EXAFS studies of binuclear iron complexes as models for hemerythrin and related proteins

Hedman, Britt; Co, Man Sung; Armstrong, William H.; Hodgson, Keith O.; Lippard, Stephen J.

doi:10.1021/ic00240a040

Cited by 23 publications

(16 citation statements)

References 8 publications

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“…However, introducing an Fe⋯P path at 3.14 Å remarkably improved the fit quality (Fit D, 2 •O 2 PPh 2 ), indicating that a phosphorus atom is present at this distance from the iron atoms in 2 •O 2 PPh 2 . Similarly, including an Fe⋯P path at 3.23 Å in addition to an Fe⋯Fe path at 3.30 Å remarkably improved the fits to the EXAFS data for [Fe 2 (O)(O 2 P(OPh) 2 ) 2 (HB(pz) 3 ) 2 ] 51. The 3.16 Å Fe⋯P distance found for 2 •O 2 PPh 2 is slightly shorter than the average 3.25 Å Fe⋯P distance seen in the crystal structure of 1 •O 2 PPh 2 , an observation consistent with the different iron oxidation states of these two complexes.…”

Section: Resultsmentioning

confidence: 87%

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂

Frisch

Martinho

et al. 2009

Inorg. Chem.

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Section: Resultsmentioning

confidence: 87%

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂

Frisch

Martinho

et al. 2009

Inorg. Chem.

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“…In cases where the metal-metal pairwise DebyeWaller factor is small (generally cases where the metal pair is rigidly bridged), strong contributions to the EXAFS signal are normally found. In contrast, for nonbridged or weakly bridged systems, the metal-metal contribution may not be clearly observable, and even if it is, interpretation may be complicated by scattering from C/N atoms in the outer shells of ligands that can mimic the metal-metal contribution (36)(37)(38).…”

Section: Resultsmentioning

confidence: 99%

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

Tan

Ensign

Ciurli

et al. 1992

Proc. Natl. Acad. Sci. U.S.A.

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The nickel/iron/sulfur center of the carbon monoxide dehydrogenase (carbon monoxide:(acceptor)oxidoreductase; EC 1.2.99.2) enzyme from Rhodospirillum rubrum (Rr-CODH) was studied by x-ray absorption spectroscopy at the Ni K edge. Extended x-ray absorption fine structure data show that the first Ni coordination shell consists of 2 S atoms at 2.23 A and 2-3 N/O atoms at 1.87 A. The edge structure indicates a distorted tetrahedral or five-coordinate Ni environment in both oxidized and reduced Rr-CODH. By comparing second-shell extended x-ray absorption fine structure data of Rr-CODH to that of (Et4N)3[NiFe3S4(SEt)4], a cubane-type cluster, it was clearly established that Ni in the Rr-CODH center is not involved in the core of a NiFe3S4 cubane cluster. One model consistent with the results is a mononuclear The metabolic pathways of certain bacteria involve conversion of CO to CO2 catalyzed by a Ni-containing enzyme, carbon monoxide dehydrogenase [CODH; carbon-monoxide: (acceptor)oxidoreductase; EC 1.2.99.2], now purified from several anaerobes (1-12). Some of these enzymes effect the synthesis of acetyl coenzyme A by means of the Wood pathway (13,14). Recent extended x-ray absorption fine structure (EXAFS) and x-ray absorption spectroscopy (XAS) edge studies of the CO-free, electron paramagnetic resonance-silent form of CODH from Clostridium thermoaceticum indicate a NiS4 (15) or =NiS2(O/N)2 (16) coordination environment with distorted square-planar or pyramidal geometry (16). EXAFS further suggests that an Fe-S cluster may be nearby (15). The CODH from Rhodospirillum rubrum (Rr-CODH) is a simpler enzyme (62-kDa monomer, 1 Ni and 8 Fe/S) that only oxidizes CO (8, 9). Isotopically induced electron paramagnetic resonance line-broadening suggests that Ni is covalently coupled to one or both Fe4S4 clusters in Rr-CODH and in other enzymes as well (17)(18)(19)(20). The possibility of an NiFe3S4 cubane-type cluster has been recognized (20), and alternative models exist in which Ni is bridged to Fe-S centers. Elucidation of the Ni-site structure is essential to understanding its role in catalysis. Toward that end, we report Ni K-edge XAS results for Rr-CODH. MATERIALS AND METHODSSample Preparations. Rr-CODH was purified and assayed as described (21). Purified Rr-CODH had a specific activity of 5200 gmol of CO oxidized per min-mg and contained 1.2 Ni and 8.1 Fe per mol of enzyme as determined by plasma emission spectroscopy. Rr-CODH samples were prepared for spectroscopic studies in an anaerobic glove box [Vacuum Atmospheres (Hawthorne, CA) Dri-Lab glove box model HE-493] containing an N2 atmosphere with <1 ppm 02. Rr-CODH samples in 100 mM Mops buffer, pH 7.5, were oxidized with indigo carmine as described (22) and were concentrated to 1.25 mM in a collodion ultrafiltration apparatus (Schleicher & Schuell). Some of the concentrated protein sample was reduced by adding sodium dithionite (5 mM final concentration dithionite). The oxidized and reduced samples were loaded into "140 IL XAS lucite cells (23 x 2 x 3 mm) wi...

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“…13 In particular Blackburn et al 35 have shown that to obtain an accurate description of the Cu-Cu distance in cytochrome oxidase, the spectrum needs to be fitted up to 16 Å −1 , while a similar conclusion was drawn by Hedman et al for the Fe-Fe distance in binuclear iron complexes. 36 Fig . 8(d) shows the WT transform of the calculated EX-AFS spectrum for the entire molecule.…”

Section: B Rhenium Diiminementioning

confidence: 99%

A wavelet analysis for the X-ray absorption spectra of molecules

Penfold

Tavernelli

Milne

et al. 2013

The Journal of Chemical Physics

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We present a Wavelet transform analysis for the X-ray absorption spectra of molecules. In contrast to the traditionally used Fourier transform approach, this analysis yields a 2D correlation plot in both R- and k-space. As a consequence, it is possible to distinguish between different scattering pathways at the same distance from the absorbing atom and between the contributions of single and multiple scattering events, making an unambiguous assignment of the fine structure oscillations for complex systems possible. We apply this to two previously studied transition metal complexes, namely iron hexacyanide in both its ferric and ferrous form, and a rhenium diimine complex, [ReX(CO)(3)(bpy)], where X = Br, Cl, or ethyl pyridine (Etpy). Our results demonstrate the potential advantages of using this approach and they highlight the importance of multiple scattering, and specifically the focusing phenomenon to the extended X-ray absorption fine structure (EXAFS) spectra of these complexes. We also shed light on the low sensitivity of the EXAFS spectrum to the Re-X scattering pathway.

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EXAFS studies of binuclear iron complexes as models for hemerythrin and related proteins

Cited by 23 publications

References 8 publications

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

A wavelet analysis for the X-ray absorption spectra of molecules

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EXAFS studies of binuclear iron complexes as models for hemerythrin and related proteins

Cited by 23 publications

References 8 publications

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O2

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O2

On the structure of the nickel/iron/sulfur center of the carbon monoxide dehydrogenase from Rhodospirillum rubrum: an x-ray absorption spectroscopy study.

A wavelet analysis for the X-ray absorption spectra of molecules

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Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂

Characterization of Two Distinct Adducts in the Reaction of a Nonheme Diiron(II) Complex with O₂