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

x-ray beam

elastic scattering

absorption

fluorescence

inelastic scattering

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

How to produce x-rays?

Large scale facilities

Synchrotron

http://www.lightsources.org/cms/?pid=1001328

European facilities: ESRF,

MaxLab, Petra III, Soleil, …

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/

Example of new synchrotrons: Petra III Hamburg

Ring was built for particle physics

Diameter about 3 kmGerman synchrotronEMBL beam lines

2015 Max IV Lund, Sweden

Sketch of synchrotron from Wikipedia

XFEL

Tiny samples Coherent diffraction and imaging Chemical reactions

http://www.xfel.eu/research/examples/nanoworld/

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

FEL

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

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

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/

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

Coherent x-ray imaging (CXDI)

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.

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).

SEM diffraction pattern reconstruction

Absorption needs to be taken into account and gives information on the sample

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.

X-ray

I0 I

t

X-ray microtomography

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

The number of radiographs is the order of 1000 and the data is several Gigabytes.

X-ray source sample detector

http://laskin.mis.hiroshimau.ac.jp/Kougi/08a/PIP/

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

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

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

X-ray

photoelectron

XAS tutorials http://xafs.org/

XANES X-ray absorption near edge structure

XANES gives information on the electronic state of the absorbing atom and the local structure surrounding it.

Data base for XANES spectra by Farrel Lyttle (http://www.esrf.fr/computing/scientific/dabax)

XANES EXAFS

Normalized absorption

EXAFS Extended x-ray absorption fine structure

Studies on the average

environment of a

selected type of atom by

its absorption

coefficient.

EXAFS gives

information of distances

and numbers of nearest

neigbours of the chosen

atom type.

8800 9000 9200 9400 96000.2

0.4

0.6

0.8

1

E (eV)

No

rma

liz

ed

ab

so

rpti

on

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.

http://en.wikipedia.org/wiki/X-ray_fluorescence

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

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

XAS: Sulfur in King Henry VIII's warship Mary Rose and Gustav II Adolf’s warship Vasa

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

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

EXAFS

XRD

XANES

e-

X-ray

Scanning experiments with a small beam

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

Y Fors, M Sandström: Sulfur and iron in shipwrecks cause conservation concerns. Chem. Soc. Rev. 2006, 35, 399-415

SO42-

(2.483 eV)

Elemental sulfur (2.473 eV)

ESRF ID21, beam size 0.5 μm

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

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

X-ray imaging of biological systems

Imaging based on soft x-ray or electron microscopyRadiation damageResolution < 100 nm

SamplesFrozen samplesDehydrated 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

X-ray scattering methods for structural studies

Size range method variations

0.1-1 nm Wide angle x-ray scattering

WAXS,

Crystallography

Element specific anomalous

scattering AWAXS, grazing

incidence x-ray diffraction

GIXD for surfaces

10-100 nm Small angle x-ray scattering

SAXS, crystallography

Element specific ASAXS,

Surfaces GISAXS

>1000 nm Ultra-low angle x-ray scattering

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

X-rays 2θ

X-ray scattering

SAXS and WAXS

WAXS

Scattering vector q, length q = 4π/λ sin θ where λ is the

wavelength and 2θ the

scattering angle

X-rays

q = k2-k1

q

monochromator sample detector

q

k1 k2

Symmetrical transmission

Symmetrical reflection

ESRF ID2

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

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 q is 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

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

k1

k2

q

dx

Crystallography of macromolecules

Cellulose I 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     

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

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

0

100

200

300

400

500

600

700

q

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

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

Crystallite size vs grain size

Grain size from electron microscopy, microtomography Crystallite size using x-ray diffraction Grains can contain several crystallites

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.pdfGlatter O, Kratky O (1982). Small Angle X-ray Scattering. http://physchem.kfunigraz.ac.at/sm/

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

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

Block co-polymers and surfactants

C16E7–D2O system

BL-15A instrument at the

Photon Factory in KEK,

Japan

M Imaia et al. Kinetic pathway of lamellar \ gyroid transition: Pretransitionand transient states. J. Chem. Phys., Vol. 115, No. 22, Dec 2001, 10525-10531

Electron density

a r

Electron density

Shape of objects in dilute solution using SAXS

Amplitude of a sphere with electron

density ρ and radius a:

F(q) = 4/3 π a3 ρ 3 (sin x –x cos x)/x3,

where x = qa.

Blue: intensity of spheres, a = 30 Å.

Green: Guinier law I ~ exp(-1/3 Rg2 q2)

ρ

http://www.embl-hamburg.de/research/unit/svergun/index.html

http://kur.web.psi.ch/sans1/SANSSoft/sasfit.html

SAXS of hydrophobin protein in a dilute solution

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

0 0.1 0.2 0.3 0.410

-10

10-5

100

q

I(q

)

Hydrophobin protein and model based on a fit to measured SAXS intensity

Crystalline structure

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

Power law behaviour of SAXS intensity from solutions

IN(q) ≈ 4π (ρ- ρ0)2 S/q4 at large q, where S is the total

area of particles and ρ- ρ0 electron density difference

Sheets I(q) ≈ const /q2

Long thin rods I(q) ≈ const /q1

e.g. Teixeira. J.Appl. Cryst. 21 1988, 781-785 and SAXS text books

I ≈ 1/q4

Flexible polymers with Gaussian statistics

Intensity is proportional to

F(q) = 2(exp(-u) + u - 1)/u2

where u = <Rg

2>q2 and <Rg2> is the

average radius of gyration

squared. <Rg

2> = (Lb)/6, where L is

the contour length and b is

the statistical segment

length.

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.

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  

Surface structures

PS

D

PS

D

αi

αf

Side view

Film surface

Soller slits

Top view

w1w2

λ = 2π/k, qxy = 2ksinθ, qz ≈ k sinαf

GIXD Grazing incidence x-ray

diffraction

Troika beam line of ESRF

Thin films with GISAXS

Structure in the film statistical information over several square

millimeters probe from surface to buried interfaces various types of environment chemical contrast of a given element can be

enhanced by performing anomalous

scattering close to a specific absorption

edge.

G Renaud, R Lazzari, F Leroy. Probing surface and interface morphology with Grazing Incidence Small Angle X-Ray Scattering. Surf Sci Rep 64 (2009) 255380http://staff.chess.cornell.edu/%7Esmilgies/gisaxs/GISAXS.php

Reflectivity studies using x-rays from laboratory source

20 nm thick film cellulose film using X-ray

tube based system

E Kontturi and Lankinen. Following the

Kinetics of a Chemical Reaction in Ultrathin

Supported Polymer Films by Reliable Mass

Density Determination with X-ray

Reflectivity. J. Am. Chem. Soc., 2010, 132,

3678–3679

18.04.23 53

αr

detectorq || z-axis

Regenerated cellulose films using GISAXS and reflectivity

• Cellulose regenerated from dimethylsilyl cellulose

• Experiments at Hasylab and ESRF

• Small-angle scattering arises from microfibril bundles.

• Electron density profile in z-direction (thickness of film)

18.04.23 54

Rossetti et al. Structures of regenerated cellulose films. Biointerphases vol 3 no 4, Dec 2008

Fast experiments with pink synchrotron beam

Kong Q., Wulff M., Lee J.H., Bratos S., Ihee H., Photochemical reaction pathways of carbon tetrabromide in solution probed by picosecond X-ray diffraction. J Am Chem Soc 129, 13584-13591 (2007)

Structure factor and radial distribution function

Carbon nanotube

Koloczek J, Hawelek L, Burian A, et al. Modelling studies of carbon nanotubes - Comparison of simulations and X-ray diffraction data. Journal of Alloys and Compounds Vol 401 Iss1-2, 46-50 SEP 29 2005

Experiment at high energy x-rays

Large scale facilities vs home laboratory

High intensity – short measurement times Example. SAXS milliseconds (home laboratory minutes)

Tunability – special methods like absorption spectroscopy

or anomalous scattering monochromatic radiation,

pink beam,

white beam

Well-collimated beam: better resolution, easier data

analysis Coherence: special methods