Advanced paramagnetic resonance spectroscopies of iron–sulfur proteins: Electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM)

AbstractThe advanced electron paramagnetic resonance (EPR) techniques, electron nuclear double resonance (ENDOR) and electron spin echo envelope modulation (ESEEM) spectroscopies, provide unique insights into the structure, coordination chemistry, and biochemical mechanism of nature's widely distributed iron–sulfur cluster (FeS) proteins. This review describes the ENDOR and ESEEM techniques and then provides a series of case studies on their application to a wide variety of FeS proteins including ferredoxins, nitrogenase, and radical SAM enzymes. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases

Characterization of an Fe≡N−NH_2 Intermediate Relevant to Catalytic N_2 Reduction to NH_3

The ability of certain transition metals to mediate the reduction of N_2 to NH_3 has attracted broad interest in the biological and inorganic chemistry communities. Early transition metals such as Mo and W readily bind N_2 and mediate its protonation at one or more N atoms to furnish M(N_xH_y) species that can be characterized and, in turn, extrude NH_3. By contrast, the direct protonation of Fe–N_2 species to Fe(N_xH_y) products that can be characterized has been elusive. Herein, we show that addition of acid at low temperature to [(TPB)Fe(N_2)][Na(12-crown-4)] results in a new S = 1/2 Fe species. EPR, ENDOR, Mössbauer, and EXAFS analysis, coupled with a DFT study, unequivocally assign this new species as [(TPB)Fe≡N–NH_2]^+, a doubly protonated hydrazido(2−) complex featuring an Fe-to-N triple bond. This unstable species offers strong evidence that the first steps in Fe-mediated nitrogen reduction by [(TPB)Fe(N_2)][Na(12-crown-4)] can proceed along a distal or “Chatt-type” pathway. A brief discussion of whether subsequent catalytic steps may involve early or late stage cleavage of the N–N bond, as would be found in limiting distal or alternating mechanisms, respectively, is also provided

The Asp1 pyrophosphatase from S. pombe hosts a [2Fe-2S]2+ cluster in vivo

AbstractThe Schizosaccharomyces pombe Asp1 protein is a bifunctional kinase/pyrophosphatase that belongs to the highly conserved eukaryotic diphosphoinositol pentakisphosphate kinase PPIP5K/Vip1 family. The N-terminal Asp1 kinase domain generates specific high-energy inositol pyrophosphate (IPP) molecules, which are hydrolyzed by the C-terminal Asp1 pyrophosphatase domain (Asp1365−920). Thus, Asp1 activities regulate the intracellular level of a specific class of IPP molecules, which control a wide number of biological processes ranging from cell morphogenesis to chromosome transmission. Recently, it was shown that chemical reconstitution of Asp1371−920 leads to the formation of a [2Fe-2S] cluster; however, the biological relevance of the cofactor remained under debate. In this study, we provide evidence for the presence of the Fe–S cluster in Asp1365−920 inside the cell. However, we show that the Fe–S cluster does not influence Asp1 pyrophosphatase activity in vitro or in vivo. Characterization of the as-isolated protein by electronic absorption spectroscopy, mass spectrometry, and X-ray absorption spectroscopy is consistent with the presence of a [2Fe-2S]2+ cluster in the enzyme. Furthermore, we have identified the cysteine ligands of the cluster. Overall, our work reveals that Asp1 contains an Fe–S cluster in vivo that is not involved in its pyrophosphatase activity.</jats:p

A low spin manganese(IV) nitride single molecule magnet

Structural, spectroscopic and magnetic methods have been used to characterize the tris(carbene) borate compound PhB(MesIm)(3)Mn equivalent to N as a four-coordinate manganese(IV) complex with a low spin (S = 1/2) configuration. The slow relaxation of the magnetization in this complex, i.e. its single-molecule magnet (SMM) properties, is revealed under an applied dc field. Multireference quantum mechanical calculations indicate that this SMM behavior originates from an anisotropic ground doublet stabilized by spin-orbit coupling. Consistent theoretical and experiment data show that the resulting magnetization dynamics in this system is dominated by ground state quantum tunneling, while its temperature dependence is influenced by Raman relaxation

Free H_2 Rotation vs Jahn−Teller Constraints in the Nonclassical Trigonal (TPB)Co−H_2 Complex

Proton exchange within the M–H_2 moiety of (TPB)Co(H_2) (Co–H_2; TPB = B(o-C_6H_4PiPr_2)_3) by 2-fold rotation about the M–H_2 axis is probed through EPR/ENDOR studies and a neutron diffraction crystal structure. This complex is compared with previously studied (SiP^(iPr)_3)Fe(H_2) (Fe–H_2) (SiP^(iPr)_3 = [Si(o-C_6H_4PiPr_2)_3]). The g-values for Co–H_2 and Fe–H_2 show that both have the Jahn–Teller (JT)-active ^2E ground state (idealized C_3 symmetry) with doubly degenerate frontier orbitals, (e)^3 = [|m_L ± 2>]^3 = [x^2 – y^2, xy]^3, but with stronger linear vibronic coupling for Co–H_2. The observation of ^1H ENDOR signals from the Co–HD complex, ^2H signals from the Co–D_2/HD complexes, but no ^1H signals from the Co–H_2 complex establishes that H_2 undergoes proton exchange at 2 K through rotation around the Co–H_2 axis, which introduces a quantum-statistical (Pauli-principle) requirement that the overall nuclear wave function be antisymmetric to exchange of identical protons (I = 1/2; Fermions), symmetric for identical deuterons (I = 1; Bosons). Analysis of the 1-D rotor problem indicates that Co–H_2 exhibits rotor-like behavior in solution because the underlying C_3 molecular symmetry combined with H_2 exchange creates a dominant 6-fold barrier to H_2 rotation. Fe–H_2 instead shows H_2 localization at 2 K because a dominant 2-fold barrier is introduced by strong Fe(3d)→ H_2(σ^*) π-backbonding that becomes dependent on the H_2 orientation through quadratic JT distortion. ENDOR sensitively probes bonding along the L_2–M–E axis (E = Si for Fe–H_2; E = B for Co–H_2). Notably, the isotropic ^1H/^2H hyperfine coupling to the diatomic of Co–H_2 is nearly 4-fold smaller than for Fe–H_2

Spectroscopic characterization of the Co-substituted C-terminal domain of rubredoxin-2

Pseudomonas putida rubredoxin-2 (Rxn2) is an essential member of the alkane hydroxylation pathway and transfers electrons from a reductase to the membrane-bound hydroxylase. The regioselective hydroxylation of linear alkanes is a challenging chemical transformation of great interest for the chemical industry. Herein, we report the preparation and spectroscopic characterization of cobalt-substituted P. putida Rxn2 and a truncated version of the protein consisting of the C-terminal domain of the protein. Our spectroscopic data on the Co-substituted C-terminal domain supports a high-spin Co(II) with a distorted tetrahedral coordination environment. Investigation of the two-domain protein Rxn2 provides insights into the metal-binding properties of the N-terminal domain, the role of which is not well understood so far. Circular dichroism, electron paramagnetic resonance and X-ray absorption spectroscopies support an alternative Co-binding site within the N-terminal domain, which appears to not be relevant in nature. We have shown that chemical reconstitution in the presence of Co leads to incorporation of Co(II) into the active site of the C-terminal domain, but not the N-terminal domain of Rxn2 indicating distinct roles for the two rubredoxin domain

XAS and EPR in Situ Observation of Ru(V) Oxo Intermediate in a Ru Water Oxidation Complex.

In this study, we combine in situ spectroelectrochemistry coupled with electron paramagnetic resonance (EPR) and X-ray absorption spectroscopies (XAS) to investigate a molecular Ru-based water oxidation catalyst bearing a polypyridinic backbone [RuII(OH2)(Py2Metacn)]2+ . Although high valent key intermediate species arising in catalytic cycles of this family of compounds have remain elusive due to the lack of additional anionic ligands that could potentially stabilize them, mechanistic studies performed on this system proposed a water nucleophilic attack (WNA) mechanism for the O-O bond formation. Employing in situ experimental conditions and complementary spectroscopic techniques allowed to observe intermediates that provide support for a WNA mechanism, including for the first time a Ru(V) oxo intermediate based on the Py2Metacn ligand, in agreement with the previously proposed mechanism

Evidence for Oxygen Binding at the Active Site of Particulate Methane Monooxygenase

Particulate methane monooxygenase (pMMO) is an integral membrane metalloenzyme that converts methane to methanol in methanotrophic bacteria. The enzyme consists of three subunits, pmoB, pmoA, and pmoC, organized in an α₃β₃γ₃ trimer. Studies of intact pMMO and a recombinant soluble fragment of the pmoB subunit (denoted as spmoB) indicate that the active site is located within the soluble region of pmoB at the site of a crystallographically modeled dicopper center. In this work, we have investigated the reactivity of pMMO and spmoB with oxidants. Upon reduction and treatment of spmoB with O₂ or H₂O₂ or pMMO with H₂O₂, an absorbance feature at 345 nm is generated. The energy and intensity of this band are similar to those of the μ-η²:η²-peroxo-Cu^II₂ species formed in several dicopper enzymes and model compounds. The feature is not observed in inactive spmoB variants in which the dicopper center is disrupted, consistent with O₂ binding to the proposed active site. Reaction of the 345 nm species with CH₄ results in the disappearance of the spectroscopic feature, suggesting that this O₂ intermediate is mechanistically relevant. Taken together, these observations provide strong new support for the identity and location of the pMMO active site

13C and 63,65Cu ENDOR studies of CO Dehydrogenase from Oligotropha carboxidovorans. Experimental Evidence in Support of a Copper–Carbonyl Intermediate

We report here an ENDOR study of an S = 1/2 intermediate state trapped during reduction of the binuclear Mo/Cu enzyme CO dehydrogenase by CO. ENDOR spectra of this state confirm that the (63,65)Cu nuclei exhibits strong and almost entirely isotropic coupling to the unpaired electron, show that this coupling atypically has a positive sign, aiso = +148 MHz, and indicate an apparently undetectably small quadrupolar coupling. When the intermediate is generated using (13)CO, coupling to the (13)C is observed, with aiso = +17.3 MHz. A comparison with the couplings seen in related, structurally assigned Mo(V) species from xanthine oxidase, in conjunction with complementary computational studies, leads us to conclude that the intermediate contains a partially reduced Mo(V)/Cu(I) center with CO bound at the copper. Our results provide strong experimental support for a reaction mechanism that proceeds from a comparable complex of CO with fully oxidized Mo(VI)/Cu(I) enzyme