X-ray free-electron lasers (XFELs) enable crystallographic structure determination beyond the limitations imposed upon synchrotron measurements by radiation damage. The need for very short XFEL pulses is relieved through gating of Bragg diffraction by loss of crystalline order as damage progresses, but not if ionization events are spatially non-uniform due to underlying elemental distributions, as in biological samples. Indeed, correlated movements of iron and sulfur ions were observed in XFEL-irradiated ferredoxin microcrystals using unusually long pulses of 80 fs. Here, we report a femtosecond time-resolved X-ray pump/X-ray probe experiment on protein nanocrystals. We observe changes in the protein backbone and aromatic residues as well as disulfide bridges. Simulations show that the latter’s correlated structural dynamics are much slower than expected for the predicted high atomic charge states due to significant impact of ion caging and plasma electron screening. This indicates that dense-environment effects can strongly affect local radiation damage-induced structural dynamics.

In this work, we analyze the application of X-ray diffraction imaging techniques to follow ultrafast structural transitions in solid materials using the example of an X-ray pump–X-ray probe experiment with a single-crystal silicon performed at a Linac Coherent Light Source. Due to the spatially non-uniform profile of the X-ray beam, the diffractive signal recorded in this experiment included contributions from crystal parts experiencing different fluences from the peak fluence down to zero. With our theoretical model, we could identify specific processes contributing to the silicon melting in those crystal regions, i.e., the non-thermal and thermal melting whose occurrences depended on the locally absorbed X-ray doses. We then constructed the total volume-integrated signal by summing up the coherent signal contributions (amplitudes) from the various crystal regions and found that this significantly differed from the signals obtained for a few selected uniform fluence values, including the peak fluence. This shows that the diffraction imaging signal obtained for a structurally damaged material after an impact of a non-uniform X-ray pump pulse cannot be always interpreted as the material’s response to a pulse of a specific (e.g., peak) fluence as it is sometimes believed. This observation has to be taken into account in planning and interpreting future experiments investigating structural changes in materials with X-ray diffraction imaging.

We present a generalized method to describe the x-ray scattering intensity of the Bragg spots in a diffraction pattern from nanocrystals exposed to intense x-ray pulses. Our method involves the subdivision of a crystal into smaller units. In order to calculate the dynamics within every unit, we employ a Monte-Carlo-molecular dynamics-ab-initio hybrid framework using real space periodic boundary conditions. By combining all the units, we simulate the diffraction pattern of a crystal larger than the transverse x-ray beam profile, a situation commonly encountered in femtosecond nanocrystallography experiments with focused x-ray free-electron laser radiation. Radiation damage is not spatially uniform and depends on the fluence associated with each specific region inside the crystal. To investigate the effects of uniform and non-uniform fluence distribution, we have used two different spatial beam profiles, Gaussian and flattop.

When matter is exposed to a high-intensity x-ray free-electron-laser pulse, the x rays excite inner-shell electrons leading to the ionization of the electrons through various atomic processes and creating high-energy-density plasma, i.e., warm or hot dense matter. The resulting system consists of atoms in various electronic configurations, thermalizing on subpicosecond to picosecond timescales after photoexcitation. We present a simulation study of x-ray-heated solid-density matter. For this we use XMDYN, a Monte Carlo molecular-dynamics-based code with periodic boundary conditions, which allows one to investigate nonequilibrium dynamics. XMDYN is capable of treating systems containing light and heavy atomic species with full electronic configuration space and three-dimensional spatial inhomogeneity. For the validation of our approach we compare for a model system the electron temperatures and the ion charge-state distribution from XMDYN to results for the thermalized system based on the average-atom model implemented in XATOM, an ab initio x-ray atomic physics toolkit extended to include a plasma environment. Further, we also compare the average charge evolution of diamond with the predictions of a Boltzmann continuum approach. We demonstrate that XMDYN results are in good quantitative agreement with the above-mentioned approaches, suggesting that the current implementation of XMDYN is a viable approach to simulate the dynamics of x-ray-driven nonequilibrium dynamics in solids. To illustrate the potential of XMDYN for treating complex systems, we present calculations on the triiodo benzene derivative 5-amino-2,4,6-triiodoisophthalic acid (I3C), a compound of relevance of biomolecular imaging, consisting of heavy and light atomic species.

X-ray free-electron lasers (XFELs) broaden horizons in X-ray crystallography. Facilitated by the unprecedented high intensity and ultrashort duration of the XFEL pulses, they enable us to investigate the structure and dynamics of macromolecules with nano-sized crystals. A limitation is the extent of radiation damage in the nanocrystal target. A large degree of ionization initiated by the incident high-intensity XFEL pulse alters the scattering properties of the atoms leading to perturbed measured patterns. In this article, the effective-form-factor approximation applied to capture this phenomenon is discussed. Additionally, the importance of temporal configurational fluctuations at high intensities, shaping these quantities besides the average electron loss, is shown. An analysis regarding the applicability of the approach to targets consisting of several atomic species is made, both theoretically and via realistic radiation-damage simulations. It is concluded that, up to intensities relevant for XFEL-based nanocrystallography, the effective-form-factor description is sufficiently accurate. This work justifies treating measured scattering patterns using conventional structure-reconstruction algorithms.

Simulation of high-intensity x-ray scattering from a crystal that is larger than the transverse x-ray beam profile is presented. We consider a crystal with a size of a micron, when irradiated by an x-ray beam having a focus of 100 nm. We discuss the methodological challenges that had to be overcome in order to calculate the x-ray scattering pattern. Our calculations enable us to identify the characteristic features of the spatial beam profile imprinted in the scattering pattern.