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We simulated Coulomb explosion dynamics due to fast ionization induced by high-intensity x-rays in six proteins that share similar atomic content and shape. We followed and projected the trajectory of the fragments onto a virtual detector, providing a unique explosion footprint. After collecting 500 explosion footprints for each protein, we utilized principal component analysis and 𝑡-distributed stochastic neighbor embedding to classify these. Results show that the classification algorithms were able to separate proteins on the basis of explosion footprints from structurally similar proteins into distinct groups. The explosion footprints, therefore, provide a unique identifier for each protein. We envision that method could be used concurrently with single-particle coherent imaging experiments to provide additional information on shape, mass, or conformation.

Charge transfer between molecules lies at the heart of many chemical processes. Here, we focus on the ultrafast electron dynamics associated with the formation of charge-transfer-to-solvent (CTTS) states following X-ray absorption in aqueous solutions of Na+, Mg2+, and Al3+ ions. To explore the formation of such states in the aqueous phase, liquid-jet photoemission spectroscopy is employed. Using the core-hole-clock method, based on Auger-Meitner (AM) decay upon 1s excitation or ionization of the respective ions, upper limits are estimated for the metal-atom electron delocalization times to the neighboring water molecules. These delocalization processes represent the first steps in the formation of hydrated electrons, which are determined to take place on a timescale ranging from several hundred attoseconds (as) below the 1s ionization threshold to only 20 as far above the 1s ionization threshold. The decrease in the delocalization times as a function of the photon energy is continuous. This indicates that the excited electrons remain in the vicinity of the studied ions even above the ionization threshold, i.e., metal-ion electronic resonances associated with the CTTS state manifolds are formed. The three studied isoelectronic ions exhibit quantitative differences in their electron energetics and delocalization times, which are linked to the character of the respective excited states. The authors investigate the X-ray-induced electron dynamics, on the sub-femtosecond timescale, of hydrated Na+, Mg2+, and Al3+ ions providing insights into the ultrafast charge-transfer processes in aqueous environments.

Collision induced unfolding is method used with ion mobility mass spectrometry to examine protein structures and their stability. Such experiments yield information about higher order protein structures, yet are unable to provide details about the underlying processes. That information can however be provided using molecular dynamics simulations. Here, we investigate the collision induced unfolding of norovirus capsid dimers from the Norwalk and Kawasaki strains by employing molecular dynamics simulations over a range of temperatures, representing different levels of activation. The dimers have highly similar structures, but the activation reveals differences in the dynamics that arises in response to the activation.

Single particle imaging of proteins in the gas phase with x-ray free-electron lasers holds great potential to study fast protein dynamics, but is currently limited by weak and noisy data. A further challenge is to discover the proteins' orientation as each protein is randomly oriented when exposed to x-rays. Algorithms such as the expand, maximize, and compress (EMC) exist that can solve the orientation problem and reconstruct the three-dimensional diffraction intensity space, given sufficient measurements. If information about orientation were known, for example, by using an electric field to orient the particles, the reconstruction would benefit and potentially reach better results. We used simulated diffraction experiments to test how the reconstructions from EMC improve with particles' orientation to a preferred axis. Our reconstructions converged to correct maps of the three-dimensional diffraction space with fewer measurements if biased orientation information was considered. Even for a moderate bias, there was still significant improvement. Biased orientations also substantially improved the results in the case of missing central information, in particular in the case of small datasets. The effects were even more significant when adding a background with 50% the strength of the averaged diffraction signal photons to the diffraction patterns, sometimes reducing the data requirement for convergence by a factor of 10. This demonstrates the usefulness of having biased orientation information in single particle imaging experiments, even for a weaker bias than what was previously known. This could be a key component in overcoming the problems with background noise that currently plague these experiments.

The present study investigates the photofragmentation behavior of iodine-enhanced nitroimidazole-based radiosensitizer model compounds in their protonated form using near-edge X-ray absorption mass spectrometry and quantum mechanical calculations. These molecules possess dual functionality: improved photoabsorption capabilities and the ability to generate species that are relevant to cancer sensitization upon photofragmentation. Four samples were investigated by scanning the generated fragments in the energy regions around C 1s, N 1s, O 1s, and I 3d-edges with a particular focus on NO2+ production. The experimental summed ion yield spectra are explained using the theoretical near-edge X-ray absorption fine structure spectrum based on density functional theory. Born-Oppenheimer-based molecular dynamics simulations were performed to investigate the fragmentation processes.

We describe a method to compute photon–matter interaction and atomic dynamics with x-ray lasers using a hybrid code based on classical molecular dynamics and collisional-radiative calculations. The forces between the atoms are dynamically determined based on changes to their electronic occupations and the formation of a free electron cloud created from the irradiation of photons in the x-ray spectrum. The rapid transition from neutral solid matter to dense plasma phase allows the use of screened potentials, reducing the number of non-bonded interactions. In combination with parallelization through domain decomposition, the hybrid code handles large-scale molecular dynamics and ionization. This method is applicable for large enough samples (solids, liquids, proteins, viruses, atomic clusters, and crystals) that, when exposed to an x-ray laser pulse, turn into a plasma in the first few femtoseconds of the interaction. We present four examples demonstrating the applicability of the method. We investigate the non-thermal heating and scattering of bulk water and damage-induced dynamics of a protein crystal using an x-ray pump–probe scheme. In both cases, we compare to the experimental data. For single particle imaging, we simulate the ultrafast dynamics of a methane cluster exposed to a femtosecond x-ray laser. In the context of coherent diffractive imaging, we study the fragmentation as given by an x-ray pump–probe setup to understand the evolution of radiation damage in the time range of hundreds of femtoseconds.

Radiation therapy uses ionizing radiation to break chemical bonds in cancer cells, thereby causing DNA damage and leading to cell death. The therapeutic effectiveness can be further increased by making the tumor cells more sensitive to radiation. Here, we investigate the role of the initial halogen atom core hole on the photofragmentation dynamics of 2-bromo-5-iodo-4-nitroimidazole, a potential bifunctional radiosensitizer. Bromine and iodine atoms were included in the molecule to increase the photoionization cross-section of the radiosensitizer at higher photon energies. The fragmentation dynamics of the molecule was studied experimentally in the gas phase using photoelectron-photoion-photoion coincidence spectroscopy and computationally using Born-Oppenheimer molecular dynamics. We observed significant changes between shallow core (I 4d, Br 3d) and deep core (I 3d) ionization in fragment formation and their kinetic energies. Despite the fact, that the ions ejected after deep core ionization have higher kinetic energies, we show that in a cellular environment, the ion spread is not much larger, keeping the damage well-localized. A study on photodissociation dynamics of 2-bromo-5-iodo-nitroimidazole - a model radiosensitizer - using coincidence spectroscopy and computational methods.

The sustainable development encompasses the search for new materials for energy storage, gas capture, separation, and solvents in industrial processes that can substitute conventional ones in an efficient and clean manner. Ionic liquids (ILs) emerged and have been advanced as alternative materials for such applications, but an obstacle is their hygroscopicity and the effects on their physical properties in the presence of humidity. Several industrial processes depend on the aqueous interfacial properties, and the main focus of this work is the water/IL interface. The behavior of the aqueous ionic liquids at the water-vacuum interface is representative for their water interfacial properties. Using X-ray photoelectron spectroscopy in combination with molecular dynamics simulations we investigate four aqueous IL systems, and provide molecular level insight on the interfacial behaviour of the ionic liquids, such as ion-pair formation, orientation and surface concentration. We find that ionic liquids containing a chloride anion have a lowered surface enrichment due to the low surface propensity of chloride. In contrast, the ionic liquids containing a bistriflimide anion are extremely surface-enriched due to cooperative surface propensity between the cations and anions, forming a two-dimensional ionic liquid on the water surface at low concentrations. Ionic liquids are interesting materials for many applications related to sustainable development, but the effects of water on their properties are insufficiently known. Using X-ray photoelectron spectroscopy and molecular dynamics simulations, we show how the surface propensity of four ionic liquids in aqueous solution vary with the molecular structure of the ions, and discuss the underlying driving forces.+image

Water and ice are routinely studied with X-rays to reveal their diverse structures and anomalous properties. We employ a hybrid collisional-radiative/molecular-dynamics method to explore how femtosecond X-ray pulses interact with hexagonal ice. We find that ice makes a phase transition into a crystalline plasma where its initial structure is maintained up to tens of femtoseconds. The ultrafast melting process occurs anisotropically, where different geometric configurations of the structure melt on different time scales. The transient state and anisotropic melting of crystals can be captured by X-ray diffraction, which impacts any study of crystalline structures probed by femtosecond X-ray lasers.

- Single particle imaging using X-ray lasers is a technique aiming to capture atomic resolution structures of biomolecules in their native state. Knowing the particle's orientation during exposure is crucial for method enhancement. It has been shown that the trajectories of sulfur atoms in a Coulomb exploding lysozyme are reproducible, providing orientation information. This study explores if sulfur atom depth influences explosion trajectory. Employing a hybrid collisional-radiative/molecular dynamics model, we analyze the X-ray laser-induced dynamics of a single sulfur ion at varying depths in water. Our findings indicate that the ion spread-depth relationship depends on pulse parameters. At a photon energy of 2 keV, high-charge states are obtained, resulting in an increase of the spread with depth. However, at 8 keV photon energy, where lower charge states are obtained, the spread is essentially independent with depth. Finally, lower ion mass results in less reproducible trajectories, opening a promising route for determining protein orientation through the introduction of heavy atoms.