bluuebunny/crossref_metadata_2025 huggingface dataset:
Evolution of Epilayer Tilt in InGaAs Metamorphic Buffer Layers Grown by HVPE
Authors: Schulte Kevin , Kuech Thomas
Published: November 2015

Tilt behavior in InxGa1-xAs metamorphic buffer layers (MBLs) grown by hydride vapor phase epitaxy (HVPE) was measured by high resolution x-ray diffraction (HRXRD). Step- and continuously-graded structures were grown on exactly (001) oriented GaAs substrates as well as on substrates with a miscut of 40→ (111)B of (001). Growth temperature and final In composition were varied as well. HRXRD Ω-F mapping was employed to independently resolve both the magnitude and direction of tilt as a function of depth throughout each structure. Tilt azimuth was initially random in growths on nominally (001) oriented substrates and changed as grading continued, moving closer to [110]. Tilt magnitude increased more linearly and to larger values as a function of xInAs in the step-graded vs. continuously graded samples. MBLs grown on 40miscut substrates tilted in the opposite direction of the miscut surface normal, and the tilt magnitude for a given xInAs was greater than for planar samples. When the tilt vectors of the miscut samples were resolved along the orthogonal [-110] and [110] directions it was found that the tilt was much stronger along the direction that the miscut was aligned, or [-110]. Tilt in the planar samples increased monotonically and to larger magnitudes along [110] compared with [-110]. The behavior on miscut samples can be attributed to the preferential generation of dislocations on slip systems which experience a larger resolved shear stress due to the miscut [1]. The tilt anisotropy in planar samples can be attributed to the fact that dislocation cores and core energies in III-V semiconductors are also anisotropic [2]. Dislocation nucleation along [110] has a higher activation energy, so a larger proportion of dislocations is likely generated by multiplication sources, creating arrays of dislocations possessing the same burgers vector. Dislocation distributions in samples grown at high temperature were found to be more uniform, overcoming these barriers.
Transformation from pyrochlore to fluorite by diffraction and X-ray spectroscopy
Authors: Kennedy Brendan , Blanchard Peter , Reynolds Emily , Zhang Zhaoming
Published: November 2015

We have studied the long-range average and local structures in a number of zirconium containing materials of the type A2B2O7 ( A = Ln or Y; B = Zr, Hf or Sn) using synchrotron X-ray and neutron powder diffraction and X-ray absorption spectroscopy. Studies of the system Gd2-xTbxZr2O7 include neutron diffraction data, obtained at λ ≍ 0.497 Å to minimise absorption, not only provide evidence for independent ordering of the anion and cation sublattices, but also suggest that the disorder transition across the pyrochlore-defect fluorite boundary of Ln2Zr2O7 is rather gradual. In general we observe that while the diffraction data indicate a clear phase transition from ordered pyrochlore to disordered defect-fluorite at specific compositions corresponding to a critical ionic radius ratio of the A and B cations (rA/rB) x ~ 1.0-1.2, X-ray absorption near-edge structure (XANES) results reveal a gradual structural evolution across the compositional range. These findings provide experimental evidence that the local disorder occurs long before the pyrochlore to defect-fluorite phase boundary as determined by X-ray diffraction, and the extent of disorder continues to develop throughout the defect-fluorite region. Where possible the experimental results were supplemented by ab initio atomic scale simulations, which provide a mechanism for disorder to initiate in the pyrochlore structure. Further, the coordination numbers of the cations in both the defect-fluorite and pyrochlore structures were predicted, and the trends agree well with the experimental XANES results. X-ray absorption measurements at the Zr L3-edge, which showed a gradual increase in the effective coordination number of the Zr from near 6-coordinate in the pyrochlore rich samples to near 7-coordinate in the defect fluorites.
Twisted crystals
Authors: Shtukenberg Alexander , Kahr Bart
Published: November 2015

Modern reviews on crystal growth and defects in crystals overlook the fact that a significant portion of materials can spontaneously grow as single crystals with twisted and bent morphologies and curved crystal lattices. Twisted crystals can be found among all types of materials (molecular crystals, salts, minerals, high polymers, metals, and elements) crystallizing in any point and space group from all types of growth media (vapor, solution, gel, glass, melt, and solid state). Their size spans over more than six orders of magnitude ranging from nm where 3D character is equivocal, to cm or dm (some of the biggest natural crystals). Here are illustrated most important features of twisted crystals as well as an analysis of mechanisms that are responsible for this mysterious phenomenon [1]. In general, formation of a twisted crystal is a complex phenomenon involving with certain requirements for dissymmetry, isomorphism, and crystal chemistry. Also critical are processes at the crystal-medium interface as well as the elasticity and plasticity of the crystalline medium. As such, twisting is strongly controlled by morphology and symmetry of the growth face. It frequently requires impurities, sometimes in extremely low concentrations. The intensity of deformation is inversely proportional to the crystal size. The phenomenon is more common when the driving force for crystallization and the temperature are high. Several mechanisms have been proposed to explain the formation of unusual curved morphologies: axial dislocation in whiskers (Eshelby twist); surface stress in polymer lamellae; surface charge and spontaneous polarization in nanoribbons; inhomogeneous fields forming around a growing crystal; and internal stress created by an inhomogeneous impurity distribution. However, most of the mechanisms proposed are insufficiently developed and need further verification and elaboration. The work was supported by the US National Science Foundation and New York University.
Are Dislocations Possible in Nanoparticles?
Authors: Ferreira Paulo
Published: November 2015

The deformation behavior of nanoscale metals continues to be an exciting area for materials research. However, in the case of single crystal 0-D nanoscale metals, no deformation experiments, to our knowledge, have been performed at the nanoscale. The one experiment closest to the nanoscale was an in-situ TEM compression of ~200 nm Si nanoparticles. However, the particle tested was too large to extract relevant information at the nanoscale and the mechanical deformation of Si is also expected to be different from that of metals. For nanoparticles it is claimed there is a conspicuous lack of dislocations, regardless of the materials processing history, even after significant deformation. Therefore, it has been suggested that dislocations cannot exist or/ do not play a role on the deformation of 0-D nanomaterials. To address this issue of the role played by dislocations in the deformation of 0-D nanomaterials, nanoparticles with diameters <20nm were compressed in-situ under phase-contrast in a transmission electron microscope (TEM). Two phase-contrast TEM experiments were done, one in a conventional TEM and the other in an aberration corrected TEM. Evidence for nucleation of dislocations and dislocation motion was observed during in-situ TEM nanoindentation, but upon unloading dislocations were no longer visible. A new model for explaining dislocation instability is introduced. In this model we consider the change in Gibbs free energy of an edge dislocation, as it moves through the nanoparticle, towards the surface. The nanoindentation experiments seem to confirm the model proposed.
Resonant X-ray scattering in low quartz to characterize the polarization light
Authors: Joly Yves , Tanaka Yoshikazu , Cabaret Delphine , Lovesey Stephen , Collins Steve
Published: November 2015

The variation with energy of the diffracted peak intensities around the absorption edges has been known for very long time. It is only very recently that resonant elastic x-ray scattering (REXS) experiments were performed on enantiomers [1], showing the sensitivity of this technique to study tiny features in these materials. In right and left low quartz, azimuthal scans of the (001) reflection intensity show the angular anisotropy by presenting a 3 fold periodicity. These scans are shifted and their amplitude oscillations vary when changing from right to left the enantiomer or when changing the light helicity. Our purpose is to show that azimuthal scans recording the (001) reflection intensity in right and left low quartz can be completely explained by the proper taking into account of the polarization characteristics of the incoming electromagnetic wave. More importantly, we show that such experiments are an excellent way to fully determine the light properties, when this one is not perfectly known. From these scans, we get 3 equations giving their relative shift, the ratio between their amplitude oscillations and the polarization rate. Consequently, without need of simulations because these equations only depend on the symmetry and the geometry, we are able to get the three unknowns which are the Stokes parameter values. Such characterization does not depend on energy, or absorbing atom atomic number. This is thus feasible at other edges or with other compounds, such as GeO2, having the same symmetry. This opens the possibility of characterizing the light polarization on a wide energy range. This study is supported by ab initio simulations on REXS and linear dichroism to validate our demonstration and to eliminate the other possibilities such as higher contribution in term of transition channels (E1E2 or E2E2) or birefringence effects.
Evaluation of Fluorescence Detectors for XAFS at High Flux Beamlines
Authors: Heald Steve
Published: November 2015

Detector technologies appropriate for fluorescence detection of XAFS are compared. The current workhorse methods of multi-element solid state detectors and filter-slit systems [1] need continued development to take full advantage of the fluxes available at modern synchrotron beamlines. These high fluxes create the potential for pushing XAFS measurements to extreme levels of diluteness (ppb) if the signal can be separated from the background. Both measurements and calculations are used to explore the ultimate limits for these technologies, and to compare them to alternative methods such as diffraction based analyzers. The measurements include the use of polycapillary optics as coupling optics for crystal analyzers and as improved slits in filter based detectors. The confocal nature of the polycapillaries significantly reduces the background for many samples, and they can be used for nearly perfect rejection of the filter refluorescence in filter based systems. The ultimate limit will be determined by processes such as inelastic scattering that produce backgrounds at the same energy as the fluorescence. These can be minimized but not eliminated by using detectors with high energy resolution.
Structural insights into DNA repair by RNase T
Authors: Hsiao Yu-Yuan , Yuan Hanna
Published: November 2015

DNA repair is generally accomplished by a coordinated effort via several types of DNA enzymes, including endonucleases, exonucleases, helicases, polymerases and ligases. Among all these DNA enzymes, the molecular functions of exonucleases, which bind at the 3′ or 5′ end of DNA and cleave one nucleotide at a time, are least understood in how they select DNA substrates for binding and trimming. Here we show that the DEDDh family exonuclease RNase T is critical for Escherichia coli resistance to various DNA damaging agents and UV radiation. RNase T specifically trims the 3′ end of structured DNA, including bulge, bubble and Y-structured DNA, and it can work with Endonuclease V to restore the deaminated base in an inosine-containing heteroduplex DNA. Our crystal structure analyses further reveal how RNase T recognizes the bulge DNA by inserting a phenylalanine into the bulge, and as a result the 3′ end of blunt-end bulge DNA can be digested by RNase T. In contrast, the homodimeric RNase T interacts with the Y-structured DNA by a different binding mode via a single protomer so that the 3′ overhang of the Y-structured DNA can be trimmed closely to the duplex region. Our data suggest that RNase T likely processes bulge and bubble DNA in the Endonuclease V-dependent DNA repair, whereas it processes Y-structured DNA in UV-induced and various other DNA repair pathways. This study thus provides mechanistic insights for RNase T and thousands of DEDDh-family exonucleases in DNA 3′-end processing.
Structure of a canonical RNase YoeB bound to the ribosome
Authors: Chen Yun , Feng Shu , Kamada Katsuhiko , Wang Han , Tang Kai , Wang Meitian , Gao Yonggui
Published: November 2015

As a typical endoribonuclease, YoeB mediates cellular adaptation in diverse bacteria by degrading mRNAs on its activation. Although the catalytic core of YoeB is thought to be identical to well-studied nucleases, this enzyme specifically targets mRNA substrates that are associated with ribosomes in vivo. However, the molecular mechanism of mRNA recognition and cleavage by YoeB, and the requirement of ribosome for its optimal activity, largely remain elusive. Here, we report the structure of YoeB bound to 70S ribosome in pre-cleavage state, revealing that both the 30S and 50S subunits participate in YoeB binding. The mRNA is recognized by the catalytic core of YoeB, of which the general base/acid (Glu46/His83) are within hydrogen-bonding distance to their reaction atoms, demonstrating an active conformation of YoeB on ribosome. Also, the mRNA orientation involves the universally conserved A1493 and G530 of 16S rRNA. In addition, mass spectrometry data indicated that YoeB cleaves mRNA following the second position at the A-site codon, resulting in a final product with a 3'–phosphate at the newly formed 3' end. Our results demonstrate a classical acid-base catalysis for YoeB-mediated RNA hydrolysis and provide insight into how the ribosome is essential for its specific activity.
HcaR Ligand and DNA Interactions in the Regulation of Catabolic Gene Expression
Authors: Joachimiak Andrzej , Joachimiak Grazyna , Bigelow Lance , Cobb Garrett , Kim Youngchang
Published: November 2015

Precise tuning of gene expression by transcriptional regulators determines the response to internal and external chemical signals and adjusts the metabolic machinery for many cellular processes. As a part of ongoing efforts by the Midwest Center for Structural Genomics, a number of transcription factors were selected to study protein-ligand and protein-DNA interactions. HcaR, a new member of the MarR/SlyA family of transcription regulators from soil bacteria Acinetobacter sp. ADP1, is an evolutionarily atypical regulator and represses hydroxycinnamate (hca) catabolic genes. Hydroxycinnamates containing an aromatic ring play diverse, critical roles in plant architecture and defense. HcaR regulates the expression of the hca catabolic operon, allowing this and related bacterial strains to utilize hydroxycinnamates: ferulate, p-coumarate, and caffeate as sole sources of carbon and energy. HcaR appears to be capable of responding to multiple aromatic ligands. These aromatic compounds bind to HcaR and reduce its affinity to the specific DNA sites. As a result, the transcription of genes encoding several catabolic enzymes is up-regulated. The HcaR structures of the apo-form and in a complex with several ligands: ferulic acid, 3,4 dihydroxybenzoic acid, vanillin and p-coumaric acid have been determined to understand how HcaR accommodates various aromatic compounds using the same binding pocket. We also have identified a potential DNA site for HcaR in the regulatory region upstream of the genes of the hca catabolic operon in Acinetobacter sp. ADP1 and have confirmed DNA binding by EMSA. The co-crystal structure of HcaR and palindromic 24-mer DNA has been determined for this DNA site. The crystal structures of HcaR, the apo-form, ligand-bound forms, and the specific DNA-bound form provide critical structural basis of protein-ligand (substrates or product) and protein-DNA interactions to understand the regulation of the expression of hydroxycinnamate (hca) catabolic genes. Our studies allow for better understanding of DNA-binding and regulation by this important group of transcription factors belonging to the MarR/SlyA families. This work was supported by National Institutes of Health grant GM094585 and by the U. S. Department of Energy, Office of Biological and Environmental Research, under contract DE-AC02-06CH11357.
Structural insight into the function of the spliceosomal helicase Aquarius
Authors: De Inessa , Bessonov Sergey , Hoeffele Romina , Santos Karine , Urlaub Henning , Luehrmann Reinhard , Pena Vladimir
Published: November 2015

Beyond participating in splicing, some spliceosomal components from higher eukaryotes play pivotal roles in coupling splicing to other RNA-processing events. The massive spliceosomal helicase Aquarius (170 kDa) is loaded at a specific location on the intron, where it acts as a molecular linker between splicing, the deposition of the exon-junction complex on the mRNA and the formation of snoRNPs from intronic segments. We have determined the crystal structures of the full-length Aquarius in complex with a non-hydrolysable ATP analog as well as with a single-stranded RNA. The structure reveals a complex molecular architecture, with a central core that resembles the RNA helicase Upf1 surrounded by several specific domains. Among them we identify an ARM-repeat domain, plus three other domains that were not observed in helicases. We could evidence that Aquarius possesses motor activity in vitro and that, strikingly, it exhibits opposite unwinding polarity versus Upf1. Crystal structure of Aquarius in complex with RNA revealed a novel mode of RNA binding by a helicase and led to the identification of structural adaptations underlying the reversal of directionality. Overall, the structure-function analysis brings insightful implications into the manner how two helicases have diverged from a common ancestor as a mean to achieve opposite polarities of translocation. Furthermore, we demonstrate that Aquarius is recruited to the spliceosome in complex with four other splicing factors and that the ARM domain is essential for the integrity of the complex. Moreover,the ARM domain makes contacts in the spliceosomal core, providing insight into the molecular basis underlying the accurate positioning of Aquarius on the intron. Following the line of these findings, we finally show that Aquarius plays an important role for the occurrence of splicing per se.
Structural basis of bacterial protein translation elongation
Authors: Gao Yonggui
Published: November 2015

Recently, better understanding of ribosome function has been achieved through structural determination. These results provided a wealth of information on how genetic codes are precisely translated into proteins that control life, as well as established the platform to put ribosome as one of the richest validated targets for antibacterial drug discovery. We discovered a new ribosome crystal form obtained from ribosome lacking subunit L9, which allows crystallization of the ribosome in the presence of elongation factors Tu and G (EF-Tu/EF-G), trapped by antibiotics kirromycin and fusidic acid, respectively. These structures for the first time at atomic level offer insight into the molecular mechanism of protein elongation, which lies at the heart of translation. In each elongation cycle, EF-G facilitates the movement of tRNA-mRNA by one codon, which is coupled to the ratchet-like rotation of the ribosome complex and is triggered by EF-G-mediated GTP hydrolysis. The structure of pre-translocational ribosome bound to EF-G trapped with a GTP analogue, sheds light on how the positioning of the catalytic residue His87 into the active site is coupled to the hydrophobic gate opening which involves the sarcin-ricin loop (SRL) and domain III of EF-G. These results provide the structural basis for the GTPase activation of EF-G. After translocation, a cognate deacylated tRNA can only move together with the codon into the ribosomal E site. We also determined the structure of a cognate tRNA bound to the ribosomal E site, representing an authentic ribosome elongation complex. Quality control in protein translation by bacterial toxin has been associated with ribosome stalling and rescue system that is critical for cell to adapt environmental stress. Finally, I will introduce our structural progress on bacterial toxin bound to ribosome towards understanding of a classical acid-base catalysis mechanism.
Structure and properties of metastable phases of m-Sb2Te3and m-Bi0.4Sb1.6Te3
Authors: Serebryanaya Nadezhda , Tatyanin Evgeny , Kruglov Ivan , Buga Sergei , Lvova Natalia , Blank Vladimir
Published: November 2015

The m-Sb2Te3 and m-Bi0.4Sb1.6Te3 metastable phases were found after high-pressure (4 GPa) and high-temperature (873 K) treatment of initial rhombohedral Sb2Te3 and Bi0.4Sb1.6Te3. These metastable phases crystallize in the same structure because they have almost identical diffraction pattern. The crystal structure of metastable phases, determined by the powder X-ray and electron diffraction methods, is monoclinic (C2/m). The cell dimensions of m-Sb2Te3 are: a=15.64(8) Å, b=4.282(8) Å, c=9.38(2) Å, β=89.700(5). The reliability factors are: RBragg=0.12, RF=0.13, χ2=4.35. There are two different types of Sb atoms: with seven-coordinated by Te atoms for Sb1 and for Sb2 – eight-coordinated by Te atoms forming composite coordination polyhedra. A comparison with the structure of pressure-induced β-Sb2Te3-phase, observed in situ under high pressure, has been made. Pressure-induced β-Sb2Te3-phase can be retained at ambient conditions as m-Sb2Te3. The annealing of m-Sb2Te3 and m-Bi0.4Sb1.6Te3 samples at 673 K during 2, 5 hours returns their structures to initial symmetry. This fact was supported by the exothermal peak found by differential scanning calorimetry. The ab initio study verified metallic character of quenched phases: the energy spectrum is consistent with the proposed monoclinic structure with short interlayer distances. The electrical resistivity and the Hall coefficient in the temperature range of T = 1.8–450 K have been measured. m-Sb2Te3 phase is superconductive at T < 2K.
Crystal Structure and Dielectric Property of Endohedral Lithium Fullerene
Authors: Aoyagi Shinobu , Sugimoto Kunihisa , Okada Hiroshi , Hoshino Norihisa , Akutagawa Tomoyuki
Published: November 2015

Endohedral lithium fullerene Li+@C60 can have a dielectric polarization by the off-centered location of the Li+ cation inside the C60 cage. The x-ray structure analysis of the PF6– salt [Li@C60](PF6) revealed that the Li+ cation occupies two off-centered equivalent positions at 20 K and hence the crystal is non-polar [1]. The disordered structure at low temperature is explained by a static orientation disorder of polar Li+@C60 cations and/or a dynamic tunneling of the Li+ cation inside the C60 cage. The Li+ tunneling would be suppressed by an intermolecular interaction at lower temperature and a dielectric phase transition might be induced. We reveal the dielectric property and crystal structure of [Li@C60](PF6) below 20 K in this study. The temperature dependence of the dielectric permittivity was measured for the single crystal down to 9 K. The dielectric permittivity increases with decreasing temperature according to the Curie-Weiss law. Such a behavior was also observed in H2O@C60 crystal but not in empty C60 crystal [2]. No dielectric phase transition was observed in H2O@C60 down to 8 K. In contrast, a dielectric anomaly suggesting a phase transition was observed in [Li@C60](PF6) around 18 K. The single-crystal x-ray diffraction experiment below 20 K was also performed at SPring-8 BL02B1. The crystal has a cubic structure at 20 K [1]. The temperature dependence of the cubic lattice constant shows no anomaly around 18 K. However, diffraction peaks that are forbidden for the given structure appear below 18 K. Thus the crystal symmetry is lowered by the dielectric phase transition. We present the result of the crystal structure analysis of the newly discovered low-temperature phase.
LEED and TEM analysis of Bismuth Telluride
Authors: Balzuweit Karla , MIlagres Thais , Nascimento Von Braun , de Carvalho Vagner , Soares Edmar , Ladeira Luiz
Published: November 2015

Bismuth Telluride has recently been identified as a 3D-topological insulator [1] as well as Graphene [2]. Topological insulators are a quite recent discovered quantum mechanics characteristic of materials where essentially the surface band structure is completely different from the bulk. Bismuth Telluride, for example has its semi-metallic behavior changed into a conducting one. However it has been well known, as an excellent thermoelectric material [3]; with relatively high thermoelectric coefficients at room temperature. Bismuth Telluride is a relatively easy material to obtain and different compositions are being studied both as bulk material and as thin films. Crystals of Bi2Te3 were Bridgman grown in a sealed quartz ampoule in a directional resistance oven at a temperature of 600oC. Conventional X-ray Laue diffraction showed patterns compatible with a single crystal along the sample except for the starting point, which was discarded. Transmission and Scanning Electron Microscopy and Low Energy Electron Diffraction (LEED) were performed. The grown crystals were cleaved and small parts were crushed on a mortar with ethanol and deposited onto a holey carbon grid. Also thin slices were cut in an ultramicrotome (Leica UC6) with a diamond knife and deposited onto a holey carbon coated grid. TEM measurements showed the presence of grains on both samples with a very small deviation from the observed crystallographic axis (0001). However LEED measurements showed only a single crystalline pattern. Electron backscatter diffraction (EBSD) studies showed large granular areas with a extremely small angular variation between the grains. It is still unclear if those differences are real or due to sample preparation artifacts and effort is being put into analyzing exactly the same piece with all the different techniques.
Application of Charge & Band-flipping to Time-of-Flight Neutron Diffraction Data
Authors: Whitfield Pamela , Coehlo Alan , Huq Ashfia , Hoffmann Christina , Wang Xiaoping
Published: November 2015

Charge-flipping has become a popular approach to ab-initio structure solution from X-ray powder diffraction data in particular due to its speed and need for minimal input other than lattice parameters. Given the appetite of charge-flipping for low d-spacing reflections, time-of-flight (TOF) neutron data should be a good match from a resolution standpoint, with easy access to high Q and lack of form-factor drop-off. One obvious issue with neutron data is the presence of elements with negative scattering lengths, where the inherent assumption of atoms always having positive `density' in the algorithm breaks down. This means that portions of the structure can be effectively invisible. Given that some of these elements (e.g. H and Mn) are commonly found in samples of interest the issue is more than simple academic curiosity. Of course such atoms can be found by difference maps, but the issue has also been addressed within the charge-flipping algorithm with the `band-flipping' modification [1]. Although Oszlányi & Sütö demonstrated the approach was viable with simulated neutron single crystal data [1], to the authors' knowledge it hasn't been used previously with experimental single crystal or powder neutron diffraction data. Powder diffraction data from POWGEN and wavelength-resolved TOF Laue single crystal data from TOPAZ at the Spallation Neutron Source have been used to probe the relative ease of charge-flipping with different TOF data using the TOPAS software package [2]. In addition the effectiveness of different customized band-flipping approaches has been tested to extract positions for positive and negative scattering elements simultaneously.
When two bad data sets are better than one
Authors: Smeets Stef , McCusker Lynne , Baerlocher Christian , Xie Dan , Zones Stacey , Wan Wei , Zou Xiaodong
Published: November 2015

High-resolution synchrotron X-ray powder diffraction (SXPD) data alone are sometimes not enough to solve the structure of a complex polycrystalline material. Such was the case for the high-silica zeolites SSZ-61 and SSZ-87, where combining data from different sources, in particular XPD and electron microscopy, was vital to success. For SSZ-61, the SXPD data feature broad peaks and a resolution of ca. 1.2 Å. Although the pattern could be indexed, structure determination failed both with the charge flipping routine in SUPERFLIP [1] and with the zeolite-specific program FOCUS [2]. The unit cell parameters and HRTEM images indicated a relationship with ZSM-12 (MTW) and SSZ-59 (SFN), so several models derived from these two frameworks were built. Eventually, after considering Si-29 MAS NMR data and the size of the organic structure directing agent (SDA), a framework model that fits all the data emerged. To complete the structure, the SDA was included as a rigid-body, and its location and orientation optimized using simulated annealing. Subsequent Rietveld refinement confirmed the structure. In contrast to SSZ-61, the SXPD pattern for SSZ-87 was quite good, and it could be indexed with a C-centered cell. However, structure solution failed, probably because of the very high degree of reflection overlap (93%). Therefore, rotation electron diffraction (RED) data [3] were collected, but they proved to be of low resolution and poor quality. Only 2 of the 7 data sets could be indexed, and these had different unit cells. Neither fit the XPD pattern directly. The problem was traced to large errors in the RED cell parameters, and eventually one RED cell could be transformed to one similar to the SXPD cell. The RED data with this cell was only 15% complete up to a resolution of 1.22 Å. Even so, the structure could be solved using a recently developed version of FOCUS that works with ED data. The SDA was found as for SSZ-61, and the structure then confirmed by Rietveld refinement.
Issues in solving complex molecular crystal structures from lab PXRD data
Authors: Shankland Kenneth
Published: November 2015

Developments (both software and methodological) in crystal structure determination from powder X-ray diffraction data have resulted in increasingly complex molecular structures now being solved from relatively low-resolution diffraction data. This can lead to the publication of structures that clearly do not meet the rigorous chemical and crystallographic standards that one normally associates with published crystal structures. As such, considerable attention should be paid to the quality of the final refined crystal structure, with chemical sense playing as important a role as the fit of the structure to the data. This presentation will focus upon some issues that impact upon the final quality of the published structure as derived from lab PXRD data, and suggest strategies for maximising the chances of a successful structure solution and refinement. These include the preparation of structural models for use in global optimisation, the use of rigid-body-type refinements, the critical assessment of output crystal structures and the use of DFT-D to validate such crystal structures. The presentation will be illustrated with examples drawn mostly from the world of pharmaceutical research and will include an introduction that puts the role of structure determination from powder diffraction data into context in terms of accessible structural complexity.
Transition between two Kosterlitz-Thouless phases in Sc-doped TiOCl
Authors: Zhang Jian , Wolfel Alexander , Bykov Maxim , Schonleber Andreas , van Smaalen Sander , Kremer Reinhard , Williamson Hailey
Published: November 2015

The compound TiOCl is a quasi-1-dimensional (1D) quantum magnet (Seidel et al., 2003). Upon cooling, TiOCl undergoes a phase transition at Tc2 = 90 K towards a state with incommensurate magnetic order, followed by a second phase transition at Tc1 = 67 K towards a spin-Peierls state (Seidel et al., 2003; Shaz et al., 2005; van Smaalen et al., 2005). Both low-temperature phases involve structural distortions that have been characterized by x-ray diffraction. The absence of any phase transitions has been reported for scandium-doped TiOCl with doping levels 0.01 < x < 0.1 for ScxTi1-xOCl (Glancy et al., 2008, 2010; Zhang et al., 2010; Aczel et al., 2011). We have synthesized ScxTi1-xOCl for x = 0.005. Based on temperature-dependent x-ray diffraction experiments and specific-hear measurements, we have found that the x = 0.005 compound transforms into incommensurate and spin-Peierls-like phases on cooling. Despite apparent large correlation lengths, these phases lack long-range order. A sluggish transformation is thus found between states of ScxTi1-xOCl that support different kinds of fluctuations.
Phase transitions toward charge density wave in the m=11.5 Mono phosphate bronze
Authors: Pérez Olivier , Kolincio Kamil , Pautrat Alain
Published: November 2015

Mono Phosphate Tungsten Bronzes (MPTB), (PO2)4(WO3)2m (m ranging from 4 to 14), are a large family of conductors of low dimensionality[1]. Their structure may be described as a regular stacking of WO3-type slabs with a thickness function of m, joined by slices of tetrahedral PO4 phosphate. Successive Peierls transitions towards charge-density wave (CDW) or spin-density wave (SDW) states are observed below different critical temperatures (TC1, TC2 ...). Structural transitions toward incommensurate modulated phases are associated with these complex electronic states. Recently an original member of MPTB, the member m=11.5 with formula (PO2)4(WO3)11(WO3)12, resulting in a regular intergrowth between m=11 and m=12 member, has been synthetized. An accurate investigation of the reciprocal space versus the temperature using single crystal X-ray diffraction shows the existence of two phase transitions at Tc1=4300C and Tc2=2800C. The ground state structure may be described with the following cell parameters a=5.3431(7) b=6.5901(9) c=40.884(6) α=93.096(2) β=93.734(2) γ=90.000(2) and the SG P-1. Both transitions associated with the occurrence of CDW are characterized by the appearance of modulation vectors (q1 and q2 associated to Tc1 and Tc2 respectively) and an increasing of the dimension of the superspace group (see figure 1). A structural study of the m=11.5 member is performed above Tc1 and below Tc1 and Tc2; an interpretation of the CDW state is then proposed. The evolution of the intensity of the satellite and main reflections around Tc1 and Tc2 is analyzed for characterizing the order parameter of the transitions. Finally, resistivity and magnetoresitance measurements of a large single crystal sample of m=11.5 MPTB are performed in a temperature interval from 2K to 300K. These measures are revealing at ~50K a possible SDW transition due to electron-electron interactions playing significant role in that material[2]. Further neutron diffraction experiment at very low temperature shall be performed to clarify this point.
Incommensurate modulated structures and luminescence in scheelites
Authors: Morozov Vladimir , Meert Katrien , Smet Philippe , Poelman Dirk , Abakumov Artem , Hadermann Joke
Published: November 2015

Scheelite (CaWO4) related compounds (A',A'')n[(B',B'')O4]m with B', B''=W and/or Mo are promising new materials for red phosphors in pc-WLEDs (phosphor-converted white-light-emitting-diode) and solid-state lasers. Scheelites can be prepared with a large concentration of vacancies in the A sublattice, giving compositions characterized by a (A'+A''):(B'O4+B''O4) ratio different from 1:1. The creation of cation vacancies in the scheelite-type framework and the ordering of A cations and vacancies are a new factor in controlling the scheelite-type structure and properties. Very often the substitution of Ca2+ by M+ and R3+ (R3+ = rare earth elements) in the scheelite-type structure leads to switching the structure from 3D to (3+n)D (n = 1,2) regime. The creation and ordering of A-cation vacancies and the effect of cation substitutions in the scheelite-type framework are investigated as a factor controlling the scheelite-type structure and luminescent properties of CaGd2(1-x)Eu2x(MoO4)4(1-y)(WO4)4y (0≤x≤1, 0≤y≤1) solid solutions. Within this series all complex molybdenum oxides have (3+2)D incommensurately modulated structures with superspace group I41/a(α,β,0)00(-β,α,0)00, while the structures of all tungstates are (3+1)D incommensurately modulated with superspace group I2/b(αβ0)00. In both cases the modulation arises due to cation-vacancy ordering at the A site. The replacement of the smaller Gd3+ by the larger Eu3+ at the A-sublattice does not affect the nature of the incommensurate modulation, but an increasing replacement of Mo6+ by W6+ switches the modulation from (3+2)D to (3+1)D regime. Acknowledgement. This research was supported by FWO (project G039211N, Flanders Research Foundation) and Russian Foundation for Basic Research (Grants 11-03-01164, and 12-03-00124).
Disorder, modulation and twinning in Λ-Co(sepulchrate) trinitrate
Authors: Schönleber Andreas , Dey Somnath , van Smaalen Sander , Larsen Finn
Published: November 2015

The organic compound Λ-Co(sepulchrate) trinitrate, [C(12)H(18)N(8)Co](3+) · 3[NO(3)](-), exhibits at room temperature a disordered structure in symmetry P6(3)22 [1,2]. The Co(sepulchrate) cation and two of the nitrate anions, all centred on three fold rotation axes, are linked via dense N–H···O hydrogen bond networks, the third nitrate anion, centred on the intersection of the two fold rotation axes, shows orientational disorder (see Figure). Three phase transitions have been observed upon cooling by means of light microscopy and spectroscopic measurements [1] and by single crystal neutron diffraction [3] at T(1) = 133 K, T(2) = 106 K and T(3) = 98 K. These phase transitions are interpreted as ordering of the disordered nitrate anions [1] and as reduction of symmetry from hexagonal to orthorhombic associated with twinning. The appearance of satellite reflections in the diffraction pattern at T(1) = 133 K indicates a modulated structure; as the positions of those satellite reflections are temperature dependent [3], the modulation is incommensurate. By single crystal X-ray diffraction at beam lines D3 and F1 of Hasylab (DESY, Hamburg) at different low temperatures we found that all observed peaks are indexable in an hexagonal setting and two q-vectors q(1)=(σ,σ,0) and q(2)=(-2σ,σ,0) with σ ≍ 0.0882. This setting is compatible with a three-fold orthorhombic twinning and one q-vector q(orth)=(2σ,0,0) for each of the three twin domains, which allows to reduce the symmetry. Structure refinement of all three low temperature phases allows to set them into relation to each other.
Reorientation of α-Fe2O3crystallites in an external magnetic field
Authors: Stękiel Michał , Przeniosło Radosław , Wardecki Dariusz , Buslaps Thomas , Jasiński Jacek
Published: November 2015

The magnetic interaction between the crystallites of weak ferromagnetic α-Fe2O3 has been studied by combining SR based X-ray diffraction with an externally applied magnetic field. The measurements were performed with several polycrystalline α-Fe2O3 [1,2] samples (dry or in suspensions) placed in a half-filled cylindrical container in ambient conditions. The axis of the cylindrical container was oriented vertically parallel to the applied dc magnetic field. The polycrystalline sample had a free surface, so the α-Fe2O3 crystallites were free to move. The full Debye-Scherrer diffraction rings were measured with a 2D pixel detector at the beamline ID-15B at ESRF. In the absence of the magnetic field the intensity distribution over azimuthal angle was a uniform, i.e. there was no texture. The applied maximal field, B=0.9T was too small to change the magnetic ordering of α-Fe2O3 but it was sufficiently strong to reorient large amount of crystallites in order to minimize the angle between their ferromagnetic moment direction and the external field. Pronounced texture patterns with clear maxima in the angular distribution of the intensity across each Debye-Scherrer ring were observed. The observed textured intensity distribution was analyzed quantitatively by using a model based on the magnetic anisotropy observed in single crystals of α-Fe2O3. The analysis yielded two important parameters: (i) the width of the angular distribution of the ferromagnetic moments directions around the external field direction, and (ii) the relative quantity of the crystallites that did reorient in the external field. The α-Fe2O3 samples were also characterized with TEM technique. The analysis of X-ray and TEM studies provide new conclusions about the magnetic interaction between the α-Fe2O3 crystallites [3]. The proposed measurement technique can be applied to study other weak ferromagnetic materials.
X-Ray induced Photostriction in Bismuth Ferrite
Authors: Nye Daniel , Keeble Dean , Gorfman Semen , Weber Mads , Kriesel Jens , Alexe Marin , Nisbet Gareth , Bhatnagar Akash , Thomas Pam
Published: November 2015

In a material with both a piezoelectric effect and the capability to form a photocurrent, photostriction can be observed – the deformation of the crystal by light. When studying photostriction, a potential method is to use x-rays to probe the unit cell in response to another light source as a stimulus, such as a laser or a diode. Given that x-rays are also photons it is plausible that they themselves produce some effect. An experiment was carried out to investigate how significant the effects of the x-rays are in producing photostriction in the absence of any other source of illumination. The material studied in this example was bismuth iron oxide, BiFeO3. A thin film with electrodes was used and it was found that the photocurrent generated by a laboratory x-ray source on the sample was of comparable level to that of a laser or diode used in the study of the bulk photoelectric effect. Using a novel, time dependent crystallographic approach, the intrinsic effect of synchrotron x-ray light on a photoferroelectric thin film has been investigated. Furthermore, we have simultaneously collected diffraction and photoelectric data, and the correlation between the electronic and structural properties will be discussed. These results could suggest that caution is necessary when interpreting photostriction data obtained with the use of x-rays.
Lattice thermal expansion of complex oxides with intrinsic anharmonicity
Authors: Murshed M. Mangir , Zhao Pei , Alekseev Evgeny , Huq Ashfia , Gesing Thorsten
Published: November 2015

The lattice thermal expansion of crystalline solids cannot be adequately modeled by Grüneisen approximation using either Einstein single harmonic frequency or Debye frequency spectrum because a true phonon spectrum does not follow either of the two kinds. The Debye model misfits to many observations due to the fact that real solids comprises of axial anisotropy, lattice waves with dispersion at the Brillouin zone boundaries, low/high frequency optical vibrations in excess of the Debye spectrum. The actual frequency distribution is a complicated function of frequency instead of a simple parabolic Debye spectrum. The frequency distribution can be simplified using power series [1] leading to singularities before and after the Debye cutoff frequency. Using multiple Debye or Einstein oscillators, or their mixtures, is also common practice to better describe the lattice expansion, however, these models extremely suffer from intrinsic anharmonicity in particular at high temperatures. It was demonstrated that even the noble monoatomic solids required inclusion of anharmonic terms in the harmonic model to better explain the observed values [2]. Worse even, when anharmonicity becomes dominant due to formation of vacancies and defects, anomalies of hard/soft modes or change of stereochemical activities of lone electron pairs (LEPs) as function of temperature. Herein we approach an extended Grüneisen approximation that includes harmonic, quasiharmonic and intrinsic anharmonic potentials to describe the internal energy of the crystal as function of temperature. The model has been applied to several complex oxides with LEPs (Bi2Ga4O9[3]) along with axial negative thermal expansion (PbFeBO4) and rigid-unit-modes (KAsW2O9) reported here. The metric parameters were obtained from quality data collected from temperature-dependent neutron and X-ray powder diffractions.
Perflourocarbon liquid under pressure: a medium for gas delivery
Authors: McKellar Scott , Sotelo Jorge , Mowat John , Wright Paul , Moggach Stephen
Published: November 2015

Materials with applications in gas storage and separation are of enormous interest across many disciplines of science. This has been driven in large part by advances in carbon sequestration technologies in line with global government targets for cleaner energy and the reduction of carbon dioxide (CO2) emissions. Potential applications in this field include the removal of CO2 from flue gas mixtures before it enters the atmosphere, for example. Porous metal-organic frameworks (MOFs) are currently seen as one of the most promising types of materials for this purpose since they combine the desired features of high porosity, thermal stability and chemical versatility. Fundamental to such research is the requirement to optimise the quantity of gas that can be stored in the MOF. Evaluation of gas storage capacities is usually performed using time-consuming gravimetric or calorimetric analyses over a range of temperatures and pressures, and often requiring gram-scale quantites of material. Here, we present a novel method for gas delivery and calculation of gas storage capacity using a perflourocarbon (PFC) liquid. PFCs have long been recognised as useful due to their predisoposition for dissolving large volumes of gases such as CO2 and oxygen. They are chemically inert hydrocarbons in which the hydrogen atoms have been replaced with fluorine. We have used a PFC containing dissolved CO2 as a pressure-transmitting liquid in an in situ high-pressure single-crystal X-ray diffraction experiment. Application of industrially-achievable pressure within a diamond anvil cell causes the CO2 to be squeezed out of the liquid into a host crystal of a porous MOF as the system seeks to fill empty space and redistribute density upon contraction. Diffraction data from a crystal of Sc2BDC3 (BDC = 1,4-benzenedicarboxylate)[1] has allowed us to determine its maximum CO2 storage capacity, which is in perfect agreement with other methods. This result is the first of its kind and the technique has several notable advantages over other methods: it requires just one experimental step, can be performed at room temperature, and requires only one single crystal of solid material.