A high-throughput energy-dispersive tender X-ray spectrometer for shot-to-shot sulfur measurements

Structural biology in the age of X-ray free-electron lasers and exascale computing

Serial femtosecond X-ray crystallography has emerged as a powerful method for investigating biomolecular structure and dynamics. With the new generation of X-ray free-electron lasers, which generate ultrabright X-ray pulses at megahertz repetition rates, we can now rapidly probe ultrafast conformational changes and charge movement in biomolecules. Over the last year, another innovation has been the deployment of Frontier, the world's first exascale supercomputer. Synergizing extremely high repetition rate X-ray light sources and exascale computing has the potential to accelerate discovery in biomolecular sciences. Here we outline our perspective on each of these remarkable innovations individually, and the opportunities and challenges in yoking them within an integrated research infrastructure.

PINK: a tender X-ray beamline for X-ray emission spectroscopy

A high-flux beamline optimized for non-resonant X-ray emission spectroscopy (XES) in the tender X-ray energy range has been constructed at the BESSY II synchrotron source. The beamline utilizes a cryogenically cooled undulator that provides X-rays over the energy range 2.1 keV to 9.5 keV. This energy range provides access to XES [and in the future X-ray absorption spectroscopy (XAS)] studies of transition metals ranging from Ti to Cu (Kα, Kβ lines) and Zr to Ag (Lα, Lβ), as well as light elements including P, S, Cl, K and Ca (Kα, Kβ). The beamline can be operated in two modes. In PINK mode, a multilayer monochromator (E/ΔE ≃ 30-80) provides a high photon flux (1014 photons s-1 at 6 keV and 300 mA ring current), allowing non-resonant XES measurements of dilute substances. This mode is currently available for general user operation. X-ray absorption near-edge structure and resonant XAS techniques will be available after the second stage of the PINK commissioning, when a high monochromatic mode (E/ΔE ≃ 10000-40000) will be facilitated by a double-crystal monochromator. At present, the beamline incorporates two von Hamos spectrometers, enabling time-resolved XES experiments with time scales down to 0.1 s and the possibility of two-color XES experiments. This paper describes the optical scheme of the PINK beamline and the endstation. The design of the two von Hamos dispersive spectrometers and sample environment are discussed here in detail. To illustrate, XES spectra of phosphorus complexes, KCl, TiO2 and Co3O4 measured using the PINK setup are presented.

Understanding Cysteine Chemistry Using Conventional and Serial X-Ray Protein Crystallography

Proteins that use cysteine residues for catalysis or regulation are widely distributed and intensively studied, with many biomedically important examples. Enzymes where cysteine is a catalytic nucleophile typically generate covalent catalytic intermediates whose structures are important for understanding mechanism and for designing targeted inhibitors. The formation of catalytic intermediates can change enzyme conformational dynamics, sometimes activating protein motions that are important for catalytic turnover. However, these transiently populated intermediate species have been challenging to structurally characterize using traditional crystallographic approaches. This review describes the use and promise of new time-resolved serial crystallographic methods to study cysteine-dependent enzymes, with a focus on the main (M^pro) and papain-like (PL^pro) cysteine proteases of SARS-CoV-2 as well as other examples. We review features of cysteine chemistry that are relevant for the design and execution of time-resolved serial crystallography experiments. In addition, we discuss emerging X-ray techniques such as time-resolved sulfur X-ray spectroscopy that may be able to detect changes in sulfur charge state and covalency during catalysis or regulatory modification. In summary, cysteine-dependent enzymes have features that make them especially attractive targets for new time-resolved serial crystallography approaches, which can reveal both changes to enzyme structure and dynamics during catalysis in crystalline samples.

Development of an experimental apparatus to observe ultrafast phenomena by tender X-ray absorption spectroscopy at PAL-XFEL

Understanding the ultrafast dynamics of molecules is of fundamental importance. Time-resolved X-ray absorption spectroscopy (TR-XAS) is a powerful spectroscopic technique for unveiling the time-dependent structural and electronic information of molecules that has been widely applied in various fields. Herein, the design and technical achievement of a newly developed experimental apparatus for TR-XAS measurements in the tender X-ray range with X-ray free-electron lasers (XFELs) at the Pohang Accelerator Laboratory XFEL (PAL-XFEL) are described. Femtosecond TR-XAS measurements were conducted at the Ru L3-edge of well known photosensitizer tris(bipyridine)ruthenium(II) chloride ([Ru(bpy)3]2+) in water. The results indicate ultrafast photoinduced electron transfer from the Ru center to the ligand, which demonstrates that the newly designed setup is applicable for monitoring ultrafast reactions in the femtosecond domain.

A von Hamos spectrometer based on highly annealed pyrolytic graphite crystal in tender x-ray domain

We have built an x-ray spectrometer in a von Hamos configuration based on a highly annealed pyrolytic graphite crystal. The spectrometer is designed to measure x-ray emission in the range of 2-5 keV. A spectral resolution E/ΔE of 4000 was achieved by recording the elastic peak of photons issued from the GALAXIES beamline at the SOLEIL synchrotron radiation facility.

Characterization of Li-S Batteries Using Laboratory Sulfur X-ray Emission Spectroscopy

Application of laboratory-based X-ray analytical techniques that are capable of a reliable characterization of the chemical state of sulfur within bulk battery cathode in parallel with electrochemical characterization is essential for further development of lithium-sulfur batteries. In this work, MeV proton-induced X-ray emission (XES) sulfur measurements were performed in ex situ mode on laboratory-synthesized sulfur standards and precycled battery cathodes. The average sulfur charge was determined from the energy shift of the Kα emission line and from the spectral shape of the Kβ emission spectrum. Finally, operando Kα XES measurements were performed to monitor reduction of sulfur within battery cathode during discharge. The experimental approach presented here provides an important step toward more routine laboratory analysis of sulfur-based battery systems and also other sulfur-neighboring low-Z bulk materials with emission energies in the tender X-ray range.

Sulfur valence-to-core X-ray emission spectroscopy study of lithium sulfur batteries

In this work, valence-to-core (VtC) Kβ sulfur X-ray emission spectroscopy (XES) was used to perform quantitative analysis of different sulfur compounds produced in a lithium sulfur (Li-S) battery during discharge. The analysis is based on the theoretical sulfur Kβ XES spectra obtained from ab initio quantum chemical calculations based on density functional theory. The emphasis is given to the Kβ sulfur XES spectra of the polysulfide molecules (Li2Sx, x = 2,,8) produced electrochemically within the Li-S battery. Ab initio molecular dynamics calculations are used further to calculate also the Kβ spectra of Li2Sx dissolved in a model solvent. Calculated spectra were directly compared with the experimental ones collected with a Johansson type tender XES spectrometer on laboratory synthesized Li2Sx reference standards and pre-cycled battery cathodes. These results demonstrate that sulfur VtC XES can be used effectively to quantitatively analyze electrochemical sulfur conversion, also in a smaller laboratory without the need for large scale synchrotron facilities.

The five-analyzer point-to-point scanning crystal spectrometer at ESRF ID26

X-ray emission spectroscopy in a point-to-point focusing geometry using instruments that employ more than one analyzer crystal poses challenges with respect to mechanical design and performance. This work discusses various options for positioning the components and provides the formulas for calculating their relative placement. Ray-tracing calculations were used to determine the geometrical contributions to the energy broadening including the source volume as given by the beam footprint on the sample. The alignment of the instrument is described and examples are given for the performance.

TEXS: in-vacuum tender X-ray emission spectrometer with 11 Johansson crystal analyzers

The design and first results of a large-solid-angle X-ray emission spectrometer that is optimized for energies between 1.5 keV and 5.5 keV are presented. The spectrometer is based on an array of 11 cylindrically bent Johansson crystal analyzers arranged in a non-dispersive Rowland circle geometry. The smallest achievable energy bandwidth is smaller than the core hole lifetime broadening of the absorption edges in this energy range. Energy scanning is achieved using an innovative design, maintaining the Rowland circle conditions for all crystals with only four motor motions. The entire spectrometer is encased in a high-vacuum chamber that allocates a liquid helium cryostat and provides sufficient space for in situ cells and operando catalysis reactors.

A versatile Johansson-type tender x-ray emission spectrometer

We present a high energy resolution x-ray spectrometer for the tender x-ray regime (1.6-5.0 keV) that was designed and operated at Stanford Synchrotron Radiation Lightsource. The instrument is developed on a Rowland geometry (500 mm of radius) using cylindrically bent Johansson analyzers and a position sensitive detector. By placing the sample inside the Rowland circle, the spectrometer operates in an energy-dispersive mode with a subnatural line-width energy resolution (∼0.32 eV at 2400 eV), even when an extended incident x-ray beam is used across a wide range of diffraction angles (∼30° to 65°). The spectrometer is enclosed in a vacuum chamber, and a sample chamber with independent ambient conditions is introduced to enable a versatile and fast-access sample environment (e.g., solid/gas/liquid samples, in situ cells, and radioactive materials). The design, capabilities, and performance are presented and discussed.

200-mm segmented cylindrical figured crystal for von Hamos x-ray spectrometer

A von Hamos Bragg crystal spectrometer at 1C beamline of Pohang Accelerator Laboratory for x-ray emission spectroscopy (XES) is described. Diced Si crystals of different orientations ([111], [110], [100], and [311]) are glued onto a planoconcave glass substrate having 250/500 mm radius of curvature. To enhance the spectrometer efficiency, the length of the crystal analyzer is kept 200 mm. The emission spectra of Cu foil and Fe foil and elastic scattering from Al foil are measured using the von Hamos geometry in which curved crystals disperse the x-rays. Spectrometer efficiency and energy resolution are measured at various x-ray photon energies. X-rays are incident at 6.54 keV, 9.00 keV, 9.205 keV, and 11.51 keV for Si(440), Si(444), Si(800), and Si(933) crystal analyzers, respectively. The cylindrical figured analyzer is placed near 80° with respect to the sample, which gives better energy resolution. The spectrometer efficiency of the Si(444) crystal analyzer increases by ∼2 times when the length of the analyzer is increased from 100 mm to 200 mm. Furthermore, to measure Fe Kα₁, Kα₂, and K_β simultaneously, we made a mixed crystal analyzer in which alternative strips of Si[111] and Si[110] are glued onto one preshaped cylindrical substrate. The enhanced efficiency and simultaneous measurement of K_α and K_β emission lines will give an edge over in situ and time-resolved x-ray emission spectroscopy studies. The information extracted with a high efficiency spectrometer from low intensity XES emission lines will be useful for the in situ elemental characterization in catalytic reactions.

Gauging aromatic conjugation and charge delocalization in the aryl silanes PhnSiH4−n (n = 0–4), with silicon K-edge XAS and TDDFT

Si K-edge X-ray absorption spectra (XAS) have been measured experimentally and calculated using time-dependent density functional theory (TDDFT) to investigate electronic structure in aryl silanes, Ph_nSiH_4−n (n = 0–4).