Mix-and-inject XFEL crystallography reveals gated conformational dynamics during enzyme catalysis
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A predictive understanding of soft x-ray near-edge absorption spectra of small molecules is an enduring theoretical challenge and of current interest for x-ray probes of molecular dynamics. We report the experimental absorption spectrum for the electron spectroscopy for chemical analysis (ESCA) molecule (ethyl trifluoroacetate) near the carbon 1s absorption edge between 285-300 eV. Furthermore, the ESCA molecule with four chemically distinct carbon sites has previously served as a theoretical benchmark for photoelectron spectra and now for photoabsorption spectra. We report a simple edge-specific approach for systematically expanding standard basis sets to properly describe diffuse Rydberg orbitals and the importance of triple excitations in equation-of-motion coupled-cluster calculations of the energy interval between valence and Rydberg excitations.
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Enzymes populate ensembles of structures necessary for catalysis that are difficult to experimentally characterize. We use time-resolved mix-and-inject serial crystallography at an x-ray free electron laser to observe catalysis in a designed mutant isocyanide hydratase (ICH) enzyme that enhances sampling of important minor conformations. The active site exists in a mixture of conformations, and formation of the thioimidate intermediate selects for catalytically competent substates. The influence of cysteine ionization on the ICH ensemble is validated by determining structures of the enzyme at multiple pH values. Large molecular dynamics simulations in crystallo and time-resolved electron density maps show that Asp 17 ionizes during catalysis and causes conformational changes that propagate across the dimer, permitting water to enter the active site for intermediate hydrolysis. ICH exhibits a tight coupling between ionization of active site residues and catalysis-activated protein motions, exemplifying a mechanism of electrostatic control of enzyme dynamics.
Understanding and harnessing X-ray quantum effects could open new frontiers in imaging and quantum optics. In this study, we measured the process of X-ray Parametric Down Conversion, where a single high-energy X-ray photon splits into two lower-energy photons. Using the SACLA X-ray Free Electron Laser in Japan at 9.83 keV, we found clear evidence that pairs of photons were produced along the energy-angle relationship that conserved both energy and momentum, as predicted for down-conversion, and consistent with quantum entanglement of X-ray photons. By matching specific photon pairs for energy and momentum conservation, we observe a signal rate of 1,250 pairs per hour, confirming that correlated photon pairs can be generated and observed in the absence of explicit time correlations. Our results show that with further refinement, the number of entangled photons produced per laser pulse could increase by an order of magnitude. This paves the way for demonstrating quantum-enhanced X-ray imaging, and confirmation of X-ray photon entanglement.
NNSA has an unmet capability gap to predict how changes in material microstructure, due to aging and new manufacturing practices, can affect performance at extremes. This capability gap is the basis for the Dynamic Mesoscale Material Science Capability (DMMSC) CD-0 that was signed in 2015 [1]. Because of the delay to the MaRIE facility approach, the Tri-Lab in March 2020 proposed separate complementary investments at the APS and LCLS to address portions of the DMMSC mission need [2].
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The Linac Coherent Light Source-II, a high-repetition-rate x-ray free electron laser, produces high average power as well as high peak power. Air is a key radiation safety element, helping to contain the FEL beams from reaching accessible areas. At high average power, air absorption can produce a high temperature and low-density channel along the x-ray beam path. In this case, the x-ray attenuation no longer follows the Beer-Lambert equation, e-μx . Air attenuation measurements were performed with x-rays focused into a gas cell at the LCLS Time-resolved AMO instrument. The air transmission was observed to significantly increase with x-ray power. Simulations were also performed, which include the thermal processes related to the high average power. In comparison to the measurements, the calculated air transmission is higher, confirming that the simulations are conservative and suitable for radiation safety analyses.
In the field of beam physics, two frontier topics have taken center stage due to their potential to enable new approaches to discovery in a wide swath of science. These areas are: advanced, high gradient acceleration techniques, and x-ray free electron lasers (XFELs). Further, there is intense interest in the marriage of these two fields, with the goal of producing a very compact XFEL. In this context, recent advances in high gradient radio-frequency cryogenic copper structure research have opened the door to the use of surface electric fields between 250 and 500 MV m -1 . Such an approach is foreseen to enable a new generation of photoinjectors with six-dimensional beam brightness beyond the current state-of-the-art by well over an order of magnitude. This advance is an essential ingredient enabling an ultra-compact XFEL (UC-XFEL). In addition, one may accelerate these bright beams to GeV scale in less than 10 m. Such an injector, when combined with inverse free electron laser-based bunching techniques can produce multi-kA beams with unprecedented beam quality, quantified by 50 nm-rad normalized emittances. The emittance, we note, is the effective area in transverse phase space (x, p x /m e c) or (y, p y /m e c) occupied by the beam distribution, and it is relevant to achievable beam sizes as well as setting a limit on FEL wavelength. These beams, when injected into innovative, short-period (1–10 mm) undulators uniquely enable UC-XFELs having footprints consistent with university-scale laboratories. We describe the architecture and predicted performance of this novel light source, which promises photon production per pulse of a few percent of existing XFEL sources. We review implementation issues including collective beam effects, compact x-ray optics systems, and other relevant technical challenges. To illustrate the potential of such a light source to fundamentally change the current paradigm of XFELs with their limited access, we examine possible applications in biology, chemistry, materials, atomic physics, industry, and medicine—including the imaging of virus particles—which may profit from this new model of performing XFEL science.
A future capability in dynamic mesoscale materials science is needed to study the limitations of materials under irreversible and extreme conditions, where these limitations are caused by nonuniformities and defects in the mesoscale. This capability gap could potentially be closed with an X-ray free-electron laser (XFEL), producing 5 × 10 10 photons with an energy of 42 keV, known as the Matter–Radiation Interactions in Extremes (MaRIE) XFEL. Over the last few years, researchers at the Los Alamos National Laboratory have developed a preconceptual design for a MaRIE-class XFEL based on existing high-brightness beam technologies, including superconducting L-band cryomodules. However, the performance of a MaRIE-class XFEL can be improved and the risk of its operation reduced by investing in emerging high-brightness beam technologies, such as the development of high-gradient normal conducting radio frequency (RF) structures. Additionally, an alternative XFEL architecture, which generates a series of high-current microbunches instead of a single bunch with uniformly high current along it, may suppress the most important emittance degradation effects in the accelerator and in the XFEL undulator. In this paper, we describe the needed dynamic mesoscale materials science capability, a MaRIE-class XFEL, and the proposed microbunched XFEL accelerator architecture in detail.
X-ray free-electron lasers (XFELs) deliver intense x-ray pulses that destroy the sample in a single shot by a Coulomb explosion. Experiments using XFEL pulse trains or the new generation of high-repetition rate XFELs require rapid sample replacement beyond those provided by the systems now used at low repletion-rate XFELs. We describe the development and characterization of a system based on a spinning disk to continuously deliver a solid sample into an XFEL interaction point at very high speeds. We tested our system at the Linac Coherent Light Source and European XFEL hard x-ray nano-focus instruments, employing it to deliver a 25 μm copper foil sample, which can be used as a gain medium for stimulated x-ray emission for the proposed x-ray laser oscillator.
Abstract Knowledge of x-ray free electron lasers’ (XFELs) pulse characteristics delivered to a sample is crucial for ensuring high-quality x-rays for scientific experiments. XFELs’ self-amplified spontaneous emission process causes spatial and spectral variations in x-ray pulses entering a sample, which leads to measurement uncertainties for experiments relying on multiple XFEL pulses. Accurate in-situ measurements of x-ray wavefront and energy spectrum incident upon a sample poses challenges. Here we address this by developing a virtual diagnostics framework using an artificial neural network (ANN) to predict x-ray photon beam properties from electron beam properties. We recorded XFEL electron parameters while adjusting the accelerator’s configurations and measured the resulting x-ray wavefront and energy spectrum shot-to-shot. Training the ANN with this data enables effective prediction of single-shot or average x-ray beam output based on XFEL undulator and electron parameters. This demonstrates the potential of utilizing ANNs for virtual diagnostics linking XFEL electron and photon beam properties.
In an X-ray free-electron laser (XFEL), a high quality relativistic electron beam from a linear accelerator traverses an array of undulator magnets to generate a high power X-ray beam by allowing the FEL to reach saturation. In many XFELs, phase shifters haven’t been commonly used or included in their designs. The importance of the phase shifter was recognized only recently. A phase shifter can be constructed using either an electromagnet (EM) or a permanent magnet (PM). EM phase shifters are heavy, complex to operate, and take more valuable longitudinal space between the undulators. Compared to EMs, the PMs have several outstanding advantages, including compactness, lighter weights, simple operation, and low maintenance. This project has developed an innovative design of fixed-gap, tunable PM-based compact phase shifter for the XFEL. While keeping the poles and gap fixed, the new design incorporates proven features from the prior work, along with novel field tuning methods, which allow the field strength to be adjusted within a reasonably large range to achieve the desired range of the phase delay control. The PM design without electric currents and power electronics associated with EMs improves reliability by reducing the number of possible points of failure and lowers the operation cost. The compactness makes it possible to use PM phase shifters in the existing XFELs with small gaps between adjacent undulators, as well as in the new XFELs without significantly increasing the FEL length. In Phase I we have accomplished the followings; 1) determined the optimum physics parameters for both weak and strong phase shifters; 2) conducted magnetic design with concrete magnetic and geometrical parameters of actual produced PM materials; 3) provided solutions to achieve precision fine tuning of the magnetic fields with unique methods; 4) elaborated a design based upon ease of manufacturing and cost analysis; and 5) produced rare-earth PM materials, which will be used for prototyping in Phase II. The phase I results provide a foundation for the research and development in the Phase II project, which will aim at building two full-size PM phase shifters and testing at SLAC National Accelerator Laboratory. This project will significantly provide the potential to bring a paradigm change in accelerator technology, replacing conventional electromagnets for many existing accelerator applications and allowing the development of new applications in completely new areas. For example, the PM FEL phase shifters can help significantly improve coherence and power of an XFEL. The proposed use of PM phase shifters will also bring significant cost savings to the construction, operation and maintenance of FEL facilities.
Emerging X-ray free electron laser (XFEL) beam sources offer new types of probes of matter with unprecedented spatial and temporal resolutions. These experimental advances must be met by robust theoretical and computational tools that provide predictive modeling capacity of the underlining electronic and structural dynamics. The latter will be essential for the design of sophisticated multi-pulse experiments and for their interpretation. The proposed research effort will focus on developing cutting- edge simulation tools for nonlinear multidimensional X-ray/optical spectroscopies and aims to address key questions in Priority Research Opportunities 1 (Probing and controlling electron motion within a molecule) and 3 (Capturing rare events and intermediate states in the transformation of matter) as mentioned in the BES Roundtable Report “Opportunities for Basic Research at the Frontiers of XFEL Ultrafast Science”. XFEL multidimensional nonlinear techniques, which combine sequences of X-ray and possibly optical pulses, provide a unique experimental toolbox for probing the dynamics of core and valence electronic excitations, as well as material structure. Predictive modeling of these dynamical processes requires the combination of analytical theory for nonlinear interactions of light and matter, robust quantum-chemical methodologies for the accurate description of electronic structure of various materials, and multiscale ab initio electron and nuclear dynamics techniques operating beyond Born-Oppenheimer approximation. These challenges will be addressed with three research thrusts (i) Develop and implement theoretical apparatus for modeling a broad range of multidimensional spectroscopic techniques enabled by present and upcoming XFEL facilities. This thrust also includes the incorporation of a computational module in the DOE supported open-source NWChem computational chemistry package as well as the development of other open-source codes ready for dissemination across a broad user base; (ii) Propose and design new multi-pulse experiments that make use of the capabilities of the incoming LCLS-II facility; (iii) Perform selected applications to specific molecular systems that can be carried out at LCLS-II and demonstrate how these X-ray sources may be used to study nonadiabatic dynamics through conical interactions, electronic correlations in multi-core excitons, and charge transfer/energy transfer processes. The proposed research will be carried out by a multi-disciplinary four-institution research team which combines academia and national laboratories and spans the broad and necessary expertise in theoretical spectroscopy, nonlinear optics, quantum chemistry, molecular non-adiabatic dynamics and code development. The work will be performed in a highly interactive team environment with junior researchers shared between institutions thus cementing cross- disciplinary interactions. The developed simulation tools will be immediately deployed for XFEL facility users, both experimentalists and theorists, via freely distributed codes and databases. Altogether, this project will facilitate establishing XFEL-based multidimensional spectroscopies as a novel diagnostic tool for monitoring electronic and structural dynamics in molecular materials.
We report resonant inelastic x-ray scattering (RIXS) spectra of neon atoms interacting with intense x-ray pulses generated using an x-ray free-electron laser (XFEL). We find that an unexpected peak emerges near the 𝐾𝛼 line of Ne, which does not coincide with any physical resonances of neon ions. We perform theoretical calculations based on a quantum-state-resolved rate-equation approach with x-ray-induced processes including possible resonant excitations. Our dynamics simulations demonstrate that a sequence of multiple resonant photoabsorption events are involved and the interplay of those multiple resonances in combination with the relatively large spectral bandwidth of XFEL radiation leads to the emergent resonance-like structure at a position where no resonances exist. Our finding offers critical guidance for future applications of high-intensity RIXS at XFEL facilities.
The metal centers in metalloenzymes and molecular catalysts are responsible for the rearrangement of atoms and electrons during complex chemical reactions, and they enable selective pathways of charge and spin transfer, bond breaking/making and the formation of new molecules. Mapping the electronic structural changes at the metal sites during the reactions gives a unique mechanistic insight that has been difficult to obtain to date. The development of X-ray free-electron lasers (XFELs) enables powerful new probes of electronic structure dynamics to advance our understanding of metalloenzymes. The ultrashort, intense and tunable XFEL pulses enable X-ray spectroscopic studies of metalloenzymes, molecular catalysts and chemical reactions, under functional conditions and in real time. In this Technical Review, we describe the current state of the art of X-ray spectroscopy studies at XFELs and highlight some new techniques currently under development. With more XFEL facilities starting operation and more in the planning or construction phase, new capabilities are expected, including high repetition rate, better XFEL pulse control and advanced instrumentation. For the first time, it will be possible to make real-time molecular movies of metalloenzymes and catalysts in solution, while chemical reactions are taking place.