XCALIB: a focal spot calibrator for intense X-ray free-electron laser pulses based on the charge state distributions of light atoms

We develop the XCALIB toolkit to calibrate the beam profile of an X-ray free-electron laser (XFEL) at the focal spot based on the experimental charge state distributions (CSDs) of light atoms. Accurate characterization of the fluence distribution at the focal spot is essential to perform the volume integrations of physical quantities for a quantitative comparison between theoretical and experimental results, especially for fluence dependent quantities. The use of the CSDs of light atoms is advantageous because CSDs directly reflect experimental conditions at the focal spot, and the properties of light atoms have been well established in both theory and experiment. To obtain theoretical CSDs, we use XATOM, a toolkit to calculate atomic electronic structure and to simulate ionization dynamics of atoms exposed to intense XFEL pulses, which involves highly excited multiple core hole states. Employing a simple function with a few parameters, the spatial profile of an XFEL beam is determined by minimizing the difference between theoretical and experimental results. We have implemented an optimization procedure employing the reinforcement learning technique. The technique can automatize and organize calibration procedures which, before, had been performed manually. XCALIB has high flexibility, simultaneously combining different optimization methods, sets of charge states, and a wide range of parameter space. Hence, in combination with XATOM, XCALIB serves as a comprehensive tool to calibrate the fluence profile of a tightly focused XFEL beam in the interaction region.Comment: 28 pages, 7 figure

Progress and Poverty—1965 Version

The first hard X-ray laser, the Linac Coherent Light Source (LCLS), produces 120 shots per second. Particles injected into the X-ray beam are hit randomly and in unknown orientations by the extremely intense X-ray pulses, where the femtosecond-duration X-ray pulses diffract from the sample before the particle structure is significantly changed even though the sample is ultimately destroyed by the deposited X-ray energy. Single particle X-ray diffraction experiments generate data at the FEL repetition rate, resulting in more than 400,000 detector readouts in an hour, the data stream during an experiment contains blank frames mixed with hits on single particles, clusters and contaminants. The diffraction signal is generally weak and it is superimposed on a low but continually fluctuating background signal, originating from photon noise in the beam line and electronic noise from the detector. Meanwhile, explosion of the sample creates fragments with a characteristic signature. Here, we describe methods based on rapid image analysis combined with ion Time-of-Flight (ToF) spectroscopy of the fragments to achieve an efficient, automated and unsupervised sorting of diffraction data. The studies described here form a basis for the development of real-time frame rejection methods, e. g. for the European XFEL, which is expected to produce 100 million pulses per hour. (C)2014 Optical Society of Americ

Multiple Ionization of Heavy Atoms by Intense X-Ray Free-Electron Laser Pulses

The photoionization of heavy atoms, krypton and xenon, by ultra-intense X-ray laser pulses was studied at the novel X-ray free-electron laser (FEL), the Linac Coherent Light Source (LCLS). Using an ion time-of-flight (TOF) spectrometer, the ion charge-state distributions were retrieved at 1.5 and 2 keV photon energies as a function of the FEL pulse energy, while large X-ray pnCCD detectors simultaneously recorded the fluorescence spectra. The experimental findings are compared to calculations by S.-K. Son and R. Santra, that are based on perturbation theory and numerically solve a large number of coupled rate equations, and to photoionization processes in light atoms observed in previous measurements at LCLS. For xenon unprecedentedly high charge states, up to Xe36+, are found at 1.5 keV photon energy, 80 fs pulse length and 2.5 mJ pulse energy, although the ground-state ionization energy exceeds the photon energy starting at Xe26+ already. As direct multi-photon ionization was demonstrated to play a minor role at X-ray energies, a different ionization pathway has to be considered here. Measured fluorescence spectra along with the theoretical analysisindicate that ionization beyond the Xe26+ threshold is enabled by densely spaced excitation resonances which can be hit within a single broadband FEL pulse for several subsequent high charge states generated during the ionization process. In contrast to the 1.5 keV case, photoionization at 2 keV photon energy only proceeds up to Xe32+, because at higher photon energy accessible resonances appear at higher charge states, which are not reached within a single shot for the pulse energies used in the present experiment. In order to demonstrate the general nature of the multiple ionization mechanism involving resonances, similar measurements were performed for krypton at 2 keV. Here, combined experimental and theoretical analysis shows that, similar to the case of xenon at 1.5 keV, the highest observed charge state, Kr21+, can only be explained by the resonance-enhanced X-ray multi-ionization process. Based on the experimental data for two exemplary elements and the general model suggested to explain the results, resonance-enhanced photoionization in intense X-ray pulses is predicted to be a general phenomenon for heavy atoms. Thus, systems containing heavy atoms with large nuclear charge Z will experience dramatically increased photoionization in certain photon energy ranges, which can either be desirable, e.g. for the efficient creation of dense plasmas of high-Z atoms, or disturbing, e.g. for coherent diffractive imaging, where local radiation damage in the vicinity of heavy atoms can be significantly enhanced

Ion induced fragmentation cross-sections of DNA constituents

Proton collision with chemical analogs for the base, the sugar and the phosphor residue of the DNA, namely pyrimidine, tetrahydrofuran and trimethyl phosphate, respectively, has been investigated. The impact energies ranged from 300 keV up to 16 MeV. For the first time, relative fragmentation cross-sections for proton impact are reported for tetrahydrofuran and trimethyl phosphate; previously reported cross sections for pyrimidine are extended for energies beyond 2500 keV. Ionization of tetrahydrofuran leads to a ring break in about 80% of all events, trimethyl phosphate predominantly fragments by bond cleavage to one of the three methyl-groups and for pyrimidine the parent ion has the highest abundance. Such comparison supports earlier findings that the sugar is the weak spot for strand breaks

Doubly and Triply Charged Species Formed from Chlorobenzene Reveal Unusual C–Cl Multiple Bonding

In free-radical halogenation of aromatics, singly charged ions are usually formed as intermediates. These stable species can be easily observed by time-of-flight mass spectrometry (TOF-MS). Here we used electron and proton beams to ionize chlorobenzene (C6H5Cl) and investigate the ions stability by TOF-MS. Additionally to the singly charged parent ion and its fragments, we find a significant yield of doubly and triply charged parent ions not previously reported. In order to characterize these species, we used high-level theoretical methods based on density functional theory (DFT), coupled-cluster (CC), and generalized valence bond (GVB) to calculate the structure, relative stabilities, and bonding of these dications and trications. The most stable isomers exhibit unusual carbon-chlorine multiple bonding: a terminal C═Cl double bond in a formyl-like CHCl moiety (1, rC–Cl = 1.621 Å) and a ketene-like C═C═Cl cumulated species (2, rC–Cl = 1.542 Å). The calculations suggest that an excited state of 2 has a nitrile-like C≡Cl triple bond structure

Radio-enhancement by gold nanoparticles and their impact on water radiolysis for x-ray, proton and carbon-ion beams.

Gold nanoparticle (GNP) radio-enhancement is a promising technique to increase the dose deposition in a tumor while sparing neighboring healthy tissue. Previous experimental studies showed effects on cell survival and tumor control for keV x-rays but surprisingly also for MV-photons, proton and carbon-ion beams. In a systematic study, we use the Monte Carlo simulation tool TOPAS-nBio to model the GNP radio-enhancement within a cell as a function of GNP concentration, size and clustering for a wide range of energies for photons, protons and, for the first time, carbon-ions. Moreover, we include water radiolysis, which has been recognized as a major pathway of GNP mediated radio-enhancement. At a GNP concentration of 0.5% and a GNP diameter of 10 nm, the dose enhancement ratio was highest for 50 keV x-rays (1.36) and decreased in the orthovoltage (1.04 at 250 keV) and megavoltage range (1.01 at 1 MeV). The dose enhancement linearly increased with GNP concentration and decreased with GNP size and degree of clustering for all radiation modalities. While the highest physical dose enhancement at 5% concentrations was only 1.003 for 10 MeV protons and 1.004 for 100 MeV carbon-ions, we find the number of hydroxyl ([Formula: see text]) altered by 23% and 3% after 1 [Formula: see text]s at low, clinically-relevant concentrations. For the same concentration and proton-impact, the G-value is most sensitive to the nanoparticle size with 46 times more radical interactions at GNPs for 2 nm than for 50 nm GNP diameter within 1 [Formula: see text]s. Nanoparticle clustering was found to decrease the number of interactions at GNPs, e.g. for a cluster of 25 GNPs by a factor of 3.4. The changes in G-value correlate to the average distance between the chemical species and the GNPs. While the radiochemistry of GNP-loaded water has yet to be fully understood, this work offers a first relative quantification of radiolysis products for a broad parameter-set

Doubly and Triply Charged Species Formed from Chlorobenzene Reveal Unusual C–Cl Multiple Bonding

In free-radical halogenation of aromatics, singly charged ions are usually formed as intermediates. These stable species can be easily observed by time-of-flight mass spectrometry (TOF-MS). Here we used electron and proton beams to ionize chlorobenzene (C₆H₅Cl) and investigate the ions stability by TOF-MS. Additionally to the singly charged parent ion and its fragments, we find a significant yield of doubly and triply charged parent ions not previously reported. In order to characterize these species, we used high-level theoretical methods based on density functional theory (DFT), coupled-cluster (CC), and generalized valence bond (GVB) to calculate the structure, relative stabilities, and bonding of these dications and trications. The most stable isomers exhibit unusual carbon-chlorine multiple bonding: a terminal CCl double bond in a formyl-like CHCl moiety (<b>1</b>, <i>r</i>_C–Cl = 1.621 Å) and a ketene-like CCCl cumulated species (<b>2</b>, <i>r</i>_C–Cl = 1.542 Å). The calculations suggest that an excited state of <b>2</b> has a nitrile-like CCl triple bond structure

Unexpected reversal of stability in strained systems containing one-electron bonds

Ring strain energy is a very well documented feature of neutral cycloalkanes, and influences their structural, thermochemical and reactivity properties. In this work, we apply density functional theory and high-level coupled cluster calculations to describe the geometry and relative stability of C6H12+˙ radical cations, whose cyclic isomers are prototypes of singly-charged cycloalkanes. Molecular ions with the mentioned stoichiometry were produced via electron impact experiments using a gaseous cyclohexane sample (20–2000 eV). From our calculations, in addition to structures that resemble linear and branched alkenes as well as distinct conformers of cyclohexane, we have found low-lying species containing three-, four- and five-membered rings with the presence of an elongated C–C bond. Remarkably, the stability trend of these ring-bearing radical cations is anomalous, and the three-membered species are up to 11.3 kcal mol−1 more stable than the six-membered chair structure. Generalized Valence Bond calculations and the Spin Coupled theory with N electrons and M orbitals were used in conjunction with the Generalized Product Function Energy Partitioning (GPF-EP) method and Interference Energy Analysis (IEA) to describe the chemical bonding in such moieties. Our results confirm that these elongated C–C motifs are one-electron sigma bonds. Our calculations also reveal the effects that drive thermochemical preference of strained systems over their strained-free isomers, and the origin of the unusual stability trend observed for cycloalkane radical cations