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X-ray photoelectron spectroscopy probes the chemical environment in a molecule at a specific atomic site. Here the authors extend this concept with a site selective trigger to follow chemical bond changes as they occur on the femtosecond time scale.

Diffraction before destruction using X-ray free-electron lasers (XFELs) has the potential to determine radiation-damage-free structures without the need for crystallization. This article presents the three-dimensional reconstruction of the Melbournevirus from single-particle X-ray diffraction patterns collected at the LINAC Coherent Light Source (LCLS) as well as reconstructions from simulated data exploring the consequences of different kinds of experimental sources of noise. The reconstruction from experimental data suffers from a strong artifact in the center of the particle. This could be reproduced with simulated data by adding experimental background to the diffraction patterns. In those simulations, the relative density of the artifact increases linearly with background strength. This suggests that the artifact originates from the Fourier transform of the relatively flat background, concentrating all power in a central feature of limited extent. We support these findings by significantly reducing the artifact through background removal before the phase-retrieval step. Large amounts of blurring in the diffraction patterns were also found to introduce diffuse artifacts, which could easily be mistaken as biologically relevant features. Other sources of noise such as sample heterogeneity and variation of pulse energy did not significantly degrade the quality of the reconstructions. Larger data volumes, made possible by the recent inauguration of high repetition-rate XFELs, allow for increased signal-to-background ratio and provide a way to minimize these artifacts. The anticipated development of three-dimensional Fourier-volume-assembly algorithms which are background aware is an alternative and complementary solution, which maximizes the use of data.

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

Measurements of the soft x-ray, self-seeding spectrum at the Linac Coherent Light Source (LCLS) free-electron laser generally display a pedestal-like distribution around the central seeded wavelength. This pedestal limits the spectral purity and can negatively affect some user applications not employing a post-undulator monochromator. In this paper, we investigate the detailed experimental characteristics of both the amplified seed and its accompanying pedestal using data from a number of separate LCLS shifts over the 2015-2018 time period. We find that the amplified seed shows excellent wavelength stability and an exponential growth rate whose dependence upon energy detuning is consistent with theory. The pedestal’s spectral distribution and integrated strength vary strongly shot by shot, independent of electron beam energy jitter. Its shot-averaged strength relative to that of the seed grows at least linearly with z and can approach values of 15% or more. The pedestal is comprised of two separate components: (1) normal self-amplified spontaneous emission (SASE) whose total strength is nominally insensitive to energy detuning and laser heater (LH) strength; (2) sideband-like emission whose strength positively correlates with that of the amplified seed and negatively with energy detuning and LH strength. We believe this latter, non-SASE component arises from comparatively long wavelength (i.e., λ∼0.3–3 μm) amplitude and phase modulations of the main seeded radiation line. Its shot to shot variability and LH sensitivity suggests an origin connected to growth of the longitudinal microbunching instability on the electron beam.

Coherent emission from a microbunched electron beam is the driving force behind the revolution in light sources, enabling x-ray free-electron lasers (FELs) to emit pulses 9 orders of magnitude brighter than previous sources. Microbunches form perpendicular to the electron travel direction, and the conventional understanding is that they shear rather than rotate in response to a transverse kick, locking FEL facilities into a single-user operating mode. In this paper, we show that microbunches rotate toward the new direction of travel if the electron beam is kicked and defocused. We provide evidence that microbunch rotation explains the unexpectedly large amount of off-axis radiation observed during experiments at the Linac Coherent Light Source. We demonstrate that LCLS can be multiplexed into at least three separate beams using this principle. Finally, we propose using a magnetic triplet to rotate microbunches through significantly larger angles without microbunch degradation. This new understanding of microbunch dynamics can lead to significantly improved multiplexing at FEL facilities, microbunch preservation through a bend, and x-ray pulses with a pulse-front tilt.

Measurements of the multishot-averaged, soft x-ray, self-seeding spectrum at the LCLS free-electron laser often have a pedestal-like distribution around the seeded wavelength, which limits the spectral purity and can negatively affect some user applications not employing a post-undulator monochromator. In this paper, we study the origins of such pedestals, focusing on longitudinal phase space modulations produced by the microbunching instability upstream of the free-electron laser (FEL) undulator. We show from theory and numerical simulation that both energy and density modulations can induce sidebands in a high-gain, seeded FEL whose fractional strength typically grows as the square of the undulator length. The results place a tight constraint on the longitudinal phase space uniformity of the electron beam for a seeded FEL, possibly requiring the amplitude of long-wavelength modulations to be much smaller than the typical incoherent energy spread if the output sideband power is to remain only a couple percent or less of the amplified seed power.

Self-seeding is a promising approach to significantly narrow the self-amplified spontaneous emission bandwidth of X-ray free-electron lasers (FELs) and hence to produce nearly transform-limited pulses. We study the radiation propagation through a grating monochromator installed at the Linac Coherent Light Source (LCLS). The monochromator design is based on a toroidal VLS grating working at a fixed incidence angle mounting without an entrance slit. It covers the spectral range from 500 eV to 1000 eV. The optical system was studied using a wave optics method to evaluate the performance of the self-seeding scheme. Our wave optics analysis takes into account the finite size of the coherent source, third-order aberrations and height error of the optical elements. Two propagation approaches are studied with time-dependent FEL simulations. In addition, the pulse-front tilt phenomenon effect is illustrated.