Role of the dispersion correction in analysis of X-ray diffraction data

Dysprosium (Dy) modified BiFeO3 [Bi1−xDyxFeO3 (x = 0.05, 0.10, and 0.15)] nanoparticles have been synthesized by a low temperature co-precipitation method. Rietveld analysis of X-ray diffraction data reveals a transformation from rhombohedral structure to orthorhombic structure with increase in the Dy concentration. From the transmission electron microscopy analysis, it is observed that the particle sizes of Bi1−xDyxFeO3 (x = 0.05, 0.10, and 0.15) nanoparticles range between 50–70, 40–50, and 30–50 nm, respectively. Raman spectra of Bi1−xDyxFeO3 (x = 0.05) belonging to rhombohedral (R3c) structure show 4A1 and 7E fundamental Raman modes in the range of 100–650 cm−1 and two-phonon scattering modes such as 2A4 (longitudinal optical), 2E8 (transverse optical (TO)), and 2E9 (TO) in the range of 950–1270 cm−1. Suppression, broadening, and shifting of Raman modes have been observed with further increase in Dy concentration. The fundamental Raman modes of Bi1−xDyxFeO3 (x = 0.15) are assigned under orthorhombic (pnma) rather than rhombohedral (R3c) as the Rietveld analysis of X-ray diffraction data predicts a structural transformation for this particular composition. A complete suppression of two phonon modes has been noticed for this composition. An anomaly in the temperature dependent dielectric studies has been observed in all the samples at the vicinity of Neel temperature indicating a magnetic ordering, and an increase in magnetization with increase of Dy concentration in BiFeO3 is noticed from the room temperature magnetic studies. P–E hysteresis loop studies show a decrease of remnant polarization (Pr) with the increase in Dy concentration and disappearance of hysteresis loop occurs for Bi1−xDyxFeO3 (x = 0.15) depicting a transformation from non-centrosymmetric (R3c) to centrosymmetric (Pnma) system.

X-Ray Diffraction and Protein Structure

Structural studies of hydrated germanium X-type zeolite via Rietveld analysis of synchrotron powder X-ray diffraction data

Rietveld refinements and spectroscopic structural studies of a Na-free carbonate apatite made by hydrolysis of monetite

Detailed analysis of X-ray diffraction data from four single crystals of eniluracil, prepared under different crystallization conditions, confirms a picture in which the crystals exhibit different degrees of disorder, which is also suggested by the computed low energy crystal structures. Since several of these crystal structures that effectively differ by an interchange of the oxygen and hydrogen atoms on C(4) and C(6) are essentially equi-energetic, growth errors that may be difficult to reverse are practically inevitable. The structural variations observed for the crystals of eniluracil studied are more appropriately described in terms of variable degrees of disorder rather than polymorphism. Analysis of the computed crystal energy landscape for interchangeable hydrogen-bonded (or other strong) motifs is, therefore, shown to be a valuable complement to X-ray diffraction and solid-state NMR for understanding and characterizing disorder in organic solid state systems. In the case of eniluracil, this detailed picture probably accounts for the challenges in devising a robust production process for this anticancer agent in the 1990s. The specific nature of the disorder accounts for different structures being obtained from powder X-ray diffraction data of different samples, and the possibility of publishable single crystal X-ray refinements also being interpreted as polymorphism rather than disorder.

Motivated by the problem of detecting changes in two-dimensional X-ray diffraction data, we propose a Bayesian spatial model for sparse signal detection in image data. Our model places considerable mass near zero and has heavy tails to reflect the prior belief that the image signal is zero for most pixels and large for an important subset. We show that the spatial prior places mass on nearby locations simultaneously being zero, and also allows for nearby locations to simultaneously be large signals. The form of the prior also facilitates efficient computing for large images. We conduct a simulation study to evaluate the properties of the proposed prior and show that it outperforms other spatial models. We apply our method in the analysis of X-ray diffraction data from a two-dimensional area detector to detect changes in the pattern when the material is exposed to an electric field.

Analysis of X-ray diffraction data on crystals of boron carbide and its derivatives reveals an increase of 1.5–3 times in the thermal vibration amplitude (Ueq) of the central atom in the XYZ group, compared to other atoms in the structure. Reasons for this phenomenon are analyzed to answer the question of whether this group is the weakest link in the structure. The effect is studied by comparing the results from nonempirical quantum-chemical calculations for the model compounds to X-ray diffraction data. The increase in Ueq is shown to be a characteristic feature of the structure of the XYZ group. The results of this work are confirmed by the data on an arbitrary site of C atom insertion into the boron carbide structure.

The refinement of electron-density distributions for non-centrosymmetric crystals from X-ray diffraction data may lead to a very good fit between model and data but to totally meaningless electron densities. This is to a large extent because varying certain parameters, or combination of parameters, in the model mainly leads to a change in the phases of the structure factors. A formal analysis of why this happens, when using multipole models, is given as well as specific examples using real data: the contributions of odd-order multipoles, which are invariant under crystal-class symmetry operations, are poorly determined. The importance of applying constraints on the models is stressed. The conclusions of this analysis can be carried over to refinements of anharmonic atomic vibrations.

Model X-ray data sets, with and without the inclusion of experimental thermal motion parameters, have been computed via Fourier transformation of ab initio molecular electron densities for 12 different molecular crystals. These datasets were then analysed with three different multipole models of varying sophistication and, from the multipole functions, molecular dipole and second moments, as well as electric field gradients (EFG's), at each nuclear site were computed and compared with results obtained from the original ab initio wavefunctions. The results provide valuable insight into the reliability of these properties, extracted in the same way from experimental X-ray data. Not all molecular systems display identical trends, but a general pattern is discernible. Specifically, dipole moments are typically underestimated by a small but significant amount (~ 10–15%), the trace of the second moment tensor is well determined but overestimated by a few per cent and electric field gradients at protons are confirmed to be well within reach of a careful charge density analysis of X-ray diffraction data.

In this paper, we propose a facile and efficient strategy for synthesizing mesoporous BaSnO3 with a surface area as large as 67 m(2)/g using a peroxo-precursor decomposition procedure. As far as we know, this is the largest surface area reported in literature for BaSnO3 materials and may have a potential to greatly promote the technological applications of this kind of functional material in the area of chemical sensors, NOx storage, and dye-sensitized solar cells. The structure evolution of the mesoporous BaSnO3 from the precursor was followed using a series of techniques. Infrared analysis indicates large amount of protons and peroxo ligands are contained in the peroxo-precursor. Although the crystal structure of the precursor appears cubic according to the analysis of X-ray diffraction data, Raman and Mössbauer spectroscopy results show that the Sn atom is offset from the center of [SnO6] octahedron. After calcination at different temperatures, the precursor gradually transforms into BaSnO3 by release of water and oxygen, and the distortion degree of [SnO6] octahedral decreases. However, a number of oxygen vacancies are generated in the calcined samples, which are further confirmed by the physical property measurement system, and they would lower the local symmetry to some content. The concentration of the oxygen vacancies reduces simultaneously as the calcination temperature increases, and their contributions to the total heat capacity of the sample are calculated based on theoretical analysis of heat capacity data in the temperature region below 10 K.

Crystallographic fragment screening is a technique for initiating drug discovery in which protein crystals are soaked or grown with high concentrations of small molecule compounds (typically MW 110-250 Da) chosen to represent fragments of potential drugs. Specific binding of these compounds to the protein is subsequently visualized in electron density maps obtained from analysis of X-ray diffraction data collected from these crystals. Theoretical and practical experience indicate that a suitably diverse library of fragment compounds containing only a few hundred compounds may be sufficient to provide a comprehensive screen of the protein target. By soaking crystals in mixtures of 3-10 compounds a fragment screen may be completed within ∼100 diffraction data sets. This data collection requirement may be met given reproducible well-diffracting protein crystals and robotic sample handling equipment at a high flux X-ray source. The leading practical issue for most crystallography laboratories that wish to launch a fragment screening project is the design and/or procurement of an appropriate fragment library. Although several off-the-shelf fragment libraries are available from chemical suppliers, the numbers, sizes, and solubility of the compounds in relatively few of these libraries are well-match to the specific needs of the crystallographic screening experiment. Informed consideration of the properties of compounds in the screening library, possibly augmented by additional filtering of available compounds with appropriate search tools, is required to design a successful experiment. The analysis of results from crystallographic fragment screening involves highly repetitive application of routine image data processing and structure refinement calculations from many very similar crystals. Efficient handling of the data applies a high-throughput structure determination methodology that conveniently packages the structure solution calculations into a single process that provides the crystallographer-analyst with ready-to-view maps for evaluating crystals for bound compounds.

The in-crystal molecular dipole moment of the nonlinear optical material 2-methyl-4-nitroaniline has been determined from a charge density analysis of x-ray diffraction data. The results indicate a considerable enhancement of the free molecule dipole moment, due to the crystal field. The analysis suggests that aspherical pseudoatoms are essential for modeling the charge distribution in a noncentrosymmetric crystal. Careful consideration must also be given to the treatment of hydrogen atoms, in the absence of complementary neutron diffraction data. An analysis of the deformation density and Laplacian of the charge density proves useful for revealing weak hydrogen bonding effects. Ab initio calculations at the Hartree–Fock double-ζ level are reported for the molecule 2-methyl-4-nitro-aniline, with and without an applied electric field. In the former case, the magnitude and direction of the applied field were determined by a dipole lattice sum, to assess the magnitude of crystal field effects. The effect was to considerably enhance the molecular dipole moment, from 9 to 20 D, in agreement with the experimentally observed enhancement. Structure factors were generated from the ab initio wave functions and subjected to multipole refinement, to effectively project the theoretical ρ(r) into the same atom-centered multipole expansion form obtained from experiment. Monopole and dipole populations obtained in this way show convincing agreement with experiment.

The reaction between a 0.5 to 1.0 micron Al film and a thick Ti substrate to form TiAl3 occurs very rapidly on heating to 635 °C and causes the Al to be confined to the surface region. After heating to 900 °C, Ti3Al is formed with little release of Al into α-Ti. Further annealing at 900 °C eventually causes the Ti3Al phase to decompose and a substantial amount of Al is released into α-Ti. The interdiffusion coefficient for Al in α-Ti at 900 °C was found to increase by less than one order of magnitude as Al is varied from 0 to 20 at. pct. These data were obtained from the (101) X-ray diffraction intensity band using polycrystalline samples. Improvements in the analysis of X-ray diffraction data for the determination of composition profiles are discussed.

X-ray diffraction and high-precision scanning electron microscopy methods were used to study the long-term evolution of the defect structure of diffusion filter-membranes Pd-Y. Analysis of X-ray diffraction data and microelectronic photographs showed that the recovery of the dislocation structure in the membranes was not uniform. Differences in the processes of hydrogen conservation in the structure of membranes are determined reversible hydrogen doping. Preservation by alloy of superstructural ordered regions was detected.

Interplay between electronic and structural properties of the misfit layered chalcogenide (LaS)1.196VS2 crystals was investigated by transport, optical measurements, angle-resolved photoemission (ARPES), Raman spectroscopy, and X-ray diffraction. Although no clear anomaly is found in temperature-dependent transport measurements, a large spectral weight transfer, around 1 eV, is observed by both optical and photoemission spectroscopies. ARPES reveals a nearly filled band with negative curvature, close enough from the Fermi level at room temperature to produce metallic-like behavior as observed in optical conductivity spectra. At low temperature, the band structure is strongly modified, yielding to an insulating state with an optical gap of 120 meV. Both Raman spectroscopy and accurate (3 + 1)D analysis of X-ray diffraction data show that, although a phase transition does not occur, structural distortions increase as temperature is decreased, and vanadium clusterization is enhanced. We found that the change...