bluuebunny/crossref_metadata_2025 huggingface dataset:
High-pressure environments of single crystal neutron diffractometer SENJU/J-PARC
Authors: Munakata Koji , Nakao Akiko , Osakabe Toyotaka , Kiyanagi Ryoji , Kaneko Koji , Ohhara Takashi , Hanashima Takayasu , Oikawa Kenichi , Tamura Itaru , Kawasaki Takuro , Komatsu Kazuki , Uwatoko Yoshiya
Published: November 2015

High-pressure technique is a powerful tool for physical property measurements and structural analyses as well as other external conditions, such as magnetic fields and temperatures. In the field of neutron experiments, measurements under high-pressure conditions are also useful and attractive; because pressure is one of important thermodynamic parameter that can be used to tune magnetic property, crystal field, and other parameters to obtain insight into the microscopic physics of many phenomena. SENJU have been constructed for a single crystal time-of-flight neutron Laue diffractometer at beamline 18 (BL18) of Materials and Life Science Experimental Facility (MLF) at Japan Proton Accelerator Research Complex (J-PARC) [1], designed in consideration of precise crystal and magnetic structure analyses for small size single crystals, 1 mm3 or less in volume: and also taking account of the neutron diffraction measurements under multiple extreme conditions. In this research we are planning to introduce high-pressure sample environments into SENJU. Two types of compact high-pressure cells have been prepared, one is clamp type piston-cylinder cell made of copper-beryllium alloy (< 2 GPa), and the other is clamp type opposite anvil cell, can be expected to reach maximum pressure of 10 GPa. A taurine single crystal (3 mm3) was enclosed in the piston-cylinder pressure cell together with deuterated glycerol (pressure transmitting medium) and pressurized up to 1 GPa. Accelerator power of J-PARC was 300 kW and the exposure time was 6 hours. We can observe many distinct Bragg reflections from the sample crystal (taurine) even through the pressure cell body, as shown in the figure. In this presentation, we will show more details and current status of high-pressure sample environments in SENJU.
Transformation pathways of structural transitions between BaMg(CO3)2polymorphs
Authors: Miletich Ronald , Pippinger Thomas , Effenberger Herta , Hofer Gregor , Lotti Paolo , Merlini Marco
Published: November 2015

In-situ investigations on BaMg(CO3)2 (= α-phase, space group R-3c) by means of single-crystal diffraction and Raman spectroscopy yield the existence of novel structural polymorphs at high-pressure (γ-phase, C2/c) and high-temperature (β-phase, R-3m) conditions. Isothermal hydrostatic compression at room temperature yield a high-pressure phase transition at Pc ≍ 2.3210.04 GPa, which is weakly first order in character and reveals significant elastic softening of the high-pressure form (α: K0 = 66.212.3 GPa, dK/dP = 2.011.8; γ: K0 = 41.910.4 GPa, dK/dP = 6.110.3). X-ray structure determination confirms a distorted but topologically similar crystal structure of the γ-phase, with Ba in twelve-fold and Mg in octahedral coordination together with characteristic CO3 units. Based on the experimental series of in-situ HPHT data points, the phase boundary of the α-to-γ-transition was determined with a Clausius-Clapeyron slope of 9.8(7) × 10-3 GPa K-1. In-situ measurements of the X-ray intensities carried out to identify the nature of the structural variation correspond to the previously reported transformation from α- to β-BaMg(CO3)2 at 343 K and 1 bar. The investigations revealed, in contrast to all X-ray diffraction data recorded at 298 K, the disappearance of the superstructure reflections and the observed reflection conditions confirm the anticipated R-3m space-group symmetry. The pathway of structural transformation follows a typically displacive fashion, involving exclusively positional shifts of the oxygen atoms for the α-β-transformation. In contrast, in the atomic displacement of the Ba atoms in addition to the three crystallographically independent oxygen sites is responsible for a comparably higher flexibility of the C2/c structure, which explains the origin of the remarkable elastic softening.
High-pressure structural behaviour of CaIrO3polymorphs
Authors: Boffa Ballaran Tiziana , Kularatne Kanchana , Trønnes Reidar
Published: November 2015

The two known polymorphs of CaIrO3 crystallize int the orthorhombic space groups Pbnm and Cmcm. These compounds have been the focus of much research in the Earth sciences community because they are isostructural with MgSiO3 perovskite and post-perovskite structures which are likely the most abundant minerals in the Earth's lower mantle. CaIrO3 post-perovskite is stable at ambient conditions and transforms at 1-3 GPa and at temperatures above 13500C to the CaIrO3 perovskite structure providing an ideal low pressure and low temperature analogue for the MgSiO3 perovskite to post-perovskite phase transformation which occurs at the extreme conditions of 125 GPa and 2500 K. However, in order to assess whether the CaIrO3 compounds can be used as analogues of MgSiO3 phases, a correct knowledge of their atomic structures and their response to changes in pressure and temperature is essential. In this study the structural behavior of both CaIrO3 polymorphs has been investigated using single-crystal X-ray diffraction at different pressures up to 10 GPa. The orthorhombic distortion of CaIrO3 perovskite derives from the cubic perovskite aristotype by tilting of the octahedral units. These tilts are very large and their variation with pressure is clearly different from the tilting reported for other Ca-oxide perovskites giving rise to a much stiffer structure. The CaIrO3 post-perovskite phase has a layered structure consisting of alternating sheets of Ca atoms and distorted IrO6 octahedra which share edges to form rows running parallel to [100]. With increasing pressure the octahedral tilting remains practically constant and compression of the post-perovskite structure occurs as a result of compression of Ca layers. With increasing temperature, instead, the octahedral tilting increases giving rise to smaller distances between oxygens of adjacent octahedra whose repulsion likely causes the transformation to the CaIrO3 perovskite structure.
Structural basis of degenerate specificity of an anti-sugar antibody
Authors: Vashisht Sharad , Kaur Kanwal , Salunke Dinakar
Published: November 2015

Although remarkable specificity of the acquired immune system was clearly being demonstrated, degenerate specificity in immune recognition is often been observed. We had started working on degenerate specificity of antibodies using peptide and sugar as a model system. Both carbohydrate antigen (me-α-Man) and peptide (DVFYPYPYASGS) were established to be equivalent in polyclonal as well as in mAb (2D10) responses (1). Thermodynamic analysis of Ag-Ab interactions had suggested the role of conformational flexibility (2) while crystallographic analysis indicated the importance of plasticity in the interactions (3) of the antigen combining site in the manifestation of molecular mimicry. It has been pointed out that even if the potential for flexibility existed, it was not being utilized while recognizing both ligands. So, in order to address this conundrum we started looking for other sugars and peptides that can bind to the mAb 2D10 with comparable affinities. Crystallographic analysis of 2D10 binding to five different sugars (me-α-Glc, α-Lac, α1-3-Mannobiose, α1-6-Mannobiose, α1-3, α1-6-Mannotriose) has given insights underlying the basis of specificity in molecular recognition. Comparison of all the structures has demonstrated that the antigen combining site for sugars is constituted of CDR H3, L1 and L3 only. All five sugars have an overlapping primary binding site (equivalent to me-α-Man interacting region). This primary sugar binding site has been shown to accommodate similar as well as dissimilar sugars by utilizing plasticity in the interacting residues available in the antigen combining site. The reducing sugar of the similar disaccharides (α1-3-Mannobiose, α1-6-Mannobiose) have been adjusted in the same direction but with utilizing different sets of interacting residues of the antibody paratope. However, the reducing sugar of a dissimilar disaccharide (α-Lac) exploits different paratope space altogether. The trisaccharide (α1-3, α1-6-Mannotriose) was accommodated in the same site by utilizing the conformational flexibility in the paratope region (mainly in CDR L1). This study had demonstrated that an affinity matured antibody may utilize at least three different strategies in order to accommodate structurally similar/dissimilar sugars.
Bovine antibodies with ultra long H3 Complementarity Determining Regions
Authors: Stanfield Robyn , Smider Vaughn , Wilson Ian
Published: November 2015

About 10% of the bovine antibody repertoire exhibit extremely long H3 complementarity determining regions (CDRs). These H3 CDRs are usually described as `loops' in the more familiar mouse and human antibody Fab structures, but the ultra long bovine H3 CDRs are actually small, cysteine-rich protein domains that vary in size from 44 to 64 amino acids. We have recently determined the structures for two bovine antibody Fab fragments, and will describe these, as well as compare them with two other previously determined bovine Fab structures (Wang et al., Cell, 2013). One new Fab has a relatively short H3 CDR region of 44 residues, with just one disulfide bond, while the other boasts one of the longest H3 CDRs, with 63 residues and four disulfide bonds. These H3 CDRs fold to form apparently rigid `stem' regions, that present the disulfide bonded `knob' domain far above the five other Fab CDR loops. Despite extreme diversity in sequence, length and disulfide bonding patterns, the CDRs share structural homology, both in their long stems and in the more variable knob regions.
Ubiquitin-dependent regulation of immune and inflammatory signaling pathways
Authors: Rittinger Katrin
Published: November 2015

Modification of proteins with ubiquitin is a key mechanism for the regulation of a wide range of cellular functions. The outcome of the modification is determined by the way ubiquitin molecules are linked to each other. Linear (M1-linked) ubiquitin chains play an important role in the regulation of immune and inflammatory signaling pathways and contribute to the activation of NF-κB. They are synthesized by the E3 ubiquitin ligase LUBAC (linear ubiquitin chain assembly complex) that is composed of at least three subunits named HOIL-1L, HOIP and SHARPIN. LUBAC belongs to the RBR (RING-inbetween-RING) family of E3 ligases that combine the properties of RING and HECT ligases and act as RING/HECT hybrids. Indeed, we have recently shown that linear ubiquitin chain synthesis proceeds via ubiquitin thioester intermediate formed by the HOIP subunit before subsequent transfer onto the target. I will present a combination of structural and biochemical data that provide a molecular explanation how this unusual E3 ligase complex promotes the synthesis of linear ubiquitin chains with high specificity, regardless of the E2 conjugating enzyme it works with.
Structural insight into autoinhibition of the NOD-like receptor NLRC4
Authors: Hu Zehan , Chai Jijie
Published: November 2015

NOD-like receptor (NLR) proteins constitute a large family of intracellular innate immune receptors. NLRs respond to pathogen-derived signature components or host-derived danger signals, oligomerizing into multiprotein signaling complexes termed inflammasomes that catalyze caspase-1 activation. The NLRC4 (NLR family caspase-recruiting domain (CARD)-containing protein 4) inflammasome is activated by bacterial pathogens carrying the bacterial flagellin or the components of type 3 secretion systems. NAIP (NLR family, apoptosis inhibitory protein) family members dictate the specificity of the NLRC4 inflammasome for different bacterial ligands, with NAIP5/6 and NAIP2 directly recognizing the bacterial flagellin and the T3SS rod protein PrgJ in mice, respectively. We recently solved the crystal structure of NLRC4 in its auotinhibition form. In the current presentation, I discuss the NLRC4 autoinhibtion mechanism and its implications for autoinhbition of other NLR members. I also touch on in vitro reconstitution of the NLRC4 inflammasome and study of its Cryo-EM structure.
Hierarchical structure of CaCO3biominerals – mesocrystals and functionalization
Authors: Schmahl Wolfgang , Griesshaber Erika , Fernandez-Diaz Lurdes , Ziegler Andreas , Kelm Klemens , Maier Bernd , Nindiyasari Fitriana , Jordan Guntram
Published: November 2015

Skeletal parts and teeth of marine organisms, avian eggshells, trilobite and isopod eyes, and many more biomineralized tissues consist of bio-calcite or bio-aragonite crystals. We explore the nano- to micro-scale architectures of these materials by electron backscatter diffraction (EBSD) and complementary techniques. In contrast to their inorganic cousins the biogenic "crystals" are hybrid composites with small amounts of organic matrix controlling morphogenesis and critically improving mechanical performance or other functions. For the biominerals meso-crystal-like structures are ubiquitous, consisting of co-oriented nano-blocks with a mosaic-spread of a few degrees, depending on the organism and on the size of the mesocrystal entity[1, 2, 3]. The nano-mosaic can be attributed to growth by nano-particle accretion from an amorphous or gel-like precursor, where relics of organic matrix cause misorientations between the crystallized nano-blocks. Recently we were able to reproduce this feature in gel-grown calcite [Nindiyasari et al., Crystal Growth and Design, in press]. The mesocrystal-co-orientation spreads on to the micro- and even millimeter-scale, frequently with a fractal nature of co-oriented hierarchical units [Maier et al., Acta Biomaterialia, accepted for publication]. The hierarchically structured morphology of the composite crystal or polycrystal is always directed by organic matrix membranes. Sea urchin teeth show a multiplex composite crystal architecture, where different subunits of engineered shapes, Mg-contents, and small misalignments are essential prerequisites for self-sharpening [1]. The figure shows an EBSD map of dendritic interdigitating calcite crystals in an avian egg shell (color coding for crystal orientation) with an misorientation profile along the grey line.
On the symmetry peculiarities of Bi2WO6single crystals
Authors: Novikova Nataliia , Dudka Alexander , Verin Igor , Van Landeghem Sam , Alekseeva Olga , Kharitonova Elena , Voronkova Valentina
Published: November 2015

Bi2WO6single crystals (a=5.452(1), b=5.433(1), c=16.435(1) Å) were studied by X-ray diffraction (MoKα radiation, diffractometer Xcalibur S, CCD-detector) and electron diffraction techniques. Bi2WO6is an archetypal x=1 member of the Aurivillius family of layered perovskites of general formula Bi2O2Ax+1BxO3x-1. Its high piezoelectric performance and nonlinear optical properties have attracted considerable attention. In addition, these crystals offer high ionic conductivity due to the fast oxygen ion transport. In recent years, this compound has been the subject of intense research in the context of catalytic applications. In this work, the Bi2WO6single crystals were grown from solution in melt of Na2WO4–NaF. There were reflections with indexes 0kl, k=2n+1, in the diffraction pattern, contradicting the sp.gr. P21ab. The structure was solved by direct methods and refined in the sp.gr. R1 (R=3.60%, Rw=3.52%). The group P21ab was found to describe the arrangement of heavy atoms Bi and W only (R=17.5%, Rw=18.68%). The structure can be described by three local groups of symmetry – each atomic layer has inherent symmetry: W atoms and O atoms in equatorial vertices of WO6-octahedra have R11b sp.gr., Bi atoms – Bm11, the rest of O atoms – B11b. The oxygen atoms between two Bi sheets can be also described by B11m sp.gr. Preliminary electron diffraction investigation of the Bi2WO6crystals indicated a presence of small amount of a minority phase B1a1 together with the main P21ab phase. The presence of B1a1 phase can be probably explained by Na content in the crystal originating from the flux. Bi2WO6single crystals were studied earlier [1]. TEM showed coherent intergrowths of two distinct modulated variants having different symmetry. This result couldn't be explained by impurity presence because of investigation of pure crystals grown from melt. The work was done with the partial support of the grant for Leading Scientific Schools NSh-1130.2014.5 and RFBR (proj.14-02-00531a).
New modular oxide structures using lone pair cations as "chemical scissors"
Authors: Batuk Maria , Batuk Dmitry , Abakumov Artem , Hadermann Joke
Published: November 2015

"It is known that lone pair cations, such as Bi3+ or Pb2+ have a flexible coordination environment that enables them to operate as ""chemical scissors"". Their flexibility reduces the strain that would otherwise be present at the interfaces separating structure modules. We have found that in complex oxides it allows many variants of interfaces, for example crystallographic shear planes or (non)conservative twin planes in structures, enabling the synthesis of new structural families. A common characteristic for all these new compounds is the presence of magnetical frustration. As a first example, this concept allowed to introduce crystallographic shear planes into the perovskite structure, a feat that was considered highly unlikely before. This allowed to generate a new anion deficient perovskite based homologous series AnBnO3n-2 (n = 4 - 6). There is magnetic frustration at the crystallographic shear plane separating the perovskite blocks, due to competing FM and AFM interactions. Also incommensurately modulated perovskites can be obtained, for example (Pb,Bi)1-xFe1+xO3-y. These arise by replacing Bi3+ with Pb2+, which introduces an oxygen deficiency, which is then accommodated by periodically spaced CS planes to reduce the coordination of the A-cations at the interface. The flexible coordination environment of Bi3+ and Pb2+ makes them ideally suited for these A cation positions. Other possibilities were encountered in BiMnFe2O6 and Bi4Fe5O13F. In BiMnFe2O6 the Bi3+ induces the existence of a non-conservative twin plane. The result is a new structure type with hcp structured modules. In Bi4Fe5O13F, the Bi3+-cations separate layers with magnetically frustrated Cairo lattices."
Structure Determination of Ho2PdSi3
Authors: Nentwich Melanie , Zschornak Matthias , Richter Carsten , Novikov Dmitri , Meyer Dirk
Published: November 2015

Holmium-Palladium-Silicide Ho2PdSi3 is a member of rare earth-transition metal silicides exhibiting a wide range of interesting magnetic and electrical properties like multiple transition temperatues. The crystal structure results from HoSi2 by substitution of Si by Pd which is ordering commensurably with a 2 × 2 × 8 superstructure confirmed by a previous XRD and a Diffraction Anomalous Fine Structure (DAFS) measurement of the super structure reflection 1/2 1/2 3/8. DAFS is a X-ray method combining the advantages of absorption and diffraction and hence offers the possibility of element and site selective studies. Thus, it was feasible to probe the local environment of Ho and Pd separately. In the following, we will present a comparison of several structure proposals of Ho2PdSi3 with experimental data from beamline E2 and BW1 of the former synchrotron DORIS III at DESY/HASYLAB.
V2C X-Ray Emission Spectroscopy as an Experimental Probe for Ligand Identity
Authors: Delgado-Jaime Mario , De Beer Serena
Published: November 2015

The development of valence-to-core (V2C) x-ray emission spectroscopy as an experimental technique for probing the electronic structure of transition metal complexes relevant to catalysis in chemistry and biology has been one of the main focuses of our group. Our level of understanding on this technique has greatly being benefited from DFT calculations based on the single particle model, as implemented in ORCA [1]. The combination of experiment and computations has allowed us to elucidate the underlying fundamental origins of the factors that affect the spectra and has also allowed us to identify specific fingerprints [2] of a diverse number of ligands and protonation states, including the signature of small light atoms in large proteins [3]. A description of the technique will be presented and their applicability will be demonstrated and discussed using different examples.
Sequence-specific DNA glycosylase found in a restriction-modification system
Authors: Miyazono Kenichi , Furuta Yoshikazu , Watanabe-Matsui Miki , Miyakawa Takuya , Ito Tomoko , Kobayashi Ichizo , Tanokura Masaru
Published: November 2015

Restriction-modification systems consist of genes that encode a restriction enzyme and a cognate modification methyltransferase. It was believed that restriction enzymes are sequence-specific endonucleases that introduce double-strand breaks at specific sites by catalyzing the cleavages of phosphodiester bonds. R.PabI is a type II restriction enzyme from a hyperthermophilic archaea Pyrococcus abyssi that recognizes 5'-GTAC-3' sequence and cleaves DNA duplexes without the addition of a divalent cation. The structural and mutational analyses of R.PabI in our previous work showed that R.PabI forms a homodimer and has a novel DNA-binding fold called a "half-pipe," which consists of a highly curved anti-parallel β-sheet. Because the structure of R.PabI shares no structural similarity to any other protein, the structural basis of the sequence-recognition and DNA-cleavage mechanisms remained unclear. In this study, we report the crystal structure of R.PabI in complex with a DNA duplex containing the R.PabI recognition sequence. The structure of the R.PabI-DNA complex shows that R.PabI unwinds a DNA duplex at a 5'-GTAC-3' site and flips the guanine and adenine bases out of the DNA helix to recognize the sequence. The electron-density map of the R.PabI-DNA complex shows that R.PabI releases adenine bases from the R.PabI recognition sequence. Biochemical assays using HPLC and MALDI-TOF MS spectrometry also support the observation that R.PabI releases adenine bases by hydrolysis. These results show that R.PabI is not an endonuclease but a sequence-specific adenine DNA glycosylase. R.PabI is the first example of a restriction enzyme that shows DNA glycosylase activity. Mutational analysis reveals the active site of the adenine DNA glycosylase activity of R.PabI. The two opposing apurinic/apyrimidinic (AP) sites generated by R.PabI are cleaved by heat promoted β elimination and/or by endogenous AP endonucleases of host cells to introduce a double-strand break.
The First Covalent Organic Framework solved by Rotation Electron Diffraction
Authors: Su Jie , Zhang Yue-Biao , Yun Yifeng , Furukawa Hiroyasu , Gándara Felipe , Duong Adam , Zou Xiaodong , Yaghi Omar
Published: November 2015

Covalent organic frameworks (COFs) represent an exciting new type of porous organic materials, which are constructed with organic building units via strong covalent bonds.[1] The structure determination of COFs is challenging, due to the difficulty in growing sufficiently large crystals suitable for single crystal X-ray diffraction, and low resolution and peak broadening for powder X-ray diffraction. Crystal structures of COFs are typically determined by modelling building with the aid of geometry principles in reticular chemistry and powder X-ray diffraction data. Here, we report the single-crystal structure of a new COF (COF-320) determined by 3D rotation electron diffraction (RED),[2] a technique applied in this context for the first time. The RED method can collect an almost complete three-dimensional electron diffraction dataset, and is a useful technique for structure determination of micron- and nanosized single crystals. To minimize electron beam damage, the RED dataset was collected at 89 K. 3D reciprocal lattice of COF-320 was reconstructed from the ED frames using the RED – data processing software[2]. As the resolution of the RED data only reached 1.6 Å, the simulated annealing parallel tempering algorithm in the FOX software package [3] was used to find a starting molecular arrangement from the 3D RED data. Finally, the crystal structure of COF-320 was solved in the space group of I-42d and refined using the SHELXL software package. The single-crystal structure of COF-320 exhibits a 3D extended framework by linking the tetrahedral organic building blocks and biphenyl linkers through imine-bonds forming a highly porous 9-fold interwoven diamond net.
Y-brass related composite structures : a (3+1)-dimensional space description
Authors: Jana Partha , Lidin Sven
Published: November 2015

The γ-brass Hume-Rothery [1] phases which adopt at VEC values near about 21/13 presently attract attention due to their structural complexity and challenge for the understanding of the underlying stabilization mechanism. Morton, by electron microscopy studies, revealed that the γ-brass regions of Cu-Zn, Ni-Zn and Pd-Zn do not only accommodate the γ-brass phase but also a bundle of structurally related, complex phases with lower symmetry than that of the γ-phase. A bundle of γ-brass related phases in the Zn-rich region of the Ni-Zn, Pd-Zn, Pt-Zn phase diagram is investigated. Their structures have been refined from single crystal X-ray diffraction data in the conventional 3D space group using supercells [2,3]. In the course of a previous investigation of the Pd-Zn system, the structures of two γ-brass related composite compounds- Pd24.3Zn75.7 and Pd21.2Zn78.8 have been described with the (3+1) dimensional space description (superspace group Xmmm(00γ)0s0 with the following lattice parameters, a = 12.929(3) Å, b = 9.112(4) Å, c = 2.5631(7) Å, q = 8/13 c* and a = 12.909(3) Å, b = 9.115(3) Å, c = 2.6052(6) Å, q = 11/18 c*, respectively) [3]. The aim of this study is to represent the structure of these previously reported phases in a coherent, modulated description to make them more readily comparable. A refinement model with a variety of modulation vectors allows to refine any intergrowth structure in the Zn rich region of the M-Zn (M=Ni,Pd,Pt) system. In order to gain an insight into expressions, cause and mechanism and structure-composition relationship for such phases, we also study the impact of substitution on the evolution of the structure of ternary derivatives of M-Zn composite compounds by the use of (3+1) formalism. For instance, substitution of zero-valent palladium and bi-valent zinc by zero-valent platinum in the structure of Pd24.3Zn75.7. This presentation will discuss about the understanding of the complexity of the atomic arrangement through the various modulation which correlates with the variation of composition of the binary and ternary phases.
Incommensurate modulation and phase transformation in a zinc tetra-thiadiazol complex
Authors: Hernandez Kristen , Zeller Matthias , Ben Nasr Cherif , Soudani Sarra
Published: November 2015

The complex of zinc nitrate with 5-(methylthio)-1,3,4-thiadiazol-2-amine crystallizes in a monoclinic setting, space group P21/n, as the tetra-thiadiazol complex [(C3H5N3S2)4(OH2)2Zn](NO3)2, with the water molecules in the apical positions of the pseudo-octahedral complex. At room temperature, the structure is characterized by large thermal libration and disorder of the thiomethyl groups, the nitrate counterions and also of one of the zinc coordinated water molecules. Upon cooling to less than 200 K, disorder and thermal libration reversibly transition to incommensurate modulation, with a q-vector of 0.337 a + 0.460 b and space group P21/n(a0g)s. At 100 K satellites up to second order are visible, and disorder and libration is completely replaced by pronounced modulation. Phase transformation, refinement strategy and parameters and modulation functions used will be presented, and the correlation between disorder above 200 K and modulation functions below this temperature will be discussed.
An Incommensurately Modulated Small-Molecule Crystal Structure
Authors: Brock Carolyn , Parkin Sean , Petříček Václav
Published: November 2015

The first diffraction patterns measured for crystals of 2-chloro-benzo-1,3,2-dithiarsole (C6H4S2AsCl) showed an exceptionally large triclinic cell. After routine data collection the structure could be solved without difficulty; 17 independent molecules were found. A successful conventional refinement of the 170 independent non-H atoms was possible if restraints were applied (similar bond lengths and angles for all molecules; rigid-bond restraints; three sets of 8 anisotropic displacement parameters for the S and C atoms). At convergence R, wR2 were 0.042, 0.107 for 859 variables, nearly 4K restraints and more than 24K unique reflections of which 8774 have I>2σ(I). All displacement ellipsoids were positive definite. The display program Mercury revealed that the molecules form ribbons with a core of closely spaced As and Cl atoms. Because the ribbon is obviously modulated, and because Z' = 17 is both very large and prime, the possibility of an incommensurate structure had to be considered. A new integration of the original frames using EVAL14 gave a modulation vector with components 5.012(2)/17, -3.187(2)/17, 8.016(3)/17; the modulation is clearly incommensurate in the b* direction. Refinement with JANA2006 (811 variables, 11,119 unique reflections, no restraints) gave R, wR2 values 0.045, 0.116. The overall packing is determined by the stacking of the aromatic rings and probably by the segregation of interacting As and Cl atoms. A conventional refinement of a disordered, average (Z' = 1) structure revealed two basic orientations of the C6S2 plane that must be correlated in several directions if impossibly short intermolecular contacts are to be avoided. Along the modulation vector q the orientation of the C6S2 plane varies smoothly, but q is not a direction in which the molecules are in contact. The reasons for the unusual modulation will be discussed, as will the signs that a modulated, high-Z' molecular crystal structure is actually incommensurate.
News from the world of modulated intermetallics
Authors: Lidin Sven , Jana Partha , Müller Carola , Piao Shuying , Ponou Simeon
Published: November 2015

The number of modulated structures with more than one modulation vector is small, and such structures often pose special problems in solving and refining. This talk will be concentrated on three such cases; The 3+4 dimensionally modulated cubic structure of digenite, the 3+2 dimensionally modulated structure of Cu3In2, the 3+2 dimensionally modulated structure of AuZn3 and the 3+2 dimensionally modulated structure of Se(Sn4)2K10. The three former cases are interesting because they are relatively weakly ordered structures where modelling is straight-forward, but the model itself is less than obvious to understand while the latter case appears highly ordered, but presents formal modelling difficulties. From these and previously known multi dimensional cases it would appear that higher order modulations are very prone to disorder. The image shows the hk0 layer from Se(Sn4)2K10.
SENJU, Extreme Environment Single Crystal Neutron Diffractometer at J-PARC
Authors: Ohhara Takashi , Kiyanagi Ryoji , Kaneko Koji , Kawasaki Takuro , Oikawa Kenichi , Tamura Itaru , Nakao Akiko , Hanashima Takayasu , Munakata Koji , Moyoshi Taketo , Kuroda Tetsuya , Yamauchi Yasuhiro , Kawamura Seiko
Published: November 2015

SENJU, a TOF-Laue single crystal neutron diffractometer at the BL18 of MLF/J-PARC, was designed for precise crystal and magnetic structure analyses under multiple extreme environments such as low-temperature, high-pressure and high-magnetic field, and also capable of taking diffraction measurements of small single crystals, less than 1.0 mm3 in volume [1]. Just after the launch of SENJU in March 2012, we newly installed and/or upgraded some sample environment devices. SENJU has a vacuum sample chamber and 37 two-dimensional scintillation detectors. Wavelength of incident neutron is 0.3 - 4.4 Å for the 1st frame and 4.6 - 8.8 Å for the 2nd frame. Because the short wavelength neutron is available and the sample position is covered by large solid angle of the detectors, wide reciprocal space within 30 Å-1 can be measured simultaneously by one measurement. As sample environment devices, 4K cryostat with 2-axes goniometer, longitudinal magnet, high-pressure cell, high temperature furnace and other devices are available or in commissioning. The most popular sample environment device on SENJU is the 4 K cryostat with a fixed-chi type 2-axes goniometer. We adopted piezo-rotators to rotate the sample crystal under vacuumed and cryo conditions. The 2-axes goniometer works stably even at 4 K and the time for cooling was 4.5 hours. A longitudinal magnet was recently installed on SENJU. The lowest temperature was 1.42 K and the maximum magnetic field was 6.85 T. A test diffraction measurement of a CeCoGe3 single crystal (1.5 x 1.5 x 3.0 mm) under 1.5 K and 0.5 T showed that Bragg reflections from the sample was clearly observed and the Bragg peaks of the sample crystal were much higher than the peaks from the magnet itself as shown in the figure. In this presentation, we will show the current status of sample environment devices for SENJU such as cryostat, magnet and other devices.
Compressibility Studies of Zirconium Based Metal-Organic Frameworks
Authors: Hobday Claire , Moggach Stephen , Morrison Carole , Duren Tina , Forgan Ross
Published: November 2015

Metal-organic frameworks (MOFs) are a well-studied class of porous materials with the potential to be used in many applications such as gas storage and catalysis.[1] UiO-67 (UiO = University of Oslo), a MOF built from zirconium oxide units connected with 4,4-biphenyldicarboxylate (BDC) linkers, forms a face centred cubic structure. Zirconium has a high affinity towards oxygen ligands making these bridges very strong, resulting in UiO-based MOFs having high chemical and thermal stability compared to other MOF structures. Moreover, UiO-67 has become popular in engineering studies due to its high mechanical stability.[2] Using high pressure x-ray crystallography we can exert MOFs to GPa pressures, experimentally exploring the mechanical stability of MOFs to external pressure. By immersing the crystal in a hydrostatic medium, pressure is applied evenly to the crystal. On surrounding a porous MOF with a hydrostatic medium composed of small molecules (e.g. methanol), the medium can penetrate the MOF, resulting in medium-dependant compression. On compressing MOF-5 (Zn4O(BDC)3) using diethylformamide as a penetrating medium, the framework was shown to have an increased resistance to compression, becoming amorphous several orders of magnitude higher in pressure than observed on grinding the sample.[3] Here we present a high-pressure x-ray diffraction study on the UiO-based MOF UiO-67, and several new synthesised derivatives built from same metal node but with altered organic linkers, allowing us to study in a systematic way, the mechanical stability of the MOF, and its pressure dependence on both the linker, and pressure medium.
Photoresponsive LB Films under Light Irradiation Observed by Time-Resolved XRR
Authors: Arakawa Etsuo , Voegeli Wolfgang , Kamezawa Chika , Iwami Ryutaro , Shirasawa Tetsuroh , Yamaguchi Yudai , Kamogawa Masashi , Nakata Masataka , Hyodo Kazuyuki , Seki Takahiro
Published: November 2015

Langmuir-Blodgett (LB) films containing azobenzene undergo reversible structural change under light irradiation because of trans-to-cis or cis-to-trans transformations of azobenzene molecules. Such films are a candidate for molecular machines. Time resolved measurements of specular X-ray reflectivity (XRR) curves were carried out for polymer specimens of azobenzene-containing polyvinil alcohol (6Az10-PVA) monolayer LB films on quartz substrates during light (365 nm or 436 nm) irradiation (1 mW/cm2). Measurements were performed with a time-resolution of 10 s using an X-ray reflectometer [1, 2], which can simultaneously measure the whole XRR curves with no need to rotate the specimen, detector or monochromator crystal. Profiles of XRR curves changed as a function of the elapsed time after initiation of the light irradiation reflecting the structural change of the film. Despite of a common belief that the photo-induced structural change occurs directly between the initial and final states, we found an evidence of the existence of the intermediate third structure. We also found that the time needed for changes in XRR curves was several times longer than for optical absorption spectroscopy (OAS) spectra reported with the same irradiation power. Details of such changes of XRR curves and structures of the film will be discussed and compared with the changes of OAS spectra. An XRR curve for the intermediate state of the 6Az10-PVA monolayer LB film specimen separated from the XRR curves measured under 365 nm light irradiation is shown in the figure together with curves for the initial and final states of the same specimen.
A study of perpendicular magnetic recording media using polarized SANS
Authors: Lister Stephen , Venkataramana Vikash , Thomson Thomas , Kohlbrecher Joachim , Takano Ken , Ikeda Yoshihiro , Heyderman Laura , Anghinolfi Luca , Heldt Georg , Lee Stephen
Published: November 2015

The study of thin film magnetic systems that are structured on the nanoscale is an area of intense interest. Small-angle neutron scattering is an extremely powerful probe of nanomagnetism in the bulk, but in thin-film systems the experiments are challenging due both to the small scattering volume available and also to scattering from other sources such as the substrate and sample environment. We have demonstrated that such experiments are however possible in magnetic films as thin as 10 nm. A good example to illustrate this is the case of perpendicular magnetic recording media. These materials are found in all modern magnetic hard drives, the data storage technology that continues to be of tremendous commercial and technological importance. These media are advanced functional multilayered materials, containing an active recording layer of only around 10 nm in thickness. This recording layer is compositionally segregated into 8 nm-sized grains of a magnetic CoCrPt alloy separated by a thin oxide shell, typically SiO2. These media have their magnetic moments oriented perpendicular to the plane of the film. Determining the local magnetic structure and reversal behavior is key to understanding the performance of perpendicular media in recording devices. Polarised SANS has proved to be a very effective tool to measure these materials at a sub-10nm length scales. The signal of interest must however also be distinguished from the scattering from other layers in the structure, some of which are also magnetic. We will present a summary of some recent results on recording media, including measurements of the grain-sized dependent switching with and without the presence of an exchange spring. We will also briefly mention experiments that demonstrate the viability of extending this approach to measurement for lithographically defined structures similar to those for application in bit-patterned media, including 2d artificial spin-ice and structurally glassy arrays.
Powder Crystallography by Combining NMR and Crystal Structure Predictions
Authors: Widdifield Cory , Baias Maria , Dumez Jean-Nicolas , Svensson Per H. , Thompson Hugh , Schantz Staffan , Day Graeme , Emsley Lyndon
Published: November 2015

State-of-the-art work in the field of NMR crystallography for molecular systems at natural abundance has recently focused on the accurate measurement of 1H chemical shift values. We will show how when coupled with crystal structure prediction (CSP) methods, this protocol is well-suited for solving the crystal structures of small to medium sized organic molecules, including cocaine and the de-novo structure determination of AZD8329.[1,2] As complementary 1D and 2D NMR experiments are needed for the 1H assignment process, other information, such as isotropic 13C chemical shift values (δiso) are measured. Unfortunately, 13C chemical shifts are not generally useful for structure determination. Additional NMR parameters that are sensitive to structure would ensure that the structure determination procedure is robust, and would provide more accurate refinements when studying larger or more challenging systems. Here, we measure 13C chemical shift tensors for a variety of prototypical organic pharmaceuticals and use density functional theory computations under the gauge-including projector augmented-wave (GIPAW) formalism to probe whether these parameters may be discriminatory for unit cell determinations and structure determination (notably when added to the CSP + 1H chemical shifts protocol).
FIDEL: A new method for SDPD of nanocrystalline organic compounds
Authors: Schmidt Martin , Habermehl Stefan , Moerschel Philipp , Eisenbrandt Pierre
Published: November 2015

Rietveld refinements generally fail, if the lattice parameters of the structural model differ more than slightly from the correct lattice parameters and the simulated reflections do not overlap with the experimental ones. For molecular crystals, we have developed a more robust fitting algorithm, which uses the cross-correlation function of calculated and experimental powder patterns, and allows a FIt with DEviating Lattice parameters (FIDEL). The method is also successful for nanocrystalline organic compounds showing only 10-20 peaks in their powder diagrams. The FIDEL method has proven to be useful for various applications, including refinements starting from (1) structure data of an isostructural chemical derivative; (2) structure data of an isostructural hydrate or solvate; (3) structure data from measurements at another temperature (e.g. for fitting a room-temperature powder diagram starting with a structure determined from a single-crystal measurement at 100K). FIDEL is also used for determining crystal structures from non-indexed powder diagrams of nanocrystalline organic compounds. Three steps are performed: (1) Prediction of possible crystal structures in various space groups using global lattice-energy minimizations by force-field methods. (2) FIDEL fit of 100 to 600 low-energy structures to the experimental powder pattern. The structure candidate leading to the correct structure results in a significantly better fit than all other structures. (3) Rietveld refinement. The FIDEL method was used to determine the hitherto unknown crystal structure of the nanocrystalline alpha-phase of 2,9-dichloroquinacridone (C20H10Cl2N2O2). The upper part of the figure shows the experimental powder pattern and the simulated powder diagram of one of the predicted low-energy structures before any fitting. The lower part displays the result of the FIDEL fit, before the Rietveld refinement.
Atom Specific Ultrafast Surface Chemistry using a Soft X-ray Laser
Authors: Nilsson Anders
Published: November 2015

Catalysis is central for many chemical energy transformations that occur at interfaces. One of the dreams is to follow catalytic reactions in real time from reactants over various intermediates to products. The prospective for the study of chemical reactions on surfaces using X-ray free-electron lasers (Linac Coherent Light Source, or LCLS, at SLAC National Accelerator Laboratory) will be presented. We induced the hot electron and phonon mediated excitation of adsorbates on Ru(0001) with synchronized excitation by a femtosecond optical laser pulse. We have followed the ultrafast evolution of the bond distortions, weakening and breaking, using x-ray absorption spectroscopy and x ray emission spectroscopy resonantly tuned to the oxygen core level with ultrashort x-ray pulses delivered from LCLS. We can directly follow the time evolution of the molecular orbitals in an atom-specific way on a subpicosecond timescale. Three examples will be shown CO desorption, Oxygen activation and CO oxidation on Ru(0001).
Combatting Drug Resistance: Lessons from the viral proteases of HIV and HCV
Authors: Schiffer Celia
Published: November 2015

Drug resistance negatively impacts the lives of millions of patients and costs our society billions of dollars by limiting the longevity of many of our most potent drugs. Drug resistance can be caused by a change in the balance of molecular recognition events that selectively weakens inhibitor binding but maintains the biological function of the target. To reduce the likelihood of drug resistance, a detailed understanding of the target's function is necessary. Both structure at atomic resolution and evolutionarily constraints on its variation is required. "Resilient" targets are less susceptible to drug resistance due to their key location in a particular pathway. This rationale was derived through crystallographic studies elucidating substrate recognition and drug resistance in HIV-1 protease and Hepatitis C (HCV) NS3/4A protease. Both are key therapeutic targets and are potentially "resilient" targets where resistant mutations occur outside of the substrate binding site. To reduce the probability of drug resistance inhibitors should be designed to fit within what we define as the "substrate envelope". These principals are likely more generally applicable to other quickly evolving diseases where drug resistance is quickly evolving. http://www.umassmed.edu/schifferlab/index.aspx
Transient electron density maps from femtosecond x-ray powder diffraction
Authors: Juvé Vincent , Zamponi Flavio , Holtz Marcel , Woerner Michael , Elsaesser Thomas
Published: November 2015

Ultrashort hard x-ray pulses are sensitive probes of structural dynamics on the picometer length and femtosecond time scales of electronic and atomic motions. Using short hard x-ray pulses as probe in a pump-probe scheme allow to do femtosecond x-ray diffraction experiments [1], which provide transient electron density maps at a femtosecond timescale with a sub-angstrom spatial resolution. In a typical femtosecond x-ray powder diffraction experiment many Debye-Scherrer rings, up to a maximum diffraction angle 2θmax, are recorded for each time delay between the optical pump and the hard x-ray probe. From the diffraction pattern, the change of the diffracted intensity of each rings are monitored. The interference of diffracted x-rays from the many unexcited cells, with known structure factors coming from steady-state measurement, and diffracted x-rays from the few excited cells allows for the detection of the transients structure factors. Problems could arise if the 3D-Fourier transform is directly used because of the abrupt end of the collected information in the reciprocal space (maximum diffraction angle 2θmax). In order to overcome this problem, the Maximum Entropy Method is apply to the data and the transient electron density maps are derived. We apply the femtosecond x-ray powder diffraction technique and the Maximum Entropy Method to study the induced transient polarization by high optical fields on ionic crystals. Such polarizations are connected to a spatial redistribution of electronic charge, which corresponds to a charge transfer between the two ionic compounds [2]. While the charge transfer originates from the anion to the cation in the LiBH and the NaBH4, the LiH exhibits a peculiar behavior: the charge transfer occurs from the cation to the anion. As result from comparison with calculations in the COHSEX framework, this behavior is due to the strong electronic correlations in the LiH [3].