Coordination Chemistry and Trace Element Biology SYNEW/Feiters2.pdf · M. C. Feiters and W. Meyer-Klaucke, in Practical Approaches to Biological Inorganic Chemistry (R. R. Crichton

Institute for Molecules and Materials

• Mini-school X-ray Absorption Spectroscopy

Martin C. Feiters, IMM, HG 03.021Institute for Molecules and Materials, Radboud University

Heijendaalsweg 153, 6525 AJ Nijmegen, NL( 024-3652016, [email protected]

Workshop X-ray Absorption Spectroscopy, SyNeW Utrecht, June 2, 2015

Coordination Chemistry and Trace Element Biology



Koningsberger building

Victor J. Koningsberger(1895 - 1966) 1934 Botany

Diek C. Koningsberger(1938 -) 1988 Inorganic Chemistry



Coordination Chemistry and Trace Element Biology

• Fe in lipoxygenases, imidazoles• Zn in HIV integrase, imidazoles and sulfurs• Binding of tungstate by bacterial proteins• Iridium complex ions and solids• Bromine in algae and haloperoxidases, EXAFS-XRD• Ni-catalyzed isocyanide polymerization, EXAFS-XANES• XES/XFEL of Mn in photosynthetic systems• XES/HERFD XAS of Fe and Mo in nitrogenase• Conclusions, prospects



K and L3 edges of biological trace elements

4 5 6 7 8 9 10 11 12 13 14

4038

.5 C

a45

57 I

4852

I

5188

IV

546

5C

r 59

89M

n 6

539

Fe 7

112

Co

770

9N

i 83

33C

u 8

979

Zn 9

659

W 1

0207

W 1

1544

As

118

67W

121

00Se

126

58

Br

1347

4

X-ray Energy (keV)

Abs

orpt

ion

(arb

itrar

y un

its)

4

Off scale: K edges of (soft) H (13.6), C (284.2), N (409.9),O (543.1), Na (1070.8), Mg (1303.0), P (2145.5),

S (2472), Cl (2822.4), and K (3608.4); (hard) Mo (20000), I (33169), and W (69525 eV).

K edges, 1s; L1, 2s;L2, 2p1/2; L3, 2p3/2

(Ir 1

1215

)



•• Activation by Activation by 1313(S)(S)ROOHROOH

• Aerobic reaction• Anaerobic reaction• Non-enzymatic

dioxygenation

A spectroscopicallyeffective working hypothesis for the lipoxygenase mechanism



Lipoxygenase: 5-6 coordinated Fe, 4 ± 1 imidazoles• Axial ligand symmetry accounts

for EPR spectra

• Cf. Reaction centre in photosynthetic bacteria



Lipoxygenase Fe coordination• Crystallographic/ spectroscopic (re)investigation: 6th ligand H2O

• Deprotonated upon oxidation to Fe(III)

• Probably the base/oxidator responsible for H-tunneling !

• Purified 1947• Fe 1973• EPR/UV-vis 1976• EXAFS 1988• 1st XRD 1993



Multiple ScatteringBesides the single scattering pathways of the photoelectron wave

A(bsorber)-B(ackscatterer)-A(bsorber) andA(bsorber)-R(emote backscatterer)-A(bsorber)

multiple scattering pathways A-B-R-A may exist.

Typically only important at low k, in XANES region (0-50 eV above edge)

Important also in the EXAFS of rigid ligand systems where the angleA-B-R-A approaches 180 o (> 140 o):

• Coordinating cyanide, isocyanide, or carbon monoxide• Coordinating rigid heteroatomic ligand:

e.g. pyridine, imidazole, pyrrole, porphyrin, N-heterocyclic carbene

When simulated with a single scattering approximation, the presence of multiple scattering is noted as amplitude and phase effects.



Important in the EXAFS of rigid ligand systems where the angleA-B-R-A approaches 180 o (> 140 o):• Coordinating carbon monoxide

• Coordinating rigid heteroatomic ligand:e. g. pyridine, imidazole,

• Metal at center of unit: octahedral, square planar

9

Multiple Scattering

N-heterocyclic carbene



FeMeIm model compound

SS + MS SS MS

Strange et al. J. Am. Chem. Soc. 109 (1987) 7157; Feiters et al. J. Am. Chem. Soc. 110 (1988) 7746


Workshop X-ray Absorption Spectroscopy, SyNeW Utrecht, June 2, 2015 11

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

-12

0

12

2 3 4 5 6 7 8 9 10 11 12 13 14

0

120

0 1 2 3 4 5 6 7 8 9 10

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

-12

0

12

2 3 4 5 6 7 8 9 10 11 12 13 14

0

120

0 1 2 3 4 5 6 7 8 9 10

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

-15

0

15

2 3 4 5 6 7 8 9 10 11 12 13 14 15

-120

0

120

0 1 2 3 4 5 6 7 8 9 10

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

-15

0

15

2 3 4 5 6 7 8 9 10 11 12 13 14 15

-120

0

120

0 1 2 3 4 5 6 7 8 9 10

CNC

NC

ZnCNC

NC

Zn(im)4 and Zn(im)6

• FT patterns comparable, EXAFS different

M. C. Feiters and W. Meyer-Klaucke, in Practical Approachesto Biological Inorganic Chemistry (R. R. Crichton and R. Louro, Editors; 2013)



Refinement in EXAFS SimulationsChoose atom type, iteratively refine parameters till minimum in fit index∆E0, threshold energy; R, distance absorber-scatterer; N, occupancy;a (= 2σ2), Debye-Waller-type factor. N(ind) = (2.Δk.ΔR)/π + 2

Single scattering: ∆E0 for the complete simulation, R, N, a for every shell

Multiple scattering: ∆E0 for the complete simulation,R, N, a (angle M-A-B) for every shell

Constrained refinement: Distances within unit fixed ∆E0 for the complete simulation, one R, one N, (one angle for unit), a for every shell

Restrained refinement: Idealized distances given, penalty added to fitindex for deviations with EXCURVE∆E0 for the complete simulation, one R, one N, (one angle for unit)a for every shell

N. Binsted, R. W. Strange, S. S. Hasnain, Biochemistry 31 (1992) 12117



Simulations of Zn imidazole complexes• left) Simulation of ‘straight’ [Zn(im)4](ClO4)2

• right) ‘tilted’ imidazole in Zn(im)2(OAc)2: camel back less pronounced, contribution of ring Cs at 3.0 Å smeared out due to large ∆R.

13

15

0

-15

120

0

-120

2 4 6 8 10 12 14 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 2 4 6 8 10 0 2 4 6 8 10R (Å) R (Å)

A B

EXA

FS *

k3/F

T/

15

0

-15

120

0

-120

2 4 6 8 10 12 14 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 2 4 6 8 10 0 2 4 6 8 10R (Å) R (Å)

A B

EXA

FS *

k3/F

T/



8

0

-8

60

0

-60

2 4 6 8 10 12 14 16 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 1 2 3 4 5 0 1 2 3 4 5 R (Å) R (Å)

A B

EXA

FS *

k3/F

T/

2 N + 1 Sat 2.0 Å 2 N at 2.0 Å

1 S at 2.3 Å

8

0

-8

60

0

-60

2 4 6 8 10 12 14 16 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 1 2 3 4 5 0 1 2 3 4 5 R (Å) R (Å)

A B

EXA

FS *

k3/F

T/

2 N + 1 Sat 2.0 Å 2 N at 2.0 Å

1 S at 2.3 Å

M. C. Feiters et al. J. Synchr. Rad. 10 (2003) 86

N and S at same and realistic distance from Zn




8

0

-8

60

0

-60

2 4 6 8 10 12 14 16 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 1 2 3 4 5 0 1 2 3 4 5 R (Å) R (Å)

B CEX

AFS

* k3

/FT/

2 N at 2.0 Å1 S at 2.3 Å

2 Im at 2.0 Å2 S at 2.3 Å

8

0

-8

60

0

-60

2 4 6 8 10 12 14 16 2 4 6 8 10 12 14 16k (Å-1) k (Å-1)

0 1 2 3 4 5 0 1 2 3 4 5 R (Å) R (Å)

B CEX

AFS

* k3

/FT/

2 N at 2.0 Å1 S at 2.3 Å

2 Im at 2.0 Å2 S at 2.3 Å

M. C. Feiters et al. J. Synchr. Rad. 10 (2003) 86

S and Im ligands to Zn in HIV-2 integrase




Camel Back

• Fe in lipoxygenases, imidazoles• Zn in HIV integrase, imidazoles and sulfurs• Binding of tungstate by bacterial proteins• Iridium complex ions and solids• Bromine in algae and haloperoxidases, EXAFS-XRD• Ni-catalyzed isocyanide polymerization, EXAFS-XANES• XES/XFEL of Mn in photosynthetic systems• XES/HERFD XAS of Mo and Fe in nitrogenase• Conclusions, prospects



Ser42

Gly41Ala40

Ser42 Ser70

Asp153

Pro154Cys155

Glu218

Tyr236

1.96

1.70

2.211.73

2.09

W2.20

Ser42

Gly41Ala40

Ser42 Ser70

Asp153

Pro154Cys155

Glu218

Tyr236

1.96

1.70

2.211.73

2.09

W2.20

Archaeal MoO42-/WO4

2- Binding Proteins• PX of Archaeoglobus fulgidus ModA with WO4

2-

• Pyrococcus furiosus WtpA: 103 stronger binding of WO42-

• MoO42-/WO4

2- very similar, protein selectivity ?

K. Hollenstein et al., Nature 448 (2007) 21; L. E. Bevers et al., J. Bacteriol. 188 (2006) 6498



MS pathways for octahedral, not tetrahedral W

K. Hollenstein et al., JBIC 14 (2009) 663-72

experimentaltotal simulationgreen, MS comp.

Archaeoglobus fulgidusModA with WO4

2-

(octahedral)

WO42- buffer

(tetrahedral) 1.79

2.24



Ir complex ion

-15

0

15

2 3 4 5 6 7 8 9 10 11 12 13 14 15

0

150

0 1 2 3 4 5 6 7 8 9 10

EXA

FS *

k3/F

T/

k (Å-1)

R (Å)

2.32

6 Å

2.32

6

Experimentaltotal simulation

SS



-60

0

60

2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19

IrO2 solid(rutile)

EXA

FS *

k3/F

T/

k (Å-1)

R (Å)

Experimentaltotal simulation

SSMS

0

250

0 1 2 3 4 5 6 7 8 9 10



Biological Halogen Accumulation in Marine Algae

Accumulation of Br- and I-in marine algae such asAscophyllum nodosum →(knotted wrack) and

F. C. Küpper et al, Planta 207 (1998) 163

← Laminaria digitata(oarweed) is mediated by V-containing haloperoxidases



Br in native VBPO (Ascophyllum nodosum)

A) B)

0 1 2 3 4 5 6 7 8 9 10

20

0

0

R (Å)

/FT/

//

Br

BrHO

R

1.90

0 1 2 3 4 5 6 7 8 9 10

20

0

0

R (Å)

/FT/

//

Br

BrHO

R

1.90

5

0

0

-5

k (Å-1)

EXA

FS *

k3

3 4 5 6 7 8 9 10 11 12 13 14

//5

0

0

-5

k (Å-1)

EXA

FS *

k3

3 4 5 6 7 8 9 10 11 12 13 14

//

Blue, electron density; red, negative Fourier-difference map contoured at a 3σ level.Original coordinates: Revised coordinates:Di-iodo with 0.5 occupancy Di-bromo

EXAFS identifies diBr-Tyr residue in native enzyme

M. C. Feiters et al.JACS 127 (2005) 15340

Weyand et al.JMB 293 (1999) 595



4.45

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

1 3 5 7 9 11 13 15

6

0

-6

0 1 2 3 4 5 6 7 8 9 10

30

0

R (Å)

/FT/

k (Å-1)

EXA

FS *

k3

1 3 5 7 9 11 13 15

6

0

-6

0 1 2 3 4 5 6 7 8 9 10

30

0

• rBr (1.87) > rCl (1.70 Å)• rK 1.44 Å

1.89

3.21

4.44

5.40

6.32

Br in Laminaria cortex:Br defect in KCl lattice

F. C. Küpper et al. J. Phycol. 50 (2014) 652



1.89

3.21

4.44

5.40

6.32

Br in bromoform precursors in Asparagopsis armata

F. C. Küpper et al. J. Phycol. 50 (2014) 652

WholeAsparagopsis

armata

2,2,-dibromo-propane

bromoform



EXAFS of solid Ni(acacR)2 complexes

R (Å)

FT

k (Å-1)

EXA

FS *

k3

-10

0

10

3 4 5 6 7 8 9 10 11 12 13

0

90

0 1 2 3 4 5 6 7 8

NiO

NiO

NiO

O

O

O

O

OOO O O

NiO

O O

O

O O= acac

3

R = p-tBuBn:2 bidentate

acac/Ni4 O @ 1.83 Å

R = H:2 bidentate acac/Ni, 4 O @ 2.03 Å+ 2 monodentate acac/Ni, 2 O @ 2.04 Å

M. C. Feiters et al. Ind. Eng. Chem. Res. 44 (2005) 8631

Association equilibria

between inactive (coordinativelysaturated) and active catalysts for Mukaiyama

epoxidation



Nor

mal

ized

Abs

orpt

ion Planar Tetrahedral

Square-planar and tetrahedral Ni(II)

Pure 1s → 4pz for planar

Ener

gy

Colpas et al., Inorg. Chem. 1991, 30, 920; Kau et al., J. Am. Chem. Soc. 109 (1987) 6433



Comparison of Methods

8320 8340 8360 8380 8400 84200.0

0.2

0.4

0.6

0.8

1.0

1.2

1.4

1.6

Nor

mal

ized

XA

NE

S

Photon energy, eV

XANES of Ni(acacH)2 (solid)

and Ni(acac-p-tBuBn)2 (dashed)

p1 (Ni-O)

p2 (O-C1)

p3 (C1-C2)

p4 (O-Ni-O)

Ni-C1

XANES MTXANES

1.941.83

1.281.28

1.431.39

10293

2.82

DFT 1.84 1.30 1.39 95 2.81

EXAFS 1.83 (1.30) (1.38) - 2.78

G. Y. Smolentsev, Phys. Rev. B 75 (2007) 144106; A. V. Soldatov, Rad. Phys. Chem. 75 (2006) 1866

Ni K edge XANES experimental (solid

line), theoretical ‘muffin-tin’ FMS

(dashed), and non-MT FDM calculations (dotted) for same set

of structural parameters



X-ray fluorescence – total yield vs. energy resolved• The hole created by inner electron excitation can be filled by electrons

from higher orbitals, which give rise to fluorescence• The total fluorescence yield is more intense for K than for L-excitation• The X-ray absorption spectrum can be measured as µf = If / I0




X-ray emission spectroscopy (XES) of MnO• 1st row transition metal (Mn2+):

Kα1 and Kα2 lines resolved, more intense than (not resolved) Kβ1and Kβ3 by order of magnitude;

• Much weaker: Kβ satellite lines Kβ2,5 and Kβ”.

• Usually present (not in Figure) for transition metals which have a total electron spin S ≠ 0 (such as Mn2+): Kβ’ line at slightly lower energy than Kβ1,3 line.

• Results from emission from the metal 3p level combined with a spin flip of a 3d electron and is therefore sensitive to the spin state of the metal ion.

29

K1 1s

K edgeexcit.

continuum

L1 2s

L2 2p1/2L3 2p3/2

M1 3sM2,3 3pM4,5 3d

K 1

K 2

K 1,3

K 2,5

Mn2+ Mn2+Glatzel & Bergmann, Coord. Chem. Rev. 249 (2005) 65



Valence-to-core (V2C)in XES of MnO

30

• Kβ satellite lines: cross-over emission line Kβ” extremely sensitive to nature coordinating ligands; involves emission from ligand’s 2s level to metal’s 1s core hole, and allows O, N and C ligands to be distinguished.

• Ligand identification information complimentary to EXAFS (← no discrimination between ligandsfrom same row of Periodic Table)

• Examples: variation in the number of O ligands to Mn in the so-called Kok cycle in PhotoSystem II; identification of central atom bound to Fe in the Fe,Mo cofactor of nitrogenase as C.


Workshop X-ray Absorption Spectroscopy, SyNeW Utrecht, June 2, 2015J. Kern et al. Science 340 (2013) 491

Simultaneous Femtosecond XAS and Diffraction …



… of Photosystem II

at Room Temperature

J. Kern et al. Science 340 (2013) 491

XRD at 5 Å resolution



XES of Fe in nitrogenase

K. M. Lancaster et al. Science 2011, 334, 974; R. Bjornsson Chem. Sci. 5 (2014) 3096

(A) Normalized V2C XES spectra of isolated FeMoco (red) and a representative fit to the data (black dashed line). (B) Comparison of the normalized V2C XES data for FeMoco (red), the MoFe protein (grey), and the ∆nifB MoFe protein (black). (Inset) V2C satellite region for Fe2O3 (red), Fe3N (blue), and MoFe protein (grey). (C) Experimental difference spectrum of FeMoco with P clusters (grey), as well as calculated difference spectra of P clusters with FeMoco containing interstitial C4- (black), N3- (blue), and O2- (red).

• V2C XES of FeMoCo Fe edge



HERFD XAS of Mo in nitrogenase• High-Energy Resolution Fluorescence Detected

(HERFD) – XANES of Mo in nitrogenase

K. M. Lancaster et al. Science 2011, 334, 974; R. Bjornsson Chem. Sci. 5 (2014) 3096

Fig. 1 Molecular structures of 3 (left), FeMoco (center) and an overlay of the two

experimental X-ray structures (right).

Fig. 2 Mo K-edge HERFD-XAS data for compounds 1–4 and MoFe protein



Overview of XAS strengths and limitations, andrelations with other techniques: Information to be obtained from XANES and XES

35

Spectral feature

Information Accuracy and correlations

Other XAS Other technique

XANESedge position Oxidation

stateRelate to model compounds; be aware of correlation with average R

∆R: EXAFS UV-visible spectra, EPR

pre-edge features

Ligandgeometry

Relate to well-characterized model compounds

N from EXAFS UV-visible spectra, EPR, crystallography

Covalency of metal-ligandbond

- XANES of other metal-and ligandedges

EPR hyperfine structure

XESKβ’ line Metal ion

spin state- - EPR, magnetic

susceptibilityKβ” line Ligand

identity- EXAFS (Z ± 1

accuracy)Crystallography


Workshop X-ray Absorption Spectroscopy, SyNeW Utrecht, June 2, 2015M. C. Feiters and W. Meyer-Klaucke, in Practical Approaches

to Biological Inorganic Chemistry (R. R. Crichton and R. Louro, Editors; 2013)

Overview of XAS strengths and limitations,and relations with other techniques: Information to be obtained from the EXAFS region of XAS

36

Spectral featureInformation Accuracy and

correlationsOther XAS Other technique

amplitude Coordination number N

20 % (± 1), correlation with Debye-Waller factor

Ligandgeometry from XANES

Crystallography

decay of amplitude with k

σ a): static or thermal disorder, distinguish by T variation

Correlated with/ spoils accuracy of N

periodicity Distance R of scatterers

if shell resolved: ±0.02 Å, correlation with threshold energy ∆E0

Edge shift from XANES

Crystallography

phase Backscatterer atom type: C, N, O (‘low Z’) vs. P, S, Cl vs. larger backscatterer

Different to distinguish atom types adjacent in Periodic Table

Unambiguous from XES Kβ”line

Crystallography

a) Debye-Waller factor





EXAFS – SAXS – WAXS @ DUBBLE

Documents

Coordination Chemistry and Trace Element Biology SYNEW/Feiters2.pdf · M. C. Feiters and W. Meyer-Klaucke, in Practical Approaches to Biological Inorganic Chemistry (R. R. Crichton