Introduction to XAFS. Applications of X-ray and neutron scattering in biology, chemistry and physics

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1 Introduction to XAFS Applications of X-ray and neutron scattering in biology, chemistry and physics Jonas Andersen, ph.d. student, DTU Chemistry Bastian Brink, ph.d. student, DTU Mechanical Engineering

2 Todays Schedule Introduction to XAFS Theory and Application Exercise 1 12:00 13:00 Lunch Break Presentation from Haldor Topsøe Exercise 2 2 DTU Chemistry, Technical University of Denmark

3 X-ray Absorption Theory The absorption coefficient - µ Transmission of electromagnetic radiation through a material Lambert Beers s Law: 3 DTU Chemistry, Technical University of Denmark

4 Introduction to XAFS Requirement: High intensity radiation source with variable energy/wavelength - Synchrotron 4 DTU Chemistry, Technical University of Denmark

5 Generation of photoelectric wave X-ray photon E>E 0 (Zn) Excess energy (E E 0 ) goes to create a photo electric wave propagating from the absorbing atom. E E 0 (Zn) Zn E 0 (Zn) is absorbed (excitation) 5 DTU Chemistry, Technical University of Denmark Isolated system

6 Backscattering of photoelectric wave N O Zn Zn S O N Interference pattern depends on: Number of backscatters Geometry of backscatters (distance/angles) Type of backscatters Energy (i.e. wavelength of photoelectric wave) 6 DTU Chemistry, Technical University of Denmark

7 X-ray absorption spectrum E 0 Cu-foil at Cu K-edge Absorbance (a.u.) The edge (E=E 0 ) EXAFS The fine structure will be extracted and analysed XANES E (ev) The fine structure is proportional to the 1D projection of the interference pattern and contains information about the coordination geometry. One spectrum two techniques: XANES and EXAFS 7 DTU Chemistry, Technical University of Denmark

8 Data reduction: Energy space Raw data + pre and post edge lines event Normalized to one absorption 8 DTU Chemistry, Technical University of Denmark

9 Data reduction: k-space Change scale from X-ray energy to Photoelectron wavenumber k-weighting to enchance features at high k values 9 DTU Chemistry, Technical University of Denmark

10 Data reduction: R-space (Fourier transform) Frequency filter. Think radial distribution function but Real and imaginary parts remember that it is not! (Depends on e.g. multiple scattering, atom types, scattering factors, phase shift) 10 DTU Chemistry, Technical University of Denmark

11 Interpretation Multiple Scattering Theory: 11 DTU Chemistry, Technical University of Denmark

12 Modelling Including only the first short scattering paths Individual contributions 12 DTU Chemistry, Technical University of Denmark

13 Modelling Including only the first short scattering paths Adding additional paths 13 DTU Chemistry, Technical University of Denmark

14 What can we see with EXAFS? EXAFS probes the local environment (within a radius of 5-7Å) around a specific element with very high accuracy. Structural information is obtained from a model fitted to the EXAFS data χχ kk = jj (kk) 2 ff eeeeee kkrr jj (kk) exp( 2kk 2 ) exp 2RR jj jj Λ kk, RR jj = RR jj + sin 2kkRR jj φφ iiii kk Least squares minimization: χχ 2 = kk χχ DDDDDDDD kk χχ MMMMMMMMMM kk 2 χχ 2 = RRRR DDDDDDDD RR RRRR MMMMMMMMMM RR 2 + IIII DDDDDDDD RR IIII MMMMMMMMMM RR 2 RR kk kk 14 DTU Chemistry, Technical University of Denmark

15 Which samples can be studied by XAFS? The sample requires a presence of an element with an accesible elemental absorption edge Concentration of the absorbing element must be high enough No need for crystalline samples. The physical state can be of any type (crystals, micro crystals, amorphous solids, liquids, solutions, tissue, cells, ) but must be homogeneous. Must be stable in the beam, and radiation damage must be avoided Applications within: Biology (metalloproteins, tissue, cells) Catalysis (active sites) Environmental science (trace metals) Pharmaceuticals 15 DTU Chemistry, Technical University of Denmark

16 The absorption of an x-ray photon Absorption Fluorescence Auger effect 16 DTU Chemistry, Technical University of Denmark

17 Data collection mode Transmission: Concentrated samples (> 10%) Thickness corresponding to edge step of about 1 E.g. 7 μm for pure Fe. Dilute samples thickness in mm range Flourescence: Dilute samples, down to ppm levels Self-absorption may dampen XAFS oscillations Flourescent radiation is re-absorbed in the sample and does not reach the detector 17 DTU Chemistry, Technical University of Denmark

18 Experimental setup Typical experiment: Transmission of intensity through a material: Absorption (high concentration): μμ EE log II 0 II Fluorescence (low concentration):μμ EE II ff II 0 18 DTU Chemistry, Technical University of Denmark

19 XAFS at Beamline I811 Experiment station K-edge: S K-edge to As K-edge L-edge: Zr L-edge to Au L-edge K-edge: Fe K-edge to Mo K-edge L-edge: Lu L-edge to Am L-edge Beam ~ 1 mm wide 19 DTU Chemistry, Technical University of Denmark

20 Scientific results XANES data 20 DTU Chemistry, Technical University of Denmark

21 XRD and XAS studies on insulin Ph. D. Christian Grundahl Frankær Characterization of Metalloproteins and Biomaterials by X-ray Absorption Spectroscopy and X-ray Diffraction 21 DTU Chemistry, Technical University of Denmark

22 Complementarity between XRD and XAS Initial model Increased resolution Single crystal X-ray diffraction Three dimensional structure of the entire protein High level of details, but often not at atomic resolution Requires single crystals of high quality X-ray absorption spectroscopy Local structure of the metal cluster (within a radius of 5 7 Å) Ultra high resolution (distances can be determined within accuracies of 0.01 Å) No crystals are required Requires a good starting model 22 DTU Chemistry, Technical University of Denmark

23 Insulin Monomer (5740 Da) consists of two peptide chains (A = 21 residues and B = 30 residues) connected by three disulfide bonds Monomers assemble to dimers Dimers assemble to hexamers in presence of divalent metal ions 23 DTU Chemistry, Technical University of Denmark

24 Insulin hexamer conformations: M 2+ sites M 2+ coordinated to three histidine residues RT 6 T 3 R 3 One M 2+ octahedral the Both other M 2+ tetrahedral octahedral 24 DTU Chemistry, Technical University of Denmark

25 Single crystal X-ray diffraction Crystallization Crystal structures Crystal growth T 6 -insulin R 6 -insulin Data collection MAX-lab, beam-line T 6 T 3 R 3 R 6 Space group R3 R3 R3 a Å Å Å c Å Å Å Molecules/as u Resolution 1.40 Å 1.30 Å 1.80 Å R merge 4.2 % 4.6 % 7.1 % I/σ(I) R R free DTU Chemistry, Technical University of Denmark Medium resolution provide good initial EXAFS models

26 Qualitative XANES XANES is a signature of the coordination geometry Octahedral Zn: high intensity white-line Tetrahedral Zn: low intensity white-line 26 DTU Chemistry, Technical University of Denmark

27 EXAFS model building Coordinates from single crystal XRD structures used as initial model Atoms within a 5.6 Å radius from Zn included in the model Models were fitted in EXCURVE 1 Distances and temperature factors refined 1 Binsted et al. (1991) EXCURV92. SERC, Daresbury Laboratory, Cheshire, UK 27 DTU Chemistry, Technical University of Denmark

28 EXAFS: T 6 -insulin Restrained refinement Octahedral coordination in both Zn sites R = N p = 19 XRD EXAFS R (Å) R (Å) 2σ 2 (Å 2 ) N ε2 (HisB10) (3) 0.012(1) Extracted EXAFS Fourier transform C ε (4) 0.020(3) C δ (3) 0.020(3) N δ (2) 0.017(3) C γ (3) 0.017(3) C β (5) 0.017(3) O w (11) 0.030(1) O w2 (axial) (3) 0.021(10) 28 DTU Chemistry, Technical University of Denmark

29 EXAFS: R 6 -insulin LeuB 6 HisB10 Extracted EXAFS Fourier transform Restrained refinement Tetrahedral coordination in both Zn sites R = N p = 19 XRD EXAFS R (Å) R (Å) 2σ 2 (Å 2 ) N ε2 (HisB10) (4) 0.007(1) C ε (2) 0.010(3) C δ (2) 0.010(3) N δ (1) 0.012(3) C γ (2) 0.012(3) C β (3) 0.012(3) O (LeuB6) (5) 0.020(9) Cl (axial) (3) 0.006(1) 29 DTU Chemistry, Technical University of Denmark

30 EXAFS: T 3 R 3 -insulin XRD EXAFS R (Å) R (Å) 2σ 2 (Å 2 ) N ε (11) 0.014(1) C ε (1) C δ (1) R Constrained = refinement NTwo p = clusters 14 Correlation Dual octahedral/tetrahedral Higher uncertainties Zn coordination N δ (4) C γ (4) C β (3) O w (15) 0.035(5) Extracted EXAFS Fourier transform N ε (11) 0.014(1) C ε (1) C δ (1) N δ (4) C γ (4) C β (3) N (SCN) (9) 0.014(1) C (SCN) (1) 30 DTU Chemistry, Technical University of Denmark S (SCN) (3)

31 Quantitative fitting of XANES Performed for T 6 and R 6 -insulin T 6 -insulin R 6 -insulin Calculation of XANES spectra on 4.5 Å clusters (from EXAFS models) using the FDMmethods, FDMNES 1 Structural parameters (distances and angles) were optimized by a multidimensional interpolation, FitIt 2 Optimized distances were in agreement with EXAFS results Optimized angles differed with up to 10 from the EXAFS results 1 Joly (2001), Phys. Rev. B 63, Smolentsev & Soldatov (2007), Comp. Mat. Sci. 39, DTU Chemistry, Technical University of Denmark

32 Comparison of XRD and XAS results with other reported Zn-site geometries The accuracy of XRD results depends on resolution of XRD structure Zn N distances in R 3 -sites (tetrahedral) EXAFS results are closer to the Zn-distances reported in small molecules, i.e. more accurate Large discrepancies between XRD and XAS results observed for the Zn O w distance in the loose octahedral T 3 - sites. 32 DTU Chemistry, Technical University of Denmark

33 In-situ spectroscopic studies of Chromium Catalysts in Ionic Liquids ATR-FTIR coupled with EXAFS 33 DTU Chemistry, Technical University of Denmark

34 Intro Glucose isomerization to fructose and following conversion to 5- (hydroxymethyl)furfural (HMF) is catalyzed by a Chromium species in the ionic liquid 1-butyl-3-methyl-imidazolium chloride ([BMIm]Cl). GGGGGGGGGGGGGG FFFFFFFFFFFFFFFF HHHHHH + 3HH 2 OO Controversy regarding coordination sphere and oxidation number. EXAFS and XANES can provide information regarding coordination sphere and oxidation state. In-situ ATR-FTIR can provide information regarding the reaction kinetics. 34 DTU Chemistry, Technical University of Denmark

35 XANES Linear combination fit of Cr(II) and Cr(III) with glucose in [BMIm]Cl Sample Cr(II)/[BMIm] Cl/Glucose Cr(III)/[BMIm ]Cl/Glucose Cr(II) amount 0.879(0.039) (0.000) Cr(III) amount 0.121(0.039) (0.000) 35 DTU Chemistry, Technical University of Denmark

36 Background corrected EXAFS data 36 DTU Chemistry, Technical University of Denmark

37 EXAFS [CrCl 6 ] 3- in [BMIm]Cl EXAFS fit Schematic drawing 37 DTU Chemistry, Technical University of Denmark 17/04/2008

38 EXAFS [CrCl 4 Glu] - in [BMIm]Cl EXAFS fit Schematic drawing 38 DTU Chemistry, Technical University of Denmark 17/04/2008

39 EXAFS [CrCl 4 Glu] 2- in [BMIm]Cl JT-distorted Cr(II) and Cr(III) (as determined by XANES) Tetrachloroglucose chromate(ii) Tetrachloroglucose chromate(iii) Bond Distance (Å) Cr-Cl 2.30 Cr-Cl z 2.40 Cr-O 1.99 Cr-Cl 2.35 Cr-O DTU Chemistry, Technical University of Denmark

40 IR results Arrhenius plot for the Cr catalyzed reaction. The Cr(II) reaction is approximate 8 times slower than the Cr(III) reaction. However with exactly same activation energy. ln(k) Coupled with XANES results the oxidation state has been determined to be ,0024 0,0026 0,0028 0,003 1/T [K-1] Anhydrous Cr(II) Anhydrous Cr(III) Linear fit (anhydrous Cr(II)) 40 DTU Chemistry, Technical University of Denmark

41 Nitrogen stabilized expanded austenite Austenitic stainless steel fcc structure of Fe,Cr,Ni Identical metallic local environments Nitriding in NH 3 atmosphere Solid solution of N Lattice expansion 41 DTU Chemistry, Technical University of Denmark

42 Nitrogen stabilized expanded austenite Untreated steel Nitrided Exercise 2! 42 DTU Chemistry, Technical University of Denmark

43 Exercises: 1: Fluorescence spectrum of aqueous solution of Cr 2+ 2: Transmission spectrum: Expanded austenite (Cr and Fe data) Raw data -> Normalization, background-removal -> Modelling 43 DTU Chemistry, Technical University of Denmark

44 Programs: Athena (Data reduction) 44 DTU Chemistry, Technical University of Denmark

45 Programs: Artemis (Modelling) etc 45 DTU Chemistry, Technical University of Denmark