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X-ray methods for nanoscience

X-ray methods for nanoscience. Ritva Serimaa Department of Physics University of Helsinki. Nanoscience III. X-rays and matter. wavelength of the order of 0.1 nm. elastic scattering. x-ray beam. absorption. inelastic scattering. fluorescence. Why structural studies?.

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X-ray methods for nanoscience

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  1. X-ray methods for nanoscience Ritva Serimaa Department of Physics University of Helsinki Nanoscience III

  2. X-rays and matter • wavelength of the order of 0.1 nm elastic scattering x-ray beam absorption inelastic scattering fluorescence

  3. Why structural studies? • Understanding the relationship of structure, properties and function of a system • Monitoring the system during its formation for tuning the structure and properties • Dependence of the structure and properties on environmental conditions like temperature or pressure HU Course 2013: Synchrotron radiation in materials research http://www.helsinki.fi/~serimaa/index-xraypk.html

  4. How to produce x-rays? Large scale facilities ESRF First x-ray free electron lasers: Flash, LCLS http://www-ssrl.slac.stanford.edu/lcls/index.html The European XFEL is constructed in Hamburg http://xfel.eu/ • Synchrotron http://www.lightsources.org/cms/?pid=1001328 • European facilities: ESRF, MaxLab, Petra III, Soleil, …

  5. Example of new synchrotrons: Petra III Hamburg • Ring was built for particle physics • Diameter about 3 km • German synchrotron • EMBL beam lines • 2015 Max IV Lund, Sweden

  6. Sketch of synchrotron from Wikipedia

  7. XFEL • Tiny samples • Coherent diffraction and imaging • Chemical reactions http://www.xfel.eu/research/examples/nanoworld/

  8. Free electron laser (FEL) • FELs are usually based on the combination of a linear accelerator followed by a high-precision insertion device. • The accelerated electrons in the insertion device bunch together more tightly than usual. • Over the length of the insertion device, the electrons in the microbunches begin to oscillate in step (coherently). http://www.lightsources.org/cms/?pid=1001328

  9. FEL http://en.wikipedia.org/wiki/Free_electron_laser

  10. X-ray lithography (XRL) with table top and ordinary synchrotrons and lasers patterned films achieved in GGe by XRL structures with resolutions of the order of 100 nm • G Brusatin et al. Design of hybrid sol–gel films for direct x-ray and electron beam nanopatterning.Nanotechnology 19 (2008) 175306 • D Minkov et al. Targets emitting transition radiation for performing X-ray lithography by the tabletop synchrotron MIRRORCLE-20SX. Nucl Instr and Meth in Phys Res A: Accelerators… Vol 590, Iss 1-3, 2008, 110-113 • M.C. Marconia and P.W. Wachulak. Extreme ultraviolet lithography with table top lasers. Progress in Quantum Electronics Vol 34, Iss 4, 2010, 173-190

  11. XFEL experimental stations 2014 • FXE femtosecond xray experiments: diffraction … • GED high energy density matter experiments, diffraction, inelastic scattering, spectroscopy • SPB single particles clusters biomolecules, coherent diffraction, resolution < 1 nm • MID materials imaging and dynamics, coherent diffraction, resolution around 10 nm • SQS small quantum systems, high resolution spectroscopy • SCS spectroscopy and coherent scattering, coherent imaging, photon correlation spectroscopy http://www.xfel.eu/research/experiment_stations/scs/

  12. FLASH, small version of the European XFEL at DESY since 2005 • FLASH is 260 m long • soft X-rays down to a wavelength of 6 nm • A coherent diffraction pattern http://hasylab.desy.de/facilities/flash/research/a_perfect_image_from_a_single_fel_shot/index_eng.html

  13. gold particles (diameter 10 nm) on a Si3N4 membrane The diffraction pattern was used to reconstruct the gold particle using the hybrid input-output (HIO) method together with the so-called shrink-wrap algorithm. Image with 5 nm spatial resolution. Coherent x-ray imaging (CXDI) SEM diffractionpatternreconstruction C. G. Schroer et al. Coherent X-Ray Diffraction Imaging with Nanofocused Illumination. PRL 101, 090801 (2008) (at ESRF ID 13) J. R. Fienup, Appl. Opt. 21, 2758 (1982). S. Marchesini et al., Phys. Rev. B 68, 140101(R) (2003).

  14. X-rays are absorbed into the material or scattered. Attenuation is described by mass attenuation constant μ/ρ [cm2/g], where ρ is the density. I = I0 exp(-(μ/ρ) ρt), where t is the thickness. I0 I X-ray t Absorption needs to be taken into account and gives information on the sample

  15. In X-ray tomography a series of radiographs are recorded for different angular positions of the sample which rotates around an axis perpendicular to the beam. Laboratory setups: cone beam, polychromatic radiation Synchrotron: parallel beam and monochromatic radiation X-ray microtomography The number of radiographs is the order of 1000 and the data is several Gigabytes. X-ray source http://laskin.mis.hiroshimau.ac.jp/Kougi/08a/PIP/ sample detector

  16. X-ray microtomography setup at Department of Physics, Helsinki University • Phoenix nanotom 180 NF • Tungsten x-ray tube • Hamamatsu flat panel detector • One experiment • 1,440 projections • The measurement time for a single image 750 ms

  17. Absorption as a function of energy • An x-ray photon is absorbed by the atom and the excess energy is transferred to an electron, which may be expelled from the atom, leaving the atom ionized X-ray http://physics.nist.gov/PhysRefData/XrayMassCoef/ElemTab/z28.html

  18. X-ray absorption spectroscopy XAS • If x-ray energy is suitable, a photoelectron will be ejected. • X-ray absorption fine structure: The outgoing electron scatters from nearest atoms. This causes oscillations in the linear absorption coefficient. • Extended x-ray absorption fine structure EXAFS • X-ray absorption near edge structure XANES photoelectron X-ray XAS tutorials http://xafs.org/

  19. XANES gives information on the electronic state of the absorbing atom and the local structure surrounding it. XANES X-ray absorption near edge structure Normalized absorption XANES EXAFS Data base for XANES spectra by Farrel Lyttle (http://www.esrf.fr/computing/scientific/dabax)

  20. Studies on the average environment of a selected type of atom by its absorption coefficient. EXAFSgivesinformation of distances and numbers of nearest neigbours of the chosen atom type. EXAFS Extended x-ray absorption fine structure

  21. Fluoresence analysis Elemental analysis Sample is irradiated by x-rays The emitted fluorescence radiation is detected. The elements are regognized on the basis of the energies of the x-ray fluorescence emittion lines. Example: J. Szlachetko et al. Application of the high-resolution grazing-emission x-ray fluorescence method for impurities control in semiconductor nanotechnology. J Appl Phys 105, 086101, 2009 http://en.wikipedia.org/wiki/X-ray_fluorescence

  22. X-ray microcopy and XANES at ESRF 2-7 keV Spot size 0.3 – 1 micrometer http://www.esrf.eu/UsersAndScience/Experiments/Imaging/ID21/ http://www-cxro.lbl.gov/BL612/index.php?content=research.html

  23. XAS: Sulfur in King Henry VIII's warship Mary Rose and Gustav II Adolf’s warshipVasa • Marine-archaeological oak timbers • XANES and synchrotron-based x-ray microspectroscopy • Iron sulfides and elemental sulfur occur in separate particles. Sandström M et al. PNAS 102 (40): 14165-14170 OCT 4 2005

  24. Synchrotron radiation X-ray microscopy since 2000 X-ray fluorescence analysis (XRF): elemental composition X-ray diffraction (XRD): crystalline impurities X-ray Absorption Near Edge Structure (XANES): the chemical state of the sulfur or iron atom Extended X-ray absorption fine structure (EXAFS): bonding of the sulfur or iron atom XRD XANES X-ray EXAFS e- Scanning experiments with a small beam

  25. Large amounts of reduced sulfur compounds abound in lignin-rich parts such as the middle lamella between the cell walls, mostly as thiols and disulfides SO42- (2.483 eV) Elemental sulfur (2.473 eV) ESRF ID21, beam size 0.5 μm Y Fors, M Sandström: Sulfur and iron in shipwreckscauseconservationconcerns. Chem. Soc. Rev. 2006, 35, 399-415

  26. Nanoparticle de-acidification of the Mary Rose • SrCO3 nanoparticles were dispersed into 2-propanol and sonicated for 1 hour. • Wood was placed in the nanoparticle medium and left for 3 days whilst being sonicated throughout. • Samples were removed from solution and rinsed with distilled water. • The sulfate is almost entirely converted to SrSO4 Eleanor J. Schofield et al. Materials Today Volume 14, Issues 7–8, July–August 2011, Pages 354–358

  27. The penetration of SrCO3 nanoparticles in Mary Rose timbers • (a) SEM micrograph of after treatment with SrCO3; (inset) EDS of strontium • (b) XRF of strontium • (c) Sulfur and strontium profile using EDS; (inset) line analysis throughout the cross-section

  28. X-ray imaging of biological systems • Imaging based on soft x-ray or electron microscopy • Radiation damage • Resolution < 100 nm • Samples • Frozen samples • Dehydrated specimens at room temperature. • Example: Scanning transmission X-ray microscopy and XANES at Carbon K absorption edge on Wood with resolution of 100 nm. XANES result: Polysaccharides are susceptible to soft X-ray irradiation induced chemical transformations GD Cody et al. Soft X-ray induced chemical modification of polysaccharides in vascular plant cell walls. J El. Spect and Rel. Phen. 170(1-3), March 2009, 57-64

  29. X-ray scattering methods for structural studies Cullity and Stock: Elements of x-ray diffraction J Als-Nielsen, D McMorrow: Elements of modern x-ray physics Feigin, Svergun: Structure analysis by small-angle X-ray and neutron scattering. http://www.embl-hamburg.de/ExternalInfo/Research/Sax/reprints/feigin_svergun_1987.pdf

  30. q = k2-k1 q X-ray scattering Scattering vector q, length q = 4π/λsinθ where λ is the wavelength and 2θ the scattering angle • SAXS and WAXS • WAXS q X-rays 2θ monochromator sample detector Symmetrical transmission Symmetrical reflection X-rays k1 k2

  31. ESRF ID2 http://www.esrf.eu/UsersAndScience/Experiments/SoftMatter/ID02/BeamlineLayout

  32. X-ray scattering WAXS, SAXS, USAXS, XRD … • Wavelength of the order of 0.1 nm • X-rays scatter from electrons. • Scattering amplitude A(q) is proportional to Fourier transform of the electron density (x): A(q) =  (y) exp(i q·y) d3y Here qis the scattering vector. • Intensity I(q) = A*A may be presented as a Fourier transform of the autocorrelation function C(z) of the electron density: • I(q) =  C(z) exp(-i q·z) d3z • Here C(z)=  (z+y) (y) d3y

  33. q k1 k2   d x Bragg law 2d sin θ = λ • Scattering vector q = k2 - k1 is perpendicular to the lattice planes. The lenght of the scattering vector |q| = 4π/λ sinθ • Bragg law in terms of q: d = 2π/q Path difference 2x x/d = sin θ 2x = 2d sin θ = λ

  34. Crystallography of macromolecules • Cellulose Ia The oriented fibrous samples prepared by aligning cellulose microcrystals from the cell wall of the freshwater alga Glaucocystis nostochinearum. Nishiyama Y, Sugiyama J, Chanzy H, Langan P. Crystal structure and hydrogen bonding system in cellulose Ia from synchrotron X-ray and neutron fiber diffraction. J Am Chem Soc 125(47), 14300-14306, 2003  

  35. Isotropic crystalline powder sample • Diffraction pattern consists of rings • Example. Silver behenate • Crystal structure from the positions of the peaks • Crystallite size from the FWHM’s of the peaks http://chemistry.library.wisc.edu/subject-guides/x-ray-crystallography.html

  36. Anisotropic crystalline sample Diffraction pattern may consists of ”spots” Crystal structure Crystallite size Preferred orientation of crystallites from the azimuthal intensity of one reflection Example: paper - cellulose and filler q

  37. Semicrystalline materials: Crystallinity from WAXS intensity • Crystallinity index = Intensity of crystalline model -------------------------------------- Experimental intensity Solid bamboo sample • Crystalline intensity from model • Amorphous pattern measured from a lignin sample. Reflection mode Transmission mode

  38. Crystallite size from the width of the reflections • Scherrer formula L = K λ/(B(2θ) cosθ),  where K is a constant, B(2θ) is the the full width at half maximum of the reflection, 2θ is the scattering angle and λ the wavelength. • Instrumental broadening of the reflection should be considered. • Extraction of a diffraction peak from the intensity curve. FWHM

  39. Crystallite size vs grain size • Grain size from electron microscopy, microtomography • Crystallite size using x-ray diffraction • Grains can contain several crystallites

  40. Small-angle x-ray scattering and diffraction • Crystal structures in length scales 1-100 nm • Macromolecules in solution: shape and size • Fractal structures: fractal dimension • Two-phase systems with sharp interfaces: spesific surface Feigin LA, Svergun DI. Structure analysis by small-angle X-ray and neutron scattering. http://www.embl-hamburg.de/ExternalInfo/Research/Sax/reprints/feigin_svergun_1987.pdf Glatter O, Kratky O (1982). Small Angle X-ray Scattering. http://physchem.kfunigraz.ac.at/sm/

  41. Small-angle diffraction: nanoporous silica Two-dimensional Hexagonal structure d-2 = 4/3 (h2 + hk + k2)/a2 Values of h and k for first peaks: 01, 10 1 1 0 2 Dirk Mter et al. Surfactant Self-Assembly in Cylindrical Silica Nanopores. J. Phys. Chem. Lett., 2010, 1 (9), pp 1442–1446

  42. Mesoporous silica F Kleitz, S Hei Choi, R Ryoo. Cubic Ia3d large mesoporous silica: synthesis and replication to platinum nanowires, carbon nanorods and carbon nanotubes. Chem. Commun., 2003, 2136-2137

  43. C16E7–D2O system BL-15A instrument at the Photon Factory in KEK, Japan Block co-polymers and surfactants M Imaia et al. Kinetic pathway of lamellar \ gyroid transition: Pretransition and transient states. J. Chem. Phys., Vol. 115, No. 22, Dec 2001, 10525-10531

  44. Electron density Shape of objects in dilute solution using SAXS Amplitude of a sphere with electron density ρand radius a: F(q) = 4/3 π a3 ρ 3 (sin x –x cos x)/x3, where x = qa. Electron density ρ a r Blue: intensity of spheres, a = 30 Å. Green: Guinier law I ~ exp(-1/3 Rg2 q2) http://www.embl-hamburg.de/research/unit/svergun/index.html http://kur.web.psi.ch/sans1/SANSSoft/sasfit.html

  45. Guinier law. At small q the intensity can be approxi-mated with a Gaussian: I(q) ≈ I(0) exp(-(1/3)(qRg)2 ) The radius of gyration Rg = ∫ρ(r)r2 dV / ∫ρ(r)dV Figure: Rg = 25.1 Å V = 45475 Å3≈ (36)3 Å3 Sphere R = 32 Å SAXS of hydrophobin protein in a dilute solution

  46. Crystalline structure Hydrophobin protein and model based on a fit to measured SAXS intensity Hakanpaa JM, Szilvay GR, Kaljunen H, Maksimainen M, Linder M, Rouvinen J. Two crystal structures of Trichoderma reesei hydrophobin HFBI -The structure of a protein amphiphile with and without detergent interaction. Protein Sci. V15, 2129-2140, 2006 http://www.embl-hamburg.de/ExternalInfo/ Research/Sax/software.html

  47. Power law behaviour of SAXS intensity from solutions • IN(q) ≈ 4π (ρ- ρ0)2 S/q4at large q, where S is the total area of particles and ρ- ρ0electron density difference • Sheets I(q) ≈ const /q2 • Long thin rods I(q) ≈ const /q1 I ≈ 1/q4 e.g. Teixeira. J.Appl. Cryst. 21 1988, 781-785 and SAXS text books

  48. Flexible polymers with Gaussian statistics • Intensity is proportional to F(q) = 2(exp(-u) + u - 1)/u2 where u = <Rg2>q2 and <Rg2> is the average radius of gyration squared. • <Rg2> = (Lb)/6, where L is the contour length and b is the statistical segment length.

  49. Dense systems: fractal aggregates • The SAXS intensity follow a power law • I ≈ 1/qa. • This can be interpreted as arising from fractal structures, if the characteristic length scale R of a fractal satisfies the condition Rq >>1. • For surface fractals the power law exponent a is between 3 and 4. It is related to surface fractal dimension Ds as a = 6 - Ds. • The Porod law, a = 4, is valid for the scattering of a compact particle with a smooth surface (Ds = 2, Dm = 3) • A power law with a < 3 is caused by a mass fractal for which a = Dm = Ds < 3. • Continuous charge density transitions can cause a to be larger than 4.

  50. μ-SAXS and microfluidics T. Pfohl et al.Trends in microfluidics with complex fluids, Chem. Phys. Chem.4 (2003), pp. 1273–1274. Piggee C. Sometimes less is more: microfluidics extends the capabilities of SAXS. Analytical Chemistry 80(11), 3948-3948, 2008  

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