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