Introduction to X-ray Absorption

Near Edge Spectroscopy (XANES)

Ritimukta Sarangi SSRL, SLAC

Stanford University June 28, 2010

1s 2s 2p 3p 3s 3d continuum

K-edge

L-edges

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.

Basics of X-ray Absorption Spectroscopy (XAS)

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

Pre-edge and Edge (XANES)

EXAFS (extended x-ray absorption fine structure)

XAS or XAFS

Abs

orpt

ion

Coe

ffici

ent (

mu)

Electronic and Geometric Information

Geometric Information

X-ray Absorption Spectrum (XANES + EXAFS Region)

  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

Importance of XAS Edges

  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

Interpretation of XAS Edges

Metal K-edge XAS

L 3p M 3d

M 4p

M 1s

ener

gy

continuum continuum

edge

edge

pre-edge

pre-edge

Metal K-pre-edge absorptions arise due to a quadrupole-allowed dipole-forbidden 1s 3d excitation (Δl = ±2) - weak Metal K-rising edge absorptions are electric dipole allowed (Δl = ±1)- Intense

Factors that Affect Metal K-edge Shape and Energy

Oxidation State

  The rising-edge and the edge maxima shift to higher energy as the oxidation state increases.

  Important consideration – similar ligand system.

Cu(II) Cu(III)

Factors that Affect Metal K-edge Shape and Energy

Oxidation State Contd

  Both Fe samples. What oxidation states do they represent?

  Both Ni samples. What oxidation states do they represent?

Fe(II) Fe(II)

Ni(II) Ni(III)

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

  Ni is special case with little change upon oxidation!

Factors that Affect Metal K-edge Shape and Energy

Coordination Number and Geometry

0.0

0.4

0.8

1.2

8980 8990 9000 9010

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

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

Coordination no: 2 3 4

x

y

z

4px,y,z

px,y

pz

px

Py,z px,y,z

Ene

rgy

Cu Cu Cu

  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

L 3p M 3d

M 4p

M 1s

Factors that Affect Metal K-edge Shape and Energy

Covalency

0.0

0.4

0.8

1.2

8980 9000 9020

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

  Energy and intensity can be correlated with metal-ligand overlap using the VBCI model.

  In comparable systems: Intensity Covalency Energy 1/Covalency

L 3p M 3d

M 4p

M 1s

L 3p M 3d

M 4p

M 1s

Shakedown

Factors that Affect Metal K-edge Shape and Energy

Pre-edge Shape and Energy

7109 7111 7113 7115

Energy ( eV )

  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

Fe N

N N

N Fe

N

N N

N

O

O

Fe N

N N

N N

N 0.0

0.4

0.8

1.2

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

Metal K-pre-edge: Quantitative Use

 Pre-edge intensity Deviation from Centrosymmetry Metal 3d-4p mixing

Fe Fe Fe Fe > > >

0.0

0.4

0.8

1.2

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

7112 7116

Sq-py Td Sq-Py* Oh

Td Oh

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

Metal K-pre-edge Energy

Cu 3dx2-y

2

ener

gy

Ligand Field

Zeff

2p

1s

  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

0.0

0.4

0.8

1.2

8980 9000 9020

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

8976 8978 8980 8982

Pre-edge Example 1 : Cobalamin

Vitamin B12 derivative: Cobalamin

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

-8.0

-4.0

0.0

4.0

8.0

0 5 10 15

k3 *

EX

AFS

k ( Å-1 )

Data courtesy Prof. Serena DeBeer

Pre-edge Example 1 : Cobalamin   Crystallography consistently gave a long Co-C distance than reasonable.

Question – Could the diffraction data have error from beam-damage/decomposition?

Me-Cbl H2O-Cbl

Me-Cbl and H2O-Cbl have similar EXAFS

0.0

0.5

1.0

1.5

7750 7850N

orm

aliz

ed A

bsor

ptio

nEnergy ( eV )

7708 7712 7716

Me-Cbl H2O-Cbl

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.

Pre-edge Example 2 : MCR

Methyl Coenzyme M Reductase

  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

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

Pre-edge Example 2 : MCR

2.41

2.26 2.09

2.25

2.05

2.08

2.32

2.08

  Do Not confirm Ni(III) state.

  Do Not show the presence of a Me group in the axial position.

  Do show increase in coordination #.

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

Pre-edge Example 2 : MCR

  Very little shift in edge energies   ~0.5 eV shift in pre-edge energy

Ni(I) > Ni(II) > Ni(III)

0.0

0.1

0.1

0.2

0.2

8330 8334 8338

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

  Large difference in pre-edge intensities

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

Pre-edge Example 2 : MCR

0.00

0.04

0.08

8328 8332 8336

Nor

mal

ized

Abs

orpt

ion

C

Energy ( eV )

DFT Calculations

  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

  EXAFS data not available to high k due to very low concentrations?   EXAFS data too weak beyond k ~ 10 Å-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

  Full multiple-scattering Theory.   The potential is generated using the Muffin-tin approach.

EXAFS: SERIES Solution

φTotal=φ1+ φ2+………… φn

MXAN: EXACT Solution

ALL Scattering Paths

  Method can be applied to dilute samples. ( k =6-7 Å-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

MXAN: Near-edge Analysis

  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).

x

y

z

R !

"

!"! #$===

N

1iii

2i

2.expi

N

1inn

.thi

2sq w/w}/]y,..),r(..y{[R

  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

Geometric Structure of N694C sLO1

Fe (His)N

N(His)

N(His)

(Ile)O (Cys)S

O(Gln)

  Structural Possibilities

Fe (His)N

N(His)

N(His)

(Cys)S

O(Gln) Fe

(His)N N(His)

N(His)

(Cys)S

O(Gln) (His)N

N(His)

N(His)

(Cys)S

H2O

Fe O

O (Gln)

Geometric Structure of N694C sLO1

Geometric Structure of N694C sLO1

1 O/N 1.96 4 O/N 2.12 1 O/N 2.49

1 O/N 1.97 3 O/N 2.12 1 S 2.28

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

F=0.136 F=0.138 F=0.150

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

F=3.71 F=0.95 F=3.91

  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.

MXAN Analysis of N694C sLO1

  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.

Summary of XANES Talk

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

Acknowledements

References

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, 595–598.

L.S. Kau et al., J. Am. Chem. Soc., 1987, 109, 6433.

R. Sarangi et. al. J. Am. Chem. Soc. 2006, 128, 8286–8296.

R. Sarangi, et al. Biochemistry 2009, 48, 3146–3156.

http://www.esrf.eu/computing/scientific/MXAN/ R. Sarangi et al., Inorg. Chem., 2008, 47,11543

Metal K- pre-edge intensity

Metal K- pre-edge energy

Rising edge-intensities in Cu(I) complexes

J.L. DuBois et al., J. Am. Chem. Soc. 2000, 122, 5775-5787.

Covalency from the rising edge

Pre-edge EXAMPLE 2

MXAN and EXAMPLE

Pre-edge EXAMPLE 1

H. A. Hassanin, et al., Dalton Trans., 2010, 39, 10626-10630