X-ray dynamical diffraction in amino acid crystals: a step towards improving structural resolution of biological moleculesviaphysical phase measurements

Abstract

1 This article will form part of a virtual special issue of the journal, presenting some highlights of the 13th Biennial Conference on HighResolution X-ray Diffraction and Imaging (XTOP2016).Keywords: invariant triplet phases; multiple diffraction; D-alanine crystals; zwitterions; synchrotron X-ray diffraction.X-ray dynamical diffraction in amino acid crystals: a step towards improving structural resolution of biological molecules via physical phase measurements In this work, experimental and data analysis procedures were developed and applied for studying amino acid crystals by means of X-ray phase measurements. The results clearly demonstrated the sensitivity of invariant triplet phases to electronic charge distribution in d-alanine crystals, providing useful information for molecular dynamics studies of intermolecular forces. The feasibility of using phase measurements to investigate radiation damage mechanisms is also discussed on experimental and theoretical grounds.

Phonon scattering mechanism in thermoelectric materials revised via resonant x-ray dynamical diffraction

“…The information extracted from the phases of the structure factors is then used to validate or select feasible model structures for the crystal. [37][38][39] The minimum crystal size for this type of experiment is, in general, ten times larger than the usual grain size found in powder samples. [40] Structure factor phases are susceptible to the differences between the vibration amplitudes of the atoms-root mean square (RMS) atomic displacements.…”

“…Reflections with phase susceptible to changes in ionic charges, resonance amplitudes, atomic positions, and occupation and DW factors have been identified by means of model structures. [37][38][39][40] For the CeFe 4 P 12 structure, the atomic planes of Ce and Fe are interleaved along [001] type directions, Fig. 1(c).…”

“…In previous applications of phase measurements, only one X-ray energy was used in each case since simple evaluation of just a few peak asymmetries allowed the validation of the proposed structural models, [37][38][39][40] as in the case of detecting hydrogen bonds between amino acid molecules. [39] By properly choosing the reference reflection with graphical help of the two-dimensional (2D) representation of Bragg cones (Supplementary Material), [54] one azimuthal scan at no particular X-ray energy had enough information to evidence the electron charges at the hydrogen bonds. Detecting hydrogen bonds in a single crystal of alanine was a proof of principle, opening new opportunities in terms of fast methods to measure electron charges at hydrogen bonds in biological molecules.…”

“…In the complete -scan performed at 8 keV, 68 peaks in the range Φ ∈ [ − 45°,+ 45°] show reliable asymmetries in terms of the non-overlapping of peaks with conflicting asymmetries. [39] Sub- Comparisons of peak asymmetries from synchrotron -scans are shown in Fig. 4(c) and 4(d),…”

Simulation of X-ray diffraction in Mn$_x$Bi$_2$Te$_{3+x}$ epitaxic films

“…In a more general approach, the dynamical diffraction theory can embrace more complex situations where many reflections are fully excited simultaneously, within the so-called multi-wave diffraction configuration. 19,20 However, for investigating Bragg reflections under specular diffraction geometry in layered materials, the theory can be significantly simplified in terms of the recursive series 2 where the reflected and transmitted amplitudes of the X-ray waves by atomic monolayers (MLs) are given in terms of the reflection and transmission coefficients,…”