Abstract:Abstract. -Radiation damage is an unavoidable process when performing structural investigations of biological macromolecules with X-rays. In crystallography this process can be limited through damage distribution in a crystal, while for single molecular imaging it can be outrun by employing short intense pulses. Secondary electron generation is crucial during damage formation and we present a study of urea, as model for biomaterial. From first principles we calculate the band structure and energy loss function… Show more
“…It is seen that the photoelectrons create more collisional electrons than do the lower-energy Auger electrons. Figure 2.The cascade of electrons generated by a single electron of energy 500, 1.5, 5 and 8 keV in a urea crystal (CON 2 H 4 ) as calculated by molecular dynamics code [40,41]. The number of secondary electrons generated is plotted as a function of time after the photon absorption event.…”
X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
“…It is seen that the photoelectrons create more collisional electrons than do the lower-energy Auger electrons. Figure 2.The cascade of electrons generated by a single electron of energy 500, 1.5, 5 and 8 keV in a urea crystal (CON 2 H 4 ) as calculated by molecular dynamics code [40,41]. The number of secondary electrons generated is plotted as a function of time after the photon absorption event.…”
X-ray free-electron lasers have opened up the possibility of structure determination of protein crystals at room temperature, free of radiation damage. The femtosecond-duration pulses of these sources enable diffraction signals to be collected from samples at doses of 1000 MGy or higher. The sample is vaporized by the intense pulse, but not before the scattering that gives rise to the diffraction pattern takes place. Consequently, only a single flash diffraction pattern can be recorded from a crystal, giving rise to the method of serial crystallography where tens of thousands of patterns are collected from individual crystals that flow across the beam and the patterns are indexed and aggregated into a set of structure factors. The high-dose tolerance and the many-crystal averaging approach allow data to be collected from much smaller crystals than have been examined at synchrotron radiation facilities, even from radiation-sensitive samples. Here, we review the interaction of intense femtosecond X-ray pulses with materials and discuss the implications for structure determination. We identify various dose regimes and conclude that the strongest achievable signals for a given sample are attained at the highest possible dose rates, from highest possible pulse intensities.
“…This fluctuation should not be neglected because it indeed contributes to the Bragg peaks to be measured. In our calculations, we do not include resonant absorption [7], shakeup and shakeoff processes [30], and impact ionization [31,32], which would generate further high charge states. Thus, the dynamical fluctuation effect would be enhanced after these processes are taken into account.…”
Section: Analysis Of the Scattering Intensitymentioning
Abstract. The high-intensity version of multiwavelength anomalous diffraction (MAD) has a potential for solving the phase problem in femtosecond crystallography with x-ray free-electron lasers (XFELs). For MAD phasing, it is required to calculate or measure the MAD coefficients involved in the key equation, which depend on XFEL pulse parameters. In the present work, we revisit the generalized KarleHendrickson equation to clarify the importance of configurational fluctuations of heavy atoms induced by intense x-ray pulses, and investigate the high-intensity cases of transmission and fluorescence measurements of samples containing heavy atoms. Based on transmission/fluorescence and diffraction experiments with crystalline samples of known structures, we propose an experimental procedure to determine all MAD coefficients at high x-ray intensity, which can be used in ab initio phasing for unknown structures.
“…The band gap of UDNB and DNB were found to be 3.27 and 2.89 eV, respectively. The earlier reported band gaps for urea and DNB are 4.74 and 2.90 eV [17,18]. The refractive index of UDNB crystal was calculated using the relation…”
Section: Energy Band Gap and Refractive Indexmentioning
confidence: 99%
“…The calculated refractive index of UDNB and DNB crystals are 2.32 and 2.43, respectively. To ensure the validity, the refractive index of urea and DNB are also calculated by the same method using the reported band gaps [17,18], and their respective values are 2.04 and 2.42, respectively.…”
Section: Energy Band Gap and Refractive Indexmentioning
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