L-Edge X-ray Absorption Spectroscopy of Dilute Systems Relevant to Metalloproteins Using an X-ray Free-Electron Laser

Probing soft X-ray induced photoreduction of a model Mn-complex at cryogenic conditions

Soft X-ray absorption spectroscopy of first row transition elements at their respective L-edges provides important information about the oxidation and spin states of the metal centers. However, the associated sample damage in radiation-sensitive samples substantially alters the electronic and chemical structures of redox-active metal centers. Here, we measure the soft X-ray spectrum of the model MnIII(acac)3 complex containing a redox-active MnIII metal center in an octahedral environment with a superconducting transition-edge sensor detector. To reduce the secondary damage resulting primarily from the diffusion of radicals and electrons, the spectra are collected at 30 K and 80 K on solid samples. Starting from the first scan, we detect the contribution of X-ray induced sample damage leading to a change in the MnII intensity. However, at low temperatures, particularly at 30 K, we do not observe a gradual increase in the radiation damage with successive scans with the X-ray beam at the same spot. At our estimated dose of 90 kGy, we find 62% of MnIII(acac)3 is still intact at 30 K. However, at room temperature, we see a gradual increase in radiation damage with increasing numbers of scans at the same spot, which is consistent with the possibility of increased diffusion rates of secondary radicals and electrons as noted in other studies.

Stimulated X-ray emission spectroscopy

We describe an emerging hard X-ray spectroscopy technique, stimulated X-ray emission spectroscopy (S-XES). S-XES has the potential to characterize the electronic structure of 3d transition metal complexes with spectral information currently not reachable and might lead to the development of new ultrafast X-ray sources with properties beyond the state of the art. S-XES has become possible with the emergence of X-ray free-electron lasers (XFELs) that provide intense femtosecond X-ray pulses that can be employed to generate a population inversion of core-hole excited states resulting in stimulated X-ray emission. We describe the instrumentation, the various types of S-XES, the potential applications, the experimental challenges, and the feasibility of applying S-XES to characterize dilute systems, including the Mn4Ca cluster in the oxygen evolving complex of photosystem II.

Probing the Dynamic Landscape: From Static to Time-Resolved X-Ray Absorption Spectroscopy to Investigate Copper Redox Chemistry in Neurodegenerative Disorders

Copper (Cu), with its ability to exist in various oxidation states, notably Cu(I) and Cu(II), plays a crucial role in diverse biological redox reactions. This includes its involvement in pathways associated with oxidative stress in neurodegenerative disorders such as Alzheimer's disease, Parkinson's disease, and Transmissible Spongiform Encephalopathies. This paper offers an overview of X-ray Absorption Spectroscopy (XAS) studies designed to elucidate the interactions between Cu ions and proteins or peptides associated with these neurodegenerative diseases. The emphasis lies on XAS specificity, revealing the local coordination environment, and on its sensitivity to Cu oxidation states. Furthermore, the paper focuses on XAS applications targeting the characterization of intermediate reaction states and explores the opportunities arising from recent advancements in time-resolved XAS at ultrabright synchrotron and Free Electron Laser radiation sources.

Toward ultrafast soft x-ray spectroscopy of organic photovoltaic devices

Novel ultrafast x-ray sources based on high harmonic generation and at x-ray free electron lasers are opening up new opportunities to resolve complex ultrafast processes in condensed phase systems with exceptional temporal resolution and atomic site specificity. In this perspective, we present techniques for resolving charge localization, transfer, and separation processes in organic semiconductors and organic photovoltaic devices with time-resolved soft x-ray spectroscopy. We review recent results in ultrafast soft x-ray spectroscopy of these systems and discuss routes to overcome the technical challenges in performing time-resolved x-ray experiments on photosensitive materials with poor thermal conductivity and low pump intensity thresholds for nonlinear effects.

Towards multimodal cellular imaging: optical and X-ray fluorescence

Imaging techniques permit the study of the molecular interactions that underlie health and disease. Each imaging technique collects unique chemical information about the cellular environment. Multimodal imaging, using a single probe that can be detected by multiple imaging modalities, can maximise the information extracted from a single cellular sample by combining the results of different imaging techniques. Of particular interest in biological imaging is the combination of the specificity and sensitivity of optical fluorescence microscopy (OFM) with the quantitative and element-specific nature of X-ray fluorescence microscopy (XFM). Together, these techniques give a greater understanding of how native elements or therapeutics affect the cellular environment. This review focuses on recent studies where both techniques were used in conjunction to study cellular systems, demonstrating the breadth of biological models to which this combination of techniques can be applied and the potential for these techniques to unlock untapped knowledge of disease states.

The role of basicity in selective C-H bond activation by transition metal-oxidos

The development of (bio)catalysts capable of selectively activating strong C-H bonds is a continuing challenge in modern chemistry. In both metalloenzymes and synthetic systems capable of activating C-H bonds, transition metal-oxido intermediates serve as the active species for reactivity whose thermodynamic properties influence the bond strengths they are capable of activating. In this Frontier article, we present current ideas of how the basicity of transition metal-oxidos impacts their reactivity with C-H bonds and present new opportunities within this field. We highlight recent insights into the role basicity plays in the activation process and its influence on mechanism, as well as the important role that secondary coordination sphere effects, such as hydrogen bonds, in tuning the basicity of the metal-oxido species is discussed.

Relativistic Orbital-Optimized Density Functional Theory for Accurate Core-Level Spectroscopy

Core-level spectra of 1s electrons of elements heavier than Ne show significant relativistic effects. We combine advances in orbital-optimized density functional theory (OO-DFT) with the spin-free exact two-component (X2C) model for scalar relativistic effects to study K-edge spectra of third period elements. OO-DFT/X2C is found to be quite accurate at predicting energies, yielding a ∼0.5 eV root-mean-square error versus experiment with the modern SCAN (and related) functionals. This marks a significant improvement over the >50 eV deviations that are typical for the popular time-dependent DFT (TDDFT) approach. Consequently, experimental spectra are quite well reproduced by OO-DFT/X2C, sans empirical shifts for alignment. OO-DFT/X2C combines high accuracy with ground state DFT cost and is thus a promising route for computing core-level spectra of third period elements. We also explored K and L edges of 3d transition metals to identify limitations of the OO-DFT/X2C approach in modeling the spectra of heavier atoms.

Plasma-Generated X-ray Pulses: Betatron Radiation Opportunities at EuPRAXIA@SPARC_LAB

EuPRAXIA is a leading European project aimed at the development of a dedicated, ground-breaking, ultra-compact accelerator research infrastructure based on novel plasma acceleration concepts and laser technology and on the development of their users’ communities. Within this framework, the Laboratori Nazionali di Frascati (LNF, INFN) will be equipped with a unique combination of an X-band RF LINAC generating high-brightness GeV-range electron beams, a 0.5 PW class laser system and the first fifth-generation free electron laser (FEL) source driven by a plasma-based accelerator, the EuPRAXIA@SPARC_LAB facility. Wiggler-like radiation emitted by electrons accelerated in plasma wakefields gives rise to brilliant, ultra-short X-ray pulses, called betatron radiation. Extensive studies have been performed at the FLAME laser facility at LNF, INFN, where betatron radiation was measured and characterized. The purpose of this paper is to describe the betatron spectrum emitted by particle wakefield acceleration at EuPRAXIA@SPARC_LAB and provide an overview of the foreseen applications of this specific source, thus helping to establish a future user community interested in (possibly coupled) FEL and betatron radiation experiments. In order to provide a quantitative estimate of the expected betatron spectrum and therefore to present suitable applications, we performed simple simulations to determine the spectrum of the betatron radiation emitted at EuPRAXIA@SPARC_LAB. With reference to experiments performed exploiting similar betatron sources, we highlight the opportunities offered by its brilliant femtosecond pulses for ultra-fast X-ray spectroscopy and imaging measurements, but also as an ancillary tool for designing and testing FEL instrumentation and experiments.

Highly efficient soft x-ray spectrometer for transient absorption spectroscopy with broadband table-top high harmonic sources

We present a novel soft x-ray spectrometer for ultrafast absorption spectroscopy utilizing table-top femtosecond high-order harmonic sources. Where most commercially available spectrometers rely on spherical variable line space gratings with a typical efficiency on the order of 3% in the first diffractive order, this spectrometer, based on a Hettrick-Underwood design, includes a reflective zone plate as a dispersive element. An improved efficiency of 12% at the N K-edge is achieved, accompanied by a resolving power of 890. The high performance of the soft x-ray spectrometer is further demonstrated by comparing nitrogen K-edge absorption spectra from calcium nitrate in aqueous solution obtained with our high-order harmonic source to previous measurements performed at the electron storage ring facility BESSY II.

Shot noise limited soft x-ray absorption spectroscopy in solution at a SASE-FEL using a transmission grating beam splitter

X-ray absorption near-edge structure (XANES) spectroscopy provides element specificity and is a powerful experimental method to probe local unoccupied electronic structures. In the soft x-ray regime, it is especially well suited for the study of 3d-metals and light elements such as nitrogen. Recent developments in vacuum-compatible liquid flat jets have facilitated soft x-ray transmission spectroscopy on molecules in solution, providing information on valence charge distributions of heteroatoms and metal centers. Here, we demonstrate XANES spectroscopy of molecules in solution at the nitrogen K-edge, performed at FLASH, the Free-Electron Laser (FEL) in Hamburg. A split-beam referencing scheme optimally characterizes the strong shot-to-shot fluctuations intrinsic to the process of self-amplified spontaneous emission on which most FELs are based. Due to this normalization, a sensitivity of 1% relative transmission change is achieved, limited by fundamental photon shot noise. The effective FEL bandwidth is increased by streaking the electron energy over the FEL pulse train to measure a wider spectral window without changing FEL parameters. We propose modifications to the experimental setup with the potential of improving the instrument sensitivity by two orders of magnitude, thereby exploiting the high peak fluence of FELs to enable unprecedented sensitivity for femtosecond XANES spectroscopy on liquids in the soft x-ray spectral region.

Parallel Broadband Femtosecond Reflection Spectroscopy at a Soft X-Ray Free-Electron Laser

X-ray absorption spectroscopy (XAS) and the directly linked X-ray reflectivity near absorption edges yield a wealth of specific information on the electronic structure around the resonantly addressed element. Observing the dynamic response of complex materials to optical excitations in pump–probe experiments requires high sensitivity to small changes in the spectra which in turn necessitates the brilliance of free electron laser (FEL) pulses. However, due to the fluctuating spectral content of pulses generated by self-amplified spontaneous emission (SASE), FEL experiments often struggle to reach the full sensitivity and time-resolution that FELs can in principle enable. Here, we implement a setup which solves two common challenges in this type of spectroscopy using FELs: First, we achieve a high spectral resolution by using a spectrometer downstream of the sample instead of a monochromator upstream of the sample. Thus, the full FEL bandwidth contributes to the measurement at the same time, and the FEL pulse duration is not elongated by a monochromator. Second, the FEL beam is divided into identical copies by a transmission grating beam splitter so that two spectra from separate spots on the sample (or from the sample and known reference) can be recorded in-parallel with the same spectrometer, enabling a spectrally resolved intensity normalization of pulse fluctuations in pump–probe scenarios. We analyze the capabilities of this setup around the oxygen K- and nickel L-edges recorded with third harmonic radiation of the free electron laser in Hamburg (FLASH), demonstrating the capability for pump–probe measurements with sensitivity to reflectivity changes on the per mill level.

Soft X-ray spectroscopy with transition-edge sensors at Stanford Synchrotron Radiation Lightsource beamline 10-1

We present results obtained with a new soft X-ray spectrometer based on transition-edge sensors (TESs) composed of Mo/Cu bilayers coupled to bismuth absorbers. This spectrometer simultaneously provides excellent energy resolution, high detection efficiency, and broadband spectral coverage. The new spectrometer is optimized for incident X-ray energies below 2 keV. Each pixel serves as both a highly sensitive calorimeter and an X-ray absorber with near unity quantum efficiency. We have commissioned this 240-pixel TES spectrometer at the Stanford Synchrotron Radiation Lightsource beamline 10-1 (BL 10-1) and used it to probe the local electronic structure of sample materials with unprecedented sensitivity in the soft X-ray regime. As mounted, the TES spectrometer has a maximum detection solid angle of 2 × 10^-3 sr. The energy resolution of all pixels combined is 1.5 eV full width at half maximum at 500 eV. We describe the performance of the TES spectrometer in terms of its energy resolution and count-rate capability and demonstrate its utility as a high throughput detector for synchrotron-based X-ray spectroscopy. Results from initial X-ray emission spectroscopy and resonant inelastic X-ray scattering experiments obtained with the spectrometer are presented.

X-ray spectroscopy with variable line spacing based on reflection zone plate optics

X-ray spectroscopy is a method, ideally suited for investigating the electronic structure of matter, which has been enabled by the rapid developments in light sources and instruments. The x-ray fluorescence lines of life-relevant elements such as carbon, nitrogen, and oxygen are located in the soft x-ray regime and call for suitable spectrometer devices. In this Letter, we present a high-resolution spectrum of liquid water, recorded with a soft x-ray spectrometer based on a reflection zone plate (RZP) design. The RZP-based spectrometer with meridional variation of line space density from 2953 to 3757 l/mm offers extremely high detection efficiency and, at the same time, medium energy resolution. We can reproduce the well-known splitting of liquid water in the lone pair regime with 10 s acquisition time.

Structure Determination of Phosphoric Acid and Phosphate Ions in Aqueous Solution Using EXAFS Spectroscopy and Large Angle X-ray Scattering

The structures of hydrated phosphoric acid and phosphate ions (H₂PO₄^-, HPO₄^2-, and PO₄^3-) in aqueous solution have been determined by P K-edge EXAFS and large angle X-ray scattering (LAXS). The P-O bond distance in all phosphate species studied is close to 1.53 Å. The P-(O)···O_aq distances have been refined to ca. 3.6 Å from the LAXS data giving a P-O···O_aq bond angle close to tetrahedral, suggesting that each oxygen or OH group of phosphoric acid and dihydrogen phosphate, on average, hydrogen bind three water molecules. The (P-)O(-H)···O_aq and (P-)O···(H-)O_aq hydrogen bonds in hydrated phosphoric acid and the H₂PO₄^- ion are shorter than the hydrogen bonds in neat water. This supports previous infrared spectroscopic studies claiming that the hydrogen bonds in hydrated phosphoric acid and phosphate ions are stronger than the hydrogen bonds in neat water. Phosphoric acid and phosphate ions can therefore be regarded as structure making solutes. This is the first study applying transmission mode X-ray absorption spectroscopy (XAS) data collection on the P K-edge. It shows that XAS spectra collected in transmission mode have a much better S/N ratio than data collected in fluorescence mode, allowing accurate determination of P-O bond distances. Furthermore, P K-edge EXAFS data collected in fluorescence mode display a higher amplitude at high k than expected due to increasing radiated volume of the sample with increasing energy as the total absorption decreases sharply with increasing energy of the X-rays. As a result, the fluorescence signal becomes nonproportional to the intensity of the X-ray beam over the EXAFS spectrum. This results in an increasing amplitude of the EXAFS function with increasing energy of the X-ray beam resulting in too small Debye-Waller coefficients.

Probing the oxidation state of transition metal complexes: a case study on how charge and spin densities determine Mn L-edge X-ray absorption energies

Transition metals in inorganic systems and metalloproteins can occur in different oxidation states, which makes them ideal redox-active catalysts. To gain a mechanistic understanding of the catalytic reactions, knowledge of the oxidation state of the active metals, ideally in operando, is therefore critical. L-edge X-ray absorption spectroscopy (XAS) is a powerful technique that is frequently used to infer the oxidation state via a distinct blue shift of L-edge absorption energies with increasing oxidation state. A unified description accounting for quantum-chemical notions whereupon oxidation does not occur locally on the metal but on the whole molecule and the basic understanding that L-edge XAS probes the electronic structure locally at the metal has been missing to date. Here we quantify how charge and spin densities change at the metal and throughout the molecule for both redox and core-excitation processes. We explain the origin of the L-edge XAS shift between the high-spin complexes MnII(acac)2 and MnIII(acac)3 as representative model systems and use ab initio theory to uncouple effects of oxidation-state changes from geometric effects. The shift reflects an increased electron affinity of MnIII in the core-excited states compared to the ground state due to a contraction of the Mn 3d shell upon core-excitation with accompanied changes in the classical Coulomb interactions. This new picture quantifies how the metal-centered core hole probes changes in formal oxidation state and encloses and substantiates earlier explanations. The approach is broadly applicable to mechanistic studies of redox-catalytic reactions in molecular systems where charge and spin localization/delocalization determine reaction pathways.

Monitoring Ultrafast Spin Crossover Intermediates in an Iron(II) Complex by Broad Band Stimulated X-ray Raman Spectroscopy

The photoinduced spin crossover dynamics of transition metal complexes is of fundamental scientific importance and is used for sensor device applications and solar energy harvesting. Current X-ray and optical spectroscopy experiments for [Fe^II(bpy)₃], an archetypal earth-abundant metal complex, show conflicting spin dynamics. We have simulated the broad band transient X-ray absorption and hybrid (broad + narrow band) X-ray stimulated Raman signals at the N and Fe K-edges of the key excited state intermediates involved in the spin crossover process of this complex. We find that these signals are much more sensitive to electron and spin populations than transition absorption and may be useful in the design of photovoltaic and artificial photosynthetic systems.

X-ray-induced sample damage at the Mn L-edge: a case study for soft X-ray spectroscopy of transition metal complexes in solution

X-ray induced sample damage can impede electronic and structural investigations of radiation-sensitive samples studied with X-rays. Here we quantify dose-dependent sample damage to the prototypical MnIII(acac)3 complex in solution and at room temperature for the soft X-ray range, using X-ray absorption spectroscopy at the Mn L-edge. We observe the appearance of a reduced MnII species as the X-ray dose is increased. We find a half-damage dose of 1.6 MGy and quantify a spectroscopically tolerable dose on the order of 0.3 MGy (1 Gy = 1 J kg-1), where 90% of MnIII(acac)3 are intact. Our dose-limit is around one order of magnitude lower than the Henderson limit (half-damage dose of 20 MGy) which is commonly employed for protein crystallography with hard X-rays. It is comparable, however, to the dose-limits obtained for collecting un-damaged Mn K-edge spectra of the photosystem II protein, using hard X-rays. The dose-dependent reduction of MnIII observed here for solution samples occurs at a dose limit that is two to four orders of magnitude smaller than the dose limits previously reported for soft X-ray spectroscopy of iron samples in the solid phase. We compare our measured to calculated spectra from ab initio restricted active space (RAS) theory and discuss possible mechanisms for the observed dose-dependent damage of MnIII(acac)3 in solution. On the basis of our results, we assess the influence of sample damage in other experimental studies with soft X-rays from storage-ring synchrotron radiation sources and X-ray free-electron lasers.

Total 3s Emission Yield as Bulk-Sensitive Probe for a True Soft X-ray Absorption Spectrum?

The detection of the true soft X-ray absorption typically needs specially prepared submicrometer thin samples for transmission measurements. Bulk experiments instead have to rely on yield methods, for example, electron yield with limitations for insulating samples, sensitivity to applied fields, and with limited bulk sensitivity. Fluorescence yield methods instead do not have those limitations but have been found to deviate, in general, from the absorption spectrum. We demonstrate that restricting the detection to the 3s fluorescence channel (with the detector at a special angle where all polarizations contribute equally) restores the true X-ray absorption spectrum for all 3d-metal L_2,3 edges. These theoretically derived results are rationalized by the lack of 3s-3d interaction in the core-excited state. Comparing X-ray absorption versus 3s-PFY for arbitrary detection geometries for both linear and circular polarized light, deviations appear that can become as large as 15%.

Direct Determination of Absolute Absorption Cross Sections at the L-Edge of Dilute Mn Complexes in Solution Using a Transmission Flatjet

The 3d transition metals play a pivotal role in many charge transfer processes in catalysis and biology. X-ray absorption spectroscopy at the L-edge of metal sites probes metal 2p-3d excitations, providing key access to their valence electronic structure, which is crucial for understanding these processes. We report L-edge absorption spectra of MnII(acac)2 and MnIII(acac)3 complexes in solution, utilizing a liquid flatjet for X-ray absorption spectroscopy in transmission mode. With this, we derive absolute absorption cross-sections for the L-edge transitions with peak magnitudes as large as 12 and 9 Mb for MnII(acac)2 and MnIII(acac)3, respectively. We provide insight into the electronic structure with ab initio restricted active space calculations of these L-edge transitions, reproducing the experimental spectra with excellent agreement in terms of shapes, relative energies, and relative intensities for the two complexes. Crystal field multiplet theory is used to assign spectral features in terms of the electronic structure. Comparison to charge transfer multiplet calculations reveals the importance of charge transfer in the core-excited final states. On the basis of our experimental observations, we extrapolate the feasibility of 3d transition metal L-edge absorption spectroscopy using the liquid flatjet approach in probing highly dilute biological solution samples and possible extensions to table-top soft X-ray sources.

L-edge spectroscopy of dilute, radiation-sensitive systems using a transition-edge-sensor array

We present X-ray absorption spectroscopy and resonant inelastic X-ray scattering (RIXS) measurements on the iron L-edge of 0.5 mM aqueous ferricyanide. These measurements demonstrate the ability of high-throughput transition-edge-sensor (TES) spectrometers to access the rich soft X-ray (100-2000 eV) spectroscopy regime for dilute and radiation-sensitive samples. Our low-concentration data are in agreement with high-concentration measurements recorded by grating spectrometers. These results show that soft-X-ray RIXS spectroscopy acquired by high-throughput TES spectrometers can be used to study the local electronic structure of dilute metal-centered complexes relevant to biology, chemistry, and catalysis. In particular, TES spectrometers have a unique ability to characterize frozen solutions of radiation- and temperature-sensitive samples.

Short-wavelength free-electron laser sources and science: a review

This review is focused on free-electron lasers (FELs) in the hard to soft x-ray regime. The aim is to provide newcomers to the area with insights into: the basic physics of FELs, the qualities of the radiation they produce, the challenges of transmitting that radiation to end users and the diversity of current scientific applications. Initial consideration is given to FEL theory in order to provide the foundation for discussion of FEL output properties and the technical challenges of short-wavelength FELs. This is followed by an overview of existing x-ray FEL facilities, future facilities and FEL frontiers. To provide a context for information in the above sections, a detailed comparison of the photon pulse characteristics of FEL sources with those of other sources of high brightness x-rays is made. A brief summary of FEL beamline design and photon diagnostics then precedes an overview of FEL scientific applications. Recent highlights are covered in sections on structural biology, atomic and molecular physics, photochemistry, non-linear spectroscopy, shock physics, solid density plasmas. A short industrial perspective is also included to emphasise potential in this area.

Soft x-ray absorption spectroscopy of metalloproteins and high-valent metal-complexes at room temperature using free-electron lasers

X-ray absorption spectroscopy at the L-edge of 3d transition metals provides unique information on the local metal charge and spin states by directly probing 3d-derived molecular orbitals through 2p-3d transitions. However, this soft x-ray technique has been rarely used at synchrotron facilities for mechanistic studies of metalloenzymes due to the difficulties of x-ray-induced sample damage and strong background signals from light elements that can dominate the low metal signal. Here, we combine femtosecond soft x-ray pulses from a free-electron laser with a novel x-ray fluorescence-yield spectrometer to overcome these difficulties. We present L-edge absorption spectra of inorganic high-valent Mn complexes (Mn ∼ 6-15 mmol/l) with no visible effects of radiation damage. We also present the first L-edge absorption spectra of the oxygen evolving complex (Mn₄CaO₅) in Photosystem II (Mn < 1 mmol/l) at room temperature, measured under similar conditions. Our approach opens new ways to study metalloenzymes under functional conditions.

XFELs for structure and dynamics in biology

The development and application of the free-electron X-ray laser (XFEL) to structure and dynamics in biology since its inception in 2009 are reviewed. The research opportunities which result from the ability to outrun most radiation-damage effects are outlined, and some grand challenges are suggested. By avoiding the need to cool samples to minimize damage, the XFEL has permitted atomic resolution imaging of molecular processes on the 100 fs timescale under near-physiological conditions and in the correct thermal bath in which molecular machines operate. Radiation damage, comparisons of XFEL and synchrotron work, single-particle diffraction, fast solution scattering, pump-probe studies on photosensitive proteins, mix-and-inject experiments, caged molecules, pH jump and other reaction-initiation methods, and the study of molecular machines are all discussed. Sample-delivery methods and data-analysis algorithms for the various modes, from serial femtosecond crystallo-graphy to fast solution scattering, fluctuation X-ray scattering, mixing jet experiments and single-particle diffraction, are also reviewed.

Iron L2,3-Edge X-ray Absorption and X-ray Magnetic Circular Dichroism Studies of Molecular Iron Complexes with Relevance to the FeMoco and FeVco Active Sites of Nitrogenase

Herein, a systematic study of a series of molecular iron model complexes has been carried out using Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) spectroscopies. This series spans iron complexes of increasing complexity, starting from ferric and ferrous tetrachlorides ([FeCl₄]^−/2–), to ferric and ferrous tetrathiolates ([Fe(SR)₄]^−/2–), to diferric and mixed-valent iron–sulfur complexes [Fe₂S₂R₄]^2–/3–. This test set of compounds is used to evaluate the sensitivity of both Fe L_2,3-edge XAS and XMCD spectroscopy to oxidation state and ligation changes. It is demonstrated that the energy shift and intensity of the L_2,3-edge XAS spectra depends on both the oxidation state and covalency of the system; however, the quantitative information that can be extracted from these data is limited. On the other hand, analysis of the Fe XMCD shows distinct changes in the intensity at both L₃ and L₂ edges, depending on the oxidation state of the system. It is also demonstrated that the XMCD intensity is modulated by the covalency of the system. For mononuclear systems, the experimental data are correlated with atomic multiplet calculations in order to provide insights into the experimental observations. Finally, XMCD is applied to the tetranuclear heterometal–iron–sulfur clusters [MFe₃S₄]^3+/2+ (M = Mo, V), which serve as structural analogues of the FeMoco and FeVco active sites of nitrogenase. It is demonstrated that the XMCD data can be utilized to obtain information on the oxidation state distribution in complex clusters that is not readily accessible for the Fe L_2,3-edge XAS data alone. The advantages of XMCD relative to standard K-edge and L_2,3-edge XAS are highlighted. This study provides an important foundation for future XMCD studies on complex (bio)inorganic systems.

A systematic Fe L_2,3-edge X-ray absorption (XAS) and X-ray magnetic circular dichroism (XMCD) study of iron tetrachlorides ([FeCl₄]^−/2−), iron tetrathiolates ([Fe(SR)₄]^−/2−), diferric and mixed-valent iron−sulfur dimers [Fe₂S₂R₄]^2−/3− and heterometal−iron−sulfur tetramers [MFe₃S₄]^3+/2+ (M = Mo, V) is reported. The changes in XAS and XMCD energies and intensities across this set of complexes are presented together with atomic multiplet calculations. The advantages of XMCD as an electronic structure probe of complex clusters are highlighted.

Highly efficient soft X-ray spectrometer based on a reflection zone plate for resonant inelastic X-ray scattering measurements

We present a newly designed compact and flexible soft X-ray spectrometer for resonant inelastic X-ray scattering (RIXS) studies within an energy range from 380 eV to 410 eV, which would include the K alpha emission lines of vital elements like nitrogen. We utilized an off-axis reflection zone plate (RZP) as the wavelength selective element with a maximum line density of 10000 l/mm. A higher energy resolution over a broader range of ± 15 eV around the designed energy was achieved by displacing the RZP. Additionally, for the first time, an actual optical side effect, the so-called comatic aberration was exploited to increase the energy resolution. First results show a resolving power in the order of 1300 for photon energy of 395 eV, which is comparable to a commercial varied line spacing grating (VLS).

K- and L-edge X-ray Absorption Spectroscopy (XAS) and Resonant Inelastic X-ray Scattering (RIXS) Determination of Differential Orbital Covalency (DOC) of Transition Metal Sites

Continual advancements in the development of synchrotron radiation sources have resulted in X-ray based spectroscopic techniques capable of probing the electronic and structural properties of numerous systems. This review gives an overview of the application of metal K-edge and L-edge X-ray absorption spectroscopy (XAS), as well as K resonant inelastic X-ray scattering (RIXS), to the study of electronic structure in transition metal sites with emphasis on experimentally quantifying 3d orbital covalency. The specific sensitivities of K-edge XAS, L-edge XAS, and RIXS are discussed emphasizing the complementary nature of the methods. L-edge XAS and RIXS are sensitive to mixing between 3d orbitals and ligand valence orbitals, and to the differential orbital covalency (DOC), that is, the difference in the covalencies for different symmetry sets of the d orbitals. Both L-edge XAS and RIXS are highly sensitive to and enable separation of and donor bonding and back bonding contributions to bonding. Applying ligand field multiplet simulations, including charge transfer via valence bond configuration interactions, DOC can be obtained for direct comparison with density functional theory calculations and to understand chemical trends. The application of RIXS as a probe of frontier molecular orbitals in a heme enzyme demonstrates the potential of this method for the study of metal sites in highly covalent coordination sites in bioinorganic chemistry.

Iron L-Edge Absorption Spectroscopy of Iron Pentacarbonyl and Ferrocene in the Gas Phase

Fe L-edge X-ray absorption spectra of gas-phase iron pentacarbonyl and ferrocene measured in total-ion yield mode are reported. Comparison to previously published spectra of free iron atoms and gaseous iron chloride demonstrates how the interplay of local atomic multiplet effects and orbital interactions in the metal-ligand bonds varies for the different systems. We find changes in the degree of metal-ligand covalency to be reflected in the measured 2p absorption onset. Orbital- or state-specific fragmentation is furthermore investigated in iron pentacarbonyl and ferrocene by analyzing the partial-ion-yield spectra at the Fe L-edge. Strong dependence of the yields of different fragments is observed in ferrocene in contrast to iron pentacarbonyl. This difference is attributed to the different degrees to which the 2p core hole is screened in the two systems and to which charge is rearranged in the Auger final states. We provide experimental benchmark spectra for new ab initio approaches for calculating metal L-edge absorption spectra of metal complexes.

Towards characterization of photo-excited electron transfer and catalysis in natural and artificial systems using XFELs

The ultra-bright femtosecond X-ray pulses provided by X-ray Free Electron Lasers (XFELs) open capabilities for studying the structure and dynamics of a wide variety of biological and inorganic systems beyond what is possible at synchrotron sources. Although the structure and chemistry at the catalytic sites have been studied intensively in both biological and inorganic systems, a full understanding of the atomic-scale chemistry requires new approaches beyond the steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure at ambient conditions, while overcoming X-ray damage to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by using the intense and ultra-short femtosecond X-ray pulses from an XFEL, where sample is probed before it is damaged. We have developed methodology for simultaneously collecting X-ray diffraction data and X-ray emission spectra, using an energy dispersive spectrometer, at ambient conditions, and used this approach to study the room temperature structure and intermediate states of the photosynthetic water oxidizing metallo-protein, photosystem II. Moreover, we have also used this setup to simultaneously collect the X-ray emission spectra from multiple metals to follow the ultrafast dynamics of light-induced charge transfer between multiple metal sites. A Mn-Ti containing system was studied at an XFEL to demonstrate the efficacy and potential of this method.

X-ray absorption spectroscopy using a self-seeded soft X-ray free-electron laser

X-ray free electron lasers (XFELs) enable unprecedented new ways to study the electronic structure and dynamics of transition metal systems. L-edge absorption spectroscopy is a powerful technique for such studies and the feasibility of this method at XFELs for solutions and solids has been demonstrated. However, the required x-ray bandwidth is an order of magnitude narrower than that of self-amplified spontaneous emission (SASE), and additional monochromatization is needed. Here we compare L-edge x-ray absorption spectroscopy (XAS) of a prototypical transition metal system based on monochromatizing the SASE radiation of the linac coherent light source (LCLS) with a new technique based on self-seeding of LCLS. We demonstrate how L-edge XAS can be performed using the self-seeding scheme without the need of an additional beam line monochromator. We show how the spectral shape and pulse energy depend on the undulator setup and how this affects the x-ray spectroscopy measurements.

Ultrafast Excited State Relaxation of a Metalloporphyrin Revealed by Femtosecond X-ray Absorption Spectroscopy

Photoexcited Nickel(II) tetramesitylporphyrin (NiTMP), like many open-shell metalloporphyrins, relaxes rapidly through multiple electronic states following an initial porphyrin-based excitation, some involving metal centered electronic configuration changes that could be harnessed catalytically before excited state relaxation. While a NiTMP excited state present at 100 ps was previously identified by X-ray transient absorption (XTA) spectroscopy at a synchrotron source as a relaxed (d,d) state, the lowest energy excited state (J. Am. Chem. Soc., 2007, 129, 9616 and Chem. Sci., 2010, 1, 642), structural dynamics before thermalization were not resolved due to the ∼100 ps duration of the available X-ray probe pulse. Using the femtosecond (fs) X-ray pulses of the Linac Coherent Light Source (LCLS), the Ni center electronic configuration from the initial excited state to the relaxed (d,d) state has been obtained via ultrafast Ni K-edge XANES (X-ray absorption near edge structure) on a time scale from hundreds of femtoseconds to 100 ps. This enabled the identification of a short-lived Ni(I) species aided by time-dependent density functional theory (TDDFT) methods. Computed electronic and nuclear structure for critical excited electronic states in the relaxation pathway characterize the dependence of the complex's geometry on the electron occupation of the 3d orbitals. Calculated XANES transitions for these excited states assign a short-lived transient signal to the spectroscopic signature of the Ni(I) species, resulting from intramolecular charge transfer on a time scale that has eluded previous synchrotron studies. These combined results enable us to examine the excited state structural dynamics of NiTMP prior to thermal relaxation and to capture intermediates of potential photocatalytic significance.

Element-specific characterization of transient electronic structure of solvated Fe(II) complexes with time-resolved soft X-ray absorption spectroscopy

Polypyridyl transition-metal complexes are an intriguing class of compounds due to the relatively facile chemical designs and variations in ligand-field strengths that allow for spin-state changes and hence electronic configurations in response to external perturbations such as pressure and light. Light-activated spin-conversion complexes have possible applications in a variety of molecular-based devices, and ultrafast excited-state evolution in these complexes is of fundamental interest for understanding of the origins of spin-state conversion in metal complexes. Knowledge of the interplay of structure and valence charge distributions is important to understand which degrees of freedom drive spin-conversion and which respond in a favorable (or unfavorable) manner. To track the response of the constituent components, various types of time-resolved X-ray probe methods have been utilized for a broad range of chemical and biological systems relevant to catalysis, solar energy conversions, and functional molecular devices. In particular, transient soft X-ray spectroscopy of solvated molecules can offer complementary information on the detailed electronic structures and valence charge distributions of photoinduced intermediate species: First-row transition-metal L-edges consist of 2p-3d transitions, which directly probe the unoccupied valence density of states and feature lifetime broadening in the range of 100 meV, making them sensitive spectral probes of metal-ligand interactions. In this Account, we present some of our recent progress in employing picosecond and femtosecond soft X-ray pulses from synchrotron sources to investigate element specific valence charge distributions and spin-state evolutions in Fe(II) polypyridyl complexes via core-level transitions. Our results on transient L-edge spectroscopy of Fe(II) complexes clearly show that the reduction in σ-donation is compensated by significant attenuation of π-backbonding upon spin-crossover. This underscores the important information contained in transient metal L-edge spectroscopy on changes in the 3d orbitals including oxidation states, orbital symmetries, and covalency, which largely define the chemistry of these complexes. In addition, ligand K-edge spectroscopy reveals the "ligand view" of the valence charge density by probing 1s-2p core-level transitions at the K-edge of light elements such as nitrogen, carbon, and oxygen. In the case of Fe(II) spin-conversion complexes, additional details of the metal-ligand interactions can be obtained by this type of X-ray spectroscopy. With new initiatives in and construction of X-ray free-electron laser sources, we expect time-resolved soft X-ray spectroscopy to pave a new way to study electronic and molecular dynamics of functional materials, thereby answering many interesting scientific questions in inorganic chemistry and material science.

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

Although the structure of enzymes and the chemistry at the catalytic sites have been studied intensively, an understanding of the atomic-scale chemistry requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the sample is destroyed. This review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.

A liquid flatjet system for solution phase soft-x-ray spectroscopy

We present a liquid flatjet system for solution phase soft-x-ray spectroscopy. The flatjet set-up utilises the phenomenon of formation of stable liquid sheets upon collision of two identical laminar jets. Colliding the two single water jets, coming out of the nozzles with 50 μm orifices, under an impact angle of 48° leads to double sheet formation, of which the first sheet is 4.6 mm long and 1.0 mm wide. The liquid flatjet operates fully functional under vacuum conditions (<10(-3) mbar), allowing soft-x-ray spectroscopy of aqueous solutions in transmission mode. We analyse the liquid water flatjet thickness under atmospheric pressure using interferomeric or mid-infrared transmission measurements and under vacuum conditions by measuring the absorbance of the O K-edge of water in transmission, and comparing our results with previously published data obtained with standing cells with Si3N4 membrane windows. The thickness of the first liquid sheet is found to vary between 1.4-3 μm, depending on the transverse and longitudinal position in the liquid sheet. We observe that the derived thickness is of similar magnitude under 1 bar and under vacuum conditions. A catcher unit facilitates the recycling of the solutions, allowing measurements on small sample volumes (∼10 ml). We demonstrate the applicability of this approach by presenting measurements on the N K-edge of aqueous NH4 (+). Our results suggest the high potential of using liquid flatjets in steady-state and time-resolved studies in the soft-x-ray regime.

A new compact soft x-ray spectrometer for resonant inelastic x-ray scattering studies at PETRA III

We present a newly designed compact grating spectrometer for the energy range from 210 eV to 1250 eV, which would include the Kα(1,2) emission lines of vital elements like C, N, and O. The spectrometer is based on a grazing incidence spherical varied line spacing grating with 2400 l/mm at its center and a radius of curvature of 58 542 mm. First, results show a resolving power of around 1000 at an energy of 550 eV and a working spectrometer for high vacuum (10(-4) mbar) environment without losing photon intensity.

Ultraviolet photochemical reaction of [Fe(III)(C2O4)3](3-) in aqueous solutions studied by femtosecond time-resolved X-ray absorption spectroscopy using an X-ray free electron laser

Time-resolved X-ray absorption spectroscopy was performed for aqueous ammonium iron(III) oxalate trihydrate solutions using an X-ray free electron laser and a synchronized ultraviolet laser. The spectral and time resolutions of the experiment were 1.3 eV and 200 fs, respectively. A femtosecond 268 nm pulse was employed to excite [Fe(III)(C2O4)3](3-) in solution from the high-spin ground electronic state to ligand-to-metal charge transfer state(s), and the subsequent dynamics were studied by observing the time-evolution of the X-ray absorption spectrum near the Fe K-edge. Upon 268 nm photoexcitation, the Fe K-edge underwent a red-shift by more than 4 eV within 140 fs; however, the magnitude of the redshift subsequently diminished within 3 ps. The Fe K-edge of the photoproduct remained lower in energy than that of [Fe(III)(C2O4)3](3-). The observed red-shift of the Fe K-edge and the spectral feature of the product indicate that Fe(III) is upon excitation immediately photoreduced to Fe(II), followed by ligand dissociation from Fe(II). Based on a comparison of the X-ray absorption spectra with density functional theory calculations, we propose that the dissociation proceeds in two steps, forming first [(CO2 (•))Fe(II)(C2O4)2](3-) and subsequently [Fe(II)(C2O4)2](2-).

Methods development for diffraction and spectroscopy studies of metalloenzymes at X-ray free-electron lasers

X-ray free-electron lasers (XFELs) open up new possibilities for X-ray crystallographic and spectroscopic studies of radiation-sensitive biological samples under close to physiological conditions. To facilitate these new X-ray sources, tailored experimental methods and data-processing protocols have to be developed. The highly radiation-sensitive photosystem II (PSII) protein complex is a prime target for XFEL experiments aiming to study the mechanism of light-induced water oxidation taking place at a Mn cluster in this complex. We developed a set of tools for the study of PSII at XFELs, including a new liquid jet based on electrofocusing, an energy dispersive von Hamos X-ray emission spectrometer for the hard X-ray range and a high-throughput soft X-ray spectrometer based on a reflection zone plate. While our immediate focus is on PSII, the methods we describe here are applicable to a wide range of metalloenzymes. These experimental developments were complemented by a new software suite, cctbx.xfel. This software suite allows for near-real-time monitoring of the experimental parameters and detector signals and the detailed analysis of the diffraction and spectroscopy data collected by us at the Linac Coherent Light Source, taking into account the specific characteristics of data measured at an XFEL.

Design and optimization of a parallel spectrometer for ultra-fast X-ray science

In the present work, different varied line space (VLS) and reflection zone plate (RZP) gratings are analyzed for their suitability in low-signal femtosecond soft X-ray spectroscopy. The need for high efficiency suggests a straightened focal line whose sharpness and residual curvature will determine the quality. One- and two-dimensional VLS structures feature an attractive trade-off between a sufficient optical performance and a strongly relaxed fabrication, due to moderate line densities which are easily accessible by e-beam lithography. Based on fanned-out RZP arrays, their continuous limit version is identified to generate an almost perfect focal line however, with an aberration level three orders of magnitude better than for the VLS gratings and well below the diffraction limit over large acceptance angles.

High energy resolution off-resonant spectroscopy for x-ray absorption spectra free of self-absorption effects

X-ray emission spectra recorded in the off-resonant regime carry information on the density of unoccupied states. It is known that by employing the Kramers-Heisenberg formalism, the high energy resolution off-resonant spectroscopy (HEROS) is equivalent to the x-ray absorption spectroscopy (XAS) technique and provides the same electronic state information. Moreover, in the present Letter we demonstrate that the shape of HEROS spectra is not modified by self-absorption effects. Therefore, in contrast to the fluorescence-based XAS techniques, the recorded shape of the spectra is independent of the sample concentration or thickness. The HEROS may thus be used as an experimental technique when precise information about specific absorption features and their strengths is crucial for chemical speciation or theoretical evaluation.