scholarly journals Hansesmarkite, Ca2Mn2Nb6O19·20H2O, a new hexaniobate from a syenite pegmatite in the Larvik Plutonic Complex, southern Norway

2017 ◽  
Vol 81 (3) ◽  
pp. 543-554 ◽  
Author(s):  
H. Friis ◽  
M. T. Weller ◽  
A. R. Kampf
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
New Mineral ◽  
Optical Orientation ◽  
X Ray Diffraction ◽  
X Ray ◽  
Naturally Occurring ◽  
Plutonic Complex ◽  
Diffraction Diagram ◽  
Southern Norway

AbstractThe new mineral hansesmarkite (IMA2015-067), Ca2Mn2Nb6O19·20H2O, was discovered at the AS Granit larvikite quarry in Tvedalen, Larvik, Vestfold, Norway. Hansesmarkite forms faintly yellow crystals up to 0.3 mm or thin coatingsin patches on gonnardite. Hansesmarkite is biaxial (+) with refractive indices (white light): α = 1.683(2), β = 1.698(2) and γ = 1.745(3); 2V(meas.) = 60.7(6)° and 2V(calc.) = 60.3°. The mineral exhibits moderate dispersion (r > v)and is pleochroic with X (almost colourless) < Y ( pale yellow) << Z (orangey yellow). The optical orientation is X ^ c = 20°, Y ^ b = 16° and Z ^ a = 5°. The empirical formula based on five electron probemicroanalyses and calculated based on Nb = 6 apfu is (Ca1.93Na0.02K0.01)∑1.96(Mn1.79Fe0.11)∑1.90Nb6O18.84·20H2O, with H2O determined from the structure solution.The mineral is triclinic, P1, with a = 9.081(4), b = 9.982(8), c = 10.60(1) Å, α = 111.07(8), β = 101.15(6), γ = 99.39(5)°, V = 850.8(13) Å3 and Z = 1. The structure was solved at 120 K because of thermalinstability of the mineral and refined to R1 = 2.50% for Fo > 4σ. The strongest reflections in the x-ray diffraction diagram are: [dobs. in Å (I)(hkl)] 9.282(36)(001), 8.610(100)(100, 011), 3.257(30)(031, 131)and 3.058(18)(130, 212). Hansesmarkite is the third naturally occurring hexaniobate in which six edge-sharing Nb-octahedra form the Lindqvist ion. These are linked via Mn-octahedra forming rods along [100] and Ca is located between the rods, creating a three dimensional structure via hydrogen bonds.

Three-dimensional X-ray diffraction imaging of process-induced dislocation loops in silicon

2011 ◽  
Vol 44 (3) ◽  
pp. 526-531 ◽  
Author(s):  
David Allen ◽  
Jochen Wittge ◽  
Jennifer Stopford ◽  
Andreas Danilewsky ◽  
Patrick McNally
Keyword(s):  
Semiconductor Industry ◽  
Three Dimensional ◽  
Crystal Defects ◽  
Three Dimensions ◽  
Dimensional Structure ◽  
Dislocation Loops ◽  
X Ray Diffraction ◽  
X Ray ◽  
Diffraction Imaging ◽  
Relationship Of

In the semiconductor industry, wafer handling introduces micro-cracks at the wafer edge and the causal relationship of these cracks to wafer breakage is a difficult task. By way of understanding the wafer breakage process, a series of nano-indents were introduced both into 20 × 20 mm (100) wafer pieces and into whole wafers as a means of introducing controlled strain. Visualization of the three-dimensional structure of crystal defects has been demonstrated. The silicon samples were then treated by various thermal anneal processes to initiate the formation of dislocation loops around the indents. This article reports the three-dimensional X-ray diffraction imaging and visualization of the structure of these dislocations. A series of X-ray section topographs of both the indents and the dislocation loops were taken at the ANKA Synchrotron, Karlsruhe, Germany. The topographs were recorded on a CCD system combined with a high-resolution scintillator crystal and were measured by repeated cycles of exposure and sample translation along a direction perpendicular to the beam. The resulting images were then rendered into three dimensions utilizing open-source three-dimensional medical tomography algorithms that show the dislocation loops formed. Furthermore this technique allows for the production of a video (avi) file showing the rotation of the rendered topographs around any defined axis. The software also has the capability of splitting the image along a segmentation line and viewing the internal structure of the strain fields.

scholarly journals The three-dimensional structure of a class-Pi glutathione S-transferase complexed with glutathione: the active-site hydration provides insights into the reaction mechanism

1998 ◽  
Vol 333 (3) ◽  
pp. 811-816 ◽  
Author(s):  
Antonio PÁRRAGA ◽  
Isabel GARCÍA-SÁEZ ◽  
Sinead B. WALSH ◽  
Timothy J. MANTLE ◽  
Miquel COLL
Keyword(s):  
Conformational Changes ◽  
Active Site ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Glutathione S Transferase ◽  
X Ray ◽  
The Right

The structure of mouse liver glutathione S-transferase P1-1 complexed with its substrate glutathione (GSH) has been determined by X-ray diffraction analysis. No conformational changes in the glutathione moiety or in the protein, other than small adjustments of some side chains, are observed when compared with glutathione adduct complexes. Our structure confirms that the role of Tyr-7 is to stabilize the thiolate by hydrogen bonding and to position it in the right orientation. A comparison of the enzyme–GSH structure reported here with previously described structures reveals rearrangements in a well-defined network of water molecules in the active site. One of these water molecules (W0), identified in the unliganded enzyme (carboxymethylated at Cys-47), is displaced by the binding of GSH, and a further water molecule (W4) is displaced following the binding of the electrophilic substrate and the formation of the glutathione conjugate. The possibility that one of these water molecules participates in the proton abstraction from the glutathione thiol is discussed.

scholarly journals Crystallization and preliminary X-ray diffraction analysis of a single variable domain of the immunoglobulin superfamily in amphioxus,Amphi-IgSF-V

2014 ◽  
Vol 70 (8) ◽  
pp. 1072-1075 ◽  
Author(s):  
Bo Jiang ◽  
Yanjie Liu ◽  
Rong Chen ◽  
Zhenbao Wang ◽  
Mansoor Tariq ◽  
...  
Keyword(s):  
Immune System ◽  
Structural Information ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Immunoglobulin Superfamily ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
System A ◽  
Human Immunoglobulins

Amphioxus is regarded as an essential animal model for the study of immune evolution. Discovery of new molecules with the immunoglobulin superfamily (IgSF) variable (V) domain in amphioxus would help in studying the evolution of IgSF V molecules in the immune system. A protein was found which just contains only one IgSF V domain in amphioxus, termedAmphi-IgSF-V; it has over 30% sequence identity to the V domains of human immunoglobulins and mammalian T-cell receptors. In order to clarify the three-dimensional structure of this new molecule in amphioxus,Amphi-IgSF-V was expressed, purified and crystallized, and diffraction data were collected to a resolution of 1.95 Å. The crystal belonged to space groupP3221, with unit-cell parametersa=b= 53.9,c= 135.5 Å. The Matthews coefficient and solvent content were calculated to be 2.58 Å3 Da−1and 52.38%, respectively. The results will provide structural information to study the evolution of IgSF V molecules in the immune system.

Metal Ion-Driven Assembly of Two New Coordination Polymers Constructed by Asymmetric Tricarboxylate and Imidazole-Containing Ligands: Syntheses, Crystal Structures, and Luminescent Properties

2015 ◽  
Vol 68 (1) ◽  
pp. 121 ◽  
Author(s):  
Wenlong Liu ◽  
Xueying Wang ◽  
Mengqiang Wu ◽  
Bing Wang
Keyword(s):  
Infrared Spectroscopy ◽  
Coordination Polymers ◽  
Metal Ion ◽  
Three Dimensional ◽  
Luminescent Properties ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
Hydrothermal Conditions ◽  
X Ray ◽  
Dimethyl Benzene

Two new coordination polymers, namely, {[Cd3(bpt)2(bimb)2]·2(H2O)}n (1) and [Zn3(bpt)2(bimb)2]n (2) (bpt = biphenyl-3,4′,5-tricarboxylate, bimb = 1,4-bis(1-imidazol-yl)-2,5-dimethyl benzene), have been obtained under hydrothermal conditions. Their structures have been determined by single-crystal X-ray diffraction analysis and further characterised by elemental analysis and infrared spectroscopy. Complex 1 exhibits a trinodal (4,4,4)-connected topology with Schläfli symbol of (4.62.83)4.(64.82). Complex 2 is also a three-dimensional structure and displays a (3,4,6)-connected topology with Schläfli symbol of (4.62)2.(42.66.85.102).(64.82). It is shown that the asymmetrically tricarboxylate can bear diverse structures regulated by metal ions. The photoluminescence behaviours of compounds 1 and 2 were also discussed.

scholarly journals Acmonidesite, a new ammonium sulfate chloride from La Fossa crater, Vulcano, Aeolian Islands, Italy

2018 ◽  
Vol 83 (1) ◽  
pp. 137-142 ◽  
Author(s):  
Francesco Demartin ◽  
Carlo Castellano ◽  
Italo Campostrini
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
New Mineral ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
Chlorine Atoms ◽  
Calculated Density ◽  
Sulfate Ions ◽  
Aeolian Islands ◽  
Fossa Crater

AbstractThe new mineral acmonidesite, (NH4,K,Pb2+,Na)9Fe42+(SO4)5Cl8, was found in an active fumarole (fumarole FA, temperature ~250°C) at La Fossa crater, Vulcano, Aeolian Islands, Sicily, Italy. It occurs on a pyroclastic breccia as brown prismatic crystals up to 0.10 mm long, in association with salammoniac, alunite and adranosite. The mineral is orthorhombic, space group C2221 (no. 20) with a = 9.841(1), b = 19.448(3) c = 17.847(3) Å, V = 3415.7(9) Å3 and Z = 4. The six strongest reflections in the powder X-ray diffraction pattern are: [dobs in Å(I)(hkl)] 8.766(100)(110), 1.805(88)(390), 5.178(45)(131), 4.250(42)(221), 2.926(42)(330) and 2.684(32)(261). The empirical formula (based on 28 anions per formula unit [pfu]) is (NH4)5.77K1.42Pb0.62Na1.24Fe3.96Mn0.08S5.04O20.16Cl7.97Br0.08. The idealised formula is (NH4,K,Pb2+,Na)9Fe42+(SO4)5Cl8. The calculated density is 2.551 g cm–3. Using single-crystal diffraction data, the structure was refined to a final R(F) = 0.0363 for 4614 independent observed reflections [I > 2σ(I)]. The structure contains two independent, distorted octahedral iron sites, Fe1 and Fe2, with the iron atoms in the 2+ oxidation state, as confirmed by the interatomic distances and bond-valence calculations (2.06 and 1.94 vu, respectively). Fe1 is surrounded by two chlorine atoms and four oxygens of the sulfate ions, with the following average distances (Å): Fe1–O 2.125 and Fe1–Cl 2.472; and Fe2 is surrounded by three chlorine atoms and three oxygens of the sulfate ions, with the following average distances (Å): Fe2–O 2.110 and Fe2–Cl 2.531. Three independent sulfate anions are also present and are connected with the iron polyhedra to form a three-dimensional structure containing voids occupied by four independent ammonium ions (two of them partially replaced by K+), one Na+/Pb2+ site and one Cl– ion.

scholarly journals Three-dimensional structure of CdX (X=Se,Te) nanocrystals by total x-ray diffraction

2007 ◽  
Vol 102 (4) ◽  
pp. 044304 ◽  
Author(s):  
S. K. Pradhan ◽  
Z. T. Deng ◽  
F. Tang ◽  
C. Wang ◽  
Y. Ren ◽  
...  
Keyword(s):  
Three Dimensional ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Three Dimensional Structure

A novel alkaline earth strontium(II) coordination polymer: poly[hexaaquatetrakis(μ5-pyridine-2,6-dicarboxylato)bis(μ4-pyridine-2,6-dicarboxylato)(μ7-sulfato)heptastrontium(II)]

2014 ◽  
Vol 70 (6) ◽  
pp. 584-587 ◽  
Author(s):  
Wei Zhang ◽  
Shu-Guang Qi ◽  
Yu-Quan Feng
Keyword(s):  
Coordination Polymer ◽  
Coordination Mode ◽  
Alkaline Earth ◽  
Three Dimensional ◽  
Dimensional Structure ◽  
Water Molecules ◽  
Stacking Interactions ◽  
X Ray Diffraction ◽  
Sulfate Anion ◽  
X Ray

The title compound, [Sr7(C7H3NO4)6(SO4)(H2O)6]n, has been synthesized by an ionothermal method using the ionic liquid 1-ethyl-3-methylimidazolium ([Emim]Br) as solvent, and characterized by elemental analysis, energy-dispersive X-ray spectroscopy, IR and single-crystal X-ray diffraction. The structure of the compound can be viewed as a three-dimensional coordination polymer composed of Sr2+cations, pyridine-2,6-dicarboxylate anions, sulfate anions and water molecules. The compound not only exhibits a three-dimensional structure with a unique coordination mode of the sulfate anion, but also features the first example of a heptanuclear strontium(II) coordination polymer. The structure is further stabilized by O—H...O hydrogen bonds and π–π stacking interactions.

Structure of the collagen fibril: some variations on a theme of tetragonally packed dimers

1980 ◽  
Vol 209 (1175) ◽  
pp. 275-297 ◽  
Keyword(s):  
Self Assembly ◽  
Collagen Fibril ◽  
Three Dimensional ◽  
Local Property ◽  
Square Lattice ◽  
Dimensional Structure ◽  
X Ray Diffraction ◽  
X Ray ◽  
Variations On A Theme ◽  
Overlap Region

A theory of the three-dimensional structure of the collagen fibril outlined by Woodhead-Galloway (1977) is discussed in greater detail and an account of the low angle X-ray diffraction pattern (Miller & Wray 1971) is obtained. Square-packed dimers form the overlap region of the fibril. In the gap region, clusters of four dimers at each of the points of a square lattice of side 3.8 nm provide the structure. Molecules are parallel to the axis of the fibril in the overlap region and tilted from the axis by a few degrees in the gap region. A brief discussion of some aspects of the self assembly of such a structure is included. In particular, it is noted that the axially projected D ( ═ 66.8 nm) period, which is a property of the Whole fibril, is not necessarily also a local property; there may be no well defined and finite small grouping of molecules that is itself D -periodic, such as is proposed in the microfibril model of the fibril (Smith 1968). On the other hand, there is strong circumstantial evidence of a D -periodic crystallographic unit cell.

scholarly journals X-Ray Diffraction of Magnetically Oriented Microcrystals of Protein

2014 ◽  
Vol 70 (a1) ◽  
pp. C349-C349
Author(s):  
Shu Tsukui ◽  
Fumiko Kimura ◽  
Kimihiko Mizutani ◽  
Bunzo Mikami ◽  
Tsunehisa Kimura
Keyword(s):  
Single Crystal ◽  
Three Dimensional ◽  
Water Soluble ◽  
Dimensional Structure ◽  
Diffraction Measurement ◽  
X Ray Diffraction ◽  
Consolidation Process ◽  
X Ray ◽  
Three Dimensional Structure

Elucidation of the three-dimensional structure of biomolecules is of great importance because the three-dimensional structure is closely related to biological functions. X-ray single-crystal analysis is powerful method to analyze the structure, but it is sometimes difficult to grow a crystal sufficiently large for conventional or even synchrotron single-crystal X-ray measurement. We recently reported on a magnetically oriented microcrystal array (MOMA) [1] that is a composite in which microcrystals are aligned three-dimensionally in polymer matrix. Microcrystals are suspended in an ultraviolet-curable monomer and rotated non-uniformly in a static magnetic field to achieve three dimensional crystal alignment. Then, the monomer is photopolymerized to maintain the achieved alignment. We have successfully demonstrated that X-ray single crystal structure determinations through MOMA are possible for low molecular weight compounds [2] as well as protein. [3] However, the method with MOMA has two drawbacks: (i) the sample microcrystals cannot be recovered from a MOMA, which is especially serious problem in case of proteins, and (ii) the alignment is deteriorated during the consolidation process, causing low resolution. In this study, we attempt to solve these problems. First, we use a water-soluble sol as microcrystalline media and consolidate the alignment by gelation, which makes the recovery of microcrystals possible. Second, a magnetically oriented microcrystal suspension (MOMS) is used for in-situ X-ray diffraction measurement, which makes the sample recovery possible and enhances the resolution. We use lysozyme as a model protein for both cases. The in-situ method with in-house X-ray diffractometer gave diffraction spots about 3.0 Å resolutions. We plan to perform the same experiment at SPring-8.

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