13. 13.
    Arndt UW, Champness JN, Phizackerley RP, Wonacott AJ (1973) A single-crystal oscillation camera for large unit cells. J Appl Crystallogr 6:457–463CrossRefGoogle Scholar
  14. 14.
    Monaco HL (1994) Experimental methods in X-ray crystallography. In: Giacovazzo C (ed) Fundamentals of crystallography. Oxford University Press, New York, pp 229–318Google Scholar
  15. 15.
    Kolb U, Gorelik T, Otten MT (2008) Towards automated diffraction tomography. Part II – cell parameter determination. Ultramicroscopy 108:763–772CrossRefGoogle Scholar
  16. 16.
    Hauptman H, Karle J (1953) The solution of the phase problem, I. The centrosymmetric crystal. Polycrystal Book Service, PittsburghGoogle Scholar
  17. 17.
    Wilson JAC (1949) The probability distribution of X-ray intensities. Acta Crystallogr 2:318–321CrossRefGoogle Scholar
  18. 18.
    Giacovazzo C (1980) Direct methods in crystallography. Academic, LondonGoogle Scholar
  19. 19.
    Dorset DL, Gilmore CJ (2000) Prospects for kinematical least-squares refinement in polymer electron crystallography. Acta Crystallogr A 56:62–67CrossRefGoogle Scholar
  20. 20.
    Burla MC, Caliandro R, Camalli M, Carrozzini B, Cascarano GL, De Caro L, Giacovazzo C, Polidori G, Siliqi D, Spagna R (2007) IL MILIONE: a suite of computer programs for crystal structure solution of proteins. J Appl Crystallogr 40:609–613CrossRefGoogle Scholar
  21. 21.
    Sheldrick GM (2008) A short history of SHELX. Acta Crystallogr A 64:112–122ADSCrossRefGoogle Scholar
  22. 22.
    Gilmore GJ (1996) Maximum entropy and Bayesian statistics in crystallography: a review of practical applications. Acta Crystallogr A 52:561–589CrossRefGoogle Scholar
  23. 23.
    Gilmore CJ, Bricogne G (1997) The mice computer program. Methods Enzymol 277:65–78CrossRefGoogle Scholar
  24. 24.
    Palatinus L, Chapuis G (2007) Superflip – a computer program for the solution of crystal structures by charge flipping in arbitrary dimensions. J Appl Crystallogr 40:786–790CrossRefGoogle Scholar
  25. 25.
    Brandenburg K, Putz H (2009) Endeavour – structure solution from powder diffraction. http://www.crystalimpact.com/endeavour/Default.htm
  26. 26.
    Coelho A (2007) TOPAS-academic V4.1, Brisbane. http://www.topas-academic.net
  27. 27.
    Favre-Nicolin V, Černý R (2002) FOX, ‘free objects for crystallography’: a modular approach to ab initio structure determination from powder diffraction. J Appl Crystallogr 35:734–743CrossRefGoogle Scholar
  28. 28.
    Favre-Nicolin V (2008) Fox, free objects for crystallography. http://objcryst.sourceforge.net
  29. 29.
    David WIF, Shankland K, Van De Streek J, Pidcock E, Motherwell WDS, Cole JC (2002) DASH: a program for crystal structure determination from powder diffraction data. J Appl Crystallogr 39:910–915CrossRefGoogle Scholar
  30. 30.
    Birkel CS, Mugnaioli E, Gorelik T, Kolb U, Panthöfer M, Tremel W (2010) Solution synthesis of a new thermoelectric Zn1+xSb nanophase and its structure determination using automated electron diffraction tomography. J Am Chem Soc 132:9881–9889CrossRefGoogle Scholar
  31. 31.
    Kolb U, Gorelik T, Mugnaioli E (2009) Automated diffraction tomography combined with electron precession: a new tool for ab initio nanostructure analysis. In: Moeck P, Hovmoeller S, Nicolopoulos S, Rouvimov S, Petrok V, Gateshki M, Fraundorf P (eds) Electron crystallography for materials research and quantitative characterization of nanostructured materials, Materials Research Society Symposia Proceedings, vol 1184, Warrendale, PA, GG01-05Google Scholar
  32. 32.
    Mugnaioli E, Gorelik T, Kolb U (2009) “Ab initio” structure solution from electron diffraction data obtained by a combination of automated diffraction tomography and precession technique. Ultramicroscopy 109:758–765CrossRefGoogle Scholar
  33. 33.
    Mugnaioli E, Kolb U (2012) Applications of automated diffraction tomography (ADT) on nanocrystalline porous materials. Micropor Mesopor Mater (in press), doi: 10.1016/j.micromeso.2012.02.024
  34. 34.
    Gemmi M, Fischer J, Merlini M, Poli S, Fumagalli P, Mugnaioli E, Kolb U (2011) A new hydrous Al-bearing pyroxene as a water carrier in subduction zones. Earth Planet Sci Lett 310:422–428ADSCrossRefGoogle Scholar
  35. 35.
    Mugnaioli E, Gorelik TE, Stewart A, Kolb U (2011) “Ab-initio” structure solution of nano-crystalline minerals and synthetic materials by automated electron tomography. In: Krivovichev SV (ed) Minerals as advanced materials II. Springer, Berlin/Heidelberg, pp 41–54CrossRefGoogle Scholar
  36. 36.
    Kolb U, Mugnaioli E, Gorelik TE (2011) Automated electron diffraction tomography – a new tool for nano crystal structure analysis. Cryst Res Technol 6:542–554CrossRefGoogle Scholar
  37. 37.
    Mugnaioli E, Sedlmaier SJ, Oekler O, Kolb U, Schnick W (2012) Ba6P12N17O9Br3 – a column-type phosphate structure solved from single-nanocrystal data obtained by automated electron diffraction tomography. Eur J Inorg Chem 2012:121–125CrossRefGoogle Scholar
  38. 38.
    Andrusenko I, Mugnaioli E, Gorelik TE, Koll D, Panthöfer M, Tremel W, Kolb U (2011) Structure analysis of titanate nanorods by automated electron diffraction tomography. Acta Crystallogr B 67:218–225CrossRefGoogle Scholar
  39. 39.
    Sedlmaier SJ, Mugnaioli E, Oekler O, Kolb U, Schnick W (2011) SrP3N5O: a highly condensed layer phosphate structure solved from a nanocrystal by automated electron diffraction tomography. Chem Eur J 17:11258–11265CrossRefGoogle Scholar
  40. 40.
    Jiang J, Jorda JL, Yu J, Baumes LA, Mugnaioli E, Diaz-Cabanas MJ, Kolb U, Corma A (2011) Synthesis and structure determination of the hierarchical meso-microporous zeolite ITQ-43. Science 333:1131–1134ADSCrossRefGoogle Scholar
  41. 41.
    Rozhdestvenskaya I, Mugnaioli E, Czank M, Depmeier W, Kolb U, Merlino S (2011) Essential features of the polytypic charoite-96 structure compared to charoite-90. Mineral Mag 75:2833–2846CrossRefGoogle Scholar
  42. 42.
    Rozhdestvenskaya I, Mugnaioli E, Czank M, Depmeier W, Kolb U, Reinholdt A, Weirich T (2010) The structure of charoite, (K,Sr,Ba,Mn)15–16(Ca,Na)32[(Si70(O,OH)180)] (OH,F)4.0*nH2O, solved by conventional and automated electron diffraction. Mineral Mag 74:159–177CrossRefGoogle Scholar
  43. 43.
    Kolb U, Gorelik TE, Mugnaioli E, Stewart A (2010) Structural characterization of organics using manual and automated electron diffraction. Polym Rev 50:385–409CrossRefGoogle Scholar
  44. 44.
    Gorelik TE, van de Streek J, Kilbinger AFM, Brunklaus G, Kolb U (2012) Ab-initio crystal structure analysis and refinement approaches of oligo p-benzamides based on electron diffraction data. Acta Crystallogr B 68:171–181CrossRefGoogle Scholar
  45. 45.
    Denysenko D, Grzywa M, Tonigold M, Schmitz B, Krkljus I, Hirscher M, Mugnaioli E, Kolb U, Hanss J, Volkmer D (2011) Elucidating gating effects for hydrogen sorption in MHU-4 type triazolate-based MOFs featuring different pore sizes. Chem Eur J 17:1837–1848CrossRefGoogle Scholar
  46. 46.
    Bellussi G, Montanari E, Di Paola E, Millini R, Carati A, Rizzo C, O’Neil Parker WJ, Gemmi M, Mugnaioli E, Kolb U, Zanardi S (2012) ECS-3: a crystalline hybrid organic–inorganic aluminosilicate with open porosity. Angew Chem 51:666–669CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media Dordrecht 2012

Authors and Affiliations

  1. 1.Institute of Physical ChemistryJohannes-Gutenberg University MainzMainzGermany

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