Characterization of Biological Samples Using Ultra-Short and Ultra-Bright XFEL Pulses.

The advent of X-ray Free Electron Lasers (XFELs) has ushered in a transformative era in the field of structural biology, materials science, and ultrafast physics. These state-of-the-art facilities generate ultra-bright, femtosecond-long X-ray pulses, allowing researchers to delve into the structure and dynamics of molecular systems with unprecedented temporal and spatial resolutions. The unique properties of XFEL pulses have opened new avenues for scientific exploration that were previously considered unattainable. One of the most notable applications of XFELs is in structural biology. Traditional X-ray crystallography, while instrumental in determining the structures of countless biomolecules, often requires large, high-quality crystals and may not capture highly transient states of proteins. XFELs, with their ability to produce diffraction patterns from nanocrystals or even single particles, have provided solutions to these challenges. XFEL has expanded the toolbox of structural biologists by enabling structural determination approaches such as Single Particle Imaging (SPI) and Serial X-ray Crystallography (SFX). Despite their remarkable capabilities, the journey of XFELs is still in its nascent stages, with ongoing advancements aimed at improving their coherence, pulse duration, and wavelength tunability.

Towards a dynamic compression facility at the ESRF.

Results of the 2018 commissioning and experimental campaigns of the new High Power Laser Facility on the Energy-dispersive X-ray Absorption Spectroscopy (ED-XAS) beamline ID24 at the ESRF are presented. The front-end of the future laser, delivering 15 J in 10 ns, was interfaced to the beamline. Laser-driven dynamic compression experiments were performed on iron oxides, iron alloys and bismuth probed by online time-resolved XAS.

New frontiers in extreme conditions science at synchrotrons and free electron lasers.

Synchrotrons and free electron lasers are unique facilities to probe the atomic structure and electronic properties of matter at extreme thermodynamical conditions. In this context, 'matter at extreme pressures and temperatures' was one of the science drivers for the construction of low emittance 4th generation synchrotron sources such as the Extremely Brilliant Source of the European Synchrotron Radiation Facility and hard x-ray free electron lasers, such as the European x-ray free electron laser. These new user facilities combine static high pressure and dynamic shock compression experiments to outstanding high brilliance and submicron beams. This combination not only increases the data-quality but also enlarges tremendously the accessible pressure, temperature and density space. At the same time, the large spectrum of available complementary x-ray diagnostics for static and shock compression studies opens unprecedented insights into the state of matter at extremes. The article aims at highlighting a new horizon of scientific opportunities based on the synergy between extremely brilliant synchrotrons and hard x-ray free electron lasers.

X-ray-Based Techniques to Study the Nano-Bio Interface.

X-ray-based analytics are routinely applied in many fields, including physics, chemistry, materials science, and engineering. The full potential of such techniques in the life sciences and medicine, however, has not yet been fully exploited. We highlight current and upcoming advances in this direction. We describe different X-ray-based methodologies (including those performed at synchrotron light sources and X-ray free-electron lasers) and their potentials for application to investigate the nano-bio interface. The discussion is predominantly guided by asking how such methods could better help to understand and to improve nanoparticle-based drug delivery, though the concepts also apply to nano-bio interactions in general. We discuss current limitations and how they might be overcome, particularly for future use in vivo.

In situ speciation and spatial mapping of Zn products during pulsed laser ablation in liquids (PLAL) by combined synchrotron methods.

Pulsed laser ablation in liquids is a hierarchical multi-step process to produce pure inorganic nanoparticle colloids. Controlling this process is hampered by the partial understanding of individual steps and structure formation. In situ X-ray methods are employed to resolve macroscopic dynamics of nanosecond PLAL as well to analyse the distribution and speciation of ablated species with a microsecond time resolution. High time resolution can be achieved by synchrotron-based methods that are capable of 'single-shot' acquisition. X-ray multicontrast imaging by a Shack-Hartmann setup (XHI) and small angle X-ray scattering (SAXS) resolve evolving nanoparticles inside the transient cavitation bubble, while X-ray absorption spectroscopy in dispersive mode opens access to the total material yield and the chemical state of the ejecta. It is confirmed that during ablation nanoparticles are produced directly as well as reactive material is detected, which is identified in the early stage as Zn atoms. Nanoparticles within the cavitation bubble show a metal signature, which prevails for milliseconds, before gradual oxidation sets in. Ablation is described by a phase explosion of the target coexisting with full evaporation. Oxidation occurs only as a later step to already formed nanoparticles.

Magnetic response of FeRh to static and dynamic disorder.

Atomic scale defects generated using focused ion as well as laser beams can activate ferromagnetism in initially non-ferromagnetic B2 ordered alloy thin film templates. Such defects can be induced locally, confining the ferromagnetic objects within well-defined nanoscale regions. The characterization of these atomic scale defects is challenging, and the mechanism for the emergence of ferromagnetism due to sensitive lattice disordering is unclear. Here we directly probe a variety of microscopic defects in systematically disordered B2 FeRh thin films that are initially antiferromagnetic and undergo a thermally-driven isostructural phase transition to a volatile ferromagnetic state. We show that the presence of static disorder i.e., the slight deviations of atoms from their equilibrium sites is sufficient to induce a non-volatile ferromagnetic state at room temperature. A static mean square relative displacement of 9 × 10-4 Å-2 is associated with the occurrence of non-volatile ferromagnetism and replicates a snapshot of the dynamic disorder observed in the thermally-driven ferromagnetic state. The equivalence of static and dynamic disorder with respect to the ferromagnetic behavior can provide insights into the emergence of ferromagnetic coupling as well as achieving tunable magnetic properties through defect manipulations in alloys.

A flexible cell for in situ combined XAS-DRIFTS-MS experiments.

A new cell for in situ combined X-ray absorption, diffuse reflectance IR Fourier transform and mass spectroscopies (XAS-DRIFTS-MS) is presented. The cell stands out among others for its achievements and flexibility. It is possible to perform XAS measurements in transmission or fluorescence modes, and the cell is compatible with external devices like UV-light and Raman probes. It includes different sample holders compatible with the different XAS detection modes, different sample forms (free powder or self-supporting pellet) and different sample loading/total absorption. Additionally, it has a small dead volume and can operate over a wide range of temperature (up to 600°C) and pressure (up to 5 bar). Three research examples will be shown to illustrate the versatility of the cell. This cell covers a wider range of applications than any other cell currently known for this type of study.

Coupled X-ray Absorption/UV-vis Monitoring of Fast Oxidation Reactions Involving a Nonheme Iron-Oxo Complex.

Time-resolved X-ray absorption (XAS) and UV-vis spectroscopies with millisecond resolution are used simultaneously to investigate oxidation reactions of organic substrates by nonheme iron activated species. In particular, the oxidation processes of arylsulfides and benzyl alcohols by a nonheme iron-oxo complex have been studied. We show for the first time that the pseudo-first-order rate constants of fast bimolecular processes in solution (milliseconds and above) can be determined by time-resolved XAS technique. By following the Fe K-edge energy shift, it is possible to detect the rate of iron oxidation state evolution that matches that of the bimolecular reaction in solution. The kinetic constant values obtained by XAS are in perfect agreement with those obtained by means of the concomitant UV-vis detection. This combined approach has the potential to provide unique insights into reaction mechanisms in the liquid phase that involve changes of the oxidation state of a metal center, and it is particularly useful in complex chemical systems where possible interferences from species present in solution could make it impossible to use other detection techniques.

Improving the quality of XAFS data.

Following the Q2XAFS Workshop and Satellite to IUCr Congress 2017 on `Data Acquisition, Treatment, Storage - quality assurance in XAFS spectroscopy', a summary is given of the discussion on different aspects of a XAFS experiment that affect data quality. Some pertinent problems ranging from sources and minimization of noise to harmonic contamination and uncompensated monochromator glitches were addressed. Also, an overview is given of the major limitations and pitfalls of a selection of related methods, such as photon-out spectroscopies and energy-dispersive XAFS, and of increasingly common applications, namely studies at high pressure, and time-resolved investigations of catalysts in operando. Advice on how to avoid or deal with these problems and a few good practice recommendations are reported, including how to correctly report results.

2D/3D Microanalysis by Energy Dispersive X-ray Absorption Spectroscopy Tomography.

X-ray spectroscopic techniques have proven to be particularly useful in elucidating the molecular and electronic structural information of chemically heterogeneous and complex micro- and nano-structured materials. However, spatially resolved chemical characterization at the micrometre scale remains a challenge. Here, we report the novel hyperspectral technique of micro Energy Dispersive X-ray Absorption Spectroscopy (µED-XAS) tomography which can resolve in both 2D and 3D the spatial distribution of chemical species through the reconstruction of XANES spectra. To document the capability of the technique in resolving chemical species, we first analyse a sample containing 2-30 µm grains of various ferrous- and ferric-iron containing minerals, including hypersthene, magnetite and hematite, distributed in a light matrix of a resin. We accurately obtain the XANES spectra at the Fe K-edge of these four standards, with spatial resolution of 3 µm. Subsequently, a sample of ~1.9 billion-year-old microfossil from the Gunflint Formation in Canada is investigated, and for the first time ever, we are able to locally identify the oxidation state of iron compounds encrusting the 5 to 10 µm microfossils. Our results highlight the potential for attaining new insights into Precambrian ecosystems and the composition of Earth's earliest life forms.

Localization and Speciation of Iron Impurities within a Fluid Catalytic Cracking Catalyst.

Fluid catalytic cracking is a chemical conversion process of industrial scale. This process, utilizing porous catalysts composed of clay and zeolite, converts heavy crude-oil fractions into transportation fuel and petrochemical feedstocks. Among other factors iron-rich reactor and feedstream impurities cause these catalyst particles to permanently deactivate. Herein, we report tomographic X-ray absorption spectroscopy measurements that reveal the presence of dissimilar iron impurities of specific localization within a single deactivated particle. Whereas the iron natural to clay in the composite seems to be unaffected by operation, exterior-facing and feedstream-introduced iron was found in two forms. Those being minute quantities of ferrous oxide, located near regions of increased porosity, and impurities rich in Fe3+ , preferentially located in the outer dense part of the particle and suggested to contribute to the formation of an isolating amorphous silica alumina envelope.

Following a Chemical Reaction on the Millisecond Time Scale by Simultaneous X-ray and UV/Vis Spectroscopy.

An innovative approach aimed at disclosing the mechanism of chemical reactions occurring in solution on the millisecond time scale is presented. Time-resolved energy dispersive X-ray absorption and UV/vis spectroscopies with millisecond resolution are used simultaneously to directly follow the evolution of both the oxidation state and the local structure of the metal center in an iron complex. Two redox reactions are studied, the former involving the transformation of FeII into two subsequent FeIII species and the latter involving the more complex FeII-FeIII-FeIV-FeIII sequence. The structural modifications occurring around the iron center are correlated to the reaction mechanisms. This combined approach has the potential to provide unique insights into reaction mechanisms in the liquid phase and represents a new powerful tool to characterize short-lived intermediates that are silent to common spectroscopic techniques.

Thermal and magnetic anomalies of α-iron: an exploration by extended x-ray absorption fine structure spectroscopy and synchrotron x-ray diffraction.

The local structure and dynamics of α-iron have been investigated by extended x-ray absorption fine structure (EXAFS) spectroscopy and x-ray diffraction (XRD) in order to shed light on some thermal and magnetic anomalies observed in the last decades. The quantitative EXAFS analysis of the first two coordination shells reveals a peculiar local vibrational dynamics of α-iron: the second neighbor distance exhibits anharmonicity and vibrational anisotropy larger than the first neighbor distance. We search for possible distortions of the bcc structure to justify the unexplained magnetostriction anomalies of α-iron and provide a value for the maximum dislocation of the central Fe atom. No thermal anomalies have been detected from the current XRD data. On the contrary, an intriguing thermal anomaly at about 150 K, ascribed to a stiffening of the Fe-Fe bonds, was found by EXAFS.

Synthesis and stability of xenon oxides Xe2O5 and Xe3O2 under pressure.

The noble gases are the most inert group of the periodic table, but their reactivity increases with pressure. Diamond-anvil-cell experiments and ab initio modelling have been used to investigate a possible direct reaction between xenon and oxygen at high pressures. We have now synthesized two oxides below 100 GPa (Xe2O5 under oxygen-rich conditions, and Xe3O2 under oxygen-poor conditions), which shows that xenon is more reactive under pressure than predicted previously. Xe2O5 was observed using X-ray diffraction methods, its structure identified through ab initio random structure searching and confirmed using X-ray absorption and Raman spectroscopies. The experiments confirm the recent prediction of Xe3O2 as a stable xenon oxide under high pressure. Xenon atoms adopt mixed oxidation states of 0 and +4 in Xe3O2 and +4 and +6 in Xe2O5. Xe3O2 and Xe2O5 form extended networks that incorporate oxygen-sharing XeO4 squares, and Xe2O5 additionally incorporates oxygen-sharing XeO5 pyramids. Other xenon oxides (XeO2, XeO3) are expected to form at higher pressures.

Probing local and electronic structure in Warm Dense Matter: single pulse synchrotron x-ray absorption spectroscopy on shocked Fe.

Understanding Warm Dense Matter (WDM), the state of planetary interiors, is a new frontier in scientific research. There exists very little experimental data probing WDM states at the atomic level to test current models and those performed up to now are limited in quality. Here, we report a proof-of-principle experiment that makes microscopic investigations of materials under dynamic compression easily accessible to users and with data quality close to that achievable at ambient. Using a single 100 ps synchrotron x-ray pulse, we have measured, by K-edge absorption spectroscopy, ns-lived equilibrium states of WDM Fe. Structural and electronic changes in Fe are clearly observed for the first time at such extreme conditions. The amplitude of the EXAFS oscillations persists up to 500 GPa and 17000 K, suggesting an enduring local order. Moreover, a discrepancy exists with respect to theoretical calculations in the value of the energy shift of the absorption onset and so this comparison should help to refine the approximations used in models.

Structural Properties and Aggregation Behavior of 1-Hexyl-3-methylimidazolium Iodide in Aqueous Solutions.

The structural properties of 1-hexyl-3-methylimidazolium iodide ([C6mim]I)/water mixtures with molar ratios ranging from 1:1 to 1:200 have been investigated using molecular dynamics (MD) simulations with extended X-ray absorption fine structure (EXAFS) experimental data. The presence of a complex network of interactions among cations, anions, and water molecules has been highlighted from the MD simulations, even if water molecules have been found to interact preferentially with the I(-) anion. The EXAFS results show that, also for the 1:1 [C6mim]I/water mixture, the water molecules are placed next to the I(-) anion, and the I(-) hydration shell becomes more and more crowded with increasing water content. Tight ion pairs have been detected in the [C6mim]I/water mixtures with molar ratios from 1:1 to 1:12, while no ionic pairs were found in the most diluted solutions. The aggregation behavior has been determined from MD simulations with the aid of S(q) functions. For the most concentrated IL/water mixtures with molar ratios between 1:1 and 1:12 the existence of long-range structural correlations has been evidenced, even if the apolar chains are not completely segregated as expected for micelle-like structures. Conversely, for the 1:200 mixture, that is above the experimental critical aggregation concentration value, the alkyl chains are completely separated from each other.

New Insights into the Nature of Co-components and Their Impact on Pd Structure: X-ray Absorption Studies on Toluene Acetoxylation Catalysts.

Co-components are a powerful tool to tune the performance of catalysts, but their nature and their impact on the catalysts is often controversially discussed. In this study X-ray absorption spectroscopy (XAS) was employed to elucidate the nature of co-components and their impact on the catalytic reaction. In anatase-supported Pd-based catalysts for the gas-phase acetoxylation of toluene, less noble co-components (e.g., Mn, Co, and Sb) spread over the support in their oxidic form and changed their valence state on stream. Incorporated atoms such as C or a small part of the Sb affect the electronic structure of Pd. For the noble Au, only a weak interaction with the support and Pd was observed during time on stream. Only XAS at the K-edges together with investigations of the Pd L-edge for a better understanding of the electronic structure, supplemented by STEM for elemental mapping, allow such detailed insights.

Melting of iron determined by X-ray absorption spectroscopy to 100 GPa.

Temperature, thermal history, and dynamics of Earth rely critically on the knowledge of the melting temperature of iron at the pressure conditions of the inner core boundary (ICB) where the geotherm crosses the melting curve. The literature on this subject is overwhelming, and no consensus has been reached, with a very large disagreement of the order of 2,000 K for the ICB temperature. Here we report new data on the melting temperature of iron in a laser-heated diamond anvil cell to 103 GPa obtained by X-ray absorption spectroscopy, a technique rarely used at such conditions. The modifications of the onset of the absorption spectra are used as a reliable melting criterion regardless of the solid phase from which the solid to liquid transition takes place. Our results show a melting temperature of iron in agreement with most previous studies up to 100 GPa, namely of 3,090 K at 103 GPa.

Local order and long range correlations in imidazolium halide ionic liquids: a combined molecular dynamics and XAS study.

A thorough characterization of the structural properties of alkylimidazolium halide ionic liquids (ILs), namely 1-alkyl-3-methylimidazolium bromide ([Cnmim]Br with n = 5, 6, 8, 10) and iodide ([C6mim]I), has been carried out by combining molecular dynamics simulations and EXAFS spectroscopy. The existence of a local order in [Cnmim]Br ILs has been evidenced, with anions and imidazolium head groups forming a local three-dimensional bonding pattern that is common to all the [Cnmim]Br IL family, regardless of the length of the alkyl chain attached to the cation. On the other hand, upon alkyl chain elongation significant differences have been highlighted in the long-range structure of these ILs. Theoretical X-ray structure factors have been calculated from MD simulations and a low q peak has been found for all [Cnmim]Br ILs, indicating the existence of long-range structural correlations. The low q peak moves to smaller q values corresponding to longer distances, increases in intensity and sharpens with increasing alkyl chain length on the cation. Similarities and differences between the ion three-dimensional arrangements in [C6mim]Br and [C6mim]I were highlighted and the structural arrangement of Br(-) and I(-) was found to be different in the proximity of the most acidic hydrogen atom of the imidazolium ring: the I(-) ion is preferentially located above and below the ring plane, while the Br(-) ion has a high probability also to be coplanar with the imidazolium ring. A quantitative analysis of the Br and I K-edge EXAFS spectra of alkylimidazolium halide ILs has been carried out based on the microscopic description of the systems derived from MD simulations. A very good agreement between theoretical and experimental EXAFS signals has been obtained, allowing us to assess the reliability of the MD structural results for all the alkylimidazolium halide ILs investigated in this work.

Combining EXAFS spectroscopy and molecular dynamics simulations to understand the structural and dynamic properties of an imidazolium iodide ionic liquid.

The structural properties of liquid 1-butyl-3-methylimidazolium iodide [C4mim]I have been investigated using an integrated approach that combines EXAFS spectroscopy and molecular dynamics (MD) simulations. A well defined first coordination shell composed on average of 4.5 I(-) ions around the imidazolium cation has been evidenced, and the structural arrangement of the I(-) ions has been found to be different in the proximity of the most acidic hydrogen atom of the imidazolium ring, as compared to the other two ring protons: in the former case the I(-) ion is not coplanar with the imidazolium ring plane, but it prefers to be above and below the plane itself, while in the latter the anion has the same probability of being or not being coplanar with the plane. A quantitative analysis of the I K-edge EXAFS spectrum of liquid [C4mim]I has been carried out starting from the structural information on the system derived from the MD simulation. This combined approach allows one to reduce the number of correlated model parameters required in the fitting of the experimental data and to increase the reliability of the EXAFS data analysis that represents a non-trivial task when dealing with disordered systems. Moreover, the good agreement between the EXAFS experimental and theoretical spectra of liquid [C4mim]I has proven the reliability of the MD results and force field employed.