Temperature-dependent iron motion in extremophile rubredoxins - no need for 'corresponding states'.

Extremophile organisms are known that can metabolize at temperatures down to - 25 °C (psychrophiles) and up to 122 °C (hyperthermophiles). Understanding viability under extreme conditions is relevant for human health, biotechnological applications, and our search for life elsewhere in the universe. Information about the stability and dynamics of proteins under environmental extremes is an important factor in this regard. Here we compare the dynamics of small Fe-S proteins - rubredoxins - from psychrophilic and hyperthermophilic microorganisms, using three different nuclear techniques as well as molecular dynamics calculations to quantify motion at the Fe site. The theory of 'corresponding states' posits that homologous proteins from different extremophiles have comparable flexibilities at the optimum growth temperatures of their respective organisms. Although 'corresponding states' would predict greater flexibility for rubredoxins that operate at low temperatures, we find that from 4 to 300 K, the dynamics of the Fe sites in these homologous proteins are essentially equivalent.

BL09XU: an advanced hard X-ray photoelectron spectroscopy beamline of SPring-8.

The BL09XU beamline of SPring-8 has been reorganized into a beamline dedicated for hard X-ray photoelectron spectroscopy (HAXPES) to provide advanced capabilities with upgraded optical instruments. The beamline has two HAXPES analyzers to cover a wide range of applications. Two sets of double channel-cut crystal monochromators with the Si(220) and (311) reflections were installed to perform resonant HAXPES analyses with a total energy resolution of less than 300 meV over a wide energy range (4.9-12 keV) while achieving a fixed-exit condition. A double-crystal X-ray phase retarder using diamond crystals controls the polarization state with a high degree of polarization over 0.9 in the wide energy range 5.9-9.5 keV. Each HAXPES analyzer is equipped with a focusing mirror to provide a high-flux microbeam. The design and performance of the upgraded instruments are presented.

Two-dimensional Kß-Kα fluorescence spectrum by nonlinear resonant inelastic X-ray scattering.

High sensitivity of the Kß fluorescence spectrum to electronic state is widely used to investigate spin and oxidation state of first-row transition-metal compounds. However, the complex electronic structure results in overlapping spectral features, and the interpretation may be hampered by ambiguity in resolving the spectrum into components representing different electronic states. Here, we tackle this difficulty with a nonlinear resonant inelastic X-ray scattering (RIXS) scheme, where we leverage sequential two-photon absorption to realize an inverse process of the Kß emission, and measure the successive Kα emission. The nonlinear RIXS reveals two-dimensional (2D) Kß-Kα fluorescence spectrum of copper metal, leading to better understanding of the spectral feature. We isolate 3d-related satellite peaks in the 2D spectrum, and find good agreement with our multiplet ligand field calculation. Our work not only advances the fluorescence spectroscopy, but opens the door to extend RIXS into the nonlinear regime.

Nuclear Resonance Vibrational Spectroscopy Definition of Peroxy Intermediates in Catechol Dioxygenases: Factors that Determine Extra- versus Intradiol Cleavage.

The extradiol dioxygenases (EDOs) and intradiol dioxygenases (IDOs) are nonheme iron enzymes that catalyze the oxidative aromatic ring cleavage of catechol substrates, playing an essential role in the carbon cycle. The EDOs and IDOs utilize very different FeII and FeIII active sites to catalyze the regiospecificity in their catechol ring cleavage products. The factors governing this difference in cleavage have remained undefined. The EDO homoprotocatechuate 2,3-dioxygenase (HPCD) and IDO protocatechuate 3,4-dioxygenase (PCD) provide an opportunity to understand this selectivity, as key O2 intermediates have been trapped for both enzymes. Nuclear resonance vibrational spectroscopy (in conjunction with density functional theory calculations) is used to define the geometric and electronic structures of these intermediates as FeII-alkylhydroperoxo (HPCD) and FeIII-alkylperoxo (PCD) species. Critically, in both intermediates, the initial peroxo bond orientation is directed toward extradiol product formation. Reaction coordinate calculations were thus performed to evaluate both the extra- and intradiol O-O cleavage for the simple organic alkylhydroperoxo and for the FeII and FeIII metal catalyzed reactions. These results show the FeII-alkylhydroperoxo (EDO) intermediate undergoes facile extradiol O-O bond homolysis due to its extra e-, while for the FeIII-alkylperoxo (IDO) intermediate the extradiol cleavage involves a large barrier and would yield the incorrect extradiol product. This prompted our evaluation of a viable mechanism to rearrange the FeIII-alkylperoxo IDO intermediate for intradiol cleavage, revealing a key role in the rebinding of the displaced Tyr447 ligand in this rearrangement, driven by the proton delivery necessary for O-O bond cleavage.

Observation of a critical charge mode in a strange metal.

Understanding the strange metallic behavior that develops at the brink of localization in quantum materials requires probing the underlying electronic charge dynamics. Using synchrotron radiation-based Mössbauer spectroscopy, we studied the charge fluctuations of the strange metal phase of ß-YbAlB4 as a function of temperature and pressure. We found that the usual single absorption peak in the Fermi-liquid regime splits into two peaks upon entering the critical regime. We interpret this spectrum as a single nuclear transition, modulated by nearby electronic valence fluctuations whose long time scales are further enhanced by the formation of charged polarons. These critical charge fluctuations may prove to be a distinct signature of strange metals.

Experimental evidence of tetrahedral symmetry breaking in SiO2 glass under pressure.

Bimodal behavior in the translational order of silicon's second shell in SiO2 liquid at high temperatures and high pressures has been recognized in theoretical studies, and the fraction of the S state with high tetrahedrality is considered as structural origin of the anomalous properties. However, it has not been well identified in experiment. Here we show experimental evidence of a bimodal behavior in the translational order of silicon's second shell in SiO2 glass under pressure. SiO2 glass shows tetrahedral symmetry structure with separation between the first and second shells of silicon at low pressures, which corresponds to the S state structure reported in SiO2 liquid. On the other hand, at high pressures, the silicon's second shell collapses onto the first shell, and more silicon atoms locate in the first shell. These observations indicate breaking of local tetrahedral symmetry in SiO2 glass under pressure, as well as SiO2 liquid.

Characterization of photoinduced normal state through charge density wave in superconducting YBa2Cu3O6.67.

The normal state of high-Tc cuprates has been considered one of the essential topics in high-temperature superconductivity research. However, compared to the high magnetic field study of it, understanding a photoinduced normal state remains elusive. Here, we explore a photoinduced normal state of YBa2Cu3O6.67 through a charge density wave (CDW) with time-resolved resonant soft x-ray scattering, as well as a high magnetic field x-ray scattering. In the nonequilibrium state where people predict a quenched superconducting state based on the previous optical spectroscopies, we experimentally observed a similar analogy to the competition between superconductivity and CDW shown in the equilibrium state. We further observe that the broken pairing states in the superconducting CuO2 plane via the optical pump lead to nucleation of three-dimensional CDW precursor correlation. Ultimately, these findings provide a critical clue that the characteristics of the photoinduced normal state show a solid resemblance to those under magnetic fields in equilibrium conditions.

Shortening X-Ray Pulse Duration via Saturable Absorption.

To shorten the duration of x-ray pulses, we present a nonlinear optical technique using atoms with core-hole vacancies (core-hole atoms) generated by inner-shell photoionization. The weak Coulomb screening in the core-hole atoms results in decreased absorption at photon energies immediately above the absorption edge. By employing this phenomenon, referred to as saturable absorption, we successfully reduce the duration of x-ray free-electron laser pulses (photon energy: 9.000 keV, duration: 6-7 fs, fluence: 2.0-3.5×10^{5} J/cm^{2}) by ∼35%. This finding that core-hole atoms are applicable to nonlinear x-ray optics is an essential stepping stone for extending nonlinear technologies commonplace at optical wavelengths to the hard x-ray region.

Nuclear Resonance Vibrational Spectroscopic Definition of the Fe(IV)2 Intermediate Q in Methane Monooxygenase and Its Reactivity.

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.

NRVS and DFT of MitoNEET: Understanding the Special Vibrational Structure of a [2Fe-2S] Cluster with (Cys)3(His)1 Ligation.

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.

Vibrational Perturbation of the [FeFe] Hydrogenase H-Cluster Revealed by 13C2H-ADT Labeling.

[FeFe] hydrogenases are highly active catalysts for the interconversion of molecular hydrogen with protons and electrons. Here, we use a combination of isotopic labeling, 57Fe 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 -13C2H2- 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 Hhyd state containing a terminal hydride at the distal Fe site. The 13C2H isotope effects were observed also in the Hhyd spectrum. DFT simulations of the spectra allowed identification of the 57Fe 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 H2 formation.

Atomic-Scale Visualization of Ultrafast Bond Breaking in X-Ray-Excited Diamond.

Ultrafast changes of charge density distribution in diamond after irradiation with an intense x-ray pulse (photon energy, 7.8 keV; pulse duration, 6 fs; intensity, 3×10^{19} W/cm^{2}) have been visualized with the x-ray pump-x-ray probe technique. The measurement reveals that covalent bonds in diamond are broken and the electron distribution around each atom becomes almost isotropic within ∼5 fs after the intensity maximum of the x-ray pump pulse. The 15 fs time delay observed between the bond breaking and atomic disordering indicates nonisothermality of electron and lattice subsystems on this timescale. From these observations and simulation results, we interpret that the x-ray-induced change of the interatomic potential drives the ultrafast atomic disordering underway to the following nonthermal melting.

Exploring Structure and Function of Redox Intermediates in [NiFe]-Hydrogenases by an Advanced Experimental Approach for Solvated, Lyophilized and Crystallized Metalloenzymes.

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 57 Fe 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.

Absolute X-ray energy measurement using a high-accuracy angle encoder.

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.

Determination of X-ray pulse duration via intensity correlation measurement of X-ray fluorescence. Erratum.

Corrections to equations and experimental results in the paper by Inoue et al. [(2019). J. Synchrotron Rad. 26, 2050-2054] are made.

Vibrational characterization of a diiron bridging hydride complex - a model for hydrogen catalysis.

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.

Hydroxy-bridged resting states of a [NiFe]-hydrogenase unraveled by cryogenic vibrational spectroscopy and DFT computations.

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.

Spectroscopic and Computational Evidence that [FeFe] Hydrogenases Operate Exclusively with CO-Bridged Intermediates.

[FeFe] hydrogenases are extremely active H2-converting enzymes. Their mechanism remains highly controversial, in particular, the nature of the one-electron and two-electron reduced intermediates called HredH+ and HsredH+. In one model, the HredH+ and HsredH+ states contain a semibridging CO, while in the other model, the bridging CO is replaced by a bridging hydride. Using low-temperature IR spectroscopy and nuclear resonance vibrational spectroscopy, together with density functional theory calculations, we show that the bridging CO is retained in the HsredH+ and HredH+ states in the [FeFe] hydrogenases from Chlamydomonas reinhardtii and Desulfovibrio desulfuricans, respectively. Furthermore, there is no evidence for a bridging hydride in either state. These results agree with a model of the catalytic cycle in which the HredH+ and HsredH+ states are integral, catalytically competent components. We conclude that proton-coupled electron transfer between the two subclusters is crucial to catalysis and allows these enzymes to operate in a highly efficient and reversible manner.

Determination of X-ray pulse duration via intensity correlation measurements of X-ray fluorescence.

A simple method using X-ray fluorescence is proposed to diagnose the duration of an X-ray free-electron laser (XFEL) pulse. This work shows that the degree of intensity correlation of the X-ray fluorescence generated by irradiating an XFEL pulse on metal foil reflects the magnitude relation between the XFEL duration and the coherence time of the fluorescence. Through intensity correlation measurements of copper Kα fluorescence, the duration of 12 keV XFEL pulses from SACLA was evaluated to be ∼10 fs.