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We have performed and analyzed the first combined 151Eu and 57Fe nuclear resonant vibrational spectroscopy (NRVS) for naturally abundant KEu(iii)[Fe(ii)(CN)6] or Eu(iii)[Fe(iii)(CN)6] complex.

Cluster multipole orderings composed of atomic high-rank multipole moments are theoretically investigated with a 5$d$-electron compound Ca$_5$Ir$_3$O$_{12}$ in mind. Ca$_5$Ir$_3$O$_{12}$ exhibits two hidden orders: One is an intermediate-temperature phase with time-reversal symmetry and the other is a low-temperature phase without time-reversal symmetry. By performing the symmetry and augmented multipole analyses for a $d$-orbital model under the hexagonal point group $D_{\rm 3h}$, we find that the 120$^{\circ}$-type ordering of the electric quadrupole corresponds to cluster electric toroidal dipole ordering with the electric ferroaxial moment, which can become the microscopic origin of the intermediate-temperature phase in Ca$_5$Ir$_3$O$_{12}$. Furthermore, based on ${}^{193}$Ir synchrotron-radiation-based M\"{o}ssbauer spectroscopy, we propose that the low-temperature phase in Ca$_5$Ir$_3$O$_{12}$ is regarded as a coexisting state with cluster electric toroidal dipole and cluster magnetic toroidal quadrupole, the latter of which is formed by the 120$^{\circ}$-type ordering of the magnetic octupole and accompanies a small uniform magnetization as a secondary effect. Our results provide a clue to two hidden phases in Ca$_5$Ir$_3$O$_{12}$., Comment: 6 pages, 4 figures, 1 table, accepted for publication in JPSJ

International audience; he biological conversion of N-2 to NH3 is accomplished by the nitrogenase family, which is collectively comprised of three closely related but unique metalloenzymes. In the present study, we have employed a combination of the synchrotron-based technique of Fe-57 nuclear resonance vibrational spectroscopy together with DFT-based quantum mechanics/molecular mechanics (QM/MM) calculations to probe the electronic structure and dynamics of the catalytic components of each of the three unique M N(2)ase enzymes (M = Mo, V, Fe) in both the presence (holo-) and absence (apo-) of the catalytic FeMco clusters (FeMoco, FeVco and FeFeco). The results described herein provide vibrational mode assignments for important fingerprint regions of the FeMco clusters, and demonstrate the sensitivity of the calculated partial vibrational density of states (PVDOS) to the geometric and electronic structures of these clusters. Furthermore, we discuss the challenges that are faced when employing NRVS to investigate large, multi-component metalloenzymatic systems, and outline the scope and limitations of current state-of-the-art theory in reproducing complex spectra.

Nature chemical biology 19(4), 498 - 506 (2023). doi:10.1038/s41589-022-01226-w, [NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H$_2$ into 2e$^−$ and 2H$^+$ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)$_2$(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN$^−$ molecules. Here, we investigated the sequential assembly of the [NiFe] cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O$_2$-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)$_2$(CO) fragment, a precursor that contained all cofactor components but remained redox inactive and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase., Published by Nature Publishing Group, Basingstoke

Inorganic chemistry 62(2), 769 - 781 (2023). doi:10.1021/acs.inorgchem.2c03278, Continued efforts are made on the development of earth-abundant metal catalysts for dehydrogenation/hydrolysis of amine boranes. In this study, complex [K-18-crown-6-ether][(NO)$_2$Fe(μ-$^{Me}$Pyr)(μ-CO)Fe(NO)$_2$] (3-K-crown, $^{Me}$Pyr = 3-methylpyrazolate) was explored as a pre-catalyst for the dehydrogenation of dimethylamine borane (DMAB). Upon evolution of H$_{2(g)}$ from DMAB triggered by 3-K-crown, parallel conversion of 3-K-crown into [(NO)$_2$Fe(N,N′-$^{Me}$PyrBH$_2$NMe$_2$)]− (5) and an iron-hydride intermediate [(NO)$_2$(CO)Fe(μ-H)Fe(CO)(NO)$_2$]$^−$ (A) was evidenced by X-ray diffraction/nuclear magnetic resonance/infrared/nuclear resonance vibrational spectroscopy experiments and supported by density functional theory calculations. Subsequent transformation of A into complex [(NO)$_2$Fe(μ-CO)$_2$Fe(NO)$_2$]$^−$ (6) is synchronized with the deactivated generation of H$_{2(g)}$. Through reaction of complex [Na-18-crown-6-ether][(NO)$_2$Fe(η$^2$-BH$_4$)] ($_4$-Na-crown) with CO(g) as an alternative synthetic route, isolated intermediate [Na-18-crown-6-ether][(NO)$_2$(CO)Fe(μ-H)Fe(CO)(NO)$_2$] (A-Na-crown) featuring catalytic reactivity toward dehydrogenation of DMAB supports a substrate-gated transformation of a pre-catalyst [(NO)$_2$Fe(μ-$^{Me}$Pyr)(μ-CO)Fe(NO)$_2$]$^−$ (3) into the iron-hydride species A as an intermediate during the generation of H$_{2(g)}$., Published by American Chemical Society, Washington, DC

Continued efforts are made on the development of earth-abundant metal catalysts for dehydrogenation/hydrolysis of amine boranes. In this study, complex [K-18-crown-6-ether][(NO)

Nuclear resonant vibrational spectroscopy (NRVS) is an excellent modern vibrational spectroscopy, in particular, for revealing site-specific information inside complicated molecules, such as enzymes. There are two different concepts about the energy calibration for a beamline or a monochromator (including a high resolution monochromator): the absolute energy calibration and the practical energy calibration. While the former pursues an as-fine-as-possible and as-repeatable-as-possible result, the latter includes the environment influenced variation from scan to scan, which often needs an in situ calibration measurement to track. However, an in situ measurement often shares a weak beam intensity and therefore has a noisy NRVS spectrum at the calibration sample location, not leading to a better energy calibration/correction in most cases. NRVS users for a long time have noticed that there are energy drifts in the vibrational spectra's zero-energy positions from scan to scan (ΔE

Methanotrophic bacteria utilize the nonheme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)2 intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both "open" and "closed" core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory to analyze the NRVS data of Q and its cryoreduced product as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q toward methane resides in the "spectator oxo" of its Fe(IV)2O2 core, in contrast to nonheme mononuclear Fe(IV)═O enzyme intermediates that H atoms abstract from weaker C-H bonds.

[NiFe]-hydrogenases are biotechnologically relevant enzymes catalyzing the reversible splitting of H$_2$ into 2 e$^- $ and 2 H$^+$ under ambient conditions. Catalysis takes place at the heterobimetallic NiFe(CN)$_2$(CO) center, whose multistep biosynthesis involves careful handling of two transition metals as well as potentially harmful CO and CN$^–$ molecules. Herein, we investigated the sequential assembly of the [NiFe]-cofactor, previously based on primarily indirect evidence, using four different purified maturation intermediates of the catalytic subunit, HoxG, of the O$_2$-tolerant membrane-bound hydrogenase from Cupriavidus necator. These included the cofactor-free apo-HoxG, a nickel-free version carrying only the Fe(CN)$_2$(CO) fragment, a precursor that contained all cofactor components but remained redox-inactive, and the fully mature HoxG. Through biochemical analyses combined with comprehensive spectroscopic investigation using infrared, electronic paramagnetic resonance, Mössbauer, X-ray absorption, and nuclear resonance vibrational spectroscopies, we obtained detailed insight into the sophisticated maturation process of [NiFe]-hydrogenase.

Ni and nitrogen-doped carbons are selective catalysts for CO2 reduction to CO (CO2R) but the hypothesized NiNx active sites are challenging to probe with traditional characterization methods. Here, we synthesize 61Ni-enriched model catalysts, termed 61NiPACN, in order to apply 61Ni Mössbauer spectroscopy using synchrotron-radiation (61Ni-SR-MS) to characterize the structure of these atomically dispersed NiNx sites. First, we demonstrate that the CO2R results and standard characterization techniques (SEM, PXRD, XPS, XANES, EXAFS) point to the existence of dispersed Ni active sites. Then, 61Ni-SR-MS reveal significant internal magnetic fields of ~5.4 T which is characteristic of paramagnetic, high spin Ni2+, in the 61NiPACN samples. Finally, theoretical calculations for a variety of Ni-Nx moieties confirm that high spin Ni2+ is stable in non-planar, tetrahedrally-distorted geometries which results in the calculated isotropic hyperfine coupling that is consistent with 61Ni-SR-MS measurements.

Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) are complementary tools for studying the vibrational and geometric structures of specific isotopically labeled molecular systems. Here we apply NRVS and DFT to characterize the trans-[57Fe(η2-H2)(H)(dppe)2][BPh4] [dppe = 1,2-bis(diphenylphosphino)ethane] complex. Heretofore, most NRVS observations have centered on the spectral region below 1000 cm-1, where the 57Fe signal is strongest. In this work, we show that state-of-the-art synchrotron facilities can extend the observable region to 2000 cm-1 and likely beyond, in measurements that require less than 1 day. The 57Fe-H stretch was revealed at 1915 cm-1, along with the asymmetric 57Fe-H2 stretch at 1774 cm-1. For a small fraction of the H2-dissociated product, the 57Fe-H stretch was detected at 1956 cm-1. The unique sensitivity to 57Fe motion and the isolated nature of the Fe-H/H2 stretching modes enabled NRVS to quantitatively analyze the sample composition.

The catalytic mechanism of [NiFe]-hydrogenases is a subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there are also a number of resting states, which are formed under oxidizing conditions. Although not directly involved in the catalytic cycle, the knowledge of their molecular structures and reactivity is important, because these states usually accumulate in the course of hydrogenase purification and may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit (HoxC) of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure resting redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe-labeled HoxC provided an unprecedented insight into the [NiFe] site modes, revealing their contributions in a spectral range otherwise superimposed by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data provide structural descriptions of the previously uncharacterized hydroxy- and water-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site., Active site vibrations of a [NiFe]-hydrogenase catalytic subunit are selectively probed by IR and NRV spectroscopy in two NiIIFeII and NiIIIFeII resting states, contributing in combination with DFT modeling to rationalized structural candidates.

The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin FeIV═O intermediate that, in most reactions, abstract a hydrogen atom from the substrate. Previously, the FeIV═O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the FeIV═O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate FeIV═O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented toward the substrate, which leads to an earlier transition state along the C-H coordinate.

Quantum electronic matter has long been understood in terms of two limiting behaviors of electrons: one of delocalized metallic states, and the other of localized magnetic states. Understanding the strange metallic behavior which develops at the brink of localization demands new probes of the underlying electronic charge dynamics. Using a state-of-the-art technique, synchrotron-radiation-based Mossbauer spectroscopy, we have studied the longitudinal charge fluctuations of the strange metal phase of beta-YbAlB4 as a function of temperature and pressure. We find that the usual single absorption peak in the Fermi-liquid regime splits into two peaks upon entering the critical regime. This spectrum is naturally interpreted as a single nuclear transition, modulated by nearby electronic valence fluctuations whose long time-scales are further enhanced, due to the formation of charged polarons. Our results represent a direct observation of critical charge fluctuations as a new signature of strange metals.

Synchrotron-radiation-based (SR-based) Mossbauer spectroscopy was applied to 193Ir 73 keV transition. Measuring the spectra of Ir metal and IrO2 at 7 K was performed to evaluate the spectrometer employing He-closed-cycle cryostats. The SR-based Mossbauer spectroscopy on 193Ir 73 keV Mossbauer transition was applied to investigate the physical properties of an intermediate valence iridium oxide Ca5Ir3O12. Efficiency of measuring spectra on operation modes of a synchrotron radiation facility was also discussed.

The Johari-Goldstein-β (JG-β) process is widely observed in a variety of glass-forming systems and recognized as an intrinsic process in deeply supercooled and glassy states. However, in some systems, e.g., glycerol, a clear sign of the JG-β process is often not apparent; for example, an isolated JG-β peak may not be observed in the dielectric relaxation spectrum. In this study, we directly investigated the angstrom-scale dynamics of glycerol through quasielastic scattering experiments using time-domain interferometry. The relaxation times of the local motions start to decouple from the timescale of the diffusion process and follow the established behavior of the JG-β process. This finding microscopically indicates the existence of the hidden JG-β process in glycerol. In addition, we succeeded in determining the decoupling temperature of the JG-β process by using the spatial-scale selectivity of the quasielastic scattering technique.

Methanotrophic bacteria utilize the non-heme diiron enzyme soluble methane monooxygenase (sMMO) to convert methane to methanol in the first step of their metabolic cycle under copper-limiting conditions. The structure of the sMMO Fe(IV)(2) intermediate Q responsible for activating the inert C-H bond of methane (BDE = 104 kcal/mol) remains controversial, with recent studies suggesting both “open” and “closed” core geometries for its active site. In this study, we employ nuclear resonance vibrational spectroscopy (NRVS) to probe the geometric and electronic structure of intermediate Q at cryogenic temperatures. These data demonstrate that Q decays rapidly during the NRVS experiment. Combining data from several years of measurements, we derive the NRVS vibrational features of intermediate Q as well as its cryoreduced decay product. A library of 90 open and closed core models of intermediate Q is generated using density functional theory (DFT) to analyze the NRVS data of Q and its cryoreduced product, as well as prior spectroscopic data on Q. Our analysis reveals that a subset of closed core models reproduce these newly acquired NRVS data as well as prior data. The reaction coordinate with methane is also evaluated using both closed and open core models of Q. These studies show that the potent reactivity of Q towards methane resides in the “spectator oxo” of its Fe(IV)(2)O(2) core, in contrast to non-heme mononuclear Fe(IV)=O enzyme intermediates that H-atom abstract from weaker C-H bonds.

Nuclear resonant vibrational spectroscopy (NRVS) is a synchrotron radiation (SR)-based nuclear inelastic scattering spectroscopy that measures the phonons (i.e., vibrational modes) associated with the nuclear transition. It has distinct advantages over traditional vibration spectroscopy and has wide applications in physics, chemistry, bioinorganic chemistry, materials sciences, and geology, as well as many other research areas. In this article, we present a scientific and figurative description of this yet modern tool for the potential users in various research fields in the future. In addition to short discussions on its development history, principles, and other theoretical issues, the focus of this article is on the experimental aspects, such as the instruments, the practical measurement issues, the data process, and a few examples of its applications. The article concludes with introduction to non-57Fe NRVS and an outlook on the impact from the future upgrade of SR rings.

The human mitochondrial protein, mitoNEET (mNT), belongs to the family of small [2Fe-2S] NEET proteins that bind their iron-sulfur clusters with a novel and characteristic 3Cys:1His coordination motif. mNT has been implicated in the regulation of lipid and glucose metabolisms, iron/reactive oxygen species homeostasis, cancer and possibly Parkinson’s disease. The geometric structure of mNT as a function of redox state and pH is critical for its function. In this study we combine (57)Fe nuclear resonance vibrational spectroscopy (NRVS) with density functional theory (DFT) calculations to understand the novel properties of this important protein.

A diiron complex containing a bridging hydride and a protonated terminal thiolate of the form [(μ,κ2-bdtH)(μ-PPh2)(μ-H)Fe2(CO)5]+ has been investigated through 57Fe nuclear resonance vibrational spectroscopy (NRVS) and interpreted using density functional theory (DFT) calculations. We report the Fe–μH–Fe wagging mode, and indications for Fe–μD stretching vibrations in the D-isotopologue, observed by 57Fe-NRVS. Our combined approach demonstrates an asymmetric sharing of the hydride between the two iron sites that yields two nondegenerate Fe–μH/D stretching vibrations. The studied complex provides an important model relevant to biological hydrogen catalysis intermediates. The complex mimics proposals for the binuclear metal sites in [FeFe] and [NiFe] hydrogenases. It is also an appealing prototype for the ‘Janus intermediate’ of nitrogenase, which has been proposed to contain two bridging Fe–H–Fe hydrides and two protonated sulfurs at the FeMo-cofactor. The significance of observing indirect effects of the bridging hydride, as well as obstacles in its direct observation, is discussed in the context of biological hydrogen intermediates., Fe–H–Fe bridging iron hydrides in model systems and metalloenzymes: benefits and challenges in revealing their vibrational signatures using NRVS spectroscopy and DFT calculations.

[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, (57)Fe nuclear resonance vibrational spectroscopy (NRVS), and density functional theory (DFT) calculations to observe and characterize the vibrational modes involving motion of the 2-azapropane-1,3-dithiolate (ADT) ligand bridging the two iron sites in the [2Fe](H) subcluster. A –(13)C(2)H(2)– ADT labeling in the synthetic diiron precursor of [2Fe](H) produced isotope effects observed throughout the NRVS spectrum. The two precursor isotopologues were then used to reconstitute the H-cluster of [FeFe] hydrogenase from Chlamydomonas reinhardtii (CrHydA1), and NRVS was measured on samples poised in the catalytically crucial H(hyd) state containing a terminal hydride at the distal Fe site. The (13)C(2)H isotope effects were observed also in the H(hyd) spectrum. DFT simulations of the spectra allowed identification of the (57)Fe normal modes coupled to the ADT ligand motions. Particularly, a variety of normal modes involve shortening of the distance between the distal Fe–H hydride and ADT N–H bridgehead hydrogen, which may be relevant to the formation of a transition state on the way to H(2) formation.

The pterin-dependent nonheme iron enzymes hydroxylate aromatic amino acids to perform the biosynthesis of neurotransmitters to maintain proper brain function. These enzymes activate oxygen using a pterin cofactor and an aromatic amino acid substrate bound to the Fe(II) active site to form a highly reactive Fe(IV) = O species that initiates substrate oxidation. In this study, using tryptophan hydroxylase, we have kinetically generated a pre-Fe(IV) = O intermediate and characterized its structure as a Fe(II)-peroxy-pterin species using absorption, Mössbauer, resonance Raman, and nuclear resonance vibrational spectroscopies. From parallel characterization of the pterin cofactor and tryptophan substrate–bound ternary Fe(II) active site before the O(2) reaction (including magnetic circular dichroism spectroscopy), these studies both experimentally define the mechanism of Fe(IV) = O formation and demonstrate that the carbonyl functional group on the pterin is directly coordinated to the Fe(II) site in both the ternary complex and the peroxo intermediate. Reaction coordinate calculations predict a 14 kcal/mol reduction in the oxygen activation barrier due to the direct binding of the pterin carbonyl to the Fe(II) site, as this interaction provides an orbital pathway for efficient electron transfer from the pterin cofactor to the iron center. This direct coordination of the pterin cofactor enables the biological function of the pterin-dependent hydroxylases and demonstrates a unified mechanism for oxygen activation by the cofactor-dependent nonheme iron enzymes.

Membrane viscosity is a fundamental property that controls molecular transport and structural rearrangements in lipid membranes. Given its importance in many cell processes, various experimental and computational methods have been developed to measure the membrane viscosity, yet the estimated values depend highly on the method and vary by orders of magnitude. Here we investigate the molecular origins of membrane viscosity by measuring the nanoscale dynamics of the lipid acyl tails using x-ray and neutron spectroscopy techniques. The results show that the membrane viscosity can be estimated from the structural relaxation times of the lipid tails.

To study metalloenzymes in detail, we developed a new experimental setup allowing the controlled preparation of catalytic intermediates for characterization by various spectroscopic techniques. The in situ monitoring of redox transitions by infrared spectroscopy in enzyme lyophilizate, crystals, and solution during gas exchange in a wide temperature range can be accomplished as well. Two O2‐tolerant [NiFe]‐hydrogenases were investigated as model systems. First, we utilized our platform to prepare highly concentrated hydrogenase lyophilizate in a paramagnetic state harboring a bridging hydride. This procedure proved beneficial for 57Fe nuclear resonance vibrational spectroscopy and revealed, in combination with density functional theory calculations, the vibrational fingerprint of this catalytic intermediate. The same in situ IR setup, combined with resonance Raman spectroscopy, provided detailed insights into the redox chemistry of enzyme crystals, underlining the general necessity to complement X‐ray crystallographic data with spectroscopic analyses., A multifunctional setup for in situ spectroscopy on gas‐processing metalloenzymes enables the controlled preparation of redox states in various sample forms. This setup allowed the first NRVS characterization of the Nia−C state of [NiFe]‐hydrogenases, provided new insights into the reductive activation of these enzymes, and revealed a so‐far unknown redox state of the oxygen‐tolerant membrane‐bound hydrogenase from R. eutropha.

International audience; The human mitochondrial protein, mitoNEET (mNT), belongs to the family of small [2Fe-2S] NEET proteins that bind their iron–sulfur clusters with a novel and characteristic 3Cys:1His coordination motif. mNT has been implicated in the regulation of lipid and glucose metabolisms, iron/reactive oxygen species homeostasis, cancer, and possibly Parkinson’s disease. The geometric structure of mNT as a function of redox state and pH is critical for its function. In this study, we combine 57Fe nuclear resonance vibrational spectroscopy with density functional theory calculations to understand the novel properties of this important protein.

Nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) are complementary tools for studying the vibrational and geometric structure of specific isotopically-labeled molecular systems. Here we apply NRVS and DFT to characterize the trans-[(57)Fe(η(2)-H(2))(H)(dppe)(2)][BPh(4)] complex. Heretofore, most NRVS observations have centered on the spectral region below 1000 cm(−1) where the (57)Fe signal is strongest. In this work, we show that state-of-the-art synchrotron facilities can extend the observable region to 2000 cm(−1) and likely beyond, in measurements that require less than one day. The (57)Fe–H stretch was revealed at 1915 cm(−1), along with the asymmetric (57)Fe–H(2) stretch at 1774 cm(−1). For a small fraction of the H(2)-dissociated product, the (57)Fe–H stretch was detected at 1956 cm(−1). The unique sensitivity to (57)Fe motion and the isolated nature of the Fe–H/H(2) stretching modes enabled NRVS to quantitatively analyze the sample composition.

The α-ketoglutarate (αKG)-dependent oxygenases catalyze a diverse range of chemical reactions using a common high-spin Fe(IV)=O intermediate and, in most reactions, abstracts a hydrogen atom from the substrate. Previously, the Fe(IV)=O intermediate in the αKG-dependent halogenase SyrB2 was characterized by nuclear resonance vibrational spectroscopy (NRVS) and density functional theory (DFT) calculations, which demonstrated that it has a trigonal-pyramidal geometry with the scissile C-H bond of the substrate calculated to be perpendicular to the Fe-O bond. Here, we have used NRVS and DFT calculations to show that the Fe(IV)=O complex in taurine dioxygenase (TauD), the αKG-dependent hydroxylase in which this intermediate was first characterized, also has a trigonal bipyramidal geometry, but with an aspartate residue replacing the equatorial halide of the SyrB2 intermediate. Computational analysis of hydrogen atom abstraction by square pyramidal, trigonal bipyramidal, and six-coordinate Fe(IV)=O complexes in two different substrate orientations (one more along [σ channel] and another more perpendicular [π channel] to the Fe-O bond) reveals similar activation barriers. Thus, both substrate approaches to all three geometries are competent in hydrogen atom abstraction. The equivalence in reactivity between the two substrate orientations arises from compensation of the promotion energy (electronic excitation within the d manifold) required to access the π channel by the significantly larger oxyl character present in the pπ orbital oriented towards the substrate, which leads to an earlier transition state along the C-H coordinate.

The catalytic mechanism of H2 conversion by [NiFe]-hydrogenase is subject of extensive research. Apart from at least four reaction intermediates of H2/H+ cycling, there is also a number of resting states, which are formed under oxidizing conditions. While not directly involved in the catalytic cycle, knowledge of their molecular structure and reactivity is important, because these states usually accumulate in the course of hydrogenase purification, and they may also play a role in vivo during hydrogenase maturation. Here, we applied low-temperature infrared (cryo-IR) and nuclear resonance vibrational spectroscopy (NRVS) to the isolated catalytic subunit, HoxC, of the heterodimeric regulatory [NiFe]-hydrogenase (RH) from Ralstonia eutropha. Cryo-IR spectroscopy revealed that the HoxC protein can be enriched in almost pure redox states suitable for NRVS investigation. NRVS analysis of the hydrogenase catalytic center is usually hampered by strong spectral contributions of the FeS clusters of the small, electron-transferring subunit. Therefore, our approach to investigate the FeS cluster-free, 57Fe labeled HoxC granted an unprecedented view onto the active site modes, including those obscured by FeS cluster-derived bands. Rationalized by density functional theory (DFT) calculations, our data allow the structural description of two hydroxy-containing resting states. Our work highlights the relevance of cryogenic vibrational spectroscopy and DFT to elucidate the structure of barely defined redox states of the [NiFe]-hydrogenase active site.

NO and O2 are detoxified in many organisms using flavodiiron proteins (FDPs). The exact coordination of the iron centre in the active site of these enzymes remains unclear despite numerous structural studies. Here, we used 57Fe nuclear resonance vibrational spectroscopy (NRVS) to probe the iron-ligand interactions in Escherichia coli FDP. This data combined with density functional theory (DFT) and 57Fe Mössbauer spectroscopy indicate that the oxidised form of FDP contains a dihydroxo-diferric Fe(III)–(µOH–)2–Fe(III) active site, while its reduction gives rise to a monohydroxo-diferrous Fe(II)–(µOH–)–Fe(II) site upon elimination of one bridging OH– ligand, thereby providing an open coordination site for NO binding. Prolonged NRVS data collection of the oxidised FDP resulted in photoreduction and formation of a partially reduced diiron center with two bridging hydroxyl ligands. These results have crucial implications for studying and understanding the mechanism of FDP as well as other non-haem diiron enzymes.

This paper presents an absolute X-ray photon energy measurement method that uses a Bond diffractometer. The proposed system enables the prompt and rapid in situ measurement of photon energies over a wide energy range. The diffractometer uses a reference silicon single-crystal plate and a highly accurate angle encoder called SelfA. The performance of the system is evaluated by repeatedly measuring the energy of the first excited state of the potassium-40 nuclide. The excitation energy is determined as 29829.39 (6) eV, and this is one order of magnitude more accurate than the previous measurement. The estimated uncertainty of the photon energy measurement was 0.7 p.p.m. as a standard deviation and the maximum observed deviation was 2 p.p.m.

[FeFe] hydrogenases are the most active H2 converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O2‐stable state called Hinact. To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in‐depth spectroscopic characterization by X‐ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O2‐stable hydrogenases and molecular catalysts., Caught in the Hinact: [FeFe] hydrogenases are highly efficient catalysts for the interconversion of H2 and H+. However, they are highly O2 sensitive. Here, the X‐ray crystal structure of an O2‐stable state of [FeFe] hydrogenase, along with comprehensive spectroscopic analysis and molecular calculations reveals the presence of a sulfur ligand bound to the active site. These results provide crucial insight into O2 stability mechanisms in proteins.

[NiFe]-hydrogenases catalyze the reversible reaction H(2) ⇄ 2H(+) + 2e(−). Their basic module consists of a large subunit, coordinating the NiFe(CO)(CN)(2) center, and a small subunit that carries electron-transferring iron-sulfur clusters. Here, we report the in vitro assembly of fully functional [NiFe]-hydrogenase starting from the isolated large and small subunits. Activity assays complemented by spectroscopic measurements revealed a native-like hydrogenase. This approach was used to label exclusively the NiFe(CO)(CN)(2) center with (57)Fe, enabling a clear view of the catalytic site by means of nuclear resonance vibrational spectroscopy. This strategy paves the way for in-depth studies of [NiFe]-hydrogenase catalytic intermediates.

Angewandte Chemie / International edition 59(38), 16786 - 16794 (2020). doi:10.1002/anie.202005208, [FeFe] hydrogenases are the most active H$_2$ converting catalysts in nature, but their extreme oxygen sensitivity limits their use in technological applications. The [FeFe] hydrogenases from sulfate reducing bacteria can be purified in an O$_2$‐stable state called Hinact. To date, the structure and mechanism of formation of Hinact remain unknown. Our 1.65 Å crystal structure of this state reveals a sulfur ligand bound to the open coordination site. Furthermore, in‐depth spectroscopic characterization by X‐ray absorption spectroscopy (XAS), nuclear resonance vibrational spectroscopy (NRVS), resonance Raman (RR) spectroscopy and infrared (IR) spectroscopy, together with hybrid quantum mechanical and molecular mechanical (QM/MM) calculations, provide detailed chemical insight into the Hinact state and its mechanism of formation. This may facilitate the design of O$_2$‐stable hydrogenases and molecular catalysts., Published by Wiley-VCH, Weinheim