Introduction to X-ray Absorption Near Edge Spectroscopy (XANES)

Ritimukta Sarangi SSRL, SLAC Stanford University June 28, 2010

Basics of X-ray Absorption Spectroscopy (XAS)

An edge results when a core electron absorbs energy equal to or greater than its binding energy. Edges are labeled according to the shell the core electron originates from. XAS is an element specific technique.
Cu K-edge ~9000 eV Cu L-edges ~930 eV Cu M-edges ~70-120 eV Fe K-edge ~7000 eV Fe L-edges ~720 eV Fe M-edges ~50-100 eV S K-edge ~2472 eV S L-edges ~200 eV

L-edges K-edge

1s

2s

2p

3s

3p 3d

continuum

X-ray Absorption Spectrum (XANES + EXAFS Region)

Absorption Coefficient (mu)

EXAFS (extended x-ray absorption fine structure) Pre-edge and Edge (XANES)

Geometric Information

Electronic and Geometric Information

XAS or XAFS

Importance of XAS Edges

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Fast data acquisition time and high signal-to-noise ratio. Can be measured at room temperature without depreciation of data quality. The pre-edge region can be used to estimate: !! Ligand-field !! Spin-State !! Centrosymmetry The rising-edge region can be used to estimate: !! Geometric Structure !! Metal-Ligand overlap via Shakedown transitions !! Ligand arrangement in certain cases !! Charge on the metal center

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Interpretation of XAS Edges

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Qualitatively !! Uses edges as a fingerprint of the electronic structure !! Compare to known model complexes !! Use in PCA analysis Molecular Orbital-Based Approach !! Obtain a more quantitative description !! Understand energy and intensity distributions using LF theory !! Works well for bound state transitions !! Fails for rising-edge and beyond. Multiple Scattering-Based Approach !! Required to simulate rising edge !! FEFF, MXAN !! Difficult to relate back to an MO-based picture Band Structure Approach !! Density of States

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Metal K-edge XAS

continuum continuum

M 4p edge M 3d L 3p energy edge pre-edge pre-edge M 1s Metal K-pre-edge absorptions arise due to a quadrupole-allowed dipole-forbidden 1s 3d excitation (!l = 2) - weak Metal K-rising edge absorptions are electric dipole allowed (!l = 1)- Intense

Factors that Affect Metal K-edge Shape and Energy

Oxidation State
Cu(II) Cu(III)

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The rising-edge and the edge maxima shift to higher energy as the oxidation state increases. Important consideration similar ligand system.

Factors that Affect Metal K-edge Shape and Energy

Oxidation State Contd
Fe(II) Fe(II) Ni(II) Ni(III)

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Both Fe samples. What oxidation states do they represent?

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Both Ni samples. What oxidation states do they represent? Ni is special case with little change upon oxidation!

Spin states are different! High-Spin (S=2) and Low-Spin (S=0)

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Factors that Affect Metal K-edge Shape and Energy

Coordination Number and Geometry
1.2

Normalized Absorption

Coordination no:
z

2 Cu

3 Cu

4 Cu

0.8
y

0.4

2-coord Cu(I) 3-coord Cu(I) 4-coord Cu(I)

8980 8990 Energy ( eV ) 9000 9010

x Energy

pz px,y 4px,y,z

px

Py,z

px,y,z

0.0

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Rising edge has strong contribution from the 1s to 4p transition. In special cases where the 4p orbital is low-lying, the energy and intensity of the edge transition can be used to estimate coordination number/geometry

Factors that Affect Metal K-edge Shape and Energy

Covalency
1.2

M 4p M 4p M 3d M 3d L 3p

Normalized Absorption

0.8

0.4

Shakedown
M 1s M 1s

0.0

8980

9000 Energy ( eV )

9020

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Energy and intensity can be correlated with metal-ligand overlap using the VBCI model. In comparable systems: Intensity Covalency Energy 1/Covalency

Factors that Affect Metal K-edge Shape and Energy

Pre-edge Shape and Energy
Normalized Absorption
1.2

0.8
O

0.4

N N N N N Fe N N N

N N

Fe

N N

N N

Fe O

0.0

7110

7130 Energy ( eV )

7150

7109

7111

7113

7115

Energy ( eV )

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Pre-edge intensity

Deviation from Centrosymmetry

Metal 3d-4p mixing

Pre-edge intensity pattern is dependent on: Spin-State b) Oxidation-State c) Ligand-Field splitting d) Multiplet-Effects Pre-edge intensity-weighted average energy is modulated by Ligand-Field strength

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Metal K-pre-edge: Quantitative Use

!!Pre-edge

intensity

Deviation from Centrosymmetry

Metal 3d-4p mixing

Fe
Sq-py
Normalized Absorption

>

Fe
Td

>

Fe
Sq-Py*

>

Fe
Oh

1.2

Td Oh
0.8

Td 4p orbitals : t2 symmetry 3d orbitals: t2 and e symmetry Mixing = Intense pre-edge Oh 4p orbitals : t1u symmetry 3d orbitals: t2g and eg symmetry No Mixing = Weak pre-edge

0.4
7112 7116

0.0

7110

7130 Energy ( eV )

7150

Metal K-pre-edge Energy

Ligand Field
Normalized Absorption

1.2

Cu 3dx2-y2
0.8

energy

Zeff 2p

0.4
8976 8978 8980 8982

0.0

8980

9000 Energy ( eV )

9020

1s

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Pre-edge intensity-weighted average energy is modulated by Ligand-Field strength Zeff or charge on the metal affects the energy of all energy levels equally, therefore has minimal effect on pre-edge energy position

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Pre-edge Example 1 : Cobalamin

Vitamin B12 derivative: Cobalamin

Problem: Determination of Co-C bond distance in Me-Cobalamin

Pre-edge Example 1 : Cobalamin

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Crystallography consistently gave a long Co-C distance than reasonable.

Question Could the diffraction data have error from beam-damage/decomposition?
8.0 4.0
Me-Cbl H2O-Cbl

1.5
Normalized Absorption

Me-Cbl H2O-Cbl

k3 * EXAFS

1.0

0.0 -4.0 -8.0 0 5 k( )

-1

0.5

7708

7712

7716

10

15

0.0

7750 Energy ( eV )

7850

Me-Cbl and H2O-Cbl have similar EXAFS

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Pre- and rising-edge data distinct

Near-edge data were used to show a) crystal structure was erroneous b) determine the Me-Co distance to atomic resolution.

Data courtesy Prof. Serena DeBeer

Pre-edge Example 2 : MCR

Methyl Coenzyme M Reductase
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1 billion tonnes of methane is generated annually by MCR. Active site contains a Ni-tetrapyrrolic cofactor called F430. Enzymatic activity is observed only in its fully reduced state - Ni(I)

Pre-edge Example 2 : MCR

Proposed Transient Intermediate

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Is a Ni(III)-Me Intermediate formed? If so whats the Ni-Me distance?

Pre-edge Example 2 : MCR

Ni(I) Ni(II) Ni(III)-Me

2.41 2.05 2.25 2.09 2.26

2.08 2.08 2.32

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Do Not confirm Ni(III) state. Do Not show the presence of a Me group in the axial position. Do show increase in coordination #.

Pre-edge Example 2 : MCR

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0.2

Very little shift in edge energies ~0.5 eV shift in pre-edge energy Ni(I) > Ni(II) > Ni(III)
Ni(I) Ni(II) Ni(III)-Me

Normalized Absorption

0.2

0.1

0.1

0.0

8330

8334 Energy ( eV )

8338

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Large difference in pre-edge intensities

Pre-edge Example 2 : MCR

DFT Calculations

Normalized Absorption

0.08

0.04

0.00 8328 8332 Energy ( eV ) 8336

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The high intensity only occurs in the case of a Ni-Me coordination. The energy of the transition is only achieved in the case on Ni(III). The intensity and energy are in the right place when a trans-axial ligand is present.

Near-edge Analysis for Structure Determination

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EXAFS data not available to high k due to very low concentrations? EXAFS data too weak beyond k ~ 10 -1 ? Sample undergoes beam-damage too fast to obtain good quality data? Comparison of data at different temperatures is required? Micro-XANES data with low signal/noise ratio? Near-edge XAS has interesting features, but EXAFS are plain ?

Multiple-Scattering Approach to XANES Data Analysis

MXAN Multiple Scattering XANes
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Full multiple-scattering Theory. The potential is generated using the Muffin-tin approach.
EXAFS: SERIES Solution MXAN: EXACT Solution

"Total="1+ "2+ "n

ALL Scattering Paths

MXAN: Near-edge Analysis

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Method can be applied to dilute samples. ( k =6-7 -1) A full multiple-scattering analysis gives important angular information. Can be applied to higher temperature samples. Since MXAN obtains an exact solution using all possible MS components the bond-distance resolution is infinite.

MXAN: Near-edge Analysis

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Fits are performed on data set : -10 eV to ~200 eV (0 eV = Edge Inflection) Initial structural parameters added as Cartesian or polar coordinates for all the atoms of a model of choice. The structural and non-structural parameters are varied iteratively (shown to have very low interdependence).
z

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R ! "

R sq = ! {[ y (..rn , $n ,..) #y
i =1

th . i

exp . 2 i

] / " }w i / ! w i
i =1

2 i

Geometric Structure of N694C sLO1

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Sepctroscopic studies on the wild-type and the mutant (N694C) protein show that N694C has a distorted active site. However no information is available on whether the S is bound

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(Ile)O (His)N

(Cys)S N(His) Fe O(Gln)

N(His)

Geometric Structure of N694C sLO1

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Structural Possibilities

(Cys)S (His)N N(His) Fe O(Gln) (His)N H 2O

(Cys)S N(His) Fe O(Gln) N(His) (His)N

(Cys)S O O N(His)

Fe

(Gln)

N(His)

N(His)

Geometric Structure of N694C sLO1

1 O/N 1.96 4 O/N 2.12 F=0.136 1 O/N 2.49

1 O/N 1.97 3 O/N 2.12 F=0.150 1 S 2.28

1 O/N 1.97 4 O/N 2.12 1 S 2.71

F=0.138

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The EXAFS fits show that the data are consistent with several different structural models (different coordinations at the Fe site)

MXAN Analysis of N694C sLO1

F=3.71

F=3.91

F=0.95

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MXAN Fits using different models gave error values that were distinctly different to differentiate between the possible local structures. The data reveal that the geometric structure is best described as a 5+1 coordinate structure with 1 long Fe-O(H2O) bond.

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Summary of XANES Talk

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The edge-region of an XAS spectrum provides a powerful spectroscopic tool for geometric and electronic structure elucidation. Information related to: Oxidation State Spin State Covalency Site-symmetry Ligand Field Local Structure A lot is still not known about the rising-edge and near-edge region. Theoretical advances will unlock this region and help us better understand our data in the future.

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Acknowledements
A special thanks to all authors of the articles, which were presented in this talk. SSRL DOE, Office of Basic Energy Sciences SMB program supported by the NIH, NCRR, Biomedical Technology Program, and the DOE, BER.

Thank You For Your Attention

References
Metal K- pre-edge intensity R. G. Shulman et al., Proc. Nat. Acad. Sci., 1976, 73, 1384. T. Westre et al., J. Am. Chem. Soc. 1997, 119, 6297-6314. J.E. Penner-Hahn et al., Chem. Phys. Lett. 1982, 88, 595598. Metal K- pre-edge energy R. Sarangi et. al. J. Am. Chem. Soc. 2006, 128, 82868296. Rising edge-intensities in Cu(I) complexes L.S. Kau et al., J. Am. Chem. Soc., 1987, 109, 6433. Covalency from the rising edge J.L. DuBois et al., J. Am. Chem. Soc. 2000, 122, 5775-5787. Pre-edge EXAMPLE 1 H. A. Hassanin, et al., Dalton Trans., 2010, 39, 10626-10630 Pre-edge EXAMPLE 2 R. Sarangi, et al. Biochemistry 2009, 48, 31463156. MXAN and EXAMPLE http://www.esrf.eu/computing/scientific/MXAN/ R. Sarangi et al., Inorg. Chem., 2008, 47,11543