47 results on '"crystal-structure"'
Search Results
2. Heptacopper(II) and dicopper(II)-adenine complexes: synthesis, structural characterization, and magnetic properties
- Author
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Félix, V. [Univ. of Aveiro (Portugal). Dept. of Chemistry and Dept. of Health Sciences]
- Published
- 2015
- Full Text
- View/download PDF
3. Synthesis, selected coordination chemistry and extraction behavior of a (phosphinoylmethyl)pyridyl N-oxide-functionalized ligand based upon a 1,4-diazepane platform
- Author
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Paine, Robert [Univ. of New Mexico, Albuquerque, NM (United States)]
- Published
- 2015
- Full Text
- View/download PDF
4. Medium range order and structural relaxation in As–Se network glasses through FSDP analysis
- Author
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Jain, H. [Lehigh Univ., Bethlehem, PA (United States). Dept. of Materials Science and Engineering]
- Published
- 2015
- Full Text
- View/download PDF
5. Computational Study of Symmetric Methylation on Histone Arginine Catalyzed by Protein Arginine Methyltransferase PRMT5 through QM/MM MD and Free Energy Simulations
- Author
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Guo, Hong [Univ. of Tennessee, Knoxville, TN (United States)]
- Published
- 2015
- Full Text
- View/download PDF
6. A 3-Dimensional Trimeric β-Barrel Model for Chlamydia MOMP Contains Conserved and Novel Elements of Gram-Negative Bacterial Porins
- Author
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Feher, Victoria A, Randall, Arlo, Baldi, Pierre, Bush, Robin M, de la Maza, Luis M, Amaro, Rommie E, and Motta, Andrea
- Subjects
Outer-Membrane Proteins ,Crystal-Structure ,Oligomerization State ,Escherichia-Coli ,Functional-Characterization ,Transmembrane Domains ,Angstrom Resolution ,Secondary Structure ,Structural Basis ,Neural-Network - Published
- 2013
7. Tight-binding model of the photosystem II reaction center: application to two-dimensional electronic spectroscopy
- Author
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Gelzinis, Andrius, Valkunas, Leonas, Fuller, Franklin D, Ogilvie, Jennifer P, Mukamel, Shaul, and Abramavicius, Darius
- Subjects
Primary Charge Separation ,Reaction-Center Complex ,Modified Redfield Theory ,Site-Directed Mutations ,Quantum Coherence ,Crystal-Structure ,Optical-Spectra ,Energy-Transfer ,Photosynthetic Complexes ,Rhodobacter-Sphaeroides - Published
- 2013
8. Inferring Epitopes of a Polymorphic Antigen Amidst Broadly Cross-Reactive Antibodies Using Protein Microarrays: A Study of OspC Proteins of Borrelia burgdorferi
- Author
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Baum, Elisabeth, Randall, Arlo Z, Zeller, Michael, Barbour, Alan G, and Chang, Yung-Fu
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Outer Surface Protein ,Early Lyme-Disease ,Linked-Immunosorbent-Assay ,Sensu-Stricto ,Hematogenous Dissemination ,Active Immunization ,Crystal-Structure ,Immune-Response ,C Ospc ,Mice - Published
- 2013
9. Homo-dimerization and ligand binding by the leucine-rich repeat domain at RHG1/RFS2 underlying resistance to two soybean pathogens
- Author
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Afzal, Ahmed J, Srour, Ali, Goil, Abhishek, Vasudaven, Sheeja, Liu, Tianyun, Samudrala, Ram, Dogra, Navneet, Kohli, Punit, Malakar, Ayan, and Lightfoot, David A
- Subjects
Receptor ,Leucine-Rich Repeat ,Ligand ,Peptide ,Cross-Link ,PredictedProtein-Structure Prediction ,Crystal-Structure ,Plant Defense ,Hierarchical Approach ,Nematode Resistance ,Receptor ,Recognition ,Perception ,Inhibition ,Evolution - Published
- 2013
10. Structural and biochemical characterization of the essential DsbA-like disulfide bond forming protein from Mycobacterium tuberculosis
- Author
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Chim, Nicholas, Harmston, Christine A, Guzman, David J, and Goulding, Celia W
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Mycobacterium Tuberculosis ,Disulfide Bond ,X-Ray Crystallography ,Dsba ,Vitamin K Epoxide Reductase ,OxidoreductaseEscherichia-Coli ,Crystal-Structure ,In-Vivo ,Vibrio-Cholerae ,Functional-Characterization ,Destabilizing Disulfide ,Folding Catalyst ,Membrane-Protein ,Formation Invivo ,Isomerase - Published
- 2013
11. Enhancing the Resilience of Human–Environment Systems: a Social Ecological Perspective
- Author
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Stokols, Daniel, Lejano, Raul Perez, and Hipp, John
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Health-Promotion ,Psychology ,Dimensions ,Framework ,Ecosystem ,Justice ,Science ,Lifeouter-membrane proteins ,crystal-structure ,oligomerization state ,escherichia-coli ,functional-characterization ,transmembrane domains ,angstrom resolution ,secondary structure ,structural basis ,neural-network - Published
- 2013
12. A Catalytic Mechanism for Cysteine N-Terminal Nucleophile Hydrolases, as Revealed by Free Energy Simulations
- Author
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Lodola, Alessio, Branduardi, Davide, De Vivo, Marco, Capoferri, Luigi, Mor, Marco, Piomelli, Daniele, and Cavalli, Andrea
- Subjects
hydrolyzing acid amidase ,bile-salt hydrolase ,scc-dftb method ,molecular-dynamics simulations ,hybrid qm/mm simulations ,penicillin-v-acylase ,crystal-structure ,enzyme catalysis ,20s proteasome ,ceramidase - Abstract
The N-terminal nucleophile (Ntn) hydrolases are a superfamily of enzymes specialized in the hydrolytic cleavage of amide bonds. Even though several members of this family are emerging as innovative drug targets for cancer, inflammation, and pain, the processes through which they catalyze amide hydrolysis remains poorly understood. In particular, the catalytic reactions of cysteine Ntn-hydrolases have never been investigated from a mechanistic point of view. In the present study, we used free energy simulations in the quantum mechanics/molecular mechanics framework to determine the reaction mechanism of amide hydrolysis catalyzed by the prototypical cysteine Ntn-hydrolase, conjugated bile acid hydrolase (CBAH). The computational analyses, which were confirmed in water and using different CBAH mutants, revealed the existence of a chair-like transition state, which might be one of the specific features of the catalytic cycle of Ntn-hydrolases. Our results offer new insights on Ntn-mediated hydrolysis and suggest possible strategies for the creation of therapeutically useful inhibitors.
- Published
- 2012
13. Structural Characterisation of Tpx from Yersinia pseudotuberculosis Reveals Insights into the Binding of Salicylidene Acylhydrazide Compounds
- Author
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Gabrielsen, Mads, Beckham, Katherine H., Feher, Victoria A., Zetterstrom, Caroline E., Wang, Dai, Muller, Sylke, Elofsson, Mikael, Amaro, Rommie E., Byron, Olwyn, and Roe, Andrew J.
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small-angle scattering ,x-ray solution ,thiol peroxidase ,escherichia-coli ,mycobacterium-tuberculosis ,biological macromolecules ,protein interactions ,crystal-structure ,iii secretion ,peroxiredoxin - Abstract
Thiol peroxidase, Tpx, has been shown to be a target protein of the salicylidene acylhydrazide class of antivirulence compounds. In this study we present the crystal structures of Tpx from Y. pseudotuberculosis (ypTpx) in the oxidised and reduced states, together with the structure of the C61S mutant. The structures solved are consistent with previously solved atypical 2-Cys thiol peroxidases, including that for “forced” reduced states using the C61S mutant. In addition, by investigating the solution structure of ypTpx using small angle X-ray scattering (SAXS), we have confirmed that reduced state ypTpx in solution is a homodimer. The solution structure also reveals flexibility around the dimer interface. Notably, the conformational changes observed between the redox states at the catalytic triad and at the dimer interface have implications for substrate and inhibitor binding. The structural data were used to model the binding of two salicylidene acylhydrazide compounds to the oxidised structure of ypTpx. Overall, the study provides insights into the binding of the salicylidene acylhydrazides to ypTpx, aiding our long-term strategy to understand the mode of action of this class of compounds.
- Published
- 2012
14. Ensemble-Based Computational Approach Discriminates Functional Activity of p53 Cancer and Rescue Mutants
- Author
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Demir, Özlem, Baronio, Roberta, Salehi, Faezeh, Wassman, Christopher D, Hall, Linda, Hatfield, G. Wesley, Chamberlin, Richard, Kaiser, Peter, Lathrop, Richard H, Amaro, Rommie E, and Gilson, Michael
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2nd-site suppressor mutations ,dna-binding domain ,molecular-dynamics ,core domain ,crystal-structure ,structural basis ,wild-type ,restoration ,simulation ,stability - Abstract
The tumor suppressor protein p53 can lose its function upon single-point missense mutations in the core DNA-binding domain ("cancer mutants''). Activity can be restored by second-site suppressor mutations ("rescue mutants''). This paper relates the functional activity of p53 cancer and rescue mutants to their overall molecular dynamics (MD), without focusing on local structural details. A novel global measure of protein flexibility for the p53 core DNA-binding domain, the number of clusters at a certain RMSD cutoff, was computed by clustering over 0.7 mu s of explicitly solvated all-atom MD simulations. For wild-type p53 and a sample of p53 cancer or rescue mutants, the number of clusters was a good predictor of in vivo p53 functional activity in cell-based assays. This number-of-clusters (NOC) metric was strongly correlated (r(2) = 0.77) with reported values of experimentally measured Delta Delta G protein thermodynamic stability. Interpreting the number of clusters as a measure of protein flexibility: (i) p53 cancer mutants were more flexible than wild-type protein, (ii) second-site rescue mutations decreased the flexibility of cancer mutants, and (iii) negative controls of non-rescue second-site mutants did not. This new method reflects the overall stability of the p53 core domain and can discriminate which second-site mutations restore activity to p53 cancer mutants.
- Published
- 2011
15. ATP Competitive Protein Kinase C Inhibitors Demonstrate Distinct State-Dependent Inhibition
- Author
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Smith, Ida M. and Hoshi, Naoto
- Subjects
crystal-structure ,catalytic domain ,phosphorylation ,binding ,suppression ,substrate ,reporter ,channels ,peptide ,complex - Abstract
We previously reported that some ATP competitive protein kinase C (PKC) inhibitors are either competitive or uncompetitive inhibitors with respect to substrate peptides. In this report, we demonstrate how the interactions between PKC and inhibitors change PKC activation kinetics. A substrate competitive inhibitor, bisindolylmaleimide I, targets activated PKC and stabilizes PKC in the activated conformation. This leads to transient activation and prolonged deactivation of PKC in the presence of bisindolylmaleimide I. In contrast, an uncompetitive substrate inhibitor, bisindolylmaleimide IV, targets quiescent PKC and stabilizes PKC in the quiescent conformation, which generates slower activation and suppressed translocation upon activation of PKC.
- Published
- 2011
16. Evolution and Distribution of the ospC Gene, a Transferable Serotype Determinant of Borrelia burgdorferi
- Author
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Barbour, Alan G and Travinsky, Bridgit
- Subjects
lyme-disease spirochete ,surface protein-c ,northeastern united-states ,sensu-stricto ,peromyscus-leucopus ,antigenic variation ,crystal-structure ,north-america ,tick vector ,mice - Abstract
Borrelia burgdorferi, an emerging bacterial pathogen, is maintained in nature by transmission from one vertebrate host to another by ticks. One of the few antigens against which mammals develop protective immunity is the highly polymorphic OspC protein, encoded by the ospC gene on the cp26 plasmid. Intragenic recombination among ospC genes is known, but the extent to which recombination extended beyond the ospC locus itself is undefined. We accessed and supplemented collections of DNA sequences of ospC and other loci from ticks in three U. S. regions (the Northeast, the Midwest, and northern California); a total of 839 ospC sequences were analyzed. Three overlapping but distinct populations of B. burgdorferi corresponded to the geographic regions. In addition, we sequenced 99 ospC flanking sequences from different lineages and compared the complete cp26 sequences of 11 strains as well as the cp26 bbb02 loci of 56 samples. Besides recombinations with traces limited to the ospC gene itself, there was evidence of lateral gene transfers that involved (i) part of the ospC gene and one of the two flanks or (ii) the entire ospC gene and different lengths of both flanks. Lateral gene transfers resulted in different linkages between the ospC gene and loci of the chromosome or other plasmids. By acquisition of the complete part or a large part of a novel ospC gene, an otherwise adapted strain would assume a new serotypic identity, thereby being comparatively fitter in an area with a high prevalence of immunity to existing OspC types. IMPORTANCE The tick-borne zoonosis Lyme borreliosis is increasing in incidence and spreading geospatially in North America. Further understanding of the evolution and genetics of its cause, Borrelia burgdorferi, in its environments fosters progress toward ecologically based control efforts. By means of DNA sequencing of a large sample collection of the pathogen from across the United States, we studied the gene for the bacterium's highly diverse OspC protein, protective immunity against which develops in animals. We found that the distributions and frequencies of types of OspC genes differed between populations of B. burgdorferi in the Northeast, the Midwest, and California. Over time, OspC genes were transferred between strains through recombinations involving the whole or parts of the gene and one or both flanks. Acquisitions of OspC genes that are novel for the region confer to recipients unique identities to host immune systems and, presumably, selective advantage when immunity to existing types is widespread among hosts.
- Published
- 2010
17. The Anopheles gambiae Odorant Binding Protein 1 (AgamOBP1) Mediates Indole Recognition in the Antennae of Female Mosquitoes
- Author
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Biessmann, Harald, Andronopoulou, Evi, Biessmann, Max R., Douris, Vassilis, Dimitratos, Spiros D., Eliopoulos, Elias, Guerin, Patrick M., Iatrou, Kostas, Justice, Robin W., Krober, Thomas, Marinotti, Osvaldo, Tsitoura, Panagiota, Woods, Daniel F., and Walter, Marika F.
- Subjects
pheromone-sensitive neurons ,culex-quinquefasciatus ,oviposition attractants ,sexual attraction ,malaria mosquito ,crystal-structure ,silkworm moth ,identification ,receptor ,expression - Abstract
Haematophagous insects are frequently carriers of parasitic diseases, including malaria. The mosquito Anopheles gambiae is the major vector of malaria in sub-Saharan Africa and is thus responsible for thousands of deaths daily. Although the role of olfaction in A. gambiae host detection has been demonstrated, little is known about the combinations of ligands and odorant binding proteins (OBPs) that can produce specific odor-related responses in vivo. We identified a ligand, indole, for an A. gambiae odorant binding protein, AgamOBP1, modeled the interaction in silico and confirmed the interaction using biochemical assays. RNAi-mediated gene silencing coupled with electrophysiological analyses confirmed that AgamOBP1 binds indole in A. gambiae and that the antennal receptor cells do not respond to indole in the absence of AgamOBP1. This case represents the first documented instance of a specific A. gambiae OBP–ligand pairing combination, demonstrates the significance of OBPs in odor recognition, and can be expanded to the identification of other ligands for OBPs of Anopheles and other medically important insects.
- Published
- 2010
18. Removal of pertechnetate from simulated nuclear waste streams using supported zerovalent iron
- Author
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Darab, John
- Subjects
Inorganic, organic, physical and analytical chemistry ,Nuclear fuel cycle and fuel materials ,CRYSTAL-STRUCTURE ,REMEDIATION ,TECHNETIUM ,SPECTROSCOPY ,CHEMISTRY ,GLASS - Abstract
The application of nanoparticles of predominantly zerovalent iron (nanoiron), either unsupported or supported, to the separation and reduction of pertechnetate anions (TcO4-) from complex waste mixtures was investigated as an alternative approach to current waste-processing schemes. Although applicable to pertechnetate-containing waste streams in general, the research discussed here was directed at two specific potential applications at the U.S. Department of Energy"s Hanford Site: (1) the direct removal of pertechnetate from highly alkaline solutions, typical of those found in Hanford tank waste, and (2) the removal of dilute pertechnetate from near-neutral solutions, typical of the eluate streams from commercial organic ion-exchange resins that may be used to remediate Hanford tank wastes. It was envisioned that both applications would involve the subsequent encapsulation of the loaded sorbent material into a separate waste form. A high surface area (>200 M2/g) base-stable, nanocrystalline zirconia was used as a support for nanoiron for tests with highly alkaline solutions, while a silica gel support was used for tests with near-neutral solutions. It was shown that after 24 h of contact time, the high surface area zirconia supported nanoiron sorbent removed about 50percent (K-d = 370 L/kg) of the pertechnetate from a pH 14 tank waste simulant containing 0.51 mM TCO4- and large concentrations of Na+, OH-, NO3-, and CO32- for a phase ratio of 360 L simulant per kg of sorbent. It was also shown that after 18 h of contact time, the silica-supported nanoiron removed >95percent pertechnetate from a neutral pH eluate simulant containing 0.076 mM TcO4_ for a phase ratio of 290 L/kg. It was determined that in all cases, nanoiron reduced the Tc(VII) to Tc(IV), or possibly to Tc(V), through a redox reaction. Finally, it was demonstrated that a mixture of 20 mass percent of the solid reaction products obtained from contacting zirconia- supported nanoiron with an alkaline waste solution containing Re(VII), a surrogate for Tc(VII), with 80 mass percent alkali borosilicate based frit heat-treated at 700 degrees C for 4 h sintered into an easily handled glass composite waste form.
- Published
- 2008
19. Removal of pertechnetate from simulated nuclear waste streams using supported zerovalent iron
- Author
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Shuh, David
- Published
- 2007
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20. A phage display selection of engrailed homeodomain mutants and the importance of residue Q50
- Author
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Simon, Matthew D., Sato, Ken, Weiss, Gregory A., and Shokat, Kevan M.
- Subjects
dna-binding specificity ,zinc-finger proteins ,recognition helix ,crystal-structure ,angstrom resolution ,complex ,interface ,sequences ,promoter ,affinity - Abstract
Mutants of engrailed homeodomain (HD) that retain DNA-binding activity were isolated using a phage display selection. This selection was used to enrich for active DNA-binding clones from a complex library consisting of over a billion members. A more focused library of mutant homeodomains consisting of all possible amino acid combinations at two DNA-contacting residues (I47 and Q50) was constructed and screened for members capable of binding tightly and specifically to the engrailed consensus sequence, TAATTA. The isolated mutants largely recapitulated the distribution of amino acids found at these positions in natural homeodomains thus validating the in vitro selection conditions. In particular, the unequivocal advantage enjoyed by glutamine at residue 50 is surprising in light of reports that minimize the importance of this residue. Here, the subtle contributions of residue Q50 are demonstrated to play a functionally important role in specific recognition of DNA. These results highlight the complex subtlety of protein–DNA interactions, underscoring the value of the first reported in vitro selection of a homeodomain.
- Published
- 2004
21. The crystal-chemistry of riebeckite, ideally Na2Fe32+ Fe23+Si8O22(OH)2: a multi-technique study.
- Author
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Susta, Umberto, Della Ventura, Giancarlo, Hawthorne, Frank C., Abdu, Yassir A., Day, Maxwell C., Mihailova, Boriana, and Oberti, Roberta
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ELECTRON probe microanalysis , *MASS spectrometry , *MOSSBAUER spectroscopy , *PLASMA spectroscopy , *SINGLE crystals - Abstract
In this work we report on a complete crystal-chemical characterization of a near end-member riebeckite from Malawi, and use the available data to critically compare information obtained from different analytical methods. The sample occurs as well-formed and very large single crystals in pegmatitic rocks. Accurate site-populations were determined by combining single-crystal structure refinement and electron microprobe analysis (EMPA). The Fe3+/Fe2+ ratio was obtained from Mössbauer spectroscopy. Lithium was quantified by Laser Ablation Inductively Coupled Plasma Mass Spectroscopy (LA-ICP-MS). Fourier-Transform Infrared (FTIR) spectra, collected both on powders and single crystals, are presented and discussed. FTIR spectra in the NIR region are also presented for the first time for this amphibole. The FTIR data are compatible with complete local ordering of A cations close to F, and complete Fe2+/Mg disorder at M (1,3). Polarized Raman-scattering data collected from single crystals confirm this conclusion. In addition, it was found that FTIR data collected on powders provide the best agreement with the site occupancies derived from chemical (EMPA and LA-ICP-MS) and crystal-chemical data, possibly because they do not depend on experimental issues such as orientation and polarization. [ABSTRACT FROM AUTHOR]
- Published
- 2018
- Full Text
- View/download PDF
22. Relationship between the Structure and Properties of Pharmaceutical Crystals
- Author
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Agam R. Sheth and David J.W. Grant
- Subjects
mechanical properties ,hydrates/solvates ,amorphous ,clathrates ,crystal-structure ,processing ,polymorphism ,physicochemical properties ,x-ray powder diffractometry ,solid state ,Technology (General) ,T1-995 ,Nuclear and particle physics. Atomic energy. Radioactivity ,QC770-798 - Abstract
The majority of drug products are solid dosage forms, most of which contain the drug substance in the crystalline state. This review considers the forces responsible for crystal packing, the various types of pharmaceutical crystals, and the methods used to determine the structure of pharmaceutical crystals. These topics provide background for the main thrust, which focuses on the importance of studying the structure of pharmaceutical crystals with particular stress on phase changes of crystal forms of drugs during pharmaceutical processing and implications of different solid forms of drugs on its mechanical properties. The present review does not consider pharmaceutical co-crystals, which could be the subject of another review.
- Published
- 2014
- Full Text
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23. Predicting cation ordering in MgAl 2 O 4 using genetic algorithms and density functional theory.
- Author
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Mohn, Chris E.
- Subjects
ALUMINUM-magnesium alloys ,GENETIC algorithms ,DENSITY functional theory ,POTENTIAL energy surfaces ,LOW temperatures - Abstract
Genetic algorithms (GAs) together with classical pair potentials and density functional theory (DFT) are used to investigate cation order in MgAl2O4(Spinel). To efficiently locate the global minimum/minima on the system potential energy surface, corresponding to the ordered and fully equilibrated low-temperature phase, local structural optimizations are essential. Such energy minimizations are expensive at the DFT level, but a comparison of the distribution of the energy minima from DFT and popular classical pair potentials allows one to rapidly tune the GA parameters. We show that GAs are able to find, not only the global minimum on the potential energy, but also other low-energy cation configurations representing possible frozen-in disordered or metastable phases after quenching. The nature of these low-energy configurations can help to interpret the extent of kinetic trapping which hampers the comparison between different experimental studies. [ABSTRACT FROM PUBLISHER]
- Published
- 2018
- Full Text
- View/download PDF
24. Investigation of the phase relations in the U-Al-Ge ternary system: Influence of the Al/Ge substitution on the properties of the intermediate phases.
- Author
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Moussa, C., El Sayah, Z., Chajewski, G., Berche, A., Dorcet, V., Pikul, A.P., Pasturel, M., Joanny, L., Stepnik, B., and Tougait, O.
- Subjects
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TERNARY system , *X-ray powder diffraction , *THERMAL analysis , *FERROMAGNETIC materials , *SOLID state chemistry - Abstract
The phase relations within the U-Al-Ge ternary system were studied for two isothermal sections, at 673 K for the whole Gibbs triangle and at 1173 K for the concentration range 25–100 at% U. The identification of the phases, their composition ranges and stability were determined by x-ray powder diffraction, scanning electron microscopy coupled to energy dispersive spectroscopy and differential thermal analysis. The tie-lines and the solubility domains were determined for the U-Ge and U-Al binaries, the UAl 3 -UGe 3 solid-solution and for the unique ternary intermediate phase U 3 Al 2−x Ge 3+x . The experimental isopleth section of the pseudo-binary UAl 3 -UGe 3 reveals an isomorphous solid solution based on the Cu 3 Au-type below the solidus. The U 3 Al 2−x Ge 3+x solid solution extends for −0.1≤x≤1.35 and −0.2≤x≤1.5 at 673 K and 1173 K respectively. It crystallizes in the I -centered tetragonal symmetry. The reciprocal lattice of several compositions of the U 3 Al 2−x Ge 3+x solid solution was examined by electron diffraction at room temperature, revealing the presence of a c -glide plane. Their crystal structure was refined by single crystal x-ray diffraction suggesting an isomorphous solid solution best described with the non-centrosymmetric space group I 4 cm in the paramagnetic domain. The magnetic measurements confirm the ferromagnetic ordering of the solid solution U 3 Al 2−x Ge 3+x with an increase of Tc with the Al content. The thermal variation of the specific heat bear out the magnetic transitions with some delocalized character of the uranium 5 f electrons. [ABSTRACT FROM AUTHOR]
- Published
- 2016
- Full Text
- View/download PDF
25. Reduced partition function ratios of iron and oxygen in goethite
- Author
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Balan, E.
- Published
- 2015
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26. Molecular and Electronic Structure of Cyclic Trinuclear Gold(I) Carbeniate Complexes: Insights for Structure/Luminescence/Conductivity Relationships
- Author
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Omary, Mohammad [University of North Texas]
- Published
- 2014
- Full Text
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27. Preparation and reactivity of macrocyclic rhodium(III) alkyl complexes
- Author
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Bakac, Andreja [Ames Lab., Ames, IA (United States); Iowa State Univ., Ames, IA (United States)]
- Published
- 2013
- Full Text
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28. Extremely low thermal conductivity in BaSb2Se4: Synthesis, characterization, and DFT studies.
- Author
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Jana, Subhendu, Panigrahi, Gopabandhu, Ummethala, Govind, Ghosh, Arghya, Malladi, Sairam K., Niranjan, Manish K., and Prakash, Jai
- Subjects
- *
THERMAL conductivity , *ELECTRONIC structure , *SINGLE crystals , *CHEMICAL bonds , *SPACE groups , *CRYSTAL structure - Abstract
We report the synthesis of black-colored crystals and a polycrystalline phase of BaSb 2 Se 4 by high-temperature reaction of elements at 1173 K and 973 K, respectively. The X-ray diffraction studies show that it crystallizes in the monoclinic P 2 1 / c space group, and the structure is composed of one-dimensional stripes of ∞ 1 [Sb 2 Se 4 ]2− that are separated by the Ba2+ cations. The optical absorption study reveals the semiconducting nature (E g = 1.3(1) eV) of the polycrystalline BaSb 2 Se 4 sample. A thermal conductivity (κ) study shows a gradual decrease of the κ -value from ∼0.39 W/mK to ∼0.29 W/mK on heating the polycrystalline sample from 300 K to 773 K. The DFT study of the electronic structure of BaSb 2 Se 4 shows that the bandgap is indirect with a magnitude in the range of ∼1.0–1.6 eV depending on the choice of XC functional. The COHP analysis has been performed to investigate the relative strengths of chemical bonding between pertinent atoms in the BaSb 2 Se 4 structure. [Display omitted] • Single crystals and polycrystalline BaSb 2 Se 4 were synthesized. • The crystal structure of BaSb 2 Se 4 was established using the SCXRD study. • A low thermal conductivity value of ∼0.29 W/mK at 773 K was found for polycrystalline BaSb 2 Se 4. • The HRTEM analysis was performed for the polycrystalline BaSb 2 Se 4. • The electronic structure of BaSb 2 Se 4 was studied using the DFT method. [ABSTRACT FROM AUTHOR]
- Published
- 2022
- Full Text
- View/download PDF
29. Stability of ironcrystal structures at 0.3–1.5 TPa.
- Author
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Godwal, B.K., González-Cataldo, F., Verma, A.K., Stixrude, Lars, and Jeanloz, Raymond
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IRON crystals , *CRYSTAL structure , *ELECTRONIC structure , *AB initio quantum chemistry methods , *MOLECULAR dynamics , *EARTH'S core - Abstract
Ab initio molecular dynamics simulations carried out for tetragonal and orthorhombic distortions of iron closely follow the results of static-lattice electronic-structure calculations in revealing that the body-centered cubic ( bcc ) phase of Fe is mechanically unstable at pressures of 0.3–1.5 TPa and temperatures up to 7000 K. Crystal-structural instabilities originate in the static lattice for the bcc configuration, and are consistent with recent results from both static and dynamic high-pressure experiments. Both theory and experiment thus show that the close-packed (hexagonal, hcp and face-centered cubic, fcc ) crystal structures of iron are those relevant to the cores of Earth-like planets. [ABSTRACT FROM AUTHOR]
- Published
- 2015
- Full Text
- View/download PDF
30. Ordered vs. disordered perovskites; structural studies of Fe-doped SrIrO3 and SrRuO3.
- Author
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Qasim, Ilyas, Blanchard, Peter E.R., Liu, Samuel, Tang, Chunguang, Kennedy, Brendan J., Avdeev, Maxim, and Kimpton, Justin A.
- Subjects
- *
STRONTIUM compounds , *PEROVSKITE , *DOPING agents (Chemistry) , *CRYSTAL structure , *NEUTRON diffraction , *SYNCHROTRONS - Abstract
Abstract: The structures of the two Fe containing perovskites Sr2IrFeO6 and SrRu0.5Fe0.5O3 have been established using a combination of synchrotron and neutron diffraction methods. Sr2IrFeO6 and SrRu0.5Fe0.5O3 are shown to be monoclinic I2/m and tetragonal I4/mcm respectively The former exhibits a rock-salt like ordering of the Fe and Ir cations and displays a sequence of phase transitions associated with the loss of the octahedral tilts upon heating; . The Fe and Ru cations are disordered in SrRu0.5Fe0.5O3 and this shows a single structural phase transition upon heating due to the loss of the in-phase tilts, viz. . In both cases XANES measurements show partial oxidation of the Fe3+ to Fe4+. The difference in the structures between the two is remarkable given the similar size of Ir5+ and Ru5+, and this is reflected in their magnetic properties. [Copyright &y& Elsevier]
- Published
- 2013
- Full Text
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31. Temperature-dependent structural studies of mullite-type Bi2Fe4O9
- Author
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Murshed, M. Mangir, Nénert, Gwilherm, Burianek, Manfred, Robben, Lars, Mühlberg, Manfred, Schneider, Hartmut, Fischer, Reinhard X., and Gesing, Thorsten M.
- Subjects
- *
MULLITE , *MOLECULAR structure , *BISMUTH compounds , *CRYSTAL structure , *TEMPERATURE effect , *NEUTRON diffraction - Abstract
Abstract: We report on the temperature-dependent structural studies on the mullite-type Bi2Fe4O9 compound. The crystal structures were determined using both powder X-ray diffraction and single crystal neutron diffraction. The thermal expansion of the cell parameters from smallest to largest occurred in the order a
- Published
- 2013
- Full Text
- View/download PDF
32. A joint computational and experimental study of a novel dioxomolybdenum(VI) complex bearing chiral N,N-dimethyllactamide ligand
- Author
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Sensato, Fabricio Ronil, Cass, Quezia Bezerra, Lopes, Bianca Rebelo, Lourenço, Tiago Campos, Zukerman-Schpector, Julio, Tiekink, Edward R.T., Longo, Elson, and Andrés, Juan
- Subjects
- *
COMPLEX compounds synthesis , *MOLYBDENUM compounds , *METAL complexes , *CHIRALITY , *AMIDES , *LIGANDS (Chemistry) , *X-ray crystallography , *MOLECULAR structure , *DENSITY functionals , *CHEMICAL bonds - Abstract
Abstract: A new cis-dioxomolybdenum complex MoO2(DMLA)2 (DMLA= N,N-dimethyllactamide) has been synthesized and characterized by X-ray crystallography, H NMR and IR spectroscopies and electronic structure calculations at DFT/B3LYP level. This compound (chemical formula C10H20MoO6N2) crystallizes in the orthorhombic space group P212121 with Z =4, a =6.9357(2)Ǻ, b =11.8761(4)Ǻ, c =17.7251(5), V =1460.00(8)Ǻ3 and renders a slightly distorted octahedral structure with two long Mo–O bonds (2.253(3)Ǻ and 2.257(3)Ǻ) trans to each of the Moand with two short Mo–O bonds of 1.942(3)4Ǻ cis to them. The Mongth are 1.715(3) and 1.704(3)Ǻ). Each lactamide ligand is bidentate; they are coordinated in their deprotonated form with the carbonyl oxygen occupying a position trans to the Mowhile the deprotonated hydroxyl oxygen is located cis to them. Structural characterization is complemented by DFT/B3LYP calculations. [Copyright &y& Elsevier]
- Published
- 2011
- Full Text
- View/download PDF
33. Crystal-structure and magnetic properties of the new ternary compound Pr117Co57Sn112
- Author
-
He, Wei, Zhang, Jiliang, Yan, Jialin, Fu, Yuechun, and Zeng, Lingmin
- Abstract
Abstract: The new ternary compound Pr117Co57Sn112 has been successfully synthesized and studied by means of X-ray powder diffraction technique. The compound Pr117Co57Sn112 crystallizes in a cubic Dy117Co57Sn112-type structure with space group (No. 225) and lattice parameter a =30.8202 (5) Å. The figure of merit for the index F 30 is 80.4 (30). Crystal-structure of Pr117Co57Sn112 has been successfully refined using the Rietveld method from X-ray diffraction data. The R-factors for the Rietveld refinement are R p =0.077, R wp =0.101 and R exp =0.032. The temperature dependence of the magnetization for the compound was also investigated in the range from 85 to 305K. The experimentally determined magnetic effective moment is μ eff =54.6 μ B per formula unit. [Copyright &y& Elsevier]
- Published
- 2010
- Full Text
- View/download PDF
34. Significance of the depth-related transition montmorillonite-beidellite in the Bouillante geothermal field (Guadeloupe, Lesser Antilles).
- Author
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Guisseau, Delphine, Mas, Patricia Patrier, Beaufort, Daniel, Girard, Jean Pierre, Inoue, Atsuyuki, Sanjuan, Bernard, Petit, Sabine, Lens, Arnaud, and Genter, Albert
- Subjects
- *
BEIDELLITE , *MONTMORILLONITE , *CRYSTALLOGRAPHY , *ELECTRON probe microanalysis , *CHEMISTRY , *MINERALOGY - Abstract
The crystal structure and crystal chemistry of dioctahedral smectites in high-enthalpy geothermal systems were investigated through samples collected in two wells drilled in the Bouillante geothermal area to understand the factors that control their vertical variation. Smectites were examined by optical and scanning electron microscopy, electron microprobe analysis, X-ray diffraction (XRD), Fourier transform infrared spectrometry (FTIR), and oxygen-isotope analysis. Smectites predominate within the upper part of the drill holes (up to 260 m depth; temperature range: 67-163 °C). The XRD, FTIR, and chemical microanalyses clearly demonstrate a transition from montmorillonite to beidellite with increasing depth and temperature that proceeded through interstratification of beidellite-like and montmorillonite-like layers. Montmorillonite predominates at temperatures below 100 °C, whereas beidellite predominates between 110 and 163 °C. However, this transition is not explained by a thermally controlled beidellitization process but appears to be related to hydrothermal fluids from which these smectites precipitated. The δ18O values of the fluids that equilibrated with smectites (-3.3 to 0.4‰) indicate that beidellitic smectite precipitated from the hot geothermal fluid associated with minor amounts of residual solutions resulting from local boiling. In the same way, montmorillonitic smectite precipitated from reacting solutions whose origin lies in the phreatic water table (±seawater contribution) associated with minor amounts of liquids resulting from the condensation of vapors escaped from the boiling zones. The mixing rate of geothermal fluid with meteoric waters exerted a major influence on the montmorillonite vs. beidellite ratio of the smectite material as underlined by the irregular depth-related smectite transition. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
35. Investigating photoluminescence and electroluminescence of iridium(III)-based blue-emitting phosphors
- Author
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Laskar, Inamur R., Hsu, Shih-Feng, and Chen, Teng-Ming
- Subjects
- *
PHOTOLUMINESCENCE , *ELECTROLUMINESCENCE , *LIGANDS (Chemistry) , *SPECTRUM analysis - Abstract
Abstract: The syntheses of two new cyclometalated ligands [2-(2′,4′-difluorophenyl)-4-tert-butylpyridine (F2 t Buppy) and 2-(2′,4′-difluorophenyl)-4-oxyhexylpyridine (F2HexOppy)] were carried out. Blue-light emitting iridium(III) complex dopants [Ir(F2 t Buppy)2(acac/pic)] (acac=acetylacetone; pic=picolinic acid) and [Ir(F2HexOppy)2(acac/pic)] were prepared using these cyclometalated ligands with acetylacetone and picolinic acid as their ancillary ligands. The structure of the complexes, [Ir(F2 t Buppy)2(acac)] and [Ir(F2 t Buppy)2(pic)] were authenticated by X-ray single-crystal structure analysis and showed an octahedral geometry. Comparative absorption and emission spectra of thin-films as well as their solution samples were studied. The variation of the lowest emitting states to their corresponding unsubstituted complexes, [Ir(F2ppy)2(acac/pic)] was also discussed. The electroluminescent (EL) device was fabricated using [Ir(F2 t Buppy)2(pic)] as the dopant (D-I) into the emitting layer and compared with two other EL devices where [Ir(F2MeOppy)2(acac)] (D-II) and FIrpic (D-III) dopants were used in the same device structure. The lower driving voltages obtained for D-I with respect to D-II and D-III devices were rationalized. The exceptional lowering of the luminance yield of the substituted dopants containing devices, D-I and D-II, to that of D-III which contains the unsubstituted dopant was also investigated. [Copyright &y& Elsevier]
- Published
- 2006
- Full Text
- View/download PDF
36. Two new microporous coordination polymers constructed by ladder-like and ribbon-like molecules with cavities
- Author
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Xu, Haitao and Li, Yadong
- Subjects
- *
POLYMERS , *MOLECULES , *HOLES , *LIGANDS (Biochemistry) - Abstract
Two novel microporous coordination polymers constructed by ladder-like and ribbon-like molecules with cavities: 2∞{[Zn(C8H3NO6)·(C10H8N2)1/2·(H2O)2]·(H2O)} (1) and 2∞[Zn(C8H3NO6)·H2O] (2) are obtained through assemble of the corner ligand and the metal Zn2+ ion. The metal Zn2+ ion of the coordination polymer (1) is in trigonal bipyramid environment: two O atoms from carboxyl groups and one N atom furnishing the equatorial plane and the other two O atoms in axes sites. For coordination polymer (2), the metal Zn2+ ion center is in tetrahedron environment: three O atoms from carboxyl groups in bottom plane and another O atom from coordination water in axis site. These infinite ladder-like or ribbon-like molecules are orderly arranged to furnish hydrophilic microporous by molecular interaction and hydrogen bonds from water molecules and carboxyl groups. And their properties are studied in this paper. [Copyright &y& Elsevier]
- Published
- 2004
- Full Text
- View/download PDF
37. SEMICRYSTALLINE AND SUPERLATTICE STRUCTURES IN BINARY MIXTURE OF LONG CHAIN n-ALKANES C194H390 AND C294H590.
- Author
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Zeng, X.B. and Ungar, G.
- Subjects
- *
CRYSTALS , *STRUCTURE-activity relationships , *ALKANES - Abstract
Binary mixtures of long chain n-alkanes from C122H246 to C294H590 have been found to form solid solutions despite their large chain length differences [Zeng and Ungar. Novel Layered Superstructures in Mixed Ultralong n-Alkanes. Phys. Rev. Lett. 2001, 86, 4875–4978]. In this article we describe a study of the binary mixture of C194H390+C294H590 (50:50 w/w) using small angle x-ray scattering. The molecular chain length difference between the two components is 100 C-atoms, the largest so far studied. In accordance with the findings on some other binary mixtures, two types of lamellar structures are found: the semicrystalline form (SCF) at high temperatures (>105°C) and the triple-layer superlattice at low temperatures (<95°C). The SCF consists of alternating crystalline and amorphous layers: C194H390 molecules are fully crystallized in the crystalline layer while C294H590 molecules traverse the crystalline layer and are only partially crystalline; their protruding tails, or cilia, constitute the amorphous layer. The superlattice is a periodic 1-D array of triple-layer units: the two outer layers in the unit contain a mixture of C194H390 and C294H590 while the surplus tails of C294H590 coalesce and interdigitate in the center and form the third, thinner crystalline layer. In the superlattice form, the unusual diffraction order dependence of the linewidth is interpreted in terms of a particular type of stacking faults. [ABSTRACT FROM AUTHOR]
- Published
- 2002
- Full Text
- View/download PDF
38. The crystal structure of the processive endocellulase CelF of Clostridium cellulolyticum in complex with a thiooligosaccharide inhibitor at 2.0 Å resolution.
- Author
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Parsiegla, Goetz, Juy, Michel, Reverbel-Leroy, Corinne, Tardif, Chantal, Belaïch, Jean-Pierre, Driguez, Hugues, and Haser, Richard
- Subjects
- *
CLOSTRIDIUM , *CELLULASE , *CELLULOSE , *HYDROLASES , *ENZYMES , *MULTIENZYME complexes - Abstract
The mesophilic bacterium Clostridium cellulolyticum exports multienzyme complexes called cellulosomes to digest cellulose. One of the three major components of the cellulosome is the processive endocellulase CelF. The crystal structure of the catalytic domain of CelF in complex with two molecules of a thiooligosaccharide inhibitor was determined at 2.0 Å resolution. This is the first three-dimensional structure to be solved of a member of the family 48 glycosyl hydrolases. The structure consists of an (αα)6-helix barrel with long loops on the N-terminal side of the inner helices, which form a tunnel, and an open cleft region covering one side of the barrel. One inhibitor molecule is enclosed in the tunnel, the other exposed in the open cleft. The active centre is located in a depression at the junction of the cleft and tunnel regions. Glu55 is the proposed proton donor in the cleavage reaction, while the corresponding base is proposed to be either Glu44 or Asp230. The orientation of the reducing ends of the inhibitor molecules together with the chain translation through the tunnel in the direction of the active centre indicates that CelF cleaves processively cellobiose from the reducing to the non-reducing end of the cellulose chain. [ABSTRACT FROM AUTHOR]
- Published
- 1998
- Full Text
- View/download PDF
39. Untersuchungen an Tetranatrium-cyclo-tetraphosphat(V) und seinen Hydraten.
- Author
-
Wiench, Dietmar and Jansen, Martin
- Abstract
A reinvestigation of the system (NaPo)/HO has been carried out. Besides the already known tetra-hydrate and anhydrous form, a mono-hydrate in the temperature range 100-120°C exists. Single crystals were obtained by crystallization from aqueous solutions containing higher alcohols (e.g. ethyleneglycol) at ∼115°C. The crystal structure was solved by X-ray methods (orthorhombic; P222; a=1365.4(2), b=1 347.5(3), c=629.1(3)pm; Z=4; 2774 diffractometer data; R=0.053). The cyclic anions exhibit point symmetry D with all terminal oxygens in eclipsed conformation. With respect to the (NaPO)-part of structure, mono-hydrate and anhydrous forms are isostructural; lattice parameters of the latter are a=1 380.8(2), b=1 363.3(2), c=602.7(2) pm. The transition mono-hydrate to anhydrous form occurs topochemically and is reversible. [ABSTRACT FROM AUTHOR]
- Published
- 1983
- Full Text
- View/download PDF
40. Na/Li substitution effect on the structural, electrical and magnetic properties of LiCr(MoO4)2 and β─Li0.87Na0.13Cr(MoO4)2.
- Author
-
Sonni, Manel, Zid, Mohamed Faouzi, Hlil, El Kebir, Zaidat, Kader, Rossignol, Cécile, and Obbade, Saïd
- Subjects
- *
IONIC conductivity measurement , *MAGNETIC properties , *IONIC conductivity , *IMPEDANCE spectroscopy , *SPECIFIC gravity , *VALENCE bonds - Abstract
The novel bi-molybdate β ─ Li 0.87 Na 0.13 Cr(MoO 4) 2 was prepared by solid state reaction route. Single crystal X-ray diffraction experiment revealed that the compound crystallizes in the triclinic system, in P −1 space group with a = 6.715 (2), b = 7.160 (3), c = 7.237 (1) Å, α = 91.16° (3), β = 110.59° (2), γ = 105.54° (3). Its crystal structure is isotypic to LiCr(MoO 4) 2 which has interesting magnetic and electrochemical properties [1–3]. Bond valence sum (BVS) and charge distribution (CHARDI) validation tools supported the structural model. The electrical properties were systematically studied by impedance spectroscopy. The ionic conductivity measurements are performed on pellets of 82% and 87% relative density for LiCr(MoO 4) 2 and β ─ Li 0.87 Na 0.13 Cr(MoO 4) 2 respectively. AC impedance spectroscopy studies show that the highest overall conductivity is σ 326°C = 7.86 × 10−7 S cm−1 Probable diffusion pathways of Li+ ions in the both structures were simulated using the bond valence sum BVS maps method. This analysis shows that the ionic transport in these materials is essentially due to simple hopping of Li+ ions parallel to (101) plane. For β ─ Li 0.87 Na 0.13 Cr(MoO 4) 2 compound, the in-situ High Temperature X-Ray Diffraction (HTXRD), in the temperature range from 25 to 650 °C, were also performed and Unit-cell thermal expansion has been discussed. The magnetic study show that these compounds present an antiferromagnetic order below the temperatures T N = 16 and 30 K for LiCr(MoO 4) 2 and β ─ Li 0.87 Na 0.13 Cr(MoO 4) 2 respectively. Image 1 • A new β ─ Li 0.87 Na 0.13 Cr(MoO 4) 2 compound was grown by solid state reaction. • Its crystal structure was determined by single-crystal X-ray diffraction. • Ionic conductivity was studied by complex impedance spectroscopy. • Li+ migration pathway was probed by the BVS model and compared to LiCr(MoO 4) 2. • Booth compounds present an antiferromagnetic order below T N. [ABSTRACT FROM AUTHOR]
- Published
- 2021
- Full Text
- View/download PDF
41. Adenine nucleobase directed supramolecular architectures based on ferrimagnetic heptanuclear copper(II) entities and benzenecarboxylate anions.
- Author
-
Pascual-Colino, Jon, Beobide, Garikoitz, Castillo, Oscar, Lodewyckx, Peter, Luque, Antonio, Pérez-Yáñez, Sonia, Román, Pascual, and Velasco, Leticia F.
- Subjects
- *
CHEMICAL structure , *CARBOXYLATES , *FERRIMAGNETIC materials , *BENZOATES , *ADENINE , *VOIDS (Crystallography) , *ANIONS , *METAL-organic frameworks - Abstract
Two planar organic anions, benzoate and benzene-1,4-dicarboxylate (terephthalate), have been selected as potential π-stacking intercalators among ferrimagnetic [Cu 7 (μ-adeninato) 6 (μ 3 -OH) 6 (μ-H 2 O) 6 2+ heptameric discrete entities. The resulting supramolecular architecture is highly dependent on the negative charge density distribution, mainly located in the carboxylate groups of the organic anions. In this sense, the benzoate anion, with just one carboxylate group, does not allow its intercalation between the adeninato ligands as it would imply a high steric hindrance among the heptameric entities. As a consequence, these benzoate anions are located inside the voids of the crystal structure reducing the accessible volume of compound [Cu 7 (μ-adeninato) 6 (μ 3 -OH) 6 (μ-H 2 O) 6 (benzoate) 2 ·~17H 2 O (1). On the contrary, the terephthalate anion, containing two carboxylate groups at opposite sites, adopts a π-stacking sandwich arrangement between two adeninato ligands that affords the porous open structure of formula [Cu 7 (μ-adeninato) 6 (μ 3 -OH) 6 (μ-H 2 O) 6 (terephthalate)·nH 2 O (2a , 2b ; n: 12 and 24, respectively). In addition to that, the less directional nature of the π-stacking interactions in comparison to the complementary hydrogen bonding based supramolecular metal-organic frameworks (SMOFs), suits them with a flexible architecture able to reversibly adsorb/desorb water (up to a 25–30% at 20 °C) altogether with the expansion/shrinkage of the crystal structure. The bridging adeninato and hydroxido ligands are effective magnetic exchange mediators to provide a S T = 5/2 ferrimagnetic state for the heptanuclear entity. Adenine directed π-π stacking interactions guide the supramolecular architectures based on ferrimagnetic heptnuclear Cu(II) entities. These materials follow our attempts in the quest for supramolecular metal-organic frameworks (SMOFs). Unlabelled Image • Adenine nucleobase as building block for supramolecular metal-organic frameworks, SMOFs. • SMOFs built up from π-stacking intercalators and metal-nucleobase based heptanuclear entities. • Influence of the negative charge density distribution of carboxylate anions in the structure. • Flexible crystal structures as atmosphere humidity adsorbents • Ferrimagnetic heptameric entities. [ABSTRACT FROM AUTHOR]
- Published
- 2020
- Full Text
- View/download PDF
42. Crystal structures of synthetic melanotekite (Pb2Fe2Si2O9), kentrolite (Pb2Mn2Si2O9), and the aluminum analogue (Pb2Al2Si2O9).
- Author
-
Dörsam, G., Liebscher, A., Wunder, B., and Franz, G.
- Subjects
- *
KENTROLITE , *MELANOTEKITE , *X-ray diffraction , *CRYSTALS , *MICROPROBE analysis , *FOURIER analysis - Abstract
Synthetic crystals of melanotekite and kentrolite were obtained at 850 °C from melt. The aluminum analogue of kentrolite Pb2Al2Si2O9 was hydrothermally synthesized at 2 GPa, 650 °C together with zoisite-(Pb) and margarite-(Pb). Synthesis products were characterized by single-crystal diffraction studies and microprobe analysis. The aluminum analogue Pb2Al2Si2O9 was observed in space group Pbcn with lattice parameters a = 6.8981(7) Å, b = 10.6906(15) Å, c = 9.7413(10) Å, and V = 718.37 ų. Fourier mappings show no irregularities of the Pb site. Melanotekite with lattice parameters a = 6.9786(6) Å, b = 11.0170(11) Å, c = 10.0895(9) Å, and V = 775.71(17) ų in space group Pbcn show a slightly deformed Pb-position in Fourier mappings. Kentrolite was observed in space group P21221 with pseudo-symmetry to Pbcn with lattice parameters a = 7.0103(5) Å, b = 11.0729 (7) Å, c = 9.9642(7) Å, and V = 773.47(11) ų. Fourier mappings of the kentrolite structure show that two different split Pb sites exist, which causes lower symmetry. The unit-cell volume of different members of the kentrolite group is a linear function of trivalent ionic radii in sixfold coordination for the elements Al, Ga, In, and also for Fe and Mn in high spin mode. The structure of Pb2M2Si2O9 (M = Al3+, Fe3+, Mn3+) is built on isolated M-octahedra chains parallel c, M-octahedra sharing alternately trans and skew edges. Each Si2O7-group is linked with their vertices to three octahedra chains. Their Si-O-Si bond angles depend on the size of M-octahedra and are 129.84° in Pb2Al2Si2O9, 131.08° in Pb2Fe2Si2O9, 128.34° and 130.33° in Pb2Mn2Si2O9. [ABSTRACT FROM AUTHOR]
- Published
- 2008
- Full Text
- View/download PDF
43. Crystal structures of synthetic melanotekite (Pb2Fe2Si2O9), kentrolite (Pb2Mn2Si2O9), and the aluminum analogue (Pb2Al2Si2O9).
- Author
-
Dörsam, G., Liebscher, A., Wunder, B., and Franz, G.
- Subjects
KENTROLITE ,MELANOTEKITE ,X-ray diffraction ,CRYSTALS ,MICROPROBE analysis ,FOURIER analysis - Abstract
Synthetic crystals of melanotekite and kentrolite were obtained at 850 °C from melt. The aluminum analogue of kentrolite Pb
2 Al2 Si2 O9 was hydrothermally synthesized at 2 GPa, 650 °C together with zoisite-(Pb) and margarite-(Pb). Synthesis products were characterized by single-crystal diffraction studies and microprobe analysis. The aluminum analogue Pb2 Al2 Si2 O9 was observed in space group Pbcn with lattice parameters a = 6.8981(7) Å, b = 10.6906(15) Å, c = 9.7413(10) Å, and V = 718.37 ų. Fourier mappings show no irregularities of the Pb site. Melanotekite with lattice parameters a = 6.9786(6) Å, b = 11.0170(11) Å, c = 10.0895(9) Å, and V = 775.71(17) ų in space group Pbcn show a slightly deformed Pb-position in Fourier mappings. Kentrolite was observed in space group P21 221 with pseudo-symmetry to Pbcn with lattice parameters a = 7.0103(5) Å, b = 11.0729 (7) Å, c = 9.9642(7) Å, and V = 773.47(11) ų. Fourier mappings of the kentrolite structure show that two different split Pb sites exist, which causes lower symmetry. The unit-cell volume of different members of the kentrolite group is a linear function of trivalent ionic radii in sixfold coordination for the elements Al, Ga, In, and also for Fe and Mn in high spin mode. The structure of Pb2 M2 Si2 O9 (M = Al3+ , Fe3+ , Mn3+ ) is built on isolated M-octahedra chains parallel c, M-octahedra sharing alternately trans and skew edges. Each Si2 O7 -group is linked with their vertices to three octahedra chains. Their Si-O-Si bond angles depend on the size of M-octahedra and are 129.84° in Pb2 Al2 Si2 O9 , 131.08° in Pb2 Fe2 Si2 O9 , 128.34° and 130.33° in Pb2 Mn2 Si2 O9 . [ABSTRACT FROM AUTHOR]- Published
- 2008
- Full Text
- View/download PDF
44. Tourmaline chemistry and the IIIB site.
- Author
-
Clark, Christine M., Wadoski, Eva R., and Freeman, Emily D.
- Subjects
- *
TOURMALINE , *BORON , *SILICATE minerals , *STEREOCHEMISTRY , *CHEMICAL structure , *STATISTICS - Abstract
Based on a large database of tourmaline crystal-structure refinements and associated electron microprobe analyses, the
bond length in the triangular (BO3) groups was found to be reasonably constant for all tourmaline species, but the B-O2 and B-O8 are variable as a function of the crystal chemistry. Tourmalines, such as elbaite, tend to have B-O2 distances significantly shorter than the B-O8 distances, whereas others, like povondraite, tend to have B-O2 distances that are longer than their B-O8 bonds. Statistical analysis of the bond-valence contributions for the nine-coordinated X-O2, and the six-coordinated Y-O2, Z-O8, and Z'-O8 bonds-as they relate to the B-O2/B-O8 bond valence-suggest that the Z'-O8 bond has the most influence over the geometry of the (BO3) triangle. This study highlights variations in what has otherwise been assumed to be a static site in the crystal structure of tourmaline-group minerals. [ABSTRACT FROM AUTHOR] - Published
- 2008
- Full Text
- View/download PDF
45. The crystal structure of pyroxenes along the jadeite--hedenbergite and jadeite--aegirine joins.
- Author
-
Nestola, F., Tribaudino, M., Ballaran, T. Boffa, Liebske, C., and Bruno, M.
- Subjects
- *
PYROXENE , *CRYSTALS , *JADEITE (Petrology) , *HEDENBERGITE , *ACMITE , *X-ray diffraction - Abstract
The crystal-structures of seven synthetic pyroxenes along the jadeite--hedenbergite (Jd57Hd43, Jd26Hd74, Jd0Hd100) and jadeite--aegirine (Jd100Ae0, Jd76Ae24, Jd35Ae65, Jd0Ae100) joins were refined using data collected by means of single-crystal X-ray diffraction (space group C2/c, R4σ between 2.2 and 3.4%). The M2 and M1 polyhedral volumes and bond lengths increase with increasing aegirine and hedenbergite content, moreover the Ca for Na substitution along the jadeite.hedenbergite join changes the M2 coordination from 6 + 2 to 4 + 4, with remarkable tilting of the tetrahedral chains. The value of the displacement parameters follows the trend UeqM2 > UeqO2 > UeqO3 > UeqO1 > UeqM1 ≈ UeqT for all samples belonging to the jadeite.aegirine join and for pure hedenbergite; in contrast,, for pyroxenes with intermediate compositions between hedenbergite and jadeite the trend is UeqO1 > UeqO2 > UeqM2 > UeqO3 > UeqM1 ≈ UeqT, with O1 and O2 having anomalously large displacement parameters, probably due to different local structural configuration around the cations with different size and charge. Cation substitution at the M1 site of Na-pyroxenes gives rise to a different structural deformation with respect of the double substitution at both the M1 and M2 sites in (Na,Ca)(M3+,M2+)Si2O6 pyroxenes as the rigid tetrahedral chains try to accommodate both the increasing size of the M1 site and the different coordination requirement of the M2 site. [ABSTRACT FROM AUTHOR]
- Published
- 2007
- Full Text
- View/download PDF
46. Position of Eukaryotic Translation Initiation Factor eIF1A on the 40S Ribosomal Subunit Mapped by Directed Hydroxyl Radical Probing
- Author
-
Yu, Yingpu, Marintchev, Assen, Kolupaeva, Victoria G., Unbehaun, Anett, Veryasova, Tatyana, Lai, Shao-Chiang, Hong, Peng, Hellen, Christopher U. T., Pestova, Tatyana V., and Wagner, Gerhard
- Subjects
Start-site Selection ,Messenger-RNA ,In-Vivo ,Crystal-Structure ,Codon Selection ,Factors 1A ,Complex ,Binding ,Release ,Hydrolysis - Abstract
The universally conserved eukaryotic initiation factor (eIF), eIF1A, plays multiple roles throughout initiation: it stimulates eIF2/GTP/Met-tRNA_i^{Met} attachment to 40S ribosomal subunits, scanning, start codon selection and subunit joining. Its bacterial ortholog IF1 consists of an oligonucleotide/oligosaccharide-binding (OB) domain, whereas eIF1A additionally contains a helical subdomain, N-terminal tail (NTT) and C-terminal tail (CTT). The NTT and CTT both enhance ribosomal recruitment of eIF2/GTP/Met-tRNA_i^{Met}, but have opposite effects on the stringency of start codon selection: the CTT increases, whereas the NTT decreases it. Here, we determined the position of eIF1A on the 40S subunit by directed hydroxyl radical cleavage. eIF1A's OB domain binds in the A site, similar to IF1, whereas the helical subdomain contacts the head, forming a bridge over the mRNA channel. The NTT and CTT both thread under Met-tRNA_i^{Met} reaching into the P-site. The NTT threads closer to the mRNA channel. In the proposed model, the NTT does not clash with either mRNA or Met-tRNA_i^{Met}, consistent with its suggested role in promoting the ‘closed’ conformation of ribosomal complexes upon start codon recognition. In contrast, eIF1A-CTT appears to interfere with the P-site tRNA-head interaction in the ‘closed’ complex and is likely ejected from the P-site upon start codon recognition.
- Published
- 2009
- Full Text
- View/download PDF
47. Binding Parameters and Thermodynamics of the Interaction of the Human Cytomegalovirus DNA Polymerase Accessory Protein, UL44, with DNA: Implications for the Processivity Mechanism
- Author
-
Loregian, Arianna, Sinigalia, Elisa, Mercorelli, Beatrice, Palù, Giorgio, and Coen, Donald Mark
- Subjects
catalytic subunit UL54 ,simplex-virus UL42 ,pol-gamma-b ,crystal-structure ,acid interactions ,primer-template ,nucleic acids ,lac repressor ,large ligands ,c-terminus - Abstract
The mechanisms of processivity factors of herpesvirus DNA polymerases remain poorly understood. The proposed processivity factor for human cytomegalovirus DNA polymerase is a DNA-binding protein, UL44. Previous findings, including the crystal structure of UL44, have led to the hypothesis that UL44 binds DNA as a dimer via lysine residues. To understand how UL44 interacts with DNA, we used filter-binding and electrophoretic mobility shift assays and isothermal titration calorimetry (ITC) analysis of binding to oligonucleotides. UL44 bound directly to double-stranded DNA as short as 12 bp, with apparent dissociation constants in the nanomolar range for DNAs > 18 bp, suggesting a minimum DNA length for UL44 interaction. UL44 also bound single-stranded DNA, albeit with lower affinity, and for either single- or double-stranded DNA, there was no apparent sequence specificity. ITC analysis revealed that UL44 binds to duplex DNA as a dimer. Binding was endothermic, indicating an entropically driven process, likely due to release of bound ions. Consistent with this hypothesis, analysis of the relationship between binding and ionic strength indicated that, on average, \(4 \pm 1\) monovalent ions are released in the interaction of each monomer of UL44 with DNA. The results taken together reveal interesting implications for how UL44 may mediate processivity.
- Published
- 2007
- Full Text
- View/download PDF
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