1

X-ray Spectroscopy A Critical Look at the Past

Accomplishments and Future Prospects

James Penner-Hahn jeph@umich.edu

Room 243Monday – Wednesday 3-5 PM and by appointmenthttp://www.chem.usyd.edu.au/~penner_j/index.htm

1. Basic Physical Principles2. Practical aspects of x-ray absorption3. Data analysis4. Near edge structure5. Spatially and temporally resolved methods6. Exotic x-ray spectroscopies

Lecture plan

Grading• Participation – 20%• Draft research proposal – 30%• Final research proposal – 50%

•Original•Feasible•Well presentedProposal forms and guidelines athttp://www-ssrl.slac.stanford.edu/users/user_admin/xray_vuv_proposal_guide.html

Proposal body – not more than 5 pages

A. DESCRIPTION OF EXPERIMENTI. BackgroundII. Previous resultsIII. Proposed ExperimentsIV. Literature cited

B. PREVIOUS EXPERIENCE WITH THE TECHNIQUES AND FACILITY

C. DETAILED SAFETY CONCERNSD. EQUIPMENT DEVELOPMENT SCHEDULEE. RESOURCES FOR PROGRAM PROJECT

Techniques for studying metal sites in proteins

• UV-visible spectroscopy• EPR spectroscopy• Magnetic susceptibility• MCD

Require open d shell

Requires I=1/2 nucleusRequires crystals• X-ray crystallography

• NMR spectroscopy

• X-ray spectroscopy

2

http://www.coe.berkeley.edu/AST/sxreuv

Absorption of x-rays by Pb

0.1

1

10

100

1000

10000

1 10 100 1000

Abs

orba

nce

(cm

2 /g)

Energy (keV)

M

L

K

10 20

L3

L2L

1

Electron binding energies of the elements

http://www.csrri.iit.edu/

Center for Synchrotron Radiation Research and Instrumentation

X-ray absorption spectroscopy

9500 9600 9700 9900Energy (eV)

XANES EXAFS

9800 10000

Abs

orpt

ion

SA

A S

E2E1

XASXAFSNEXAFS

3

X-ray absorption spectroscopy

-10

-5

0

5

10

0 2 4 6 8 10 12

EXA

FS•k

3

k (Å -1)

Amplitude

Frequency

Phase

Shape

→

coordinationnumber

→

bondlength

→

scatterer

→

scattererInformation Content of EXAFS

• Bond length ± 0.02 Å (accuracy)• Bond length ±0.005 Å (precision)• Coordination number (lower limit) ± 1 • Ligation type (Z) ± 10

Rmax < ~ 4 Å

Scott, R. A. "Measurement of Metal-Ligand Distances by EXAFS" Methods Enzymol. 1985, 117, 414-459.

Teo, B. K. EXAFS: Basic Principles and Data Analysis; Springer-Verlag: New York, 1986.

Scott, R.A., “X-Ray Absorption Spectroscopy” in Physical Methods in Bioinorganic Chemistry, Que, L. (Ed)., 2000, University Science Books.

Penner-Hahn, J.E., “X-Ray Absorption Spectroscopy”, in Comp. Coord. Chem. II, Vol. 2, 2004.

Levina A, Armstrong R.S., Lay P.A., “Three-dimensional structure determination using multiple-scattering analysis of XAFS: applications to metalloproteins and coordination chemistry” Coord. Chem. Rev. 2005, 249, 141-160.

Dependence of XANES on Oxidation State

0

400

800

6535 6555 6575 6595Energy (eV)

Nor

mal

ized

Abs

orpt

ion

II/II

II/III

III/III

III/IV

Mn(V)=O has intense pre-edge transition, not seen in Mn(III) analog

NiN4 vs NiS4

NiN6 vs NiS6

NiN4; Td vs D4h

4

X-ray Fluorescence

K

L

M

Kα

Kβ

X-ray fluorescence lines

21

31

2

12

12,15

K

L1

L1L2L3

K

M1

M5

N1

N7

αα

ααβ

ββ

ββ l

23p221p2

2s

X-ray fluorescence spectra give element sensitivity

Ar

FeCo

Cu

Zn

0

500

1000

1500

2000

0 2 4 6 8 10

Cou

nts/

sec

Energy (eV)

Elastic scatter

Advantages of XAFSDirect structural determination for:• Any form of matter• Any isotope• Any spin stateDirect determination of oxidation state

•Bulk spectroscopy (average structure)•Little angular information•Gives only local structural information•Limited sensitivity

•Requires synchrotron x-ray source

Disadvantages of XAFS

http://learntech.uwe.ac.uk/radscience/x-ray_tube

5

Bremsstrahlungradiation

Synchrotrons produce intense, tunable x-ray beams

6

http://www.synchrotron.vic.gov.au

22 July 2005

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?

The Zn site in MetE has ZnS2(O/N)2ligation.

-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 7Four

ier

Tra

nsfo

rm M

agni

tude

R + α (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

Four

ier

Tra

nsfo

rm M

agni

tude

R + α (Å)

Native

+SeHcy+Hcy

MetH (ZnS3O)

MetE (ZnS2NO)

Combination of Zn + Se EXAFS consistent with only a small distortion from tetrahedral

geometry in substrate-bound enzyme

7

J. Am. Chem. Soc., 112 (10) 1990p. 4031-4032

p. 4032-4034

EXAFS shows that CN–

does not remain bound

0 1.5 3 4.5 6 7.5

Four

ierT

rans

form

Mag

nitu

de

R + (Å)

CuCN•2LiCl

Cu-Nearest NeighborCu-C?N

Cu-C?N-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

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

Titration of CuI+ n PhLi shows isosbesticbehavior 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

8

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-

Cu

Cl

Cl

Cl

Cl Cl

Cl

CuCl

Cl

Cl

ClCl

Cl

Cu

Cl

Cl

Cl

Cl Cl

Cl

+