bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural characterisation of retromer complexes
Authors: Norwood Suzanne , Leneva Natalya , Ghai Rajesh , Cowieson Nathan , Duff Anthony , Wood Kathleen , Collins Brett
Published: November 2015

Retromer is a peripheral membrane protein complex that plays a critical role in a broad range of physiological, developmental and pathological processes including Wnt signalling, toxin transport and amyloid production in Alzheimer's disease. The classical mammalian retromer complex consists of a core heterotrimeric cargo recognition sub-complex (VPS26, VPS29 and VPS35) associated with a dimer of proteins from the SNX–BAR sorting nexin family that drives membrane deformation and tubulation. By recruiting the cargo-selective sub-complex to the forming tubules, the SNX–BAR coat complex mediates the retrograde transport of proteins from endosomes to the trans-Golgi network. Recent studies, however, have highlighted the molecular and functional diversity of retromer and the identification of new interacting proteins has revealed that the role of retromer extends to aspects of endosome-to-plasma membrane sorting and regulation of signalling events. Emerging evidence indicates that cargo specificity is mediated by specific sorting nexins. These include SNX3, involved in the trafficking of the Wntless/MIG-14 protein, and SNX27, a PX-FERM protein that mediates the retrieval of the β2-adrenergic receptor.Using the MX and SAXS/WAXS beamlines at the Australian Synchrotron, we have acquired crystallographic and small angle scattering data to determine how the core cargo recognition sub-complex assembles and to characterise the retromer-associated sorting nexins. We are using this structural information in combination with biochemical and biological studies in a synergistic approach to understand retromer-mediated endosomal protein sorting and how this fascinating protein complex contributes to a diverse set of cellular processes. The retromer complex is conserved across all eukaryotes. We are also currently exploring the structure of these proteins in the thermophilic fungus Chaetomium thermophilum and initial crystallisation experiments have produced some promising results.
Time-Resolved SAXS experiments with low sample consumption
Authors: Matsui Tsutomu , Liu Ping , Carter Lester , Weiss Thomas
Published: November 2015

Using Time-Resolved Small Angle X-ray Scattering (TR-SAXS) on the millisecond time scale to investigate biological systems is an extremely powerful tool to detect possible intermediate states that form during the course of the reaction and gain detailed insight into the sequence of events along the reaction pathway. However the use of TR-SAXS has often been difficult due to the large amount of sample typically required for such experiments. Here we report on our recent development of a fast TR-SAXS setup using a customized stopped-flow mixer. This new setup allows us to obtain a TR-SAXS data set from as little as 30ul of sample volume. It also eliminates the sample consuming priming of the tubing inside the stopped flow and thus substantially reduces the sample amount required for such experiments. An automatic wash cycle for the sample cell (capillary) is employed after every single shot to ensure that the capillary is clean and no residues remain in the cell from the previous measurement.
Analytical calculation of the radius of gyration of regular shapes and polyhedra
Authors: Kriechbaum Manfred
Published: November 2015

The radius of gyration (Rg) is one of the most common parameters to be extracted from small-angle X-ray/neutron scattering (SAXS, SANS) measurements of nanoparticles and combines information about size, shape, symmetry and homogeneity in one single value. The analytical expressions for Rg are well known for simple geometric shapes (spheres, ellipsoids, cylinders, cubes). In this work, the analytical equations for Rg for other homogeneous (constant electron or scattering length density) shapes like cones, pyramids, paraboloids, hemispheres or tori are derived and are compiled in this poster. In this approach, the Rg of different 3-dimensional objects can be composed of a 2-dimensional cross-sectional (Rc) and of a perpendicular (h) contribution. Thus, Rg2is the linear sum of both: Rg2= f1*Rc2+ f2*h2, with h being the height or diameter of the object in the perpendicular direction to the cross-section and f1 and f2 being multiplicative factors with values depending on the geometric shape. The cross-sectional area can be (semi-)circular, (semi-)elliptic, n-polygonal or rhombic, resulting in a conical, pyramidal, ellipsoidal or paraboloidal 3D-shape, depending on the perpendicular component. A mirror-symmetry in the cross-sectional plane may be present (e.g. ellipsoids, bi-cones or bi-pyramids) or absent (e.g. hemispheres or single cones or pyramids). General equations of Rc for regular (equilateral) n-polygons will be given, but also for non-equilateral polygonal (rectangular, triangular) and rhombic cross-sections. Furthermore, the analytical equations of Rg of nanoscaled particles of high symmetry, in particular of convex polyhedra like the 5 Platonic solids (tetra-, hexa-, octa-, dodeca- and icosa-hedron) or the 13 Archimedean solids and their duals (Catalan solids) are presented, for the solid, for the hollow (faces only) and as well as for the skeletal (edges only) and dot (vertices only) shape.
Microfluidic dialysis on the beamline: experiment and theory
Authors: Gillilan Richard , Skou Søren , Jensen Thomas , Vestergaard Bente , Skou Magda
Published: November 2015

Biological small angle x-ray solution scattering requires sufficient sample concentration to yield good signal while at the same time avoiding interparticle interference or the formation of unwanted oligomers or aggregates. The mere act of concentrating some samples risks rendering them unfit for SAXS measurements and the limit to which a sample may be concentrated before problems occur is often unknown a priori; aggregation is not generally regarded as a reversible process. At the same time, sample behavior at high concentrations is increasingly important not just for characterization of equilibria, or e.g. applications in the pharmaceutical industry, but also for understanding potential molecular crowding effects. We have constructed a microfluidic dialysis setup that permits on-demand concentration of protein samples at the beamline. Rather than generating dilution series to explore concentration effects, this approach produces true "concentration series", efficiently working from dilute sample upward. We experimentally demonstrate that useful concentrations can be achieved on practical timescales and that buffer exchange can be performed. Convection-diffusion modeling shows that the dialysis chip may actually retard aggregates, thus resulting in some degree of incidental sample purification. Based on model projections, the theoretical limits and potential of chip-dialysis will be described.
CryoSAXS as a Method for Measuring Low Resolution Macromolecular Structure
Authors: Hopkins Jesse , Katz Andrea , Meisburger Stephen , Warkentin Matthew , Gillilan Richard , Pollack Lois , Thorne Robert
Published: November 2015

Small angle X-ray scattering (SAXS) is an increasingly popular technique for obtaining low resolution structural information from macromolecules and complexes in solution. Biomolecular SAXS signals can rapidly degrade due to radiation damage, so that flow or oscillating cells and large total sample volumes may be required. For particularly sensitive or hard to produce samples, such as of light sensitive proteins, metalloenzymes, and large complexes, and studies where multiple buffer conditions are probed sample consumption may be prohibitive. We describe cryo-cooling of samples to 100 K to prevent X-ray induced radiation damage. We identify SAXS-friendly cryoprotectant conditions that suppress ice formation upon cooling, and compare cryoSAXS profiles obtained in window-free variable-path-length cells with room temperature measurements for a variety of standard molecules. We obtain data sufficient for envelope reconstructions using scattering volumes as small as 20 nL, and find good agreement between cryoSAXS data and known atomic structures. We also discuss work on developing low-volume fixed path-length sample holders for cryoSAXS. Cryo-cooled samples can withstand doses that are 2-3 orders of magnitude higher than typically used for SAXS at room temperature, comparable to those used in cryo-crystallography. While practical challenges remain, cryoSAXS opens the possibility of studies exploiting high brightness X-ray sources and mail-in high-throughput SAXS. This work is funded by the NSF (DBI-1152348).
Function of polyketide synthases from the SAXS structure of a complete module
Authors: Davison Jack , Dorival Jonathan , Rabeharindranto Hery , Mazon Hortense , Chagot Benjamin , Gruez Arnaud , Weissman Kira
Published: November 2015

The modular polyketide synthases (PKS), common to many bacterial antibiotic-producers, are huge multienzyme, multidomain systems which can be likened to molecular assembly lines.1 An understanding of the structural and mechanistic aspects which underpin interdomain cooperation during biosynthesis by modular PKS is crucial to ongoing efforts to re-engineer these systems for the production of novel compounds of medicinal value.2 Previous attempts to solve the structures of PKS modules by X-ray crystallography have been unsuccessful, likely due to the high, inherent flexibility of the multienzymes. Here, we have employed an alternative technique, small-angle X-ray scattering (SAXS), in combination with NMR structure elucidation and homology modelling of individual domains, to obtain the first low-resolution structural data on an entire apo PKS module. The model system comprises a multidomain region of the virginiamycin M1 PKS from Streptomyces virginiae, a target of relevance for its involvement in production of the commercial antibiotic dalfopristin. The investigated region, which comprises a ketosynthase (KS) and two consecutive acyl carrier protein (ACP) domains, interacts with a wide range of protein partners, including notably, a complex of discrete enzymes responsible for β-methylation of the polyketide, and the N-terminus of the downstream PKS protein, VirFG.3 In our solved structure (Fig. 1), the homodimeric KS, which is flanked by well-folded linker regions, occupies the center of the module. While the first ACP is located close to the KS, the second is situated at the end of a flexible linker, and mobile. Taken together, these data provide a physical explanation for the functional non-equivalence previously observed for certain tandem ACPs of this class of PKS. Furthermore, the overall open shape of the module renders the second ACP highly accessible, which may be critical for its interaction with its multiple in trans catalytic partners. Finally, our analysis redefines the function of a putative dimerization motif of tandem ACPs as a docking domain, suggesting that the module likely adopts a more closed form in order to affect transfer of the chain extension intermediate to the subsequent module.
SAXS, WAXS, MD, Protein fluctuations and function
Authors: Makowski Lee , Zhou Hao , Wang Yu Jing
Published: November 2015

Conformational mobility is essential to many protein functions and design of therapies for a broad spectrum of human diseases depends on a deep understanding the linkage between protein structure, intramolecular motions and function. Methods for screening small molecules and mutations that alter fluctuations are essential for improved understanding of this linkage. To what extent do changes in intramolecular motions lead to changes in function? To address this question, we are using a combination of wide-angle x-ray solution scattering (WAXS) and molecular dynamics (MD) to generate novel insights into the magnitude, form and functional consequences of intramolecular motions of proteins in solution. WAXS has proven unexpectedly sensitive to the intramolecular motions of proteins in solution and can detect changes in flexibility generated by single amino acid replacements or binding of small molecule ligands. Here we formulate the effect of structural fluctuations on WAXS data in such a way as to make possible direct experimental assessment of the range of motion that proteins explore in solution. The approach differs from other strategies by treating it as an inverse source problem, deriving flexibility parameters directly from data rather than from an ensemble of structures generated to predict the data.
Precision of the single crystal neutron diffractometer SENJU at J-PARC
Authors: Noda Yukio , Kiyanagi Ryoji , Ohhara Takashi , Kawasaki Takuro , Oikawa Kenichi , Kaneko Koji , Tamura Itaru , Hanashima Takayasu , Moyoshi Taketo , Nakao Akiko , Munakata Koji , Kuroda Tetuya
Published: November 2015

"SENJU" is a newly built pulsed neutron single crystal diffractometer at J-PARC/MLF for structural research of inorganic and organic materials with relatively small cell sizes under multiple extreme environments, such as low temperature and a high magnetic field. Since the launch of the instrument in 2012, SENJU has been commissioned and now tuned to be capable of crystal and magnetic structure analyses with a sample as tiny as 1mm cube or less. SENJU has the total of 37 two-dimensional scintillation detectors installed. Groups of 3 detectors are accommodated in detector banks and 12 detector banks are placed so as to cylindrically surround the sample chamber (Figure), and additional one detector is settled at the bottom. The instrumental parameters including the positions of the detectors and the neutron flight path length were determined in order to obtain accurate lattice parameters of samples. Since the instrumental parameters correlate with each other, series of different measurements were needed in order to obtain unique values for each parameter. As the first step of the procedure, a powder diffraction pattern of diamond was measured in order to determine the scattering angle of 90 [deg] utilizing the nature that a Bragg reflection vertically lines up at 90 [deg]. Simultaneously, we determined the neutron path length L1 from the neutron source to the sample position. As a next step, a Bragg reflection was repeatedly measured as the sample crystal was rotated with small steps. From this data, the equatorial plane on the detectors and the distance between the sample and the detectors L2 were determined. As a third step, many Bragg reflections from a sample with known lattice constants were measured and from the positions of the reflections the positions of each detector were determined. As a result, the lattice parameters can be obtained with the accuracy of about 0.05 % using the determined instrumental parameters.
Materials behavior under Fast Compression or Decompression
Authors: Shen Guoyin , Sinogeikin Stanislav , Smith Jesse
Published: November 2015

Phase transformation pathways are strongly influenced by the time dependence of the driving mechanism (compression, thermal transfer, strain, irradiation, etc). While thermal rate has been widely used for centuries for enhancing materials properties such as hardened steels or metallic glasses through rapid cooling, the application of compression rate is relatively new. Yet it drives rich new physics, novel chemistry, exceptional energy materials, and new routes of materials synthesis, and has become an important impetus in studying materials metastability, phase growth, and transition kinetics. In this talk, we will outline recently developed capabilities at HPCAT at the Advanced Photon Source for studying materials behavior under fast compression or decompression, including both single event loading or unloading and multiple, repetitive ramping events. A few recent studies will be highlighted. For example, a compression rate of 17 TPa per second has been reached in a piezo-driven diamond anvil cell; fast compression experiments significantly improve the precision in thermal equation of state determinations; the feasibility of controlled formation of metastable phases of Si and Ge has been demonstrated under controlled decompression rate; the phase transition kinetics of B1-B2 transitions in NaCl and KCl have been studied under various compression and decompression rates.
Laser-Based Dynamic Compression of Solids to Ultrahigh Pressures
Authors: Duffy Thomas , Wang Jue , Coppari Federica , Smith Raymond , Eggert Jon , Collins Gilbert
Published: November 2015

Laser-based dynamic compression provides new opportunities to study the structures and properties of materials to ultrahigh pressure conditions. In this technique, high-powered laser beams are used to ablate a sample surface and by reaction a compression wave is generated and propagate through the sample. By controlling the shape and duration of the laser pulse, either shock or ramp (shockless) compression can be produced. Diagnostics include velocity interferometry (from which the stress-density response of the material can be determined) and x-ray diffraction from which structural information is obtained. Magnesium oxide is a fundamental ionic solid which has been extensively examined at high pressures. Theoretical studies predict a change in MgO from a rocksalt (B1) crystal structure to a cesium chloride (B2) structure at pressures of about 400–600 GPa but diamond anvil cell experiments have not been able to reach these pressures. Here we present dynamic X-ray diffraction measurements of ramp-compressed magnesium oxide. We show that a solid–solid phase transition, consistent with a transformation to the B2 structure occurs near 600 GPa. On further compression, this structure remains stable to 900 GPa. Our results provide an experimental benchmark to the equations of state and transition pressure of magnesium oxide, and may help constrain interior properties of super-Earth extrasolar planets. We have also examined the high-pressure behavior of molybdenum under both shock and ramp loading. The melting curves and high-pressure phase diagrams of transition metals have been controversial, and Mo is an excellent test case for resolving these discrepancies. We have conducted shock compression experiments on Mo with an X-ray diffraction diagnostic to address previous claims of high-pressure phase transitions and to determine the location of the Hugoniot melting point. We have also carried out ramp compression experiments to test predictions of phase transitions in Mo at ultrahigh pressures and low temperatures.
The roles of chirality and polarity in novel multiferroics: MnSb2O6and Cu3Nb2O8
Authors: Johnson Roger , Chapon Laurent , Cao Kun , Manuel Pascal , Bombardi Alessandro , Nair Sunil , Cheong Sang-Wook , Radaelli Paolo
Published: November 2015

At room temperature Cu3Nb2O8 has a centrosymmetric, triclinic crystal structure. If cooled below 24 K, the copper magnetic moments order with a complex, generalized helicoidal magnetic structure that breaks inversion symmetry, giving rise to ferroelectricity. Unusually, the direction of the induced electric polarization vector with respect to the helicoidal spin rotation cannot be reconciled by conventional theories of magneto-electric coupling. Instead, we show that the observed multiferroic properties of Cu3Nb2O8 may be explained through a phenomenological analysis based upon coupling between the magnetic chirality, electric polarity, and a structural axial rotation. Trigonal MnSb2O6 crystallizes with a chiral crystal structure. Typically, magnetic materials with a chiral crystal lattice order with a chiral magnetic structure, where the magnetic exchange interactions and anisotropies follow the symmetry of the lattice. The magnetism of MnSi is a classic example of this scenario, in which exotic skyrmion phases emerge out of a helical magnetic state. To the contrary, we show that the low temperature magnetic structure of MnSb2O6 is cycloidal, described by a magnetic polarity as opposed to a chirality. We demonstrate through ab-initio calculations that this magnetic structure is in fact the ground state of the symmetric-exchange Heisenberg spin Hamiltonian, which has higher symmetry than the underlying crystal lattice. Furthermore, the phenomenology may be understood by considering the coupling between structural chirality, magnetic polarity, and a magnetic axial rotation. As a result, we predict MnSb2O6 to be multiferroic with a weak ferroelectric polarization.
Growth and optical characterisation of thiourea (nh2csnh2) single crystals
Authors: Chhaganlal Kishorkumar , Adroja Deepakkumar
Published: November 2015

The beauty of single crystals are very much fascinating. The flatness of their faces and sharpness of their color gives us deep satisfaction. Thiourea (NH2CSNH2) is an organic material. Organic single crystals have several applications in modern frontline technologies like electronics, photonics, optoelectronics and non linear optics(NLO). The authors have successfully grown Thiourea crystals using relatively simple and inexpensive slow evaporation of aqueous solution technique with different intensities (watt) and frequencies (Hertz) as their growth conditions. The observation suggest that in absence of light the growth period is very long and crystals are opaque by increasing the intensities of light and using different filters ,the growth period reduces and transparencies increases. Crystals obtained have hexagonal and tetragonal shapes with different optical qualities. The average size of the crystals were varied in size from 40mmX28mmX1mm to 1.5mmX1.5mmX0.5mm.Grown crystals were optically characterized by UV-Vis –NIR spectroscopy, Ellipsometry, Laser Dispersion and Second Harmonic Generation studiers. The thiourea has a good transmittance and lower cut off wavelength is 280 nm. Spectra reveal the presence of absorption peak between 200nm to 280nm. crystals have a direct band gap about 4.0 eV. Selected crystals were polished for Ellipsometric study using variable angle spectroscopic Ellipsometry using operating wavelength between 240-1700nm, angle of incidence between 20° to 90°,data were taken with wavelength interval of 50nm and angle of incidence in interval of 0.5°.The polarization state of light incident upon the sample may decomposed into s and p component. Using the fundamental equation the relation between refractive incidences and Brewster angle was obtained. SHG and laser dispersion study suggest high potential application of these crystals.
The electron charge density distribution in a non linear optical compound
Authors: Fodil Hamzaoui , Abdelkader Chouaih
Published: November 2015

The 4, 4 dimethyl amino-cyanobiphenyl crystal (DMACB) is characterized by its nonlinear optical properties. The intra molecular charge transfer of this molecule (figure-1) results mainly from the electronic transmission of the electro-acceptor (Cyano) and the electro-donor (Di-Methyl-Amino) groups [1]. An accurate electron charge density distribution around the molecule has been calculated from a high-resolution X-ray diffraction study. The data were collected at 123 K using graphite-monochromated Mo-Kα radiation. The crystal structure has been validated and deposited at the Cambridge Crystallographic Data Centre with the deposition number CCDC 876507. The refinement was carried using the multipolar model of Hansen and Coppens [2]. We have explored systematically the main molecule planes. The different sections show clearly the accumulation of the electron charge density along the chemical bonding. The oxygen lone pairs have been perfectly localized. The charge density function has been used for the calculation of the molecular dipole moment and the electrostatic potential around the molecule [3]. The obtained results show clearly the nature of electron charge transfer in the DMACB compound.
Accurate structure refinement from 3D electron diffraction data
Authors: Palatinus Lukáš , Corrêa Cinthia , Mouillard Gwladys , Boullay Philippe , Jacob Damien
Published: November 2015

Structure determination from electron diffraction data has seen an enormous progress over the past few years. At present, complex structures with hundreds of atoms in the unit cell can be solved from electron diffraction using the concept of electron diffraction tomography (EDT), possibly combined with precession electron diffraction (PED) [1]. Unfortunately, the initial model is typically optimized using the kinematical approximation to calculate model diffracted intensities. This approximation is quite inaccurate for electron diffraction and leads to high figures of merit and inaccurate results with unrealistically low standard uncertainties. The obvious remedy to the problem is the use of dynamical diffraction theory to calculate the model intensities in structure refinement. This technique has been known and used before, but it has not become very popular, because good fits could be obtained only for sufficiently perfect and sufficiently thin crystals. It has been shown recently on several zone-axis patterns [2] that the quality of the refinement can be improved by using precession electron diffraction. In the present contribution we demonstrate that the same approach can be successfully used to refine crystal structures against non-oriented patterns acquired by EDT combined with PED (PEDT in short). Because the PEDT technique provides three-dimensional diffraction information, it can be used for a complete structure refinement. Several test examples demonstrate that the dynamical structure refinement yields better figures of merit and more accurate results than the refinement using kinematical approximation.
Structural analysis of Ni3Si2by EDT and dynamical refinement
Authors: Corrêa Cinthia , Klementová Mariana , Palatinus Lukáš
Published: November 2015

Transition metal silicides are known for properties such as low resistivity, high melting point, low cost and low toxicity, which are of great interest for applications in current silicon nanotechnology such as nano-complementary metal-oxide semiconductor (CMOS) devices, photovoltaics and ohmic contacts. In all these technologies the materials are used on nanoscale. To gain better insight into their properties, it is necessary to be able to determine the structure of the nanoparticles of these materials. Electron diffraction tomography combined with the precession electron diffraction (PED) are ideal techniques for structural analysis of nanocrystals. In this work Ni3Si2 nanowires with diameter of 25 nm were analyzed by EDT both with and without PED. The structure was refined using the kinematical and dynamical diffraction theory. The results show that the best results can be obtained of EDT and PED.
TEM Random & Ultra-fast Precession ED Tomography for analysis of nm crystals
Authors: Nicolopoulos Stavros , Gemmi Mauro , Eggeman Alexander , Midgley Paul , Galanis Athanassios
Published: November 2015

Since the invention of Precession Electron Diffraction (PED) in Transmission Electron Microscopy (TEM) by Vincent & Midgley [1] in 1994 and mainly after the introduction of dedicated PED devices to different TEM, the structure of various nano-sized crystals have been solved by Electron Crystalography. The most popular technique that was recently developed based on beam precession is the 3D Precession Diffraction Tomography (PEDT) [2]. A series of ED patterns are collected every 10while the sample is tilted around the goniometer axis. By the automatic measurement of ED intensities (ADT 3D software), the unit cell, crystal symmetry and the detailed crystal structure can be determined. A large number of crystal structures, such as complex metals, alloys, organic pigments, MOF, catalysts etc., have been solved by the 3D PEDT technique. A drawback of 3D PEDT (especially for beam sensitive materials) is the long acquisition times (45–120 min), due to the time consuming step of tracking the crystal under the beam during tilting. To deal with this problem, we have developed two novel approaches: the Random Electron Diffraction Tomography (rPEDT) technique and the Ultra-Fast 3D diffraction tomography (UF PEDT) [3]. By rPEDT technique, a sample area (few microns), where several crystals in different (random) orientations are present, is scanned rapidly using an ASTAR precession device (NanoMEGAS SPRL). PED patterns of all scanned crystals are collected by a fast speed CCD camera (up to 120 frames/sec; 8/12 bit). Concerning UF PEDT, the data acquisition time can be 10-20 times faster compared to hitherto 3D PEDT procedure. UF PEDT can be applied when the crystal shift is stable and reproducible during tilting the sample for a specific tilt range. Thus, such crystals can be tracked by shifting the beam following the crystal displacement during tilting (using ASTAR beam scanning). Obtained PED patterns can be recorded with a fast CCD camera, while crystal is tilted. As a conclusion, rPEDT and UF-PEDT can be considered as breakthrough techniques in electron crystallography as they can be performed in any commercial TEM. Both techniques reduce considerable 3D intensity data acquisition time, and allow the analysis of unknown compounds, including beam sensitive organic crystals, as fast techniques prevents crystal beam damage. The authors acknowledge financial support from EU ESTEEM-2 project (European Network for Electron Microscopy www.esteem2.eu).
A new Li-Mn-Ge-O phase solved by combining 3D electron diffraction methods
Authors: Klein Holger , Kodjikian Stéphanie , Lepoittevin Christophe , Ding Lei , Colin Claire , Darie Céline , Bordet Pierre
Published: November 2015

Pyroxene compounds are a common form of natural minerals and have been studied as such for a long time. More recently the research on quasi-one-dimensional magnetic and multiferroïc materials has renewed the interest in pyroxenes of the stoichiometry AMX2O6 (A = alkali metal, M = transition metal, X = Si or Ge), since the magnetic M3+ ions form chains. Chemical substitution on the A and M sites can change the magnetic coupling along these chains making this system a rich field for the exploration of new phases of interesting magnetic properties [1]. In this work we report the discovery of a new phase in the Li-Mn-Ge-O system. A HP-HT solid state reaction was performed on a mixture of nominal stoichiometry LiMnGe2O6 during 1 h at a temperature of 8500C and a pressure of 3 GPa in a belt press. Powder X-ray diffraction yielded a diffractogram that could not be indexed by known phases of this system. An electron diffraction study in a transmission electron microscope was conducted in order to identify any unknown phases. In the case of structures that promise interesting properties a more targeted synthesis can then be undertaken. For the purpose of this work, we studied one of several unknown phases in the powder in more detail. From standard selected area electron diffraction the unit cell was determined to be triclinic with cell parameters a = 2.51 nm, b = 1.30 nm, c = 1.30 nm, α = 96.00, β = 98.80and γ = 80.80. No comparable unit cell could be found in the databases neither in this system nor with different A, M or X ions. Intensities were recorded by in-zone axis precession electron diffraction and by electron diffraction tomography. Combining the data from both methods yielded the first model of the structure which we will present here.
Combing electron diffraction techniques for structure solution
Authors: Stewart Andrew
Published: November 2015

The last few years have seen a revolution in the field of 3D electron diffraction or diffraction tomography. We have moved from only acquiring a few low index zone axis patterns to full tomographic data sets recording all accessible areas of reciprocal space. These new larger data sets have made it easier for structure solution techniques such as direct methods from the x-ray world to be applied to the electron diffraction data for structure solution. While structure solution with tomographic electron diffraction is non trivial when compared to the x-ray case it is significantly easier than it was a few years ago. Mugnaioli et al. We are now in a situation where the most difficult and time consuming step can be the assignment of the space group to a data set. Electron diffraction has many advantages over the x-ray case in terms of the manner in which we can manipulate the electron beam. This allows the collection to convergent beam diffraction (CBD) or large angle convergent beam diffraction (LACBED) patterns, via the recently developed technique by Beanland et al. These techniques can make the assignment of space group significantly easier affair, and the path to structure solution a lot smoother. We will present the combination of data from tomographic, selected area (SA) and nano-beam (NBD) datasets, with diffraction from tomographic LACBED experiments where using the strengths of each technique can be leveraged for a much quicker route to structure solution.
Single Crystal 3D Rotation Electron Diffraction from Nano-sized Crystals
Authors: Zou Xiaodong
Published: November 2015

Electron crystallography is an important technique for structure analysis of nano-sized materials. Crystals too small or too complicated to be studied by X-ray diffraction can be investigated by electron crystallography. However, conventional TEM methods requires high TEM skills and strong crystallographic knowledge, which many synthetic materials scientists and chemists do not have. We recently developed the software-based Rotation Electron Diffraction (RED) method for automated collection and processing of 3D electron diffraction data. Complete single crystal 3D electron diffraction data can be collected from nano- and micron-sized crystals in less than one hour by combining electron beam tilt and goniometer tilt, which are controlled by the RED – data collection software.3 The unit cell, possible space groups and electron diffraction intensities can be obtained from the RED data using the RED data processing software. The figure below illustrates the data collection and data processing of a zeolite silicalite-1 by RED. 1427 ED frames were collected in less than 1 hour from a crystal of 800 x 400 x 200 nm in size. A 3D reciprocal lattice of silicalite-1 was reconstructed from the ED frames, from which the unit cell parameters and space group were determined (P21/n, a=20.02Å, b=20.25Å, c=13.35Å, alfa=90.130, beta=90.740, gamma=90.030. It was possible to cut the 3D reciprocal lattice perpendicular to any directions and study the reflection conditions. The reflection intensities could be extracted. The structure of the calcined silicalite-1 could be solved from the RED data by routine direct methods using SHELX-97. All 78 unique Si and O atoms could be located and refined to an accuracy better than 0.08 Å. The RED method has been applied for structure solution of a wide range of crystals and shown to be very powerful and efficient. Now a structure determination can be achieved within a few hours, from the data collection to structure solution. We will present several examples including unknown inorganic compounds, metal-organic frameworks and organic structures solved from the RED data. Different parameters that affect the RED data quality and thus the structure determination will be discussed. The methods are general and can be applied to any crystalline materials.
1D to 2D Na-Ion Diffusion Linked to Structural Transitions in Na0.7CoO2
Authors: Medarde Marisa , Mena Mattia , Gavilano Jorge , Pomjakushina Ekaterina , Sugiyama Jun , Kamazawa Kazuya , Pomjakushin Vladimir , Sheptyakov Denis , Battlog Bertram , Ott Hans-Rudolf , Mansson Martin , Juranyi Fanni
Published: November 2015

One of the most important scientific problems faced by our society is how to convert and store clean energy. In order to achieve a significant progress in this field we need to understand the fundamental dynamical processes that govern the transfer of energy on an atomic scale. For many energy devices such as solid-state batteries and solid-oxide fuel cells, this means understanding and controlling the complex mechanisms of ion diffusion in solid matter. Because of the unusual evolution of correlated electronic properties (frustrated magnetism and superconductivity), the layered Co-oxide family NaxCoO2 (0<x<1), object of this work, has been extensively studied during the last decade. More recently it has also attracted the attention of applied sciences, mainly because of its structural similarity with LixCoO2, one of the most common Li-ion battery electrodes. In view of the larger abundance of Na in the earth crust with respect to Li, Na-ion batteries enjoy an increased attention. Hence we decided to investigate the Na-ion diffusion in this material, whose possible use as cathode for solid-state rechargeable batteries has recently been proposed [1]. The present study reports the observation of a crossover from quasi-1D to 2D Na-ion diffusion in Na0.7CoO2. High resolution neutron powder diffraction data indicate the existence of two structural transitions at T1=290K and T2=400K [2]. We present here evidence indicating that both transitions are closely related to changes in the Na-ion mobility. Analysis of the anomalies in the Na-Na distances, the Debye-Waller factors and the scattering density in the paths connecting neighbouring Na sites strongly suggest that Na-ion diffusion starts at T1, although for T1<TT2, coinciding with the equalization of all first-neighbor Na-Na distances in the structure [2]. These findings provide new insight on the subtle mechanisms controlling the Na-ion diffusion in the NaxCoO2 family and could be used for the design of related energy materials with improved functional properties. Fig. 1. Fourier difference maps of the z = 0.25 Na planes at T = 50, 320 and 450 K showing the evolution of the residual scattering density in the paths connecting the Na1 and Na2 sites (from ref.[2]).
Electrochemical Conversion: Beyond the First Cycle
Authors: Kinnibrugh Tiffany , Wiaderek Kamila , Borkiewicz Olaf , Pereira Nathalie , Amatucci Glenn , Chupas Peter , Chapman Karena
Published: November 2015

Conversion based electrode materials offer increased energy storage compared to conventional intercalation materials due to the multiple electrons that reacts per metal ion. However, loss in capacities upon repeated cycling has limited the development of this technology for commercial application. Most structural studies focus on the first discharge-charge cycle [1,2,3]. To understand the loss in capacities with repeated cycling, studies must be extended beyond the first cycle. In conversion reactions, large structural transformations occur such that the electrode is reduced to the nanoscale. Pair distribution function (PDF) analysis is well suited to characterize the structural changes occurring in such nanomaterials. Conversion based iron fluorides (FeF3, FeF2, and FeOF) have been a focus of both structural and mechanistic studies [1,2,3]. An in-depth PDF analysis of what happens beyond the first cycle will be presented for these.
Analysis of processes in Li-ion batteries by time-of-flight neutron diffraction
Authors: Bobrikov Ivan , Balagurov Anatoly , Hu Chih-Wei , Lee Chih-Hao , Deleg Sangaa
Published: November 2015

Ex-situ and in-situ neutron diffraction experiments were performed at HRFD time-of-flight (TOF) diffractometer (IBR-2 long-pulsed reactor, JINR) to characterize the entire battery system based on LiFePO4 and V-added LiFePO4 electrodes during electrochemical cycling and to find additional information about crystal structure of electrodes. Another purpose of this work was checking possibilities for in-situ experiments with real Li-ion batteries at the IBR-2 pulsed reactor. An important advantage of TOF method is the possibility to work at the fixed geometry of the experiment, which allows selecting the optimal battery orientation relative to the directions of the incident and scattered neutron beams and, thus, to minimize the difficulties associated with complex internal structure of the battery. It was shown that charge/discharge process of Li-based real Li-ion battery can be effectively studied by TOF technique at the IBR-2 pulsed reactor. Three full charge/discharge cycles were realized at room temperature (~170C) with slow rate. The step-like appearance of several LiCn phases was observed and the volume fractions of LiFePO4 and FePO4 structural phases at different states of charge were determined. The analysis of changes in cathode material microstructure when doped with vanadium showed a significant increase in the density of defects, which correlates with better electrochemical properties of V-added LiFePO4 compared to pure LiFePO4.
Operando studies of nanoscale olivine cathodes for Li-ion batteries
Authors: Ravnsbaek Dorthe , Xiang Kai , Xing Wenting , Gionet Paul , Chiang Yet-Ming , Chupas Peter , Chapman Karena , Chiang Yet-Ming
Published: November 2015

Compounds of interest for ion storage in advanced batteries frequently exhibit phase transformations, driven by large and variable electrochemical driving forces inherent to practical use. Understanding how materials variables (e.g. composition, nanoscale-crystallite size and dynamic electrochemical conditions) affect the phase transition is of vital importance for practical applications as the reversibility and stability of these structural transformations determine the energy, power, and lifetime of the system. Due to its outstanding power, safety and cycle-life olivine LiFePO4 (LFP) has during the past decade become a widely used, and one of the most well-studied, lithium ion battery cathode materials. It is well-established that for LiFePO4 the storage/release of lithium is accompanied by a first-order phase transition between lithiated and delithiated states. However, it would be a mistake to conclude that the behavior of pure LFP is representative of all olivines, in particular the vast range of doped and mixed-metal olivines that are also of interest for their advantageous electrochemical properties.1,2 Utilizing operando synchrotron radiation powder X-ray diffraction (SR-PXD), we demonstrate here, by systematic screening of the electrochemical driven phase transitions in a series of LiMnyFe1-yPO4 (y =0.1-0.8) powders, a completely different phase transformation mode dominated by formation of metastable solid solutions for nanoscale LMFP compared to the binary lithiation states within the extremely well-studied case of LFP. Through Rietveld refinement the misfit strains during phase transformations are examined, revealing small elastic misfits between phases within the extended solid solution regime. On the basis of the time- and state-of-charge dependence of the olivine structure parameters, we propose a coherent transformation mechanism, and finally, we bring evidence that the observed metastability is enabled by particle size reduction to the nanoscale.
X-Ray Diffraction of Magnetically Oriented Microcrystals of Protein
Authors: Tsukui Shu , Kimura Fumiko , Mizutani Kimihiko , Mikami Bunzo , Kimura Tsunehisa
Published: November 2015

Elucidation of the three-dimensional structure of biomolecules is of great importance because the three-dimensional structure is closely related to biological functions. X-ray single-crystal analysis is powerful method to analyze the structure, but it is sometimes difficult to grow a crystal sufficiently large for conventional or even synchrotron single-crystal X-ray measurement. We recently reported on a magnetically oriented microcrystal array (MOMA) [1] that is a composite in which microcrystals are aligned three-dimensionally in polymer matrix. Microcrystals are suspended in an ultraviolet-curable monomer and rotated non-uniformly in a static magnetic field to achieve three dimensional crystal alignment. Then, the monomer is photopolymerized to maintain the achieved alignment. We have successfully demonstrated that X-ray single crystal structure determinations through MOMA are possible for low molecular weight compounds [2] as well as protein. [3] However, the method with MOMA has two drawbacks: (i) the sample microcrystals cannot be recovered from a MOMA, which is especially serious problem in case of proteins, and (ii) the alignment is deteriorated during the consolidation process, causing low resolution. In this study, we attempt to solve these problems. First, we use a water-soluble sol as microcrystalline media and consolidate the alignment by gelation, which makes the recovery of microcrystals possible. Second, a magnetically oriented microcrystal suspension (MOMS) is used for in-situ X-ray diffraction measurement, which makes the sample recovery possible and enhances the resolution. We use lysozyme as a model protein for both cases. The in-situ method with in-house X-ray diffractometer gave diffraction spots about 3.0 Å resolutions. We plan to perform the same experiment at SPring-8.
Low Resolution Refinement with ProSMART, COOT and REFMAC5
Authors: Thorn Andrea , Nicholls Rob , Emsley Paul , Long Fei , Murshudov Garib
Published: November 2015

Membrane proteins and large assemblies are currently a major focus of molecular biology and molecular medicine. Due to their size and flexibility, these structures may only yield poor quality crystals for which diffraction intensities can be measured to merely mid-low resolution. Nevertheless, these data contain valuable structural information. Here, it will be shown how new features in COOT [1], REFMAC5 [2] and ProSMART [3] can help to exploit low resolution data for model building and refinement, as well as aid model validation. Refinement at low resolution can be stabilised with regularisers, such as jelly-body and external restraints. These allow to routinely obtain good quality models even in cases where only low-resolution data are available (e.g. >3Å). External restraints (available for protein and DNA/RNA) exploit structural prior knowledge, utilising the assertion that local interatomic distances should agree with previous observations. Sources for such prior knowledge include isomorphous and homologous structures, hydrogen bonding patterns, and typical conformations of secondary structure elements. Importantly, global rigidity is not enforced by these restraints – the approach presented allows for dramatic conformational differences between target and reference models. Consequently, restraints may be generated using homologous reference models resolved in different crystal forms. COOT facilitates model building at low resolution by removing degrees of freedom through so-called "backrub rotamers" and torsion angle restraints, as well as providing semi-automatic building options such as model morphing and jiggle fit . Map sharpening and blurring, now available in both COOT and REFMAC5, can be employed to provide further insight regarding the validity of a model, as well as aiding the model building process. General guidelines for the application of these features are provided, along with examples demonstrating their usage.