bluuebunny/crossref_metadata_2025 huggingface dataset:
Processing Twinned-Modulated and Composite Structures from CCD / CMOS Images
Authors: Campana Charles , Kaercher Joerg , Chambers John , Petricek Vaclav
Published: November 2015

The Bruker APEX2 [1] software suite includes a full set of crystallographic programs for the solution and refinement of routine crystal structures. In addition to the standard tools required for routine problems, a number of advanced tools are also provided for analysis of non-merohedral twins and modulated structures. These tools include the CELL_NOW [2], SADABS [2] and TWINABS [2] programs and a Reciprocal Lattice Viewer with a q-vector analysis option. The Bruker SAINT [2] program is routinely used for the integration of image data collected with Bruker CCD (APEX II) or CMOS (PHOTON 100) two-dimensional detectors as part of the APEX2 software suite. SAINT has many advanced features for the processing of non-routine datasets. For example, a variety of new options have been implemented to facilitate the simultaneous integration of multiple domains for twinned and composite structures. Higher dimensional crystallography may be used to integrate modulated structures with up to three q-vectors. The output data for modulated structures may be output in either HKL5 or HKLF6 format suitable for input into the JANA2006[3] program. We will present results for one twinned-modulated structure and one composite structure to illustrate the use of the respective advanced options in SAINT to integrate images and JANA2006 to refine the structures.
Temperature-induced phase transitions for amino acids with linear side chains
Authors: Görbitz Carl Henrik , Karen Pavel , Dusek Michal , Petříček Václav
Published: November 2015

Two polymorphs are known to exist under ambient conditions for a number of amino acids (three for glycine). While investigations at high pressure have revealed a number of additional polymorphs, temperature-induced changes are rare. Low-temperature structures with modified side-chain conformations were identified for L- and DL-cysteine. Furthermore, racemates with linear side chains, such as DL-methionine and the non-standard DL-aminobutyric acid (DL-Abu), DL-aminopentanoic acid (DL-norvaline, DL-Nva) and DL-aminohexanoic acid (DL-norleucine, DL-Nle), undergo major crystalline rearrangements on transitions between P21/c and C2/c space groups [1], some of them entropy driven (disordering). As for the corresponding enantio-pure amino acids, we recently described related P21 and I2 structures at 105 K for L-Abu, both with Z' = 4 [2]. A short side-chain C–C bond (1.426 Å) in the only available CSD entry for L-Nle (at 298 K) [3] lead us to suspect that disorder could have been overlooked in the original refinement. L-Nva has not been described previously. We now present single-crystal X-ray determinations between 105 and 405 K for L-Abu, L-Nva and L-Nle, showing phase behavior of unprecedented complexity. For L-Abu and L-Nva we find three different forms in this temperature interval, while four different phases were found for L-Nle. Its known C2 structure with Z' = 1 prevails between 200 and 390 K, and the side chain is indeed disordered 2:1 over two positions. Above 390 K disorder is extensive; the space group remains C2 but cell parameters change. Upon cooling new low-temperature forms are observed at 200 and 170 K. Both are modulated, but to a different extent: data collected at 100 K reveal an almost commensurate phase, while the 180 K phase is fully incommensurate. This is, to our knowledge, the first observation of modulated structures for an amino acid, and also the first observations of major crystalline rearrangements akin to those seen for the corresponding racemates.
The High Magnetic Field Magnet for Neutron Studies at Helmholtz Zentrum Berlin
Authors: Smeibidl Peter , Prokes Karel , Bird Mark , Prokhnenko Oleksandr , Ehmler Hartmut , Tennant David
Published: November 2015

High magnetic fields can create exotic states which challenge our basic understanding of matter. This requires a deep and precise knowledge of the spatial ordering of atoms and associated magnetic moments. Particularly interesting would be to disclose magnetic field dependency of various fluctuations and collective modes. Such information can be obtained from neutron scattering experiments. The Helmholtz Zentrum Berlin (HZB) is known for its sample environment that is available for both internal and external users. Presently, a project that combines dedicated scattering instrument (EXED) with a horizontal hybrid solenoid magnet with tapered 300cones is being finalized at HZB. To achieve an optimal performance, a 13 T superconducting Nb3Sn cable-in-conduit coil is combined with resistive insert coils of 12 T to 18 T (see figure), depending on electric power (between 4.4 and 8.0 MW), to give a maximum of 25 to 31 T. The magnet that has been developed in collaboration with the National High Magnetic Field Laboratory of Florida State University, Tallahassee, FL, USA [1] provides a 50 mm diameter room temperature bore. For sample cooling a 3He cryostat with a pulse tube precooling stage is being developed. The magnet will be permanently mounted at the dedicated time-of-flight instrument EXED at the end of a multispectral neutron guide NL4a, about 76 m away from the neutron source. The EXED instrument is optimized for diffraction under restricted geometrical conditions and is being upgraded to include inelastic option. This unique experimental setup is supposed to play a major role in high-field neutron studies and should be ready for use in early 2015. The contribution describes not only the most important design features of the system, the outline of the building for the technical infrastructure and the status of the installation and commissioning but also the scientific possibilities and limitations of the setup.
Phase transitions and enhanced conductivity of CaC2under high pressure
Authors: Li Kuo , Zheng Haiyan , Tulk Chris. , Ivanov Ilia , Yang Wenge , Guthrie Malcolm , Zhao Yusheng , Mao Ho-kwang
Published: November 2015

Calcium carbide is widely used in the industry for the production of acetylene and other purposes. Its phase transitions under ambient pressure have been studied since 1930s [1]. In recent years, with the development of high pressure science, its phase transitions under high pressure attracted more attentions [2], and its physical properties such as conductivity and superconductivity were focused [3]. Up to now, most of the researches on CaC2 under high pressure are theoretical, and experimental investigations are expected to figure out the structural transitions. In this work, we investigated the structural transitions of CaC2 (phase I, tetragonal, I4/mmm) up to ~30 GPa by powder XRD, neutron diffraction, and neutron PDF analysis on the recovered samples, and measured the conductivity of CaC2 up to ~20 GPa. XRD data are employed to refine the unit cell parameters, based on which the equation of state is fitted. As identified by series of fittings, the tetragonal phase stabilizes up to 10 GPa, above which it has a minor phase transition. The crystal structures were refined by the structural model of phase I with in-situ neutron diffraction data. Both of the bond length of C-C triple bond and the nearest intergroup C...C distance show a turning point at around 10-12 GPa. The critical pressure is in consistent with the predicted phase transition from phase I to phase VI (monoclinic, I2/m), though the phase VI can't be identified and refined with the data under the current resolution. The resistivity of CaC2 decreases from 1000 Ω·m at 2 GPa to 0.0001 Ω·m at 22 GPa, which can be attributed to the compression of intergroup C...C distance from 0.335nm to 0.315nm. The resistivity-pressure curve also shows a turning point at ~10GPa, corresponding to the phase transition. Above 18 GPa, CaC2 starts to amorphize, which is reversible but sluggish. The C22- may get connected to each other, as observed in the neutron PDF data of the recovered sample.
Phase behavior and thermoelastic properties of SnMo2O8under hydrostatic pressure
Authors: Gallington Leighanne , Wilkinson Angus , Rosa de Araujo Luiza , Evans John
Published: November 2015

SnMo2O8has been shown to exhibit very different phase behavior and thermal expansion from previously studied members of the AM2O8family.1At high temperatures, SnMo2O8, ZrW2O8, and ZrMo2O8assume cubic structures with orientationally disordered MO4tetrahedra; however, their behavior is widely divergent at lower temperatures. ZrMo2O8maintains its disordered structure and continues to display negative thermal expansion (NTE). While cubic symmetry is retained when cooling ZrW2O8, its WO4tetrahedra become ordered, and its NTE increases in magnitude. Rapid cooling of SnMo2O8leads to a cubic structure that only minimally differs from its high temperature form.1Slowly heating this cubic phase results in a transformation to a rhombohedral (γ) structure with ordered MoO4tetrahedra that is not isostructural to any known phases of ZrW2O8and ZrMo2O8.1In stark contrast to ZrW2O8, and ZrMo2O8, all SnMo2O8phases exhibit positive thermal expansion.1In the current work, the phase behavior and thermoelastic properties of cubic SnMo2O8under hydrostatic conditions were investigated via in situ synchrotron x-ray powder diffraction in a recently designed sample environment.2Previous studies of ZrW2O8and ZrMo2O8in this environment have shown that pressure-induced disordering of MO4tetrahedra, which only occurred in the orientationally ordered low temperature ZrW2O8phase, was linked to both elastic softening on heating and enhancement of NTE.3At 298K, cubic SnMo2O8is significantly softer (κT =30GPa) than ZrW2O8 (64GPa) and ZrMo2O8(43GPa).3Unlike ZrW2O8, which softens upon heating to 516K (ΔκT = -9GPa), SnMo2O8stiffens (+5GPa) more than ZrMo2O8(+2GPa).3The phase behavior of SnMo2O8under pressure also differs from that of ZrW2O8and ZrMo2O8. Compression elevated the γ->cubic transition temperature significantly: at ambient temperature, this transition occurs at ~435K; at 310MPa, it occurs at ~490K.
Giant pressure-induced volume collapse in the pyrite mineral MnS2
Authors: Kimber Simon
Published: November 2015

Dramatic volume collapses under pressure are fundamental to geochemistry. In transition metal materials, collapses are usually driven by so-called 'spin state' transitions- the interplay between the single-ion crystal field and the size of the magnetic moment. Here we show [1] that the classical S= 5/2 mineral Hauerite (MnS2) undergoes an unprecedented (ca. 22 %) volume collapse driven by a conceptually new magnetic mechanism. Using synchrotron x-ray diffraction, we show that cold compression induces the formation of a disordered intermediate. However, using an evolutionary algorithm we predict a new structure with edge-sharing chains is stable. This is confirmed as the thermodynamic ground state by in-situ laser heating. We show that magnetism is globally absent in the new phase, as the low-spin quantum S=1/2 moments are quenched by dimerisation. Our results show how the emergence of metal-metal bonding can stabilise giant spin-lattice coupling in Earth's minerals.
Spherical neutron polarimetry in multiferroics under external stimuli
Authors: Hutanu Vladimir , Sazonov Andrew , Roth Georg , Oh In-Hwan , Baum Max , Stein Jonas , Braden Markus , Murakawa Hiroshi , Tokura Yoshinori , Bordacs Sandor , Kezsmarki Istvan , Nafradi Balint
Published: November 2015

Study of multiferroics, materials simultaneously having more than one primary ferroic order parameter, is a hot topic of material sciences. The most extensively studied class of these compounds is the family of magnetoelectric multiferroics, where ferroelectricity can be induced by various types of magnetic orderings via the relativistic spin-orbit interaction. As a consequence of the cross coupling between spins and electric polarization, the spectacular control of the ferroelectric polarization by external magnetic field and the manipulation of the magnetic order via electric field can often be realized in these systems. Depending on the symmetry and microscopic mechanism of the multiferroicity the coupling energy between magnetic and electric ordering parameters can significantly vary. Classical neutron diffraction often fails in the precise determining of the complex magnetic structure in the multiferroics due to the presence of the statistically distributed domains in the macroscopic sample. Using spherical neutron polarimetry (SNP), known also as 3D polarization analysis, it is possible not only to precisely determine the complex magnetic structure, but also to investigate in-situ its evolution with external parameters and to control the magnetic domains distribution under the influence of the external electric or/and magnetic field. Here we will present some SNP results on few different multiferroic materials. In some of them, e.g. square lattice 2D antiferromagnet Ba2CoGe2O7, even strong electric field does not change the magnetic order. However rater week magnetic field is sufficient to create a mono-domain structure and to rotate spins in the plane. In other e.g. incommensurate (spiral) magnetic structure of the TbMnO3, solely electric field is sufficient to fully control the chirality of the magnetic structure. In the case of Cr2O3 both electric and magnetic fields should be applied in parallel in order to switch between the different antiferromagnetic domains.
Vortex Lattice Studies in Type-II Superconductors by SANS
Authors: Eskildsen Morten
Published: November 2015

When a type-II superconductor is placed in a magnetic field, it is threaded by swirling whirlpools of electric current known as vortices. The vortices behave like massive entities and provide a unique probe into the nature of the superconducting state in the host material. Furthermore, the collective vortex behavior is of crucial importance for practical applications since vortex motion will lead to dissipation. I will discuss two recent vortex lattice (VL) studies using small-angle neutron scattering (SANS) that exemplify the continuous evolution of this technique. In the first example we used SANS to determine the superconducting anisotropy of Sr2RuO4 (SRO) that is among the few superconductors believed to exhibit p-wave pairing [1]. While there is significant experimental support for unconventional pairing, there is a discrepancy between the anisotropies of the upper critical field and the Fermi surface. Taking advantage of the significant transverse VL field component that arises due to the large anisotropy of SRO we measured the superconducting anisotropy ≍ 60, roughly three times greater than the upper critical field anisotropy. This result imposes significant constraints on possible models of triplet pairing in SRO. In the second example we used a stop-motion technique to study VL transition dynamics in MgB2 [2,3]. Here the VL exhibit extensive metastability in connection with a second order rotational phase transition that cannot be understood based on the single VL domain free energy or vortex pinning. Instead, we have proposed that a jamming of VL domains acting as granular entities is responsible for the metastability. We have performed extensive SANS experiments, as the VL is driven from the metastable to the ground state by small-amplitude AC magnetic field oscillations. This shows a dual power-law behavior indicating a two-step process for the transition to the ground state. Supported by the US Department of Energy (Grant No. DE-FG02-10ER46783).
Development of SuperHRPD, a TOF neutron powder diffractomter at J-PARC
Authors: Kamiyama Takashi , Shuki Torii , Lee Sanghyun , Miao Ping , Yonemura Masao , Ishikawa Yoshihisa , Noda Yukio , Tomiyasu Ryoko
Published: November 2015

SuperHRPD is one of six time-of-flight neutron powder diffractometers in the Materials and Life Science Experimental Facility (MLF) of the Japan Proton Accelerator Research Complex (J-PARC). SuperHRPD is looking at a newly developed high resolution moderator which gives narrow & symmetrical neutron pulse with less tails. With using this moderator and lower repetition rate of 25Hz as well as the flight path shorter than 100 m, a high resolution and wide dynamical range is attainable with limited loss of neutrons. The designed highest resolution of SuperHRPD is as high as Δd/d = 0.035 % in the backward bank. Although unplanned shutdown for two years due to the earthquake and the Hadron radiation accident, SuperHRPD has been upgraded repeatedly by the scattering chamber replacement, the increase of detector solid angle, and the improvement of the detector systems, and improvement of resolution. Sample environments cover 4 K – 1000 K, 10GPa and 14 T with up to d = 40 Å. It is emphasized the magnet was designed to detect tiny structural changes precisely as well as magnetic reflections up to 14 T. After three years of operation, we confirmed higher resolution can reduce systematic errors in structural analyses. The current status of SuperHRPD will be reported.
Diffraction/Scattering Tomography on multi-phase crystalline/amorphous materials
Authors: Alvarez-Murga Michelle , Bleuet Pierre , Lepoittevin Christophe , Boudet Nathalie , Gabarino Gaston , Salamat Ashkan , Tucoulou Remi , Mezouar Mohamed , Hodeau Jean-Louis
Published: November 2015

By suitably combining diffraction/scattering and tomography (DSCT), it is possible to access to selective submicron 2D/3D structural and micro-structural information, which cannot be obtained from separate, independent diffraction and tomography experiments. DSCT is used to discriminate between multi-phase crystalline and amorphous materials, especially when the similarities in densities limit the use of other methods. In addition, this method is sensitive to local variation of the crystalline state, texture, grain size or strains inside the object and can allow simultaneous 3D mappings of such properties. The DSCT phase-selectivity can be easily combined with fluorescence and absorption for added chemical and density resolution allowing multi-modal analyses. As samples can be used in their original state, this method can be applied without cutting or polishing them. Moreover the setup can be adapted with specific sample environments in order to monitor phase and microstructure evolution as a function of an externally controlled parameter with a non-invasive approach. After a first report on in 1998 [1], since 2008 capabilities of DSCT have been demonstrated using x-rays on complex materials as diverse as biological tissue, pigments, Portland cements, Carbon-based materials, Uranium-based nuclear fuel, Ni/Al2O3 catalysts or amorphous systems [2]. More recently, the technique has evolved towards quantitative characterization of the microstructure and stress/strain through either Rietveld or Peak Profile analyses and also pair distribution function techniques (PDF) and their application to nanostructured materials [3]. In this poster contribution, we briefly review the principle and methodology of pencil-beam based x-ray DSCT which is two-fold: (i) selective structural imaging and (ii) extraction of selective scattered patterns of ultra-minor phases.
Crystal Structures of Pigment Red 57:1
Authors: Hammer Sonja , Bekö Sándor , Glinnemann Jürgen , Schmidt Martin
Published: November 2015

Zeitschrift für Kristallographie, Angewandte Chemie, The New York Times, The Sun, El Pais, La Republica, Le Monde, Shanghai Daily, and many more journals and newspapers are printed with Pigment Red 57:1. P.R.57:1 (C18H12CaN2O6S · n H2O, n = 0,1,3) is the most important organic red pigment with a production of more than 50,000 tons per year and an annual sales volume of more than 200 million Euro.[1] In printing ink the pigment is not dissolved, but finely dispersed. Consequently its solid-state properties are maintained. Like most pigments, P.R.57:1 occurs in different crystal phases with different colours. Upon synthesis a trihydrate is formed. Drying at 500C generates a monohydrate with magenta shade, which is used for printing inks. The monohydrate is thermally stable up to temperatures higher than 1900C before it releases water to yield a hygroscopic anhydrous phase with dull dark magenta shade. For all three phases the growth of single crystals is impeded by the low solubility of the pigment in most media. The crystal structures of all three forms were determined from in-house X-ray powder data.[2] The structures were solved by real-space methods with simulated annealing. Subsequently a Rietveld refinement with restraints on bond lengths, bond angles and planar groups was performed. All three phases crystallize in space-group type P21/c, Z = 4. The trihydrate and the monohydrate show eightfold coordination of the Ca ions, the anhydrate a sevenfold one. Apparently the increasing anion-cation interactions lead to the observed colour shift. The arrangement of cations and anions is similar in all three forms. The crystal structures exhibit double layers, one polar, one nonpolar. The polar layer consists of water molecules, calcium ions, sulfonate, keto and carboxylate groups, held together mostly by hydrogen bonds and Coulomb interactions. The nonpolar layer contains naphthalene and toluene moieties.
Structures of 2 new sulfates, Na2M(SO4)2(M=Co, Ni), with rare SO42-coordination
Authors: Fry Allyson , Phelan William , McQueen Tyrel
Published: November 2015

In this study the structures of two new sulfates, Na2M(SO4)2(M=Co, Ni), were determined via both single crystal diffraction and neutron and laboratory X-ray diffraction data. The structural analysis was initiated with single crystal diffraction of the cobalt analogue and while this elucidated the cation positions the oxygen positions were still elusive. Therefore, combined Rietveld refinements of laboratory and neutron powder diffraction data was performed employing both hard constraints and soft restraints. The 5 K neutron data of both compounds are isostructural with the room temperature data as shown by Rietveld refinements. Refinements show that the transition metal ions are in a pseudo octahedral coordination that is better represented by a trigonal bipyramid, where one of the ligands is an edge of a SO42-tetrahedra. This rare coordination of sulfate tetrahedra was corroborated by spectroscopic techniques: UV-vis, Raman, and infrared. Additionally these compounds adopt large unit cells within the space group C2/c: Na2Co(SO4)2vol=4137.17(1)Å3and Na2Ni(SO4)2vol=4080.17(5) Å3.
Combining powder diffraction with TEM for solving modulated structures
Authors: Abakumov Artem
Published: November 2015

In many materials competing interactions of different nature may give rise to incommensurate modulations causing extreme structure complexity. Ab initio solution of the modulated structures even with using high quality synchrotron X-ray and/or neutron powder diffraction data appears to be a very challenging problem due to weakness of the satellite reflections, ambiguity in the determination of the modulation vector(s) and superspace symmetry and difficulties in building the initial model for further Rietveld refinement. These problems can be resolved or, at least, mitigated if the diffraction, imaging and spectroscopic advanced transmission electron microscopy techniques are combined with the analysis of powder diffraction data. Complete reconstruction of the reciprocal space, structure solution using quasi-kinematical electron diffraction data, mapping projected scattering density in the unit cell, visualization of the light atoms, displacive and occupational ordering, mapping chemical composition and coordination number can be utilized to reveal the nature of incommensurate modulations and construct the reliable model for the refinement from powder diffraction data. The benefit of the strategy of combining the powder diffraction data with the reciprocal and real space information obtained using aberration-corrected scanning transmission electron microscopy will be illustrated on the examples of the transition metal oxides: Li3xNd2/3-xTiO3 perovskites with frustrated incommensurately modulated octahedral tilting pattern [1]; perovskites (Bi,Pb)1-xFe1+xO3-y, modulated by crystallographic shear planes [2]; CaGd2(1-x)Eu2x(MoO4)4(1-y)(WO4)4y scheelites with incommensurately modulated ordering of cation vacancies [3].
Why was the structure of the niobium silicate AM-11 so difficult to solve?
Authors: McCusker Lynne , Massüger Lars , Xie Dan , Grässlin Jürgen , Smeets Stef , Baerlocher Christian , Wan Wei , Zou Xiaodong
Published: November 2015

The synthesis of the polycrystalline niobium silicate catalyst AM-11 was first reported in 1998 [1], but its structure proved to be elusive. In 2007 we received two samples from the Aveiro group. At the time, we were looking for a material suitable for the application of the texture method of structure solution, and AM-11 seemed to be ideal for this purpose. One of the samples had needle and the other platelet morphology, and textured samples could be prepared in both cases. The conventional powder diffraction pattern could be indexed on a hexagonal, an orthorhombic or a monoclinic unit cell, so this was the first issue to be resolved. The texture measurements quickly revealed that the crystal system was orthorhombic, but the structure resisted solution. We then tried applying the precession electron diffraction technique in combination with high-resolution powder diffraction data, but beyond confirming the orthorhombic symmetry, these data did not help us to solve the structure. Another attempt was made with a new sample and an improved texture setup, but to no avail. Rotation electron diffraction data and high-resolution transmission electron microscopy images showed that some disorder was present and helped to define the space group, but the structure remained a mystery. The powder charge-flipping routine in Superflip [2], yielded tantalizingly clear electron density maps, but they could not be interpreted sensibly. The unit cell parameters were seen to be related to those of the titanium silicate zorite [3] (one axis doubled in AM-11), so the problem was taken up once again last year. By starting with a simplified zorite framework structure with Nb in place of Ti, and performing what amounts to manual Fourier recycling, the surprisingly simple structure (1Nb, 3 Si, 9 O), which is significantly different from zorite, finally revealed itself. There is some stacking disorder, but the structure is otherwise innocuous. What made it so difficult to solve?
A computational–experimental approach for automated crystal structure solution
Authors: Wolverton Chris
Published: November 2015

Crystal structure solution from diffraction experiments is one of the most fundamental tasks in materials science, chemistry, physics and geology. Unfortunately, numerous factors render this process labour intensive and error prone. Experimental conditions, such as high pressure or structural metastability, often complicate characterization. Furthermore, many materials of great modern interest, such as batteries and hydrogen storage media, contain light elements such as Li and H that only weakly scatter X-rays. Finally, structural refinements generally require significant human input and intuition, as they rely on good initial guesses for the target structure. To address these many challenges, we demonstrate a new hybrid approach, first-principles-assisted structure solution (FPASS), which combines experimental diffraction data, statistical symmetry information and first-principles-based algorithmic optimization to automatically solve crystal structures. We demonstrate the broad utility of FPASS to clarify four important crystal structure debates: the hydrogen storage candidates MgNH and NH3BH3; Li2O2, relevant to Li–air batteries; and high-pressure silane, SiH4.
Preparing for SwissFEL: Exploring the limits of time-resolved X-ray spectroscopy
Authors: Milne Chris , Szlachetko Jakub , Penfold Tom , Chergui Majed , Abela Rafael
Published: November 2015

Using x-ray absorption spectroscopy (XAS) and x-ray emission spectroscopy (XES) to probe laser-excited samples we can obtain excited-state structural and electronic dynamical information not available through other techniques.[1] One of the restrictions of most synchrotron-based implementations of this technique is the three-orders of magnitude mismatch between x-ray and laser repetition rates (MHz Vs. kHz). By using a laser capable of generating significant pulse energies at MHz repetition rates we can eliminate this discrepancy, thus greatly reducing measurement times and enhancing achievable signal-to-noise ratios.[2] Several examples that demonstrate the strength of this technique will be presented, including probing the electron relaxation in photoexcited TiO2 nanoparticles in solution and resolving the dynamical structural changes associated with ligand rebinding in the protein myoglobin under physiological conditions. The ability to extend these types of measurements into the femtosecond regime at Experimental Station A[3] at the SwissFEL hard X-ray free electron laser, which is under construction at the Paul Scherrer Institute (Villigen, Switzerland), will be discussed.
Crystal structure of the Vif-interaction domain of the anti-viral APOBE3F
Authors: Nakashima Masaaki , Kitamura Shingo , Kurosawa Teppei , Ode Hirotaka , Kawamura Takashi , Imahashi Mayumi , Yokomaku Yoshiyuki , Watanabe Nobuhisa , Sugiura Wataru , Iwatani Yasumasa
Published: November 2015

Human cells express a family of cytidine deaminases, called APOBEC3 (A3) (A3A, B, C, D, F, G, and H). The family enzymes, especially A3G and A3F potentially inhibit replication of retroviruses including HIV-1. However, HIV-1 overcomes the A3-mediated antiviral system by expressing a virus-encoded antagonist, viral infectivity factor (Vif) protein. In HIV-1-infected cells, Vif specifically binds with A3 followed by proteasomal degradation of A3. Hence, inhibition of the interaction between A3 and Vif is an attractive strategy for developing novel anti-HIV-1 drugs. To date, we have determined the first crystal structure of A3 with Vif-binding interface, A3C (PDB ID: 3VOW). In addition, our extensive mutational analysis, based on the A3C structure, revealed that structural features of the Vif-binding interface are highly conserved among A3C, DE, and F [1]. However, more recently, Bohn et al. and Karen et al. have shown the crystal structures of mutant A3F C-terminal domain (CTD) which is responsible for the Vif interaction, and have predicted more extended area, including our identified residues, for the interface on the A3F CTD [2][3]. To clarify the Vif-binding interface of A3F, we sought to determine the crystal structure of the wild-type A3F CTD and evaluated contributions of the additional residues for the Vif-interaction interface by virological method. First, we have successfully determined the crystal structure of A3F CTD at 2.75 Å resolution. Furthermore, we have identified four additional residues unique on the A3F CTD but not A3C for Vif interaction, which are located in the vicinity of our previously reported interface. These results demonstrated that the structural features of Vif-binding interface are indeed conserved between A3C and A3F. Taken together, these results will provide the fine-tuned structure information to understand the binding between A3 and Vif and to facilitate a development of novel anti-HIV-1 compounds targeting A3 proteins.
Structural basis for a novel model for myotoxic activity on phospholipases A2
Authors: Fontes Marcos , Fernandes Carlos , dos Santos Juliana , Salvador Guilherme , Borges Rafael , Magro Angelo , Cardoso Fabio , Dreyer Thiago
Published: November 2015

Envenoming due to snakebites is an important public health problem in many tropical and subtropical countries which, in addition to mortality, may result in permanent sequelae as a consequence of local tissue damage, i.e. necrosis and hemorrhage. Toxins that play a leading role in the complex pathogenesis of these feared venom actions have been identified as members of the phospholipase A2 (PLA2) and metalloproteinase protein families. Phospholipases A2 are enzymes responsible for cellular membrane disruption through Ca2+-dependent hydrolysis of phospholipids. A class of these proteins (Lys49-PLA2s) does not show catalytic activity but can exert a pronounced local myotoxic effect that is not neutralized by serum therapy. After more than 20 years of structural, biochemical and biological studies with this class of proteins, its biological mechanism still remain not totally understood. Here, based in a comprehensive study including over than 30 crystallographic structures, Small Angle X-ray Scattering, Dynamic Light Scattering, Isothermal Titration Calorimetry, Biochemical, Bioinformatics, Phylogenic and Myografic experiments, we proposed a complete myotoxic mechanism. This work confirms the biological dimer indicated by recent studies in which both C-termini are in the dimeric interface. In this configuration, we propose that the myotoxic site of these toxins is composed by the Lys 20, Lys115 and Arg118 residues. The extensive structural analysis also include: (i) the function of hydrophobic long-chain molecules as Lys49-PLA2s inhibitors, (ii) the role of Lys122, previously indicated as being responsible for Lys49-PLA2s catalytic inactivity, (iii) a structural comparison of the Ca2+-binding loop region between Lys49 and Asp49-PLA2s, (iv) the importance of Tyr119 residue, (v) the role of different classes of inhibitors and (vi) the role of hydrophobic knuckle. Taking into account all these issues we were able to propose a complete mechanism of action of these proteins and also proposed the different ways to inhibit them. These results may be useful to guide new experiments that can definitively clarify the action mechanism of snake venom PLA2s and lead to the design of structure-based inhibitors to complement the serum therapy.
Structural and thermal analyses of a hydrolysis compound of thalidomide
Authors: Otogawa Kohei , Ogino Yosyisuki , Ishikawa Kazuhiko , Tanaka Makoto , Shiro Motoo , Osaka Tutsuya , Asahi Toru
Published: November 2015

Thalidomide (TD) is a historically famous chiral drug. After prescription as a safe hypnotic, TD was suspected of contributing to teratogenicity, resulting in prohibition of the use of TD. TD and its derivatives, however, have attracted a renewed attention since their therapeutic effects for Hansen's disease and multiple myeloma were demonstrated. Meanwhile TD has been known to suffer from spontaneous hydrolysis with complicated pathways, leading to the production of various metabolites of TD. Therefore, we are now facing the difficulty in specifying the compounds which cause desired and/or adverse effects in the drug mechanism of TD. In a previous study, pure hydrolytic products of TD were synthesized and assayed for production-inhibitory activity of TNF-α, a kind of cytokine that induces inflammation. This study has showed that some products, especially α-(2-carboxybenzamido)glutarimide (CBG), exhibit high potency for the inhibition of TNF-α production compared to original TD. The hydrolytic products of TD thus are found to greatly attribute to the pharmacological effect of TD. For comprehending effects of the hydrolytic products, it is much significant to perform physicochemical analysis of them because their properties are deeply related to molecular stability and interaction with receptor proteins. In this study, we thus aim to investigate the physicochemical properties of CBG employing X-ray crystal structural analysis and thermal analyses. Single crystals of racemic and enantiomeric CBG were grown by solvent evaporation methods. On the crystallization, we chose alcoholic solvents such as methanol and ethanol. Surprisingly, crystals grown from the CBG solutions have indicated the same crystal structure of TD with high reproducibility. This unique result is likely to represent dehydration of CBG in non-aqueous solvents, which has not been reported so far. The detailed mechanism is under investigation.
In-line SEC-SAXS and MALS/DLS/RI for the Analysis of Polydisperse Macromolecules
Authors: Acerbo Alvin , Cook Michael , Miller Bill , Smith Scott , Kriksunov Irina , Szebenyi Doletha , Gillilan Richard
Published: November 2015

Small Angle X-ray Scattering (SAXS) is a powerful tool for the structural analysis of biological macromolecules in solution and has seen a surge in popularity amongst structural biologists in the past decade. In part, this is because SAXS benefits greatly from the sensitivity and throughput that can be achieved at modern high brightness synchrotron sources. However, the critical need for highly monodisperse samples in SAXS analysis can be a challenge, and as such a number of labs have moved to develop in-line Size Exclusion Chromatography (SEC) at the beamline. Real-time SAXS on elution profiles not only improves monodispersity of samples and provides information on possible oligomeric states, but it also offers new modes of data analysis that can take advantage of the inherent concentration profiles underlying elution peaks and distributions of partially resolved species. Efforts to extend the synergy between SEC and SAXS to other biophysical methods are ongoing. The newly commissioned G1 BioSAXS facility at MacCHESS now offers the option of combining real-time SEC-SAXS with multi-angle static (MALS) and dynamic (DLS) light scattering along with refractive index (RI) detection. In this talk we give a brief overview of the performance and capabilities of the new BioSAXS station at MacCHESS with emphasis on detection limits and signal quality. We then discuss how the complementary light scattering techniques can be combined to offer new insights for complex inhomogeneous samples in terms of biological information and data quality assessment. We also discuss the limitations and possible future developments of these approaches as biologists seek to investigate more dynamic systems as well as shorter time scales.
Automation for BioSAXS experiments at BM29 of the ESRF
Authors: Brennich Martha , Round Adam , Pernot Petra , Kieffer Jérôme , De Maria Antolinos Alejandro , Ohlsson Staffan , Maillot Benoit , Gordon Elspeth , McSweeney Sean
Published: November 2015

Small Angle X-ray Scattering (SAXS) experiments of macromolecules (proteins, nucleic acids, ...) in solution can provide a wealth of information concerning structure, dynamics and therefore function. However, correct interpretation of results depends critically on data quality. To achieve this, well defined acquisition protocols and immediate feedback are essential. At beamline BM29 at ESRF, BioSAXS data are acquired in a temperature controlled flow through capillary. Samples and buffers can be loaded into the capillary via a robotic liquid handling sample changer (SC) [1] or by connecting the capillary to the outlet of a size exclusion chromatography (SEC) setup [2]. Samples loaded by the SC can be passed through the beam to avoid unwanted effects caused by radiation damage. All recorded data are immediately analyzed to give user-oriented feedback on estimated molecular weight, size, possible radiation damage and inter-particle effects, quality of background correction, etc. Subsequent downstream analysis, also carried out autmatically, results in the calculation of molecular envelopes for solution structures. The information management system ISPyBB (Information System for Protein crystallography Beamlines and BioSAXS) logs and presents all information on data acquisition and analysis and allows users to easily compare the results of different data acquisitions and to decide whether further measurements or changes of acquisition parameters are necessary. The combination of these tools allows non-expert users to carry out BioSAXS experiments autonomously, thereby making the technique accessible to a broader community.
Single molecule study of cytoskeleton and membrane dynamics
Authors: Sun Yujie
Published: November 2015

Molecular motors are proteins that convert chemical energy directly into mechanical work in the cell, driving many cellular processes. Given their intrinsic unsynchronous nature, single molecule fluorescence and manipulation techniques are nearly the ultimate tools to understand the mechanisms of molecular motors. I will talk about single molecule fluorescence studies of cytoskeleton associated motors, and their roles in cellular trafficking and membrane shaping of intra-cellular structures.
Nuclear Enhanced MEM Used to Analyze Local Distortions in Lead Chalcogenides
Authors: Christensen Sebastian , Bindzus Niels , Christensen Mogens , Brummerstedt Iversen Bo
Published: November 2015

We introduce a novel method for reconstructing nuclear density distributions (NDDs): Nuclear Enhanced X-ray Maximum Entropy Method (NEXMEM). NEXMEM offers an alternative route to experimental NDDs, exploiting the superior quality of synchrotron X-ray data compared to neutron data. The method was conceived to analyse local distortions in the thermoelectric lead chalcogenides, PbX (X = S, Se, Te). Thermoelectric materials are functional materials with the unique ability to interconvert heat and electricity, holding much promise for green energy solutions such as waste heat recovery. The extraordinary thermoelectric performance of binary lead chalcogenides has caused huge research activity, but the mechanisms governing their unexpected low thermal conductivity still remain a controversial topic. It has been proposed to result from giant anharmonic phonon scattering or from local fluctuating dipoles on the Pb site.[1,2] No macroscopic symmetry change are associated with these effects, rendering them invisible to conventional crystallographic techniques. For this reason PbX was until recently believed to adopt the ideal, undistorted rock-salt structure. In the present study, we investigate PbX using multi-temperature synchrotron powder X-ray diffraction data in combination with the maximum entropy method (MEM) and NEXMEM. In addition NEXMEM has been validated by testing against simulated powder diffraction data of PbTe with known displacements of Pb. The increased resolution of NEXMEM proved essential for resolving Pb-displacement of 0.2 Å in simulated data. The figure below shows Pb in the (100) plane for MEM, NEXMEM and the actual NDD of the test structure. Our findings outline the extent of disorder in lead chalcogenides, promoting our understanding of this class of high-performance thermoelectric materials. Furthermore we introduce NEXMEM which can be used for widespread characterization of subtle atomic features in crystals with unusual properties.
New developments in the BayMEM Suite
Authors: Hübschle Christian , van Smaalen Sander
Published: November 2015

The program suite BayMEM consists of the programs PRIOR, BayMEM and EDMA. It is intended to apply the Maximum Entropy Method (MEM) to ordinary and modulated structures[1]. The PRIOR program is intended to calculate the prior density for the MEM calculation, but it has been recently shown that it can be used to calculate the dynamic charge density from multipolar refinements[2] as well. As a new functionality it is now also possible to calculate the electrostatic potential from the dynamic deformation density by the method described by Steward and Spackman[3]. We will present a new MapConverter program which allows to convert electron density stored in different file formats into an other. It is also possible to rearrange and cut the density in such a way, that it is possible, to have clear view of one molecule, not obscured by its symmetry mates, in a molecular viewer like MoleCoolQt for example.
Pseudo-Mackay clusters in the Al-Pd-Co System
Authors: Sugiyama Kazumasa , Suzuki Syota , Simura Rayko
Published: November 2015

A great number of complicated intermetallic compounds were reported in binary and ternary alloy systems of Al with transition metals. Al–Co–Pd is one of the most interesting alloys, since a variety of crystalline phases associated with quasicrystals has been reported [1]. Among these crystalline phases, the structures of ε-phases are closely associated with Al3Pd, which is an important crystalline approximant for the decagonal phase with a period of 1.6 nm. W-phase is another approximant for the decagonal phase and its structural information is useful for understanding the columnar unit in the decagonal phase with a periodicity of 0.8 nm [2]. On the other hand, some crystalline phases associated with the icosahedral phase were also found in this Al-Pd-Co system. C2–phase, R-phase (R¯3: a = 2.91 nm, c = 1.32 nm) and F-phase (Pa3: a = 2.44 nm) are classified into this category. In particular, the structures of R-phase and F-phase consist of a variety of pseudo-Mackay clusters similar to those found in 1/1-AlCuRu and the trigonal χ-AlPdRe. As an example, the structure of R-phase shows two types of pMCs. These pMCs can be ranked by their atomic arrangements of the first shells, nevertheless every outer shell is a harmony of an Al-icosidodecahedron and a Co/Pd-icosahedron. These pMCs interpenetrate each other by sharing edges of Co/Pd-icosahedra and the interstitial space is subsequently filled by the smaller Al-icosahedra around Pd/Al sites [3]. The characteristic structural motifs for R-phase and F-phase readily suggest the importance of pMC as a fundamental structural unit for icosahedral quasicrystals.
In-situ HRTEM observations of growth process of decagonal quasicrystals
Authors: Nagao Keisuke , Nishimoto Kazue , Inuduka Tomoaki , Edagawa Keiichi
Published: November 2015

Quasicrystals possess quasiperiodicity, where the structure cannot be described simply by the repetition of unit cell like conventional crystals. This fact raises the question of how quasicrystals grow, i.e., what physical mechanism makes the growth of quasicrystals possible. While crystals can grow by copying a unit cell via local atomic interactions, nonlocal structural information seems to be required in the growth of quasicrystals. This problem has attracted much attention ever since the first discovery of a quasicrystal in 1984, and several theoretical growth models [1] have been proposed. However, no experimental studies have so far been reported, and it is still unclear whether these theoretical growth models apply to real quasicrystals. In the present study, we have conducted in-situ high-temperature electron microscopic (HRTEM: High-Resolution Transmission Electron Microscopy) observations of the growth process of decagonal quasicrystals to elucidate the growth mechanism. The growth processes of a decagonal quasicrystal of Al70.8Ni19.7Co9.5were observed by HRTEM in the temperature range 1073-1173K. Tiling patterns with edge length of about 2nm were constructed from a series of HRTEM images. They were analysed in the framework of the projection method. Here, we followed the procedures in our previous work [2]. We have already reported the results of some observations and analyses elsewhere [3]. However, the growth processes of them were on a small scale, and the results were indefinite. Recently, we have succeeded in observing a growth process on a massive scale. In this paper, we present the results of this observation and subsequent analyses, and discuss the growth mechanism of the quasicrystal.
Synthesis and thermal stability of Au-based quasicrystals and its approximants
Authors: Kotajima Takahiro , Hiroto Takanobu , Tamura Ryuji
Published: November 2015

Various Tsai-type quasicrystals and crystalline approximants have been found in a variety of systems. These compounds are made of Tsai-type icosahedral clusters. Recently, the existence of long-range magnetic orders was reported in Cd6R and Au-SM-R approximants[1,2]. Therefore, it is of interest to investigate the magnetic properties of new alloys systems which are also composed of Tsai-type clusters. In the present work, in order to search new Tsai-type quasicrystals as well as approximants, we have investigated the phase constitution and phase stability in the Au-In-R(R=rare-earth) systems. In this research, alloys of various compositions were prepared by arc melting and were subsequently annealed under various conditions. The phase constitution and phase stability were investigated by X-ray diffraction and differential thermal analysis. As a result, we have observed the formation of 1/1 approximants in the Au-In-R systems and found that they are stable up to high temperatures of ~1000K. The formation condition and stability of icosahedral quasicrytals will be also reported in the presentation.