X-ray Emission Spectroscopy at X-ray Free Electron Lasers: Limits to Observation of the Classical Spectroscopic Response for Electronic Structure Analysis

X-ray Emission Spectroscopy of Single Protein Crystals Yields Insights into Heme Enzyme Intermediates

Enzyme reactivity is often enhanced by changes in oxidation state, spin state, and metal-ligand covalency of associated metallocofactors. The development of spectroscopic methods for studying these processes coincidentally with structural rearrangements is essential for elucidating metalloenzyme mechanisms. Herein, we demonstrate the feasibility of collecting X-ray emission spectra of metalloenzyme crystals at a third-generation synchrotron source. In particular, we report the development of a von Hamos spectrometer for the collection of Fe Kβ emission optimized for analysis of dilute biological samples. We further showcase its application in crystals of the immunosuppressive heme-dependent enzyme indoleamine 2,3-dioxygenase. Spectra from protein crystals in different states were compared with relevant reference compounds. Complementary density functional calculations assessing covalency support our spectroscopic analysis and identify active site conformations that correlate to high- and low-spin states. These experiments validate the suitability of an X-ray emission approach for determining spin states of previously uncharacterized metalloenzyme reaction intermediates.

Effects of x-ray free-electron laser pulse intensity on the Mn K 1,3 x-ray emission spectrum in photosystem II-A case study for metalloprotein crystals and solutions

In the last ten years, x-ray free-electron lasers (XFELs) have been successfully employed to characterize metalloproteins at room temperature using various techniques including x-ray diffraction, scattering, and spectroscopy. The approach has been to outrun the radiation damage by using femtosecond (fs) x-ray pulses. An example of an important and damage sensitive active metal center is the Mn4CaO5 cluster in photosystem II (PS II), the catalytic site of photosynthetic water oxidation. The combination of serial femtosecond x-ray crystallography and Kβ x-ray emission spectroscopy (XES) has proven to be a powerful multimodal approach for simultaneously probing the overall protein structure and the electronic state of the Mn4CaO5 cluster throughout the catalytic (Kok) cycle. As the observed spectral changes in the Mn4CaO5 cluster are very subtle, it is critical to consider the potential effects of the intense XFEL pulses on the Kβ XES signal. We report here a systematic study of the effects of XFEL peak power, beam focus, and dose on the Mn Kβ1,3 XES spectra in PS II over a wide range of pulse parameters collected over seven different experimental runs using both microcrystal and solution PS II samples. Our findings show that for beam intensities ranging from ∼5 × 1015 to 5 × 1017 W/cm2 at a pulse length of ∼35 fs, the spectral effects are small compared to those observed between S-states in the Kok cycle. Our results provide a benchmark for other XFEL-based XES studies on metalloproteins, confirming the viability of this approach.

Advances and challenges in time-resolved macromolecular crystallography

Conformational changes within biological macromolecules control a vast array of chemical reactions in living cells. Time-resolved crystallography can reveal time-dependent structural changes that occur within protein crystals, yielding chemical insights in unparalleled detail. Serial crystallography approaches developed at x-ray free-electron lasers are now routinely used for time-resolved diffraction studies of macromolecules. These techniques are increasingly being applied at synchrotron radiation sources and to a growing diversity of macromolecules. Here, we review recent progress in the field, including visualizing ultrafast structural changes that guide the initial trajectories of light-driven reactions as well as capturing biologically important conformational changes on slower time scales, for which bacteriorhodopsin and photosystem II are presented as illustrative case studies.

Dynamic Structural Biology Experiments at XFEL or Synchrotron Sources

Macromolecular crystallography (MX) leverages the methods of physics and the language of chemistry to reveal fundamental insights into biology. Often beautifully artistic images present MX results to support profound functional hypotheses that are vital to entire life science research community. Over the past several decades, synchrotrons around the world have been the workhorses for X-ray diffraction data collection at many highly automated beamlines. The newest tools include X-ray-free electron lasers (XFELs) located at facilities in the USA, Japan, Korea, Switzerland, and Germany that deliver about nine orders of magnitude higher brightness in discrete femtosecond long pulses. At each of these facilities, new serial femtosecond crystallography (SFX) strategies exploit slurries of micron-size crystals by rapidly delivering individual crystals into the XFEL X-ray interaction region, from which one diffraction pattern is collected per crystal before it is destroyed by the intense X-ray pulse. Relatively simple adaptions to SFX methods produce time-resolved data collection strategies wherein reactions are triggered by visible light illumination or by chemical diffusion/mixing. Thus, XFELs provide new opportunities for high temporal and spatial resolution studies of systems engaged in function at physiological temperature. In this chapter, we summarize various issues related to microcrystal slurry preparation, sample delivery into the X-ray interaction region, and some emerging strategies for time-resolved SFX data collection.

Recent results in time resolved serial femtosecond crystallography at XFELs

Time-resolved serial femtosecond crystallography (tr-SFX) methods exploit slurries of crystalline samples that range in size from hundreds of nanometers to a few tens of micrometers, at near-physiological temperature and pressure, to generate atomic resolution models and probe authentic function with the same experiment. 'Dynamic structural biology' is often used to encompass the research philosophy and techniques. Reaction cycles for tr-SFX studies are initiated by photons or ligand addition/mixing strategies, wherein the latter are potentially generalizable across enzymology. Thus, dynamic structural biology often creates stop-motion molecular movies of macromolecular function. In metal-dependent systems, complementary spectroscopic information can also be collected from the same samples and X-ray pulses, which provides even more detailed mechanistic insights. These types of experimental data also complement quantum mechanical and classical dynamics numerical calculations. Correlated structural-functional results will yield more detailed mechanistic insights and will likely translate into better drugs and treatments impacting human health, and better catalysis for clean energy and agriculture.

Femtosecond electronic structure response to high intensity XFEL pulses probed by iron X-ray emission spectroscopy

We report the time-resolved femtosecond evolution of the K-shell X-ray emission spectra of iron during high intensity illumination of X-rays in a micron-sized focused hard X-ray free electron laser (XFEL) beam. Detailed pulse length dependent measurements revealed that rapid spectral energy shift and broadening started within the first 10 fs of the X-ray illumination at intensity levels between 10¹⁷ and 10¹⁸ W cm^-2. We attribute these spectral changes to the rapid evolution of high-density photoelectron mediated secondary collisional ionization processes upon the absorption of the incident XFEL radiation. These fast electronic processes, occurring at timescales well within the typical XFEL pulse durations (i.e., tens of fs), set the boundary conditions of the pulse intensity and sample parameters where the widely-accepted ‘probe-before-destroy’ measurement strategy can be adopted for electronic-structure related XFEL experiments.

Chemical Sensitivity of Kβ and Kα X-ray Emission from a Systematic Investigation of Iron Compounds

K-fluorescence X-ray emission spectroscopy (XES) is receiving growing interest in all fields of natural sciences to investigate the local spin. The spin sensitivity in Kβ (Kα) XES stems from the exchange interaction between the unpaired 3p (2p) and the 3d electrons, which is greater for Kβ than for Kα. We present a thorough investigation of a large number of iron-bearing compounds. The experimental spectra were analyzed in terms of commonly used quantitative parameters (Kβ_1,3-first moment, Kα₁-full width at half-maximum, and integrated absolute difference -IAD-), and we carefully examined the difference spectra. Multiplet calculations were also performed to elucidate the underlying mechanisms that lead to the chemical sensitivity. Our results confirm a strong influence of covalency on both Kβ and Kα lines. We establish a reliable spin sensitivity of Kβ XES as it is dominated by the exchange interaction, whose variations can be quantified by either Kβ_1,3-first moment or Kβ-IAD and result in a systematic difference signal line shape. We find an exception in the Kβ XES of Fe³⁺ and Fe²⁺ in water solution, where a new difference spectrum is identified that cannot be reproduced by scaling the exchange integrals. We explain this by strong differences in orbital mixing between the valence orbitals. This result calls for caution in the interpretation of Kβ XES spectral changes as due to spin variations without a careful analysis of the line shape. For Kα XES, the smaller exchange interaction and the influence of other electron-electron interactions make it difficult to extract a quantity that directly relates to the spin.

Inception of electronic damage of matter by photon-driven post-ionization mechanisms

"Probe-before-destroy" methodology permitted diffraction and imaging measurements of intact specimens using ultrabright but highly destructive X-ray free-electron laser (XFEL) pulses. The methodology takes advantage of XFEL pulses ultrashort duration to outrun the destructive nature of the X-rays. Atomic movement, generally on the order of >50 fs, regulates the maximum pulse duration for intact specimen measurements. In this contribution, we report the electronic structure damage of a molecule with ultrashort X-ray pulses under preservation of the atoms' positions. A detailed investigation of the X-ray induced processes revealed that X-ray absorption events in the solvent produce a significant number of solvated electrons within attosecond and femtosecond timescales that are capable of coulombic interactions with the probed molecules. The presented findings show a strong influence on the experimental spectra coming from ionization of the probed atoms' surroundings leading to electronic structure modification much faster than direct absorption of photons. This work calls for consideration of this phenomenon in cases focused on samples embedded in, e.g., solutions or in matrices, which in fact concerns most of the experimental studies.