lecture 3.jphgroup/xas_course/harbin/lecture3.pdf1 lecture 3. applications of x-ray spectroscopy to...
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1
Lecture 3.Applications of x-ray spectroscopy
to inorganic chemistry
1. Bioinorganic chemistry/enzymology
2. Organometallic Chemistry
3. Battery materials
MetE (cobalamin independent MetSyn) contains Zn
Zn is tightly boundZn is required for activityIs Zn involved in reaction, or does it play a
structural role?
2
The Zn site in MetE has ZnS2(O/N)2
ligation.
-4
0
4
8
2 4 6 8 10 12
EX
AF
S•k
3
k (Å-1)
0
5
10
15
20
0 1 2 3 4 5 6 7Fou
rier
Tra
nsfo
rm M
agni
tude
R + (Å)
Native+Hcy
Addition of homocysteine changes ligation to ZnS3(O/N).
Changes in ligation are due to homocysteine binding to Zn
0
10
20
30
40
50
60
0 1 2 3 4 5 6 7
Fou
rier
Tra
nsfo
rm M
agni
tude
R + (Å)
Native
+SeHcy+Hcy
MetH (ZnS3O)
MetE (ZnS2NO)
3
Combination of Zn + Se EXAFS consistent with only a small distortion from tetrahedral
geometry in substrate-bound enzyme
J. Am. Chem. Soc., 112 (10) 1990p. 4031-4032
p. 4032-4034
4
EXAFS shows that CN–
does not remain bound
0 1.5 3 4.5 6 7.5
Four
ier
Tra
nsfo
rmM
agni
tude
R + (Å)
CuCN•2LiCl
Cu-Nearest Neighbor
Cu-CNCu-CN-Cu
CuCN•2LiCl + MeLi
CuCN•2LiCl + 2 MeLi
Structures of cyanocuprates in THF
Cu C NN
CCu
Cu
Cl
MeLi
MeLi
Cu C NMe
Cu MeMe
C NLi Li
5
Solution speciation of CuI+PhLiPhLi + CuI “phenylcopper”
2PhLi+ CuI “diphenylcuprate”
1:1 Cu4Ph4(Me2S)2
Cu5Mes5
1.2:1 [Cu5Ph6]–
1.5:1 [Cu4LiPh6]–
[Cu4MgPh6]
2:1 [CuPh2]–
[CuPh2Li]2
[Cu3Li2Ph6]–
Crystalline phenyl:copper species
0
50
100
150
200
250
300
8970 8980 8990 9000 9010 9020
Nor
mal
ized
Abs
orba
nce
Energy ( eV )
n=0.0
n=0.2
n=0.4
n=0.6
n=0.8
n=1.0
n=1.1
n=1.2
Titration of CuI+ n PhLi shows isosbestic behavior up to 1.2 equivalents
6
Titration of CuI+ n PhLi shows isosbestic behavior from 1.2-2.0 equivalents
0
50
100
150
200
250
300
8970 8980 8990 9000 9010 9020
Nor
mal
ized
Abs
orba
nce
Energy ( eV )
n=2.0n=1.8
n=1.7n=1.5n=1.4n=1.3n=1.2
EXAFS data support XANES speciation
[Cu5Ph6]–
[CuI2]–
[CuPh2]–
0 0.5 1 1.5 20
0.2
0.4
0.6
0.8
1
PhLi / CuI Ratio
Cu
Com
posi
tion
1.2
CuI2-
Cu5Ph6-
CuPh2-
7
In-situ X-ray Absorption Spectroscopy
Aniruddha Deb et al. J. Synchrotron Rad. (2004). 11, 497–504
In-situ X-ray Absorption Spectroscopy
8
Charge/Discharge at 0.1C
Li3V1.9Mg0.15(PO4)3
- Cut off : 3.0 V-4.5V
- Charge: 121 mAh/g- Discharge: 104
mAh/g
Li3V1.9Mg0.15(PO4)3
- Cut off : 3.0 V-4.8V
- Charge: 136 mAh/g- Discharge: 100
mAh/g
Li3V1.9Mg0.15(PO4)3
Energy(eV)
5460 5480 5500 5520
No
rmal
ized
In
ten
sity
0
200
400
600
800
5464 5468 54720
20
40
60
Charge: 3.0-4.5V
Energy(eV)
5460 5480 5500 5520
No
r,m
ali
zed
In
ten
sity
0
200
400
600
800
5464 5468 54720
20
40
60
Discharge: 3.0-4.5V
Between 3.0-4.5V No change shown in the pre-edge region for a cut off of 4.5V Between 3-4.5V changes in the edge, observed, showing oxidation
state change No significant eg-t2g splitting observed in the pre-edge region Octahedral structure preserved
9
Energy (eV)
5460 5480 5500 5520
No
rma
lize
d I
nte
ns
ity
0
200
400
600
800
2D Graph 1
5464 5468 5472 54760
50
100
150
200
Discharge 2.0-4.8V
Energy (eV)
5460 5480 5500 5520
No
rma
lize
d I
nte
ns
ity
0
200
400
600
800
5464 5468 5472 54760
50
100
150
200
Charge:3.0-4.8V
Li3V1.9Mg0.15(PO4)3
Above 4.5V and below 3.0V Above 4.5V change in edge consistent with formation of tetrahedral
V4+ or V5+. XANES change is largely irreversible. Possible structural change below 3.0V as the
pre-edge intensity increases
Li(Ni0.4Co0.15Al0.05Mn0.4)O2
10
Li(Ni0.4Co0.15Al0.05Mn0.4)O2
Li(Ni0.4Co0.15Al0.05Mn0.4)O2
11
Li(Ni0.4Co0.15Al0.05Mn0.4)O2
12
Applications of EXAFS to Crystallographically
Characterized Materials
Cu
Cl
Cl
Cl
Cl Cl
Cl
CuCl
Cl
Cl
Cl
Cl
Cl
Cu
Cl
Cl
Cl
ClCl
Cl
+
13
Polarized XAS
x-ray beam
Fluorescence Detector
Crystal or other oriented sample
Samplepositioner
Polarized XAFS of Mo/Fe/S clusters
Fe
S
FeMo
S
SS
S
S
MoFe
S
Fe
SS
SFe S Fe
R+ (Å)
Fou
rier
Tra
nsfo
rm M
agni
tude
Flank, Weininger, Mortenson, & Cramer, J. Am. Chem. Soc., 108. 1049.
14
Examples using XANES to determine electronic
structure
X-ray absorption spectroscopyXANES EXAFS
Abs
orpt
ion
3s 3p3d
4s4p1s
15
1s3d transitions
• Dipole forbidden (L = 2) for centrosymmetric complexes
• Weak, but not absent, for all first row transition metals
• Possible mechanisms– 3d+4p mixing (not possible for centrosymmetric
complexes
– vibronic coupling
– direct quadrupole coupling
Orientation dependence of 1s3d transition
0
100
200
300
400
500
8960 8980 9020 9060
Energy (eV)
9000 9040
Abs
orba
nce
e
Cu
Cl
Cl Cl
Cl
k
90o
0o
16
Four-fold periodicity to 1s3d transition
(degrees)
0 90 180 270 360
Cu
Cu
Cl
Cl Cl
Cl
e
k
e
k
Theoret ical
<s | xy |dx2-y2> = 0<s | xy | dxy > ° 0
Experiment al
Quadrupole transitions – L=2
≠ 0
17
Selection rules for quadrupole transitions
xzxz
yzyz
xyxy
yxyx
zz
cso
2
2
22
22
222
coscos2cossinsincos52
sincos2coscossincos52
2sincoscos2sinsin52
2coscoscos2sinsinsin52
sincossin56
2222
22
Brouder, C. J. Phys. Condens. Matter, 2 (1990) 701-738
1s3d transitions for Fe porphyrins
0
5
10
15
20
25
7110 7112 7114 7116 7118
Nor
mal
ized
Abs
orpt
ion
Energy(eV)
x2-y
2
d
xyd
18
Isolated 1s3d for Fe(OEP)(2-MeIm)
0
5
10
15
20
25
7110 7112 7114 7116 7118
Nor
mal
ized
Abs
orpt
ion
Energy(eV)
xy x2
-y2dd
xz+yzd
z2d
dxy
dxz,yz
dz2
dx2-y2
0.00 eV
0.50 eV
1.70 eV
2.20 eV
XANES for Fe(III) complexes
Roe et al., J. Am. Chem. Soc., 106, 1676
.
4 coordinate
5 coordinate
6 coordinate
Energy (eV)
.
Percent Fe 4p character
5 10 15 20
5
10
15
25
20
19
1s3d intensity
• Weak for square–planar complexes
• Strong for tetrahedral complexes
• Correlates with coordination number
Electronic information is (often) enhanced by studying L-edge rather
than K-edge
20
Multiplet effects
SGDPF)3()3()3()2()2()1(Ti
D)3()3()3()2()2()1(Ti
S)3()3()2()2()1(Ti
111332626222
21626223
1626224
dpspss
dpspss
pspss
01
3,4,51
1,2,31
0,1,23
2,3,432626222
25,2
321626223
01626224
SGDPF)3()3()3()2()2()1(Ti
D)3()3()3()2()2()1(Ti
S)3()3()2()2()1(Ti
dpspss
dpspss
pspss
16252262622 )3()3()3()2()2()1()3()3()2()2()1( dpspsspspss
L edge of Ti4+
150 )3()2()3( dpd
43
33
23
33
23
13
33
23
13
31
21
11
01 F,F,F,D,D,D,PP,P,F,D,PS
Allowed transitions: J = ±1 13
13
11
01 D,P,PS
Simulations of L edges
DeGroot, Coord. Chem. Rev. 2005, 249, 31–63
21
But – life is not really this simple – need to consider ligand field:d2 terms vs ligand field
Ti4+ in the presence of a ligand field
10Dq=1.8 eV
22
Determination of Oxidation State
Kau et al., J. Am. Chem. Soc., 1987, 109, 6433
L2Cu+1 L3Cu+1
L4Cu+1Cu+2
23
By defining “generic” Cu(I) and Cu(II) XANES
can determine change in Cu oxidation state
Sensitivity of XANES to geometry is consistent with expected density of unoccupied Cu 4p orbitals
CuS2
CuS3
24
Theoretical calculations of XANES
Rehr and Ankudinov, Coord. Chem. Rev. 2005, 249 131–140
Mean-free path increases dramatically for energies near the edge – accounts for some of
the difficult with XANES caculations
Penn, Phys. Rev. B 35, 1987 482–486
25
The difficulty of simulating XANES is aalso due (in part) to multiple scattering
N
NH
Zn
Scattering probability as a function of scattering angle
Barton and Shirley, Phys. Rev. B 1985, 32, 1892
Ni
26
Importance of linear multiple scattering
J. Am. Chem. Soc. 1996, 118, 8623-8638
MXAN can simulate XANES spectra (at least for some compounds under some conditions)
Benfatto et al, J. Synchr.Rad. 2003. 10, 51-57;J. Am. Chem. Soc. 2004, 126, 15618-15623
Fe(CN)63–
27
XANES studies are not limited to metals
George and Gorbaty, J. Am. Chem. Soc. 1979 101, 3182
Ligand edges show pronounced dependence on metal identity
Hedman, et al., J. Am. Chem. Soc. 1990, 112, 1643
24CuCl
24ZnCl
28
Pre-edge transition due to M3d+L3p
mixing
24CuCl
Changes in pre-edge intensity correlate with changes in covalency
29
XANES (and potentially EXAFS)
as a probe of solution structure
XANES spectra show only very small changes with added thiolate
-50
0
50
100
150
200
250
300
350
9450 9600 9750 9900
Abs
orp
tion
(cm
2 /g)
Energy (eV)
Zn(SR)4
2-
Zn(SR)4
2- +
200 mM (TMA)RS
30
Conventional normalization misses changes in XANES
MBACK reveals subtle changes when thiolate is added
Equilibria for Zn(SPh)42- in DMSO
TMASRR)Zn(DMSO)(S 3 TMAZn(SR)4
KD,IP = 0.010.009 M2
TMAZn(SR)24
TMAZn(SR)4
KIP = 13 4 M-1
SRR)Zn(DMSO)(S 32
4Zn(SR)
KD= 0.130.12 M
Wilker and Lippard, Inorg. Chem. (1997) 36, 969.
For 5 mM Zn, >75% dissociation
31
Flow system can be used for time resolved measurements
Requirements (for reasonable sample volumes):•Rapid scanning•Small sample (i.e., small beam)
32
Flow direction
t=0
t=T
x-ray
[Reactants]
capillary 1 L/sec=1 mm/sec
100 m beam→100 ms resolution
33
Oxidation of Mn(III)hmpab by oxone is slow at 0º C
34
Oxidation is significantly faster at room temperature
Reaction appears to be first order in Mn and oxone
35
Initial rate it temperature dependentG‡=23 kJ/mol
However, product that is formed is Mn(IV)=O not Mn(V)=O
36
6540 6550 6560 6570 6580 6590 6600-100
0
100
200
300
400
500
600
700
800
Increasing time
Mn(III) shows significant radiation damageRoom temperature, 30 minute scans
6540 6550 6560 6570 6580 6590 6600-100
0
100
200
300
400
500
600
700
800
Low temperature (4K) reduces but does not eliminate radiation damage
Low temperature can’t be used if thermochromic
37
6530 6540 6550 6560 6570 6580 6590 6600 6610 6620-100
0
100
200
300
400
500
600
700
800
Flowing fluid samples can prevent radiation damageMn3+(salpn)(acac) in Acetone + 15% H2O
Flow rate = 0.05 - 6.4 L/s
Residence time in beam = 2 s - 16 ms