Qualitative and MO-Based Approach to XAS Edges...MO Based Approach Molecular Orbital-Based Approach Obtain a more quantitative description ... e.g: Ni 1s is the deepest orbital so

Qualitative and MO-Based

Approach to XAS Edges

Ritimukta Sarangi SSRL, SLAC

Stanford University July 01, 2011

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)

  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.

Interpretation of XAS Edges

Metal K-pre-edge: Qualitative Use

0.0

0.4

0.8

1.2

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

All are heme species – What information can you glean from the Edges? Oxidation State? Geometry? Other Axial Ligands? Spin State?

1 2 3

Metal K-pre-edge of 1

Molecule Energy @ 0.6 Intensity Fe(III) S=1/2 7124.3 Fe(III) S=5/2 7124.1 Fe(II) S=0 7123.9 Fe(II) S=2 7121.5 Fe(II) S=2 7121.2

1 7121.7

Rising edge energy squarely falls in the Fe(II) region – {Maybe slightly higher than Fe (II) S=4}

Oxidation State? = Fe(II) Geometry? Other Axial Ligands? Spin State?

0.0

0.4

0.8

1.2

8980 9000 9020

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

Cu(II) Cu(III)

square planar

Intense rising edge features indicate: covalent systems in sq-planar environment


Oxidation State? = Fe(II) Geometry? = Square planar Other Axial Ligands? = None Spin State? Spin State? S= 1

Fe

NN

N N


0.2

0.6

1.0

1.4

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

Molecule Energy @ 0.6 Intensity Fe(III) S=1/2 7124.3 Fe(III) S=5/2 7124.1 Fe(II) S=0 7123.9

2 7121.4 Fe(II) S=2 7121.2

Rising edge energy squarely falls in the Fe(II) region (S=2)

No intense edge feature : Not square planar Fe N

N N

N L

Fe N

N N

N L

L Square Pyramidal Octahedral

Oxidation State? = Fe(II) Geometry? Other Axial Ligands? Spin State?


7108 7110 7112 7114 7116

Energy ( eV )

7108 7110 7112 7114 7116

Energy ( eV )

Square Pyramidal

Fe N

N N

N N

Fe N

N N

N N

N Octahedral

0.0

0.4

0.8

1.2

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

7109 7111 7113 7115

Energy ( eV )

Shape of pre-edge feature = Octahedral

Oxidation State? = Fe(II) Geometry? = Octahedral Other Axial Ligands? = Yes, 2 Spin State? S=2

Fe

NN

N N

O(L)(L)O O = O(L)


Molecule Energy @ 0.6 Intensity Fe(III) S=1/2 7124.3 Fe(III) S=5/2 7124.1 Fe(II) S=0 7123.9

2 7124.0

Fe(II) and Fe(III) can have same edge eV!

3d

1s

Fe(III) S=1/2 Fe(III) S=5/2 Fe(II) S=0

0.0

0.4

0.8

1.2

7110 7130 7150

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )


Fe(III) S=1/2 Fe(III) S=5/2 Fe(II) S=0

7110 7112 7114

2nd

Dvt

Inte

nsity

Energy ( eV )

Energy and intensity pattern indicate that the molecule is Fe(II) and S=0, low-spin.

Oxidation State? = Fe(II) Geometry? Other Axial Ligands? Spin State? S=0

Fe N

N N

N L

Fe N

N N

N L

L Square Pyramidal Octahedral


7108 7110 7112 7114 7116

Energy ( eV )

Square Pyramidal

Fe N

N N

N N

Fe N

N N

N N

N Octahedral

Intensity of pre-edge feature = Octahedral

Oxidation State? = Fe(II) Geometry? = Octahedral Other Axial Ligands? = Yes, 2 Spin State? S=0

Fe

NN

N N

N(L)(L)N NL=

MO Based Approach

  Molecular Orbital-Based Approach   Obtain a more quantitative description   Understand energy and intensity distributions using LF theory   Works well for bound state transitions   Unsuccessful for rising-edge and beyond.

Pre-edge Example 1 : 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)

Different MCR Species

Proposed Transient Intermediate

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

MCR: EXAFS Information

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

Ni-OX = 2.12 Å Ni-CH3 = 1.98 ÅNi-OH2 = 2.13 Å

2.08

2.32

2.08

MCRMe Possible Axial Coordination

  The ligand in the putative Ni(III)-Me can be Me or H2O or OX

MCR: Ni K Pre-edge and Near-edge

  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

DFT Calculations

! UKS B3LYP tightscf opt PAL4 SlowConv grid4 nofinalgrid ! COSMO(water) %output PrintLevel Normal Print[P_MOs] 1 Print[P_Overlap] 1 end %basis basis TZVP end %scf maxiter 500 end %Method SpecialGridAtoms 28 SpecialGridIntAcc 7 end * xyz +1 2 Ni 0.00000 0.00000 -0.00000 newgto "CP(PPP)" end N 1.45459 1.60491 0.25726 C 3.45823 0.20034 0.06731 . ………. ……….. .………. *

Geometry optimization

Level of theory : DFT Functional: hybrid Basis sets: reasonable size Solvation? Convergence criteria? Input Structure? Charge and Spin State?

DFT Calculations TD-DFT Calculation of the XAS K-edge ! UKS B3LYP tightscf PAL4 SlowConv grid4 nofinalgrid COSMO(water)

!Moread noiter %moinp "1.gbw" %output PrintLevel Normal Print[P_MOs] 1 Print[P_Overlap] 1 end %basis basis TZVP end %tddft OrbWin[0] = 0,0,203,216 OrbWin[1] = 0,0,201,214 Nroots 15 Maxdim 150 Doquad True end %Method SpecialGridAtoms 28 SpecialGridIntAcc 7 end * xyz +1 2 Ni 0.00000 0.00000 -0.00000 newgto "CP(PPP)" end N 1.45459 1.60491 0.25726 C 3.45823 0.20034 0.06731 . ………. ……….. .………. *

  * Choose orbitals for transition “from” and “to”.

e.g: Ni 1s is the deepest orbital so its 0,0 and the valence levels start at 203 for the alpha set and 201 for beta set.

  Perform the calculation and they apply the correct broadening to the calculated stick plots.

e.g: For Ni the broadening is ~1.5 eV

0.00

0.04

0.08

8328 8332 8336

Nor

mal

ized

Abs

orpt

ion

C

Energy ( eV )

Calculated and Experimental Spectra

  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.

MO Based Approach- Example 2

[CoII(14-TMC)(MeCN)](ClO4)2 [CoIII(14-TMC)(O2)](ClO4) H2O2 + base

known crystal structure

final structure solved by EXAFS

[CoII(15-TMC)(MeCN)](ClO4)2 [Co?(15-TMC)(O2)](ClO4) H2O2 + base

d7, S=3/2 d6, S=1

d7, ?? d?, ??

14-membered

15-membered

Electronic Configuration

[CoII(14-TMC)(MeCN)](ClO4)2

d7, S=3/2

3d

[CoIII(14-TMC)(O2)](ClO4)2

d6, S=1

3d

14-TMC EXAFS and Near-edge

0.2

0.6

1.0

1.4

7710 7730 7750 7770

Nor

mal

ized

Abs

orpt

ion

Energy ( eV )

[CoII(14-TMC)MeCN]2+

[Co(14-TMC)O2]+

7707 7709 7711 7713

1 eV edge-shift = oxidation 1.1 eV pre-edge shift ~ oxidation

FT shift to lower R = shorter Co-N/O distances = oxidation

  Combination of Co K-edge and EXAFS data show: oxidation occurs, bond length shorten and O2 binds

  Combination of XAS and EXAFS with DFT shows that the spin state of the O2

bound form can only be S=1, not S=0 and not S=2

14- and 15-TMC Precursor Data

  14-TMC and 15-TMC look quite different! 1st shell intensity higher 2nd shell intensity present in 15-TMC peak at R’ ~4 Å.

1st Shell

2nd shell

R’ ~ 4 Å peak

14- and 15-TMC Co K Pre-edge

But what about spin states?

d7, S=3/2

3d

High-Spin

d7, S=1/2

3d

Low-Spin

Would this difference in spin state result in a difference in the pre-edge spectral shape ?

DFT Calculation

d7, S=1/2

3d

Low-Spin

  DFT clearly shows that the species is low-spin.   Makes sense – additional ligand increases the eg and t2g split   Results in low-spin ground state.

Experiment Low-Spin High-Spin

15-TMC EXAFS

[CoII(15-TMC)(MeCN)2](ClO4)2 [Co?(15-TMC)(O2)](ClO4) H2O2 + base

d7, S=1/2 d?, ??

[CoII(15-TMC)(MeCN)2](ClO4)2 [CoIII(15-TMC)(O2)(MeCN)](ClO4) H2O2 + base

d7, S=1/2 d6, S=0

d6, S=1

3d

Spin-State of O2 bound 15-TMC

d6, S=0

3d

  14-TMC to 15-TMC the edge shifts to higher energy – high to low spin   14-TMC to 15-TMC the pre-edge becomes sharper – 1 peak – low spin

[CoII(15-TMC)(MeCN)2](ClO4)2 [CoIII(15-TMC)(O2)(MeCN)](ClO4) H2O2 + base

d7, S=1/2 d6, S=0

Geometric Structure from Near-edge Data : Multiple Scattering Approach using MXAN

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

A Simple Example FEFF and MXAN Fits to the data of solvated Bromide – Room Temperature Data

0.0

0.4

0.8

1.2

40 120

Nor

mal

ized

Abs

orpt

ion

Energy(eV)

0.0

0.4

0.8

1.2

0 40 120

Nor

mal

ized

Abs

orpt

ion

Energy(eV)

6-coordinate

6-coordinate 8-coordinate

8-coordinate

  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)



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

Documents

Qualitative and MO-Based Approach to XAS Edges...MO Based Approach Molecular Orbital-Based Approach Obtain a more quantitative description ... e.g: Ni 1s is the deepest orbital so