15.4.

2011
1
Elementary EXAFS analysis
Assuming an isotropic sample and independent particle model the
XAFS data is modelled by:
g(q) = Z N
j
S
j
(q) F
j
(q) exp(-Mq
2
) exp(-2r
j
//
j
(q))
sin(2qr
j
+
j
(q))/r
j
2
N
j
number of neighbours at distancer
j
from the central atom
S
j
is amplitude reduction factor due to many body effects
F
j
(q) the backscattering amplitude
Mdamping factor
/
j
the electron mean free path, and

j
the phase shift.
This formula is called the EXAFS equation.
Elementary EXAFS analysis
The factor exp(-2r
j
//
j
(q)) comes from the life-time of the excited
state.
The factor exp(-Mq
2
) is a temperature factor.
The trigonometric factor arises from the phase difference between
the outgoing and backscattered parts of |f>. Distance difference is
2r
j
.
Distinguishing neighbouring atoms: The backscattering amplitude
F
j
(q) is spesific for an atom and allows identification of the
neighbours of the resonant atom. Complications: the temperature
factor damps the amplitude.
The phase shift
j
(q) depends both on the central atom and the
backscattering atom:
j
(q) = 2
jcentral
(q) +
jback
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Mass absorption coefficient of
Ni
http://physics.nist.gov/PhysRefData/XrayMassCoef/ElemTab/z2
8.html
Sharp discontinuities at
K, LI, LII, LIII, M,
absorption edges
Discontinuities
correspond to
wavelengths of the
incident beam sufficient
to eject an L, M, N
electron from the atom.
Background subtraction
The contribution of non-resonant atoms
and higher shells is subtracted by
extrapolating the pre-edge behaviour in
the EXAFS region.
Try:
3 degree polynomial
Cubic splines
The background below and above the
edge are different.
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Cu foil
Linear fit
to pre-
edge data
works
here fine.
8.5 9 9.5 10 10.5 11 11.5
-0.5
0
0.5
1
1.5
2
2.5
3
3.5
fitted background
Data from Bruce Ravels EXAFS course
http://cars9.uchicago.edu/~ravel/talks/course/exercises.html
E [keV]
Cu foil
Not very
serious
fitting trial
with a third
degree
polynomial
8.5 9 9.5 10 10.5 11 11.5
-0.5
0
0.5
1
1.5
2
2.5
3
Fitted polynomial
Data from Bruce Ravels EXAFS course
http://cars9.uchicago.edu/~ravel/talks/course/exercises.html
E [keV]
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Cu foil
Edge
position by
the point of
inflection
method.
E0 =8.979
keV
8.5 9 9.5 10 10.5 11 11.5
-200
-100
0
100
200
300
400
500
Derivative for finding E0
Data from Bruce Ravels EXAFS course
http://cars9.uchicago.edu/~ravel/talks/course/exercises.html
X(k)
The functiong is damped rapidly.
Weighting with k, k
2
or k
3
is used.
For analysing the data, calculation of
FT|Xk
n
| is useful.
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Cu foil
Weighting with
q
3
2 4 6 8 10 12 14 16 18
-150
-100
-50
0
50
100
\Chi function
Data from Bruce Ravels EXAFS course
http://cars9.uchicago.edu/~ravel/talks/course/exercises.html
q [1/]
Calculated g-function of Co
Tabulated values of
backscattering
amplitudes and
phases 2
jcentral
(q)
and
jback
from Datax-
database.
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Radial function
Since X-function consists of sin-functions,
Fourier transform reveals the frequences.
Modified radial distribution function
rdf(r) ~ } w(k) k
n
X(k) exp(ikr) dk,
where w(k) is a filter function. The integration is
from the minimum of k to the maximum of k.
The positions do not give real atomic distances.
There is a shift, which depends on the choice of
E
0
and n. That is why fitting is needed.
Examples of filters
Hanning and box filters
Satisfactory filter for X may be
something between: box with
smooth corners
Discrete Fourier transforms of
the filters.
Fourier transforms of Hanning
and Hamming windows do not
show ripples, but are quite
broad smearing the filtered rdf.
0 20 40 60 80 100
0
0.2
0.4
0.6
0.8
1
1.2
1.4


hanning
box
480 490 500 510 520 530 540 550
0
0.2
0.4
0.6
0.8
1


hanning
box
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Cu foil
Pseudo RDF
Blue curve with box
filter
Green curve with
Hanning window
Use as mild filtering
as possible!
0 1 2 3 4 5 6
0
50
100
150
200
250
300
350
pseudo-RDF
Data from Bruce Ravels EXAFS course
http://cars9.uchicago.edu/~ravel/talks/course/exercises.html
R []
One way to examine the data: inverse transform
and compare to experimental X-function
Works for isolated peaks of the
rdf, e.g. 1 coordination shell
Choose the filter carefully!
Box results in ripples
Hamming and Hanning
filters are the other
extreme.
Pt
O
r = 2
Serimaa et al. Inorg. Chem., 36 (24),
5574 -5579, 1997
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Example.
Retention of Cu iby lignocellulosic
material (LS).
(a) Radial structure function of
the first shell and its numerical
simulation.
(b) First-shell fit of the EXAFS
function of CuLS system.
Experimental first-shell filtered
data in the 0.85-2.24 range
(dotted line) and best fit (solid
curve) modeled as Cu-O
contributions. Experimental
phase and amplitude functions
were extracted from the
EXAFS spectrum of the
Cu(CH
3
CO
2
)
2
reference
compound.
L. Dupont et al. EXAFS and XANES Studies of Retention of Copper and Lead
by a Lignocellulosic Biomaterial Environ. Sci. Technol. 36, 2002, 5062-5066.
Fitting a model
Fit a multi-shell model to X(k) k
n
The radial function may contain spurious
oscillations, thus it is better to fit a model
to k-space function. Theoretical
amplitudes and phase functions are used.
The parameters to be determined are the
atomic distances, coordination numbers
and Debye-Waller factors.
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Pt-complexes
Serimaa et al. Inorg. Chem., 36 (24), 5574 -
5579, 1997
Fourier transform FT(X k3) from EXAFS
data of platinum uridine green sulfate
(exp. x-marks) with models (solid line):
(a) mononuclear model (2), (b) dinuclear
model (3), (c) mixture model.
Pt-N, Pt-O
Pt-Pt, Pt-light
element
The information content
Number of parameters one can reliably
extract
N = (2/n) K R
where K and R are the Fourier transform
and the fitting range
Example. K range is (3.0-12.0) 1/, and R
range (1.0-3.0) , number of parameters
11-12.
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Programs: FEFF
Rehr, J . J .; Albers, R. C.; Zabinsky, S. I.
Phys. Rev. Lett. 1992, 69, 3397.
Ankudinov, A. L.; Bouldin, C.; Rehr, J . J .;
Sims, J .; Hung, H. Phys. Rev. B 2002, 65,
104107
FEFF project home page
http://leonardo.phys.washington.edu/feff/
FEFF
FEFF is an automated program for ab
initio multiple scattering calculations of X-
ray Absorption Fine Structure (XAFS) and
X-ray Absorption Near-Edge Structure
(XANES) spectra for clusters of atoms.
The code yields scattering amplitudes and
phases to be used in analysis of
experimental XAS data.
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FEFF phase shifts
Self-consistent or overlapped atom
potentials are necessary for the calculation
of the scattering phase shifts.
Self-consistent calculations are often
essential for XANES, especially for cases
with significant charge transfer.
Although the effect of self-consistency on
EXAFS is small, such calculations give an
accurate determination of E
0
.
FEFF
Ab initio self-consistent real space multiple-scattering
code for simultaneous calculations of x-ray-absorption
spectra and electronic structure.
Extended X-ray-absorption fine structure (EXAFS), full multiple
scattering calculations of various X-ray absorption spectra (XAS)
and projected local densities of states (LDOS)
The spectra include x-ray absorption near edge structure
(XANES)
X-ray natural and magnetic circular dichroism (XNCD and
XMCD), spin polarized X-ray absorption spectra (SPXAS and
SPEXAFS), non-resonant X-ray emission spectra (XES),
X-ray scattering amplitude (Thomson and anomalous parts)
Calculation of electron energy loss spectroscopy (EELS) is also
possible, but is much less automated in this release.
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Example. Multiple scattering
Fourier transform
associated with a
metallic platinum
foil calculated with
and without multiple
scattering
contributions.
Bazin et al. J . Phys.
Chem. B 1997, 101,
11040-11050.
Program Viper
K.V.Klementiev, HASYLAB / DESY
The program is designed for XAFS-
data processing with maximum visual
control
Preliminary data analysis
glitch- and step-corrections
Energy calibration
Deconvolution of absorption coefficient
with monochromator resolution curve
and/or core-hole lifetime
deconvolution.
The extraction of EXAFS-part, (k).
(i) by a spline drawn through the knots
varied to minimize the low-r EXAFS FT
part;
(ii) by a smoothing spline and
(iii) by a Bayesian smoothing curve.
(k) extraction can be verified
simultaneously by Fourier-transform.
(k) or (E) can be corrected by user-
defined functions f(k) or f(E) to correct,
for example, the fluorescence self-
absorption.
The function f(E) may refer to the
theoretical tables of absorption
coefficients incorporated into the
program.
Errors of (k) are calculated by various
ways in order to validate the spectrum
extension.
Fast Fourier analysis, k-weighting,
several windowing functions.
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Program Viper
Fitting procedures for the first few coordination shells:
By ordinary EXAFS formula. Multiple-edge refinement is possible.
Using the radial distribution function RDF(r) specified by a user-
defined formula, parameters of which then are varied.
Using the oscillatory potential U(r) of the absorber-scatterer pair.
All fit parameters can be fixed and constrained or related to the
homogeneous parameters of the other shells (wells) by user-defined
functions.
Fitting is done either in k- or in r-space.
Scattering amplitudes and phases must be calculated by other
programs (FEFF format is recognized) or can be extracted by
VIPER from a reference spectrum.
Statistical 2- and F- tests can be performed at user request.
Program GNXAS
Filipponi, A. & Di Cicco, A. (1995). Phys.
Rev. B, 52, 15135-15149.
Filipponi, A., Di Cicco, A. & Natoli, C. R.
(1995). Phys. Rev. B, 52, 15122-15134.
Filipponi, A., Di Cicco, A., Tyson, T. A. &
Natoli, C. R. (1991). Solid State Commun.
78, 256-268
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Programs: GNXAS
The GNXAS package for EXAFS data analysis is based
on multiple-scattering (MS) calculations and a rigorous
fitting procedure of the raw experimental data.
The main characteristic of the software are:
Atomic phase shifts calculations in the muffin-tin approximation
based on atom self-consistent relativistic calculations. Account
for the neighbors is taken.
Inclusion of inelastic losses through complex Hedin-Lundqvist
potential.
Calculation of MS signals associated with two, three, and four
atom configurations using advanced algorithms.
GNXAS features
The fitting procedure that allows:
to fit simultaneously any number of spectra containing
any number of edges,
to use directly the raw data without any pre-analysis,
to account for complex background multi-electron
excitation features,
to use various model peaks for the pair, triplet and
quadruplet distribution functions, including non Gaussian
models and extremal cases.
to treat liquid phase or disordered systems and
extract reliable g(r) functions in the short range,
to perform a rigorous statistical error analysis and plot
two-dimensional correlation maps.
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Analysis programs
http://www.esrf.eu/computing/scientific/08-
CARD/CARD.html
A novel code for the analysis of extended x-ray
absorption fine structure (EXAFS) data collected in total
reflection mode (reflEXAFS) is presented.
The procedure calculates the theoretical fine structure
signals appearing in the reflectivity spectrum starting
from the ab initio EXAFS calculations.
These signals are then used in structural refinement
(including multiple scattering paths)
Kemp
A flexible script called KEMP has been developed and
implemented at the XAS beamline at EMBL Hamburg.
Kemp automatically processes fluorescence XAS data.
The script includes dead time correction, energy
calibration, selection of fluorescence detector channels,
as well as the extraction of x-ray absorption near-edge
structure and extended x-ray-absorption fine structure.
The output is quickly available and thus can be included
in the design of further experiments, which results in a
more efficient use of the beam time.
Malgorzata Korbas, Daniel Fulla Marsa, and Wolfram Meyer-
Klaucke. Rev. Sci. Instrum. 77, 063105 (2006)
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Older program EXCURV
EXCURV98 package
Binsted N (1998) EXCURV98: CCLRC Daresbury
laboratory computer program
Binsted N, Strange RW, Hasnain SS (1992) Constrained
and restrained refinement in EXAFS data analysis with
curved wave theory. Biochemistry 31:1211712125
Binsted, N. & Hasnain, S. S. (1996). J. Synchrotron Rad.
3, 185-196
Gurman, S. J ., Binsted, N. & Ross, I. (1984). J. Phys. C,
17, 143-151
Gurman, S. J ., Binsted, N. & Ross, I. (1986). J . Phys. C,
19, 1845-1861
EXAFS of solutions
Direct Modeling of EXAFS Spectra from
Molecular Dynamics Simulations. Palmer, B. J .;
Pfund, D. M.; Fulton, J . L.J . Phys. Chem.;
(Article); 1996; 100(32); 13393-13398.
Understanding the Effects of Concentration on
the Solvation Structure of Ca
2+
in Aqueous
Solution. I: The Perspective on Local Structure
from EXAFS and XANES. Fulton, J . L.; Heald, S.
M.; Badyal, Y. S.; Simonson, J . M.J . Phys.
Chem. A.; (Article); 2003; 107(23); 4688-4696
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Models
A set of polarizable ion-water intermolecular potential models were
developed that accurately describe solvation enthalpies and
structural properties of Ca
2+
and Sr
2+
in aqueous solution.
The molecular dynamics (MD) results were coupled to electron
scattering simulations in order to generate the Ca
2+
and Sr
2+
EXAFS
spectra.
MD-XAFS spectra were found to be in good agreement with the
corresponding experimental measurements including both the ion-
oxygen and the ion-hydrogen distances for the first hydration shell.
This work demonstrates that the combinati on of MD-EXAFS,
and the corresponding experiment measurement provides a
powerful tool i n the analysis of the solvati on structure of
aqueous ionic solutions.
Liem X. Dang et al. EXAFS Spectra of the Dilute Solutions of Ca2+and
Sr2+in Water and Methanol. J . Phys. Chem. B, 107 (50), 14119 -
14123, 2003.