Introduction to X-ray Absorption Spectroscopy

Bruce Ravel
Synchrotron Science Group
National Institute of Standards and Technology
&
Beamline for Materials Measurements
National Synchrotron Light Source II

MSAE E8235x
Columbia University
September 30, 2015

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 This Talk

This is a long talk.

We’ll take a break in the middle.

Cartoon
c Wayno and Dan Piraro
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Part 1

The basic physics and

chemistry of X-ray
Absorption

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This Talk

This talk is an introduction to the inner-shell spectroscopies, XAS and

XRF.

Outline
An overview of the basic physics of inner shell spectroscopies
An introduction to XAS and XRF beamline instrumentation
A flavor of the sorts of science that can be accomplished with XAS and
XRF, including examples from my own research and my beamline.

My hope is that you will leave with a sense of how XAS and XRF might
be applied to your research.

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XAS and XRF

X-ray Absorption Spectroscopy

and
X-Ray Fluorescence spectroscopy

These are inner shell spectroscopies.

Inner shell means that an x-ray Spectroscopy means that some
interacts primarily with a deep-core aspect of the interaction changes as
electron rather than with a valence a function of photon energy.
electron.

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XAS and XRF

X-ray Absorption Spectroscopy

and
X-Ray Fluorescence spectroscopy

These are inner shell spectroscopies.

Inner shell means that an x-ray Spectroscopy means that some
interacts primarily with a deep-core aspect of the interaction changes as
electron rather than with a valence a function of photon energy.
electron.

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XAS and XRF

X-ray Absorption Spectroscopy

and
X-Ray Fluorescence spectroscopy

These are inner shell spectroscopies.

Inner shell means that an x-ray Spectroscopy means that some
interacts primarily with a deep-core aspect of the interaction changes as
electron rather than with a valence a function of photon energy.
electron.

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The basic physical process in XAS and XRF

n=4 N edges
n=3 M edges
n=2 L edges
X-
ra
y
in

n=1 K edge

1 An incoming photon interacts with a deep-core electron. Shown here, a 1s

electron is excited for a K-edge spectrum.
2 The deep-core electron is promoted to some unoccupied state above the
Fermi energy, propagates away, and leaves behind a core-hole.
3 A short time later (1 or 2 femtoseconds), a higher-lying electron decays
into the core-hole and emits a photon.
4 Alternately, the energy from the higher-lying electron can be used to emit
an Auger electron.
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The basic physical process in XAS and XRF

n=4 N edges
n=3 M edges
n=2 L edges

n=1 K edge

1 An incoming photon interacts with a deep-core electron. Shown here, a 1s

electron is excited for a K-edge spectrum.
2 The deep-core electron is promoted to some unoccupied state above the
Fermi energy, propagates away, and leaves behind a core-hole.
3 A short time later (1 or 2 femtoseconds), a higher-lying electron decays
into the core-hole and emits a photon.
4 Alternately, the energy from the higher-lying electron can be used to emit
an Auger electron.
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The basic physical process in XAS and XRF

X-r
ay n=4 N edges
o ut n=3 M edges
n=2 L edges

n=1 K edge

1 An incoming photon interacts with a deep-core electron. Shown here, a 1s

electron is excited for a K-edge spectrum.
2 The deep-core electron is promoted to some unoccupied state above the
Fermi energy, propagates away, and leaves behind a core-hole.
3 A short time later (1 or 2 femtoseconds), a higher-lying electron decays
into the core-hole and emits a photon.
4 Alternately, the energy from the higher-lying electron can be used to emit
an Auger electron.
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The basic physical process in XAS and XRF

Au n=4 N edges
g er
e-
ou n=3 M edges
t
n=2 L edges

n=1 K edge

1 An incoming photon interacts with a deep-core electron. Shown here, a 1s

electron is excited for a K-edge spectrum.
2 The deep-core electron is promoted to some unoccupied state above the
Fermi energy, propagates away, and leaves behind a core-hole.
3 A short time later (1 or 2 femtoseconds), a higher-lying electron decays
into the core-hole and emits a photon.
4 Alternately, the energy from the higher-lying electron can be used to emit
an Auger electron.
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Elements and Beamlines

K- or L-edges measured at a soft-X-ray beamline

K-edges measured at a hard-X-ray beamline
L-edges measured at a hard-X-ray beamline

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Characteristic energies
Each element has a characteristic set of excitation and fluorescence energies.

Iron: Z=26

Edge Energy (eV) Line Transition Energy (eV) Strength

K 7112 Kα1 K-L3 6405.2 0.580
L3 706.8 Kα2 K-L2 6392.1 0.294
L2 719.9 Kβ1 K-M3 7059.3 0.082
L1 844.6 Kβ3 K-M2 7059.3 0.043
Kβ5 K-M4,5 7110.0 0.001

Uranium: Z=92

Edge Energy Line Transition Energy Strength

K 115606 Lα1 L3-M5 13614.0 0.686
L3 17166 Lα2 L3-M4 13438.0 0.077
L2 20948 Lβ2 L3-N4,5 16387.7 0.181
L1 21757 Lβ5 L3-O4,5 17063.2 0.038
Lβ6 L3-N1 15727.0 0.013
L` L3-M1 11618.0 0.005
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A simple picture of X-ray absorption

An incident x-ray of energy E is absorbed, destroying a core electron of
binding energy E0 and emitting a photo-electron with kinetic energy
(E − E0 ). The core state is eventually filled, ejecting a fluorescent x-ray
or an Auger electron.

An empty final state is required.

No available state,
no absorption!
When the incident x-ray energy is
larger than the binding energy,
there is a sharp increase in
absorption.

For an isolated atom, µ(E ) has a sharp step at the core-level binding
energy and is a smooth function of energy above the edge.
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X-ray absorption in condensed matter

The ejected photo-electron can scatter from neighboring atoms. R has
some relationship to λ and there is a phase shift associated with the
scattering event. Thus the outgoing and scattered waves interfere.

The scattering of the photo-electron

wave function interferes with itself.

µ(E ) depends on the density of

states with energy (E − E0 ) at the
absorbing atom.

This interference at the absorbing atom will vary with energy, causing
the oscillations in µ(E ).
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XAS and Valence State

As the valence increases

Mn0 → Mn2+ → Mn3+ → Mn4+
the edge position shifts to higher
energy.

XAS is a direct measure of valence state

Since each element has its own edge energy, an element’s valence can
be measured even in a heterogeneous sample
Since x-rays are deeply penetrating into matter, samples often require
only preparation
No assumption of symmetry or periodicity is made, so the sample can
be crystalline, amorphous, thin film, in solution, surface sorbed, · · · ,
whatever

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XAS and Local Atomic Structure

The different Mn species display big differences
in the fine structure beyond the edge as the
valence increases (Mn0 , Mn2+ , Mn3+ , Mn4+ ).
The white line and subsequent oscillations are
quite different.

The oscillatory portion of the spectrum can be

isolated and ...

... Fourier transformed. This FT function can be

interpreted to yield partial pair distribution
functions of atoms about the absorber. The
Mn-O distances are different for the Mn2+ ,
Mn3+ , and Mn4+ and clearly different from the
Mn-Mn distance in Mn metal.

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XAS and Local Atomic Structure

The different Mn species display big differences
in the fine structure beyond the edge as the
valence increases (Mn0 , Mn2+ , Mn3+ , Mn4+ ).
The white line and subsequent oscillations are
quite different.

The oscillatory portion of the spectrum can be

isolated and ...

... Fourier transformed. This FT function can be

interpreted to yield partial pair distribution
functions of atoms about the absorber. The
Mn-O distances are different for the Mn2+ ,
Mn3+ , and Mn4+ and clearly different from the
Mn-Mn distance in Mn metal.

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XAS and Local Atomic Structure

The different Mn species display big differences
in the fine structure beyond the edge as the
valence increases (Mn0 , Mn2+ , Mn3+ , Mn4+ ).
The white line and subsequent oscillations are
quite different.

The oscillatory portion of the spectrum can be

isolated and ...

... Fourier transformed. This FT function can be

interpreted to yield partial pair distribution
functions of atoms about the absorber. The
Mn-O distances are different for the Mn2+ ,
Mn3+ , and Mn4+ and clearly different from the
Mn-Mn distance in Mn metal.

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Fluorescence from Many Elements

X-ray fluorescence is a spectroscopy in which the incident energy is
fixed and the energy dependence of the secondary photons is measured.

Every element with an edge below the incident energy will fluoresce.
Glass with every 2nd element Ca–Ge, incident energy = 11153 eV

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Fluorescence from A Sediment Sample

Here are the XRF spectra with incident beams above and below the U
LIII edge for a sediment heavily contaminated with uranium.

When combined with a standard measured under identical

conditions, element concentrations can be quantified.

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Using the Fluorescence Spectrum for XAS

We can place a region of interest (ROI) around the U Lα peak and
measure its variation as a function of incident energy.

In this way, we measure signal only from the absorber and reject all
other photons entering the detector.

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Typical optics for an XAS beamline

Collimating mirror

Makes the divergent

rays from the source
parallel, setting the Total external
beam size (20 mm × reflection off a
3 mm at BMM) paraboloid or torroid
surface

All instrumentation images are from FMB Oxford Beamlines Ltd.

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Typical optics for an XAS beamline

Monochromator

Bragg diffraction from

a Si crystal to pass a
narrow bandwidth
from the pink beam
Change energy by
changing angle

All instrumentation images are from FMB Oxford Beamlines Ltd.

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Typical optics for an XAS beamline

Focusing mirror

Total external
reflection from a
torroid surface, bent
such that rays focus
to a spot

All instrumentation images are from FMB Oxford Beamlines Ltd.

Photo of mirror is from ESRF ID09B Introduction to X-ray Absorption Spectroscopy
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Typical optics for an XAS beamline

Harmonic rejection
mirror

Flat mirror redirects

beam from mono and
M2
Set at an angle that
passes the
fundamental but
absorbs harmonics
All instrumentation images are from FMB Oxford Beamlines Ltd.
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A typical XAS hutch (NSLS X23A2, R.I.P.)

Ionization chambers
• Current amplifier

•
X­ray

Filled with inert gas

High Voltage

Gas-filled capacitors. Incoming photon

ionizes a gas molecule. The electron
cascade produces a measurable current.

Transmission XAS
µ(E ) = ln(I0 /It ), i.e. Beers’ Law for
X-rays

Photo is of the hutch from NSLS beamline X23A2 Introduction to X-ray Absorption Spectroscopy
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A typical XAS hutch (NSLS X23A2, R.I.P.)

Energy discriminating
fluorescence detector

Silicon drift diode measures energy of

each photon deposited

Fluorescence XAS
µ(E ) ∝ If /I0

Photo is of the hutch from NSLS beamline X23A2 Introduction to X-ray Absorption Spectroscopy
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A typical XAS hutch (NSLS X23A2, R.I.P.)

Sample stage
• Hard X-rays are deeply penetrating
into matter, so the stage could be:
Cryostat
Furnace
Pressure cell
Electrochemistry cell
Stop-flow cell
Gas flow reactor
etc. etc. etc.

Real samples under real conditions

Photo is of the hutch from NSLS beamline X23A2 Introduction to X-ray Absorption Spectroscopy
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What is meant by “deeply penetrating”?

The Í Center for X-ray Optics provides a tool for estimating the
attenuation of X-rays as they pass through matter.
Í http://henke.lbl.gov/optical constants/atten2.html

So, windows made of low-Z materials can be quite thick and still pass
hard X-rays. This allows deployment of specialized sample environ-
ments for use in XAS experiments.

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Acronyms

XANES X-ray Absorption Near-Edge Structure

NEXAFS Near-Edge X-ray Absorption Fine Structure

XANES and NEXAFS are exactly the same thing. Historically, the soft
X-ray community says “NEXAFS” while the hard X-ray community says
“XANES”.

Both acronyms refer to the portion of the XAS (X-ray Absorption

Spectroscopy) measurement in the vicinity of the absorption edge.

The Extended X-ray Absorption Fine Structure is oscillatory data

extending hundreds of volts above the edge.

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Some vocabulary
Words commonly used to describe specific parts of the XANES spectrum.

pre-edge Small (or large, certainly white line Large, prominent peak
meaningful!) features between the just above the edge, particularly
Fermi energy and the threshold in L or M edge spectra
edge The main rising part of XAS
spectrum
near-edge Characteristic features
above the edge
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Part 2

Understanding XANES

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Speciation at a glance: Coordination

Here is Cr K edge data for tetragonally coordinated, hexavalent
K2 CrVI O7 and hexagonally coordinated, trivalent CrIII
2 O3 . Trivalent Cr is
insoluble and non-toxic. Hexavalent Cr is readily soluble and highly
toxic.

K2 CrO7

Cr2 O3

It is very easy to tell “good” Cr from “bad” Cr in a XANES measurement.

data from Í http://cars9.uchicago.edu/~newville/ModelLib/search.html Introduction to X-ray Absorption Spectroscopy

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Speciation at a glance: Crystallinity

SiO2 is found in two forms∗ under standard conditions: crystalline (the
mineral quartz) and amorphous (common glass).

Again, these are readily distinguished by a XANES measurement.

∗ Wikipedia identifies 14 other metastable, high-T, or high-P forms of SiO .
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Speciation at a glance: Oxidation

There is an 11 eV shift from S2− to S6+

with lots of variation among species.
S speciation is of importance across a
broad range of disciplines, including life
science, catalysis, petroleum science,
photovoltaics, environmental science and
more.
P and Cl are similarly rich in their XAS.

Sulfur K-edge x-ray absorption spectroscopy of petroleum asphaltenes and model

compounds, G.N. George, M.L. Gorbaty, J. Am. Chem. Soc. (1989) 111:9,
3182 Í DOI: 10.1021/ja00191a012 Introduction to X-ray Absorption Spectroscopy
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Oxidation and edge position

There is a relationship between 3.5 0

Re metal
4+
Re O2

Edge position (eV)

Re6+O3
formal valence of a metal and 3 NH4Re7+O4

the position of the edge in the

2.5

Normalized Absorption
XANES spectrum. Here is Re
2
metal along with 4+, 6+, and 0 1 2 3 4 5 6 7
Formal valence
7+ oxides of Re. 1.5

The shift to higher energy is, to 1

first order, a Coulomb effect. 0.5

Less charge on the atom means

0
10510 10520 10530 10540 10550 10560 10570 10580 10590 10600
less screening of the core. Energy (eV)

Some more examples:

Mo S.P. Cramer et al. J. Am. Chem. Soc., 98:5, pp 1287 (1976)
Í DOI: 10.1021/ja00421a053
V J. Wong et al. Phys. Rev. B30, 5596–5610 (1984) Í DOI: 10.1103/PhysRevB.30.5596

Simultaneous XAFS measurements of multiple samples, B. Ravel, C. Scorzato, D.P.

Siddons, S.D. Kelly and S.R. Bare, J. Synchrotron Rad. (2010) 17, 380-385
Í DOI: 10.1107/S0909049510006230 Introduction to X-ray Absorption Spectroscopy
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Mixed phases

Here we see trivalent V2 O3 ,

pentavalent V2 O5 and an
unknown Vanadium
compound plotted together.

Like in the Cr example, we see a distinct difference between

6-coordinated and 4-coordinated V.

Our unknown is partially reduced, as can be seen by the reduction in

pre-edge peak and the left-ward shift of the main edge.

Later we will discuss ways of determining the content of the unknown.

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Evolution of redox state

The edge features are often large enough that their evolution can be
measured in an in situ experiment.

Here we see the kinetics of

CrIII → CrVI oxidation by
Mn oxide over the course of
four minutes of reaction
time. Each scan was
measured in 3 second.

The in situ experiment could involve a chemical reaction, a change in

temperature, electrochemical cycling, and so on.
Kinetics of Chromium(III) Oxidation by Manganese(IV) Oxides Using Quick Scanning
X-ray Absorption Fine Structure Spectroscopy (Q-XAFS), G. Landrot, M.
Ginder-Vogel, and D.L. Sparks, Environ. Sci. Technol., (2010) 44:1, pp 143-149
Í DOI: 10.1021/es901759w Introduction to X-ray Absorption Spectroscopy
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Ligands

We see a significant edge

shift between aqueous As3+
and aqueous As5+ , as we
expect. Note that the As3+
and As5+ methionine
solutions are similar, but
shifted to lower energy.

The same shift is seen

between divalent hematite
(Fe2 O3 ) and divalent pyrite
(FeS2 ).

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Fingerprinting

Fingerprint, tr.v.
To identify by means of a distinctive mark or characteristic.

One of the most powerful uses of XANES data is to simply identify what is in
front of the beam.
Looking back at the CrIII /CrVI example, what might you say about the valence of
the chromium contained in coal combustion residue?

K2 CrO7

Cr2 O3

Quantifying Hazardous Species in Particulate Matter Derived from

Fossil-Fuel Combustion, F.E. Huggins, et al., Environ. Sci. Technol.
(2004) 38:6, 1836 Í DOI: 10.1021/es0348748 Introduction to X-ray Absorption Spectroscopy
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Categorizing spectra

In an study of Ti-containing standard materials, the different

coordination environments were found to aggregate when plotting
pre-edge peak height v. peak position.

Here we see the data from

the reference below along
with Ti K-edge data from
various Zirconolite
(CaZrTi2 O7 ) samples,
including the one from the
self-absorption slide.

F. Farges, G.E. Brown Jr., J.J. Rehr, Coordination chemistry of Ti (IV) in silicate glasses and melts:
I. XAFS study of titanium coordination in oxide model compounds , Geochim. Cosmochim/ Acta,
60:16, 3023, 1996, Í DOI: 10.1016/0016-7037(96)00144-5 Introduction to X-ray Absorption Spectroscopy
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XANES and disorder

The details of the XANES can often give information about structural
disorder about the absorbing atom.

EuTiO3 is a true cubic perovskite. PbTiO3 is a tetragonally distorted

perovskite with substantial disorder in the oxygen octahedron.
Consequently, the pre-edge peak is much larger for PbTiO3 .

B. Ravel, E. A. Stern, R. I. Vedrinskii, V. Kraizman, Local structure and the

phase transitions of BaTiO3 Ferroelectrics, 206:1 (1998) 407,
Í DOI: 10.1080/00150199808009173 Introduction to X-ray Absorption Spectroscopy
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Why are local disorder and the pre-edge peak

related?

XAS is a dipole transition. The photoelectron changes angular momentum

by 1: ` ± 1.
For a K-edge spectrum, the initial state is s: ` = 0. Thus the final state
must be ` = 1.
Ti has a filled p shell but a completely empty d shell.
With centro-symmetry, as in a true perovskite, the p and d states cannot
hybridize. Broken symmetry leads to mixing of p and d states around the
Fermi level.
Disorder-driven admixture of d character results in an enhanced pre-edge
peak.

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Analysis

There are a number of ways to get quantitative results from XANES

spectra. Here’s an incomplete list:
Linear Combination Fitting
Interpret data by comparison with standards
Peak Fitting
Fit peak-like and step-like line-shapes to the XANES data
Principle Components Analysis
Decompose an ensemble of data into a mathematical basis
Difference Spectra
Subtract one normalized spectrum from another

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LCF

The working assumption of LCF

The spectrum from an unknown sample can be understood as a linear
superposition of the spectra of two or more known samples.

That is:

+ = +

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Economic geology (I)

One way that gold deposits form is by having Au chloride fluids rise
from the deep earth, wash over cyanobacteria colonies, and reduce to
metallic gold.

Before
We simulated this process at the
Au3+Cl beamline by exposing cyanobacteria
to an Au3+ solution and “watching”
the evolution of the Au XAS from
Exposed Au3+ to Au0 .

Questions
What is the rate constant?
After
Is there an intermediate species?

M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous

Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol.
40(20) p. 6304-6309. (2006) Í DOI: 10.1021/es061040r Introduction to X-ray Absorption Spectroscopy
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Economic geology (II)

Over the course of the time series,

We see that 7 minutes after
the white line ∼ 11921 shrinks
injection, the data strongly
while the bump ∼ 11945 grows,
resemble the Au3+ Cl. After one
suggesting the reduction to Au
week, the data resemble Au metal.
metal.

M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous

Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol.
40(20) p. 6304-6309. (2006) Í DOI: 10.1021/es061040r Introduction to X-ray Absorption Spectroscopy
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Economic geology (III)

We can analyze these data as a We can plot out the contributions

linear combination of species, from these species as a function of
including Au3+ Cl, Au metal, and time to get a sense of reaction rates.
Au1+ sulfide.

M. Lengke et el., Mechanisms of Gold Bioaccumulation by Filamentous

Cyanobacteria from Gold(III)-Chloride Complex, Environ. Sci. Technol.
40(20) p. 6304-6309. (2006) Í DOI: 10.1021/es061040r Introduction to X-ray Absorption Spectroscopy
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Peak fitting

The working assumption of peak fitting

A spectrum can be meaningfully deconstructed into a set of step-like
(atan or erfc) and peak (Gaussian, Lorentzian, Voight) functions.

In this case, various Gaussians are interpreted

as the main 1s-π ∗ or Rydberg/mixed valence
transitions and two higher energy (1s-2π ∗ )
transition in the C K-edge XANES of a
sediment.

This sort of analysis is most meaningful when performed across an

ensemble of related data. The drawback is that the physical
significance of the line-shapes is sketchy, at best.
T. Schäfer, et al., Organic Geochemistry, 36:4, (2005) 567, Í DOI: 10.1016/j.orggeochem.2004.10.011 Introduction to X-ray Absorption Spectroscopy
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XANES Information XANES Fingerprinting XANES Analysis

XANES: Principle Components Analysis

PCA is a bit of linear algebra which breaks down an ensemble of related data
into abstract components.

The components can then be used to try to construct a standard as a test to see
whether that standard is present in the ensemble.

The number of species

represented in the
ensemble is related to the
number of statistically
significant components.

S.R. Wasserman, J. Phys. IV France (1997) C2-203-C2-205; Í DOI: 10.1051/jp4/1997163

S.R. Wasserman et al., J. Synchrotron Rad. (1999) 6, 284-286; Í DOI: 10.1107/S0909049599000965
+ references therein Introduction to X-ray Absorption Spectroscopy
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Difference Spectra
Difference spectra
Subtract one spectrum from another.

The most common use is for X-ray Magnetic Difference spectra can also be
Circular Dichroism (XMCD) used to highlight a subtle
change in a data sequence.

The areas under the difference spectra tell you

about moment and magnetic ordering.
Here, hydogenation of the Pt
X-ray magnetic circular dichroism study on CeFe2, A. Delobbe, et al.,
Europhys. Lett. 43 320 (1998), Í DOI: 10.1209/epl/i1998-00359-2
nanoparticles alters the Pt DOS
Pt data courtesy of Simon Bare Introduction to X-ray Absorption Spectroscopy
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Part 3

Understanding EXAFS

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A simple picture of X-ray absorption

An incident x-ray of energy E is absorbed, destroying a core electron of
binding energy E0 and emitting a photo-electron with kinetic energy
(E − E0 ). The core state is eventually filled, ejecting a fluorescent x-ray
or an Auger electron.

An empty final state is required.

No available state,
no absorption!
When the incident x-ray energy is
larger than the binding energy,
there is a sharp increase in
absorption.

For an isolated atom, µ(E ) has a sharp step at the core-level binding
energy and is a smooth function of energy above the edge.
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X-ray absorption in condensed matter

The ejected photo-electron can scatter from neighboring atoms. R has
some relationship to λ and there is a phase shift associated with the
scattering event. Thus the outgoing and scattered waves interfere.

The scattering of the photo-electron

wave function interferes with itself.

µ(E ) depends on the density of

states with energy (E − E0 ) at the
absorbing atom.

This interference at the absorbing atom will vary with energy, causing
the oscillations in µ(E ).
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Computing X-ray Absorption from First

Principles
In XAS we measure the dipole mediated[1] transition
of an electron in a deep core[2] state |ii into an
unoccupied[3] state |f i:
1. A photon interacts
with an electron
Fermi’s Golden Rule 2. Typically a 1s, 2s, or
EfP
>EF  2 2p electron
µ(E ) ∝ hf |ˆ
 · r|ii δ(Ef ) 3. A bound or
f continuum state not
already containing
Broadly speaking, there are two ways to solve this an electron
equation: 4. Easy — basic
quantum mechanics
1 Accurately represent |ii[4] and |f i[5] , then evaluate the
5. Hard work, lots of
integral directly. This is the approach taken, for computation
example, by molecular orbital theory. 6. G is also called a
Green’s function.
2 Use multiple scattering theory, AKA propagator
formalism[6] :
µ(E ) ∝ − π1 Im hi|ˆ
∗ · r G(r , r 0 ; E )ˆ
 · r 0 |iiΘ(E − EF ).

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Real Space Multiple Scattering

In multiple scattering theory, all the hard work is in computing the

Green’s function.
G the function that describes all possible ways for a
photoelectron to interact with the surrounding atoms
G0 the function that describes how an electron propagates
between two points in space
t the function that describes how a photo-electron scatters
from a neighboring atom

Expanding the Green’s function

−1 0
G = 1 − G0 t G (XANES)
=G0 + G0 t G0 + G0 t G0 t G0 + G0 t G0 t G0 t G0 + ... (EXAFS)

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Scattering Paths

−1 0
Full multiple scattering (XANES): Solving G = 1 − G0 t G
considers ALL paths within some cluster of atoms:
single scattering path double scattering path triple scattering path
x x x x x x x x

(2 legs) (3 legs) (4 legs)

EXAFS path expansion

The clever thing about feff is that each term is further expanded as
a sum of all paths of that order.
G0 t G0 is expanded as a sum of single scattering paths
G0 t G0 t G0 is a sum of all double scattering paths
and so on.

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Real space multiple scattering in pictures

Here are some examples (in two
dimensions) of single, double, and
triple scattering paths.
For SS, feff expands G0 t G0 ,
computing the three SS paths
shown and all others (up to some
maximum length).
SS and collinear MS paths tend to
be the dominant contributions to
the EXAFS.

The trick to EXAFS analysis

Somehow evaluate each path and choose which ones to include in a
fit.

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Real space multiple scattering in pictures

Here are some examples (in two
dimensions) of single, double, and
triple scattering paths.
For SS, feff expands G0 t G0 ,
computing the three SS paths
shown and all others (up to some
maximum length).
SS and collinear MS paths tend to
be the dominant contributions to
the EXAFS.

The trick to EXAFS analysis

Somehow evaluate each path and choose which ones to include in a
fit.

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The EXAFS equation

For each kind of path, we evaluate the EXAFS equation:
2 2
(NΓ S02 )FΓ (k)e −2σΓ k
χ(k, Γ) = sin (2kRΓ + ΦΓ (k))e −2RΓ /λ(k) (1)
2 kRΓ2
X
χtheory (k) = χ(k, Γ) (2)
Γ

RΓ = R0,Γ + ∆RΓ (3)

p
k =N (E0 − ∆E0 ) (4)

The terms in blue come from theory. (I use a thing called feff).
feff treats SS and MS paths equivalently. FΓ and φΓ are the effective
scattering amplitude and phase shift for the path.

The strategy of EXAFS analysis

In ifeffit the terms in red are not themselves the fitting parameters.
They are written in terms of the actual fitting parameters.

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FeS2 structure
The Fe atom is surrounded by an
octahedron of S atoms
6 S nearest neighbors at 2.257 Å
6 S next nearest neighbors at
3.445 Å
2 S scatterers at 3.594 Å
12 Fe scatterers at 4.167 Å

Somehow add up the contributions

from each of the scatterers and from
all the MS paths involving those
scatterers.

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Path expansion
2 2
(NΓ S02 )FΓ (k)e −2σΓ k
χ(k, Γ) = sin (2kRΓ + ΦΓ (k))e −2RΓ /λ(k) (1)
2 kRΓ2
X
χtheory (k) = χ(k, Γ) (2)
Γ

RΓ = R0,Γ + ∆RΓ (3)

p
k =N (E0 − ∆E0 ) (4)

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Path expansion
2 2
(NΓ S02 )FΓ (k)e −2σΓ k
χ(k, Γ) = sin (2kRΓ + ΦΓ (k))e −2RΓ /λ(k) (1)
2 kRΓ2
X
χtheory (k) = χ(k, Γ) (2)
Γ

RΓ = R0,Γ + ∆RΓ (3)

p
k =N (E0 − ∆E0 ) (4)

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Minerology (I)
A deep understanding of the nuclear fuel cycle requires study of “exotic”
pentavalent uranium minerals that can form under specific mine or
storage facility conditions. One such mineral,
UV (H2 O)2 (UVI O2 )2 O4 (OH)+4·H2 O, has recently been synthesized.

XRD is an indirect measure of valence — XAS is a direct measure!

N. Belai et el., Pentavalent Uranium Oxide via Reduction of [UO2 ]2+
Under Hydrothermal Reaction Conditions, Inorg. Chem., 2008, 47 (21),
pp 10135-10140, Í DOI: 10.1021/ic801534m Introduction to X-ray Absorption Spectroscopy
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Minerology (II)
XAS on UV (H2 O)2 (UVI O2 )2 O4 (OH)+4·H2 O

XANES data EXAFS analysis

We see evidence of UV by the The crystal structure refined from the

intermediate edge position between our XRD is consistent with the EXAFS
UIV and UVI standards. data.
N. Belai et el., Pentavalent Uranium Oxide via Reduction of [UO2 ]2+
Under Hydrothermal Reaction Conditions, Inorg. Chem., 2008, 47 (21),
pp 10135-10140, Í DOI: 10.1021/ic801534m Introduction to X-ray Absorption Spectroscopy
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Dielectric materials (I)

Tantalum oxynitrides are a class of dielectric materials with high K

which is tunable by selection of the A cation. By mixing A cations, a
temperature-constant dielectric is possible.

First principles DFT on BaTaO2 N suggests that the different ionic radii
of O and N introduce substantial disorder around the Ta atom.
B. Ravel et al., Role of local disorder in the dielectric response of
BaTaO2 N, Phys. Rev. B73, p. 184121 (2006),
Í DOI: 10.1103/PhysRevB.73.184121 Introduction to X-ray Absorption Spectroscopy
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Dielectric materials (II)

The DFT results in a rather complex coordination environment about the

Ta atom — much more complex than the simple perovskite structure.

With some effort, this complexity can be incorporated into the data
analysis. The EXAFS data are shown to be (mostly) consistent with the
DFT results.
B. Ravel et al., Role of local disorder in the dielectric response of
BaTaO2 N, Phys. Rev. B73, p. 184121 (2006),
Í DOI: 10.1103/PhysRevB.73.184121 Introduction to X-ray Absorption Spectroscopy
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EXAFS analysis can be quite elaborate...

Manganese zinc ferrite

nanoparticles
Each element can occupy each
either metal site
Oxygen vacancies can exist
Oxygen Data collected at 3 edges and on
Octahedral various sample preparations
site A fitting model was created using
Tetrahedral all the data simultaneously and
site considering occupancies of each
metal on each site, oxygen
vacancy, and nanoparticle
undercoordination

S. Calvin et el., Multiedge refinement of extended x-ray-absorption fine structure of manganese zinc
ferrite nanoparticles, Phys. Rev. B 66(22) p. 224405. (2002), Í DOI: 10.1103/PhysRevB.66.224405
Ferrite image from Í http://wikis.lib.ncsu.edu/index.php/Image:Size21.png
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Part 4

A real-world example

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My vegetable garden

When I bought my house, there was a wooden deck off the dining room.
I replaced this with a paving stone patio and converted the adjacent
plot of ground into a vegetable garden.

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Wood preservative

The wood used to make the deck was

treated with the wood preservative
chromated copper arsentate (CCA), which
is chromium-bearing analogue of copper
orthoarsente, Cu3 (AsO4 )2 ·4H2 O.

CCA-treated wood is known to leach all three elements into surround-

ing soils. I had some questions:
1 How much As is in the soil? Is it higher near the patio than elsewhere
in the garden? (Use XRF)
2 What chemical species is the As in the soil? (Use XAS)

The orthoarsenate image is from Wikimedia commons and is in the public domain.
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XRF spectra
I took soil samples from a few centimeters below the
surface from a spot adjecent to the old deck and from a
spot 5 meters away and slightly uphill.
Here are the XRF spectra from those two spots:

There is a clear enhancement of both As and Cr in the soil adjacent to

the old deck. The As is enhanced roughly two-fold.
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As standards
As a point of reference, here are the XAS spectra from two inorganic As
standards, As3+ 5+
2 O3 and As2 O5 .

Note that the edge of As5+ standard is shifted substantially to higher

energy and that the first peak is much enhanced.
As5+ is water soluble, thus more mobile than As3+ .
Also As5+ is quite toxic.
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XAS from the soil samples

Here are the raw µ(E ) data from

the two soil locations. Sure enough,
the signal from the site adjacent to
the old deck is enhanced by about
a factor of 2.

Should I be worried about eating produce from my garden?

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XAS from the soil samples

Here are the raw µ(E ) data from Here are the normalized data
the two soil locations. Sure enough, compared to standards. The As is
the signal from the site adjacent to slightly reduced, but predominantly
the old deck is enhanced by about As5+ . As in soil is well known to
a factor of 2. bind to soil particles as As5+ .

Should I be worried about eating produce from my garden?

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XAS from the soil samples

Here are the raw µ(E ) data from Here are the normalized data
the two soil locations. Sure enough, compared to standards. The As is
the signal from the site adjacent to slightly reduced, but predominantly
the old deck is enhanced by about As5+ . As in soil is well known to
a factor of 2. bind to soil particles as As5+ .

Should I be worried about eating produce from my garden?

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XRF spectra from plant leaves

Here are XRF spectra

from the leaf of a squash
plant growing in the soil
adjacent to the old deck.

Although toxic As5+ is present in the soil in elevated quantities, very

little is taken up by the plants growing that soil.

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XRF spectra from plant leaves

Here are XRF spectra

from the leaf of a squash
plant growing in the soil
adjacent to the old deck.

Although toxic As5+ is present in the soil in elevated quantities, very

little is taken up by the plants growing that soil.

The squash were delicious!

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More information

About NSLS-II
Í http://www.bnl.gov/ps
About synchrotron science
Í http://www.lightsources.org/
About X-ray Absorption Spectroscopy
Í http://www.xafs.org/
Í XAFS for Everyone by Scott Calvin

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Information about XAS

Í http://xafs.org/Tutorials

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Free∗ XAS software

Í http://bruceravel.github.io/demeter/

∗ Free of cost, freely available source code, freely redistributable

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