bluuebunny/crossref_metadata_2025 huggingface dataset:
Effect of thickness and Si substrate morphology in La0.7Sr0.3MnO3/Si thin films
Authors: Wang Hsiao-Tsu , Wu Mau- Kuen , Shao Yu-Cheng , Wang Yu-Fu , Hsieh Shang-Hsien , Singh Shashi- Bhushan , Chong Cheong-Wei , Lin Jauyn-Grace , Tsai Huang-Ming , Lin Hong-Ji , Lee Jyh-Fu , Pong Way- faung
Published: November 2015

Investigation has been made on atomic, electronic structures and magnetic properties of La0.7Sr0.3MnO3 (LSMO) on Si substrate. The effect of different thickness of LSMO and different morphological [flat and nano-pyramid (NP)] of Si substrate are studied in present work. The result of Mn K-edge extended x-ray absorption fine structure indicates the more disorder of local atomic structure of first shell (Mn-O bound) in the thinner LSMO/Si film. The Mn L3,2-edge x-ray absorption near-edge structure shows the presence of Mn2+ ion on the sample. Furthermore, the Mn L3,2-edge x-ray magnetic circular dichroism reveals that the thinner film (LSMO/Si) has highest magnetic moment, in comparison to that of thick LSMO/Si and LSMO/Si-NP samples. This finding suggests that the appearance Mn2+ may play an important role in magnetic behavior of hetero-junction LSMnO/Si and Si-NP.
EXAFS studies of the metal coordination environments in mixed Ti/Zr silicates
Authors: Hall Reece , Readman Jennifer
Published: November 2015

Microporous materials have a wide range of commercial uses from ion-exchangers to catalysts and have been used in the treatment of nuclear waste. The acidity associated with legacy waste pools often limits the effectiveness of these zeolites due to a loss of crystallinity. Microporous titanium silicates display different structural characteristics compared to conventional zeolites. Sitinakite, KNa2Ti4Si2O13(OH)·4H2O and the synthetic niobium doped analogue are being used as ion-exchange materials for the removal of Cs+and Sr2+from nuclear waste . Natisite is a layered titanium silicate with titanium in an unusual 5 coordinate square pyramidal environment. Natisite, Na2TiSiO5, crystallises in the tetragonal space group P4/nmm. [1, 2] A series of samples have been prepared with varying levels of zirconium doping ranging from 10% to 50%. Powder x-ray diffraction (PXRD) showed no obvious impurities attributed to zirconium containing phase. X-Ray Fluorescence (XRF) was carried out and showed the presence of zirconium indicating that doping had been successful. Ion-exchange experiments were carried out on the doped and undoped natiste samples using Cs and Co containing solutions. It was found that increasing the levels of zirconium increased the affinity towards Cs with the undoped materials taking up very little Cs. The rate of exchange with Co seemed to increase as the zirconium level was increased within the sample. This suggests that the presence of zirconium in the framework has a considerable effect on the ion-exchange properties of natisite. EXAFS has been useful in determining the coordination environment of titanium and zirconium in order to help fully understand the chemistry of this material. Also it has helped with determining if the exchanged Cs and Co have a preference for the sites close to Zr rather than Ti. It is therefore believed that the inclusion of zirconium in the natisite framework has potential use as an ion-exchanger in the nuclear industry.
The $100 million question: Do we need to apply informatics to crystallization?
Authors: Newman Janet , Fazio Vincent , Schmidt Breon , Peat Thomas
Published: November 2015

The PDB is currently growing at a rate of about 9000 structures annually, and 90% of these have been determined by X-ray diffraction methods. Each structure is the result of one or more crystals. Not every protein crystallises nor do all crystals diffract well enough; it has been estimated that of every 10 proteins that are purified, four will show some sign of crystallisation and one will crystallise robustly enough to obtain a structure1. Using these numbers, and making some educated guesses (for example, that most proteins are tested in 1000 crystallisation trials1) these 8000 structures represent 80,000 purified proteins, and 80,000,000 crystallisation trials which are set up each year. The cost of consumables, chemicals and direct labour to set up those trials varies, but can be estimated to be $0.1- $1, excluding the cost of the protein sample and any automation, suggesting that the structural biology community spends between 10 and 100 million each year on crystallisation. Any tools or insight that we can get from data mining or taking a computational approach to rationalize this process may not only profoundly change structural biology, but will make it much less expensive as well. We will discuss approaches to data mining, data standards, and software tools to enable a more rational approach to the process of crystallogenesis.
High-resolution and low-dose X-ray crystal structure of Photosytem II
Authors: Tanaka Ayako , Kawakami Keisuke , Umena Yasufumi , Kamiya Nobuo
Published: November 2015

Photosystem II (PSII) is a large multi-subunit membrane protein embedded in thylakoid membranes as a dimeric form with molecular weight of 700 kDa. The oxygen-evolving complex (OEC) of PSII is the heart of photosynthesis to split water molecules and to produce electrons and protons. The X-ray crystal structure of PSII was reported recently at a resolution of 1.9 Å with an averaged coordinate error (DPI) of 0.11 Å [1]. The chemical composition of OEC was fixed to as Mn4CaO5(H2O)4, and the structure was unambiguously determined for the first time including all amino-acid residues and oxo-bridging oxygen atoms ligated to the metal atoms.After the structure determination, two problems are newly showed up. One is the resolution problem. The resolution of 1.9 Å is extremely high in comparison with that of crystal structure previously reported [2], however, it is not enough to obtain precise information for bond lengths between metals and oxo-bridging oxygen atoms in OEC. The other is the X-ray reduction problem on Mn atoms. The reflection intensities were measured by a slide-oscillation method at a low X-ray dose of 0.85 MGy. According to the EXAFS studies reported by Glöckner et al. [3], the dose value corresponded to that 25% of OEC in crystal was damaged into Mn(II) aqua complexes. In order to overcome these problems, we have succeeded to get high quality crystals of PSII, which show much higher resolution and isomorphism. The high isomorphism is very important to obtain low-dose data using multiple crystals. Sixteen partial datasets were reduced using XDS and merged to a resolution of 1.77 Å. The calculated X-ray dose was 0.11 MGy, only 13 % of that for the 1.9 Å resolution data. Based on the merged data, structure determination is underway.
Transhydrogenase coupling proton translocation and hydride transfer
Authors: Leung Josephine , Schurig-Briccio Lici , Yamaguchi Mutsuo , Moeller Arne , Speir Jeffrey , Gennis Robert , Stout Charles
Published: November 2015

Nicotinamide nucleotide transhydrogenase (TH) is a homodimeric 200 kDa membrane protein that is associated with glucose homeostasis in diabetes: mice with mutations or deletions in the TH-encoding gene exhibit glucose intolerance and impaired secretion of insulin [1-2]. TH couples hydride transfer between nicotinamide nucleotides to proton translocation between the matrix (in) and the intermembrane space (out) of mitochondria (or between the cytosol and the periplasm in prokaryotes) [3]: NADH + NADP + H+(out) ⇌ NAD + NADPH + H+(in). Each TH monomer contains three domains: a soluble 40 kDa NAD(H)-binding domain (domain I), a 40kDa membrane-intercalated proton channel (domain II), and a soluble 20 kDa NADP(H)-binding domain (domain III), which is connected to domain II. Hydride transfer between nucleotides occurs between domain I and domain III; and proton translocation is carried out in domain II [3]. The mechanism of TH is unknown due to the lack of structures of the transmembrane domain and the intact enzyme. We have solved three crystal structures of the membrane-intercalated domain II of Thermus thermophilus TH at 2.8-3.0 Å using selenomethionine derivatives and mercury derivatives of crystals obtained in the lipidic cubic phase. Four crystal structures of the soluble domains have also been obtained at 1.8-2.4 Å. Using the higher resolution structures of the subunits, we have determined the structure of the entire TH complex at 6.9 Å by crystallography, and 18 Å by single-particle cryogenic electron microscopy. The intact TH structure reveals that domain III subunits violate the local 2-fold symmetry: one has its NADP(H) binding site 'face-up' to interact with domain I for hydride transfer; the other 'face-down' to interact with domain II for proton translocation. An alternating mechanism of the NADP(H) binding domains provides insights into how TH couples hydride transfer to proton motive force.
Crystal Structure of AcrB Complexed with Linezolid at 3.5Å Resolution
Authors: Hung Li-Wei , Kim Heungbok , Murakami Satoshi , Gupta Goutam , Kim Chang-Yub , Terwilliger Thomas
Published: November 2015

"We present the crystal structure of AcrB in complex with Linezolid[1]. AcrB is an inner-membrane Resistance-Nodulation-Division efflux pump and is part of the AcrAB-TolC multidrug-resistance tripartite efflux system in E. Coli. Crystal structures of AcrB by itself as well as several drug-bound complexes have been structurally characterized. Linezolid is an approved oxazolidinone antibiotic used for the treatment of serious infections caused by Gram-positive bacteria that are resistant to other antibiotics, and has been called a ""reserve antibiotic"", a drug of last resort against potentially intractable infections. This antibiotic inhibits bacterial protein synthesis by specifically binding to the 50S ribosomal subunit. Linezolid has no clinically significant effect on most Gram-negative bacteria. This is thought to be a result of relatively low intracellular concentration of Linezolid due to efflux, but there is no direct evidence yet to support this hypothesis. This membrane protein-drug complex shows that an antibiotic specific to Gram-positive bacteria can also bind an efflux pump from E. coli, a Gram-negative bacterium. The crystal structure of AcrB and Linezolid complex reveals that Linezolid binds to the A385/F386 loops of the symmetric trimers of AcrB in the same fashion as several other antibiotics that are extruded by efflux pumps. A conformational change of a loop in the bottom of the periplasmic cleft is also observed."
Composition profiles across MIMs for resistive switching studied by EDS and EELS
Authors: Hanzig Florian , Veselý Josef , Motylenko Mykhaylo , Leuteritz Astrid , Mähne Hannes , Mikolajick Thomas , Rafaja David
Published: November 2015

Resistive switching in MIM (metal-insulator-metal) stacks is an effect that enables a promising data storage technology which is able to overcome the size limitations of conventional non-volatile memories. The resistive switching effect was already demonstrated for several binary as well as ternary transition metal oxides (TiO2, NiO, SrTiO3, Nb2O5) [1,2]. The current models of the switching mechanisms suggest the important role of defects like oxygen vacancies [3]. Here, we report on the local structural and electronic properties of transition metal oxides embedded in MIM stacks that were obtained by using transmission electron microscopy and electron spectroscopy. We focus on the development of the stoichiometry across the MIM stack for amorphous and partial crystalline niobium oxides. Therefore, electron energy loss spectra (EELS) as well as the energy dispersive X-ray spectra (EDS) were collected on the atomic scale utilizing a nanometer probe in the scanning transmission electron microscope (STEM). The differences in the oxygen content among the electrodes and the concentration profiles at the metal/oxide interfaces in particular were investigated in dependence on the preparation method and on the electrode material. Besides, focusing on the electron loss near edge structure (ELNES) of the oxygen K edge we employed simulations using FEFF9 to describe the modifications of the electronic structure with variations in the oxygen content.
Single-crystal diffraction data from powder samples via SFX
Authors: Zhang Tao , Jin Shifeng , Gu Yuanxin , He Yao , Fan Haifu
Published: November 2015

With the serial femtosecond crystallography (SFX) [1] using hard X-ray free-electron laser as light source, it is possible to obtained three-dimensional single-crystal diffraction data from powder samples consisting of submicron crystal grains. This offers two advantages. First, complicated crystal structures far beyond the ability of powder X-ray diffraction analysis now can be solved easily; second, mixtures of two or more crystalline components can be examined in a single experiment. The percentage of each component can be determined accurately and the crystal structure of them can be solved readily. Simulating calculations were performed with a mixture of two different kinds of zeolites. The program suite CrystFEL [2] was used for simulating SFX diffraction patterns, diffraction indexing and Monte-Carlo integration of diffraction intensities. The program suite SHELX [3] was used for structure determination. Satisfactory results have been obtained and will be discussed in detail.
High-performance, quantum mechanics-based macromolecular x-ray refinement
Authors: Borbulevych Oleg , Westerhoff Lance
Published: November 2015

"Modern, structure based drug discovery (SBDD) is dependent upon accurate protein:ligand structure determination and characterization. In conventional x-ray refinement, the geometry of the ligand within the active site is modeled according to the practitioner's beliefs as expressed in the form of stereochemical restraints provided by the ligand library or CIF file. Further, metal centers, bound species, and so on can be difficult to refine correctly without significant human intervention. Our work has addressed this problem through the integration of DivCon6 - a linear scaling, semiempirical, quantum mechanics (SE-QM) functional - with the Phenix refinement package. With Phenix/DivCon[1], SE-QM is used in ""real-time"" during each microcycle over the course of the refinement. With its inclusion of electrostatics, charge transfer, polarization, dispersion, hydrogen bonds, etcetera, this method is a much more rigorous, robust alternative to conventional stereochemical restraints and is better able to accurately model protein:ligand structures without ""tweaking"" any restraints. We report PM6 refinement results for several key examples including structures with metal coordination spheres, covalent bonds, and other exotic protein:ligand chemistry situations. When compared with the originally deposited PDB structures, we found in all cases that QM refinement leads to ligand structures with much lower strain, and in some cases, the improvement is dramatic and as much 10+ fold. At the same time, SE-QM methods are better able to capture the influence of the surrounding structure (e.g. active site) on the ligand. These interactions are particularly interesting in SBDD as they are often the targets for lead design and optimization, and examples that illustrate how these interactions are captured with SE-QM will also be discussed."
SHELXT: Integrating space group determination and structure solution
Authors: Sheldrick George
Published: November 2015

SHELXT is intended for robust routine solution of small molecule crystal structures. It makes the simple but powerful assumption that the structure consists of resolved atoms, but unlike classical direct methods it is not required that the atoms are 'equal'. This enables it to succeed with poor or incomplete data but makes it unsuitable for structures that are twinned, modulated or contain severe (e.g. 'whole molecule') disorder. SHELXT is a dual-space program that starts with a Patterson minimum superposition and iteratively applies the random omit procedure (also used in SHELXD) with data expanded to space group P1, but does not use phase probability relations or solvent flipping. In the SHELX system it will probably obsolete SHELXS but not SHELXD, which is better for large equal-atom and twinned structures. SHELXT reads any legal SHELX format .ins and (HKLF3 or 4) .hkl files. It extracts the Laue group and tries to find space groups in this Laue group and origin shifts to fit the phases from the best P1 solution, and makes an approximate assignment of element types using the elements specified on the SFAC instruction (and maybe a couple more). This is followed by an isotropic refinement and an attempt to assign the absolute structure if the space group is non-centrosymmetric. It is hoped to release SHELXT as part of the SHELX system (http://shelx.uni-ac.gwdg.de/SHELX/index.php) in time for the 2014 Montreal IUCr Meeting.
Aperiodic 3D tiling by self-similar substitution method using solid unit
Authors: Watanabe Yasunari
Published: November 2015

"There are two important aperiodic tiling methods. One is a projection method and the other is self-similar substitution method. Author applied projection and substitution method to several quasi-periodic tiling [1a] [1b] [1c] [2a] [2b] [2c]. Quantity of the information for research of aperiodic tiling except quasi-periodic tiling is not so large as that of quasi-periodic tiling. Author shows one of the substitution example. that is a ""pentomino tile"" which is made of five unit squares. First generation of a ""pentomino tile"" is composed of two original pentominos and chiral two original pentominos [3]. Author considered 3D solid body unit similar to exterior view of car-body as shown in figure, then succeeded in first generation tile using the body unit. In this study, author consider a relation between substitution and crystallographic rotation matrix and translation matrix and discuss general formulation of self-similar substitution. Caption of Figure: (left-hand) original generation, (center) First generation, (right-hand) Second generation"
Structural similarity of sign systems as the basis of metalanguage of culture
Authors: Talanov Valery
Published: November 2015

The problem of structural similarity of various sign systems is discussed. People`s creative works of art and models of chemical structures, genetic and linguistic codes are compared. Structural similarity (sometimes isomorphism) of sign systems, relating to various spheres of culture, is objective reason of possibility of universal metalanguage creation. What proofs are provided? Many ornaments on mausoleums and mosques in Islamic art precisely correspond to motives of structures of inorganic crystals in polyhedral representation, especially structures of silicates. An interesting example of structural isomorphism is the structure of architectural masterpieces with geode surfaces and fullerenes molecules structures. Fullerene structures and geodetic domes are also structurally similar to the forms of some biological organisms, for example, to the simple viruses and radiolyariyas. Structural analogy of inorganic substances with spiral structures and world art is highlighted. For example, according to a structural motive of a double spiral of a DNA molecule the sculpture «The Rape of the Sabines» (1583) by Giambologna is constructed. This sculpture is created 370 years prior to D. Watson and F. Crick great discovery. Studying of medieval Islamic decorative art showed that some geometrical ornaments were constructed on the principles which were close to models of quasicrystal geometry of alloys. The types of structural similarity of sign systems are classified into three groups: order structures; algebraic structures; topological structures. Various types of symmetry belong to order structures. Structural similarity of sign systems is described by different types of symmetry. In the author's opinion symmetry is one of the universal metalanguage of culture [1].
The Rose Windows of Gothic Cathedrals: Art, Symmetry and Beyond
Authors: Abad-Zapatero Cele
Published: November 2015

The magnificent rose windows of the Gothic cathedrals have been the object of wonder and fascination to architects, artists and human beings alike, since they were used to emphasize the splendor of Gothic architecture, its lightness of forms and luminosity of interiors. There is considerable amount of literature on the theme including studies on the stone tracery and the stained glass, and a website created by a prominent author in the field (www.therosewindow.com, [1]) is an excellent resource. A brief reference in the classic book Symmetry by H. Weyl [2] suggested that rose windows were indeed excellent examples of planar point group symmetry. However, a rigorous and systematic study of this particular facet of these masterpieces has never been done. Preliminary results of the frequency of different symmetrical arrangements for more than five hundred windows have been recently published [3] and will be presented. In addition, detailed analysis of certain examples of rose windows and iconic macromolecular structures suggest that various symmetrical figures and entities that are part of our world can have symbolic meaning. They can be described by the rigorous framework of group theory in mathematics but they have also been used through history to convey different thoughts, insights and perceptions of the artists (and scientists) as designers and executors of the cosmological view of the times. A project aimed at extending these studies in the future will be presented.
Basic Ammonothermal Growth of GaN in Silver Lined Autoclave
Authors: Pimputkar Siddha , Kawabata Shinichiro , Speck James , Nakamura Shuji
Published: November 2015

Gallium Nitride (GaN) and its alloys form a promising material system for optoelectronic and electronic devices. Heteroepitaxial growth of GaN on sapphire and SiC, while viable, introduces threading dislocations (between 1E8 – 1E11 cm^-2), mismatches in thermal expansion coefficients, and limitations on available growth orientations other than the polar, <0001> directions. With a push towards longer wavelengths, higher output powers at higher efficiencies with reduced droop for LEDs, non-polar and semi-polar oriented devices are becoming increasingly important, though need currently lacking, large area, bulk GaN substrates. A solution is the ammonothermal growth technique, which entails dissolving a GaN feedstock in a supercritical ammonia solution containing sodium (P < 270 MPa, T = 500–600 °C) and re-crystallizing the material on a GaN seed. Improvements in growth rate are needed to reduce cost and increase throughput. To that end, an ultra high purity (UHP) growth environment was created within a typical Ni-Cr superalloy autoclave by introducing a silver capsule. 40 basic ammonothermal growth runs were performed on hydride vapor phase epitaxy (HVPE) GaN seed crystals. The capsule design significantly reduced concentrations of transition metals in the GaN crystals (<1x1E17 cm^-3) while improving the transparency to α(450 nm) = 2.2 cm^-1. Total growth rates improved from 200 to 344130 μm/day for c-plane and from 34 to 4612 μm/day for m-plane growth. Degradation in crystal quality based on the full width at half maximum of the ω-rocking curve using X-ray diffraction when compared to the seed crystal was only observed for Ga-face growth on c-plane oriented seeds, presumably due to poor nucleation. Cracking in thick growth layers was observed due to strain originating from the HVPE seed crystals. Differences in the total system pressure profiles were analyzed and the observed pressure drop due to outward diffusion of hydrogen during growth was modeled.
Defect evolution in high-quality 4H-SiC grown by solution method
Authors: Harada Shunta , Tagawa Miho , Ujihara Toru
Published: November 2015

Silicon carbide (SiC) has been receiving great interest due to its potential application as a next-generation power device. For the high-performance SiC power device, a high-quality SiC wafer is necessary. Commercial SiC wafers are usually produced by physical vapor transport (PVT) method. The crystal quality of the commercial wafers has been improved and the density of micropipes which cause the degradation of break down voltage has been almost eliminated. However, thousands of dislocations still exist in the wafers. Solution growth is one of the methods to achieve high-quality crystal growth because the condition of solution growth is close to thermal equilibrium. Many researchers studied top-seeded solution growth (TSSG) method for the high-quality bulk growth of SiC. So far high growth rate (2 mm/h) and large diameter growth (3 inches) has been demonstrated by this method. Recently we have investigated the defect evolution during the solution growth of SiC. In the solution-growth crystal, threading screw dislocations (TSDs) propagating to the growth direction was converted to defects on the basal planes by macrosteps formed on the growth surface. By using the vicinal seed crystal, we can successfully form a large number of macrosteps on the growth surface and most of TSDs were efficiently converted to the defect on the basal planes. The defects on the basal planes are propagating to the direction vertical to the growth direction and are finally wiped out as the growth proceeds. Actually by utilizing the TSD conversion during the solution growth, we obtained high-quality crystal with very low TSD density. The TSD density of the solution growth crystal was only 30 cm-2, which is two-order magnitude lower than that of the commercial wafers.
Structural basis of DNA sequence recognition by the response regulator PhoP
Authors: He Xiaoyuan , Wang Shuishu
Published: November 2015

The PhoP-PhoR two-component system plays a key role in regulating virulence of Mycobacterium tuberculosis. The response regulator PhoP is a transcription regulator, and it regulates expression of more than 100 genes. PhoP belongs to the OmpR/PhoB subfamily of response regulators. Despite extensive research in recent years, the molecular mechanism of DNA sequence recognition by this large subfamily of response regulators is not fully understood, especially the role of the N-terminal regulatory domain on DNA binding of the effector domain. Here we present a crystal structure of the full-length PhoP in complex with a direct-repeat DNA sequence. PhoP binds to DNA as a dimer. The two effector domains bind in tandem, each interacting with a half site of the direct repeat DNA. The DNA recognition helix inserts into the major groove, reading the sequence of a 7-bp motif. The wing residues interact with the downstream sequence, with a conserved arginine side chain inserting into the minor groove. Surprisingly, the regulatory domain also forms a tandem arrangement, instead of the anticipated symmetric dimer. The regulatory domain of the upstream protomer interacts with both domains of the downstream protomer. The structural elements of the alpha4-beta5-alpha5 face, which often found to be involved in dimer interface of the regulatory domain, play important roles in the interactions between the protomers. The crystal structure explains why PhoP recognizes direct repeats of two 7-bp motifs with a strict spacing of 4 bp and the highly cooperative binding of the two monomers. Detailed analysis of the structure along with analysis of the DNA sequence requirements and ITC measurements of protein-DNA binding interactions will be presented.
Structural Studies of the DCC-Ribosome Complex
Authors: Nielsen Maja , Kidmose Rune , Flygaard Rasmus , Jenner Lasse
Published: November 2015

During neuronal development axons are guided by a gradient of the signal molecule netrin, which attracts extending neurons by binding to the DCC (Deleted in Colorectal Cancer) Receptor. It has been shown that the intracellular domain of the DCC receptor interacts directly with the ribosome, and that this interaction is crucial for axon guidance(1). However structural insights into this interaction are still lacking. Our aim is therefore to determine the crystal structure of the DCC-ribosome complex. As membrane proteins can be challenging to crystalize, especially together with a huge macromolecular complex as the ribosome, a cloned fragment of the intracellular domain of the human DCC receptor will be used. Tcherkezian et al. showed that the interaction with the ribosome occurs through the ribosomal protein L5(1), which is conserved from S. cerevisiae to humans. We therefore decided to use the 80S S. cerevisiae ribosome because crystallization conditions are known and well-established (2). Furthermore, in the crystals of S. cerevisiae there is a large solvent channel passing by ribosomal protein L5(2), making it likely that we can soak fragments of the DCC receptor into crystals of S. cerevisiae ribosome. In order to screen for soluble fragments of the DCC receptor that can be used for soaking, a random PCR expression approach first described by Kawasaki and Inagaki(3), where random PCR fragments are inserted into a vector containing GFP was used. This method resulted in several soluble fragments covering the P1 domain that was shown to be responsible for ribosome binding(1). These fragments are now being purified, and will be tested for ribosome binding, and subsequently in soaking and co-crystallisation experiments. Progress will be presented.
Understanding disease mutations from the crystal structure of SOX9 with DNA
Authors: Das Debanu , Yumoto Fumiaki , Kuchenbecker Kristopher , Deacon Ashley , Fletterick Robert , Wilson Ian
Published: November 2015

SRY(Sex determining Region Y)-box or SOX transcription factors are important in early development and maintenance of different cell pools after birth. Of the ~20 SOX proteins (SRY, SOX1-SOX15, SOX17, SOX18, SOX21 and SOX30), SOX2, SOX9 and SOX10 mutations are primarily disease-associated: SOX2 with Combined Pituitary Hormone Deficiency, Microphthalmia, Septo-optic dysplasia and anophthalmic syndrome; SOX9 with Campomelic Dysplasia (affects development of the reproductive and skeletal system); and SOX10 (~94% sequence identity to SOX9) with Waardenburg Syndrome (affects audition and pigmentation in hair, eyes and skin; and specifically with WS types 2 and 4). As part of our Protein Structure Initiative (PSI)-Biology partnership, we performed structural and mutational analyses including x-ray crystallography and surface plasmon resonance assays, on the DNA-binding HMG domain of SOX9 with duplex DNA. Crystals were obtained in C222 space group and the structure was determined by molecular replacement to 2.77 Å resolution with final Rcryst/Rfree of 24.8/27.8%. The overall structure of the SOX9-DNA complex is similar to other SOX/SRY protein complexes. The SOX9-DNA protein-DNA interactions suggested a panel of mutations to assay for biochemical activity, which allowed us to understand the molecular basis of five mutations identified in Campomelic Dysplasia. These mutated residues have direct contact with DNA as well as indirect contacts, i.e., these mutations lead to allosteric secondary structure changes in the protein, which affect residues in direct contact with DNA. Due to the very high sequence identity between SOX9 and SOX10, our crystal structure also helps to rationalize the effect of SOX10 mutations in Waardenburg Syndrome. This work is supported by NIH grants U54 GM094586 and U01 GM094614. SSRL operations are funded by DOE BES, and the SSRL SMB program by DOE BER, NIH NCRR BTP and NIH NIGMS.
A Ten-Day Course for Chemical Crystallography
Authors: Stern Charlotte , Oliver Allen , Sarjeant Amy
Published: November 2015

Crystallography has long been a subject excluded from core curricula in undergraduate and graduate Chemistry programs. Occasionally offered as an elective or special topics course, crystallography remains a "black box" technique to many researchers who rely on it for verification of their work. Students interested in learning the theory and in-depth practical applications are often left to their own devices and seek out workshops, special courses, or one-on-one training. Currently, the authors host a ten-day intensive course on chemical crystallography, covering theory, hands-on experimental technique, and structure solution and refinement for both single crystal and powder X-ray diffraction. Here we describe the features of the course, the general curriculum and the demographics of attendees and faculty instructors.
Diiron(IV)oxo Crystal Structure Modeling Intermediate Q of Methane Monooxygenase
Authors: Rohde Gregory , Xue Genqiang , Que, Jr. Lawrence
Published: November 2015

Nonheme iron enzymes catalyze a wide variety of reactions by O2 activation, including the biosynthesis of the antibiotic chloramphenicol, the radical initiator in the production of deoxyribonucleotides from ribonucleotides by ribonucleotide reductase intermediate X (RNRX) in all eukaryotic life-forms and the selective oxidation of methane to methanol by the soluble form of methane monoxygenase intermediate Q (sMMOQ).[1] High-valent diiron active intermediates have been identified for both sMMOQ and RNRX and are formulated as a diiron(IV)-bis-µ-oxo and a mixed valent Fe(III)Fe(IV)-bis-µ-oxo respectively.[1] Previously, the crystal structure of a mixed-valent Fe(III)Fe(IV)-bis-µ-oxo model complex was reported.[2] A high-yielding synthesis of the reported diiron(IV)-bis-µ-oxo has allowed for the successful structural solution of a high-valent diiron(IV) model complex for sMMOQ.[3] This sMMOQ model complex, along with four other diiron-bis-µ-oxo model complexes in different oxidation and protonation states are compared to sMMOQ and RNRX and related to the mechanism of O2 activation by nonheme enzymes.
A collection of magnetic structures with cif-like files as a database seed
Authors: Gallego Samuel , Perez-Mato J. Manuel , Tasci Emre , Elcoro Luis , Aroyo Mois , Momma Koichi , Madariaga Gotzon
Published: November 2015

We report the release within the Bilbao Crystallographic server [1] of a webpage providing detailed quantitative information on a representative set of published magnetic structures. Under the name of MAGNDATA (www.cryst.ehu.es/magndata) more than 140 entries are available. Each magnetic structure has been saved making use of magnetic symmetry, i.e. Shubnikov magnetic groups for commensurate structures, and magnetic superspace groups for incommensurate ones. This ensures a unified communication method and a robust and unambiguous description of both atomic positions and magnetic moments. The origin and main crystallographic axes of the parent phase are usually kept, with the cost of often using a non-standard setting for the magnetic symmetry. The magnetic point group is also given, so that the allowed macroscopic tensor properties can be derived. The fact that magnetic structures are being described according to various methods, often with ambiguous information, has forced an elaborate interpretation and transformation of the original data. For this purpose the freely available internet tools MAXMAGN [1] and ISODISTORT [2] have been our essential tools. Most of the analyzed structures happen to possess maximal magnetic symmetries within the constraints imposed by the magnetic propagation vector, and the relevant model could be derived in a straightforward manner using MAXMAGN [1]. In a few cases a lower symmetry is realized, but then it corresponded to one isotropy subgroup of one or several irreducible representations (irreps) of the paramagnetic grey space group, and ISODISTORT [2] could be applied to model the structure. Although the structure description is done using magnetic groups, the active irrep(s) are also given in most cases. The entries of the collection can be retrieved in a cif-like format, which is supported by internet tools as STRCONVERT [1] and ISOCIF [2], the visualization program VESTA [3], and some refinement programs (JANA2006, FULLPROF). Each entry also includes Vesta files that allow the visualization of a single magnetic unit cell.
Competing Superexchange Interactions in Double Perovskite Osmates
Authors: Morrow Ryan , Woodward Patrick
Published: November 2015

Double perovskites, A2BB'O6, containing mixed transition metal ions have exhibited numerous desirable properties such as colossal magnetoresistance, half metallic transport, and high temperature ferrimagnetism. However, a predictive understanding of the superexchange mechanisms which control the magnetism of these materials when they are insulating and B is 3d transition metal and B' is a 4d or 5d transition metal has remained elusive. In this work, a number of insulating double perovskite osmates, A2BOsO6 (A=Sr,Ca,La; B=Cr,Fe,Co,Ni) have been chosen and studied using magnetometry, specific heat, XMCD, and neutron powder diffraction techniques in order to systematically probe the effects of electronic configuration and bonding geometry on the magnetic ground state. It is concluded that the magnetic properties of these materials are controlled by a competition between short range B–O–Os and long range superexchange interactions which are sensitive to bonding geometry resulting in tunability of the magnetic ground state.
Perovskites in low dimensional multi-layer structure types
Authors: Liu Samuel , Miiller Wojciech , Liu Yun , Blanchard Peter , Avdeev Max , Kennedy Brendan , Ling Chris
Published: November 2015

This study introduces examples of structure property relationships within the multi-layered Sillen-Aurivillius family (shown in Figure) and aims to investigate the effect of chemical doping and lattice matching effects. The first example involves doping 1/3 of the n = 3 ferroelectric perovskite layers with magnetic transition metal cations in Bi5PbTi3O14Cl [1] with charge balancing by removing Pb2+for Bi3+. A statistical 1:2 distribution of M3+and Ti4+across all three perovskite layers was found in Bi6Ti2MO14Cl, M = Cr3+, Mn3+, Fe3+, resulting in highly strained structures (enhancing the ferroelectricity compared to Bi5PbTi3O14Cl) and pronounced spin-glass behavior below Tirr(0) = 4.46 K. Ferroelectric transitions were observed at high temperature for each of the new compounds. Ferroelectric properties were also measured on Bi6Ti2FeO14Cl using piezoresponse force microscopy showing hysteretic phase behavior. A new n = 2 Sillen-Aurivillius compound Bi3Sr2Nb2O11Br, based on Bi3Pb2Nb2O11Cl [2], was synthesized by simultaneously replacing Pb2+with Sr2+and Cl-with Br-. Inter-layer mismatch prevented the formation of Bi3Sr2Nb2O11Cl and Bi3Pb2Nb2O11Br. Sr2+doping reduces the impact of the stereochemically active 6s2lone pair found on Pb2+and Bi3+, resulting in a stacking contraction in the lattice parameters by 1.22 % and an expansion of the a-b plane by 0.25 %, improving inter-layer compatibility with Br-. X-ray Absorption Near Edge Structure spectra analysis shows that the ferroelectric distortion of the B-site cation is less apparent in Bi3Sr2Nb2O11Br compared to Bi3Pb2Nb2O11Cl. Variable-temperature neutron diffraction data show no evidence for a ferroelectric distortion.
Distribution of mixed-valence ions in Mn1+xFe2-xO4ferrites
Authors: Aoyagi Yoshio , Okube Maki , Sasaki Satoshi
Published: November 2015

Mn ferrite has a spinel structure to show the ferrimagnetism, where the magnetic moments show a collinear ferrimagnetic ordering between tetrahedral A and octahedral B sites. Since Mn2+ and Fe3+ have the same electronic configuration, it is not easy to determine the cation distribution of Mn ferrite from usual magnetization measurements. Especially in Mn ferrite, both Mn2+ and Fe3+ have a large spin polarization to give strong magnetic moments through the super exchange interaction between the two sites. Replacing Fe3+ by Mn2+ and Mn4+, the ferrimagnetic property weakens through magnetic balance between the sites. Since Mn and Fe ions may have multiple valences in the oxide structure, the scheme of site preference, based on careful study of various valence states, has been investigated for Mn1+xFe2-xO4. Single crystals for Mn1+xFe2-xO4 (x = 0.05, 0.20, 1.36 and 1.50) were synthesized from stoichiometric proportions of Mn3O4 and Fe3O4 in an evacuated silica capsule at 1353 K for 96 h. Each of spherical or parallel-piped crystals, ranging 0.05 to 0.08 mm, was mounted on the glass fiber. Conventional intensity measurements were made using a Rigaku AFC-5S four-circle diffractometer with a graphite (002) monochromator for Mo Kα radiation. Least-squares refinements were made to obtain atomic parameters, converged with R factors ranging 0.023 to 0.029. The site occupancy of Mn and Fe atoms was then determined on the basis of the resonant scattering effect at the Fe K absorption edge (λ = 1.7535 Å), by using a vertical-type four-circle diffractometer at PF-BL-10A. The results show that 89, 82, 100 and 100 percent of Mn atoms occupy the A site for the four samples, respectively. In the third step of analyses, absorption experiments were performed at PF-BL-6C. XANES and XMCD spectra were used at Mn and Fe K edges for determining the valence states of Mn and Mn ions. Finally, the distribution of mixed-valence ions for Mn1.20Fe1.80O4 was determined by the valence-difference contrast method, where the intensity data were collected for a spherical single crystal of 0.08 mm in a diameter at both threshold and pre-edge regions of Mn K edge, by using an AFC-5u four-circle diffractometer installed in PF-BL-6C. The site occupancy with the valence state will be discussed in the presentation, compared with the other type of transition-metal ferrites.
Magnetic ordering in double perovskites with 4d and 5d elements
Authors: Greedan John , Thompson Corey , Marjerrison Casey , Gaulin Bruce , Luke Graeme
Published: November 2015

B-site ordered double perovskites of the type AA′BB′O6 have attracted attention recently due to unusual and unpredictable modes of magnetic order. Of particular interest are materials where AA′ = Ba, Sr or La and B′ = Mo,Ru,Os and Re and B is a diamagnetic ion such as Li+,Na+,Ca2+, Mg2+, Zn2+ or Cd2+.Crystal symmetries encountered are Fm-3m, I4/m and P21/n as a function of the Goldschmidt tolerance factor which in turn impose local symmetries at the magnetic B′ site of m-3m, 4/m and -1, respectively. The magnetic ions have electronic configurations 4d1, 4d3,5d1, 5d2 and 5d3 with nominal spins, S = 1/2,1 and 3/2. Spin orbit coupling is very large, reaching ~ 0.5eV for the 5d ions, and plays a more important role than in the more familiar 3d-based magnetic materials. Geometric frustration, the B′ ion sublattice is f.c.c., based on edge sharing tetrahedra, also is of critical importance. Observed magnetic ground states range from spin glasses (without apparent disorder), collective spin singlets, ferromagnets and antiferromagnets. Often, ordered moments are a small fraction of a Bohr magneton. Systematic behavior is elusive. For example Ba2YReO6 and Ba2CaOsO6 (both Fm-3m) have the same unit cell constant to within .01 % and both are based on 5d2 ions but the former is a highly unconventional spin glass and the latter orders antiferromagnetically below 50K. Recent results on this class of magnetic materials will be described in the context of existing theories.
High-pressure synthesis, structure, phase relation of polar LiNbO3-type ZnTiO3
Authors: Inaguma Yoshiyuki , Aimi Akihisa , Shirako Yuichi , Sakurai Daichi , Mori Daisuke , Kojitani Hiroshi , Akaogi Masaki , Katsumata Tetsuhiro , Nakayama Masanobu
Published: November 2015

Ferroelectricity, piezoelectricity, pyroelectricity, and second-order nonlinear optical behavior are technologically important. Because these properties are attributable to the noncentrosymmetric (NCS) structure[1], the search for materials exhibiting such characteristics must begin with a search of NCS materials. Among them, LiNbO3-type (LN-type) compounds with a chemical formula of ABX3 exhibit NSC structures with hexagonal polar space group R3c whose BX6 octahedra three-dimensionally share their corners the same as perovskite-type compounds[2]. In LN-type compounds, the A cation - B cation repulsion directs the spontaneous polarization along c-axis(Fig. 1). Therefore, we might find attractive functional properties by the selection of constituent ions based on their having a naturally occurring polar LN-type structure attributable to the cation-cation repulsion. With the ideas mentioned above, we have investigated the high-pressure synthesis and characterization of novel LN-type oxides such as ZnSnO3, PbNiO3, CdPbO3 as well as known MnMO3 (M = Ti, Sn). Recently, we have successfully synthesized a polar LN-type titanate ZnTiO3 (LN-ZTO) under high pressure and high temperature [3]. The first principles calculation indicates that LN-ZTO is a meta-stable phase obtained by the transformation in the decompression process from the perovskite-type phase, which is stable at high pressure and high temperature. The Rietveld structural refinement reveals that LN-ZTO exhibits greater intra-distortion of the TiO6 in LN-ZTO than that of the SnO6 in LN-type ZnSnO3 (LN-ZSO). The estimated spontaneous polarization are greater than those of LN-ZSO, which is attributed to the great displacement of Ti along c-axis and the greater Born effective charge of Ti (+6.1) than that of Sn (+4.1). Furthermore, the spontaneous polarization of LN-ZTO is greater than that of LiNbO3, indicating that LN-ZTO, like LiNbO3, is a candidate ferroelectric material with high performance. The second harmonic generation (SHG) response of LN-ZTO is 24 times greater than that of LN-ZSO. The findings indicate that the intra-octahedral distortion, spontaneous polarization, and SHG response are caused by the stabilization of the polar LN-type structure and reinforced by the second-order Jahn-Teller effect attributable to the orbital interaction between oxygen ions and d0 ions such as Ti4+. We also discuss the relationship between the intra-distortion of BO6 and polarity in several LN-type oxides.
Charge density study of the first mixed-valent tetraphosphete
Authors: Breuers Verena , Lehmann Christian , Frank Walter
Published: November 2015

The first λ3,λ5-tetraphosphete contains a 4π-electron four-membered ring as the central structural unit of a dispirocyclic system and can thus be classified as an analogue to diphosphetes and cyclodiphosphazenes. According to its crystal structure the central P4unit exhibits not only P–P bonds which are of equal length (P1–P2 2,139(1) Å, P1–P2A 2,142(1) Å), but also rhombic distortion (P1–P2–P1A 79,4(1)0, P2–P1–P2A 100,6(1)0).[1] Therefore its electronic structure cannot be described as 'Phosphacyclobutadiene' but either as a bis(ylide) or as a system with delocalized double bonds. After various quantum chemical calculations and an extensive examination of its reaction and coordination behavior failed to answer this question, we addressed the problem via a detailed analysis of its charge density distribution. The experimental charge density based on high resolution X-ray diffraction data collected at low temperature is determined by multipole least squares refinement using the program packageXD2006.[2] In a first step, the static deformation density exhibits charge density which is located mainly outside of the P4ring plane at the λ3-phosphorus atoms but simultaneously redistributed into the P–P bond area. In addition to that, a study of its topological properties and an inspection of the Laplacian of the electron density according to Bader's `Quantum Theory of Atoms in Molecules' (QTAIM)[3] further highlight the bonding features. They reveal polar Si–N, Si–C and P–N bonds with a decreasing amount of electrostatic contribution as well as four valence shell charge concentrations (thus sp3hybridization) at each of the phosphorus atoms. Finally supported by theoretical calculations, the results illustrate the unique bonding situation in the P4unit combining a high ylidic character with unusual not exclusively sigma-like P–P bonds.