The role of X-ray spectroscopy in understanding the geometric and electronic structure of nitrogenase

AbstractX-ray absorption (XAS) and X-ray emission spectroscopy (XES) provide element specific probes of the geometric and electronic structures of metalloprotein active sites. As such, these methods have played an integral role in nitrogenase research beginning with the first EXAFS studies on nitrogenase in the late 1970s. Herein, we briefly explain the information that can be extracted from XAS and XES. We then highlight the recent applications of these methods in nitrogenase research. The influence of X-ray spectroscopy on our current understanding of the atomic structure and electronic structure of iron molybdenum cofactor (FeMoco) is emphasized. Contributions of X-ray spectroscopy to understanding substrate interactions and cluster biosynthesis are also discussed. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases

Re-evaluating the Cu K pre-edge XAS transition in complexes with covalent metal–ligand interactions

Three [Me2NN]Cu(h2 -L2) complexes (Me2NN ¼ HC[C(Me)NAr]2; L2 ¼ PhNO (2), ArF 2N2 (3), PhCH]CH2 (4); Ar ¼ 2,6-Me2-C6H3; ArF ¼ 3,5-(CF3)2-C6H3) have been studied by Cu K-edge X-ray absorption spectroscopy, as well as single- and multi-reference computational methods (DFT, TD-DFT, CASSCF, MRCI, and OVB). The study was extended to a range of both known and theoretical compounds bearing 2p-element donors as a means of deriving a consistent view of how the pre-edge transition energy responds in systems with significant ground state covalency. The ground state electronic structures of many of the compounds under investigation were found to be strongly influenced by correlation effects, resulting in ground state descriptions with majority contributions from a configuration comprised of a Cu(II) metal center anti-ferromagentically coupled to radical anion O2, PhNO, and ArF 2N2 ligands. In contrast, the styrene complex 4, which displays a Cu K pre-edge transition despite its formal d10 electron configuration, exhibits what can best be described as a Cu(I):(styrene)0 ground state with strong pbackbonding. The Cu K pre-edge features for these complexes increase in energy from 1 to 4, a trend that was tracked to the percent Cu(II)-character in the ground state. The unexpected shift to higher preedge transition energies with decreasing charge on copper (QCu) contributed to an assignment of the pre-edge features for these species as arising from metal-to-ligand charge transfer instead of the traditional Cu1s / Cu3d designation

Metal-only Lewis pairs between group 10 metals and Tl(I) or Ag(I): insights into the electronic consequences of Z-type ligand binding†

Complexes bearing electron rich transition metal centers, especially those displaying coordinative unsaturation, are well-suited to form reverse-dative σ-interactions with Lewis acids. Herein we demonstrate the generality of zerovalent, group 10 m-terphenyl isocyanide complexes to form reverse-dative σ-interactions to Tl(I) and Ag(I) centers. Structural and spectroscopic investigations of these metal-only Lewis pairs (MOLPs) has allowed insight into the electronic consequences of Lewis-acid ligation within the primary coordination sphere of a transition metal center. Treatment of the bis-isocyanide complex, Pt(CNArDipp2)2 (ArDipp2 = 2,6-(2,6-(i-Pr)2C6H3)2C6H3) with TlOTf (OTf = [O3SCF3]−) yields the Pt/Tl MOLP [TlPt(CNArDipp2)2]OTf (1). 1H NMR and IR spectroscopic studies on 1, and its Pd congener [TlPd(CNArDipp2)2]OTf (2), demonstrate that the M → Tl interaction is labile in solution. However, treatment of complexes 1 and 2 with Na[BArF4] (ArF = 3,5-(CF3)2C6H3) produces [TlPt(CNArDipp2)2]BArF4 (3) and [TlPd(CNArDipp2)2]BArF4 (4), in which Tl(I) binding is shown to be static by IR spectroscopy and, in the case of 3, 195Pt NMR spectroscopy as well. This result provides strong evidence that the M → Tl linkages can be attributed primarily to σ-donation from the group 10 metal to Tl, as loss of ionic stabilization of Tl by the triflate anion is compensated for by increasing the degree of M → Tl σ-donation. In addition, X-ray Absorption Near-Edge Spectroscopy (XANES) on the Pd/Tl and Ni/Tl MOLPs, [TlPd(CNArDipp2)2]OTf (2) and [TlNi(CNArMes2)3]OTf, respectively, is used to illustrate that the formation of a reverse-dative σ-interaction with Tl(I) does not alter the spectroscopic oxidation state of the group 10 metal. Also reported is the ability of M(CNArDipp2)2 (M = Pt, Pd) to form MOLPs with Ag(I), yielding the complexes [AgM(CNArDipp2)2]OTf (5, M = Pt; 6, M = Pd). As was determined for the Tl-containing MOLPs 1–4, it is shown that the spectroscopic oxidation states of the group 10 metal in 5 and 6 are essentially unchanged compared to the zerovalent precursors M(CNArDipp2)2. However, in the case of 5 and 6, the formation of a dative M → Ag σ-bonding interaction facilitates the binding of Lewis bases to the group 10 metal trans to Ag, illustrating the potential of acceptor fragments to open up new coordination sites on transition metal complexes without formal, two-electron oxidation

Revisiting the Mössbauer Isomer Shifts of the FeMoco Cluster of Nitrogenase and the Cofactor Charge

Despite decades of research, the structure–activity relationship of nitrogenase is still not understood. Only recently was the full molecular structure of the FeMo cofactor (FeMoco) revealed, but the charge and metal oxidation states of FeMoco have been controversial. With the recent identification of the interstitial atom as a carbide and the more recent revised oxidation-state assignment of the molybdenum atom as Mo(III), here we revisit the Mössbauer properties of FeMoco. By a detailed error analysis of density functional theory-computed isomer shifts and computing isomer shifts relative to the P-cluster, we find that only the charge of [MoFe7S9C]1– fits the experimental data. In view of the recent Mo(III) identification, the charge of [MoFe7S9C]1– corresponds to a formal oxidation-state assignment of Mo(III)3Fe(II)4Fe(III), although due to spin delocalization, the physical oxidation state distribution might also be interpreted as Mo(III)1Fe(II)4Fe(2.5)2Fe(III), according to a localized orbital analysis of the MS = 3/2 broken symmetry solution. These results can be reconciled with the recent spatially resolved anomalous dispersion study by Einsle et al. that suggests the Mo(III)3Fe(II)4Fe(III) distribution, if some spin localization (either through interactions with the protein environment or through vibronic coupling) were to take place.We thank E. Bill for valuable discussions and comments on the manuscript. S.D. and F.N. acknowledge the Max Planck Society for funding. This work was supported by the European Research Council (ERC) under the European Union’s Seventh Framework Programme (FP/2007-2013) ERC Grant Agreement No. 615414 (S.D.). R.B. acknowledges support from the Icelandic Research Fund, Grant Nos. 141218051 and 162880051 and the Univ. of Iceland Research Fund.Peer Reviewe

Type-zero copper proteins

Many proteins contain copper in a range of coordination environments, where it has various biological roles, such as transferring electrons or activating dioxygen. These copper sites can be classified by their function or spectroscopic properties. Those with a single copper atom are either type 1, with an intense absorption band near 600 nm, or type 2, with weak absorption in the visible region. We have built a novel copper(ii) binding site within structurally modified Pseudomonas aeruginosa azurins that does not resemble either existing type, which we therefore call 'type zero'. X-ray crystallographic analysis shows that these sites adopt distorted tetrahedral geometries, with an unusually short Cu–O (G45 carbonyl) bond. Relatively weak absorption near 800 nm and narrow parallel hyperfine splittings in electron paramagnetic resonance spectra are the spectroscopic signatures of type zero copper. Cyclic voltammetric experiments demonstrate that the electron transfer reactivities of type-zero azurins are enhanced relative to that of the corresponding type 2 (C112D) protein

Modern X-ray spectroscopy:XAS and XES in the laboratory

X-ray spectroscopy is an important tool for scientific analysis. While the earliest demonstration experiments were realised in the laboratory, with the advent of synchrotron light sources most of the experiments shifted to large scale synchrotron facilities. In the recent past there is an increased interest to perform X-ray experiments also with in-house laboratory sources, to simplify access to X-ray absorption and X-ray emission spectroscopy, in particular for routine measurements. Here we summarise the recent developments and comment on the most representative example experiments in the field of in-house laboratory X-ray spectroscopy. We first give an introduction and some historic background on X-ray spectroscopy. This is followed by an overview of the detection techniques used for X-ray absorption and X-ray emission measurements. A short paragraph also puts related high energy resolution and resonant techniques into context, though they are not yet feasible in the laboratory. At the end of this section the opportunities using wavelength dispersive X-ray spectroscopy in the laboratory are discussed. Then we summarise the relevant details of the recent experimental laboratory setups split into two separate sections, one for the recent von Hamos setups, and one for the recent Johann/Johansson type setups. Following that, focussing on chemistry and catalysis, we then summarise some of the notable X-ray absorption and X-ray emission experiments and the results accomplished with in-house setups. In a third part we then discuss some applications of laboratory X-ray spectroscopy with a particular focus on chemistry and catalysis.</p

Calcium Valence-to-Core X-ray Emission Spectroscopy: A Sensitive Probe of Oxo Protonation in Structural Models of the Oxygen-Evolving Complex

Calcium is an abundant, nontoxic metal that finds many roles in synthetic and biological systems including the oxygen-evolving complex (OEC) of photosystem II. Characterization methods for calcium centers, however, are underdeveloped compared to those available for transition metals. Valence-to-core X-ray emission spectroscopy (VtC XES) selectively probes the electronic structure of an element’s chemical environment, providing insight that complements the geometric information available from other techniques. Here, the utility of calcium VtC XES is established using an in-house dispersive spectrometer in combination with density functional theory. Spectral trends are rationalized within a molecular orbital framework, and Kβ_(2,5) transitions, derived from molecular orbitals with primarily ligand p character, are found to be a promising probe of the calcium coordination environment. In particular, it is shown that calcium VtC XES is sensitive to the electronic structure changes that accompany oxo protonation in Mn₃CaO₄-based molecular mimics of the OEC. Through correlation to calculations, the potential of calcium VtC XES to address unresolved questions regarding the mechanism of biological water oxidation is highlighted

Identification of a spin-coupled Mo(III) in the nitrogenase iron-molybdenum cofactor

International audienceNitrogenase is a complex enzyme that catalyzes the formation of ammonia utilizing a MoFe7S9C cluster. The presence of a central carbon atom was recently revealed, finally completing the atomic level description of the active site. However, important prerequisites for understanding the mechanism - the total charge, metal oxidation states and electronic structure are unknown. Herein we present high-energy resolution fluorescence detected Mo K-edge X-ray absorption spectroscopy of nitrogenase. Comparison to FeMo model complexes of known oxidation state indicates that the Mo in the FeMo cofactor of nitrogenase is best described as Mo(III), in contrast to the universally accepted Mo(IV) assignment. The oxidation state assignment is supported by theoretical calculations, which reveal the presence of an unusual spin-coupled Mo(III) site. Although so far Mo(III) was not reported to occur in biology the suggestion raises interesting parallels with the known homogenous Mo catalysts for N-2 reduction, where a Mo(III) compound is the N-2-binding species. It also requires a reassignment of the Fe oxidation states in the cofacto

The Nonphysiological Reductant Sodium Dithionite and [FeFe] Hydrogenase: Influence on the Enzyme Mechanism.

[FeFe] hydrogenases are highly active enzymes for interconverting protons and electrons with hydrogen (H2). Their active site H-cluster is formed of a canonical [4Fe-4S] cluster ([4Fe-4S]H) covalently attached to a unique [2Fe] subcluster ([2Fe]H), where both sites are redox active. Heterolytic splitting and formation of H2 takes place at [2Fe]H, while [4Fe-4S]H stores electrons. The detailed catalytic mechanism of these enzymes is under intense investigation, with two dominant models existing in the literature. In one model, an alternative form of the active oxidized state Hox, named HoxH, which forms at low pH in the presence of the nonphysiological reductant sodium dithionite (NaDT), is believed to play a crucial role. HoxH was previously suggested to have a protonated [4Fe-4S]H. Here, we show that HoxH forms by simple addition of sodium sulfite (Na2SO3, the dominant oxidation product of NaDT) at low pH. The low pH requirement indicates that sulfur dioxide (SO2) is the species involved. Spectroscopy supports binding at or near [4Fe-4S]H, causing its redox potential to increase by ∼60 mV. This potential shift detunes the redox potentials of the subclusters of the H-cluster, lowering activity, as shown in protein film electrochemistry (PFE). Together, these results indicate that HoxH and its one-electron reduced counterpart Hred′H are artifacts of using a nonphysiological reductant, and not crucial catalytic intermediates. We propose renaming these states as the "dithionite (DT) inhibited"states Hox-DTi and Hred-DTi. The broader potential implications of using a nonphysiological reductant in spectroscopic and mechanistic studies of enzymes are highlighted

Localized Electronic Structure of Nitrogenase FeMoco Revealed by Selenium K-edge High Resolution X-ray Absorption Spectroscopy

The size and complexity of Mo-dependent nitrogenase, a multicomponent enzyme capable of reducing dinitrogen to ammonia, have made a detailed understanding of the FeMo cofactor (FeMoco) active site electronic structure an ongoing challenge. Selective substitution of sulfur by selenium in FeMoco affords a unique probe wherein local Fe–Se interactions can be directly interrogated via high-energy resolution fluorescence detected X-ray absorption spectroscopic (HERFD XAS) and extended X-ray absorption fine structure (EXAFS) studies. These studies reveal a significant asymmetry in the electronic distribution of the FeMoco, suggesting a more localized electronic structure picture than is typically assumed for iron–sulfur clusters. Supported by experimental small molecule model data in combination with time dependent density functional theory (TDDFT) calculations, the HERFD XAS data is consistent with an assignment of Fe2/Fe6 as an antiferromagnetically coupled diferric pair. HERFD XAS and EXAFS have also been applied to Se-substituted CO-inhibited MoFe protein, demonstrating the ability of these methods to reveal electronic and structural changes that occur upon substrate binding. These results emphasize the utility of Se HERFD XAS and EXAFS for selectively probing the local electronic and geometric structure of FeMoco