Electron diffraction data: new perspectives

Transcription

1 Electron diffraction data: new perspectives Lukáš Palatinus Institute of Physics ASCR, Prague, Czechia

2 Outline Electron diffraction why and why not, when and when not? Oriented diffraction patterns the beauty and the betrayal of symmetry precession to the rescue!? Electron diffraction tomography A weapon of mass structure production, finally! But... Dynamical refinement from (P)EDT What God has joined together let not man separate (Mk 10:9) Outlook Quo vadis, electron crystallography?

3 Electron vs. X-ray diffraction X-rays electrons weak interaction with crystal simple description of diffraction by kinematical theory little radiation damage possibility of diffraction in various environments (hp, gasses) large crystals (>> 1 mm) or powder diffraction -> problems with mixtures and impurities strong interaction with crystal complicated description of diffraction by dynamical theory radiation damage experiment in vacuum small crystals down to X nm analysis of mixtures and impurities

4 Electron vs. X-ray diffraction X-rays electrons Diffraction mostly kinematical Diffraction strongly dynamical q Fg f ( g)exp(2 ig r ) i 1 i I gi F gi 2 i

5 Dynamical diffraction the Bloch-wave method S g S = exp 2πitA I gi S i1 2

6 Dynamical diffraction the Bloch-wave method 0 U g1 U g2 U g3 U g4 S = exp 2πitA I gi S i1 2 U g1 2KS g1 U g1 g 2 U g1 g 3 U g1 g 4 U g2 U g2 g 1 2KS g2 U g2 g 3 U g2 g 4 U g3 U g3 g 1 U g3 g 2 2KS g3 U g3 g 4 U g4 U g4 g 1 U g4 g 2 U g4 g 3 2KS g4

7 Dynamical diffraction - multislice Scattering: ψ (x, y) = ψ(x, y)exp (iδφ x, y ) Propagation: ψ (x, y) = ψ x, y exp πi x2 + y 2 λ z Image:

8 Dynamical diffraction S = exp 2πitA I gi S i1 2

9 Dynamical diffraction S = exp 2πitA 2K n Each intensity is a function of: - Crystal thickness - Crystal orientation - Structure factors of all sufficiently excited beams

10 Oriented diffraction patterns

11 Oriented diffraction patterns very useful for determination of lattice parameters and 220 symmetry beautiful spot patterns and CBED patterns computationally (more) easily tractable the strongest dynamical effects structure solution possible, but very cumbersome Sr 25 Fe 30 O 77 ; opy.cz/html/1450.html 220 Al-Cu-Fe quasicrystal; h/research_highlights/research_hig hlight_07.html Silicon [110] GaAs [1-10]; 211/ pdf

12 Precession electron diffraction Vincent & Midgley, Ultramicrosocopy 53 (1994)

13 Precession electron diffraction

14 Precession electron diffraction PED = integrating the diffracted intensities over many orientations of the incident beam around a circle For symmetry determination: more reflections in one diffraction pattern, more obvious systematic absences, easier access to HOLZ lines, better symmetry orthopyroxene [001] no precession For structure solution: intensities are more kinematical more generally, the ordering of intensities is much closer to kinematical than non-precessed data. For structure refinement: less sensitive to crystal thickness and orientation, more sensitive to structural parameters precession - 2.4

15 Precession electron diffraction PED = integrating the diffracted intensities over many orientations of the incident beam around a circle For symmetry determination: more reflections in one diffraction pattern, more obvious systematic absences, easier access to HOLZ lines, better symmetry CaTiO3 non-oriented no precession For structure solution: intensities are more kinematical more generally, the ordering of intensities is much closer to kinematical than non-precessed data. For structure refinement: less sensitive to crystal thickness and orientation, more sensitive to structural parameters precession 2.0

16 R2 [%] Precession electron diffraction Number of steps t=110nm t=40nm

17 Structure solution from oriented patterns Problems: low coverage, tedious data collection, strong dynamical effects even with precession

18 Electron diffraction tomography

19 Electron diffraction tomography

20 Electron diffraction tomography RED Stockholm school ADT Mainz school

21 EDT examples P. Boullay, N. Barrier and L. Palatinus, Inorg. Chem. 52 (2013)

22 EDT examples ε-fe 2 O 3, data collection and processing Mariana Klementová

23 Electron diffraction tomography complete or almost complete diffraction data conceptually simple, fast and potentially fully automatic experiment easy solution of structures by ab initio methods Poor figures of merit, unreliable atomic positions, unreliable e.s.d.s structure R obs [%] average [Å] max [Å] barite Li 4 Ti 8 Ni 3 O Zn 5 Cl 4 (BTDD) 3 32? 0.2 (rigid bodies and soft constr.) natrolite charoite Na 2 Ti 6 O Examples from Kolb et al., Cryst. Res. Technol. 46

24 Electron diffraction tomography Why is the refinement so poor? Because of the dynamical difraction

25 Dynamical refinement S = exp 2πitA/2K n I gi S i1 2 a ii = 2KS gi, i = 1, N beams a ij = U gi g j, i, j = 1, N beams Dynamical refinement = leastsquares refinement with I calc calculated with the dynamical diffraction theory

26 Dynamical refinement - specifics data selection a key to success: g max : the maximum resolution of the experimetal data (typically 1.4 Å -1 ) S g max : maximum excitation error of the experimental data R Sg max : The ratio between S g and the amplitude of the precesion motion at g

27 Dynamical refinement - specifics - Each experimental frame is treated separately. Reflections are not merged accross frames - Symmetry-equivalent reflections are not merged - Each frame has a separate scale factor - Crystal thickness is refined - Exact orientation of the crystal w.r.t. incident beam for each frame is important and must be known - Data selection procedure is important!

28 Dynamical refinement and PED why bother? Own et al. (2006), Acta Cryst. A62 Palatinus et al. (2013), Acta Cryst. A69 Price to pay: much longer computing times!

29 Dynamical refinement and PED why bother? Paracetamol form II two data sets precession angle Data set I Data set II tilt step tilt range R obs 9% 35%

30 wr(all) Dynamical refinement practical procedure Analyze data and extract intensities Set up the parameters of refinement, calculate thickness plots to indentify starting thickness Import the data to Jana. All information is stored in CIF format and imported automatically Run standard leastsquares refinement. Refine structure parameters, sample thickness, scales of individual patterns. Palatinus et al. (2015), Acta Cryst. A69 Fine-tune the orientation of individual patterns thickness

31 Dynamical refinement test results material kinematical dynamical computing time per ADRA / MDRA R1 ADRA / MDRA R1 cycle (desktop PC) kaolinite / / m 24 s Remark inverted structure R1=8.19 Ni 2 Si / / s 15 nm nanowire Ni 3 Si / / m 27s 35 nm nanowire PrVO / / m 52 s mayenite / / m 20 s orthopyro xene / / m partially occupied O visible in the difference Fourier partial occupancies of Fe/Mg refined to accuracy better than 2% Palatinus et al., Acta Cryst. B 2015a,b; Correa et al., J. Alloys Comp. 2016

32 Current challenges Can we still improve the fit to get to the typical x-ray levels of accuracy and figures of merit? Can we find data collection protocols that do not require PED and still can be well refined? Can we port the dynamical refinement strategy to macromolecules and is it necessary? Develop random diffraction tomography for the solution of really unstable crystals We need an appropriate instrument!

33 Future of electron crystallography Presentation of the method, more widespread use Use of special cameras with improved signal-to-noise ratio Random diffraction tomography, combination of diffraction from many crystals