Qualitative and MO-Based Approach to XAS Edges...MO Based Approach Molecular Orbital-Based Approach...
Transcript of Qualitative and MO-Based Approach to XAS Edges...MO Based Approach Molecular Orbital-Based Approach...
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
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ized
Abs
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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
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ized
Abs
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Energy ( eV )
Cu(II) Cu(III)
square planar
Intense rising edge features indicate: covalent systems in sq-planar environment
Metal K-pre-edge of 1
Oxidation State? = Fe(II) Geometry? = Square planar Other Axial Ligands? = None Spin State? Spin State? S= 1
Fe
NN
N N
Metal K-pre-edge of 2
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?
Metal K-pre-edge of 2
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
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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)
Metal K-pre-edge of 3
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
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Abs
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Energy ( eV )
Metal K-pre-edge of 3
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
Metal K-pre-edge of 3
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
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ized
Abs
orpt
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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
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Abs
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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
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Abs
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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
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0.8
1.2
40 120
Nor
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Abs
orpt
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Energy(eV)
0.0
0.4
0.8
1.2
0 40 120
Nor
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Abs
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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)
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