bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural Characterization of PLZF-Corepressor Complexes
Authors: Zhai Andrew , Privé Gilbert
Published: November 2015

Promyelocytic Leukemia Zinc Finger (PLZF) encodes a transcription factor containing an N-terminal BTB domain as well as 9 C-terminal C2H2 Zinc Finger repeats. PLZF represses genes necessary for the differentiation of haematopoietic progenitors as well as spermatogonia and therefore plays a crucial role in stem cell renewal. It accomplishes this by recruiting large, multi-protein repressor complexes to its targets genes. In order to understand the structural behavior of PLZF within the context of these complexes, we are employing a multi-disciplinary approach to identify proteins involved in direct interactions with PLZF, including the use of a loss of function mutation within the BTB domain. Our data identifies known corepressors Sin3A, SMRT, HOXA5 and other members of HDAC complexes family as potential direct interacting partners. Progress towards solving the crystal structure of the PLZF BTB domain bound to its corepressors will be presented.
The unique regulation of Fe-S cluster biogenesis in a Gram-positive bacterium
Authors: Santos Joana , Macedo-Ribeiro Sandra , Pereira Pedro
Published: November 2015

The ubiquitous iron-sulfur (Fe-S) cluster-containing proteins are involved in countless biological routes and play crucial roles for the functioning of both prokaryotic and eukaryotic cells. The transcription factor IscR, of the helix–turn–helix family, was first implicated in repressing expression of the ISC (Iron Sulfur Cluster biogenesis) pathway and was shown to contain a [2Fe–2S] cluster. Promoters controlled by IscR belong to two distinct sequence groups [1] and the [2Fe-2S] cluster of IscR was shown to be essential for regulation of type-1 promoters (isc, yadR, yhgI), while apo-IscR is responsible for the regulation of type-2 promoters [2]. The proposed model for IscR action consists on a mechanism for Fe-S biogenesis fine-tuned by the cellular Fe-S cluster status. Despite recent advances in understanding the regulation of isc and suf operons by environmental signals, the features of IscR target-site recognition and the structural changes that alter the DNA binding specificity of IscR upon ligation of the [2Fe-2S] cluster are unknown. To understand how IscR recognizes two different DNA motifs, we solved the three-dimensional structures of free apo-IscR and of its complex with a type-2 target sequence, the hya promoter from the hydrogenase-1 operon [3]. These experimental models revealed some of the molecular details of the unusual environmentally modulated recognition of two distinct promoter consensus sequences by IscR, using a single predicted helix–turn–helix DNA binding motif. To our knowledge, IscR is the only transcription factor that is active in both the apo and holo-forms and which displays cofactor-mediated modulation of its DNA binding specificity. This work was funded by Fundação para a Ciência e a Tecnologia (Portugal) through grant PTDC/BBB-BEP/2127/2012 (EU-FEDER funding through COMPETE FCOMP-01-0124-FEDER-028116) and PhD fellowship SFRH/BD/66461/2009 to JAS.
DNA binding and dimerization specificities of Basic Zipper transcription factors
Authors: Pogenberg Vivian , Consani-Textor Larissa , Wilmanns Matthias
Published: November 2015

The ability of basic zipper transcription factors to form homo- or heterodimers provides a paradigm for combinatorial control of eukaryotic gene expression. In a first study, we clarified the specificity of the MIcrophthalmia-associated Transcription Factor [1]. To achieve this, we solved three crystal structures: two structures of MITF in complex with DNA duplexes encompassing two different target motifs (E-box and M-box) and one APO-structure. We then analyzed interactions between these DNA elements and several MITF mutants with documented mice phenotypes, using complementary techniques. The comparison of these experiments together with available biological data reveals the particular mechanism of DNA recognition by MITF. Moreover we demonstrated how a shift in the leucine zipper register limits the choice of the homotypic dimerization partner among the other b-HLH-Zip transcription factors. In a second study, we wondered how facultative dimerization results in alternative DNA-binding repertoires on distinct regulatory elements [2]. In this respect, the hematopoietic b-Zip transcription factor MafB, is a good model, since it has the ability to form homo- and heterodimers with a few other transcription factors. We first determined two high-resolution structures of MafB as a homodimer and as a heterodimer with c-Fos bound to variants of the Maf-recognition element (MARE). The two structures revealed several unexpected and specific coiled coil interactions. Based on these findings, we have engineered two MafB mutants with opposite dimerization preferences. One of them indeed showed a strong preference for MafB/c-Fos heterodimerization. In addition this variant enabled a selection of heterodimer- favoring over homodimer-specific MARE variants, demonstrating that protein/protein and protein/DNA interactions are interconnected. Our data provide a new concept for transcription factor design to selectively activate dimer-specific pathways and binding repertoires.
Crystal structure of human cytosolic aspartyl-tRNA synthetase
Authors: Park Sang Ho , Kim Kyung Rok , Kim Hyoun Sook , Rhee Kyung Hee , Kim Byung-Gyu , Kim Dae Gyu , Park Mi Seul , Kim Hyun-Jung , Kim Sunghoon , Han Byung Woo
Published: November 2015

Human cytosolic aspartyl-tRNA synthetase (DRS) catalyzes the attachment of the amino acid aspartic acid to its cognate tRNA and it is a component of the multi-tRNA synthetase complex (MSC) which has been known to be involved in unexpected signaling pathways. Here, we report the crystal structure of DRS at 2.25 Å resolution. DRS is a homodimer with a dimer interface 3,750.5 Å2which comprises of 16.6% of the monomeric surface area. Our structure reveals the C-terminal end of the N-helix which is considered as a unique addition in DRS, and its conformation further supports the switching model of the N-helix for the transfer of tRNAAsp to elongation factor 1α. From our analyses of the crystal structure and post-translational modification of DRS, we suggest that the phosphorylation of Ser146 provokes the separation of DRS from the MSC and provides the binding site for an interaction partner with unforeseen functions.
Translational control by diverse RNA folds that recognize the metabolite preQ1
Authors: Liberman Joseph , Salim Mohammad , Belashov Ivan , Wedekind Joseph
Published: November 2015

Typical paradigms of translational regulation utilize proteins, whereas riboswitches are economical, RNA-based elements that govern gene expression without protein partners. Present in all domains of life, riboswitches are commonly located in the 5´-untranslated regions of bacterial mRNAs where they establish feedback loops that respond to cellular levels of a specific small-molecule effector. Here we present the novel crystal structure of the recently discovered preQ1-III (class 3) riboswitch at 2.85 Å resolution. The 101-nucleotide switch features an internal loop pseudoknot (iPK) that coaxially stacks upon flanking helices P2 and P3. PreQ1(7-aminomethyl-7-deazaguanine) – the last soluble intermediate in the biosynthesis of the hypermodified tRNA base queuosine (Scheme I) – binds to form a major groove base triple of the form U·preQ1·C that utilizes highly conserved pyrimidine bases that help define this riboswitch class. This mode of effector binding involves non-canonical Watson-Crick pairing reminiscent of the phylogenetically unrelated preQ1-II (class 2) riboswitch. Remarkably, both riboswitch classes utilize dual U·A-U base triples that stack against the ligand. The respective nine-nucleotide motifs and their preQ1ligands superimpose with an rmsd of 0.4 Å; the class 2 and 3 structures are otherwise unrelated. The class 3 preQ1binding pocket also includes contributions from junctions that connect the P2-iPK-P3 coaxial stack with perpendicularly positioned helix P4. Of special interest is the observation that P4 can form a hairpin-loop pseudoknot (hPK) with the ribosome binding site (RBS) of the mRNA, suggesting a mode of ligand-dependent RBS sequestration. Biochemical experiments describing the preQ1dependence of hPK formation will be presented, as well as a comparison to known, translational class 1 and 2 preQ1riboswitch structures [1-3]. Implications for bacterial translational control will be discussed based on this diverse riboswitch family.
Proteopedia: Bridging the Rift Between 3D Structure & Function of Biomacromolecules
Authors: Sussman Joel , Prilusky Jaime
Published: November 2015

Proteopedia is a wiki web resource, http://proteopedia.org, which aids in understanding of the structure/function relationship of biomacromolecules. The `3D' images on each page are surrounded by descriptive text containing hyperlinks that change the appearance (view, representations, colors or labels) of the adjacent 3D structure to reflect the concept discussed in the text (see figure below). This makes the complex structural information readily accessible and comprehensible, even to non-structural biologists. Using Proteopedia, scientists and students can easily create descriptions of biomacromolecules linked to their 3D structure, e.g., a page on the way inhibitors block HIV Protease, http://proteopedia.org/w/HIV-1_protease. Pages can be viewed on computers and tablets via the molecular viewer JSmol. Content is being added by ~2,600 Proteopedia's users from more than 50 countries, in a dozen different languages, including Arabic, Russian & Chinese. Members of the scientific community are invited to request a Proteopedia user account, at no cost, to create and edit pages, see: http://proteopedia.org/w/Special:RequestAccount.
Cr(II) complex: water reductant and starting compound for new Cr(III) compounds
Authors: Crochet Aurelien , Brog Jean-Pierre , Fromm Katharina
Published: November 2015

The use of alkali aryloxide reagents in organo-metallic synthesis often depends on their solubility, a property derived from their structure. The regain of interest of alkali aryloxides also originates from the discovery of high-temperature superconducting compounds, which has generated a great interest in the formation of oxide materials and other ceramics. Thus, many alkoxides of yttrium and copper are common precursors for oxide materials. Moreover, the synthesis of heterobimetallic alkoxides has provided a facile route for obtaining soluble, volatile, and generally monomeric species. These heterobimetallic complexes can thus serve as valuable precursors for making metal oxides but it is not the only possible application for this type of compounds. These complexes can be used as starting compounds for syntheses of more complex structures. In this work, the salt elimination and ligand exchange reaction of chromium(II) chloride with lithium phenoxide yields a mixed metal lithium-chromium(II) phenoxide. Using this latter as intermediately formed starting material and combining the substitution reaction with an oxidation process, we have gained access to new polynuclear chromium(III) aryloxide complexes. While a 1D coordination polymer based on chromium(III) is obtained in a first reaction by serendipity, the controlled addition of water to the Cr(II) complex leads to three new discrete chromium(III) cluster compounds. The use of deuterated species allowed to confirm the oxidation based on the addition of water by detection of H2, HD and D2. During these investigations, we have also identified a THF-adduct of chromium(II) chloride, used in the literature as precursor in numerous syntheses, but with a hitherto unknown structure. Figure 1: Oxidation of a Cr(II) complex by water and formation of a new Cr(III) complex.
Crystal Growth to Foster Inquiry–Based Learning: First Year Science Laboratory
Authors: Rabeh Wael , Bernstein Joel
Published: November 2015

Crystals play an important and ubiquitous role in our everyday life with applications in medicine, industry, agriculture, and biotechnology. With the recent trends toward inquiry-based learning in undergraduate science teaching laboratory, we developed a crystals growth laboratory for first year students. While one objective is to learn how to grow and handle crystals, the laboratory is designed to foster the acquisition of basic scientific knowledge and hands on experience to develop critical laboratory skills. In this sense, it is targeted for students with diverse backgrounds and, in accord with the liberal arts curriculum at NYU Abu Dhabi readily includes non-science majors. The original inspiration for the lab came from the 1960 classic book "Crystals and Crystal Growing" by Holden and Singer. We have expanded on the emphasis there on inorganic salt crystals to require students to crystallize macromolecules as well, in a research driven environment. Similar to projects carried in more advanced courses, students write an outline of their project that is developed into a full proposal through a literature search stimulated by in class discussions and peer-review. Some of the learning goals include the ability to design and manage a research project, propose ideas and methods to explore the topic of interest, learn various techniques and equipment common in a science laboratory, the ability to analyze data, acquire best practices in lab safety, and most importantly develop their scientific writing skills. Following 4-5 weeks of crystal growing and characterization, students present their data at the end of the semester Crystal Growth Symposium first presenting a 5 minute flash poster-presentation followed by a poster session. The symposium is a collective effort to enhance the students' presentation and communication skills and to showcase and encouraging high quality of research. While still evolving, the laboratory has seen a variety of mainly student-initiated investigations not only exploring a variety of methods to grow crystals, but also in exploring the effect of magnetic field, vibration, temperature, or pH on crystal growth. We will present organizational details of the laboratory program and present examples of many posters that have been generated during four years of operating the laboratory.
Integrating Chemical Crystallography into Advanced Undergraduate Laboratories
Authors: Tanski Joseph
Published: November 2015

As scientific educators, it is important to mentor students in using state-of-the-art instrumentation and in the communication of new knowledge. Just as chemical crystallography and complimentary spectroscopic techniques such as NMR can be fast, effective tools to experimentally determine the structure of molecules and enhance students learning of molecular structure, they can also provide an inspiring opportunity for students to write short, scientific journal style reports that can be edited and published in collaboration with a mentor. This contribution will focus on incorporating X-ray crystallography into an advanced undergraduate integrated laboratory class as part of a discovery based exercise where the students do not know the identity of their small molecule organic compound, and the publication of the resulting crystal structures. The structures of some recently published examples are shown below. With examples of past student projects and published structures, topics will include: sample choice, the discovery based molecular structure determination lab module, structure validation, analysis and discussion of intermolecular interactions such as hydrogen bonding, π-stacking, halogen-halogen interactions, and C-H···X (X = O, N, halogen) interactions, and the writing of descriptions of crystal and molecular structures for publication in collaboration with undergraduate students. This work was supported by grants from the U.S. National Science Foundation, No. 0521237 & 0911324.
Teaching in a Secondary School: Crystal Growth and Basics of Crystallography
Authors: Rychkov Denis , Losev Evgeniy , Boldyreva Elena
Published: November 2015

Nowadays, secondary education provides a broad variety of different compulsory courses giving a solid basis for further student's progress at the university. However, there is an opinion that in this system we are losing the sense of adventures, discoveries and research. Now the main question is if we can efficiently combine compulsory subjects and open classrooms in order to support students in their self-realization needs and provoke interest in mundane school subjects. The educational course for pupils «Crystal Growth – from School Desk to Leading Scientific Research» began several years ago with close cooperation between Novosibirsk State University, the Institute of Solid State Chemistry and Mechanochemistry SB RAS and School #162 of Novosibirsk. The aim of the course is to provide further education in Chemistry and Crystallography via laboratory work and lectures, complementing the standard school program. We provide a targeted syllabus for students from 7 to 17 years old, covering related scientific topics starting from crystal symmetry to the basics of physical chemistry. Through close communication and interaction, pupils develop skills in growing crystals, paying particular attention to obtaining large single crystals of different substances. During the course, pupils crystallize more than 15 different substances using at least 5 different methods and their modifications. At the end of every year, the students are given the opportunity to carry out a personal project, calling on the new knowledge they have obtained from the course. Thus we can assume that an efficient program was developed and realized to support personal ideas and research for school students, based on compulsory subjects and modern experimental techniques. The work was supported by the grant of Dmitry Zimin Fund "Dynasty" "Entertaining Science for pupils" No.DP-55/13, Development Program of University Student Association, NSU, App. No.2012-PSO-225, City Hall grant for young scientists.
3D printing of crystallographic models for interdisciplinary college education
Authors: Moeck Peter , Kaminsky Werner , Snyder Trevor
Published: November 2015

Crystallographic models of molecule and crystal structures, crystal morphologies, Bravais lattices, space and point group symmetries, highly local and extended crystal defects, ... can all be encoded in the Crystallographic Information Framework (CIF) file format. While 3D printing has been available for at least 20 years, cost and performance improvements have only recently made 3D printing practical for usage by college educators and the general public. There is also an industry wide 3D printing standard, the STL file format. Virtual reality freeware programs that include conversions from CIF to STL are openly available [1]. The more than 250,000 entries Crystallography Open Database (COD) has in recent years developed into the world's premier open-access source for CIFs of structures of small molecules and small to medium sized unit cell crystals [2]. The International Advisory Board of the COD also supports a related project [3a], which provides CIFs for interdisciplinary college education. Three of these "COD offspring" databases have started to provide for free downloads of STL files of small molecules, crystal morphologies, and grain boundaries [3b]. These 3D printing files were created directly from the CIFs in these databases. It is now up to interested college educators to develop new pedagogy in teaching crystallography on the basis of 3D models that can be printed out from these files. To facilitate further developments in this field, there is a web portal of open-access crystallography resources to which all interested college educators are invited to contribute [3c].
Structure and Dynamics of DNA-bound Ruthenium Complexes
Authors: Hall James , O'Sullivan Kyra , Niyazi Hakan , Sanchez-Weatherby Juan , Winter Graeme , Sorensen Thomas , Cardin David , Quinn Susan , Kelly John , Cardin Christine
Published: November 2015

Since the 1980s, there has been great interest in how polypyridyl ruthenium complexes bind to DNA. This is due to their photoactive properties[1], which have great potential in photodynamic therapy, as they are able to damage DNA upon photoirradiation. However, there has been significant debate over the precise binding sites of these complexes due to the lack of definitive structural information. Presented here are several high resolution crystal structures showing how these complexes can bind to short DNA oligonucleotides. With each new structure we are able to answer questions about the binding geometry and step specificity which could explain the observations obtained from biophysical measurements in solution. We have shown that the complexes bind by intercalation as well as confirming a previously proposed binding mode, semi-intercalation. We have also shown that the complexes bind with a high level of sequence specificity[2], preferring TA steps over AT and CG and that each enantiomer can bind with a different orientation[3] (Figure 1). One obvious advantage to working with crystal samples is that they possess a well defined molecular structure, which can be determined and is therefore known. Spectroscopic experiments, with data collected in the picosecond and nanosecond timescale, will also be reported with these systems.
Crystal structure of metallo-DNA duplex containing T-Hg(II)-T base pairs
Authors: Kondo Jiro , Yamada Tom , Hirose Chika , Okamoto Itaru , Tanaka Yoshiyuki , Ono Akira
Published: November 2015

The DNA duplex containing mercury-mediated base pairs (T-Hg(II)-T) is an attractive biomacromolecular nanomaterials. In a recent study, it was confirmed that the Hg(II) ion significantly stabilizes a DNA duplex by binding selectively to a T-T mispair [1]. Based on the phenomenon observed, a DNA-based sensing system that selectively and sensitively detects Hg(II) ions in aqueous solution was developed [2]. In the present study, we have solved the first crystal structure of a B-form DNA duplex containing two consecutive T-Hg(II)-T base pairs [3]. The Hg(II) ion occupies the center between two T residues. The geometry of the T-Hg(II)-T base pair is very similar to that of the canonical Watson-Crick base pairs. The distance of N3-Hg(II) bond is 2.0 Å, suggesting that the N3 nitrogen releases an imino-proton even at neutral pH (pKa of N3 position of T is 9.8) and directly bonds to Hg(II). In the B-form DNA, the helical axis runs through the center of base pairs, and the Hg(II) ions are therefore aligned along the helical axis. The distance between the two neighboring Hg(II) ions is 3.3 Å. The relatively short Hg(II)-Hg(II) distance indicates that the metallophilic attraction could exit between them and may stabilize the B-form duplex. To support this, the DNA duplex is largely distorted and adopts an unusual non-helical conformation in the absence of Hg(II). In conclusion, the Hg(II) ion is essential for maintaining the B-form conformation of the DNA duplex containing T-T mispairs. The structure of the Hg(II)-DNA hybrid duplex itself and the Hg(II)-induced structural switching from the non-helical form to the B-form provide the basis for the structure-based design of metal-conjugated nucleic acid nanomaterials.
Biomimetic resorcinarene-based copper(II) complex
Authors: Višnjevac Aleksandar , Gout Jérôme , Bistri-Aslanoff Olivia , Reinaud Olivia
Published: November 2015

"The synthesis, structural characterization, as well as the chemical activity studies of a Cu(II) ""bowl complex", based on the resorcin[4]arene scaffold with three imidazole-containing coordinating arms grafted at the large rim, is presented. This complex is a biomimetic model of a metalloenzyme active site where a cofacial triade of amino-acid residues holds the metal ion in the active site [1]. The trisimidazole ligand reacts with a stoichiometric amount of copper(II) perchlorate to produce a Cu(II) diperchloratocomplex 1. Spectroscopic studies revealed a 5-coordinate SBP environment for the Cu(II) center provided by three imidazole arms, and two extra donors, one embedded in the resorcinarene cavity, the other exposed to the solvent, in exo position. These two labile sites are occupied by either coordinating solvent molecules or residual water, and are readily displaced by carboxylate donors, the position of which (endo or exo) is under tight control of the bowl-cavity. The reaction of 1 with CH3COONa led to a formation of the Cu(II) acetatocomplex 2. Molecular structure of 2 features a rigidified resorcinarene bowl, which was constructed by the addition of the four methylene bridges between the eight hydroxyl groups of the octol precursor [2]. The isolated resorcinarene basket reveals an approximate, non-crystallographic, 4mm point symmetry, and can easily host small guest molecules. Three methylimidazole-containing coordination arms at the large rim coordinate the Cu (II) ion. Its coordination sphere is completed by two O atoms from the intra-cavity bound acetate. The electron donors form a distorted square pyramide, where one of the nitrogens is at the appical position. The endo-coordination of the acetate is supported by an extensive network of intramolecular C-H···O and C-H···π interactions. Complex 2 crystallizes in P21/c space group; a=32.3310 (4)Å, b=11.5490 (1)Å, c=21.6020 (2)Å, beta=102.281(3)0."
Molybdenum and tungsten oxidoreductase model chemistry
Authors: Schulzke Carola , Fischer Christian
Published: November 2015

After introducing the general topic of molybdenum and tungsten dependent oxidoreductases[1] our group's strategic approaches relating to issues posed by the structures and functions of these enzymes' cofactors will be presented. Cofactor related questions will be discussed in detail which, at least to some extent, could be answered by model synthesis and crystallographic plus spectroscopic and/or electrochemical evaluation. These are in particular the influence, the type of coordination to the peptide may have on the catalytic performance, the choice of metal (molybdeum versus tungsten) in these enzymes and the respective evolutionary change in preference.[2,3] Finally some exciting and entirly unanticipated crystallographic discoveries will be presented.These are for instance unusual binding motifs, coordination polymer structures, hydrogen bonding and additional non-covalent interactions between dithiolene sulfur ligand atoms and potassium and sodium counter ions.
Large in-plane deformation of RuO6octahedron and ferromagnetism of bulk SrRuO3
Authors: Lee Sanghyun , Zhang J. R. , Torii S. , Choi Seongil , Cho Deok-Yong , Kamiyama T. , Yu Jaejun , McEwen K. A. , Park Je-Geun
Published: November 2015

Glazer tilting system with tilting and rotation of oxygen octahedron, can describe ABO3 perovskite structure effectively. In highest symmetry, Pm-3m(No. 221) crystal structure is a0a0a0 without tilting and rotation. If temperature is lower, the different atomic radius of A and B causes tilting and rotation of BO6 octahedron. Glazer tiling notation of Pbnm(No. 62, cab lattice) orthorhombic structure is a-a-c+ with antiphase tilting along [110]cubic and in-phase rotation along [001]cubic for neighboring octahedron. SrRuO3 is rare example of itinerant ferromagnetic among 4d oxides. It shows zero thermal expansion, so called Invar effect below ferromagnetic transition(Tc=165 K). Otherwise, paramagnetic CaRuO3 has same Pbnm crystal structure without magnetic transition. To understand Invar effect and ferromagnetism of SrRuO3, We carried out high resolution Time-of-flight powder neutron diffraction using SuperHRPD beamline in J-PARC, with the best resolution Δd/d=0.03% of backscattering bank. Itinerant ferromagnetic SrRuO3 shows 50 fetometer increase of  mean bond below ferromagnetic transition while paramagnetic CaRuO3 shows decrease of  and follows well by the usual thermal expansion. For SrRuO3, Glazer tilting with deformation of RuO6 octahedron explains Invar effect and why lattice a is larger than lattice b in Pbnm structure. The increased  mean bond is considered as coupled order parameter with ferromagnetic transition. The band width of CaRuO3 is almost constant in the whole temperature range whereas ones of SrRuO3 decrease at low temperature. Then more localized Ru 4d orbitals probably contribute ferromagnetic transition.
Crystal structures of 2D coordination networks in [M(bbtr)3](ClO4)2(M=Mn, Cd)
Authors: Kusz Joachim , Nowak Maria , Bronisz Robert , Szklarz Grzegorz
Published: November 2015

[Fe(bbtr)3](ClO4)2 (bbtr=1,4-di(1,2,3-triazol-1-yl)butane) represents a spin crossover (SCO) system where the first coordination sphere consists of 1,2,3-triazole rings coordinated by exodentate nitrogen atoms [1]. Iron(II) ion is linked to six other iron(II) ions by bbtr ligands. This creates two dimensional (2D) polymeric layers. SCO is abrupt, accompanied by hysteresis loop. In the cooling mode P-3 -> P-1 structural phase transition precedes SCO. The non-magnetic structural transformation is accompanied by reorganization of weak intermolecular interactions and shift of 2D layers with respect to each other. Surprisingly, an analog [Fe(bbtr)3](BF4)2, does not exhibit in cooling mode neither thermally SCO nor structural phase transition [2]. To clarify the role of structural phase transition on SCO we have performed structural modifications by exchanging the kind of anions and/or metal ions. An exchange of perchlorate on triflate anion involves deeper structural changes. A topology of the polymeric layer remains the same, but the SCO is shifted to higher temperature and structural phase transition is not observed. The studies of isostructural zinc(II) analogs confirmed the crucial role of anion in the occurrence of non-magnetic structural phase transition. The [Zn(bbtr)3](ClO4)2 exhibites P-3 -> P-1 structural phase transition which is not present in tetrafluoroborate analog [2]. We expand studies on other hexacoordinating metal(II) ions. Reactions between manganese(II) or cadmium(II) perchlorates and bbtr in acetonitrile lead to [M(bbtr)3](ClO4)2 (M=Mn, Cd) complexes. Single crystal X-ray diffraction studies revealed that both compounds create a 2D polymeric networks. The temperature dependence of lattice parameters for these complexes showed that, in contrast to [Fe(bbtr)3](ClO4)2 and [Zn(bbtr)3](ClO4)2 systems, the structural phase transition is not present. This work was funded by the Polish National Science Centre Grant No. DEC-2011/01/B/ST5/06311.
Proton conduction mechanism and phase transition of (Rb,K)3H(SeO4)2
Authors: Kiyanagi Ryoji , Matsuo Yasumitsu , Ishikawa Yoshihisa , Noda Yukio , Ohhara Takashi , Kawasaki Takuro , Oikawa Kenichi , Kaneko Koji , Tamura Itaru , Hanashima Takayasu , Munakata Koji , Nakao Akiko , Kawakita Yukinobu
Published: November 2015

The materials represented as M3H(XO4)2 (M = alkaline metal, X = S or Se) are known to exhibit high protonic conductivities at moderately high temperature. The high protonic conductivity emerges upon a structural phase transition and hydrogen bonds become directionally disordered. The protonic conduction is presumably realized through the disordered hydrogen bonds, but no experimental evidence has been reported. Meanwhile, although the mechanism of the protonic conduction is considered to be the same among this group of materials, the transition temperature (Tc) varies depending on the elements of M and X. For example, the material with M = Rb and X = Se undergoes the transition at 440 K while with M = K and X = Se the transition occurs at 390 K. Since the chemical characteristics of Rb and K are, as a principal, the same, some structural features may play crucial roles in triggering the phase transition. In order to clarify the mechanism of the proton conduction in the superprotonic phase and the relation between the crystal structure and Tc, structural studies on Rb3H(SeO4)2 at high temperature and solid solutions of Rb3H(SeO4)2 and K3H(SeO4)2 (Rb3-xKxH(SeO4)2, x=0,1,2,3) were conducted by means of single crystal neutron diffraction at FONDER at JRR-3M and SENJU at J-PARC/MLF. The proton density distribution map obtained from the high temperature neutron diffraction experiment clearly demonstrates 2-dimensional continuous spread of the proton distribution, which is considered to be the proton conduction path (figure). The structure analyses of Rb3-xKxH(SeO4)2 revealed that K ions tend to occupy one of two possible sites. As the concentration of K ion increases, the distortion of SeO4 appears to be enhanced. The variation of the distortion is consistent with the variation of the transition temperature, suggesting the close relationship between the distortion and the phase transition temperature.
Orbital Order and Structural Phase Transitions in Vanadium Spinel FeV2O4
Authors: Kawaguchi Shogo , Ishibashi Hiroki , Mori Shigeo , Kim Jungeun , Kato Kenichi , Takata Masaki , Nakao Hironori , Yamasaki Yuichi , Kubota Yoshiki
Published: November 2015

Orbital degrees of freedom plays an important role in condensed matter physics because it is strongly related with phase transitions and induces the fascinating physical properties. A spinel oxide FeV2O4is one of the peculiar examples because this compound has double orbital degrees of freedom at both Fe2+and V3+ions. Furthermore, this material represents exotic physical properties [1,2], i.e.; multiferroic, large magnetostriction, and successive structural transitions with decreasing temperature: cubic - tetragonal (c < a: tetraHT, 138K) - orthorhombic (orthoHT, 108 K) - tetragonal (c > a: tetraLT, 68 K). However, the origin of structural transitions and physical properties is controversial until now. In order to clarify the origin, we have performed synchrotron x-ray diffraction experiments at low temperatures at beamline BL02B2 (for the powder samples) in SPring-8 and BL-4C (for the single crystal) of the Photon Factory, KEK. Furthermore, we have carried out the magnetization and the specific heat measurements using polycrystalline samples and single crystal of FeV2O4. We have firstly found another orthorhombic phase (orthoLT) below 30 K in the polycrystalline sample of FeV2O4, shown in figure 1. The Rietveld analysis was performed, and the overall qualities of fittings were fairly good. In order to investigate the details of the orbital state of Fe2+and V3+in FeV2O4, we have performed the normal mode analysis, which is based on static displacements of the tetrahedron of FeO4and octahedron of VO6. In the orthoLT phase, we found the orbital order of Fe2+ions, which is mixture of 3z2-r2and y2-z2orbitals, without change of orbital order of V3+ions. This result indicates that the origin of the orthoLT phase is derived from the competition between cooperative Jahn-Teller effect and relativistic spin-orbit coupling of Fe2+ions. We also discuss the origins of the other phase transitions considering the orbital state of V3+and Fe2+ions, and then the orbital dilution effect, where the structural and magnetic properties are investigated by using powder samples substituted for Fe2+and V3+ions by other ions (Mn2+and Fe3+) with no orbital degrees of freedom.
Structural and magnetic properties of spinel compound Fe1+xCoxV2O4
Authors: Ishibashi Hiroki , Iwane Hiroki , Kawaguchi Shogo , Kubota Yoshiki
Published: November 2015

Vanadium spinel oxides AV2O4have attracted much attention for recent years because they show the peculiar physical properties which are caused by competition and cooperation of spin, orbital and lattice degrees of freedom. Among such compounds, FeV2O4is a unique compound showing successive phase transitions: cubic to tetragonal (c < a) at ~140 K, from tetragonal to orthorhombic accompanied by ferrimagnetic transition at ~110 K and from orthorhombic to tetragonal (c > a) at ~70 K with decreasing temperature. It is suggested that these phase transitions originate from the orbital degrees of freedom of both Fe2+ions at A-site (tetrahedral site) and V3+ones at B-site (octahedral site), however, the origin remains controversial. In the present study, we investigate the substitution effect of Fe2+with Co2+having no orbital degrees of freedom to clarify the role of the orbital degree of Fe2+at the A-site. We carried out magnetization and specific heat measurements and synchrotron powder diffraction experiments by the Debye-Scherrer camera at the beamline BL-8B at Photon Factory in KEK. For x ≤ 0.1, the successive structural transitions similar to that observed in FeV2O4occur although the transition temperature of cubic-to-tetraLT transition rapidly decreases with increasing x. For 0.2≤ x ≤ 0.6, the only structural transition from cubic to tetragonal (c < a) was observed, however, the transition temperatures were somewhat different from the ferrimagnetic transition ones. On the other hand, for x ≥ 0.7, the crystal structure remains cubic down to 10 K similar to that of CoV2O4. These structural properties are discussed in terms of the orbital states of Fe2+ions obtained by the normal mode analysis, and they are compared with the results of the specific heat and magnetization measurements.
Crystal and magnetic structure of new perovskite-based lead iron oxychlorides
Authors: Batuk Maria , Batuk Dmitry , Abakumov Artem , Hadermann Joke
Published: November 2015

The hematophanite Pb4Fe3O8Cl crystal structure is built of incomplete perovskite Pb4Fe3O8 blocks separated by layers of chlorine atoms [1,2]. Each perovskite block consists of a corner-sharing FeO6 octahedral layer sandwiched between the sheets of the FeO5 square pyramids. We have proven that the thickness of the perovskite block in the hematophanite structure can be extended to two and even three octahedral layers forming homologous series with the general formula An+1BnO3n–1Cl (where hematophanite is the n=3 member). The n=4 members with composition Pb4BiFe4O11Cl and Pb5Fe3TiO11Cl have been synthesized. We were also able to introduce Aurivillius-type PbBiO2 blocks between the hematophanite blocks forming another new homologous series [PbBiO2]An+1BnO3n-1Cl2. Two successive members with n=3 (Pb5BiFe3O10Cl2) and n=4 (Pb5Bi2Fe4O13Cl2 and isostructural Pb5BiFe3TiO13Cl2) have been obtained. The crystal and magnetic structure has been determined and refined in a wide temperature range (1.5 – 700 K) using a combination of neutron powder diffraction (NPD) and electron microscopy techniques (electron diffraction, high angle annular dark field scanning transmission electron microscopy (STEM), atomic resolution STEM-EDX). Using NPD and STEM-EDX data we demonstrated that Ti4+ cations occupy both octahedral and square-pyramidal sites. This makes these structural types rare examples of Ti4+ in five-fold oxygen coordination environment. Pb4BiFe4O11Cl and Pb5Fe3TiO11Cl are antiferromagnetically (AFM) ordered below 600(10) and 450(10) K, respectively. Pb5BiFe3O10Cl2, Pb5Bi2Fe4O13Cl2 and Pb5BiFe3TiO13Cl2 demonstrate signs of local magnetic ordering below ~600, ~600 and ~400 K, respectively. However, the long range magnetic ordering does not set in and the magnetic reflections appear enormously broadened merging into a halo. Presumably, AFM ordering establishes within the perovskite blocks but is disrupted along the c-axis, because of a high thickness of the non-magnetic modules.
Nanoscale phase coexistence at the metal-insulator transition in Cu(Ir1–xCrx)2S4
Authors: Bozin Emil , Knox Kevin , Juhas Pavol , Hor Yew San , Mitchell John , Billinge Simon
Published: November 2015

Increasingly, nanoscale phase coexistence and hidden broken symmetry states are being found in the vicinity of metal-insulator transitions (MIT), for example, in high temperature superconductors, heavy fermion and colossal magnetoresistive materials, but their importance and possible role in the MIT and related emergent behaviors is not understood. Despite their ubiquity, they are hard to study because they produce weak diffuse signals in most measurements. Here we propose Cu(Ir1–xCrx)2S4 as a model system for studying nanoscale phase coexistence at the MIT, where robust local structural signals lead to key new insights. We demonstrate by x-ray scattering measurements and atomic pair distribution function approach a hitherto unobserved coexistence of a Ir4+ charge-localized dimer phase and Cr-ferromagnetism. The resulting phase diagram that takes into account the short range dimer order, is highly reminiscent of a generic MIT phase diagram similar to the cuprates. The results represent the first observation of nanoscale phase coexistence in iridates [1]. We suggest that the presence of quenched strain from dopant ions acts as an arbiter deciding between the competing ground states.
Identifying the correct d-block element with aspherical scattering factors
Authors: Dittrich Birger , Roesky Herbert , Singh Amit , Sidhu Navdeep
Published: November 2015

"Element assignment in single-crystal X-ray diffraction (XRD) is based on the number of electrons of a particular atom, so that neighboring elements in the periodic table are often hard to distinguish. 3d-block carbene complexes, e.g. [1], provide examples where the situation is even worse: use of the independent-atom model (IAM) leads to significantly better figures of merit for the element left to the correct one in the periodic table, and the element can hence not be identified by XRD using the IAM without prior chemical knowledge. This is readily explained by the characteristics of the ligand, which can cause electron-deficiency at the metal center. Hence Cu instead of Zn gives a significantly better fit to the diffraction data in the IAM in our example, although the heavier element is unambiguously present. Rearrangements in the aspherical valence electron-density distribution (EDD) hence forbid to reliably distinguish and to correctly identify the metal atom in such coordination compounds with conventional methodology, whereas aspherical scattering factors allow a correct assignment. These findings clearly illustrate the need to sometimes go beyond ""spherical-atoms"". We show how ""whole molecule"" aspherical scattering factors derived from theoretical computations within the Hansen/Coppens mutlipole model EDD description [2a] can be successfully used in least-squares refinement. A related approach is Hirshfeld-atom refinement [2b], but for network structures, disordered molecules and those with atoms on special positions this approach is not always technically feasible. The suggested modeling procedure is based on the invariom database [3] and its capability to predict quantum chemical X-H bond distances involving hydrogen, and is amenable to d-block compounds where all-electron calculations are possible. Due to the important role of aspherical EDD in the vicinity of the central atom we expect that similar behavior will occur in linear and square-planar, but not in tetrahedral and octahedral coordination."
Locating Cu in Zeolite SSZ-13 by Synchrotron PXRD Using Maximum Entropy Method
Authors: Andersen Casper , Bremholm Martin , Vennestrøm Peter , Blichfeld Anders , Lundegaard Lars , Iversen Bo
Published: November 2015

Efficient elimination of environmentally harmful gaseous NOx compounds from automotive diesel emission remains a challenging task. State-of-the-art zeolites with the chabazite framework containing catalytically active Cu2+ (Cu-SSZ-13) have been commercialized as NOx after-treatment catalysts in diesel-powered vehicles, due to its superior activity, selectivity, and durability.[1] However, to meet current and future legislative demands, continuous improvement is of fundamental interest. Prerequisites for an in depth understanding and further improvements, are detailed complete structural models of the Cu-loaded catalyst. This may be achieved by the use of high resolution synchrotron powder X-ray diffraction (PXRD) and iterative Rietveld analysis and Maximum Entropy Method (MEM). Since the content of Cu2+ is low, a protonated system (H-SSZ-13) and model system with monovalent Ag+ ions (Ag-SSZ-13) are also examined. The protonated and dehydrated H-SSZ-13 shows perfectly empty voids, i.e. no water residue or other non-framework species. The H-SSZ-13 structure is used as the initial model for the MEM calculations. For Ag-SSZ-13 MEM analysis clearly pinpoints the Ag+ ion as being located in the 6-ring shifted into the chabazite cage (Figure 1), consistent with the generally accepted site for Ag+ ions in chabazite and reveals the strength of the iterative Rietveld/MEM analysis. For the more challenging case of Cu-SSZ-13 it was still possible through careful analysis and reasoning to locate two separate positions for the Cu2+ in Cu-SSZ-13 (Figure 1). The B site has been suggested by several other studies, but never confirmed experimentally.[2] This is the most complete structural description of zeolite SSZ-13 with stabilizing and catalytically active Cu2+ ions.[3]
Electron density of molecular crystals at high pressure from synchrotron data
Authors: Macchi Piero , Casati Nicola , Kleppe Annette , Jephcoat Andrew
Published: November 2015

Accurate electron density mapping is quite a common practice for crystals cooled at low temperature and accurately measured. This is not true for species under external perturbation, due to complicated experimental conditions. Studying molecular crystals in excited states is a challenge, Coppens(2009), and a purely experimental electron density mapping is not possible at present. So far, the same limitation affected molecular crystals at high pressure, with only few attempts to use theoretical multipoles to fit experimental data, Fabbiani (2011). Here we report on the first unconstrained multipolar model, refined for syn-l,6;8,13 biscarbonyl[14]annulene (BCA) at P=7.7 GPa. BCA was the subject of a low temperature data collection by Destro (1995). The molecule (close to C2v symmetry) has a fair aromaticity, but it progressively localizes double and single bonds as a function of pressure. At 7.7 GPa the geometrical distortion is quite evident and mirrored by the electron density. The experiment, carried out at Diamond Light Source, was possible combining: a) high energy (40 Kev) to overcome the resolution problems caused by diamond anvil cells and reduce absorption and extinction; b) microfocused beam (30 micron) to minimize spurious X-ray diffusion; c) two crystals in the DAC, to increase data coverage; d) sufficient pressure to quench atomic motion. The final agreement is obviously worse than what typically obtained at ambient pressure. However, the model is satisfactory because: a) the deformation density is sensible and in agreement with the calculated one; b) the distribution of residuals is normal and no significant error is evident. The study proves that aromatic molecules are more reactive when squeezed, in keeping with the recent theoretical study by Hoffmann et al. on benzene. The Figure shows the static deformation density of BCA in 3D, obtained from a multipolar model refined against the experimental structure factors.
X-ray powder diffraction for charge density studies
Authors: Als-Nielsen Jens
Published: November 2015

Issues concerning optimal powder diffraction at synchrotron sources for charge density studies will be discussed. These include beam qualities (energy, bandwidth, brillance, flux) as well as sample environmnet (vaccuum, capillary, temperature) and detector type (image plate, crystal analyzer). Simple on-line analysis in obtaining structure factors will be presented.