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Preview: Acta Crystallographica Section A

Acta Crystallographica Section A

Acta Crystallographica Section A: Foundations and Advances covers theoretical and fundamental aspects of the structure of matter. The journal is the prime forum for research in diffraction physics and the theory of crystallographic structure determination

Published: 2015-07-01


MicroED data collection and processing


MicroED, a method at the intersection of X-ray crystallography and electron cryo-microscopy, has rapidly progressed by exploiting advances in both fields and has already been successfully employed to determine the atomic structures of several proteins from sub-micron-sized, three-dimensional crystals. A major limiting factor in X-ray crystallography is the requirement for large and well ordered crystals. By permitting electron diffraction patterns to be collected from much smaller crystals, or even single well ordered domains of large crystals composed of several small mosaic blocks, MicroED has the potential to overcome the limiting size requirement and enable structural studies on difficult-to-crystallize samples. This communication details the steps for sample preparation, data collection and reduction necessary to obtain refined, high-resolution, three-dimensional models by MicroED, and presents some of its unique challenges.

Identification of inversion domains in KTiOPO4via resonant X-ray diffraction


A novel method is presented for the identification of the absolute crystallographic structure in multi-domain polar materials such as ferroelectric KTiOPO4. Resonant (or `anomalous') X-ray diffraction spectra collected across the absorption K edge of Ti (4.966 keV) on a single Bragg reflection demonstrate a huge intensity ratio above and below the edge, providing a polar domain contrast of ∼270. This allows one to map the spatial domain distribution in a periodically inverted sample, with a resolution of ∼1 µm achieved with a microfocused beam. This non-contact, non-destructive technique is well suited for samples of large dimensions (in contrast with traditional resonant X-ray methods based on diffraction from Friedel pairs), and its potential is particularly relevant in the context of physical phenomena connected with an absence of inversion symmetry, which require characterization of the underlying absolute atomic structure (such as in the case of magnetoelectric coupling and multiferroics).

Theoretical study of the properties of X-ray diffraction moiré fringes. I


A detailed and comprehensive theoretical description of X-ray diffraction moiré fringes for a bicrystal specimen is given on the basis of a calculation by plane-wave dynamical diffraction theory. Firstly, prior to discussing the main subject of the paper, a previous article [Yoshimura (1997). Acta Cryst. A53, 810–812] on the two-dimensionality of diffraction moiré patterns is restated on a thorough calculation of the moiré interference phase. Then, the properties of moiré fringes derived from the above theory are explained for the case of a plane-wave diffraction image, where the significant effect of Pendellösung intensity oscillation on the moiré pattern when the crystal is strained is described in detail with theoretically simulated moiré images. Although such plane-wave moiré images are not widely observed in a nearly pure form, knowledge of their properties is essential for the understanding of diffraction moiré fringes in general.

Diaphony, a measure of uniform distribution, and the Patterson function


This paper reviews the number-theoretic concept of diaphony, a measure of uniform distribution for number sequences and point sets based on a Fourier theory approach, and its relation to crystallographic concepts like the largest interplanar spacing of a lattice, the structure-factor equation and the Patterson function.

Algorithm for systematic peak extraction from atomic pair distribution functions


The study presents an algorithm, ParSCAPE, for model-independent extraction of peak positions and intensities from atomic pair distribution functions (PDFs). It provides a statistically motivated method for determining parsimony of extracted peak models using the information-theoretic Akaike information criterion (AIC) applied to plausible models generated within an iterative framework of clustering and chi-square fitting. All parameters the algorithm uses are in principle known or estimable from experiment, though careful judgment must be applied when estimating the PDF baseline of nanostructured materials. ParSCAPE has been implemented in the Python program SrMise. Algorithm performance is examined on synchrotron X-ray PDFs of 16 bulk crystals and two nanoparticles using AIC-based multimodeling techniques, and particularly the impact of experimental uncertainties on extracted models. It is quite resistant to misidentification of spurious peaks coming from noise and termination effects, even in the absence of a constraining structural model. Structure solution from automatically extracted peaks using the Liga algorithm is demonstrated for 14 crystals and for C60. Special attention is given to the information content of the PDF, theory and practice of the AIC, as well as the algorithm's limitations.

Approximation of virus structure by icosahedral tilings


Viruses are remarkable examples of order at the nanoscale, exhibiting protein containers that in the vast majority of cases are organized with icosahedral symmetry. Janner used lattice theory to provide blueprints for the organization of material in viruses. An alternative approach is provided here in terms of icosahedral tilings, motivated by the fact that icosahedral symmetry is non-crystallographic in three dimensions. In particular, a numerical procedure is developed to approximate the capsid of icosahedral viruses by icosahedral tiles via projection of high-dimensional tiles based on the cut-and-project scheme for the construction of three-dimensional quasicrystals. The goodness of fit of our approximation is assessed using techniques related to the theory of polygonal approximation of curves. The approach is applied to a number of viral capsids and it is shown that detailed features of the capsid surface can indeed be satisfactorily described by icosahedral tilings. This work complements previous studies in which the geometry of the capsid is described by point sets generated as orbits of extensions of the icosahedral group, as such point sets are by construction related to the vertex sets of icosahedral tilings. The approximations of virus geometry derived here can serve as coarse-grained models of viral capsids as a basis for the study of virus assembly and structural transitions of viral capsids, and also provide a new perspective on the design of protein containers for nanotechnology applications.

Pairwise correlations in layered close-packed structures


Given a description of the stacking statistics of layered close-packed structures in the form of a hidden Markov model, analytical expressions are developed for the pairwise correlation functions between the layers. These may be calculated analytically as explicit functions of model parameters or the expressions may be used as a fast, accurate and efficient way to obtain numerical values. Several examples are presented, finding agreement with previous work as well as deriving new relations.

Topological crystallography of gas hydrates


A new approach to the investigation of the proton-disordered structure of clathrate hydrates is presented. This approach is based on topological crystallography. The quotient graphs were built for the unit cells of the cubic structure I and the hexagonal structure H. This is a very convenient way to represent the topology of a hydrogen-bonding network under periodic boundary conditions. The exact proton configuration statistics for the unit cells of structure I and structure H were obtained using the quotient graphs. In addition, the statistical analysis of the proton transfer along hydrogen-bonded chains was carried out.

Iterative projection algorithms in protein crystallography. II. Application


Iterative projection algorithms (IPAs) are a promising tool for protein crystallographic phase determination. Although related to traditional density-modification algorithms, IPAs have better convergence properties, and, as a result, can effectively overcome the phase problem given modest levels of structural redundancy. This is illustrated by applying IPAs to determine the electron densities of two protein crystals with fourfold non-crystallographic symmetry, starting with only the experimental diffraction amplitudes, a low-resolution molecular envelope and the position of the non-crystallographic axes. The algorithm returns electron densities that are sufficiently accurate for model building, allowing automated recovery of the known structures. This study indicates that IPAs should find routine application in protein crystallography, being capable of reconstructing electron densities starting with very little initial phase information.

Temperature- and energy-dependent phase shifts of resonant multiple-beam X-ray diffraction in germanium crystals


This paper reports temperature- and energy-dependent phase shifts of resonant multiple-beam X-ray diffraction in germanium crystals, involving forbidden (002) and weak (222) reflections. Phase determination based on multiple-beam diffraction is employed to estimate phase shifts from (002)-based \{(002)(375)(37\overline{3})\} four-beam cases and (222)-based \{ (222)(\overline{5}3\overline{3})\} three-beam cases in the vicinity of the Ge K edge for temperatures from 20 K up to 300 K. The forbidden/weak reflections enhance the sensitivity of measuring phases at resonance. At room temperature, the resonance triplet phases reach a maximum of 8° for the four-beam cases and −19° for the three-beam cases. It is found that the peak intensities and triplet phases obtained from the (002) four-beam diffraction are related to thermal motion induced anisotropy and anomalous dispersion, while the (222) three-beam diffraction depends on the aspherical covalent electron distribution and anomalous dispersion. However, the electron–phonon interaction usually affects the forbidden reflections with increasing temperatures and seems to have less effect on the resonance triplet phase shifts measured from the (002) four-beam diffraction. The resonance triplet phase shifts of the (222) three-beam diffraction versus temperature are also small.

The atomic anisotropic displacement tensor – completing the picture


A simplified approach for calculating the equivalent isotropic displacement parameter is presented and the transformation property of the tensor representation U to point-group operations is analysed. Complete tables have been compiled for the restrictions imposed upon the tensor owing to the site symmetry associated with all special positions as listed in Hahn [(2011), International Tables for Crystallography, Vol. A, Space-group Symmetry, 5th revised ed. Chichester: John Wiley and Sons, Ltd].