Preliminary X-ray Data Analysis of Crystalline Hibiscus Chlorotic Ringspot Virus

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cheng, A.; Speir, J; Yuan, Y

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3Synchrotron .2 Amore » resolution and allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 . Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV.« less

Fluorescence kinetics of PSII crystals containing Ca(2+) or Sr(2+) in the oxygen evolving complex.

PubMed

van Oort, Bart; Kargul, Joanna; Maghlaoui, Karim; Barber, James; van Amerongen, Herbert

2014-02-01

Photosystem II (PSII) is the pigment-protein complex which converts sunlight energy into chemical energy by catalysing the process of light-driven oxidation of water into reducing equivalents in the form of protons and electrons. Three-dimensional structures from x-ray crystallography have been used extensively to model these processes. However, the crystal structures are not necessarily identical to those of the solubilised complexes. Here we compared picosecond fluorescence of solubilised and crystallised PSII core particles isolated from the thermophilic cyanobacterium Thermosynechococcus elongatus. The fluorescence of the crystals is sensitive to the presence of artificial electron acceptors (K3Fe(CN)3) and electron transport inhibitors (DCMU). In PSII with reaction centres in the open state, the picosecond fluorescence of PSII crystals and solubilised PSII is indistinguishable. Additionally we compared picosecond fluorescence of native PSII with PSII in which Ca(2) in the oxygen evolving complex (OEC) is biosynthetically replaced by Sr(2+). With the Sr(2+) replaced OEC the average fluorescence decay slows down slightly (81ps to 85ps), and reaction centres are less readily closed, indicating that both energy transfer/trapping and electron transfer are affected by the replacement. Copyright © 2013. Published by Elsevier B.V.

Nanocrystalline ordered vanadium carbide: Superlattice and nanostructure

NASA Astrophysics Data System (ADS)

Kurlov, A. S.; Gusev, A. I.; Gerasimov, E. Yu.; Bobrikov, I. A.; Balagurov, A. M.; Rempel, A. A.

2016-02-01

The crystal structure, micro- and nanostructure of coarse- and nanocrystalline powders of ordered vanadium carbide V8C7 have been examined by X-ray and neutron diffraction and electron microscopy methods. The synthesized coarse-crystalline powder of ordered vanadium carbide has flower-like morphology. It was established that the real ordered phase has the composition V8C7-δ (δ ≅ 0.03) deviating from perfect stoichiometric composition V8C7. The vanadium atoms forming the octahedral environment □V6 of vacant sites in V8C7-δ are displaced towards the vacancy □. The presence of carbon onion-like structures was found in the vanadium carbide powders with a small content of free (uncombined) carbon. The nanopowders of V8C7-δ carbide with average particle size of 20-30 nm produced by high-energy milling of coarse-crystalline powder retain the crystal structure of the initial powder, but differ in the lattice deformation distortion anisotropy.

The 2.3 {angstrom} crystal structure of cholera toxin B subunit pentamer: Choleragenoid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Rong-Guang; Westbrook, M.L.; Maulik, P.R.

1996-02-01

Cholera toxin, a heterohexameric AB{sub 5} enterotoxin released by Vibrio cholera, induces a profuse secretory diarrhea in susceptible hosts. Choleragenoid, the B subunit pentamer of cholera toxin, directs the enzymatic A subunit to its target by binding to GM{sub 1} gangliosides exposed on the luminal surface of intestinal epithelial cells. We have solved the crystal structure of choleragenoid at 2.3 {Angstrom} resolution by combining single isomorphous replacement with non-crystallographic symmetry averaging. The structure of the B subunits, and their pentameric arrangement, closely resembles that reported for the intact holotoxin (choleragen), the heat-labile enterotoxin from E. coli, and for a choleragenoid-GM{submore » 1} pentasaccharide complex. In the absence of the A subunit the central cavity of the B pentamer is a highly solvated channel. The binding of the A subunit or the receptor pentasaccharide to choleragenoid has only a modest effect on the local stereochemistry and does not perceptibly alter the subunit interface.« less

Preferential nucleation during polymorphic transformations

DOE PAGES

Sharma, H.; Sietsma, J.; Offerman, S. E.

2016-08-03

Polymorphism is the ability of a solid material to exist in more than one phase or crystal structure. Polymorphism may occur in metals, alloys, ceramics, minerals, polymers, and pharmaceutical substances. Unresolved are the conditions for preferential nucleation during polymorphic transformations in which structural relationships or special crystallographic orientation relationships (OR’s) form between the nucleus and surrounding matrix grains. We measured in-situ and simultaneously the nucleation rates of grains that have zero, one, two, three and four special OR’s with the surrounding parent grains. These experiments show a trend in which the activation energy for nucleation becomes smaller – and thereforemore » nucleation more probable - with increasing number of special OR’s. As a result, these insights contribute to steering the processing of polymorphic materials with tailored properties, since preferential nucleation affects which crystal structure forms, the average grain size and texture of the material, and thereby - to a large extent - the final properties of the material.« less

Influence of nano-size inclusions on spall fracture of copper single crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Razorenov, S. V.; Ivanchihina, G. E.; Kanel, G. I.

2007-12-12

Spall experiments have been carried out for copper in different structural states. The samples were copper single crystals, crystals of Cu+0.1% Si, copper crystals with silica particles of 180 nm average size, and polycrystalline copper. In experiments, the free surface velocity histories were recorded with the VISAR. The recovered samples were studied using optical microscopy and SEM. Solid solution Cu+0.1% Si demonstrates slower spall process than pure copper crystals. At longer pulse durations its spall strength is slightly less than that of pure crystals but approaches the latter with decreasing pulse duration. Fracture of copper with silica inclusions is completedmore » much faster. The spall strength of this material is close to that of Cu+0.1% Si crystals at longer pulse duration and approaches the strength of polycrystalline copper with decreasing the load duration. Fractography of the spall surfaces correlates with the free surface velocity histories. The main fracture surface of the Cu+0.1% Si grains consists of net of dimples {approx}4 {mu}m to 40 {mu}m mean diameter. The fracture surfaces of copper with silica inclusions is covered by a net of dimples of 1 {mu}m to 5 {mu}m size.« less

Characterizing RNA ensembles from NMR data with kinematic models

PubMed Central

Fonseca, Rasmus; Pachov, Dimitar V.; Bernauer, Julie; van den Bedem, Henry

2014-01-01

Functional mechanisms of biomolecules often manifest themselves precisely in transient conformational substates. Researchers have long sought to structurally characterize dynamic processes in non-coding RNA, combining experimental data with computer algorithms. However, adequate exploration of conformational space for these highly dynamic molecules, starting from static crystal structures, remains challenging. Here, we report a new conformational sampling procedure, KGSrna, which can efficiently probe the native ensemble of RNA molecules in solution. We found that KGSrna ensembles accurately represent the conformational landscapes of 3D RNA encoded by NMR proton chemical shifts. KGSrna resolves motionally averaged NMR data into structural contributions; when coupled with residual dipolar coupling data, a KGSrna ensemble revealed a previously uncharacterized transient excited state of the HIV-1 trans-activation response element stem–loop. Ensemble-based interpretations of averaged data can aid in formulating and testing dynamic, motion-based hypotheses of functional mechanisms in RNAs with broad implications for RNA engineering and therapeutic intervention. PMID:25114056

Synthesis, crystal structure, Hirshfeld surface analysis, spectroscopic characterization, reactivity study by DFT and MD approaches and molecular docking study of a novel chalcone derivative

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Pillai, Renjith Raveendran; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-05-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethyl)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in monoclinic crystal system in P21/c space group, unit cell parameters a = 16.7629 (12) Å, b = 13.9681 (10) Å, c = 5.8740 (4) Å, β = 96.3860 (12)° and Z = 4. Hirshfeld surface analysis revealed that the molecular structure is dominated by H⋯H, C⋯H/H⋯C, Br⋯F/F⋯Br and F⋯F contacts. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed.

Crystallization and preliminary crystallographic analysis of Abp, a GH27 β-L-arabinopyranosidase from Geobacillus stearothermophilus.

PubMed

Lansky, Shifra; Salama, Rachel; Solomon, Vered H; Belrhali, Hassan; Shoham, Yuval; Shoham, Gil

2013-06-01

Geobacillus stearothermophilus T-6 is a thermophilic soil bacterium that possesses an extensive system for the utilization of hemicellulose. The bacterium produces a small number of endo-acting extracellular enzymes that cleave high-molecular-weight hemicellulolytic polymers into short decorated oligosaccharides, which are further hydrolysed into the respective sugar monomers by a battery of intracellular glycoside hydrolases. One of these intracellular processing enzymes is β-L-arabinopyranosidase (Abp), which is capable of removing β-L-arabinopyranose residues from naturally occurring arabino-polysaccharides. As arabino-polymers constitute a significant part of the hemicellulolytic content of plant biomass, their efficient enzymatic degradation presents an important challenge for many potential biotechnological applications. This aspect has led to an increasing interest in the biochemical characterization and structural analysis of this and related hemicellulases. Abp from G. stearothermophilus T-6 has recently been cloned, overexpressed, purified, biochemically characterized and crystallized in our laboratory, as part of its complete structure-function study. The best crystals obtained for this enzyme belonged to the primitive orthorhombic space group P2(1)2(1)2(1), with average unit-cell parameters a = 107.7, b = 202.2, c = 287.3 Å. Full diffraction data sets to 2.3 Å resolution have been collected for both the wild-type enzyme and its D197A catalytic mutant from flash-cooled crystals at 100 K, using synchrotron radiation. These data are currently being used for a high-resolution three-dimensional structure determination of Abp.

On the Coupling Mechanism of Equiaxed Crystal Generation with the Liquid Flow Driven by Natural Convection During Solidification

NASA Astrophysics Data System (ADS)

Stefan-Kharicha, Mihaela; Kharicha, Abdellah; Wu, Menghuai; Ludwig, Andreas

2018-02-01

The influence of the melt flow on the solidification structure is bilateral. The flow plays an important role in the solidification pattern, via the heat transfer, grain distribution, and segregations. On the other hand, the crystal structure, columnar or equiaxed, impacts the flow, via the thermosolutal convection, the drag force applied by the crystals on the melt flow, etc. As the aim of this research was to further explore the solidification-flow interaction, experiments were conducted in a cast cell (95 * 95 * 30 mm3), in which an ammonium chloride-water solution (between 27 and 31 wt pct NH4Cl) was observed as it solidified. The kinetic energy (KE) of the flow and the average flow velocity were calculated throughout the process. Measurements of the volume extension of the mush in the cell and the velocity of the solid front were also taken during the solidification experiment. During the mainly columnar experiments (8 cm liquid height) the flow KE continuously decreased over time. However, during the later series of experiments at higher liquid height (9.5 cm), the flow KE evolution presented a strong peak shortly after the start of solidification. This increase in the total flow KE correlated with the presence of falling equiaxed crystals. Generally, a clear correlation between the strength of the flow and the occurrence of equiaxed crystals was evident. The analysis of the results strongly suggests a fragmentation origin of equiaxed crystals appearing in the melt. The transition from purely columnar growth to a strongly equiaxed rain (CET) was found to be triggered by (a) the magnitude of the coupling between the flow intensity driven by the equiaxed crystals, and (b) the release and transport of the fragments by the same flow recirculating within the mushy zone.

Optical and morphological properties of sol gel derived titanium dioxide films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sharma, A. B.; Sharma, S. K.; M, Vishwas

2015-08-28

Titanium oxide (Titania) thin films were synthesized on different substrates via the sol-gel dip-coating method using alkoxide solution. Some selected samples were also prepared with different percentage of Lead (Pb). The influence of Pb addition in precursor sol on the optical properties of titanium dioxide thin films was studied. The optical transmittance in the visible region has increased with increase in weight percentage of lead. The refractive index was slightly decreased with Pb addition. Crystallization of these coatings was achieved through thermal annealing at temperatures above 400 °C. The structural properties and surface morphology of the crystallized coatings were studiedmore » by Scanning Electron Microscopy. Increase in average grain size from 250 nm to 350 nm with increase in Pb concentration is observed. Films were appeared to more coarse with increase in Pb addition. An increase in Pb addition resulted increase in average roughness from 12 nm to 25 nm.« less

The bifoil photodyne: a photonic crystal oscillator.

PubMed

Lugo, J E; Doti, R; Sanchez, N; de la Mora, M B; del Rio, J A; Faubert, J

2014-01-15

Optical tweezers is an example how to use light to generate a physical force. They have been used to levitate viruses, bacteria, cells, and sub cellular organisms. Nonetheless it would be beneficial to use such force to develop a new kind of applications. However the radiation pressure usually is small to think in moving larger objects. Currently, there is some research investigating novel photonic working principles to generate a higher force. Here, we studied theoretically and experimentally the induction of electromagnetic forces in one-dimensional photonic crystals when light impinges on the off-axis direction. The photonic structure consists of a micro-cavity like structure formed of two one-dimensional photonic crystals made of free-standing porous silicon, separated by a variable air gap and the working wavelength is 633 nm. We show experimental evidence of this force when the photonic structure is capable of making auto-oscillations and forced-oscillations. We measured peak displacements and velocities ranging from 2 up to 35 microns and 0.4 up to 2.1 mm/s with a power of 13 mW. Recent evidence showed that giant resonant light forces could induce average velocity values of 0.45 mm/s in microspheres embedded in water with 43 mW light power.

The bifoil photodyne: a photonic crystal oscillator

PubMed Central

Lugo, J. E.; Doti, R.; Sanchez, N.; de la Mora, M. B.; del Rio, J. A.; Faubert, J.

2014-01-01

Optical tweezers is an example how to use light to generate a physical force. They have been used to levitate viruses, bacteria, cells, and sub cellular organisms. Nonetheless it would be beneficial to use such force to develop a new kind of applications. However the radiation pressure usually is small to think in moving larger objects. Currently, there is some research investigating novel photonic working principles to generate a higher force. Here, we studied theoretically and experimentally the induction of electromagnetic forces in one-dimensional photonic crystals when light impinges on the off-axis direction. The photonic structure consists of a micro-cavity like structure formed of two one-dimensional photonic crystals made of free-standing porous silicon, separated by a variable air gap and the working wavelength is 633 nm. We show experimental evidence of this force when the photonic structure is capable of making auto-oscillations and forced-oscillations. We measured peak displacements and velocities ranging from 2 up to 35 microns and 0.4 up to 2.1 mm/s with a power of 13 mW. Recent evidence showed that giant resonant light forces could induce average velocity values of 0.45 mm/s in microspheres embedded in water with 43 mW light power. PMID:24423985

Structure and temperature-dependent phase transitions of lead-free Bi 1/2Na 1/2TiO 3-Bi 1/2K 1/2TiO 3-K 0.5Na 0.5NbO 3 piezoceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anton, Eva-Maria; Schmitt, Ljubomira Ana; Hinterstein, Manuel

2014-05-28

Structure and phase transitions of (1-y)((1-x)Bi 1/2Na 1/2TiO 3-xBi 1/2K 1/2TiO 3)-yK 0.5Na 0.5NbO 3 (x; y) piezoceramics (0.1 ≤ x ≤ 0.4; 0 ≤ y ≤ 0.05) were investigated by transmission electron microscopy, neutron diffraction, temperature-dependent x-ray diffraction, and Raman spectroscopy. The local crystallographic structure at room temperature (RT) does not change by adding K 0.5Na 0.5NbO 3 to Bi 1/2Na 1/2TiO 3-xBi 1/2K 1/2TiO 3 for x = 0.2 and 0.4. The average crystal structure and microstructure on the other hand develop from mainly long-range polar order with ferroelectric domains to short-range order with polar nanoregions displaying amore » more pronounced relaxor character. The (0.1; 0) and (0.1; 0.02) compositions exhibit monoclinic Cc space group symmetry, which transform into Cc + P4bm at 185 and 130 °C, respectively. This high temperature phase is stable at RT for the morphotropic phase boundary compositions of (0.1; 0.05) and all compositions with x = 0.2. For the compositions of (0.1; 0) and (0.1; 0.02), local structural changes on heating are evidenced by Raman; for all other compositions, changes in the long-range average crystal structure were observed.« less

Pseudosymmetric features of non-centrosymmetric AB type crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gazhulina, A.P., E-mail: asyagazhulina@yandex.ru; Marychev, M.O.

2016-07-15

This work is supplement to our previous investigation (Gazhulina and Marychev, 2015) [1]. We have considered pseudosymmetric features with respect to the operation of inversion (pseudoinversion) for 340 non-centrosymmetric AB type crystals. Analysis of the features of particular structure types allowed us to determine the positions of pseudoinversion centers, subdivide them into separate types, and classify the entire set of crystals studied with respect to the types of pseudoinversion centers and peculiarities of the behavior of the degree of pseudoinversion depending on the ratio of atomic numbers of A and B components. For each group of crystals, average values andmore » lower boundaries of the maximum pseudoinversion are determined and distribution with respect to the degree of pseudoinversion is constructed. - Graphical abstract: A group of 340 non-centrosymmetric AB type crystals have been considered for their pseudosymmetry features with respect to the operation of inversion. Positions of pseudoinversion centers, subdivision of them into separate types, classification of the entire set of crystals studied with respect to the types of pseudoinversion centers and peculiarities of the behavior of the degree of pseudoinversion are established and discussed. Display Omitted - Highlights: • We consider pseudoinversion of 340 non-centrosymmetric AB type crystals. • AB type crystals are divided into three groups with respect to pseudoinversion. • Positions and types of pseudoinversion centers are determined. • Lower boundaries of the maximum pseudoinversion are determined.« less

Monoclinic deformation of calcite crystals at ambient conditions

NASA Astrophysics Data System (ADS)

Przeniosło, R.; Fabrykiewicz, P.; Sosnowska, I.

2016-09-01

High resolution synchrotron radiation powder diffraction shows that the average crystal structure of calcite at ambient conditions is described with the trigonal space group R 3 bar c but there is a systematic hkl-dependent Bragg peak broadening. A modelling of this anisotropic peak broadening with the microstrain model from Stephens (1999) [15] is presented. The observed lattice parameters' correlations can be described by assuming a monoclinic-type deformation of calcite crystallites. A quantitative model of this monoclinic deformation observed at ambient conditions is described with the space group C 2 / c . The monoclinic unit cell suggested at ambient conditions is related with the monoclinic unit cell reported in calcite at high pressure (Merrill and Bassett (1975) [10]).

Detailed analysis of Honeywell In-Space Accelerometer data - STS-32. [crystal microstructure response to different types of residual acceleration

NASA Technical Reports Server (NTRS)

Rogers, Melissa J. B.; Alexander, J. I. D.; Schoess, Jeff

1993-01-01

The Honeywell In-Space Accelerometer (HISA) system collected data in the mid-deck area of the Shuttle Columbia during the flight of STS-32, January 1990. The resulting data were to be used to investigate the response of crystal microstructure to different types of residual acceleration. The HISA is designed to detect and record transient and oscillatory accelerations. The sampling and electronics package stored averaged accelerations over two sampling periods; two sampling rates were available: 1 Hz and 50 Hz. Analysis of the HISA data followed the CMMR Acceleration Data Processing Guide, considering in-house computer modelling of a float-zone indium crystal growth experiment. Characteristic examples of HISA data showing the response to the primary reaction control system, Orbiter Maneuvering System operations, and crew treadmill activity are presented. Various orbiter structural modes are excited by these and other activities.

Polymorphic transition of solid-fats dispersed systems — its characterization by a novel method and scanning electron microscopy observation

NASA Astrophysics Data System (ADS)

Hirokawa, Norio; Ueda, Masahiro; Harano, Yoshio

1994-08-01

Solid-fats dispersed systems, such as margarine, butter and cacao-butter, were characterized by a novel method based on liquid permeation under pressure, for the simultaneous measurement of a solid-content ɛ p and an average diameter dp of solid particles (fats crystals) in them. Further, micro-structures of these systems were observed by a scanning electron microscope (SEM). As the result, it has been clarified that the spherical fats crystals of several μm in size appeared in the initial solid-fats products are agglomerates of fine particles of ca. 0.1 μm and that these fine particles are uniformly redispersed during an annealing treatment accompanying the reduction of ɛ p and dp. It is strongly suggested that this phenomenon is caused by a transition of fat crystals into a more stable polymorph.

Fabrication technology of Si face and m face on 4H-SiC (0001) epi-layer based on molten KOH etching

NASA Astrophysics Data System (ADS)

Lin, Wen-kui; Zeng, Chun-hong; Sun, Yu-hua; Zhang, Xuan; Li, Zhe; Yang, Tao-tao; Ju, Tao; Zhang, Bao-shun

2018-02-01

Additional scattering of electrons in the complex MOSFET channel caused by off-cut angle of (0001) 4H-SiC wafer, makes accurate crystal face acquisition much desired. Molten KOH was used to etch the circular grooves on the SiC wafer surface in muffle furnace, and hexagonal grooves with SiC crystal symmetry were obtained. Average etching rates at 500°C along <11-20> and <1-100> direction were about 4.826 um/min and 4.112 um/min, respectively,with a etching anisotropy ratio of 1.18. The m face was obtained by controlling the etching time and Si face was obtained by selfstopping effect. The method we developed in this paper has potential applications in the accurate crystal face acquisition of (0001) 4H-SiC epi-wafer, and the preparation of structures based on 4H-SiC.

Crystal structure, chemical composition, and extended defects of the high-Tc (Bi,Pb)2Sr2Ca(n)-1CunO4 + 2n + delta compounds.

PubMed

Eibl, O

1995-02-15

This paper summarizes results obtained by high-resolution transmission electron microscopy on the crystal structure and microstructure of the (Bi,Pb)2Sr2Ca(n)-1CunO4 + 2n + delta high-Tc superconducting oxides. The experimental basis for the work presented here are high-resolution structure images obtained at ultra-thin (3 nm) areas of carefully prepared transmission electron microscope (TEM) samples. The analysis was carried out on a 400 kV TEM equipped with a pole piece yielding 0.17 nm point-to-point resolution. From the images obtained the projected crystal potential of the cations can be extracted directly, as confirmed by detailed image simulation. Structural analysis of the oxygen sublattice remains an unsolved problem by high-resolution TEM (HRTEM), mainly because of the small scattering factors, and thus the contribution of the oxygen sublattice to the image contrast is small. The (BiPb)2Sr2Ca(n)-1CunO4 + 2n + delta phases are modulated structures that can be understood as an average structure plus a superimposed displacement field. The crystal structure consists of BiO double layers and perovskite-type cuboids (containing Sr, Ca, Cu, and O), which are sandwiched between the BiO double layers. The displacement field can be directly analyzed by HRTEM, and the largest displacement amplitudes of 70 pm were determined for the Bi atoms in the n = 1 compound. The chemical composition of the n = 2 and n = 3 compounds was determined by EDX in the TEM for the cation sublattice. A significant (Ca + Sr) deficiency (approximately 10%) with respect to Cu was found. The (Sr + Ca)/Cu mole fraction ratio was 1.31 for the Bi-2212 phase and 1.14 for the Bi(Pb)-2223 phase. The oxygen content cannot be determined by EDX in the TEM with the accuracy necessary for a correlation with electrical and superconducting properties. The defect structure present in these materials, that is, intergrown lamellae with different crystal structures and equal or different chemical compositions, stacking faults, and grain boundaries, is summarized. The importance of grain boundaries for understanding and improving superconducting properties is emphasized.

Investigation of the thermal and optical performance of a spatial light modulator with high average power picosecond laser exposure for materials processing applications

NASA Astrophysics Data System (ADS)

Zhu, G.; Whitehead, D.; Perrie, W.; Allegre, O. J.; Olle, V.; Li, Q.; Tang, Y.; Dawson, K.; Jin, Y.; Edwardson, S. P.; Li, L.; Dearden, G.

2018-03-01

Spatial light modulators (SLMs) addressed with computer generated holograms (CGHs) can create structured light fields on demand when an incident laser beam is diffracted by a phase CGH. The power handling limitations of these devices based on a liquid crystal layer has always been of some concern. With careful engineering of chip thermal management, we report the detailed optical phase and temperature response of a liquid cooled SLM exposed to picosecond laser powers up to 〈P〉  =  220 W at 1064 nm. This information is critical for determining device performance at high laser powers. SLM chip temperature rose linearly with incident laser exposure, increasing by only 5 °C at 〈P〉  =  220 W incident power, measured with a thermal imaging camera. Thermal response time with continuous exposure was 1-2 s. The optical phase response with incident power approaches 2π radians with average power up to 〈P〉  =  130 W, hence the operational limit, while above this power, liquid crystal thickness variations limit phase response to just over π radians. Modelling of the thermal and phase response with exposure is also presented, supporting experimental observations well. These remarkable performance characteristics show that liquid crystal based SLM technology is highly robust when efficiently cooled. High speed, multi-beam plasmonic surface micro-structuring at a rate R  =  8 cm2 s-1 is achieved on polished metal surfaces at 〈P〉  =  25 W exposure while diffractive, multi-beam surface ablation with average power 〈P〉  =100 W on stainless steel is demonstrated with ablation rate of ~4 mm3 min-1. However, above 130 W, first order diffraction efficiency drops significantly in accord with the observed operational limit. Continuous exposure for a period of 45 min at a laser power of 〈P〉  =  160 W did not result in any detectable drop in diffraction efficiency, confirmed afterwards by the efficient parallel beam processing at 〈P〉  =  100 W. Hence, no permanent changes in SLM phase response characteristics have been detected. This research work will help to accelerate the use of liquid crystal spatial light modulators for both scientific and ultra high throughput laser-materials micro-structuring applications.

Goldquarryite, a new Cd-bearing phosphate mineral from the Gold Quarry mine, Eureka County, Nevada

USGS Publications Warehouse

Roberts, Andrew C.; Cooper, M.A.; Hawthorne, F.C.; Gault, Robert A.; Jensen, M.C.; Foord, E.E.

2003-01-01

Goldquarryite, idealized formula CuCd2Al3(PO44F2(H2O)10(H2O 2, structure-derived formula (Cu0.70???0.30??1.00(Cd1.68Ca0.32??2.00Al3 (PO44F2(H2O)10[(H2O 1.60F0.40]??2.00, is triclinic, space group P1, with unit-cell parameters derived from crystal structure: a = 6.787(1), b = 9.082(2), c = 10.113(2) A??, ?? = 101.40(1)??, ?? = 104.27(1)??, ?? = 102.51(1)??, V = 568.7(3) A??3, a:b:c: = 0.7473:1:1.1135, Z = 1. The strongest seven reflections in the X-ray powder-diffraction pattern are [d(A??)(I)(hkl)]: 9.433(100)(001); 4.726(30)(002); 3.700(30)(022); 3.173(30b)(122, 113, 120, 003); 3.010(30)(122, 212); 2.896(30)(211); 2.820(50)(022). The mineral occurs on a single specimen collected from the 5,425-foot bench, Gold Quarry mine, Eureka County, Nevada, as isolated clusters of radiating sprays of crystals and as compact parallel crystal aggregates, which are both found on and between breccia fragments. Sprays and aggregates never exceed 3 mm in longest dimension and typically average about 0.5 mm in size. Goldquarryite is a late-stage supergene mineral associated with opal, carbonate-fluorapatite and hewettite, on a host rock composed principally of brecciated and hydrothermally rounded jasperoid fragments which have been lightly cemented by late-stage silicification. Individual euhedral crystals are acicular to bladed, elongate [100], with a length-to-width ratio of approximately 20:1; the maximum size is 1.5 mm but most crystals do not exceed 0.4 mm in length. Forms are {010}, {001} major and {100} very minor. The mineral is pleochroic; translucent (masses) to transparent (crystals); very pale blue to blue-gray (crystals) or blue (masses); with a white streak and a vitreous to glassy luster. Goldquarryite is brittle, lacks cleavage, has an irregular fracture, and is nonfluorescent; hardness (Mohs') is estimated at 3-4; measured density is 2.78(1) g/cm3 (sink-float techniques using methylene iodide-acetone mixtures), calculated density is 2.81 g/cm3 (for formula and unit-cell parameters derived from crystal structure). Optically, it is biaxial positive, ?? = 1.570, ?? = 1.573, ?? = 1.578; 2V (meas.) = ???30??, 2V (calc.) = 76??; dispersion r < v, strong. Average electron-microprobe analysis: K2O = 0.17, CuO = 5.33, CaO = 1.25, NiO = 0.23, ZnO = 0.05, CdO = 26.24, Al2O3 = 15.22, V2O3 = 0.05, P2O5 = 28.04, F = 3.63, H2O (calculated assuming stoichiometry) = [22.19], -O = F = -1.53, total = 100.87 weight %, corresponding to [(Cu0.66Ni0.03Zn0.01) ??0.70.

A finite-strain homogenization model for viscoplastic porous single crystals: I - Theory

NASA Astrophysics Data System (ADS)

Song, Dawei; Ponte Castañeda, P.

2017-10-01

This paper presents a homogenization-based constitutive model for the finite-strain, macroscopic response of porous viscoplastic single crystals. The model accounts explicitly for the evolution of the average lattice orientation, as well as the porosity, average shape and orientation of the voids (and their distribution), by means of appropriate microstructural variables playing the role of internal variables and serving to characterize the evolution of both the "crystallographic" and "morphological" anisotropy of the porous single crystals. The model makes use of the fully optimized second-order variational method of Ponte Castañeda (2015), together with the iterated homogenization approach of Agoras and Ponte Castañeda (2013), to characterize the instantaneous effective response of the porous single crystals with fixed values of the microstructural variables. Consistent homogenization estimates for the average strain rate and vorticity fields in the phases are then used to derive evolution equations for the associated microstructural variables. The model is 100% predictive, requiring no fitting parameters, and applies for porous viscoplastic single crystals with general crystal anisotropy and average void shape and orientation, which are subjected to general loading conditions. In Part II of this work (Song and Ponte Castañeda, 2017a), results for both the instantaneous response and the evolution of the microstructure will be presented for porous FCC and HCP single crystals under a wide range of loading conditions, and good agreement with available FEM results will be shown.

Molybdenum Oxide Nitrides of the Mo2(O,N,□)5 Type: On the Way to Mo2O5.

PubMed

Weber, Dominik; Huber, Manop; Gorelik, Tatiana E; Abakumov, Artem M; Becker, Nils; Niehaus, Oliver; Schwickert, Christian; Culver, Sean P; Boysen, Hans; Senyshyn, Anatoliy; Pöttgen, Rainer; Dronskowski, Richard; Ressler, Thorsten; Kolb, Ute; Lerch, Martin

2017-08-07

Blue-colored molybdenum oxide nitrides of the Mo 2 (O,N,□) 5 type were synthesized by direct nitridation of commercially available molybdenum trioxide with a mixture of gaseous ammonia and oxygen. Chemical composition, crystal structure, and stability of the obtained and hitherto unknown compounds are studied extensively. The average oxidation state of +5 for molybdenum is proven by Mo K near-edge X-ray absorption spectroscopy; the magnetic behavior is in agreement with compounds exhibiting Mo V O 6 units. The new materials are stable up to ∼773 K in an inert gas atmosphere. At higher temperatures, decomposition is observed. X-ray and neutron powder diffraction, electron diffraction, and high-resolution transmission electron microscopy reveal the structure to be related to VNb 9 O 24.9 -type phases, however, with severe disorder hampering full structure determination. Still, the results demonstrate the possibility of a future synthesis of the potential binary oxide Mo 2 O 5 . On the basis of these findings, a tentative suggestion on the crystal structure of the potential compound Mo 2 O 5 , backed by electronic-structure and phonon calculations from first principles, is given.

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales.

PubMed

Márk, Géza I; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Order-disorder effects in structure and color relation of photonic-crystal-type nanostructures in butterfly wing scales

NASA Astrophysics Data System (ADS)

Márk, Géza I.; Vértesy, Zofia; Kertész, Krisztián; Bálint, Zsolt; Biró, László P.

2009-11-01

In order to study local and global order in butterfly wing scales possessing structural colors, we have developed a direct space algorithm, based on averaging the local environment of the repetitive units building up the structure. The method provides the statistical distribution of the local environments, including the histogram of the nearest-neighbor distance and the number of nearest neighbors. We have analyzed how the different kinds of randomness present in the direct space structure influence the reciprocal space structure. It was found that the Fourier method is useful in the case of a structure randomly deviating from an ordered lattice. The direct space averaging method remains applicable even for structures lacking long-range order. Based on the first Born approximation, a link is established between the reciprocal space image and the optical reflectance spectrum. Results calculated within this framework agree well with measured reflectance spectra because of the small width and moderate refractive index contrast of butterfly scales. By the analysis of the wing scales of Cyanophrys remus and Albulina metallica butterflies, we tested the methods for structures having long-range order, medium-range order, and short-range order.

Low-temperature solvothermal synthesis of EuS hollow microspheres

DOE Office of Scientific and Technical Information (OSTI.GOV)

Peng, Yong; Wang, Hong; Li, Peng

2014-09-15

Graphical abstract: Synthesis of EuS hollow microspheres at low-temperature via solvothermal method for the first time. - Highlights: • We adopt an improved method to synthesise the (Phen)Eu(Et{sub 2}CNS{sub 2}){sub 3} in deionized water. • We have successfully synthesised the EuS hollow microsphere at 230 °C in acetonitrile. • The price of acetonitrile is more inexpensive, so the price of preparation was reduced. - Abstract: EuS crystals are synthesized by low-temperature solvothermal decomposition of the single source precursor complex (Phen)Eu(Et{sub 2}CNS{sub 2}){sub 3} in acetonitrile. X-ray powder diffraction, scanning electron microscopy, granulocyte diameter statistical analysis, surface energy-dispersive X-ray spectroscopy analysis,more » and UV–vis absorption spectroscopy are used to characterize the structure and properties of the obtained EuS crystals. The results show that the formed EuS crystals are uniform hollow microspheres with a typical cubic phase structure of rock salt and the average particle size of 2.01 μm. The mechanisms for the thermal decomposition of the precursor complex and the formation of the EuS hollow microspheres are postulated based on the experimental observations and previous reports.« less

Crystallization and textural porosity of synthetic clay minerals.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Carrado, K. A.; Csencsits, R.; Thiyagarajan, P.

2002-12-01

The crystallization of synthetic layered magnesium silicate hectorite clays from both silica sol and organosilane sources is compared. For the silica sol-derived clays, a templating method is employed wherein organic or polymeric molecules are included during clay crystallization that are then removed from the composites via calcination. The mechanism of silane-derived hectorite formation is followed by XRD, TGA, 29Si MAS NMR, and small angle X-ray scattering (SAXS), and results are compared to those obtained for the sol-derived hectorite. The mechanism appears to be similar but the rate is approximately doubled when the silane is used rather than silica sol. Analyticalmore » transmission electron microscopy (TEM) is exploited to glean structural morphology information towards resolving the nature of the resulting pore network structures. Results are compared with nitrogen adsorption-desorption isotherm behavior; dominant hysteresis loops are present in the type IV isotherms. Pore size distributions based on both the adsorption and desorption isotherms are compared. Small angle neutron scattering (SANS) experiments reveal that the average particle size increases as synthetic laponite < sol-derived hectorite < silane-derived hectorite < natural hectorite. Contrast matching SANS studies in aqueous and organic solvents are carried out to extract information about pore accessibility.« less

Ferroelectrics under the Synchrotron Light: A Review.

PubMed

Fuentes-Cobas, Luis E; Montero-Cabrera, María E; Pardo, Lorena; Fuentes-Montero, Luis

2015-12-30

Currently, an intensive search for high-performance lead-free ferroelectric materials is taking place. ABO₃ perovskites (A = Ba, Bi, Ca, K and Na; B = Fe, Nb, Ti, and Zr) appear as promising candidates. Understanding the structure-function relationship is mandatory, and, in this field, the roles of long- and short-range crystal orders and interactions are decisive. In this review, recent advances in the global and local characterization of ferroelectric materials by synchrotron light diffraction, scattering and absorption are analyzed. Single- and poly-crystal synchrotron diffraction studies allow high-resolution investigations regarding the long-range average position of ions and subtle global symmetry break-downs. Ferroelectric materials, under the action of electric fields, undergo crystal symmetry, crystallite/domain orientation distribution and strain condition transformations. Methodological aspects of monitoring these processes are discussed. Two-dimensional diffraction clarify larger scale ordering: polycrystal texture is measured from the intensities distribution along the Debye rings. Local order is investigated by diffuse scattering (DS) and X-ray absorption fine structure (XAFS) experiments. DS provides information about thermal, chemical and displacive low-dimensional disorders. XAFS investigation of ferroelectrics reveals local B-cation off-centering and oxidation state. This technique has the advantage of being element-selective. Representative reports of the mentioned studies are described.

Incorporation of fragmentation into a volume average solidification model

NASA Astrophysics Data System (ADS)

Zheng, Y.; Wu, M.; Kharicha, A.; Ludwig, A.

2018-01-01

In this study, a volume average solidification model was extended to consider fragmentation as a source of equiaxed crystals during mixed columnar-equiaxed solidification. The formulation suggested for fragmentation is based on two hypotheses: the solute-driven remelting is the dominant mechanism; and the transport of solute-enriched melt through an interdendritic flow in the columnar growth direction is favorable for solute-driven remelting and is the necessary condition for fragment transportation. Furthermore, a test case with Sn-10 wt%Pb melt solidifying vertically downward in a 2D domain (50 × 60 mm2) was calculated to demonstrate the model’s features. Solidification started from the top boundary, and a columnar structure developed initially with its tip growing downward. Furthermore, thermo-solutal convection led to fragmentation in the mushy zone near the columnar tip front. The fragments transported out of the columnar region continued to grow and sink, and finally settled down and piled up in the bottom domain. The growing columnar structure from the top and pile-up of equiaxed crystals from the bottom finally led to a mixed columnar-equiaxed structure, in turn leading to a columnar-to-equiaxed transition (CET). A special macrosegregation pattern was also predicted, in which negative segregation occurred in both columnar and equiaxed regions and a relatively strong positive segregation occurred in the middle domain near the CET line. A parameter study was performed to verify the model capability, and the uncertainty of the model assumption and parameter was discussed.

Nickel nanofibers synthesized by the electrospinning method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ji, Yi; Zhang, Xuebin, E-mail: zzhhxxbb@126.com; Zhu, Yajun

2013-07-15

Highlights: ► The nickel nanofibers have been obtained by electrospinning method. ► The nickel nanofibers had rough surface which was consisted of mass nanoparticles. ► The average diameter of nickel nanofibers is about 135 nm and high degree of crystallization. ► The Hc, Ms, and Mr were estimated to be 185 Oe, 51.9 and 16.9 emu/g respectively. - Abstract: In this paper, nickel nanofibers were prepared by electrospinning polyvinyl alcohol/nickel nitrate precursor solution followed by high temperature calcination in air and deoxidation in hydrogen atmosphere. The thermal stability of the as-electrospun PVA/Ni(NO{sub 3}){sub 2} composite nanofibers were characterized by TG–DSC.more » The morphologies and structures of the as-prepared samples were characterized by X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR), field-emission scanning electronmicroscope (FE-SEM) and field-emission transmission electron microscopy (FE-TEM). The hysteresis loops (M–H loops) were measured by Physical Property Measurement System (PPMS). The results indicate that: the PVA and the nickel nitrate were almost completely decomposed at 460 °C and the products were pure nickel nanofibers with face-centered cubic (fcc) structure. Furthermore, the as-prepared nickel nanofibers had a continuous structure with rough surface and high degree of crystallization. The average diameter of nickel nanofibers was about 135 nm. The nanofibers showed a stronger coercivity of 185 Oe than value of bulk nickel.« less

Production of crystalline refractory metal oxides containing colloidal metal precipitates and useful as solar-effective absorbers

DOEpatents

Narayan, Jagdish; Chen, Yok

1983-01-01

This invention is a new process for producing refractory crystalline oxides having improved or unusual properties. The process comprises the steps of forming a doped-metal crystal of the oxide; exposing the doped crystal in a bomb to a reducing atmosphere at superatmospheric pressure and a temperature effecting precipitation of the dopant metal in the crystal lattice of the oxide but insufficient to effect net diffusion of the metal out of the lattice; and then cooling the crystal. Preferably, the cooling step is effected by quenching. The process forms colloidal precipitates of the metal in the oxide lattice. The process may be used, for example, to produce thermally stable black MgO crystalline bodies containing magnetic colloidal precipitates consisting of about 99% Ni. The Ni-containing bodies are solar-selective absorbers, having a room-temperature absorptivity of about 0.96 over virtually all of the solar-energy spectrum and exhibiting an absorption edge in the region of 2 .mu.m. The process parameters can be varied to control the average size of the precipitates. The process can produce a black MgO crystalline body containing colloidal Ni precipitates, some of which have the face-centered-cubic structure and others of which have the body-centered cubic structure. The products of the process are metal-precipitate-containing refractory crystalline oxides which have improved or unique optical, mechanical, magnetic, and/or electronic properties.

Effect of sintering temperature on physical, structural and optical properties of wollastonite based glass-ceramic derived from waste soda lime silica glasses

NASA Astrophysics Data System (ADS)

Almasri, Karima Amer; Sidek, Hj. Ab Aziz; Matori, Khamirul Amin; Zaid, Mohd Hafiz Mohd

The impact of different sintering temperatures on physical, optical and structural properties of wollastonite (CaSiO3) based glass-ceramics were investigated for its potential application as a building material. Wollastonite based glass-ceramics was provided by a conventional melt-quenching method and followed by a controlled sintering process. In this work, soda lime silica glass waste was utilized as a source of silicon. The chemical composition and physical properties of glass were characterized by using Energy Dispersive X-ray Fluorescence (EDXRF) and Archimedes principle. The Archimedes measurement results show that the density increased with the increasing of sintering temperature. The generation of CaSiO3, morphology, size and crystal phase with increasing the heat-treatment temperature were examined by field emission scanning electron microscopy (FESEM), Fourier transforms infrared reflection spectroscopy (FTIR), and X-ray diffraction (XRD). The average calculated crystal size gained from XRD was found to be in the range 60 nm. The FESEM results show a uniform distribution of particles and the morphology of the wollastonite crystal is in relict shapes. The appearance of CaO, SiO2, and Ca-O-Si bands disclosed from FTIR which showed the formation of CaSiO3 crystal phase. In addition to the calculation of the energy band gap which found to be increased with increasing sintering temperature.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kelleher, Alan; Liu, Zhuyun; Seid, Christopher A.

LJL143, a salivary protein from L. longipalpis, was produced using P. pastoris and crystallized in space group P2{sub 1}2{sub 1}2{sub 1}. Leishmaniasis is a neglected vector-borne disease with a global prevalence of over 12 million cases and 59 000 annual deaths. Transmission of the parasite requires salivary proteins, including LJL143 from the New World sandfly Lutzomyia longipalpis. LJL143 is a known marker of sandfly exposure in zoonotic hosts. LJL143 was crystallized from soluble protein expressed using Pichia pastoris. X-ray data were collected to 2.6 Å resolution from orthorhombic crystals belonging to space group P2{sub 1}2{sub 1}2{sub 1}, with average unit-cellmore » parameters a = 57.39, b = 70.24, c = 79.58 Å. The crystals are predicted to have a monomer in the asymmetric unit, with an estimated solvent content of 48.5%. LJL143 has negligible homology to any reported structures, so the phases could not be determined by molecular replacement. All attempts at S-SAD failed and future studies include experimental phase determination using heavy-atom derivatives.« less

STXM-XANES Analysis of Organic Matter in Dark Clasts and Halite Crystals in Zag and Monahans Meteorites

NASA Technical Reports Server (NTRS)

Kebukawa, Y.; Zolensky, M. E.; Fries, M.; Nakato, A.; Kilcoyne, A. L. D.; Takeichi, Y.; Suga, H.; Miyamoto, C.; Rahman, Z.; Kobayashi, K.;

Oxygen binding by alpha(Fe2+)2beta(Ni2+)2 hemoglobin crystals.

PubMed Central

Bruno, S.; Bettati, S.; Manfredini, M.; Mozzarelli, A.; Bolognesi, M.; Deriu, D.; Rosano, C.; Tsuneshige, A.; Yonetani, T.; Henry, E. R.

2000-01-01

Oxygen binding by hemoglobin fixed in the T state either by crystallization or by encapsulation in silica gels is apparently noncooperative. However, cooperativity might be masked by different oxygen affinities of alpha and beta subunits. Metal hybrid hemoglobins, where the noniron metal does not bind oxygen, provide the opportunity to determine the oxygen affinities of alpha and beta hemes separately. Previous studies have characterized the oxygen binding by alpha(Ni2+)2beta(Fe2+)2 crystals. Here, we have determined the three-dimensional (3D) structure and oxygen binding of alpha(Fe2+)2beta(Ni2+)2 crystals grown from polyethylene glycol solutions. Polarized absorption spectra were recorded at different oxygen pressures with light polarized parallel either to the b or c crystal axis by single crystal microspectrophotometry. The oxygen pressures at 50% saturation (p50s) are 95 +/- 3 and 87 +/- 4 Torr along the b and c crystal axes, respectively, and the corresponding Hill coefficients are 0.96 +/- 0.06 and 0.90 +/- 0.03. Analysis of the binding curves, taking into account the different projections of the alpha hemes along the optical directions, indicates that the oxygen affinity of alpha1 hemes is 1.3-fold lower than alpha2 hemes. Inspection of the 3D structure suggests that this inequivalence may arise from packing interactions of the Hb tetramer within the monoclinic crystal lattice. A similar inequivalence was found for the beta subunits of alpha(Ni2+)2beta(Fe2+)2 crystals. The average oxygen affinity of the alpha subunits (p50 = 91 Torr) is about 1.2-fold higher than the beta subunits (p50 = 110 Torr). In the absence of cooperativity, this heterogeneity yields an oxygen binding curve of Hb A with a Hill coefficient of 0.999. Since the binding curves of Hb A crystals exhibit a Hill coefficient very close to unity, these findings indicate that oxygen binding by T-state hemoglobin is noncooperative, in keeping with the Monod, Wyman, and Changeux model. PMID:10794410

Crystal structure of fac-tri-chlorido-[tris-(pyridin-2-yl-N)amine]-chromium(III).

PubMed

Yamaguchi-Terasaki, Yukiko; Fujihara, Takashi; Nagasawa, Akira; Kaizaki, Sumio

2015-01-01

In the neutral complex mol-ecule of the title compound, fac-[CrCl3(tpa)] [tpa is tris-(pyridin-2-yl)amine; C15H12N4], the Cr(III) ion is bonded to three N atoms that are constrained to a facial arrangement by the tpa ligand and by three chloride ligands, leading to a distorted octa-hedral coordination sphere. The average Cr-N and Cr-Cl bond lengths are 2.086 (5) and 2.296 (4) Å, respectively. The complex mol-ecule is located on a mirror plane. In the crystal, a combination of C-H⋯N and C-H⋯Cl hydrogen-bonding inter-actions connect the mol-ecules into a three-dimensional network.

Raman study of ? crystals

NASA Astrophysics Data System (ADS)

Pimenta, M. A.; Oliveira, M. A. S.; Bourson, P.; Crettez, J. M.

1997-09-01

In this work we present a polarized Raman study of 0953-8984/9/37/020/img7 single crystals for several values of the concentration 0953-8984/9/37/020/img8 made using different scattering geometries. The Raman spectra, composed of broad bands, have been fitted in accordance with a symmetry analysis which allowed us to assign the vibrational modes, and determine their frequencies and damping constants. The results are compatible with an average hexagonal symmetry for the solid solutions with x in the range 0953-8984/9/37/020/img9. In each of the spectra we found two bands at about 590 and 0953-8984/9/37/020/img10, probably associated with the existence of 0953-8984/9/37/020/img11 structures in the solid solutions.

Crystal structure, thermal expansivity, and elasticity of OH-chondrodite: Trends among dense hydrous magnesium silicates

DOE PAGES

Ye, Yu; Jacobsen, Steven D.; Mao, Zhu; ...

2015-04-01

Here, we report the structure and thermoelastic properties of OH-chondrodite. The sample was synthesized at 12 GPa and 1523 K, coexisting with hydroxyl-clinohumite and hydrous olivine. The Fe content Fe/(Fe+Mg) is 1.1 mol%, and the monoclinic unit-cell parameters are: a = 4.7459(2) Å, b = 10.3480(7) Å, c = 7.9002(6) Å, α = 108.702(7)°, and V = 367.50(4) Å3. At ambient conditions the crystal structure was refined in space group P 21/b from 1915 unique reflection intensities measured by single-crystal x-ray diffraction. The volume thermal expansion coefficient was measured between 150 and 800 K, resulting in α V = 2.8(5)×10more » -9(K -2) × T + 40.9(7) × 10 -6(K -1) – 0.81(3)(K)/T 2, with an average value of 38.0(9)×10 -6 K -1. Brillouin spectroscopy was used to measure a set of acoustic velocities from which all thirteen components (C ij) of the elastic tensor were determined. The Voigt-Reuss-Hill average of the moduli yield for the adiabatic bulk modulus, K S0 = 117.9(12) GPa, and for shear modulus, G 0 = 70.1(5) GPa. The Reuss bound on the isothermal bulk modulus (K T0) is 114.2(14) GPa. From the measured thermodynamic properties, the Grüneisen parameter (γ) is calculated to be 1.66(4). Fitting previous static compression data using our independently measured bulk modulus (isothermal Reuss bound) as a fixed parameter, we refined the first pressure derivative of the bulk modulus, K T’ = 5.5(1). Systematic trends between H 2O content and physical properties are evaluated among dense hydrous magnesium silicate (DHMS) phases along the forsterite-brucite join.« less

The effect of Eu{sup 2+} doping concentration on luminescence properties of Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+} yellow phosphor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Song, Yue; Liu, Quansheng, E-mail: liuqs@cust.edu.cn; School of Physics, JiLin University, No. 2699 Qianjin Street, Changchun 130012

2013-10-15

Graphical abstract: - Highlights: • The concentration quenching mechanism of Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+}can be interpreted by the dipole–dipole (d–d) interaction of Eu{sup 2+} ions. • The average electronegativity of O{sup 2−} ions located around Eu{sup 2+} ion is 1.9991 eV. • The optimum concentration of Eu{sup 2+} ions in Sr{sub 3}B{sub 2}O{sub 6} is 7 mol%. • Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+} is a hexagonal crystal structure. - Abstract: The Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+} yellow phosphors were synthesized by high-temperature solid state reaction method. The crystal structure and optical properties of the Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+}more » phosphor was studied. Results indicate that Sr{sub 3}B{sub 2}O{sub 6}:Eu{sup 2+} has a hexagonal crystal structure. The excitation spectrum indicates that this phosphor can be effectively excited by ultraviolet light of near 390 nm and blue light of 460 nm. The emission spectrum shows a intense broad band spectrum peaking at 566 nm, which corresponds to the 4f{sup 6}({sup 7}F)5d ({sup 2}e{sub g})→{sup 8}S{sub 7/2} (4f{sup 7})transition of Eu{sup 2+} ion. The excitation spectrum is a broad asymmetric excitation band extending from 300 nm to 500 nm and the main excitation peak is at 468 nm. The average electronegativity of O{sup 2−} ions located around Eu{sup 2+} ion is 1.9991 eV. The optimum concentration of Eu{sup 2+} is 7 mol%. The concentration quenching mechanism can be interpreted by the dipole–dipole (d–d) interaction of Eu{sup 2+} ions.« less

Thermal effects in high average power optical parametric amplifiers.

PubMed

Rothhardt, Jan; Demmler, Stefan; Hädrich, Steffen; Peschel, Thomas; Limpert, Jens; Tünnermann, Andreas

2013-03-01

Optical parametric amplifiers (OPAs) have the reputation of being average power scalable due to the instantaneous nature of the parametric process (zero quantum defect). This Letter reveals serious challenges originating from thermal load in the nonlinear crystal caused by absorption. We investigate these thermal effects in high average power OPAs based on beta barium borate. Absorption of both pump and idler waves is identified to contribute significantly to heating of the nonlinear crystal. A temperature increase of up to 148 K with respect to the environment is observed and mechanical tensile stress up to 40 MPa is found, indicating a high risk of crystal fracture under such conditions. By restricting the idler to a wavelength range far from absorption bands and removing the crystal coating we reduce the peak temperature and the resulting temperature gradient significantly. Guidelines for further power scaling of OPAs and other nonlinear devices are given.

Enhanced performance of photonic crystal GaN light-emitting diodes with graphene transparent electrodes

NASA Astrophysics Data System (ADS)

Ge, Hai-Liang; Xu, Chen; Xu, Kun; Xun, Meng; Wang, Jun; Liu, Jie

2015-03-01

The two-dimensional (2D) triangle lattice air hole photonic crystal (PC) GaN-based light-emitting diodes (LED) with double-layer graphene transparent electrodes (DGTE) have been produced. The current spreading effect of the double-layer graphene (GR) on the surface of the PC structure of the LED has been researched. Specially, we found that the part of the graphene suspending over the air hole of the PC structure was of much higher conductivity, which reduced the average sheet resistance of the graphene transparent conducting electrode and improved the current spreading of the PC LED. Therefore, the work voltage of the DGTE-PC LED was obviously decreased, and the output power was greatly enhanced. The COMSOL software was used to simulate the current density distribution of the samples. The results show that the etching of PC structure results in the degradation of the current spreading and that the graphene transparent conducting electrode can offer an uniform current spreading in the DGTE-PC LED. PACS: 85.60.Jb; 68.65.Pq; 42.70.Qs

Structural evolution in three and four-layer Aurivillius solid solutions: A comparative study versus relaxor properties

NASA Astrophysics Data System (ADS)

Tellier, Jenny; Boullay, Philippe; Ben Jennet, Dorra; Mercurio, Daniele

2008-02-01

Two solid solutions of three-layer Ba xBi 4- xNb xTi 3- xO 12 (0 ≤ x ≤ 1.2) and four-layer Aurivillius compounds (Na 0.5Bi 0.5) 1- xBa xBi 4Ti 4O 15 (0 ≤ x ≤ 1), which both present a ferroelectric to relaxor-like transition with increasing x, were synthesized by solid state reaction. The evolution of their crystal structures, as a function of x, was performed using Rietveld refinements from X-ray powder diffraction data. As x increases, the average crystal structures become less distorted with respect to the archetypal high temperature tetragonal one and the coordination number of Bi 3+ in M 2O 2 layers continuously changes from {4 + 2} to {4}. The relaxor behaviour which appears in samples for a tolerance factor t > 0.96 is associated with a general static disorder in A and M sites together with the presence of some Ba 2+ cations in M 2O 2 layers (less than 10%).

Polyacrylonitrile nanofiber as polar solvent N,N-dimethyl formamide sensor based on quartz crystal microbalance technique

NASA Astrophysics Data System (ADS)

Rianjanu, A.; Julian, T.; Hidayat, S. N.; Suyono, E. A.; Kusumaatmaja, A.; Triyana, K.

2018-04-01

Here, we describe an N,N-dimethyl formamide (DMF) vapour sensor fabricated by coating polyacrylonitrile (PAN) nanofiber structured on quartz crystal microbalance (QCM). The PAN nanofiber sensors with an average diameter of 225 nm to 310 nm were fabricated via electrospinning process with different mass deposition on QCM substrate. The nanostructured of PAN nanofiber offers a high specific surface area that improved the sensing performance of nanofiber sensors. Benefiting from that fine structure, and high polymer-solvent affinity between PAN and DMF, the development of DMF sensors presented good response at ambient temperature. Since there is no chemical reaction between PAN nanofiber and DMF vapour, weak physical interaction such absorption and swelling were responsible for the sensing behavior. The results are indicating that the response of PAN nanofiber sensors has more dependency on the nanofiber structure (specific surface area) rather than its mass deposition. The sensor also showed good stability after a few days sensing. These findings have significant implications for developing DMF vapour sensor based on QCM coated polymer nanofibers.

Structure and stability of solid Xe(H 2) n

DOE PAGES

Somayazulu, Maddury; Dera, Przemyslaw; Smith, Jesse; ...

2015-03-10

Mixtures of xenon and molecular hydrogen form a series of hexagonal, van der Waals compounds at high pressures and at 300 K. Synchrotron, x-ray, single crystal diffraction studies reveal that below 7.5 GPa, Xe(H 2) 8 crystallizes in a P3¯m1 structure that displays pressure-induced occupancy changes of two pairs of xenon atoms located on the 2c and 2d sites (while the third pair on yet another 2c site remains fully occupied). The occupancy becomes 1 at the P3¯m1 to R3 transition and all the xenon atoms occupy the 3d sites in the high-pressure structure. These pressure-induced changes in occupancy coincidemore » with volume changes that maintain the average Xe:H 2 stoichiometry fixed at 1:8. Furthermore, the synchrotron x-ray diffraction and Raman measurements show that this unique hydrogen-bearing compound that can be synthesized at 4.2 GPa and 300 K, quenched at low temperatures to atmospheric pressure, and retained up to 90 K on subsequent warming.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Vibrational Properties of Anhydrous and Partially Hydrated Uranyl Fluoride

DOE PAGES

Anderson, Brian B.; Kirkegaard, Marie C.; Miskowiec, Andrew J.; ...

2017-01-01

Uranyl fluoride (UO 2F 2) is a hygroscopic powder with two main structural phases: an anhydrous crystal and a partially hydrated crystal of the same R¯3m symmetry. The formally closed-shell electron structure of anhydrous UO 2F 2 is amenable to density functional theory calculations. We use density functional perturbation theory (DFPT) to calculate the vibrational frequencies of the anhydrous crystal structure and employ complementary inelastic neutron scattering and temperature-dependent Raman scattering to validate those frequencies. As a model closed-shell actinide, we investigated the effect of LDA, GGA, and non-local vdW functionals as well as the spherically-averaged Hubbard +U correction onmore » vibrational frequencies, electronic structure, and geometry of anhydrous UO 2F 2. A particular choice of U eff = 5.5 eV yields the correct U Oyl bond distance and vibrational frequencies for the characteristic Eg and A1g modes that are within the resolution of experiment. Inelastic neutron scattering and Raman scattering suggest a degree of water coupling to the lattice vibrations in the more experimentally accessible partially hydrated UO 2F 2 system, with the symmetric O-U-O stretching vibration shifted approximately 47 cm -1 lower in energy compared to the anhydrous structure. Evidence of water interaction with the uranyl ion is present from a two-peak decomposition of the uranyl stretching vibration in the Raman spectra and anion hydrogen stretching vibrations in the inelastic neutron scattering spectra. A first-order dehydration phase transition temperature is definitively identified to be 125 °C using temperature-dependent Raman scattering.« less

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE PAGES

Taddei, Keith M.; Sturza, M.; Chung, Duck -Yung; ...

2015-09-14

By simultaneously displaying magnetism and superconductivity in a single phase, the iron-based superconductors provide a model system for the study of magnetism's role in superconductivity. The class of intercalated iron selenide superconductors is unique among these in having the additional property of phase separation and coexistence of two distinct phases—one majority phase with iron vacancy ordering and strong antiferromagnetism, and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfully synthesized separate frommore » the majority phase. In order to better understand this minority phase, a series of high-quality Cs xFe 2–ySe 2 single crystals with (0.8 ≤ x ≤ 1;0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show that the average I4/mmm structure of the minority phase is distinctly different from the high-temperature I4/mmm parent structure. Moreover, single-crystal diffraction reveals the presence of discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from three-dimensional Cs vacancy ordering. This model predicts a 25% vacancy of the Cs site in the minority phase which is consistent with the site's refined occupancy. Magnetization measurements performed in tandem with neutron single-crystal diffraction provide evidence that the minority phase is the host of superconductivity. Lastly, our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the nominal valence of iron.« less

Cesium vacancy ordering in phase-separated C s x F e 2 - y S e 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Taddei, K. M.; Sturza, M.; Chung, D. Y.

2015-09-01

By simultaneously displaying magnetism and superconductivity in a single phase, the iron based superconductors provide a model system for the study of magnetism’s role in superconductivity. The class of intercalated iron selenide superconductors is unique amongst these in having the additional property of phase separation and coexistence of two distinct phases - one majority phase with iron vacancy ordering and strong antiferromagnetism and the other a poorly understood minority microscopic phase with a contested structure. Adding to the intrigue, the majority phase has never been found to show superconductivity on its own while the minority phase has never been successfullymore » synthesized separate from the majority phase. In order to better understand this minority phase, a series of high quality CsxFe2-ySe2 single crystals with (0.8 ≤ x ≤ 1; 0 ≤ y ≤ 0.3) were grown and studied. Neutron and x-ray powder diffraction performed on ground crystals show the average structure of the minority phase to be I4/mmm, however, the temperature evolution of its lattice parameters shows it to be distinct from the high temperature I4/mmm parent structure. Neutron and x-ray diffraction experiments performed on single crystal samples reveal the presence of previously unobserved discrete superlattice reflections that remove the degeneracy of the Cs sites in both the majority and minority phases and reduce their structural symmetries from body-centered to primitive. Group theoretical analysis in conjunction with structural modeling shows that the observed superlattice reflections originate from a three-dimensional Cs vacancy ordering in the minority phase. This model predicts a 25% vacancy of the Cs site which is consistent with the site’s refined occupancy. Magnetization measurements performed in tandem with neutron single crystal diffraction provide evidence that the minority phase is the host of superconductivity. Our results also reveal a superconducting dome in which the superconducting transition temperature varies as a function of the valence of iron.« less

Structural, microstructural and vibrational analyses of the monoclinic tungstate BiLuWO{sub 6}

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ait Ahsaine, H.; Taoufyq, A.; Institut Matériaux Microélectronique et Nanosciences de Provence, IM2NP, UMR CNRS 7334, Université de Toulon, BP 20132, 83957 La Garde Cedex

2014-10-15

The bismuth lutetium tungstate phase BiLuWO{sub 6} has been prepared using a solid state route with stoichiometric mixtures of oxide precursors. The obtained polycrystalline phase has been characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), transmission electron microscopy (TEM), and Raman spectroscopy. In the first step, the crystal structure has been refined using Rietveld method: the crystal cell was resolved using monoclinic system (parameters a, b, c, β) with space group A2/m. SEM images showed the presence of large crystallites with a constant local nominal composition (BiLuW). TEM analyses showed that the actual local structure could be better representedmore » by a superlattice (a, 2b, c, β) associated with space groups P2 or P2/m. The Raman spectroscopy showed the presence of vibrational bands similar to those observed in the compounds BiREWO{sub 6} with RE=Y, Gd, Nd. However, these vibrational bands were characterized by large full width at half maximum, probably resulting from the long range Bi/Lu disorder and local WO{sub 6} octahedron distortions in the structure. - Graphical abstract: The average structure of BiLuWO{sub 6} determined from X-ray diffraction data can be represented by A2/m space group. Experimental Electron Diffraction patterns along the [0vw] zone axes of the monoclinic structure and associated simulated patterns show the existence of a monoclinic superstructure with space group P2 or P2/m. - Highlights: • A new monoclinic BiLuWO{sub 6} phase has been elaborated from solid-state reaction. • The space group of the monoclinic disordered average structure should be A2/m. • Transmission electron microscopy leads to a superlattice with P2/m space group. • Raman spectroscopy suggests existence of local disorder.« less

Effect of hydrogen on deformation structure and properties of CMSX-2 nickel-base single-crystal superalloy

NASA Technical Reports Server (NTRS)

Dollar, M.; Bernstein, I. M.; Walston, S.; Prinz, F.; Domnanovich, A.

1987-01-01

Material used in this study was a heat of the alloy CMSX-2. This nickel-based superalloy was provided in the form of oriented single crystals, solutionized for 3 hrs at 1315 C. It was then usually heat treated as follows: 1050 C/16h/air cool + 850 C/48h/air cool. The resulting microstructure is dominated by cuboidal, ordered gamma precipitates with a volume fraction of about 75% and an average size of 0.5 microns. In brief, the most compelling hydrogen induced-changes in deformation structure are: (1) enhanced dislocation accumulation in the gamma matrix; and (2) more extensive cross-slip of superdislocations in the gamma precipitates. The enhanced dislocation density in gamma acts to decrease the mean free path of a superdislocation, while easier cross slip hinders superdislocation movement by providing pinning points in the form of sessile jobs. Both processes contribute to the increase of flow stress and the notable work hardening that occurs prior to fracture.

Highly transparent ceramics with disordered crystal structure

NASA Astrophysics Data System (ADS)

Osipov, V. V.; Khasanov, O. L.; Solomonov, V. I.; Shitov, V. A.; Orlov, A. N.; Platonov, V. V.; Spirina, A. V.; Luk'yashin, K. E.; Dvilis, E. S.

2010-08-01

A highly transparent ceramic has been synthesized from Nd3+:Y2O3 to which 6 mol. % ZrO2 and 25 mol. % Sc2O3 or Lu2O3 were added for disordering the crystal structure. Nanopowders with an average particle size of 10-15 nm served as an initial material. They were compacted by the method of uniaxial static pressing combined with ultrasonic action on nanoparticles. The compacting pressure was 200 MPa; the power of the ultrasonic generator was 1.5 kW. It has been shown that the replacement of Y by isovalent Sc and Lu ions and by heterovalent Zr ions reduces the content of pores and the sizes of crystallites. The transparency of the Nd3+:Y2O3 ceramic with these additives reaches a maximum of 82.2%, and the 40% intensity level spectral band corresponding to the 4F3/2 → 4I11/2 transition widens from 11.4 to 40 nm.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Xuetian; An, Ke; Bai, Jianmin

Sodium ion batteries are being considered as an alternative to lithium ion batteries in large-scale energy storage applications owing to the low cost. In this paper, a novel titanate compound, NaAlTi 3O 8, was successfully synthesized and tested as a promising anode material for sodium ion batteries. Powder X-ray Diffraction (XRD) and refinement were used to analyze the crystal structure. Electrochemical cycling tests under a C/10 rate between 0.01 - 2.5 V showed that ~83 mAh/g capacity could be achieved in the second cycle, with ~75% of which retained after 100 cycles, which corresponds to 0.75 Na + insertion andmore » extraction. The influence of synthesis conditions on electrochemical performances was investigated and discussed. Finally, NaAlTi 3O 8 not only presents a new anode material with low average voltage of ~0.5 V, but also provides a new type of intercalation anode with a crystal structure that differentiates from the anodes that have been reported.« less

Surface analysis of Fe-Co-Mo electrolytic coatings

NASA Astrophysics Data System (ADS)

Yar-Mukhamedova, G. Sh; Sakhnenko, N. D.; Ved', M. V.; Yermolenko, I. Yu; Zyubanova, S. I.

2017-06-01

Coatings Fe-Co-Mo with a composition of 47 at.% iron, 28 at.% Cobalt and 25 at.% Molybdenum were deposited from citrate electrolyte using pulse electrolysis mode. Scanning electron and atomic force microscopy have established the surface morphology and topography. It was identified the parts with a globular structure which have an average size of 0.2-0.5μm and singly located sharp grains. Within the same scan area sites with developed surface were detected the topography of which is identical to the crystal structure of cobalt with the crystallites size of 0.2-1.75μm. The parameters Ra and Rq for parts with different morphology as well as average characteristics of coatings demonstrated the low roughness of the surface. It is found that the coercive force of Fe-Co-Mo films is 7-10 Oe, which allow us to classify the Fe-Co-Mo coatings as soft magnetic materials.

Large moments in bcc FexCoyMnz ternary alloy thin films

NASA Astrophysics Data System (ADS)

Snow, R. J.; Bhatkar, H.; N'Diaye, A. T.; Arenholz, E.; Idzerda, Y. U.

2018-02-01

The elemental magnetic moments and the average atomic moment of 10-20 nm thick single crystal bcc (bct) FexCoyMnz films deposited on MgO(001) have been determined as a function of a broad range of compositions. Thin film epitaxy stabilized the bcc structure for 80% of the available ternary compositional space compared to only a 23% stability region for the bulk. The films that display ferromagnetism represent 60% of the available compositional possibilities compared to 25% for the bulk. A maximum average atomic moment of 3.25 ± 0.3 μB/atom was observed for a bcc Fe9Co62Mn29 film (well above the limit of the Slater-Pauling binary alloy curve of 2.45 μB/atom). The FexCoyMnz ternary alloys that exhibit high moments can only be synthesized as ultrathin films since the bcc structure is not stable in the bulk for those compositions.

THz polariton laser using an intracavity Mg:LiNbO₃ crystal with protective Teflon coating.

PubMed

Ortega, Tiago A; Pask, Helen M; Spence, David J; Lee, Andrew J

2017-02-20

An enhancement in the performance of a THz polariton laser based on an intracavity magnesium-doped lithium niobate crystal (Mg:LiNbO₃) in surface-emitted (SE) configuration is demonstrated resulting from the deposition of a protective Teflon coating on the total internal reflection surface of the crystal. In this cavity geometry the resonating fields undergo total internal reflection (TIR) inside the lithium niobate, and laser damage to that surface can be a limiting factor in performance. The protective layer prevents laser damage to the crystal surface, enabling higher pump power, yielding higher THz output power and wider frequency tuning range. With the unprotected crystal, narrow-band THz output tunable from 1.50 to 2.81 THz was produced, with maximum average output power of 20.1 µW at 1.76 THz for 4 W diode pump power (limited by laser damage to the crystal). With the Teflon coating, no laser damage to the crystal was observed, and the system produced narrow-band THz output tunable from 1.46 to 3.84 THz, with maximum average output power of 56.8 µW at 1.76 THz for 6.5 W diode pump power. This is the highest average output power and the highest diode-to-terahertz conversion efficiency ever reported for an intracavity terahertz polariton laser.

Local Crystal Structure of Antiferroelectric Bi2Mn4/3Ni2/3O6 in Commensurate and Incommensurate Phases Described by Pair Distribution Function (PDF) and Reverse Monte Carlo (RMC) Modeling.

PubMed

Szczecinski, Robert J; Chong, Samantha Y; Chater, Philip A; Hughes, Helen; Tucker, Matthew G; Claridge, John B; Rosseinsky, Matthew J

2014-04-08

The functional properties of materials can arise from local structural features that are not well determined or described by crystallographic methods based on long-range average structural models. The room temperature (RT) structure of the Bi perovskite Bi 2 Mn 4/3 Ni 2/3 O 6 has previously been modeled as a locally polar structure where polarization is suppressed by a long-range incommensurate antiferroelectric modulation. In this study we investigate the short-range local structure of Bi 2 Mn 4/3 Ni 2/3 O 6 , determined through reverse Monte Carlo (RMC) modeling of neutron total scattering data, and compare the results with the long-range incommensurate structure description. While the incommensurate structure has equivalent B site environments for Mn and Ni, the local structure displays a significantly Jahn-Teller distorted environment for Mn 3+ . The local structure displays the rock-salt-type Mn/Ni ordering of the related Bi 2 MnNiO 6 high pressure phase, as opposed to Mn/Ni clustering observed in the long-range average incommensurate model. RMC modeling reveals short-range ferroelectric correlations between Bi 3+ cations, giving rise to polar regions that are quantified for the first time as existing within a distance of approximately 12 Å. These local correlations persist in the commensurate high temperature (HT) phase, where the long-range average structure is nonpolar. The local structure thus provides information about cation ordering and B site structural flexibility that may stabilize Bi 3+ on the A site of the perovskite structure and reveals the extent of the local polar regions created by this cation.

Investigation of Methods to Eliminate Voltage Delay in Li/SOCl2 Cells.

DTIC Science & Technology

1980-05-01

of storage at 550C the surface was completely covered with cubic crystals averaging about 8 pim on an edge (Figure 24). The lithium surface stored at...completely covered with cubic crystals, showing no smooth undercoating at all (Figure 25). The average crystal diameter was approximately 3.3 pim , with a...used. ithi timl acgu ire0d A Ci yst al I me surt ace, oil dr n torage at elevated temlper aI Ite t. T[he out lace, showed ch[ ott ine by EPAC except

Revisiting the blind tests in crystal structure prediction: accurate energy ranking of molecular crystals.

PubMed

Asmadi, Aldi; Neumann, Marcus A; Kendrick, John; Girard, Pascale; Perrin, Marc-Antoine; Leusen, Frank J J

2009-12-24

In the 2007 blind test of crystal structure prediction hosted by the Cambridge Crystallographic Data Centre (CCDC), a hybrid DFT/MM method correctly ranked each of the four experimental structures as having the lowest lattice energy of all the crystal structures predicted for each molecule. The work presented here further validates this hybrid method by optimizing the crystal structures (experimental and submitted) of the first three CCDC blind tests held in 1999, 2001, and 2004. Except for the crystal structures of compound IX, all structures were reminimized and ranked according to their lattice energies. The hybrid method computes the lattice energy of a crystal structure as the sum of the DFT total energy and a van der Waals (dispersion) energy correction. Considering all four blind tests, the crystal structure with the lowest lattice energy corresponds to the experimentally observed structure for 12 out of 14 molecules. Moreover, good geometrical agreement is observed between the structures determined by the hybrid method and those measured experimentally. In comparison with the correct submissions made by the blind test participants, all hybrid optimized crystal structures (apart from compound II) have the smallest calculated root mean squared deviations from the experimentally observed structures. It is predicted that a new polymorph of compound V exists under pressure.

Targeted Basic Studies of Ferroelectric and Ferroelastic Materials for Piezoelectric Transducer Applications.

DTIC Science & Technology

1983-03-01

PLZT ceramics. Low temperature studies on pure and doped PZTs have given the first clear indi- cation of the intrinsic (averaged) single domain...8217 11 4.0 PYROELECTRIC MATERIALS 27 4.1 Micro Composites 27 4.2 ’ Doped ’ Tungsten Bronze and TGS Structure Single Crystals 28 5.0 FERROELECTRIC...differences in piezo- electric activity, coupling constant and permittivity between differently doped PZTs are extrinsic and freeze out at 4°K. Extending

Influence of arsenic flow on the crystal structure of epitaxial GaAs grown at low temperatures on GaAs (100) and (111)A substrates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Galiev, G. B.; Klimov, E. A.; Vasiliev, A. L.

The influence of arsenic flow in a growth chamber on the crystal structure of GaAs grown by molecular-beam epitaxy at a temperature of 240°C on GaAs (100) and (111)A substrates has been investigated. The flow ratio γ of arsenic As4 and gallium was varied in the range from 16 to 50. GaAs films were either undoped, or homogeneously doped with silicon, or contained three equidistantly spaced silicon δ-layers. The structural quality of the annealed samples has been investigated by transmission electron microscopy. It is established for the first time that silicon δ-layers in “low-temperature” GaAs serve as formation centers ofmore » arsenic precipitates. Their average size, concentration, and spatial distribution are estimated. The dependence of the film structural quality on γ is analyzed. Regions 100–150 nm in size have been revealed in some samples and identified (by X-ray microanalysis) as pores. It is found that, in the entire range of γ under consideration, GaAs films on (111)A substrates have a poorer structural quality and become polycrystalline beginning with a thickness of 150–200 nm.« less

Dynamo Catalogue: Geometrical tools and data management for particle picking in subtomogram averaging of cryo-electron tomograms.

PubMed

Castaño-Díez, Daniel; Kudryashev, Mikhail; Stahlberg, Henning

2017-02-01

Cryo electron tomography allows macromolecular complexes within vitrified, intact, thin cells or sections thereof to be visualized, and structural analysis to be performed in situ by averaging over multiple copies of the same molecules. Image processing for subtomogram averaging is specific and cumbersome, due to the large amount of data and its three dimensional nature and anisotropic resolution. Here, we streamline data processing for subtomogram averaging by introducing an archiving system, Dynamo Catalogue. This system manages tomographic data from multiple tomograms and allows visual feedback during all processing steps, including particle picking, extraction, alignment and classification. The file structure of a processing project file structure includes logfiles of performed operations, and can be backed up and shared between users. Command line commands, database queries and a set of GUIs give the user versatile control over the process. Here, we introduce a set of geometric tools that streamline particle picking from simple (filaments, spheres, tubes, vesicles) and complex geometries (arbitrary 2D surfaces, rare instances on proteins with geometric restrictions, and 2D and 3D crystals). Advanced functionality, such as manual alignment and subboxing, is useful when initial templates are generated for alignment and for project customization. Dynamo Catalogue is part of the open source package Dynamo and includes tools to ensure format compatibility with the subtomogram averaging functionalities of other packages, such as Jsubtomo, PyTom, PEET, EMAN2, XMIPP and Relion. Copyright © 2016. Published by Elsevier Inc.

Characterization of bubble core and cloudiness in Yb3+:Sr5(PO4)3F crystals using Micro-Raman spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cui, Y; Roy, U N; Bai, L

Ytterbium doped strontium fluoroapatite Yb{sup 3+}:Sr{sub 5}(PO{sub 4}){sub 3}F (Yb: S-FAP) crystals have been used in High Average Power Laser systems as gain medium. Growth induced defects associated with the crystal often affect their performance. In order to improve the crystal quality and its optical applications, it is imperative to understand the nature of these defects. In this study, we utilize Micro-Raman spectroscopy to characterize two common growth-induced defects: bubble core and cloudiness. We find the bubble core consist of voids and microcrystals of Yb: S-FAP. These microcrystals have very different orientation from that of the pure crystal outside themore » bubble core. In contrast to a previous report, neither Sr{sub 3}(PO{sub 4}){sub 2} nor Yb{sub 2}O{sub 3} are observed in the bubble core regions. On the other hand, the cloudy regions are made up of the host materials blended with a structural deformation along with impurities which include CaCO{sub 3}, YbPO{sub 4}, SrHPO{sub 4} and Sr{sub 2}P{sub 2}O{sub 7}. The impurities are randomly distributed in the cloudy regions. This analysis is necessary for understanding and eliminating these growth defects in Yb:S-FAP crystals.« less

Local structural distortion and electrical transport properties of Bi(Ni 1/2Ti 1/2)O 3 perovskite under high pressure

DOE PAGES

Zhu, Jinlong; Yang, Liuxiang; Wang, Hsiu -Wen; ...

2015-12-16

Perovskite-structure materials generally exhibit local structural distortions that are distinct from long-range, average crystal structure. The characterization of such distortion is critical to understanding the structural and physical properties of materials. In this work, we combined Pair Distribution Function (PDF) technique with Raman spectroscopy and electrical resistivity measurement to study Bi(Ni 1/2Ti 1/2)O 3 perovskite under high pressure. PDF analysis reveals strong local structural distortion at ambient conditions. As pressure increases, the local structure distortions are substantially suppressed and eventually vanish around 4 GPa, leading to concurrent changes in the electronic band structure and anomalies in the electrical resistivity. Wemore » find, consistent with PDF analysis, Raman spectroscopy data suggest that the local structure changes to a higher ordered state at pressures above 4 GPa.« less

Local structural distortion and electrical transport properties of Bi(Ni1/2Ti1/2)O3 perovskite under high pressure.

PubMed

Zhu, Jinlong; Yang, Liuxiang; Wang, Hsiu-Wen; Zhang, Jianzhong; Yang, Wenge; Hong, Xinguo; Jin, Changqing; Zhao, Yusheng

2015-12-16

Perovskite-structure materials generally exhibit local structural distortions that are distinct from long-range, average crystal structure. The characterization of such distortion is critical to understanding the structural and physical properties of materials. In this work, we combined Pair Distribution Function (PDF) technique with Raman spectroscopy and electrical resistivity measurement to study Bi(Ni1/2Ti1/2)O3 perovskite under high pressure. PDF analysis reveals strong local structural distortion at ambient conditions. As pressure increases, the local structure distortions are substantially suppressed and eventually vanish around 4 GPa, leading to concurrent changes in the electronic band structure and anomalies in the electrical resistivity. Consistent with PDF analysis, Raman spectroscopy data suggest that the local structure changes to a higher ordered state at pressures above 4 GPa.

Interfacial kinetics in nanosized Au/Ge films: An in situ TEM study

NASA Astrophysics Data System (ADS)

Kryshtal, Aleksandr P.; Minenkov, Alexey A.; Ferreira, Paulo J.

2017-07-01

We investigate the morphology and crystalline structure of Au/Ge films in a wide range of temperatures by in situ TEM heating. Au/Ge films with Au mass thickness of 0.2-0.3 nm and Ge thickness of 5 nm were produced in vacuum by the sequential deposition of components on a carbon substrate at room temperature. It has been shown that particles with an average size of 4 nm, formed by Au film de-wetting, melt on the germanium substrate at temperatures 110-160 °C, which are below the eutectic temperature for the bulk. The effect of crystallization-induced capillary motion of liquid eutectic particles over Ge surface has been found in this work. Formation of metastable fcc phase of Ge has been observed at the liquid-germanium interface and behind the moving particle. Formation of a liquid phase with its subsequent crystallization at the metal-semiconductor interface seems to play a key role in the metal-induced crystallization effect.

Nanotwin and phase transformation in tetragonal Pb(Fe1/2Nb1/2)1-xTixO3 single crystal

NASA Astrophysics Data System (ADS)

Tu, C.-S.; Tseng, C.-T.; Chien, R. R.; Schmidt, V. Hugo; Hsieh, C.-M.

2008-09-01

This work is a study of phase transformation in (001)-cut Pb(Fe1/2Nb1/2)1-xTixO3 (x =48%) single crystals by means of dielectric permittivity, domain structure, and in situ x-ray diffraction. A first-order T(TNT)-C(TNT) phase transition was observed at the Curie temperature TC≅518 K upon zero-field heating. T, TNT, and C are tetragonal, tetragonal nanotwin, and cubic phases, respectively. T(TNT) and C(TNT) indicate that minor TNT domains reside in the T and C matrices. Nanotwins, which can cause broad diffraction peak, remain above TC≅518 K and give an average microscopic cubic symmetry in the polarizing microscopy. Colossal dielectric permittivity (>104) was observed above room temperature with strong frequency dispersion. This study suggests that nanotwins can play an important role in relaxor ferroelectric crystals while phase transition takes place. The Fe ion is a potential candidate as a B-site dopant for enhancing dielectric permittivity.

Crystal cryocooling distorts conformational heterogeneity in a model Michaelis complex of DHFR

PubMed Central

Keedy, Daniel A.; van den Bedem, Henry; Sivak, David A.; Petsko, Gregory A.; Ringe, Dagmar; Wilson, Mark A.; Fraser, James S.

2014-01-01

Summary Most macromolecular X-ray structures are determined from cryocooled crystals, but it is unclear whether cryocooling distorts functionally relevant flexibility. Here we compare independently acquired pairs of high-resolution datasets of a model Michaelis complex of dihydrofolate reductase (DHFR), collected by separate groups at both room and cryogenic temperatures. These datasets allow us to isolate the differences between experimental procedures and between temperatures. Our analyses of multiconformer models and time-averaged ensembles suggest that cryocooling suppresses and otherwise modifies sidechain and mainchain conformational heterogeneity, quenching dynamic contact networks. Despite some idiosyncratic differences, most changes from room temperature to cryogenic temperature are conserved, and likely reflect temperature-dependent solvent remodeling. Both cryogenic datasets point to additional conformations not evident in the corresponding room-temperature datasets, suggesting that cryocooling does not merely trap pre-existing conformational heterogeneity. Our results demonstrate that crystal cryocooling consistently distorts the energy landscape of DHFR, a paragon for understanding functional protein dynamics. PMID:24882744

Coherent diffraction imaging of nanoscale strain evolution in a single crystal under high pressure

PubMed Central

Yang, Wenge; Huang, Xiaojing; Harder, Ross; Clark, Jesse N.; Robinson, Ian K.; Mao, Ho-kwang

2013-01-01

The evolution of morphology and internal strain under high pressure fundamentally alters the physical property, structural stability, phase transition and deformation mechanism of materials. Until now, only averaged strain distributions have been studied. Bragg coherent X-ray diffraction imaging is highly sensitive to the internal strain distribution of individual crystals but requires coherent illumination, which can be compromised by the complex high-pressure sample environment. Here we report the successful de-convolution of these effects with the recently developed mutual coherent function method to reveal the three-dimensional strain distribution inside a 400 nm gold single crystal during compression within a diamond-anvil cell. The three-dimensional morphology and evolution of the strain under pressures up to 6.4 GPa were obtained with better than 30 nm spatial resolution. In addition to providing a new approach for high-pressure nanotechnology and rheology studies, we draw fundamental conclusions about the origin of the anomalous compressibility of nanocrystals. PMID:23575684

Coherent diffraction imaging of nanoscale strain evolution in a single crystal under high pressure.

PubMed

Yang, Wenge; Huang, Xiaojing; Harder, Ross; Clark, Jesse N; Robinson, Ian K; Mao, Ho-kwang

2013-01-01

The evolution of morphology and internal strain under high pressure fundamentally alters the physical property, structural stability, phase transition and deformation mechanism of materials. Until now, only averaged strain distributions have been studied. Bragg coherent X-ray diffraction imaging is highly sensitive to the internal strain distribution of individual crystals but requires coherent illumination, which can be compromised by the complex high-pressure sample environment. Here we report the successful de-convolution of these effects with the recently developed mutual coherent function method to reveal the three-dimensional strain distribution inside a 400 nm gold single crystal during compression within a diamond-anvil cell. The three-dimensional morphology and evolution of the strain under pressures up to 6.4 GPa were obtained with better than 30 nm spatial resolution. In addition to providing a new approach for high-pressure nanotechnology and rheology studies, we draw fundamental conclusions about the origin of the anomalous compressibility of nanocrystals.

Ultrastable, high efficiency picosecond green light generation using K3B6O10Br series nonlinear optical crystals

NASA Astrophysics Data System (ADS)

Hou, Z. Y.; Xia, M. J.; Wang, L. R.; Xu, B.; Yan, D. X.; Meng, L. P.; Liu, L. J.; Xu, D. G.; Zhang, L.; Wang, X. Y.; Li, R. K.; Chen, C. T.

2017-09-01

Two perovskite-structure K3B6O10Br1-x Cl x (x  =  0 and 0.5) series nonlinear optical crystals were thoroughly investigated for their picosecond 532 nm laser pulses abilities and high power outputs were achieved via second harmonic generation (SHG) technique for the first time. SHG conversion efficiency of 57.3% with a 13.2 mm length K3B6O10Br (KBB) crystal was achieved using a laser source of pulse repetition rate of 10 Hz and pulse width of 25 ps, which is the highest conversion efficiency of ps visible laser based on KBB crystal. And by employing an 80 MHz, 10 ps fundamental laser beam, maximum power outputs of 12 W with K3B6O10Br0.5Cl0.5 (KBBC) and 11.86 W with KBB crystals were successfully demonstrated. Furthermore, the standard deviation jitters of the average power outputs are less than 0.6% and 1.17% by KBB and KBBC, respectively, showing ultrastable power stabilities favorable for practical applications. In addition, the other optical parameters including acceptance angle and temperature bandwidth were also investigated.

Neutron transmission measurements of poly and pyrolytic graphite crystals

NASA Astrophysics Data System (ADS)

Adib, M.; Abbas, Y.; Abdel-Kawy, A.; Ashry, A.; Kilany, M.; Kenawy, M. A.

The total neutron cross-section measurements of polycrystalline graphite have been carried out in a neutron wavelength from 0.04 to 0.78 nm. This work also presents the neutron transmission measurements of pyrolytic graphite (PG) crystal in a neutron wavelength band from 0.03 to 0.50 nm, at different orientations of the PG crystal with regard to the beam direction. The measurements were performed using three time-of-flight (TOF) spectrometers installed in front of three of the ET-RR-1 reactor horizontal channels. The average value of the coherent scattering amplitude for polycrystalline graphite was calculated and found to be bcoh = (6.61 ± 0.07) fm. The behaviour of neutron transmission through the PG crystal, while oriented at different angles with regard to the beam direction, shows dips at neutron wavelengths corresponding to the reflections from (hkl) planes of hexagonal graphite structure. The positions of the observed dips are found to be in good agreement with the calculated ones. It was also found that a 40 mm thick PG crystal is quite enough to reduce the second-order contamination of the neutron beam from 2.81 to 0.04, assuming that the incident neutrons have a Maxwell distribution with neutron gas temperature 330 K.

Compressive auto-indexing in femtosecond nanocrystallography

DOE Office of Scientific and Technical Information (OSTI.GOV)

Maia, Filipe; Yang, Chao; Marchesini, Stefano

2010-09-20

Ultrafast nanocrystallography has the potential to revolutionize biology by enabling structural elucidation of proteins for which it is possible to grow crystals with 10 or fewer unit cells. The success of nanocrystallography depends on robust orientation-determination procedures that allow us to average diffraction data from multiple nanocrystals to produce a 3D diffraction data volume with a high signal-to-noise ratio. Such a 3D diffraction volume can then be phased using standard crystallographic techniques."Indexing" algorithms used in crystallography enable orientation determination of a diffraction data from a single crystal when a relatively large number of reflections are recorded. Here we show thatmore » it is possible to obtain the exact lattice geometry from a smaller number of measurements than standard approaches using a basis pursuit solver.« less

Preparation and optical characteristics of ZnSe nanocrystals doped glass by sol gel in situ crystallization method

NASA Astrophysics Data System (ADS)

Hao, Haiyan; Yao, Xi; Wang, Minqiang

2007-01-01

Homogeneous ZnSe nanocrystals doped SiO 2 glass was successfully prepared by sol-gel in situ crystallization method. The structure of the doped ZnSe nanocrystals was studied by X-ray diffraction (XRD). ZnSe nanocrystals in silica were about 4-10 nm analysed by transmission electron microscopy (TEM), which was consistent with the results of XRD estimated using Scherrer's formular. The quantum size effect in ZnSe nanocrystals was evidenced from the blue-shifts of the optical absorption edge, and the average size of ZnSe nanocrystals was estimated by the magnitude of blue shift according to the L.E. Brus' effective mass model. The size of ZnSe nanocrystals depending on annealing time and temperature was further discussed using XRF.

Preparation of (Ga1−xZnx)(N1−xOx) Photocatalysts from the Reaction of NH3 with Ga2O3/ZnO and ZnGa2O4: In Situ Time-Resolved XRD and XAFS Studies

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, H.; Wen , W; Wang, Q

Hibiscus chlorotic ringspot virus (HCRSV) is a positive-sense monopartite single-stranded RNA virus that belongs to the Carmovirus genus of the Tombusviridae family, which includes carnation mottle virus (CarMV). The HCRSV virion has a 30 nm diameter icosahedral capsid with T = 3 quasi-symmetry containing 180 copies of a 38 kDa coat protein (CP) and encapsidates a full-length 3.9 kb genomic RNA. Authentic virus was harvested from infected host kenaf leaves and was purified by saturated ammonium sulfate precipitation, sucrose density-gradient centrifugation and anion-exchange chromatography. Virus crystals were grown in multiple conditions; one of the crystals diffracted to 3.2 A resolutionmore » Ad allowed the collection of a partial data set. The crystal belonged to space group R32, with unit-cell parameters a = b = 336.4, c = 798.5 A. Packing considerations and rotation-function analysis determined that there were three particles per unit cell, all of which have the same orientation and fixed positions, and resulted in tenfold noncrystallography symmetry for real-space averaging. The crystals used for the structure determination of southern bean mosaic virus (SBMV) have nearly identical characteristics. Together, these findings will greatly aid the high-resolution structure determination of HCRSV.« less

Recrystallization-Induced Surface Cracks of Carbon Ions Irradiated 6H-SiC after Annealing.

PubMed

Ye, Chao; Ran, Guang; Zhou, Wei; Shen, Qiang; Feng, Qijie; Lin, Jianxin

2017-10-25

Single crystal 6H-SiC wafers with 4° off-axis [0001] orientation were irradiated with carbon ions and then annealed at 900 °C for different time periods. The microstructure and surface morphology of these samples were investigated by grazing incidence X-ray diffraction (GIXRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Ion irradiation induced SiC amorphization, but the surface was smooth and did not have special structures. During the annealing process, the amorphous SiC was recrystallized to form columnar crystals that had a large amount of twin structures. The longer the annealing time was, the greater the amount of recrystallized SiC would be. The recrystallization volume fraction was accorded with the law of the Johnson-Mehl-Avrami equation. The surface morphology consisted of tiny pieces with an average width of approximately 30 nm in the annealed SiC. The volume shrinkage of irradiated SiC layer and the anisotropy of newly born crystals during annealing process produced internal stress and then induced not only a large number of dislocation walls in the non-irradiated layer but also the initiation and propagation of the cracks. The direction of dislocation walls was perpendicular to the growth direction of the columnar crystal. The longer the annealing time was, the larger the length and width of the formed crack would be. A quantitative model of the crack growth was provided to calculate the length and width of the cracks at a given annealing time.

Crystal engineering of ibuprofen compounds: From molecule to crystal structure to morphology prediction by computational simulation and experimental study

NASA Astrophysics Data System (ADS)

Zhang, Min; Liang, Zuozhong; Wu, Fei; Chen, Jian-Feng; Xue, Chunyu; Zhao, Hong

2017-06-01

We selected the crystal structures of ibuprofen with seven common space groups (Cc, P21/c, P212121, P21, Pbca, Pna21, and Pbcn), which was generated from ibuprofen molecule by molecular simulation. The predicted crystal structures of ibuprofen with space group P21/c has the lowest total energy and the largest density, which is nearly indistinguishable with experimental result. In addition, the XRD patterns for predicted crystal structure are highly consistent with recrystallization from solvent of ibuprofen. That indicates that the simulation can accurately predict the crystal structure of ibuprofen from the molecule. Furthermore, based on this crystal structure, we predicted the crystal habit in vacuum using the attachment energy (AE) method and considered solvent effects in a systematic way using the modified attachment energy (MAE) model. The simulation can accurately construct a complete process from molecule to crystal structure to morphology prediction. Experimentally, we observed crystal morphologies in four different polarity solvents compounds (ethanol, acetonitrile, ethyl acetate, and toluene). We found that the aspect ratio decreases of crystal habits in this ibuprofen system were found to vary with increasing solvent relative polarity. Besides, the modified crystal morphologies are in good agreement with the observed experimental morphologies. Finally, this work may guide computer-aided design of the desirable crystal morphology.

Production, purification and preliminary X-ray crystallographic studies of adeno-associated virus serotype 1

DOE Office of Scientific and Technical Information (OSTI.GOV)

Miller, Edward B.; Gurda-Whitaker, Brittney; Govindasamy, Lakshmanan

2006-12-01

Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. Crystals of baculovirus-expressed adeno-associated virus serotype 1 (AAV1) capsids have been grown in the rhombohedral space group R32 (unit-cell parameters a = 254.7 Å, α = 62.3°) and shown to diffract X-rays to at least 2.5 Å resolution. The diffraction data were subsequently processed and reduced with an overall R{sub sym} of 12.3% and a completeness of 89.0%. Based on the unit-cellmore » volume, rotation-function and translation-function results and packing considerations, there is one virus capsid (60 viral proteins) per unit cell and there are ten viral proteins per crystallographic asymmetric unit. The AAV1 capsid shares both the twofold and threefold crystallographic symmetry operators. The AAV1 data have been initially phased using a polyalanine model (based on the crystal structure of AAV4) to 4.0 Å resolution and the structure determination and refinement is in progress using tenfold noncrystallographic symmetry electron-density averaging.« less

Density profile of strongly correlated spherical Yukawa plasmas

NASA Astrophysics Data System (ADS)

Bonitz, M.; Henning, C.; Ludwig, P.; Golubnychiy, V.; Baumgartner, H.; Piel, A.; Block, D.

2006-10-01

Recently the discovery of 3D-dust crystals [1] excited intensive experimental and theoretical activities [2-4]. Details of the shell structure of these crystals has been very well explained theoretically by a simple model involving an isotropic Yukawa-type pair repulsion and an external harmonic confinement potential [4]. On the other hand, it has remained an open question how the average radial density profile, looks like. We show that screening has a dramatic effect on the density profile, which we derive analytically for the ground state. Interestingly, the result applies not only to a continuous plasma distribution but also to simulation data for the Coulomb crystals exhibiting the above mentioned shell structure. Furthermore, excellent agreement between the continuum model and shell models is found [5]. [1] O. Arp, D. Block, A. Piel, and A. Melzer, Phys. Rev. Lett. 93, 165004 (2004). [2] H. Totsuji, C. Totsuji, T. Ogawa, and K. Tsuruta, Phys. Rev. E 71, 045401 (2005) [3] P. Ludwig, S. Kosse, and M. Bonitz, Phys. Rev. E 71, 046403 (2005) [4] M. Bonitz, D. Block, O. Arp, V. Golubnychiy, H. Baumgartner, P. Ludwig, A. Piel, and A. Filinov, Phys. Rev. Lett. 96, 075001 (2006) [5] C. Henning, M. Bonitz, A. Piel, P. Ludwig, H. Baumgartner, V. Golubnichiy, and D. Block, submitted to Phys. Rev. E

Synthesis, characterization and computational study of the newly synthetized sulfonamide molecule

NASA Astrophysics Data System (ADS)

Murthy, P. Krishna; Suneetha, V.; Armaković, Stevan; Armaković, Sanja J.; Suchetan, P. A.; Giri, L.; Rao, R. Sreenivasa

2018-02-01

A new compound N-(2,5-dimethyl-4-nitrophenyl)-4-methylbenzenesulfonamide (NDMPMBS) has been derived from 2,5-dimethyl-4-nitroaniline and 4-methylbenzene-1-sulfonyl chloride. Structure was characterized by SCXRD studies and spectroscopic tools. Compound crystallized in the monoclinic crystal system with P21/c space group a = 10.0549, b = 18.967, c = 8.3087, β = 103.18 and Z = 4. Type and nature of intermolecular interaction in crystal state investigated by 3D-Hirshfeld surface and 2D-finger print plots revealed that title compound stabilized by several interactions. The structural and electronic properties of title compound have been calculated at DFT/B3LYP/6-311G++(d,p) level of theory. Computationally obtained spectral data was compared with experimental results, showing excellent mutual agreement. Assignment of each vibrational wave number was done on the basis of potential energy distribution (PED). Investigation of local reactivity descriptors encompassed visualization of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) surfaces, visualization of Fukui functions, natural bond order (NBO) analysis, bond dissociation energies for hydrogen abstraction (H-BDE) and radial distribution functions (RDF) after molecular dynamics (MD) simulations. MD simulations were also used in order to investigate interaction of NDMPMBS molecule with 1WKR and 3ETT proteins protein.

Highly Dynamic Anion-Quadrupole Networks in Proteins.

PubMed

Kapoor, Karan; Duff, Michael R; Upadhyay, Amit; Bucci, Joel C; Saxton, Arnold M; Hinde, Robert J; Howell, Elizabeth E; Baudry, Jerome

2016-11-01

The dynamics of anion-quadrupole (or anion-π) interactions formed between negatively charged (Asp/Glu) and aromatic (Phe) side chains are for the first time computationally characterized in RmlC (Protein Data Bank entry 1EP0 ), a homodimeric epimerase. Empirical force field-based molecular dynamics simulations predict anion-quadrupole pairs and triplets (anion-anion-π and anion-π-π) are formed by the protein during the simulated trajectory, which suggests that the anion-quadrupole interactions may provide a significant contribution to the overall stability of the protein, with an average of -1.6 kcal/mol per pair. Some anion-π interactions are predicted to form during the trajectory, extending the number of anion-quadrupole interactions beyond those predicted from crystal structure analysis. At the same time, some anion-π pairs observed in the crystal structure exhibit marginal stability. Overall, most anion-π interactions alternate between an "on" state, with significantly stabilizing energies, and an "off" state, with marginal or null stabilizing energies. The way proteins possibly compensate for transient loss of anion-quadrupole interactions is characterized in the RmlC aspartate 84-phenylalanine 112 anion-quadrupole pair observed in the crystal structure. A double-mutant cycle analysis of the thermal stability suggests a possible loss of anion-π interactions compensated by variations of hydration of the residues and formation of compensating electrostatic interactions. These results suggest that near-planar anion-quadrupole pairs can exist, sometimes transiently, which may play a role in maintaining the structural stability and function of the protein, in an otherwise very dynamic interplay of a nonbonded interaction network as well as solvent effects.

Applications of the Cambridge Structural Database in organic chemistry and crystal chemistry.

PubMed

Allen, Frank H; Motherwell, W D Samuel

2002-06-01

The Cambridge Structural Database (CSD) and its associated software systems have formed the basis for more than 800 research applications in structural chemistry, crystallography and the life sciences. Relevant references, dating from the mid-1970s, and brief synopses of these papers are collected in a database, DBUse, which is freely available via the CCDC website. This database has been used to review research applications of the CSD in organic chemistry, including supramolecular applications, and in organic crystal chemistry. The review concentrates on applications that have been published since 1990 and covers a wide range of topics, including structure correlation, conformational analysis, hydrogen bonding and other intermolecular interactions, studies of crystal packing, extended structural motifs, crystal engineering and polymorphism, and crystal structure prediction. Applications of CSD information in studies of crystal structure precision, the determination of crystal structures from powder diffraction data, together with applications in chemical informatics, are also discussed.

GRID: a high-resolution protein structure refinement algorithm.

PubMed

Chitsaz, Mohsen; Mayo, Stephen L

2013-03-05

The energy-based refinement of protein structures generated by fold prediction algorithms to atomic-level accuracy remains a major challenge in structural biology. Energy-based refinement is mainly dependent on two components: (1) sufficiently accurate force fields, and (2) efficient conformational space search algorithms. Focusing on the latter, we developed a high-resolution refinement algorithm called GRID. It takes a three-dimensional protein structure as input and, using an all-atom force field, attempts to improve the energy of the structure by systematically perturbing backbone dihedrals and side-chain rotamer conformations. We compare GRID to Backrub, a stochastic algorithm that has been shown to predict a significant fraction of the conformational changes that occur with point mutations. We applied GRID and Backrub to 10 high-resolution (≤ 2.8 Å) crystal structures from the Protein Data Bank and measured the energy improvements obtained and the computation times required to achieve them. GRID resulted in energy improvements that were significantly better than those attained by Backrub while expending about the same amount of computational resources. GRID resulted in relaxed structures that had slightly higher backbone RMSDs compared to Backrub relative to the starting crystal structures. The average RMSD was 0.25 ± 0.02 Å for GRID versus 0.14 ± 0.04 Å for Backrub. These relatively minor deviations indicate that both algorithms generate structures that retain their original topologies, as expected given the nature of the algorithms. Copyright © 2012 Wiley Periodicals, Inc.

Novel Gyroscopic Mounting for Crystal Oscillators to Increase Short and Medium Term Stability under Highly Dynamic Conditions.

PubMed

Abedi, Maryam; Jin, Tian; Sun, Kewen

2015-06-17

In this paper, a gyroscopic mounting method for crystal oscillators to reduce the impact of dynamic loads on their output stability has been proposed. In order to prove the efficiency of this mounting approach, each dynamic load-induced instability has been analyzed in detail. A statistical study has been performed on the elevation angle of the g-sensitivity vector of Stress Compensated-cut (SC-cut) crystals. The analysis results show that the proposed gyroscopic mounting method gives good performance for host vehicle attitude changes. A phase noise improvement of 27 dB maximum and 5.7 dB on average can be achieved in the case of steady state loads, while under sinusoidal vibration conditions, the maximum and average phase noise improvement are as high as 24 dB and 7.5 dB respectively. With this gyroscopic mounting method, random vibration-induced phase noise instability is reduced 30 dB maximum and 8.7 dB on average. Good effects are apparent for crystal g-sensitivity vectors with low elevation angle φ and azimuthal angle β. under highly dynamic conditions, indicating the probability that crystal oscillator instability will be significantly reduced by using the proposed mounting approach.

Intrinsic crystal phase separation in the antiferromagnetic superconductor Rb(y)Fe(2-x)Se2: a diffraction study.

PubMed

Yu Pomjakushin, V; Krzton-Maziopa, A; Pomjakushina, E V; Conder, K; Chernyshov, D; Svitlyk, V; Bosak, A

2012-10-31

The crystal and magnetic structures of the superconducting iron-based chalcogenides Rb(y)Fe(2-x)Se(2) have been studied by means of single-crystal synchrotron x-ray and high-resolution neutron powder diffraction in the temperature range 2-570 K. The ground state of the crystal is an intrinsically phase-separated state with two distinct-by-symmetry phases. The main phase has the iron vacancy ordered √5 × √5 superstructure (I4/m space group) with AFM ordered Fe spins. The minority phase does not have √5 × √5-type of ordering and has a smaller in-plane lattice constant a and larger tetragonal c-axis and can be well described by assuming the parent average vacancy disordered structure (I4/mmm space group) with the refined stoichiometry Rb(0.60(5))(Fe(1.10(5))Se)(2). The minority phase amounts to 8-10% mass fraction. The unit cell volume of the minority phase is 3.2% smaller than the one of the main phase at T = 2 K and has quite different temperature dependence. The minority phase merges with the main vacancy ordered phase on heating above the phase separation temperature T(P) = 475 K. The spatial dimensions of the phase domains strongly increase above T(P) from 1000 to >2500 Å due to the integration of the regions of the main phase that were separated by the second phase at low temperatures. Additional annealing of the crystals at a temperature T = 488 K, close to T(P), for a long time drastically reduces the amount of the minority phase.

In-situ and real-time growth observation of high-quality protein crystals under quasi-microgravity on earth.

PubMed

Nakamura, Akira; Ohtsuka, Jun; Kashiwagi, Tatsuki; Numoto, Nobutaka; Hirota, Noriyuki; Ode, Takahiro; Okada, Hidehiko; Nagata, Koji; Kiyohara, Motosuke; Suzuki, Ei-Ichiro; Kita, Akiko; Wada, Hitoshi; Tanokura, Masaru

2016-02-26

Precise protein structure determination provides significant information on life science research, although high-quality crystals are not easily obtained. We developed a system for producing high-quality protein crystals with high throughput. Using this system, gravity-controlled crystallization are made possible by a magnetic microgravity environment. In addition, in-situ and real-time observation and time-lapse imaging of crystal growth are feasible for over 200 solution samples independently. In this paper, we also report results of crystallization experiments for two protein samples. Crystals grown in the system exhibited magnetic orientation and showed higher and more homogeneous quality compared with the control crystals. The structural analysis reveals that making use of the magnetic microgravity during the crystallization process helps us to build a well-refined protein structure model, which has no significant structural differences with a control structure. Therefore, the system contributes to improvement in efficiency of structural analysis for "difficult" proteins, such as membrane proteins and supermolecular complexes.

High-speed prediction of crystal structures for organic molecules

NASA Astrophysics Data System (ADS)

Obata, Shigeaki; Goto, Hitoshi

2015-02-01

We developed a master-worker type parallel algorithm for allocating tasks of crystal structure optimizations to distributed compute nodes, in order to improve a performance of simulations for crystal structure predictions. The performance experiments were demonstrated on TUT-ADSIM supercomputer system (HITACHI HA8000-tc/HT210). The experimental results show that our parallel algorithm could achieve speed-ups of 214 and 179 times using 256 processor cores on crystal structure optimizations in predictions of crystal structures for 3-aza-bicyclo(3.3.1)nonane-2,4-dione and 2-diazo-3,5-cyclohexadiene-1-one, respectively. We expect that this parallel algorithm is always possible to reduce computational costs of any crystal structure predictions.

The influence of high pressure to crystalline and magnetic structure of Ba 2 FeMoO 6

NASA Astrophysics Data System (ADS)

Turchenko, V. A.; Kalanda, N. A.; Kovalev, L. V.; Yarmolich, M. V.; Petrov, A. V.; Lukin, Ye V.; Doroshkevich, A. S.; Balasoiu, M.; Lupu, N.; Savenko, B. N.

2018-03-01

The behavior of the crystalline and magnetic structure of Ba 2 FeMoO 6 compound in a wide pressure range from 0 to 4.7 GPa was studied. The crystal structure of ceramic sample was described in the framework of SG I4/mmm (No 139) and contains less 10% of anti-site defects. The change of tetragonal structure (I4/mmm) was not observed in all measured pressure range. It was shown multidirectional influence of ambient pressure onto the average interionic distances of metal-ligand in oxygen octahedrons of FeO 6 and MoO 6. For tetragonal structure of Ba 2 FeMoO 6 were determined coefficients of the linear and all-round compressibility. The influence of ambient pressure on the value of magnetic moment of iron sublattice was shown.

Structural investigations in helium charged titanium films using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Wan, Chubin; Zhou, Xiaosong; Wang, Yuting; Li, Shina; Ju, Xin; Peng, Shuming

2014-01-01

The crystal structure and local atomic arrangements surrounding Ti atoms were determined for He-charged hexagonal close-packed (hcp) Ti films and measured at glancing angles by synchrotron radiation X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively. The charged specimens were prepared by direct current magnetron sputtering with a He/Ar mixture. He atoms with a relatively medium concentration (He/Ti atomic ratio as high as 17 at.%) were incorporated evenly in the deposited films. XRD results showed the changes in the peak intensities in Ti films with different He contents. EXAFS Fourier Transform analysis indicated that the average Ti-Ti distance decreased significantly, and proved the existence of phase transition.

Structural, morphological and optical studies of F doped SnO2 thin films

NASA Astrophysics Data System (ADS)

Chandel, Tarun; Thakur, Vikas; Dwivedi, Shailendra Kumar; Zaman, M. Burhanuz; Rajaram, Poolla

2018-05-01

Highly conducting and transparent FTO (flourine doped tin Oxide) thin films were grown on the glass substrates using a low cost spray pyrolysis technique. The films were characterized for their structural, morphological and optical studies using XRD, SEM and UV-Vis spectroscopy. XRD studies show that the FTO films crystallize in Tetragonal cassiterite structure. Morphological analysis using SEM show that the films are uniformly covered with spherical grains albeit high in surface roughness. The average optical transmission greater than 80% in the visible region along with the appearance of interference fringes in the transmission curves confirms the high quality of the films. Electrical studies show that the films exhibit sheet resistance below 10 Ω ϒ-1.

A review on the synthesis, crystal growth, structure and physical properties of rare earth based quaternary intermetallic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C., E-mail: sebastiancp@jncasr.ac.in

2016-04-15

This review highlights the synthesis and crystal growth of quaternary intermetallic compounds based on rare earth metals. In the first part of this review, we highlight briefly about intermetallics and their versatile properties in comparison to the constituent elements. In the next part, we have discussed about various synthesis techniques with more focus on the metal flux technique towards the well shaped crystal growth of novel compounds. In the subsequent parts, several disordered quaternary compounds have been reviewed and then outlined most known ordered quaternary compounds with their complex structure. A special attention has been given to the ordered compoundsmore » with structural description and relation to the parent binary and ternary compounds. The importance of electronic and structural feature is highlighted as the key roles in designing these materials for emerging applications. - Graphical abstract: Rare earth based quaternary intermetallic compounds crystallize in complex novel crystal structures. The diversity in the crystal structure may induce unique properties and can be considered them as future materials. - Highlights: • Crystal growth and crystal structure of quaternary rare earth based intermetallics. • Structural complexity of quaternary compounds in comparison to the parent compounds. • Novel quaternary compounds display unique crystal structure.« less

Likelihood-based modification of experimental crystal structure electron density maps

DOEpatents

Terwilliger, Thomas C [Sante Fe, NM

2005-04-16

A maximum-likelihood method for improves an electron density map of an experimental crystal structure. A likelihood of a set of structure factors {F.sub.h } is formed for the experimental crystal structure as (1) the likelihood of having obtained an observed set of structure factors {F.sub.h.sup.OBS } if structure factor set {F.sub.h } was correct, and (2) the likelihood that an electron density map resulting from {F.sub.h } is consistent with selected prior knowledge about the experimental crystal structure. The set of structure factors {F.sub.h } is then adjusted to maximize the likelihood of {F.sub.h } for the experimental crystal structure. An improved electron density map is constructed with the maximized structure factors.

Construction, MD simulation, and hydrodynamic validation of an all-atom model of a monoclonal IgG antibody.

PubMed

Brandt, J Paul; Patapoff, Thomas W; Aragon, Sergio R

2010-08-04

At 150 kDa, antibodies of the IgG class are too large for their structure to be determined with current NMR methodologies. Because of hinge-region flexibility, it is difficult to obtain atomic-level structural information from the crystal, and questions regarding antibody structure and dynamics in solution remain unaddressed. Here we describe the construction of a model of a human IgG1 monoclonal antibody (trastuzumab) from the crystal structures of fragments. We use a combination of molecular-dynamics (MD) simulation, continuum hydrodynamics modeling, and experimental diffusion measurements to explore antibody behavior in aqueous solution. Hydrodynamic modeling provides a link between the atomic-level details of MD simulation and the size- and shape-dependent data provided by hydrodynamic measurements. Eight independent 40 ns MD trajectories were obtained with the AMBER program suite. The ensemble average of the computed transport properties over all of the MD trajectories agrees remarkably well with the value of the translational diffusion coefficient obtained with dynamic light scattering at 20 degrees C and 27 degrees C, and the intrinsic viscosity measured at 20 degrees C. Therefore, our MD results likely represent a realistic sampling of the conformational space that an antibody explores in aqueous solution. 2010 Biophysical Society. Published by Elsevier Inc. All rights reserved.

Flat-on ambipolar triphenylamine/C60 nano-stacks formed from the self-organization of a pyramid-sphere-shaped amphiphile.

PubMed

Liang, Wei-Wei; Huang, Chi-Feng; Wu, Kuan-Yi; Wu, San-Lien; Chang, Shu-Ting; Cheng, Yen-Ju; Wang, Chien-Lung

2016-04-21

A giant amphiphile, which is constructed with an amorphous nano-pyramid (triphenylamine, TPA) and a crystalline nano-sphere (C 60 ), was synthesized. Structural characterization indicates that this pyramid-sphere-shaped amphiphile ( TPA-C 60 ) forms a solvent-induced ordered phase, in which the two constituent units self-assemble into alternating stacks of two-dimensional (2D) TPA and C 60 nano-sheets. Due to the complexity of the molecular structure and the amorphous nature of the nano-pyramid, phase formation was driven by intermolecular C 60 -C 60 interactions and the ordered phase could not be reformed from the TPA-C 60 melt. Oriented crystal arrays of TPA-C 60 , which contain flat-on TPA/C 60 nano-stacks, can be obtained via a PDMS-assisted crystallization (PAC) technique. The flat-on dual-channel supramolecular structure of TPA-C 60 delivered ambipolar and balanced charge-transport characteristics with an average μ e of 2.11 × 10 -4 cm 2 V -1 s -1 and μ h of 3.37 × 10 -4 cm 2 V -1 s -1 . The anisotropic charge-transport ability of the pyramid-sphere-shaped amphiphile was further understood based on the lattice structure and the lattice orientation of TPA-C 60 revealed from electron diffraction analyses.

The Crystal Structure and RNA-Binding of an Orthomyxovirus Nucleoprotein

PubMed Central

Zheng, Wenjie; Olson, John; Vakharia, Vikram; Tao, Yizhi Jane

2013-01-01

Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ∼12 nts of RNA, shorter than the 24–28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions. PMID:24068932

Predicting side-chain conformations of methionine using a hard-sphere model with stereochemical constraints

NASA Astrophysics Data System (ADS)

Virrueta, A.; Gaines, J.; O'Hern, C. S.; Regan, L.

2015-03-01

Current research in the O'Hern and Regan laboratories focuses on the development of hard-sphere models with stereochemical constraints for protein structure prediction as an alternative to molecular dynamics methods that utilize knowledge-based corrections in their force-fields. Beginning with simple hydrophobic dipeptides like valine, leucine, and isoleucine, we have shown that our model is able to reproduce the side-chain dihedral angle distributions derived from sets of high-resolution protein crystal structures. However, methionine remains an exception - our model yields a chi-3 side-chain dihedral angle distribution that is relatively uniform from 60 to 300 degrees, while the observed distribution displays peaks at 60, 180, and 300 degrees. Our goal is to resolve this discrepancy by considering clashes with neighboring residues, and averaging the reduced distribution of allowable methionine structures taken from a set of crystallized proteins. We will also re-evaluate the electron density maps from which these protein structures are derived to ensure that the methionines and their local environments are correctly modeled. This work will ultimately serve as a tool for computing side-chain entropy and protein stability. A. V. is supported by an NSF Graduate Research Fellowship and a Ford Foundation Fellowship. J. G. is supported by NIH training Grant NIH-5T15LM007056-28.

Numerical simulation of flow and mass transfer for large KDP crystal growth via solution-jet method

NASA Astrophysics Data System (ADS)

Yin, Huawei; Li, Mingwei; Hu, Zhitao; Zhou, Chuan; Li, Zhiwei

2018-06-01

A novel technique of growing large crystals of potassium dihydrogen phosphate (KDP) named solution-jet method is proposed. The aim is to increase supersaturation on the pyramidal face, especially for crystal surface regions close to the rotation axis. The fluid flow and surface supersaturation distribution of crystals grown under different conditions were computed using the finite-volume method. Results indicate that the time-averaged supersaturation of the pyramidal face in the proposed method significantly increases and the supersaturation difference from the crystal center to edge clearly decreases compared with the rotating-crystal method. With increased jet velocity, supersaturation on the pyramidal face steadily increases. Rotation rate considerably affects the magnitude and distribution of the prismatic surface supersaturation. With increased crystal size, the mean value of surface supersaturation averaged over the pyramid gradually decreases; conversely, standard deviation increases, which is detrimental to crystal growth. Moreover, the significant roles played by natural and forced convection in the process of mass transport are discussed. Results show that further increased jet velocity to 0.6 m/s renders negligible the effects of natural convection around the pyramid. The simulation for step propagation indicates that solution-jet method can promote a steady step migration and enhance surface morphology stability, which can improve the crystal quality.

Polymer-Induced Heteronucleation for Protein Single Crystal Growth: Structural Elucidation of Bovine Liver Catalase and Concanavalin A Forms

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

Obtaining single crystals for X-ray diffraction remains a major bottleneck in structural biology; when existing crystal growth methods fail to yield suitable crystals, often the target rather than the crystallization approach is reconsidered. Here we demonstrate that polymer-induced heteronucleation, a powerful technique that has been used for small molecule crystallization form discovery, can be applied to protein crystallization by optimizing the heteronucleant composition and crystallization formats for crystallizing a wide range of protein targets. Applying these advances to two benchmark proteins resulted in dramatically increased crystal size, enabling structure determination, for a half century old form of bovine liver catalasemore » (BLC) that had previously only been characterized by electron microscopy, and the discovery of two new forms of concanavalin A (conA) from the Jack bean and accompanying structural elucidation of one of these forms.« less

Fluid and Crystallized Intelligence--Theory and Research in Later Adulthood.

ERIC Educational Resources Information Center

Willis, Sherry L.; Baltes, Paul B.

Two studies examined modifiability in intellectual functioning in older adults. The fluid-crystallized theory provided a theory base for the research. (Fluid intelligence follows a normative decline through adulthood, while crystallized intelligence remains stable or even increases.) In the first study thirty subjects (average age 69.2)…

Multimode theory of plasmon excitation at a metal - photonic crystal interface

NASA Astrophysics Data System (ADS)

Kuznetsova, T. I.; Raspopov, N. A.

2017-12-01

Surface plasmon excitation at a photonic crystal - metal interface is studied taking into account multiple scattering of an initial light wave on a periodical crystal structure. The analysis is focused on calculating characteristics of the eigenwaves in a one-dimensional crystal, which comprise a set of harmonics with the wavevectors separated from each other by the value of the crystal lattice wavevector. Reflection from the crystal - metal interface binds the amplitudes of propagating and evanescent modes. Calculations show that for the dielectric characteristics of a synthetic opal and a substrate made of a real metal with a ruby laser radiation used as the initial wave, the fulfilment of plasmon resonance conditions leads to a local increase in the surface plasmon amplitude by a factor of 6.4 - 9 as compared to the average amplitude of the initial wave. As a rule, the effect can only be obtained for a single surface wave, all other waves being substantially weaker than the main plasmon. There is a specific case where the resonance condition holds for two modes simultaneously. In this case, two oppositely directed fluxes of equal intensity are generated at the interface. The resonance condition breaks at a small deviation of the incident angle of the initial wave θ from the normal direction (|θ| ⩾ 10-4 rad). In the latter case, the picture is asymmetric: at angles |θ| ⩾ 5 × 10-3 rad, only one plasmon remains intensive. The local density of electromagnetic energy at the photonic crystal - metal interface may exceed the corresponding value of the initial wave by a factor of 40 - 80.

Investigation for the amorphous state of ER-34122, a dual 5-lipoxygenase/cyclooxygenase inhibitor with poor aqueous solubility, in HPMC solid dispersion prepared by the solvent evaporation method.

PubMed

Kushida, Ikuo; Gotoda, Masaharu

2013-10-01

ER-34122, a poorly water-soluble dual 5-lipoxygenase/cyclooxygenase inhibitor, exists as a crystalline form. According to an Oak Ridge thermal ellipsoid plot drawing, carbonyl oxygen O (5) makes an intermolecular hydrogen bond with the hydrogen bonded to N (3) in the crystal structure. The FTIR and the solid-state ¹³C NMR spectra suggest that the network is spread out in the amorphous state and the hydrogen bonding gets weaker than that in the crystalline phase, because the carbonyl signals significantly shift in both spectra. When amorphous ER-34122 was heated, crystallization occurred at around 140°C. Similar crystallization happened in the solid dispersion; however, the degree of crystallization was much lower than that observed in the pure amorphous material. Also, the DSC thermogram of the solid dispersion did not show any exothermic peaks implying crystallization. The heat of fusion (ΔHf) determined in the pure amorphous material was nearly equal to that for the crystalline form, whereas the ΔHf value obtained in the solid dispersion was less than a third of them. These data prove that crystallization of the amorphous form is dramatically restrained in the solid dispersion system. The carbonyl wavenumber shifts in the FTIR spectra indicate that the average hydrogen bond in the solid dispersion is lower than that in the pure amorphous material. Therefore, HPMC will suppress formation of the intermolecular network observed in ER-34122 crystal and preserve the amorphous state, which is thermodynamically less stable, in the solid dispersed system.

Physical and Structural Studies on the Cryo-cooling of Insulin Crystals

NASA Technical Reports Server (NTRS)

Lovelace, J.; Bellamy, H.; Snell, E. H.; Borgstahl, G.

2003-01-01

Reflection profiles were analyzed from microgravity-(mg) and earth-grown insulin crystals to measure mosaicity (h) and to reveal mosaic domain structure and composition. The effects of cryocooling on single and multi-domain crystals were compared. The effects of cryocooling on insulin structure were also re-examined. Microgravity crystals were larger, more homogeneous, and more perfect than earth crystals. Several mg crystals contained primarily a single mosaic domain with havg of 0.005deg. The earth crystals varied in quality and all contained multiple domains with havg of 0.031deg. Cryocooling caused a 43-fold increase in h for mg crystals (havg=0.217deg) and an %fold increase for earth crystals (havg=0.246deg). These results indicate that very well-ordered crystals are not completely protected from the stresses associated with cryocooling, especially when structural perturbations occur. However, there were differences in the reflection profiles. For multi-mosaic domain crystals, each domain individually broadened and separated from the other domains upon cryo-cooling. Cryo-cooling did not cause an increase in the number of domains. A crystal composed of a single domain retained this domain structure and the reflection profiles simply broadened. Therefore, an improved signal-to-noise ratio for each reflection was measured from cryo-cooled single domain crystals relative to cryo-cooled multi-domain crystals. This improved signal, along with the increase in crystal size, facilitated the measurement of the weaker high- resolution reflections. The observed broadening of reflection profiles indicates increased variation in unit cell dimensions which may be linked to cryo-cooling-associated structural changes and disorder.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

Martín-Islán, Africa P; Martín-Ramos, Daniel; Sainz-Díaz, C Ignacio

2008-02-01

An experimental and theoretical investigation on crystal forms of the popular and ubiquitous pharmaceutical Minoxidil is presented here. A new crystallization method is presented for Minoxidil (6-(1-piperidinyl)-2,4-pyrimidinediamide 3-oxide) in ethanol-poly(ethylene glycol), yielding crystals with good quality. The crystal structure is determined at low temperature, with a final R value of 0.035, corresponding to space group P2(1) (monoclinic) with cell dimensions a = 9.357(1) A, b = 8.231(1) A, c = 12.931(2) A, and beta = 90.353(4) degrees . Theoretical calculations of the molecular structure of Minoxidil are set forward using empirical force fields and quantum-mechanical methods. A theoretical prediction for Minoxidil crystal structure shows many possible polymorphs. The predicted crystal structures are compared with X-ray experimental data obtained in our laboratory, and the experimental crystal form is found to be one of the lowest energy polymorphs.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ozkendir, Osman Murat, E-mail: ozkendir@gmail.com

Highlights: • Crystal and electronic structure properties of Nd{sub x}Ti{sub 1−x}BO{sub 2+d} structure were investigated. • New crystal structures for Nd–Ti complexes are determined. • Distortions in the crystal structure were observed as a result of Boron shortage. • Prominent change in electronic properties of the samples with the increasing Nd amount. - Abstract: Neodymium substituted TiBO{sub 3} samples were investigated according to their crystal, electric and electronic properties. Studies were conducted by X-ray absorption fine structure spectroscopy (XAFS) technique for the samples with different substitutions in the preparation processes. To achieve better crystal structure results during the study, XRDmore » pattern results were supported by extended-XAFS (EXAFS) analysis. The electronic structure analysis were studied by X-ray absorption near-edge structure spectroscopy (XANES) measurements at the room temperatures. Due to the substituted Nd atoms, prominent changes in crystal structure, new crystal geometries for Nd-Ti complexes, phase transitions in the crystals structure were detected according to the increasing Nd substitutions in the samples. In the entire stages of the substitutions, Nd atoms were observed as governing the whole phenomena due to their dominant characteristics in Ti geometries. Besides, electrical resistivity decay was determined in the materials with the increasing amount of Nd substitution.« less

High-throughput crystallization screening.

PubMed

Skarina, Tatiana; Xu, Xiaohui; Evdokimova, Elena; Savchenko, Alexei

2014-01-01

Protein structure determination by X-ray crystallography is dependent on obtaining a single protein crystal suitable for diffraction data collection. Due to this requirement, protein crystallization represents a key step in protein structure determination. The conditions for protein crystallization have to be determined empirically for each protein, making this step also a bottleneck in the structure determination process. Typical protein crystallization practice involves parallel setup and monitoring of a considerable number of individual protein crystallization experiments (also called crystallization trials). In these trials the aliquots of purified protein are mixed with a range of solutions composed of a precipitating agent, buffer, and sometimes an additive that have been previously successful in prompting protein crystallization. The individual chemical conditions in which a particular protein shows signs of crystallization are used as a starting point for further crystallization experiments. The goal is optimizing the formation of individual protein crystals of sufficient size and quality to make them suitable for diffraction data collection. Thus the composition of the primary crystallization screen is critical for successful crystallization.Systematic analysis of crystallization experiments carried out on several hundred proteins as part of large-scale structural genomics efforts allowed the optimization of the protein crystallization protocol and identification of a minimal set of 96 crystallization solutions (the "TRAP" screen) that, in our experience, led to crystallization of the maximum number of proteins.

Folding of Polymer Chains in Early Stage of Crystallization

NASA Astrophysics Data System (ADS)

Yuan, Shichen; Miyoshi, Toshikazu

Understanding the structural formation of long polymer chains in the early stage of crystallization is one of the long-standing problems in polymer science. Using solid state NMR, we investigated chain trajectory of isotactic polypropylene in the mesomorphic nano-domains formed via rapid and deep quenching. Comparison of experimental and simulated 13C-13C Double Quantum (DQ) buildup curves demonstrated that instead of random re-entry models and solidification models, individual chains in the mesomorphic form iPP adopt adjacent reentry sequences with an average folding number of = 3-4 (assuming an adjacent re-entry fraction of of 100%) during mesomorphic formation process via nucleation and growth in the early stage. This work was financially supported by the National Science Foundation (Grant DMR-1105829 and 1408855) and startup funds from the UA.

Crystal structure of fac-tri­chlorido­[tris­(pyridin-2-yl-N)amine]­chromium(III)

PubMed Central

Yamaguchi-Terasaki, Yukiko; Fujihara, Takashi; Nagasawa, Akira; Kaizaki, Sumio

2015-01-01

In the neutral complex mol­ecule of the title compound, fac-[CrCl3(tpa)] [tpa is tris­(pyridin-2-yl)amine; C15H12N4], the CrIII ion is bonded to three N atoms that are constrained to a facial arrangement by the tpa ligand and by three chloride ligands, leading to a distorted octa­hedral coordination sphere. The average Cr—N and Cr—Cl bond lengths are 2.086 (5) and 2.296 (4) Å, respectively. The complex mol­ecule is located on a mirror plane. In the crystal, a combination of C—H⋯N and C—H⋯Cl hydrogen-bonding inter­actions connect the mol­ecules into a three-dimensional network. PMID:25705455

High-throughput crystal-optimization strategies in the South Paris Yeast Structural Genomics Project: one size fits all?

PubMed

Leulliot, Nicolas; Trésaugues, Lionel; Bremang, Michael; Sorel, Isabelle; Ulryck, Nathalie; Graille, Marc; Aboulfath, Ilham; Poupon, Anne; Liger, Dominique; Quevillon-Cheruel, Sophie; Janin, Joël; van Tilbeurgh, Herman

2005-06-01

Crystallization has long been regarded as one of the major bottlenecks in high-throughput structural determination by X-ray crystallography. Structural genomics projects have addressed this issue by using robots to set up automated crystal screens using nanodrop technology. This has moved the bottleneck from obtaining the first crystal hit to obtaining diffraction-quality crystals, as crystal optimization is a notoriously slow process that is difficult to automatize. This article describes the high-throughput optimization strategies used in the Yeast Structural Genomics project, with selected successful examples.

A novel structure of gel grown strontium cyanurate crystal and its structural, optical, electrical characterization

NASA Astrophysics Data System (ADS)

Divya, R.; Nair, Lekshmi P.; Bijini, B. R.; Nair, C. M. K.; Gopakumar, N.; Babu, K. Rajendra

2017-12-01

Strontium cyanurate crystals with novel structure and unique optical property like mechanoluminescence have been grown by conventional gel method. Transparent crystals were obtained. The single crystal X-ray diffraction analysis reveals the exquisite structure of the grown crystal. The crystal is centrosymmetric and has a three dimensional polymeric structure. The powder X ray diffraction analysis confirms its crystalline nature. The functional groups present in the crystal were identified by Fourier transform infrared spectroscopy. Elemental analysis confirmed the composition of the complex. A study of thermal properties was done by thermo gravimetric analysis and differential thermal analysis. The optical properties like band gap, refractive index and extinction coefficient were evaluated from the UV visible spectral analysis. The etching study was done to reveal the dislocations in the crystal which in turn explains mechanoluminescence emission. The mechanoluminescence property exhibited by the crystal makes it suitable for stress sensing applications. Besides being a centrosymmetric crystal, it also exhibits NLO behavior. Dielectric properties were studied and theoretical calculations of Fermi energy, valence electron plasma energy, penn gap and polarisability have been done.

Inorganic Crystal Structure Database (ICSD)

National Institute of Standards and Technology Data Gateway

SRD 84 FIZ/NIST Inorganic Crystal Structure Database (ICSD) (PC database for purchase)   The Inorganic Crystal Structure Database (ICSD) is produced cooperatively by the Fachinformationszentrum Karlsruhe(FIZ) and the National Institute of Standards and Technology (NIST). The ICSD is a comprehensive collection of crystal structure data of inorganic compounds containing more than 140,000 entries and covering the literature from 1915 to the present.

Microgravity

NASA Image and Video Library

1992-06-25

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

Zeolites

NASA Technical Reports Server (NTRS)

1992-01-01

Zeolites are crystalline aluminosilicates that have complex framework structures. However, there are several features of zeolite crystals that make unequivocal structure determinations difficult. The acquisition of reliable structural information on zeolites is greatly facilitated by the availability of high-quality specimens. For structure determinations by conventional diffraction techniques, large single-crystal specimens are essential. Alternatively, structural determinations by powder profile refinement methods relax the constraints on crystal size, but still require materials with a high degree of crystalline perfection. Studies conducted at CAMMP (Center for Advanced Microgravity Materials Processing) have demonstrated that microgravity processing can produce larger crystal sizes and fewer structural defects relative to terrestrial crystal growth. Principal Investigator: Dr. Albert Sacco

From molecule to solid: The prediction of organic crystal structures

NASA Astrophysics Data System (ADS)

Dzyabchenko, A. V.

2008-10-01

A method for predicting the structure of a molecular crystal based on the systematic search for a global potential energy minimum is considered. The method takes into account unequal occurrences of the structural classes of organic crystals and symmetry of the multidimensional configuration space. The programs of global minimization PMC, comparison of crystal structures CRYCOM, and approximation to the distributions of the electrostatic potentials of molecules FitMEP are presented as tools for numerically solving the problem. Examples of predicted structures substantiated experimentally and the experience of author’s participation in international tests of crystal structure prediction organized by the Cambridge Crystallographic Data Center (Cambridge, UK) are considered.

Crystals of Janus colloids at various interaction ranges

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preisler, Z.; Soft Condensed Matter, Debye Institute for Nanomaterials Science, Utrecht University, Princetonplein 5, 3584 CC Utrecht; Vissers, T.

We investigate the effect of interaction range on the phase behaviour of Janus particles with a Kern-Frenkel potential. Specifically, we study interaction ranges Δ = 0.1σ, 0.3σ, 0.4σ, 0.5σ with σ the particle diameter, and use variable box shape simulations to predict crystal structures. We found that changing the interaction range beyond 0.2σ drastically increases the variety of possible crystal structures. In addition to close-packed structures, we find body-centered tetragonal and AA-stacked hexagonal crystals, as well as several lamellar crystals. For long interaction ranges and low temperatures, we also observe an extremely large number of metastable structures which compete withmore » the thermodynamically stable ones. These competing structures hinder the detection of the lowest-energy crystal structures, and are also likely to interfere with the spontaneous formation of the ground-state structure. Finally, we determine the gas-liquid coexistence curves for several interaction ranges, and observe that these are metastable with respect to crystallization.« less

Fully automatic characterization and data collection from crystals of biological macromolecules.

PubMed

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander; Nurizzo, Didier; Bowler, Matthew W

2015-08-01

Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.

Surface phase separation, dewetting feature size, and crystal morphology in thin films of polystyrene/poly(ε-caprolactone) blend.

PubMed

Ma, Meng; He, Zhoukun; Li, Yuhan; Chen, Feng; Wang, Ke; Zhang, Qing; Deng, Hua; Fu, Qiang

2012-12-01

Thin films of polystyrene (PS)/poly(ε-caprolactone) (PCL) blends were prepared by spin-coating and characterized by tapping mode force microscopy (AFM). Effects of the relative concentration of PS in polymer solution on the surface phase separation and dewetting feature size of the blend films were systematically studied. Due to the coupling of phase separation, dewetting, and crystallization of the blend films with the evaporation of solvent during spin-coating, different size of PS islands decorated with various PCL crystal structures including spherulite-like, flat-on individual lamellae, and flat-on dendritic crystal were obtained in the blend films by changing the film composition. The average distance of PS islands was shown to increase with the relative concentration of PS in casting solution. For a given ratio of PS/PCL, the feature size of PS appeared to increase linearly with the square of PS concentration while the PCL concentration only determined the crystal morphology of the blend films with no influence on the upper PS domain features. This is explained in terms of vertical phase separation and spinodal dewetting of the PS rich layer from the underlying PCL rich layer, leading to the upper PS dewetting process and the underlying PCL crystalline process to be mutually independent. Copyright © 2012 Elsevier Inc. All rights reserved.

Crystal Face Distributions and Surface Site Densities of Two Synthetic Goethites: Implications for Adsorption Capacities as a Function of Particle Size.

PubMed

Livi, Kenneth J T; Villalobos, Mario; Leary, Rowan; Varela, Maria; Barnard, Jon; Villacís-García, Milton; Zanella, Rodolfo; Goodridge, Anna; Midgley, Paul

2017-09-12

Two synthetic goethites of varying crystal size distributions were analyzed by BET, conventional TEM, cryo-TEM, atomic resolution STEM and HRTEM, and electron tomography in order to determine the effects of crystal size, shape, and atomic scale surface roughness on their adsorption capacities. The two samples were determined by BET to have very different site densities based on Cr VI adsorption experiments. Model specific surface areas generated from TEM observations showed that, based on size and shape, there should be little difference in their adsorption capacities. Electron tomography revealed that both samples crystallized with an asymmetric {101} tablet habit. STEM and HRTEM images showed a significant increase in atomic-scale surface roughness of the larger goethite. This difference in roughness was quantified based on measurements of relative abundances of crystal faces {101} and {201} for the two goethites, and a reactive surface site density was calculated for each goethite. Singly coordinated sites on face {210} are 2.5 more dense than on face {101}, and the larger goethite showed an average total of 36% {210} as compared to 14% for the smaller goethite. This difference explains the considerably larger adsorption capacitiy of the larger goethite vs the smaller sample and points toward the necessity of knowing the atomic scale surface structure in predicting mineral adsorption processes.

Exploring Solid-State Structure and Physical Properties: A Molecular and Crystal Model Exercise

ERIC Educational Resources Information Center

Bindel, Thomas H.

2008-01-01

A crystal model laboratory exercise is presented that allows students to examine relations among the microscopic-macroscopic-symbolic levels, using crystalline mineral samples and corresponding crystal models. Students explore the relationship between solid-state structure and crystal form. Other structure-property relationships are explored. The…

A Multiscale Computational Model Combining a Single Crystal Plasticity Constitutive Model with the Generalized Method of Cells (GMC) for Metallic Polycrystals.

PubMed

Ghorbani Moghaddam, Masoud; Achuthan, Ajit; Bednarcyk, Brett A; Arnold, Steven M; Pineda, Evan J

2016-05-04

A multiscale computational model is developed for determining the elasto-plastic behavior of polycrystal metals by employing a single crystal plasticity constitutive model that can capture the microstructural scale stress field on a finite element analysis (FEA) framework. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, the stand-alone GMC is applied for studying simple material microstructures such as a repeating unit cell (RUC) containing single grain or two grains under uniaxial loading conditions. For verification, the results obtained by the stand-alone GMC are compared to those from an analogous FEA model incorporating the same single crystal plasticity constitutive model. This verification is then extended to samples containing tens to hundreds of grains. The results demonstrate that the GMC homogenization combined with the crystal plasticity constitutive framework is a promising approach for failure analysis of structures as it allows for properly predicting the von Mises stress in the entire RUC, in an average sense, as well as in the local microstructural level, i.e. , each individual grain. Two-three orders of saving in computational cost, at the expense of some accuracy in prediction, especially in the prediction of the components of local tensor field quantities and the quantities near the grain boundaries, was obtained with GMC. Finally, the capability of the developed multiscale model linking FEA and GMC to solve real-life-sized structures is demonstrated by successfully analyzing an engine disc component and determining the microstructural scale details of the field quantities.

A Multiscale Computational Model Combining a Single Crystal Plasticity Constitutive Model with the Generalized Method of Cells (GMC) for Metallic Polycrystals

PubMed Central

Ghorbani Moghaddam, Masoud; Achuthan, Ajit; Bednarcyk, Brett A.; Arnold, Steven M.; Pineda, Evan J.

2016-01-01

A multiscale computational model is developed for determining the elasto-plastic behavior of polycrystal metals by employing a single crystal plasticity constitutive model that can capture the microstructural scale stress field on a finite element analysis (FEA) framework. The generalized method of cells (GMC) micromechanics model is used for homogenizing the local field quantities. At first, the stand-alone GMC is applied for studying simple material microstructures such as a repeating unit cell (RUC) containing single grain or two grains under uniaxial loading conditions. For verification, the results obtained by the stand-alone GMC are compared to those from an analogous FEA model incorporating the same single crystal plasticity constitutive model. This verification is then extended to samples containing tens to hundreds of grains. The results demonstrate that the GMC homogenization combined with the crystal plasticity constitutive framework is a promising approach for failure analysis of structures as it allows for properly predicting the von Mises stress in the entire RUC, in an average sense, as well as in the local microstructural level, i.e., each individual grain. Two–three orders of saving in computational cost, at the expense of some accuracy in prediction, especially in the prediction of the components of local tensor field quantities and the quantities near the grain boundaries, was obtained with GMC. Finally, the capability of the developed multiscale model linking FEA and GMC to solve real-life-sized structures is demonstrated by successfully analyzing an engine disc component and determining the microstructural scale details of the field quantities. PMID:28773458

Recrystallization-Induced Surface Cracks of Carbon Ions Irradiated 6H-SiC after Annealing

PubMed Central

Ye, Chao; Ran, Guang; Zhou, Wei; Shen, Qiang; Feng, Qijie; Lin, Jianxin

2017-01-01

Single crystal 6H-SiC wafers with 4° off-axis [0001] orientation were irradiated with carbon ions and then annealed at 900 °C for different time periods. The microstructure and surface morphology of these samples were investigated by grazing incidence X-ray diffraction (GIXRD), scanning electron microscopy (SEM), and transmission electron microscopy (TEM). Ion irradiation induced SiC amorphization, but the surface was smooth and did not have special structures. During the annealing process, the amorphous SiC was recrystallized to form columnar crystals that had a large amount of twin structures. The longer the annealing time was, the greater the amount of recrystallized SiC would be. The recrystallization volume fraction was accorded with the law of the Johnson–Mehl–Avrami equation. The surface morphology consisted of tiny pieces with an average width of approximately 30 nm in the annealed SiC. The volume shrinkage of irradiated SiC layer and the anisotropy of newly born crystals during annealing process produced internal stress and then induced not only a large number of dislocation walls in the non-irradiated layer but also the initiation and propagation of the cracks. The direction of dislocation walls was perpendicular to the growth direction of the columnar crystal. The longer the annealing time was, the larger the length and width of the formed crack would be. A quantitative model of the crack growth was provided to calculate the length and width of the cracks at a given annealing time. PMID:29068408

Novel Gyroscopic Mounting for Crystal Oscillators to Increase Short and Medium Term Stability under Highly Dynamic Conditions

PubMed Central

Abedi, Maryam; Jin, Tian; Sun, Kewen

2015-01-01

In this paper, a gyroscopic mounting method for crystal oscillators to reduce the impact of dynamic loads on their output stability has been proposed. In order to prove the efficiency of this mounting approach, each dynamic load-induced instability has been analyzed in detail. A statistical study has been performed on the elevation angle of the g-sensitivity vector of Stress Compensated-cut (SC-cut) crystals. The analysis results show that the proposed gyroscopic mounting method gives good performance for host vehicle attitude changes. A phase noise improvement of 27 dB maximum and 5.7 dB on average can be achieved in the case of steady state loads, while under sinusoidal vibration conditions, the maximum and average phase noise improvement are as high as 24 dB and 7.5 dB respectively. With this gyroscopic mounting method, random vibration-induced phase noise instability is reduced 30 dB maximum and 8.7 dB on average. Good effects are apparent for crystal g-sensitivity vectors with low elevation angle φ and azimuthal angle β. under highly dynamic conditions, indicating the probability that crystal oscillator instability will be significantly reduced by using the proposed mounting approach. PMID:26091393

A top-down approach to crystal engineering of a racemic Δ2-isoxazoline.

PubMed

Lombardo, Giuseppe M; Rescifina, Antonio; Chiacchio, Ugo; Bacchi, Alessia; Punzo, Francesco

2014-02-01

The crystal structure of racemic dimethyl (4RS,5RS)-3-(4-nitrophenyl)-4,5-dihydroisoxazole-4,5-dicarboxylate, C13H12N2O7, has been determined by single-crystal X-ray diffraction. By analysing the degree of growth of the morphologically important crystal faces, a ranking of the most relevant non-covalent interactions determining the crystal structure can be inferred. The morphological information is considered with an approach opposite to the conventional one: instead of searching inside the structure for the potential key interactions and using them to calculate the crystal habit, the observed crystal morphology is used to define the preferential lines of growth of the crystal, and then this information is interpreted by means of density functional theory (DFT) calculations. Comparison with the X-ray structure confirms the validity of the strategy, thus suggesting this top-down approach to be a useful tool for crystal engineering.

Interacting quasi-band theory for electronic states in compound semiconductor alloys: Wurtzite structure

NASA Astrophysics Data System (ADS)

Kishi, Ayaka; Oda, Masato; Shinozuka, Yuzo

2016-05-01

This paper reports on the electronic states of compound semiconductor alloys of wurtzite structure calculated by the recently proposed interacting quasi-band (IQB) theory combined with empirical sp3 tight-binding models. Solving derived quasi-Hamiltonian 24 × 24 matrix that is characterized by the crystal parameters of the constituents facilitates the calculation of the conduction and valence bands of wurtzite alloys for arbitrary concentrations under a unified scheme. The theory is applied to III-V and II-VI wurtzite alloys: cation-substituted Al1- x Ga x N and Ga1- x In x N and anion-substituted CdS1- x Se x and ZnO1- x S x . The obtained results agree well with the experimental data, and are discussed in terms of mutual mixing between the quasi-localized states (QLS) and quasi-average bands (QAB): the latter bands are approximately given by the virtual crystal approximation (VCA). The changes in the valence and conduction bands, and the origin of the band gap bowing are discussed on the basis of mixing character.

NaAlTi 3O 8, A Novel Anode Material for Sodium Ion Battery

DOE PAGES

Ma, Xuetian; An, Ke; Bai, Jianmin; ...

2017-03-13

Sodium ion batteries are being considered as an alternative to lithium ion batteries in large-scale energy storage applications owing to the low cost. In this paper, a novel titanate compound, NaAlTi 3O 8, was successfully synthesized and tested as a promising anode material for sodium ion batteries. Powder X-ray Diffraction (XRD) and refinement were used to analyze the crystal structure. Electrochemical cycling tests under a C/10 rate between 0.01 - 2.5 V showed that ~83 mAh/g capacity could be achieved in the second cycle, with ~75% of which retained after 100 cycles, which corresponds to 0.75 Na + insertion andmore » extraction. The influence of synthesis conditions on electrochemical performances was investigated and discussed. Finally, NaAlTi 3O 8 not only presents a new anode material with low average voltage of ~0.5 V, but also provides a new type of intercalation anode with a crystal structure that differentiates from the anodes that have been reported.« less

Computational carbohydrate chemistry: what theoretical methods can tell us

PubMed Central

Woods, Robert J.

2014-01-01

Computational methods have had a long history of application to carbohydrate systems and their development in this regard is discussed. The conformational analysis of carbohydrates differs in several ways from that of other biomolecules. Many glycans appear to exhibit numerous conformations coexisting in solution at room temperature and a conformational analysis of a carbohydrate must address both spatial and temporal properties. When solution nuclear magnetic resonance data are used for comparison, the simulation must give rise to ensemble-averaged properties. In contrast, when comparing to experimental data obtained from crystal structures a simulation of a crystal lattice, rather than of an isolated molecule, is appropriate. Molecular dynamics simulations are well suited for such condensed phase modeling. Interactions between carbohydrates and other biological macromolecules are also amenable to computational approaches. Having obtained a three-dimensional structure of the receptor protein, it is possible to model with accuracy the conformation of the carbohydrate in the complex. An example of the application of free energy perturbation simulations to the prediction of carbohydrate-protein binding energies is presented. PMID:9579797

Salvage of failed protein targets by reductive alkylation.

PubMed

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins.

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

Tan, Kemin; Kim, Youngchang; Hatzos-Skintges, Catherine; Chang, Changsoo; Cuff, Marianne; Chhor, Gekleng; Osipiuk, Jerzy; Michalska, Karolina; Nocek, Boguslaw; An, Hao; Babnigg, Gyorgy; Bigelow, Lance; Joachimiak, Grazyna; Li, Hui; Mack, Jamey; Makowska-Grzyska, Magdalena; Maltseva, Natalia; Mulligan, Rory; Tesar, Christine; Zhou, Min; Joachimiak, Andrzej

2014-01-01

The growth of diffraction-quality single crystals is of primary importance in protein X-ray crystallography. Chemical modification of proteins can alter their surface properties and crystallization behavior. The Midwest Center for Structural Genomics (MCSG) has previously reported how reductive methylation of lysine residues in proteins can improve crystallization of unique proteins that initially failed to produce diffraction-quality crystals. Recently, this approach has been expanded to include ethylation and isopropylation in the MCSG protein crystallization pipeline. Applying standard methods, 180 unique proteins were alkylated and screened using standard crystallization procedures. Crystal structures of 12 new proteins were determined, including the first ethylated and the first isopropylated protein structures. In a few cases, the structures of native and methylated or ethylated states were obtained and the impact of reductive alkylation of lysine residues was assessed. Reductive methylation tends to be more efficient and produces the most alkylated protein structures. Structures of methylated proteins typically have higher resolution limits. A number of well-ordered alkylated lysine residues have been identified, which make both intermolecular and intramolecular contacts. The previous report is updated and complemented with the following new data; a description of a detailed alkylation protocol with results, structural features, and roles of alkylated lysine residues in protein crystals. These contribute to improved crystallization properties of some proteins. PMID:24590719

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds

PubMed Central

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C.; Orimo, Shin-ichi

2016-01-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures. PMID:27032978

Extending the applicability of the Goldschmidt tolerance factor to arbitrary ionic compounds.

PubMed

Sato, Toyoto; Takagi, Shigeyuki; Deledda, Stefano; Hauback, Bjørn C; Orimo, Shin-ichi

2016-04-01

Crystal structure determination is essential for characterizing materials and their properties, and can be facilitated by various tools and indicators. For instance, the Goldschmidt tolerance factor (T) for perovskite compounds is acknowledged for evaluating crystal structures in terms of the ionic packing. However, its applicability is limited to perovskite compounds. Here, we report on extending the applicability of T to ionic compounds with arbitrary ionic arrangements and compositions. By focussing on the occupancy of constituent spherical ions in the crystal structure, we define the ionic filling fraction (IFF), which is obtained from the volumes of crystal structure and constituent ions. Ionic compounds, including perovskites, are arranged linearly by the IFF, providing consistent results with T. The linearity guides towards finding suitable unit cell and composition, thus tackling the main obstacle for determining new crystal structures. We demonstrate the utility of the IFF by solving the structure of three hydrides with new crystal structures.

From screen to structure with a harvestable microfluidic device.

PubMed

Stojanoff, Vivian; Jakoncic, Jean; Oren, Deena A; Nagarajan, V; Poulsen, Jens-Christian Navarro; Adams-Cioaba, Melanie A; Bergfors, Terese; Sommer, Morten O A

2011-08-01

Advances in automation have facilitated the widespread adoption of high-throughput vapour-diffusion methods for initial crystallization screening. However, for many proteins, screening thousands of crystallization conditions fails to yield crystals of sufficient quality for structural characterization. Here, the rates of crystal identification for thaumatin, catalase and myoglobin using microfluidic Crystal Former devices and sitting-drop vapour-diffusion plates are compared. It is shown that the Crystal Former results in a greater number of identified initial crystallization conditions compared with vapour diffusion. Furthermore, crystals of thaumatin and lysozyme obtained in the Crystal Former were used directly for structure determination both in situ and upon harvesting and cryocooling. On the basis of these results, a crystallization strategy is proposed that uses multiple methods with distinct kinetic trajectories through the protein phase diagram to increase the output of crystallization pipelines.

Environmentally safe oil-field reagents for development and operation of oil-gas deposits

NASA Astrophysics Data System (ADS)

Fakhreeva, A. V.; Manaure, D. A.; Dokichev, V. A.; Voloshin, A. I.; Telin, A. G.; Tomilov, Yu V.; Nifantiev, N. E.

2018-04-01

Sodium-carboxymethylcellulose and arabinogalactane inhibits the crystallization of calcium carbonate from a supersaturated aqueous solution at 80°C. The sizes of formed crystals CaCO3 in the presence of arabinogalactane, sodium-carboxymethylcellulose and neonol AF 9-10 decrease on an average 7-12 μm and a change of their structure. It is expected, that the mechanism of inhibitionis in specific adsorption polysaccharides and neonol on occurring crystalline surface of the calcium carbonate, both at the expense of electrostatic interaction of functional groups with Ca2+ ions, located on the surface of the crystal, and due to coordination and hydrogen bonds with oxygen atoms and HO-groups of additives. Oil-water emulsion rheology in the presence of neonol AF 9-10 has been studied. It is shown that neonol AF 9-10 decrease viscosity natural water-oil emulsion by 25 times. Addition of 5% neonol to water-oil emulsion leads to formation more than 20 stable emulsion forms of different density and composition. New highly effective “green” oilfield reagents have been developed on the basis of neonol and natural polysaccharides.

Crystalline ricin D, a toxic anti-tumor lectin from seeds of Ricinus communis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wei, C.H.; Koh, C.

1978-03-25

A toxic lectin, ricin D, present in the seeds of Ricinus communis has been purified and crystallized in a form suitable for high resolution crystallographic structure studies. This protein is different from a previously found form of ricin (also present in the same seeds), the only ricin for which a preliminary x-ray investigation has been reported so far. Ricin D crystallizes from an aqueous solution in an orthorhombic unit cell of symmetry P2/sub 1/2/sub 1/2/sub 1/ and a = 79.0, b = 114.7, and c = 72.8 A. The asymmetric unit contains one molecule with an average molecular weight ofmore » 62,400. The crystal is fairly stable to x-radiation and has a water content of approximately 54% by volume. It appears to comprise two closely related species of proteins, the major species corresponding to ricin D and the other presumably corresponding to a deamidation product of ricin D. The two species have nearly identical molecular size and amino acid compositions, but different charges.« less

All-fiber mode-locked laser via short single-wall carbon nanotubes interacting with evanescent wave in photonic crystal fiber.

PubMed

Li, Yujia; Gao, Lei; Huang, Wei; Gao, Cong; Liu, Min; Zhu, Tao

2016-10-03

We report an all-fiber passively mode-locked laser based on a saturable absorber fabricated by filling short single-wall carbon nanotubes into cladding holes of grapefruit-type photonic crystal fiber. The single-wall carbon nanotube is insensitive to polarization of light for its one-dimensional structure, which suppresses the polarization dependence loss. Carbon nanotubes interact with photonic crystal fiber with ultra-weak evanescent field, which enhances the damage threshold of the saturable absorber and improves the operating stability. In our experiment, conventional soliton with a pulse duration of 1.003 ps and center wavelength of 1566.36 nm under a pump power of 240 mW is generated in a compact erbium-doped fiber laser cavity with net anomalous dispersion of -0.4102 ps². The signal to noise ratio of the fundamental frequency component is ~80 dB. The maximum average output power of the mode-locked laser reaches 9.56 mW under a pump power of 360 mW. The output power can be further improved by a higher pump power.

Process Research on Polycrystalline Silicon Material (PROPSM)

NASA Technical Reports Server (NTRS)

Culik, J. S.

1983-01-01

The performance limiting mechanisms in large grain (greater than 1-2 mm in diameter) polycrystalline silicon was investigated by measuring the illuminated current voltage (I-V) characteristics of the minicell wafer set. The average short circuit current on different wafers is 3 to 14 percent lower than that of single crystal Czochralski silicon. The scatter was typically less than 3 percent. The average open circuit voltage is 20 to 60 mV less than that of single crystal silicon. The scatter in the open circuit voltage of most of the polycrystalline silicon wafers was 15 to 20 mV, although two wafers had significantly greater scatter than this value. The fill factor of both polycrystalline and single crystal silicon cells was typically in the range of 60 to 70 percent; however several polycrystalline silicon wafers have fill factor averages which are somewhat lower and have a significantly larger degree of scatter.

Structural and optical properties of WTe2 single crystals synthesized by DVT technique

NASA Astrophysics Data System (ADS)

Dixit, Vijay; Vyas, Chirag; Pathak, V. M.; Soalanki, G. K.; Patel, K. D.

2018-05-01

Layered transition metal di-chalcogenide (LTMDCs) crystals have attracted much attention due to their potential in optoelectronic device applications recently due to realization of their monolayer based structures. In the present investigation we report growth of WTe2 single crystals by direct vapor transport (DVT) technique. These crystals are then characterized by energy dispersive analysis of x-rays (EDAX) to study stoichiometric composition after growth. The structural properties are studied by x-ray diffraction (XRD) and selected area electron diffraction (SAED) is used to confirm orthorhombic structure of grown WTe2 crystal. Surface morphological properties of the crystals are also studied by scanning electron microscope (SEM). The optical properties of the grown crystals are studied by UV-Visible spectroscopy which gives direct band gap of 1.44 eV for grown WTe2 single crystals.

Octoxy capped Si nanoparticles synthesized by homogeneous reduction of SiCl4 with crown ether alkalide.

PubMed

Sletnes, M; Maria, J; Grande, T; Lindgren, M; Einarsrud, M-A

2014-02-07

Blue-green luminescent octoxy capped Si nanoparticles were synthesized via homogeneous reduction of SiCl4 with the crown ether alkalide K(+)(15-crown-5)2K(-) in tetrahydrofuran. The Si nanoparticles were characterized with respect to size, crystal structure, morphology, surface termination, optical properties and stability. Si diamond structure nanoparticles with narrow size distributions, and average diameters ranging from 3 to 7 nm were obtained. A finite-size effect on the lattice dimensions was observed, in the form of an expansion of the [220] lattice planes of smaller Si nanoparticles. The concentration of SiCl4 was found to be the most important parameter governing the particle size and size distribution. The octoxy capped particles were stable under an ambient atmosphere for at least one month, but exposure to water made them prone to oxidation. An average radiative recombination lifetime of 8.8 ns was measured for the blue-green luminescence. The luminescence appears to originate from surface defects, rather than from quantum confinement.

The application of tailor-made force fields and molecular dynamics for NMR crystallography: a case study of free base cocaine

PubMed Central

Neumann, Marcus A.

2017-01-01

Motional averaging has been proven to be significant in predicting the chemical shifts in ab initio solid-state NMR calculations, and the applicability of motional averaging with molecular dynamics has been shown to depend on the accuracy of the molecular mechanical force field. The performance of a fully automatically generated tailor-made force field (TMFF) for the dynamic aspects of NMR crystallography is evaluated and compared with existing benchmarks, including static dispersion-corrected density functional theory calculations and the COMPASS force field. The crystal structure of free base cocaine is used as an example. The results reveal that, even though the TMFF outperforms the COMPASS force field for representing the energies and conformations of predicted structures, it does not give significant improvement in the accuracy of NMR calculations. Further studies should direct more attention to anisotropic chemical shifts and development of the method of solid-state NMR calculations. PMID:28250956

Solvent effects on the crystal growth structure and morphology of the pharmaceutical dirithromycin

NASA Astrophysics Data System (ADS)

Wang, Yuan; Liang, Zuozhong

2017-12-01

Solvent effects on the crystal structure and morphology of pharmaceutical dirithromycin molecules were systematically investigated using both experimental crystallization and theoretical simulation. Dirithromycin is one of the new generation of macrolide antibiotics with two polymorphic forms (Form I and Form II) and many solvate forms. Herein, six solvates of the dirithromycin, including acetonitrile, acetonitrile/water, acetone, 1-propanol, N,N-dimethylformamide (DMF) and cyclohexane, were studied. Experimentally, we crystallized the dirithromycin molecules in different solvents by the solvent evaporating method and measured the crystal structures with the X-ray diffraction (XRD). We compared these crystal structures of dirithromycin solvates and analyzed the solvent property-determined structure evolution. The solvents have a strong interaction with the dirithromycin molecule due to the formation of inter-molecular interactions (such as the hydrogen bonding and close contacts (sum of vdW radii)). Theoretically, we calculated the ideal crystal habit based on the solvated structures with the attachment growth (AE) model. The predicted morphologies and aspect ratios of dirithromycin solvates agree well with the experimental results. This work could be helpful to better understand the structure and morphology evolution of solvates controlled by solvents and guide the crystallization of active pharmaceutical ingredients in the pharmaceutical industry.

Synthesis and morphology of Ba1-xRE2x/3Nb2O6 nanocrystals with tungsten bronze structure in RE2O3-BaO-Nb2O5-B2O3 glasses (RE: Sm, Eu, Gd, Dy, Er)

NASA Astrophysics Data System (ADS)

Ida, H.; Shinozaki, K.; Honma, T.; Oh-ishi, K.; Komatsu, T.

2012-12-01

Ba1-xRE2x/3Nb2O6 nanocrystals with a tetragonal tungsten bronze (TTB) structure are synthesized using a conventional glass crystallization technique in 2.3RE2O3-27.4BaO-34.3Nb2O5-36B2O3 (mol%) (RE=Sm, Eu, Gd, Dy, and Er) glasses. One sharp crystallization peak is observed at ∼670 °C in both powdered and bulk glasses, and the formation of Ba1-xRE2x/3Nb2O6 nanocrystals with unit cell parameters of a∼1.24 nm and c∼0.39 nm was confirmed. It is found from high resolution transmission electron microscope observations that the morphology of Ba1-xRE2x/3Nb2O6 nanocrystals is ellipsoidal. Their average particle size is in the range of 15-60 nm and decreases with decreasing ionic radius of RE3+ being present in the precursor glasses. The optical transparent crystallized glass (bulk) shows the total photoluminescence (PL) quantum yield of 53% in the visible region of Eu3+ ions, suggesting a high potential of Ba1-xRE2x/3Nb2O6 nanocrystals as PL materials.

Transition to collapsed tetragonal phase in CaFe2As2 single crystals as seen by 57Fe Mössbauer spectroscopy

NASA Astrophysics Data System (ADS)

Bud'ko, Sergey L.; Ma, Xiaoming; Tomić, Milan; Ran, Sheng; Valentí, Roser; Canfield, Paul C.

2016-01-01

Temperature dependent measurements of 57Fe Mössbauer spectra on CaFe2As2 single crystals in the tetragonal and collapsed tetragonal phases are reported. Clear features in the temperature dependencies of the isomer shift, relative spectra area, and quadrupole splitting are observed at the transition from the tetragonal to the collapsed tetragonal phase. From the temperature dependent isomer shift and spectral area data, an average stiffening of the phonon modes in the collapsed tetragonal phase is inferred. The quadrupole splitting increases by ˜25 % on cooling from room temperature to ˜100 K in the tetragonal phase and is only weakly temperature dependent at low temperatures in the collapsed tetragonal phase, in agreement with the anisotropic thermal expansion in this material. In order to gain microscopic insight about these measurements, we perform ab initio density functional theory calculations of the electric field gradient and the electron density of CaFe2As2 in both phases. By comparing the experimental data with the calculations we are able to fully characterize the crystal structure of the samples in the collapsed-tetragonal phase through determination of the As z coordinate. Based on the obtained temperature dependent structural data we are able to propose charge saturation of the Fe-As bond region as the mechanism behind the stabilization of the collapsed-tetragonal phase at ambient pressure.

Molecular Dynamic Simulation of Space and Earth-Grown Crystal Structures of Thermostable T1 Lipase Geobacillus zalihae Revealed a Better Structure.

PubMed

Ishak, Siti Nor Hasmah; Aris, Sayangku Nor Ariati Mohamad; Halim, Khairul Bariyyah Abd; Ali, Mohd Shukuri Mohamad; Leow, Thean Chor; Kamarudin, Nor Hafizah Ahmad; Masomian, Malihe; Rahman, Raja Noor Zaliha Raja Abd

2017-09-25

Less sedimentation and convection in a microgravity environment has become a well-suited condition for growing high quality protein crystals. Thermostable T1 lipase derived from bacterium Geobacillus zalihae has been crystallized using the counter diffusion method under space and earth conditions. Preliminary study using YASARA molecular modeling structure program for both structures showed differences in number of hydrogen bond, ionic interaction, and conformation. The space-grown crystal structure contains more hydrogen bonds as compared with the earth-grown crystal structure. A molecular dynamics simulation study was used to provide insight on the fluctuations and conformational changes of both T1 lipase structures. The analysis of root mean square deviation (RMSD), radius of gyration, and root mean square fluctuation (RMSF) showed that space-grown structure is more stable than the earth-grown structure. Space-structure also showed more hydrogen bonds and ion interactions compared to the earth-grown structure. Further analysis also revealed that the space-grown structure has long-lived interactions, hence it is considered as the more stable structure. This study provides the conformational dynamics of T1 lipase crystal structure grown in space and earth condition.

Effects of Al-Impurity Type on Formation Energy, Crystal Structure, Electronic Structure, and Optical Properties of ZnO by Using Density Functional Theory and the Hubbard-U Method.

PubMed

Wu, Hsuan-Chung; Chen, Hsing-Hao; Zhu, Yu-Ren

2016-08-01

We systematically investigated the effects of Al-impurity type on the formation energy, crystal structure, charge density, electronic structure, and optical properties of ZnO by using density functional theory and the Hubbard-U method. Al-related defects, such as those caused by the substitution of Zn and O atoms by Al atoms (Al s(Zn) and Al s(O) , respectively) and the presence of an interstitial Al atom at the center of a tetrahedron (Al i(tet) ) or an octahedron (Al i(oct) ), and various Al concentrations were evaluated. The calculated formation energy follows the order E f (Al s(Zn) ) < E f (Al i(tet) ) < E f (Al i(oct) ) < E f (Al s(O) ). Electronic structure analysis showed that the Al s(Zn) , Al s(O) , Al i(tet) , and Al i(oct) models follow n -type conduction, and the optical band gaps are higher than that of pure ZnO. The calculated carrier concentrations of the Al s(O) and Al i(tet) /Al i(oct) models are higher than that of the Al s(Zn) model. However, according to the curvature of the band structure, the occurrence of interstitial Al atoms or the substitution of O atoms by Al atoms results in a high effective mass, possibly reducing the carrier mobility. The average transmittance levels in the visible light and ultraviolet (UV) regions of the Al s(Zn) model are higher than those of pure ZnO. However, the presence of an interstitial Al atom within the ZnO crystal reduces transmittance in the visible light region; Al s(O) substantially reduces the transmittance in the visible light and UV regions. In addition, the properties of ZnO doped with various Al s(Zn) concentrations were analyzed.

Use of Crystal Structure Informatics for Defining the Conformational Space Needed for Predicting Crystal Structures of Pharmaceutical Molecules.

PubMed

Iuzzolino, Luca; Reilly, Anthony M; McCabe, Patrick; Price, Sarah L

2017-10-10

Determining the range of conformations that a flexible pharmaceutical-like molecule could plausibly adopt in a crystal structure is a key to successful crystal structure prediction (CSP) studies. We aim to use conformational information from the crystal structures in the Cambridge Structural Database (CSD) to facilitate this task. The conformations produced by the CSD Conformer Generator are reduced in number by considering the underlying rotamer distributions, an analysis of changes in molecular shape, and a minimal number of molecular ab initio calculations. This method is tested for five pharmaceutical-like molecules where an extensive CSP study has already been performed. The CSD informatics-derived set of crystal structure searches generates almost all the low-energy crystal structures previously found, including all experimental structures. The workflow effectively combines information on individual torsion angles and then eliminates the combinations that are too high in energy to be found in the solid state, reducing the resources needed to cover the solid-state conformational space of a molecule. This provides insights into how the low-energy solid-state and isolated-molecule conformations are related to the properties of the individual flexible torsion angles.

Frequency-doubled green picosecond laser based on K3B6O10Br nonlinear optical crystal

NASA Astrophysics Data System (ADS)

Meng, Luping; Zhang, Ling; Hou, Zhanyu; Wang, Lirong; Xu, Hui; Shi, Meng; Wang, Lingwu; Yang, Yingying; Qi, Yaoyao; He, Chaojian; Yu, Haijuan; Lin, Xuechun; Su, Fufang; Xia, Mingjun; Li, Rukang

2018-05-01

We report a frequency-doubled green picosecond (ps) laser based on K3B6O10Br (KBB) nonlinear optical crystal with cutting angle of θ = 34.7° and φ = 30°. Through intracavity frequency doubling using a type I phase-matched KBB crystal with dimensions of 4 mm × 4 mm × 13.2 mm, the average output power of 185.00 mW green ps laser was obtained with a repetition rate of 80 MHz and pulse width of 25.0 ps. In addition, we present external frequency doubling using KBB crystal. The average output power of 3.00 W green ps laser was generated with a repetition rate of 10 kHz and pulse width of 38.1 ps, which corresponds to a pulse energy of 0.30 mJ and a peak power 7.89 MW, respectively. The experimental results show that KBB crystal is a promising nonlinear optical material.

Two distinct crystallization processes in supercooled liquid

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tane, Masakazu, E-mail: mtane@sanken.osaka-u.ac.jp; Kimizuka, Hajime; Ichitsubo, Tetsu

2016-05-21

Using molecular dynamics simulations we show that two distinct crystallization processes, depending on the temperature at which crystallization occurs, appear in a supercooled liquid. As a model for glass-forming materials, an Al{sub 2}O{sub 3} model system, in which both the glass transition and crystallization from the supercooled liquid can be well reproduced, is employed. Simulations in the framework of an isothermal-isobaric ensemble indicate that the calculated time-temperature-transformation curve for the crystallization to γ(defect spinel)-Al{sub 2}O{sub 3} exhibited a typical nose shape, as experimentally observed in various glass materials. During annealing above the nose temperature, the structure of the supercooled liquidmore » does not change before the crystallization, because of the high atomic mobility (material transport). Thus, the crystallization is governed by the abrupt crystal nucleation, which results in the formation of a stable crystal structure. In contrast, during annealing below the nose temperature, the structure of the supercooled liquid gradually changes before the crystallization, and the formed crystal structure is less stable than that formed above the nose temperature, because of the restricted material transport.« less

Correlation of Intermolecular Acyl Transfer Reactivity with Noncovalent Lattice Interactions in Molecular Crystals: Toward Prediction of Reactivity of Organic Molecules in the Solid State.

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

Intermolecular acyl transfer reactivity in several molecular crystals was studied, and the outcome of the reactivity was analyzed in the light of structural information obtained from the crystals of the reactants. Minor changes in the molecular structure resulted in significant variations in the noncovalent interactions and packing of molecules in the crystal lattice, which drastically affected the facility of the intermolecular acyl transfer reactivity in these crystals. Analysis of the reactivity vs crystal structure data revealed dependence of the reactivity on electrophile···nucleophile interactions and C-H···π interactions between the reacting molecules. The presence of these noncovalent interactions augmented the acyl transfer reactivity, while their absence hindered the reactivity of the molecules in the crystal. The validity of these correlations allows the prediction of intermolecular acyl transfer reactivity in crystals and co-crystals of unknown reactivity. This crystal structure-reactivity correlation parallels the molecular structure-reactivity correlation in solution-state reactions, widely accepted as organic functional group transformations, and sets the stage for the development of a similar approach for reactions in the solid state.

Electrodeposited Ni-Co films from electrolytes with different Co contents

NASA Astrophysics Data System (ADS)

Karpuz, Ali; Kockar, Hakan; Alper, Mursel; Karaagac, Oznur; Haciismailoglu, Murside

2012-02-01

The properties of electrodeposited Ni-Co films produced from electrolyte consisted of nickel sulfamate, cobalt sulfate and boric acid were investigated as a function of Co content in the films. The compositional analysis performed by an energy dispersive X-ray spectroscopy demonstrated that the Co content of the films increases as the cobalt sulfate concentration in the electrolyte increases. The anomalous codeposition behavior was observed for all concentrations. The crystal structure was analyzed using an X-ray diffraction technique. The face centered cubic (fcc) structure was observed in the films containing from 0 at.% Co to 58 at.% Co. For the higher atomic Co contents (64 at.% and 80 at.%), a mixed phase of dominantly fcc and hexagonal closed packed (hcp) structure was observed although the (10.0) and (10.1) hcp peaks had minor intensities in the patterns. Surface micrographs obtained from a scanning electron microscope revealed that the film surface has a rougher appearance as the Co content increases. Magnetic measurements showed that the saturation magnetization gradually increased with increasing Co content of the films. The coercivity, Hc can be controlled by the structural parameters such as average grain size and crystal structure. The results also indicated that the optimum film composition was 28-40 at.% Co since the lower Hc and higher magnetoresistance (MR) values with very smooth or slightly granular surfaces were achieved at this Co content. It is revealed that Co content has an important effect on structural, magnetic and MR properties of the Ni-Co films.

Structural investigations in helium implanted cubic zirconia using grazing incidence XRD and EXAFS spectroscopy

NASA Astrophysics Data System (ADS)

Kuri, G.; Degueldre, C.; Bertsch, J.; Döbeli, M.

2010-06-01

The crystal structure and local atom arrangements surrounding Zr atoms were determined for a helium implanted cubic stabilized zirconia (CSZ) using X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy, respectively, measured at glancing angles. The implanted specimen was prepared at a helium fluence of 2 × 10 16 cm -2 using He + beams at two energies (2.54 and 2.74 MeV) passing through a 8.0 μm Al absorber foil. XRD results identified the formation of a new rhombohedral phase in the helium embedded layer, attributed to internal stress as a result of expansion of the CSZ-lattice. Zr K-edge EXAFS data suggested loss of crystallinity in the implanted lattice and disorder of the Zr atoms environment. EXAFS Fourier transforms analysis showed that the average first-shell radius of the Zr sbnd O pair in the implanted sample was slightly larger than that of the CSZ standard. Common general disorder features were explained by rhombohedral type short-range ordered clusters. The average structural parameters estimated from the EXAFS data of unimplanted and implanted CSZ are compared and discussed. Potential of EXAFS as a local probe of atomic-scale structural modifications induced by helium implantation in CSZ is demonstrated.

Prediction and theoretical characterization of p-type organic semiconductor crystals for field-effect transistor applications.

PubMed

Atahan-Evrenk, Sule; Aspuru-Guzik, Alán

2014-01-01

The theoretical prediction and characterization of the solid-state structure of organic semiconductors has tremendous potential for the discovery of new high performance materials. To date, the theoretical analysis mostly relied on the availability of crystal structures obtained through X-ray diffraction. However, the theoretical prediction of the crystal structures of organic semiconductor molecules remains a challenge. This review highlights some of the recent advances in the determination of structure-property relationships of the known organic semiconductor single-crystals and summarizes a few available studies on the prediction of the crystal structures of p-type organic semiconductors for transistor applications.

The potential for the indirect crystal structure verification of methyl glycosides based on acetates' parent structures: GIPAW and solid-state NMR approaches

NASA Astrophysics Data System (ADS)

Szeleszczuk, Łukasz; Gubica, Tomasz; Zimniak, Andrzej; Pisklak, Dariusz M.; Dąbrowska, Kinga; Cyrański, Michał K.; Kańska, Marianna

2017-10-01

A convenient method for the indirect crystal structure verification of methyl glycosides was demonstrated. Single-crystal X-ray diffraction structures for methyl glycoside acetates were deacetylated and subsequently subjected to DFT calculations under periodic boundary conditions. Solid-state NMR spectroscopy served as a guide for calculations. A high level of accuracy of the modelled crystal structures of methyl glycosides was confirmed by comparison with published results of neutron diffraction study using RMSD method.

Structural properties of a family of hydrogen-bonded co-crystals formed between gemfibrozil and hydroxy derivatives of t-butylamine, determined directly from powder X-ray diffraction data

NASA Astrophysics Data System (ADS)

Cheung, Eugene Y.; David, Sarah E.; Harris, Kenneth D. M.; Conway, Barbara R.; Timmins, Peter

2007-03-01

We report the formation and structural properties of co-crystals containing gemfibrozil and hydroxy derivatives of t-butylamine H 2NC(CH 3) 3-n(CH 2OH) n, with n=0, 1, 2 and 3. In each case, a 1:1 co-crystal is formed, with transfer of a proton from the carboxylic acid group of gemfibrozil to the amino group of the t-butylamine derivative. All of the co-crystal materials prepared are polycrystalline powders, and do not contain single crystals of suitable size and/or quality for single crystal X-ray diffraction studies. Structure determination of these materials has been carried out directly from powder X-ray diffraction data, using the direct-space Genetic Algorithm technique for structure solution followed by Rietveld refinement. The structural chemistry of this series of co-crystal materials reveals well-defined structural trends within the first three members of the family ( n=0, 1, 2), but significantly contrasting structural properties for the member with n=3.

Structural, morphological and optical studies of ripple-structured ZnO thin films

NASA Astrophysics Data System (ADS)

Navin, Kumar; Kurchania, Rajnish

2015-11-01

Ripple-structured ZnO thin films were prepared on Si (100) substrate by sol-gel spin-coating method with different heating rates during preheating process and finally sintered at 500 °C for 2 h in ambient condition. The structural, morphological and photoluminescence (PL) properties of the nanostructured films were analyzed by X-ray diffraction (XRD), atomic force microscopy (AFM), scanning electron microscopy (SEM) and PL spectroscopy. XRD analysis revealed that films have hexagonal wurtzite structure and texture coefficient increases along (002) plane with preheating rate. The faster heating rate produced higher crystallization and larger average crystallite size. The AFM and SEM images indicate that all the films have uniformly distributed ripple structure with skeletal branches. The number of ripples increases, while the rms roughness, amplitude and correlation length of the ripple structure decrease with preheating rates. The PL spectra show the presence of different defects in the structure. The ultraviolet emission improved with the heating rate which indicates its better crystallinity.

Macroscopic and bulk-controlled elastic modes in an interaction of interstitial alcali metal cations within a face-centered cubic crystalline fullerine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tatarenko, V.A.; Tsysman, C.L.; Oltarzhevskaya, Y.T.

1994-12-31

The calculations in a majority of previous works for the fulleride (AqC{sub 60}) crystals were performed within the framework of the rigid-lattice model, neglecting the distoration relaxation of the host fullerene (C{sub 60}) crystal caused by the interstitial alkali-metal (A) cations. However, an each cation is a source of a static distoration field, and the resulting field is a superposition of such fields generated by all cations. This is a reason why the host-crystal distortions depend on the A-cations configurations, i.e. on a type of a spatial bulk distribution of interstitial cations. This paper seeks to find a functional relationmore » between the amplitudes of the doping-induced structure-distortion waves and of statistic concentration ones. A semiphenomenological model is constructed here within the scope of statistical-thermodynamic treatment and using the lattice-statistics simulation method. In this model the effects due to the presence of q solute A cations over available interstices (per unit cell) on the statistic inherent reorientation and/or displacements of the solvent molecules from the average-lattice sites as well as on the lattice parameter a of the elastically-anysotropic cubic C{sub 60} crystal are taken into account.« less

A Crystal-Physical Model of Electrotransfer in the Superionic Conductor Pb1 - x Sc x F2 + x ( x = 0.1)

NASA Astrophysics Data System (ADS)

Sorokin, N. I.

2018-04-01

The frequency (ν = 10-1-107 Hz) dependences of electrical conductivity σ(ν) of single crystals of superionic conductor Pb0.9Sc0.1F2.1 (10 mol % ScF3) with fluorite type structure (CaF2) in the temperature range 153-410 K have been investigated. The static bulk conductivity σ dc =1.5 × 10-4 S/cm and average hopping frequency ν h = 1.5 × 107 Hz of charge carriers (mobile ions F-) at room temperature (293 K) have been defined from the σ dc (ν) experimental curves. Enthalpies of thermoactivated processes of ionic conductivity σ dc ( T) (Δ H σ = 0.393 ± 0.005 eV) and dielectric relaxation ν h ( T) (Δ H h = 0.37 ± 0.03 eV) coincide within their errors. A crystal-physical model of fluorine-ion transport in a Pb0.9Sc0.1F2.1 crystal lattice has been proposed. The characteristic parameters of charge carriers have been calculated: concentration n mob = 2.0 × 1021 cm-3, the distance of the hopping d ≈ 0.5 nm and mobility μmob = 4.5 × 10-7 cm2/s V (293 K).

Macroscopic and bulk-controlled elastic modes in an interaction of interstitial alcali metal cations within a face-centered cubic crystalline fullerine

NASA Technical Reports Server (NTRS)

Tatarenko, Valentine A.; Tsysman, Constantin L.; Oltarzhevskaya, Yelena T.

1995-01-01

The calculations in a majority of previous works for the fulleride (AqC-60) crystals were performed within the framework of the rigid-lattice model, neglecting the distortion relaxation of the host fullerene (C-60) crystal caused by the interstitial alkali-metal (A) cations. However, an each cation is a source of a static distortion field, and the resulting field is a superposition of such fields generated by all cations. This is a reason why the host-crystal distortions depend on the A-cations configurations, i.e. on a type of a spatial bulk distribution of interstitial cations. The given paper seeks to find a functional relation between the amplitudes of the doping-induced structure-distortion waves and of static concentration ones. A semiphenomenological model is constructed here within the scope of statistical-thermodynamic treatment and using the lattice-statistics simulation method(*). In this model the effects due to the presence of q solute A cations over available interstices (per unit cell) on the static inherent reorientation and/or displacements of the solvent molecules from the 'average-lattice' sites' as well as on the lattice parameter a of a elastically-anysotropic 'cubic' C-60 crystal are taken into account.

The Question of Impurities in Macromolecule Crystal Quality Improvement in Microgravity

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.; Pusey, Marc L.; Sportiello, Michael G.; Todd, Paul; Bellamy, Henry; Borgstahl, Gloria E.; Pokros, Matthew; Cassanto, John M.

2000-01-01

While macromolecule impurities may affect crystal size and morphology the over-riding question is how do macromolecule impurities effect crystal X-ray quality and diffraction resolution. In the case of chicken egg white lysozyme previous researchers have reported that crystals grown in the presence of ovalbumin, ovotransferrin, and turkey egg white lysozyme show no difference in diffraction resolution compared to those grown in pure solutions. One impurity however, a naturally occurring lysozyme dimer, does negatively impact the X-ray crystal properties. For this impurity it has been reported that crystal quality improvement in microgravity may be due to improved impurity partitioning during crystallization. In this study we have examined the incorporation of the dimer into lysozyme crystals, both on the ground and in microgravity experiments, and have performed detailed X-ray analysis of the crystals using a new technique for finely probing the mosaicity of the crystal at the Stanford Synchrotron Radiation Laboratory. Dimer partitioning was not significantly different in microgravity compared to the ground based experiments, although it is significantly better than that previously reported in microgravity. Mosaicity analysis of pure crystals, 1422 indexed reflections (microgravity) and 752 indexed reflections (ground), gave average results of 0.0066 and 0.0092 degrees (FWHM) respectively. The microgravity crystals also provided an increased signal to noise. Dimer incorporation increased the average mosaicity in microgravity but not on the ground. However, dimer incorporation did greatly reduce the resolution limit in both ground and microgravity grown crystals. The data is being treated anisotropically to explore these effects. These results indicate that impurity effects in microgravity are complex and that the conditions or techniques employed may greatly affect the role of impurities.

In-situ study on growth units of Ba2Mg(B3O6)2 crystal

NASA Astrophysics Data System (ADS)

Lv, X. S.; Sun, Y. L.; Tang, X. L.; Wan, S. M.; Zhang, Q. L.; You, J. L.; Yin, S. T.

2013-05-01

BMBO (Ba2Mg(B3O6)2 crystal) is an excellent birefringent crystal and a potential stimulated Raman scattering (SRS) crystal. In this paper, high temperature Raman spectroscopy was used to in-situ study the melt structure near a BMBO crystal-melt interface. [B3O6]3- groups were found in this region. The result reveals that both of BaO bonds and MgO bonds are the weak bonds in the BMBO crystal structure. During the melting process, the crystal structure broke into Ba2+ ions, Mg2+ ions and [B3O6]3- groups. Our experimental results confirmed that the well-developed faces of BMBO crystals are the (001), (101) and (012) faces. Based on attachment energy theory, the crystal growth habit was discussed. The (001) (101) and (012) crystal faces linked by the weak BaO bonds and MgO bonds have smaller attachment energies and slower growth rates, and thus present in the final morphology. The (012) crystal face has a multi-terrace structure, which suggests that BMBO crystal grows with a layer-by-layer mode.

Influence of GTP/GDP and magnesium ion on the solvated structure of the protein FtsZ: a molecular dynamics study.

PubMed

Jamous, Carla; Basdevant, Nathalie; Ha-Duong, Tap

2014-01-01

We present here a structural analysis of ten extensive all-atom molecular dynamics simulations of the monomeric protein FtsZ in various binding states. Since the polymerization and GTPase activities of FtsZ depend on the nature of a bound nucleotide as well as on the presence of a magnesium ion, we studied the structural differences between the average conformations of the following five systems: FtsZ-Apo, FtsZ-GTP, FtsZ-GDP, FtsZ-GTP-Mg, and FtsZ-GDP-Mg. The in silico solvated average structure of FtsZ-Apo significantly differs from the crystallographic structure 1W59 of FtsZ which was crystallized in a dimeric form without nucleotide and magnesium. The simulated Apo form of the protein also clearly differs from the FtsZ structures when it is bound to its ligand, the most important discrepancies being located in the loops surrounding the nucleotide binding pocket. The three average structures of FtsZ-GTP, FtsZ-GDP, and FtsZ-GTP-Mg are overall similar, except for the loop T7 located at the opposite side of the binding pocket and whose conformation in FtsZ-GDP notably differs from the one in FtsZ-GTP and FtsZ-GTP-Mg. The presence of a magnesium ion in the binding pocket has no impact on the FtsZ conformation when it is bound to GTP. In contrast, when the protein is bound to GDP, the divalent cation causes a translation of the nucleotide outwards the pocket, inducing a significant conformational change of the loop H6-H7 and the top of helix H7.

Elasticity of α-Cristobalite: A Silicon Dioxide with a Negative Poisson's Ratio

NASA Astrophysics Data System (ADS)

Yeganeh-Haeri, Amir; Weidner, Donald J.; Parise, John B.

1992-07-01

Laser Brillouin spectroscopy was used to determine the adiabatic single-crystal elastic stiffness coefficients of silicon dioxide (SiO_2) in the α-cristobalite structure. This SiO_2 polymorph, unlike other silicas and silicates, exhibits a negative Poisson's ratio; α-cristobalite contracts laterally when compressed and expands laterally when stretched. Tensorial analysis of the elastic coefficients shows that Poisson's ratio reaches a maximum value of -0.5 in some directions, whereas averaged values for the single-phased aggregate yield a Poisson's ratio of -0.16.

Cross-Linking Studies of Lysozyme Nucleation

NASA Technical Reports Server (NTRS)

Forsythe, Elizabeth; Pusey, Marc

2000-01-01

Tetragonal chicken egg white crystals consist of 4(sub 3) helices running in alternating directions, the helix rows having a two fold symmetry with each other. The unit cell consists of one complete tetrameric turn from each of two adjacent helices (an octamer). PBC analysis indicates that the helix intermolecular bonds are the strongest in the crystal, therefore likely formed first. AFM analysis of the (110) surface shows only complete helices, no half steps or bisected helices being found, while AFM line scans to measure the growth step increments show that they are multiples of the 4(sub 3) helix tetramer dimensions. This supports our thesis that the growth units are in fact multiples of the four molecule 4(sub 3) helix unit, the "average" growth unit size for the (110) face being an octamer (two turns about the helix) and the (101) growth unit averaging about the size of a hexamer. In an effort to better understand the species involved in the crystal nucleation and growth process, we have initiated an experimental program to study the species formed in solution compared to what is found in the crystal through covalent cross-linking studies. These experiments use the heterobifunctional cross-linking agent aminoethyl-4-azidonitroanaline (AEANA). An aliphatic amine at one end is covalently attached to the protein by a carbodiimide-mediated reaction, and a photo reactive group at the other can be used to initiate crosslinking. Modifications to the parent structure can be used to alter the distance between the two reactive groups and thus the cross-linking agents "reach". In practice, the cross-linking agent is first coupled to the asp101 side chain through the amine group. Asp101 lies within the active site cleft, and previous work with fluorescent probes had shown that derivatives at this site still crystallize in the tetragonal space group. This was also found to be the case with the AEANA derivative, which gave red tetragonal crystals. The protein now has a reactive group that can be photoactivated at a specific point in the nucleation or crystal growth process to "capture" protein molecules bound within reach of the crosslinking agent. If those bound protein molecules have a defined geometric relationship with the capturing molecule, such as would be found in a crystal, then the photoreacted cross-linking site should be consistent. Random protein interactions, typical of an amorphous precipitate or interaction, would show a random cross-linking reaction. The results of these and other experiments will be presented.

OPCPA modeling using YCOB as the non-linear crystal

NASA Astrophysics Data System (ADS)

Pires, Hugo; Cardoso, Luis; Wemans, João; João, Celso; Figueira, Gonçalo

2010-04-01

In this work, we evaluate numerically the performance of the nonlinear crystal yttrium calcium oxyborate (YCOB) as the gain medium in a noncollinear, angularly dispersed beam OPCPA configuration, and compare it to other well-studied crystals. In particular, we study its use in the context of an ultrahigh peak and average power amplifier setup. Possible bandwidths are assessed.

Structural analysis of β-glucosidase mutants derived from a hyperthermophilic tetrameric structure

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Mishima, Yumiko; Maeno, Yuka; Ishikawa, Kazuhiko

2014-01-01

β-Glucosidase from Pyrococcus furiosus (BGLPf) is a hyperthermophilic tetrameric enzyme which can degrade cellooligosaccharides to glucose under hyperthermophilic conditions and thus holds promise for the saccharification of lignocellulosic biomass at high temperature. Prior to the production of large amounts of this enzyme, detailed information regarding the oligomeric structure of the enzyme is required. Several crystals of BGLPf have been prepared over the past ten years, but its crystal structure had not been solved until recently. In 2011, the first crystal structure of BGLPf was solved and a model was constructed at somewhat low resolution (2.35 Å). In order to obtain more detailed structural data on BGLPf, the relationship between its tetrameric structure and the quality of the crystal was re-examined. A dimeric form of BGLPf was constructed and its crystal structure was solved at a resolution of 1.70 Å using protein-engineering methods. Furthermore, using the high-resolution crystal structural data for the dimeric form, a monomeric form of BGLPf was constructed which retained the intrinsic activity of the tetrameric form. The thermostability of BGLPf is affected by its oligomeric structure. Here, the biophysical and biochemical properties of engineered dimeric and monomeric BGLPfs are reported, which are promising prototype models to apply to the saccharification reaction. Furthermore, details regarding the oligomeric structures of BGLPf and the reasons why the mutations yielded improved crystal structures are discussed. PMID:24598756

Multiple solvent crystal structures of ribonuclease A: An assessment of the method

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

The multiple solvent crystal structures (MSCS) method uses organic solvents to map the surfaces of proteins. It identifies binding sites and allows for a more thorough examination of protein plasticity and hydration than could be achieved by a single structure. The crystal structures of bovine pancreatic ribonuclease A (RNAse A) soaked in the following organic solvents are presented: 50% dioxane, 50% dimethylformamide, 70% dimethylsulfoxide, 70% 1,6-hexanediol, 70% isopropanol, 50% R,S,R-bisfuran alcohol, 70% t-butanol, 50% trifluoroethanol, or 1.0M trimethylamine-N-oxide. This set of structures is compared with four sets of crystal structures of RNAse A from the protein data bank (PDB) andmore » with the solution NMR structure to assess the validity of previously untested assumptions associated with MSCS analysis. Plasticity from MSCS is the same as from PDB structures obtained in the same crystal form and deviates only at crystal contacts when compared to structures from a diverse set of crystal environments. Furthermore, there is a good correlation between plasticity as observed by MSCS and the dynamic regions seen by NMR. Conserved water binding sites are identified by MSCS to be those that are conserved in the sets of structures taken from the PDB. Comparison of the MSCS structures with inhibitor-bound crystal structures of RNAse A reveals that the organic solvent molecules identify key interactions made by inhibitor molecules, highlighting ligand binding hot-spots in the active site. The present work firmly establishes the relevance of information obtained by MSCS.« less

A hybrid phononic crystal for roof application.

PubMed

Wan, Qingmian; Shao, Rong

2017-11-01

Phononic crystal is a type of acoustic material, and the study of phononic crystals has attracted great attention from national research institutions. Meanwhile, noise reduction in the low-frequency range has always encountered difficulties and troubles in the engineering field. In order to obtain a unique and effective low-frequency noise reduction method, in this paper a low frequency noise attenuation system based on phononic crystal structure is proposed and demonstrated. The finite element simulation of the band gap is consistent with the final test results. The effects of structure parameters on the band gaps were studied by changing the structure parameters and the band gaps can be controlled by suitably tuning structure parameters. The structure and results provide a good support for phononic crystal structures engineering application.

Crystallized N-terminal domain of influenza virus matrix protein M1 and method of determining and using same

NASA Technical Reports Server (NTRS)

Luo, Ming (Inventor); Sha, Bingdong (Inventor)

2000-01-01

The matrix protein, M1, of influenza virus strain A/PR/8/34 has been purified from virions and crystallized. The crystals consist of a stable fragment (18 Kd) of the M1 protein. X-ray diffraction studies indicated that the crystals have a space group of P3.sub.t 21 or P3.sub.2 21. Vm calculations showed that there are two monomers in an asymmetric unit. A crystallized N-terminal domain of M1, wherein the N-terminal domain of M1 is crystallized such that the three dimensional structure of the crystallized N-terminal domain of M1 can be determined to a resolution of about 2.1 .ANG. or better, and wherein the three dimensional structure of the uncrystallized N-terminal domain of M1 cannot be determined to a resolution of about 2.1 .ANG. or better. A method of purifying M1 and a method of crystallizing M1. A method of using the three-dimensional crystal structure of M1 to screen for antiviral, influenza virus treating or preventing compounds. A method of using the three-dimensional crystal structure of M1 to screen for improved binding to or inhibition of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the manufacture of an inhibitor of influenza virus M1. The use of the three-dimensional crystal structure of the M1 protein of influenza virus in the screening of candidates for inhibition of influenza virus M1.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

NASA Astrophysics Data System (ADS)

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-04-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex.

PubMed

Zhou, X Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Suino-Powell, Kelly M; Boutet, Sébastien; Williams, Garth J; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2016-04-12

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhou, X. Edward; Gao, Xiang; Barty, Anton

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

PubMed Central

Zhou, X. Edward; Gao, Xiang; Barty, Anton; Kang, Yanyong; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Suino-Powell, Kelly M.; Boutet, Sébastien; Williams, Garth J.; Wang, Meitian; Li, Dianfan; Caffrey, Martin; Chapman, Henry N.; Spence, John C.H.; Fromme, Petra; Weierstall, Uwe; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2016-01-01

Serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solved with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes. PMID:27070998

X-ray laser diffraction for structure determination of the rhodopsin-arrestin complex

DOE PAGES

Zhou, X. Edward; Gao, Xiang; Barty, Anton; ...

2016-04-12

Here, serial femtosecond X-ray crystallography (SFX) using an X-ray free electron laser (XFEL) is a recent advancement in structural biology for solving crystal structures of challenging membrane proteins, including G-protein coupled receptors (GPCRs), which often only produce microcrystals. An XFEL delivers highly intense X-ray pulses of femtosecond duration short enough to enable the collection of single diffraction images before significant radiation damage to crystals sets in. Here we report the deposition of the XFEL data and provide further details on crystallization, XFEL data collection and analysis, structure determination, and the validation of the structural model. The rhodopsin-arrestin crystal structure solvedmore » with SFX represents the first near-atomic resolution structure of a GPCR-arrestin complex, provides structural insights into understanding of arrestin-mediated GPCR signaling, and demonstrates the great potential of this SFX-XFEL technology for accelerating crystal structure determination of challenging proteins and protein complexes.« less

Monosodium urate crystal deposition associated with the progress of radiographic grade at the sacroiliac joint in axial SpA: a dual-energy CT study.

PubMed

Zhu, Junqing; Li, Aiwu; Jia, Ertao; Zhou, Yi; Xu, Juan; Chen, Shixian; Huang, Yinger; Xiao, Xiang; Li, Juan

2017-05-02

Previous studies have revealed that ankylosing spondylitis (AS), as the progenitor of axial spondyloarthritis (AxSpA), has been characterized by the insidiously progressive nature of sacroiliitis and spondylitis. Dual-energy computed tomography (DECT) has recently been used to analyse the deposition of monosodium urate (MSU) crystals with higher sensitivity and specificity. However, it remains unclear whether the existence of the MSU crystal deposition detected by DECT at the sacroiliac joint in patients with AxSpA also is associated with the existing structural damage. Here, we performed this study to show the DECT MSU crystal deposits in AxSpA patients without coexisting gout and to ascertain the relationship between the MSU crystal deposition and the structural joint damage of sacroiliac joints. One hundred and eighty-six AxSpA patients without coexisting gout were recruited. The plain radiographs of the sacroiliac joint were obtained, along with the DECT scans at the pelvis and the clinical variables. All statistics based on the left or right sacroiliac joint damage grading (0-4) were calculated independently. Bivariate analysis and ordinal logistic regression was performed between the clinical features and radiographic grades at the sacroiliac joint. At the pelvis, large quantities of MSU crystal deposition were found in patients with AxSpA. The average MSU crystal volume at the left sacroiliac joint, the right sacroiliac joint, and the pelvis were 0.902 ± 1.345, 1.074 ± 1.878, and 5.272 ± 9.044 cm 3 , values which were correlated with serum uric acid concentrations (r = 0.727, 0.740, 0.896; p < 0.001). In bivariate analysis, wide clinical variables were associated with the changes in sacroiliac joint damage. Further, the AxSpA duration, BASFI score, and the volume of MSU crystal at both sides of sacroiliac joint were associated with the progress of radiographic grade at the sacroiliac joints in the ordinal logistic models (left AOR = 1.180, 3.800, 1.920; right AOR = 1.190, 3.034, 1.418; p < 0.01). Large quantities of MSU crystal deposition detected by DECT were found at the pelvis in AxSpA patients without coexisting gout. In addition to AxSpA duration and BASFI score, the MSU crystal deposition at the sacroiliac joint is associated with the progress of radiographic grade at sacroiliac joints in those patients.

Statistical Analysis of Crystallization Database Links Protein Physico-Chemical Features with Crystallization Mechanisms

PubMed Central

Fusco, Diana; Barnum, Timothy J.; Bruno, Andrew E.; Luft, Joseph R.; Snell, Edward H.; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis. PMID:24988076

Statistical analysis of crystallization database links protein physico-chemical features with crystallization mechanisms.

PubMed

Fusco, Diana; Barnum, Timothy J; Bruno, Andrew E; Luft, Joseph R; Snell, Edward H; Mukherjee, Sayan; Charbonneau, Patrick

2014-01-01

X-ray crystallography is the predominant method for obtaining atomic-scale information about biological macromolecules. Despite the success of the technique, obtaining well diffracting crystals still critically limits going from protein to structure. In practice, the crystallization process proceeds through knowledge-informed empiricism. Better physico-chemical understanding remains elusive because of the large number of variables involved, hence little guidance is available to systematically identify solution conditions that promote crystallization. To help determine relationships between macromolecular properties and their crystallization propensity, we have trained statistical models on samples for 182 proteins supplied by the Northeast Structural Genomics consortium. Gaussian processes, which capture trends beyond the reach of linear statistical models, distinguish between two main physico-chemical mechanisms driving crystallization. One is characterized by low levels of side chain entropy and has been extensively reported in the literature. The other identifies specific electrostatic interactions not previously described in the crystallization context. Because evidence for two distinct mechanisms can be gleaned both from crystal contacts and from solution conditions leading to successful crystallization, the model offers future avenues for optimizing crystallization screens based on partial structural information. The availability of crystallization data coupled with structural outcomes analyzed through state-of-the-art statistical models may thus guide macromolecular crystallization toward a more rational basis.

Eukaryotic major facilitator superfamily transporter modeling based on the prokaryotic GlpT crystal structure.

PubMed

Lemieux, M Joanne

2007-01-01

The major facilitator superfamily (MFS) of transporters represents the largest family of secondary active transporters and has a diverse range of substrates. With structural information for four MFS transporters, we can see a strong structural commonality suggesting, as predicted, a common architecture for MFS transporters. The rate for crystal structure determination of MFS transporters is slow, making modeling of both prokaryotic and eukaryotic transporters more enticing. In this review, models of eukaryotic transporters Glut1, G6PT, OCT1, OCT2 and Pho84, based on the crystal structures of the prokaryotic GlpT, based on the crystal structure of LacY are discussed. The techniques used to generate the different models are compared. In addition, the validity of these models and the strategy of using prokaryotic crystal structures to model eukaryotic proteins are discussed. For comparison, E. coli GlpT was modeled based on the E. coli LacY structure and compared to the crystal structure of GlpT demonstrating that experimental evidence is essential for accurate modeling of membrane proteins.

High chloride content calcium silicate glasses.

PubMed

Chen, Xiaojing; Karpukhina, Natalia; Brauer, Delia S; Hill, Robert G

2017-03-08

Chloride is known to volatilize from silicate glass melts and until now, only a limited number of studies on oxychloride silicate glasses have been reported. In this paper we have synthesized silicate glasses that retain large amounts of CaCl 2 . The CaCl 2 has been added to the calcium metasilicate composition (CaO·SiO 2 ). Glasses were produced via a melt quench route and an average of 70% of the chloride was retained after melting. Up to 31.6 mol% CaCl 2 has been successfully incorporated into these silicate glasses without the occurrence of crystallization. 29 Si MAS-NMR spectra showed the silicon being present mainly as a Q 2 silicate species. This suggests that chloride formed Cl-Ca(n) species, rather than Si-Cl bonds. Upon increasing the CaCl 2 content, the T g reduced markedly from 782 °C to 370 °C. Glass density and glass crystallization temperature decreased linearly with an increase in the CaCl 2 content. However, both linear regressions revealed a breakpoint at a CaCl 2 content just below 20 mol%. This might be attributed to a significant change in the structure and is also correlated with the nature of the crystallizing phases formed upon heat treatment. The glasses with less than 19.2 mol% CaCl 2 crystallized to wollastonite, whilst the compositions with CaCl 2 content equal to or greater than 19.2 mol% are thought to crystallize to CaCl 2 . In practice, the crystallization of CaCl 2 could not occur until the crystallization temperature fell below the melting point of CaCl 2 . The implications of the results along with the high chloride retention are discussed.

The use of small-molecule structures to complement protein–ligand crystal structures in drug discovery

PubMed Central

Cole, Jason C.

2017-01-01

Many ligand-discovery stories tell of the use of structures of protein–ligand complexes, but the contribution of structural chemistry is such a core part of finding and improving ligands that it is often overlooked. More than 800 000 crystal structures are available to the community through the Cambridge Structural Database (CSD). Individually, these structures can be of tremendous value and the collection of crystal structures is even more helpful. This article provides examples of how small-molecule crystal structures have been used to complement those of protein–ligand complexes to address challenges ranging from affinity, selectivity and bioavailability though to solubility. PMID:28291759

Kinetic Control of Aqueous Hydrolysis: Modulating Structure/Property Relationships in Inorganic Crystals

NASA Astrophysics Data System (ADS)

Neilson, James R.

2011-12-01

A grand challenge in materials science and chemistry revolves around the preparation of materials with desired properties by controlling structure on multiple length scales. Biology approaches this challenge by evolving tactics to transform soluble precursors into materials and composites with macro-scale and atomic precision. Studies of biomineralization in siliceous sponges led to the discovery of slow, catalytic hydrolysis of molecular precursors in the biogenesis of silica skeletal elements with well defined micro- and nano-scale architectures. However, the role of aqueous hydrolysis in the limit of kinetic control is not well understood; this allows us to form a central hypothesis: that the kinetics of hydrolysis modulate the structures of materials and their properties. As a model system, the diffusion of a simple hydrolytic catalyst (such as ammonia) across an air-water interface into a metal salt solution reproduces some aspects of the chemistry found in biomineralization, namely kinetic and vectorial control. Variation of the catalyst concentration modulates the hydrolysis rate, and thus alters the resulting structure of the inorganic crystals. Using aqueous solutions of cobalt(II) chloride, each product (cobalt hydroxide chloride) forms with a unique composition, despite being prepared from identical mother liquors. Synchrotron X-ray total scattering methods are needed to locate the atomic positions in the material, which are not aptly described by a traditional crystallographic unit cell due to structural disorder. Detailed definition of the structure confirms that the hydrolysis conditions systematically modulate the arrangement of atoms in the lattice. This tightly coupled control of crystal formation and knowledge of local and average structures of these materials provides insight into the unusual magnetic properties of these cobalt hydroxides. The compounds studied show significant and open magnetization loops with little variation with composition or structure, yet subtle and systematic changes in the mean-field spin interaction strength and spin entropy loss. Meanwhile, neutron powder diffraction reveals a fully compensated Ńeel state; a detailed analysis of the local structure defines the aperiodic clusters of polyhedra responsible for magnetic order. The rate of hydrolysis of metal precursors modulates the disposition of these polyhedral clusters. The strategy of kinetically controlling aqueous hydrolysis also extends to the formation of stoichiometrically ordered bimetallic crystals [MSn(OH)6], where the hydrolysis behavior for dissimilar metal cations must be controlled via counteranions or precursor selection. In the formation of these ordered double perovskite hydroxides, the rate of hydrolysis is held constant in the limit of kinetic control. Instead, the propensities of different cations to undergo controlled hydrolysis are probed by their ability to form ordered crystals. Collectively, these studies demonstrate how systematic variation in the kinetic conditions of materials preparation and the character of each solute control the structure and properties of materials, with a precision not attainable through traditional or near-equilibrium approaches.

Transition from Irradiation-Induced Amorphization to Crystallization in Nanocrystalline Silicon Carbide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jiang, Weilin; Jiao, Liang; Wang, Haiyan

2011-12-01

Response to irradiation of nanocrystalline 3C-SiC is studied using 2 MeV Au+ ions near the critical temperature for amorphization and is compared to the behavior of its monocrystalline counterpart under the identical irradiation conditions. The irradiated samples have been characterized using in-situ ion channeling, ex-situ x-ray diffraction, and helium ion microscopy. Compared to monocrystalline 3C-SiC, a faster amorphization process in the nanocrystalline material (average grain size = 3.3 nm) is observed at 500 K. However, the nanograin grows with increasing ion fluence at 550 K and the grain size tends to saturate at high fluences. The striking contrast demonstrates amore » sharp transition from irradiation-induced interface-driven amorphization at 500 K to crystallization at 550 K. The results could show potential impacts of nanocrystalline SiC on nuclear fuel cladding and structural components of next-generation nuclear energy systems.« less

Efficient laser emission from cladding waveguide inscribed in Nd:GdVO(4) crystal by direct femtosecond laser writing.

PubMed

Liu, Hongliang; Tan, Yang; Vázquez de Aldana, Javier R; Chen, Feng

2014-08-01

We report on the fabrication of depressed cladding waveguides in Nd:GdVO(4) laser crystal by using femtosecond laser inscription. The cross section of the structure is a circular shape with a diameter of 150 μm. Under the optical pump at 808 nm, the continuous wave (cw) as well as pulsed (Q-switched by graphene saturable absorber) waveguide lasing at 1064 nm has been realized, supporting guidance of both TE and TM polarizations. The maximum output power of 0.57 W was obtained in the cw regime, while the maximum pulse energy of the pulsed laser emissions was up to 19 nJ (corresponding to a maximum average output power of 0.33 W, at a resonant frequency of 18 MHz). The slope efficiencies achieved for the cw and pulsed Nd:GdVO(4) waveguide lasers were as high as 68% and 52%, respectively.

Research on spectrum broadening covering visible light of a fiber femtosecond optical frequency comb for absolute frequency measurement

NASA Astrophysics Data System (ADS)

Xing, Shuai; Wu, Tengfei; Li, Shuyi; Xia, Chuanqing; Han, Jibo; Zhang, Lei; Zhao, Chunbo

2018-03-01

As a bridge connecting microwave frequency and optical frequency, femtosecond laser has important significance in optical frequency measurement. Compared with the traditional Ti-sapphire femtosecond optical frequency comb, with the advantages of compact structure, strong anti-interference ability and low cost, the fiber femtosecond optical frequency comb has a wider application prospect. An experiment of spectrum broadening in a highly nonlinear photonic crystal fiber pumped by an Er-fiber mode-locked femtosecond laser is studied in this paper. Based on optical amplification and frequency doubling, the central wavelength of the output spectrum is 780nm and the average power is 232mW. With the femtosecond pulses coupled into two different photonic crystal fibers, the coverage of visible spectrum is up to 500nm-960nm. The spectral shape and width can be optimized by changing the polarization state for satisfying the requirments of different optical frequencies measurement.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Preston, Daniel N; Peterson, Paul D; Kien - Yin, Lee

Structural damage in energetic materials plays a significant role in the probability of nonshock initiation events. Damage may occur in the form of voids or cracks either within crystals or in binder-rich regions between crystals. These cracks affect whether hotspots generated by impact will quench or propagate under non-shock insult. For this study, we have separately engineered intracrystalline and inter-crystalline cracks in to the HMX-based PBX 9501. Intra-crystalline cracks were created by subjecting HMX to forward and reverse solid-to-solid phase transformations prior to formulation. Inter-crystalline cracks were induced by compressing formulated samples of PBX 9501 at an average strain ratemore » of 0.00285 S{sup -1}. Both sets of pre-damaged explosives were then impact tested using the LANL Type 12 Drop Weight-Impact Machine and their sensitivities compared to nondamaged PBX 9501. Results of these tests clearly show significant differences in sensitivity between damaged and non-damaged PBX 9501.« less

Why don't we find more polymorphs?

PubMed

Price, Sarah L

2013-08-01

Crystal structure prediction (CSP) studies are not limited to being a search for the most thermodynamically stable crystal structure, but play a valuable role in understanding polymorphism, as shown by interdisciplinary studies where the crystal energy landscape has been explored experimentally and computationally. CSP usually produces more thermodynamically plausible crystal structures than known polymorphs. This article illustrates some reasons why: because (i) of approximations in the calculations, particularly the neglect of thermal effects (see §1.1); (ii) of the molecular rearrangement during nucleation and growth (see §1.2); (iii) the solid-state structures observed show dynamic or static disorder, stacking faults, other defects or are not crystalline and so represent more than one calculated structure (see §1.3); (iv) the structures are metastable relative to other molecular compositions (see §1.4); (v) the right crystallization experiment has not yet been performed (see §1.5) or (vi) cannot be performed (see §1.6) and the possibility (vii) that the polymorphs are not detected or structurally characterized (see §1.7). Thus, we can only aspire to a general predictive theory for polymorphism, as this appears to require a quantitative understanding of the kinetic factors involved in all possible multi-component crystallizations. For a specific molecule, analysis of the crystal energy landscape shows the potential complexity of its crystallization behaviour.

Fully automatic characterization and data collection from crystals of biological macromolecules

DOE Office of Scientific and Technical Information (OSTI.GOV)

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to themore » optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.« less

Hydrogen-bond coordination in organic crystal structures: statistics, predictions and applications.

PubMed

Galek, Peter T A; Chisholm, James A; Pidcock, Elna; Wood, Peter A

2014-02-01

Statistical models to predict the number of hydrogen bonds that might be formed by any donor or acceptor atom in a crystal structure have been derived using organic structures in the Cambridge Structural Database. This hydrogen-bond coordination behaviour has been uniquely defined for more than 70 unique atom types, and has led to the development of a methodology to construct hypothetical hydrogen-bond arrangements. Comparing the constructed hydrogen-bond arrangements with known crystal structures shows promise in the assessment of structural stability, and some initial examples of industrially relevant polymorphs, co-crystals and hydrates are described.

X-ray transparent microfluidic chip for mesophase-based crystallization of membrane proteins and on-chip structure determination

DOE PAGES

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.; ...

2014-08-21

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. In addition, we validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

X-ray Transparent Microfluidic Chip for Mesophase-Based Crystallization of Membrane Proteins and On-Chip Structure Determination

DOE Office of Scientific and Technical Information (OSTI.GOV)

Khvostichenko, Daria S.; Schieferstein, Jeremy M.; Pawate, Ashtamurthy S.

2014-10-01

Crystallization from lipidic mesophase matrices is a promising route to diffraction-quality crystals and structures of membrane proteins. The microfluidic approach reported here eliminates two bottlenecks of the standard mesophase-based crystallization protocols: (i) manual preparation of viscous mesophases and (ii) manual harvesting of often small and fragile protein crystals. In the approach reported here, protein-loaded mesophases are formulated in an X-ray transparent microfluidic chip using only 60 nL of the protein solution per crystallization trial. The X-ray transparency of the chip enables diffraction data collection from multiple crystals residing in microfluidic wells, eliminating the normally required manual harvesting and mounting ofmore » individual crystals. We validated our approach by on-chip crystallization of photosynthetic reaction center, a membrane protein from Rhodobacter sphaeroides, followed by solving its structure to a resolution of 2.5 Å using X-ray diffraction data collected on-chip under ambient conditions. A moderate conformational change in hydrophilic chains of the protein was observed when comparing the on-chip, room temperature structure with known structures for which data were acquired under cryogenic conditions.« less

Toward Fully in Silico Melting Point Prediction Using Molecular Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhang, Y; Maginn, EJ

2013-03-01

Melting point is one of the most fundamental and practically important properties of a compound. Molecular computation of melting points. However, all of these methods simulation methods have been developed for the accurate need an experimental crystal structure as input, which means that such calculations are not really predictive since the melting point can be measured easily in experiments once a crystal structure is known. On the other hand, crystal structure prediction (CSP) has become an active field and significant progress has been made, although challenges still exist. One of the main challenges is the existence of many crystal structuresmore » (polymorphs) that are very close in energy. Thermal effects and kinetic factors make the situation even more complicated, such that it is still not trivial to predict experimental crystal structures. In this work, we exploit the fact that free energy differences are often small between crystal structures. We show that accurate melting point predictions can be made by using a reasonable crystal structure from CSP as a starting point for a free energy-based melting point calculation. The key is that most crystal structures predicted by CSP have free energies that are close to that of the experimental structure. The proposed method was tested on two rigid molecules and the results suggest that a fully in silico melting point prediction method is possible.« less

Integrative interactive visualization of crystal structure, band structure, and Brillouin zone

NASA Astrophysics Data System (ADS)

Hanson, Robert; Hinke, Ben; van Koevering, Matthew; Oses, Corey; Toher, Cormac; Hicks, David; Gossett, Eric; Plata Ramos, Jose; Curtarolo, Stefano; Aflow Collaboration

The AFLOW library is an open-access database for high throughput ab-initio calculations that serves as a resource for the dissemination of computational results in the area of materials science. Our project aims to create an interactive web-based visualization of any structure in the AFLOW database that has associate band structure data in a way that allows novel simultaneous exploration of the crystal structure, band structure, and Brillouin zone. Interactivity is obtained using two synchronized JSmol implementations, one for the crystal structure and one for the Brillouin zone, along with a D3-based band-structure diagram produced on the fly from data obtained from the AFLOW database. The current website portal (http://aflowlib.mems.duke.edu/users/jmolers/matt/website) allows interactive access and visualization of crystal structure, Brillouin zone and band structure for more than 55,000 inorganic crystal structures. This work was supported by the US Navy Office of Naval Research through a Broad Area Announcement administered by Duke University.

Sixty years from discovery to solution: crystal structure of bovine liver catalase form III

DOE Office of Scientific and Technical Information (OSTI.GOV)

Foroughi, Leila M.; Kang, You-Na; Matzger, Adam J.

2012-03-27

The crystallization and structural characterization of bovine liver catalase (BLC) has been intensively studied for decades. Forms I and II of BLC have previously been fully characterized using single-crystal X-ray diffraction. Form III has previously been analyzed by electron microscopy, but owing to the thinness of this crystal form an X-ray crystal structure had not been determined. Here, the crystal structure of form III of BLC is presented in space group P212121, with unit-cell parameters a = 68.7, b = 173.7, c = 186.3 {angstrom}. The asymmetric unit is composed of the biological tetramer, which is packed in a tetrahedronmore » motif with three other BLC tetramers. This higher resolution structure has allowed an assessment of the previously published electron-microscopy studies.« less

Aqueous trifluorethanol solutions simulate the environment of DNA in the crystalline state.

PubMed

Kypr, J; Chládková, J; Zimulová, M; Vorlícková, M

1999-09-01

We took 28 fragments of DNA whose crystal structures were known and used CD spectroscopy to search for conditions stabilising the crystal structures in solution. All 28 fragments switched into their crystal structures in 60-80% aqueous trifluorethanol (TFE) to indicate that the crystals affected the conformation of DNA like the concentrated TFE. The fragments crystallising in the B-form also underwent cooperative TFE-induced changes that took place within the wide family of B-form structures, suggesting that the aqueous and crystal B-forms differed as well. Spermine and magnesium or calcium cations, which were contained in the crystallisation buffers, promoted or suppressed the TFE-induced changes of several fragments to indicate that the crystallisation agents can decide which of the possible structures is adopted by the DNA fragment in the crystal.

Low pH overrides the need of calcium ions for the shape-function relationship of calmodulin: resolving prevailing debates.

PubMed

Pandey, Kalpana; Dhoke, Reema R; Rathore, Yogendra Singh; Nath, Samir K; Verma, Neha; Bawa, Simranjot; Ashish

2014-05-15

Calmodulin (CaM) regulates numerous cellular functions by sensing Ca(2+) levels inside cells. Although its structure as a function of the Ca(2+)-bound state remains hotly debated, no report is available on how pH independently or in interaction with Ca(2+) ions regulates shape and function of CaM. From SAXS data analysis of CaM at different levels of Ca(2+)-ion concentration and buffer pH, we found that (1) CaM molecules possess a Gaussian-chain-like shape in solution even in the presence of Ca(2+) ion or at low pH, (2) the global shape of apo CaM is very similar to its NMR structure rather than the crystal structures, (3) about 16 Ca(2+) ions or more are required per CaM molecule in solution to achieve the four-Ca(2+)-bound crystal structure, (4) low pH alone can impart shape changes in CaM similar to Ca(2+) ions, and (5) at different [Ca(2+)]/[CaM] ratio or pH values, the predominant shape of CaM is essentially a weighted average of its apo and fully activated shape. Results were further substantiated by analysis of sedimentation coefficient values from analytical ultracentrifugation and peptide binding assays using two peptides, each known to preferentially bind the apo or the Ca(2+)-activated state.

Self-powdering and nonlinear optical domain structures in ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals formed in glass

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tsukada, Y.; Honma, T.; Komatsu, T., E-mail: komatsu@mst.nagaokaut.ac.j

Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3}, (GMO), crystals are formed through the crystallization of 21.25Gd{sub 2}O{sub 3}-63.75MoO{sub 3}-15B{sub 2}O{sub 3} glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 {mu}m spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called 'self-powdering phenomenon during crystallization' in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and amore » spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO{sub 4}){sup 2-} tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals. - Graphical abstract: This figure shows the polarized optical photograph at room temperature for a particle (piece) obtained by a heat treatment of the glass at 590 deg. C for 2 h in an electric furnace in air. This particle was obtained through the self-powdering behavior in the crystallization of glass. The periodic domain structure is observed. Ferroelastic beta'-Gd{sub 2}(MoO{sub 4}){sub 3} crystals are formed in the particle, and second harmonic generations are detected, depending on the domain structure.« less

Macromolecular Crystallization in Microgravity

NASA Technical Reports Server (NTRS)

Snell, Edward H.; Helliwell, John R.

2004-01-01

The key concepts that attracted crystal growers, macromolecular or solid state, to microgravity research is that density difference fluid flows and sedimentation of the growing crystals are greatly reduced. Thus, defects and flaws in the crystals can be reduced, even eliminated, and crystal volume can be increased. Macromolecular crystallography differs from the field of crystalline semiconductors. For the latter, crystals are harnessed for their electrical behaviors. A crystal of a biological macromolecule is used instead for diffraction experiments (X-ray or neutron) to determine the three-dimensional structure of the macromolecule. The better the internal order of the crystal of a biological macromolecule then the more molecular structure detail that can be extracted. This structural information that enables an understanding of how the molecule functions. This knowledge is changing the biological and chemical sciences with major potential in understanding disease pathologies. Macromolecular structural crystallography in general is a remarkable field where physics, biology, chemistry, and mathematics meet to enable insight to the basic fundamentals of life. In this review, we examine the use of microgravity as an environment to grow macromolecular crystals. We describe the crystallization procedures used on the ground, how the resulting crystals are studied and the knowledge obtained from those crystals. We address the features desired in an ordered crystal and the techniques used to evaluate those features in detail. We then introduce the microgravity environment, the techniques to access that environment, and the theory and evidence behind the use of microgravity for crystallization experiments. We describe how ground-based laboratory techniques have been adapted to microgravity flights and look at some of the methods used to analyze the resulting data. Several case studies illustrate the physical crystal quality improvements and the macromolecular structural advances. Finally, limitations and alternatives to microgravity and future directions for this research are covered.

Feasibility of one-shot-per-crystal structure determination using Laue diffraction

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cornaby, Sterling; CHESS; Szebenyi, Doletha M. E.

Structure determination was successfully carried out using single Laue exposures from a group of lysozyme crystals. The Laue method may be a viable option for collection of one-shot-per-crystal data from microcrystals. Crystal size is an important factor in determining the number of diffraction patterns which may be obtained from a protein crystal before severe radiation damage sets in. As crystal dimensions decrease this number is reduced, eventually falling to one, at which point a complete data set must be assembled using data from multiple crystals. When only a single exposure is to be collected from each crystal, the polychromatic Lauemore » technique may be preferable to monochromatic methods owing to its simultaneous recording of a large number of fully recorded reflections per image. To assess the feasibility of solving structures using single Laue images from multiple crystals, data were collected using a ‘pink’ beam at the CHESS D1 station from groups of lysozyme crystals with dimensions of the order of 20–30 µm mounted on MicroMesh grids. Single-shot Laue data were used for structure determination by molecular replacement and correct solutions were obtained even when as few as five crystals were used.« less

Construction of crystal structure prototype database: methods and applications.

PubMed

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-26

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Construction of crystal structure prototype database: methods and applications

NASA Astrophysics Data System (ADS)

Su, Chuanxun; Lv, Jian; Li, Quan; Wang, Hui; Zhang, Lijun; Wang, Yanchao; Ma, Yanming

2017-04-01

Crystal structure prototype data have become a useful source of information for materials discovery in the fields of crystallography, chemistry, physics, and materials science. This work reports the development of a robust and efficient method for assessing the similarity of structures on the basis of their interatomic distances. Using this method, we proposed a simple and unambiguous definition of crystal structure prototype based on hierarchical clustering theory, and constructed the crystal structure prototype database (CSPD) by filtering the known crystallographic structures in a database. With similar method, a program structure prototype analysis package (SPAP) was developed to remove similar structures in CALYPSO prediction results and extract predicted low energy structures for a separate theoretical structure database. A series of statistics describing the distribution of crystal structure prototypes in the CSPD was compiled to provide an important insight for structure prediction and high-throughput calculations. Illustrative examples of the application of the proposed database are given, including the generation of initial structures for structure prediction and determination of the prototype structure in databases. These examples demonstrate the CSPD to be a generally applicable and useful tool for materials discovery.

Aqueous cholesteric liquid crystals using uncharged rodlike polypeptides. Polypeptide vesicles by conformation-specific assembly. Ordered chiral macroporous hybrid silica-polypeptide composites

NASA Astrophysics Data System (ADS)

Bellomo, Enrico Giuseppe

2005-07-01

Aqueous cholesteric liquid crystals using uncharged rodlike polypeptides . The aqueous, lyotropic liquid-crystalline phase behavior of an alpha helical polypeptide, has been studied using optical microscopy and X-ray scattering. Solutions of optically pure polypeptide were found to form cholesteric liquid crystals at volume fractions that decreased with increasing average chain length. At very high volume fractions, the formation of a hexagonal mesophase was observed. The pitch of the cholesteric phase could be varied by a mixture of enantiomeric samples, where the pitch increased as the mixture approached equimolar. The cholesteric phases could be untwisted, using either magnetic field or shear flow, into nematic phases, which relaxed into cholesterics upon removal of field or shear. We have found that the phase diagram of this polypeptide in aqueous solution parallels that of poly(gamma-benzyl glutamate) in organic solvents, thus providing a useful system for liquid-crystal applications requiring water as solvent. Polypeptide vesicles by conformation-specific assembly. We have found that block copolymers composed of polypeptide segments provide significant advantages in controlling both the function and supramolecular structure of bioinspired self-assemblies. Incorporation of the stable chain conformations found in proteins into block copolymers was found to provide an additional element of control, beyond amphiphilicity and composition that defines self-assembled architecture. The abundance of functionality present in amino acids, and the ease by which they can be incorporated into these materials, also provides a powerful mechanism to impart block copolypeptides with function. This combination of structure and function work synergistically to enable significant advantages in the preparation of therapeutic agents as well as provide insight into design of self-assemblies beginning to approach the complexity of natural structures such as virus capsids. Ordered chiral macroporous hybrid silica-polypeptide composites. The mineralization of organic templates has been investigated as an effective way to control the size and structure of inorganic frameworks. Hybrid structures incorporating polypeptide with silica have been prepared and characterized using X-ray scattering, TGA, SEM and TEM. The results support the interaction between silica and polymer to form ordered chiral macroporous structures that can be easily controlled by polymer molecular weight and volume fraction.

High-resolution crystal structure of copper amine oxidase from Arthrobacter globiformis: assignment of bound diatomic molecules as O2.

PubMed

Murakawa, Takeshi; Hayashi, Hideyuki; Sunami, Tomoko; Kurihara, Kazuo; Tamada, Taro; Kuroki, Ryota; Suzuki, Mamoru; Tanizawa, Katsuyuki; Okajima, Toshihide

2013-12-01

The crystal structure of a copper amine oxidase from Arthrobacter globiformis was determined at 1.08 Å resolution with the use of low-molecular-weight polyethylene glycol (LMW PEG; average molecular weight ∼200) as a cryoprotectant. The final crystallographic R factor and Rfree were 13.0 and 15.0%, respectively. Several molecules of LMW PEG were found to occupy cavities in the protein interior, including the active site, which resulted in a marked reduction in the overall B factor and consequently led to a subatomic resolution structure for a relatively large protein with a monomer molecular weight of ∼70,000. About 40% of the presumed H atoms were observed as clear electron densities in the Fo - Fc difference map. Multiple minor conformers were also identified for many residues. Anisotropic displacement fluctuations were evaluated in the active site, which contains a post-translationally derived quinone cofactor and a Cu atom. Furthermore, diatomic molecules, most likely to be molecular oxygen, are bound to the protein, one of which is located in a region that had previously been proposed as an entry route for the dioxygen substrate from the central cavity of the dimer interface to the active site.

Morphology and current-voltage characteristics of nanostructured pentacene thin films probed by atomic force microscopy.

PubMed

Zorba, S; Le, Q T; Watkins, N J; Yan, L; Gao, Y

2001-09-01

Atomic force microscopy was used to study the growth modes (on SiO2, MoS2, and Au substrates) and the current-voltage (I-V) characteristics of organic semiconductor pentacene. Pentacene films grow on SiO2 substrate in a layer-by-layer manner with full coverage at an average thickness of 20 A and have the highest degree of molecular ordering with large dendritic grains among the pentacene films deposited on the three different substrates. Films grown on MoS2 substrate reveal two different growth modes, snowflake-like growth and granular growth, both of which seem to compete with each other. On the other hand, films deposited on Au substrate show granular structure for thinner coverages (no crystal structure) and dendritic growth for higher coverages (crystal structure). I-V measurements were performed with a platinum tip on a pentacene film deposited on a Au substrate. The I-V curves on pentacene film reveal symmetric tunneling type character. The field dependence of the current indicates that the main transport mechanism at high field intensities is hopping (Poole-Frenkel effect). From these measurements, we have estimated a field lowering coefficient of 9.77 x 10(-6) V-1/2 m1/2 and an ideality factor of 18 for pentacene.

Fabrication and Probabilistic Fracture Strength Prediction of High-Aspect-Ratio Single Crystal Silicon Carbide Microspecimens With Stress Concentration

NASA Technical Reports Server (NTRS)

Nemeth, Noel N.; Evans, Laura J.; Jadaan, Osama M.; Sharpe, William N., Jr.; Beheim, Glenn M.; Trapp, Mark A.

2005-01-01

Single crystal silicon carbide micro-sized tensile specimens were fabricated with deep reactive ion etching (DRIE) in order to investigate the effect of stress concentration on the room-temperature fracture strength. The fracture strength was defined as the level of stress at the highest stressed location in the structure at the instant of specimen rupture. Specimens with an elliptical hole, a circular hole, and without a hole (and hence with no stress concentration) were made. The average fracture strength of specimens with a higher stress concentration was larger than the average fracture strength of specimens with a lower stress concentration. Average strength of elliptical-hole, circular-hole, and without-hole specimens was 1.53, 1.26, and 0.66 GPa, respectively. Significant scatter in strength was observed with the Weibull modulus ranging between 2 and 6. No fractographic examination was performed but it was assumed that the strength controlling flaws originated from etching grooves along the specimen side-walls. The increase of observed fracture strength with increasing stress concentration was compared to predictions made with the Weibull stress-integral formulation by using the NASA CARES/Life code. In the analysis isotropic material and fracture behavior was assumed - hence it was not a completely rigorous analysis. However, even with these assumptions good correlation was achieved for the circular-hole specimen data when using the specimen data without stress concentration as a baseline. Strength was over predicted for the elliptical-hole specimen data. Significant specimen-to-specimen dimensional variation existed in the elliptical-hole specimens due to variations in the nickel mask used in the etching. To simulate the additional effect of the dimensional variability on the probabilistic strength response for the single crystal specimens the ANSYS Probabilistic Design System (PDS) was used with CARES/Life.

Confirming the Revised C-Terminal Domain of the MscL Crystal Structure

PubMed Central

Maurer, Joshua A.; Elmore, Donald E.; Clayton, Daniel; Xiong, Li; Lester, Henry A.; Dougherty, Dennis A.

2008-01-01

The structure of the C-terminal domain of the mechanosensitive channel of large conductance (MscL) has generated significant controversy. As a result, several structures have been proposed for this region: the original crystal structure (1MSL) of the Mycobacterium tuberculosis homolog (Tb), a model of the Escherichia coli homolog, and, most recently, a revised crystal structure of Tb-MscL (2OAR). To understand which of these structures represents a physiological conformation, we measured the impact of mutations to the C-terminal domain on the thermal stability of Tb-MscL using circular dichroism and performed molecular dynamics simulations of the original and the revised crystal structures of Tb-MscL. Our results imply that this region is helical and adopts an α-helical bundle conformation similar to that observed in the E. coli MscL model and the revised Tb-MscL crystal structure. PMID:18326638

A Low-Cost System Based on Image Analysis for Monitoring the Crystal Growth Process.

PubMed

Venâncio, Fabrício; Rosário, Francisca F do; Cajaiba, João

2017-05-31

Many techniques are used to monitor one or more of the phenomena involved in the crystallization process. One of the challenges in crystal growth monitoring is finding techniques that allow direct interpretation of the data. The present study used a low-cost system, composed of a commercial webcam and a simple white LED (Light Emitting Diode) illuminator, to follow the calcium carbonate crystal growth process. The experiments were followed with focused beam reflectance measurement (FBRM), a common technique for obtaining information about the formation and growth of crystals. The images obtained in real time were treated with the red, blue, and green (RGB) system. The results showed a qualitative response of the system to crystal formation and growth processes, as there was an observed decrease in the signal as the growth process occurred. Control of the crystal growth was managed by increasing the viscosity of the test solution with the addition of monoethylene glycol (MEG) at 30% and 70% in a mass to mass relationship, providing different profiles of the RGB average curves. The decrease in the average RGB value became slower as the concentration of MEG was increased; this reflected a lag in the growth process that was proven by the FBRM.

[Fine stereo structure for natural organic molecules, a preliminary study. II. Melting point influenced by structure factors].

PubMed

Lu, Y; Zheng, Q; Lu, D; Ma, P; Chen, Y

1995-06-01

Crystal structures of two compounds from Tripterygium wilfordii Hook f. have been determined by X-ray diffraction method. Structure factors influencing melting point of solid state have been analysed. Crystal class (or space group), recrystallization solvent, force between molecules and fine changes of molecular structures will all cause melting point changes of crystal substance.

On crystal versus fiber formation in dipeptide hydrogelator systems.

PubMed

Houton, Kelly A; Morris, Kyle L; Chen, Lin; Schmidtmann, Marc; Jones, James T A; Serpell, Louise C; Lloyd, Gareth O; Adams, Dave J

2012-06-26

Naphthalene dipeptides have been shown to be useful low-molecular-weight gelators. Here we have used a library to explore the relationship between the dipeptide sequence and the hydrogelation efficiency. A number of the naphthalene dipeptides are crystallizable from water, enabling us to investigate the comparison between the gel/fiber phase and the crystal phase. We succeeded in crystallizing one example directly from the gel phase. Using X-ray crystallography, molecular modeling, and X-ray fiber diffraction, we show that the molecular packing of this crystal structure differs from the structure of the gel/fiber phase. Although the crystal structures may provide important insights into stabilizing interactions, our analysis indicates a rearrangement of structural packing within the fibers. These observations are consistent with the fibrillar interactions and interatomic separations promoting 1D assembly whereas in the crystals the peptides are aligned along multiple axes, allowing 3D growth. This observation has an impact on the use of crystal structures to determine supramolecular synthons for gelators.

Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity.

PubMed

Owens, Gwen E; New, Danielle M; Olvera, Alejandra I; Manzella, Julia Ashlyn; Macon, Brittney L; Dunn, Joshua C; Cooper, David A; Rouleau, Robyn L; Connor, Daniel S; Bjorkman, Pamela J

2016-10-01

Huntington's disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and microgravity-grown crystals had a slightly improved mosaicity (decreased by 0.03°) and diffraction resolution (decreased by 0.2 Å) compared with control crystals grown on Earth. However, the highest resolution and lowest mosaicity crystals were formed on Earth, and the highest-quality crystal overall was formed on Earth after return from microgravity.

Comparative analysis of anti-polyglutamine Fab crystals grown on Earth and in microgravity

PubMed Central

Owens, Gwen E.; New, Danielle M.; Olvera, Alejandra I.; Manzella, Julia Ashlyn; Macon, Brittney L.; Dunn, Joshua C.; Cooper, David A.; Rouleau, Robyn L.; Connor, Daniel S.; Bjorkman, Pamela J.

2016-01-01

Huntington’s disease is one of nine neurodegenerative diseases caused by a polyglutamine (polyQ)-repeat expansion. An anti-polyQ antigen-binding fragment, MW1 Fab, was crystallized both on Earth and on the International Space Station, a microgravity environment where convection is limited. Once the crystals returned to Earth, the number, size and morphology of all crystals were recorded, and X-ray data were collected from representative crystals. The results generally agreed with previous microgravity crystallization studies. On average, microgravity-grown crystals were 20% larger than control crystals grown on Earth, and microgravity-grown crystals had a slightly improved mosaicity (decreased by 0.03°) and diffraction resolution (decreased by 0.2 Å) compared with control crystals grown on Earth. However, the highest resolution and lowest mosaicity crystals were formed on Earth, and the highest-quality crystal overall was formed on Earth after return from microgravity. PMID:27710941

A STUDY OF DISLOCATION STRUCTURE OF SUBBOUNDARIES IN MOLYBDENUM SINGLE CRYSTALS,

DTIC Science & Technology

MOLYBDENUM, *DISLOCATIONS), GRAIN STRUCTURES(METALLURGY), SINGLE CRYSTALS, ZONE MELTING, ELECTRON BEAM MELTING, GRAIN BOUNDARIES, MATHEMATICAL ANALYSIS, ETCHED CRYSTALS, ETCHING, ELECTROEROSIVE MACHINING, CHINA

Multi Resonance Shear Mode Transducers

DTIC Science & Technology

2016-11-21

burden for this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing...ABSTRACT Crystallographic engineering of single crystal relaxor-based ferroelectrics was used to design broadband, compact, high power, low frequency...using multiple d36 crystal geometries or combinations of d36 and other crystal cuts. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17

Self-powdering and nonlinear optical domain structures in ferroelastic β‧-Gd2(MoO4)3 crystals formed in glass

NASA Astrophysics Data System (ADS)

Tsukada, Y.; Honma, T.; Komatsu, T.

2009-08-01

Ferroelastic β'-Gd 2(MoO 4) 3, (GMO), crystals are formed through the crystallization of 21.25Gd 2O 3-63.75MoO 3-15B 2O 3 glass (mol%), and two scientific curious phenomena are observed. (1) GMO crystals formed in the crystallization break into small pieces with a triangular prism or pyramid shape having a length of 50-500 μm spontaneously during the crystallizations in the inside of an electric furnace, not during the cooling in air after the crystallization. This phenomenon is called "self-powdering phenomenon during crystallization" in this paper. (2) Each self-powdered GMO crystal grain shows a periodic domain structure with different refractive indices, and a spatially periodic second harmonic generation (SHG) depending on the domain structure is observed. It is proposed from polarized micro-Raman scattering spectra and the azimuthal dependence of second harmonic intensities that GMO crystals are oriented in each crystal grain and the orientation of (MoO 4) 2- tetrahedra in GMO crystals changes periodically due to spontaneous strains in ferroelastic GMO crystals.

Correlation between hierarchical structure of crystal networks and macroscopic performance of mesoscopic soft materials and engineering principles.

PubMed

Lin, Naibo; Liu, Xiang Yang

2015-11-07

This review examines how the concepts and ideas of crystallization can be extended further and applied to the field of mesoscopic soft materials. It concerns the structural characteristics vs. the macroscopic performance, and the formation mechanism of crystal networks. Although this subject can be discussed in a broad sense across the area of mesoscopic soft materials, our main focus is on supramolecular materials, spider and silkworm silks, and biominerals. First, the occurrence of a hierarchical structure, i.e. crystal network and domain network structures, will facilitate the formation kinetics of mesoscopic phases and boost up the macroscopic performance of materials in some cases (i.e. spider silk fibres). Second, the structure and performance of materials can be correlated in some way by the four factors: topology, correlation length, symmetry/ordering, and strength of association of crystal networks. Moreover, four different kinetic paths of crystal network formation are identified, namely, one-step process of assembly, two-step process of assembly, mixed mode of assembly and foreign molecule mediated assembly. Based on the basic mechanisms of crystal nucleation and growth, the formation of crystal networks, such as crystallographic mismatch (or noncrystallographic) branching (tip branching and fibre side branching) and fibre/polymeric side merging, are reviewed. This facilitates the rational design and construction of crystal networks in supramolecular materials. In this context, the (re-)construction of a hierarchical crystal network structure can be implemented by thermal, precipitate, chemical, and sonication stimuli. As another important class of soft materials, the unusual mechanical performance of spider and silkworm silk fibres are reviewed in comparison with the regenerated silk protein derivatives. It follows that the considerably larger breaking stress and unusual breaking strain of spider silk fibres vs. silkworm silk fibres can be interpreted according to the synergistically correlated hierarchical structures of the domain and crystal networks, which can be quantified by the hierarchical structural correlation and the four structural parameters. Based on the concept of crystal networks, the new understanding acquired will transfer the research and engineering of mesoscopic materials, particularly, soft functional materials, to a new phase.

Computed crystal energy landscapes for understanding and predicting organic crystal structures and polymorphism.

PubMed

Price, Sarah Sally L

2009-01-20

The phenomenon of polymorphism, the ability of a molecule to adopt more than one crystal structure, is a well-established property of crystalline solids. The possible variations in physical properties between polymorphs make the reliable reproduction of a crystalline form essential for all research using organic materials, as well as quality control in manufacture. Thus, the last two decades have seen both an increase in interest in polymorphism and the availability of the computer power needed to make the computational prediction of organic crystal structures a practical possibility. In the past decade, researchers have made considerable improvements in the theoretical basis for calculating the sets of structures that are within the energy range of possible polymorphism, called crystal energy landscapes. It is common to find that a molecule has a wide variety of ways of packing with lattice energy within a few kilojoules per mole of the most stable structure. However, as we develop methods to search for and characterize "all" solid forms, it is also now usual for polymorphs and solvates to be found. Thus, the computed crystal energy landscape reflects and to an increasing extent "predicts" the emerging complexity of the solid state observed for many organic molecules. This Account will discuss the ways in which the calculation of the crystal energy landscape of a molecule can be used as a complementary technique to solid form screening for polymorphs. Current methods can predict the known crystal structure, even under "blind test" conditions, but such successes are generally restricted to those structures that are the most stable over a wide range of thermodynamic conditions. The other low-energy structures can be alternative polymorphs, which have sometimes been found in later experimental studies. Examining the computed structures reveals the various compromises between close packing, hydrogen bonding, and pi-pi stacking that can result in energetically feasible structures. Indeed, we have observed that systems with many almost equi-energetic structures that contain a common interchangeable motif correlate with a tendency to disorder and problems with control of the crystallization product. Thus, contrasting the computed crystal energy landscape with the known crystal structures of a given molecule provides a valuable complement to solid form screening, and the examination of the low-energy structures often leads to a rationalization of the forms found.

Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental 129Xe NMR Spectroscopy

PubMed Central

Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J.; Laitinen, Risto; Jokisaari, Jukka

2017-01-01

Abstract An approach is presented for the structure determination of clathrates using NMR spectroscopy of enclathrated xenon to select from a set of predicted crystal structures. Crystal structure prediction methods have been used to generate an ensemble of putative structures of o‐ and m‐fluorophenol, whose previously unknown clathrate structures have been studied by 129Xe NMR spectroscopy. The high sensitivity of the 129Xe chemical shift tensor to the chemical environment and shape of the crystalline cavity makes it ideal as a probe for porous materials. The experimental powder NMR spectra can be used to directly confirm or reject hypothetical crystal structures generated by computational prediction, whose chemical shift tensors have been simulated using density functional theory. For each fluorophenol isomer one predicted crystal structure was found, whose measured and computed chemical shift tensors agree within experimental and computational error margins and these are thus proposed as the true fluorophenol xenon clathrate structures. PMID:28111848

Hydrothermal crystal growth of oxides for optical applications

NASA Astrophysics Data System (ADS)

McMillen, Colin David

2007-12-01

The manipulation of light has proven to be an integral part of today's technology-based society. In particular, there is great interest in obtaining coherent radiation in all regions of the optical spectrum to advance technology in military, medical, industrial, scientific and consumer fields. Exploring new crystal growth techniques as well as the growth of new optical materials is critical in the advancement of solid state optics. Surprisingly, the academic world devotes little attention to the growth of large crystals. This shortcoming has left gaps in the optical spectrum inaccessible by solid state devices. This dissertation explores the hydrothermal crystal growth of materials that could fill two such gaps. The first gap exists in the deep-UV region, particularly below 200 nm. Some materials such as LiB3O5 and beta-BaB2O4 can generate coherent light at wavelengths as low as 205 nm. The growth of these materials was explored to investigate the feasibility of the hydrothermal method as a new technique for growing these crystals. Particular attention was paid to the descriptive chemistry surrounding these systems, and several novel structures were elucidated. The study was also extended to the growth of materials that could be used for the generation of coherent light as low as 155 nm. Novel synthetic schemes for Sr2Be2B2O7 and KBe2BO 3F2 were developed and the growth of large crystals was explored. An extensive study of the structures, properties and crystal growth of related compounds, RbBe2BO3F2 and CsBe2BO 3F2, was also undertaken. Optimization of a number of parameters within this family of compounds led to the hydrothermal growth of large, high quality single crystal at rates suitable for large-scale growth. The second gap in technology is in the area of high average power solid state lasers emitting in the 1 mum and eye-safe (>1.5 mum) regions. A hydrothermal technique was developed to grow high quality crystals of Sc 2O3 and Sc2O3 doped with suitable lanthanide activator ions. Preliminary spectroscopic studies were performed and large crystals were again grown at rates suitable for commercial production. The synthesis of ultra-high purity Ln2O3 (Ln = Sc, Y, La-Lu) nanoparticles was also explored to advance the development of ceramic-based solid state lasers. Crystal growth is a complex task involving a great number of intricacies that must be understood and balanced. This dissertation has advanced the art and science of growing crystals, and documented the development of large, high quality crystals of advanced optical materials The materials and hydrothermal crystal growth techniques developed over the course of this work represent important progress toward controlling the optical spectrum.

Crystallographic Topology 2: Overview and Work in Progress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Johnson, C.K.

1999-08-01

This overview describes an application of contemporary geometric topology and stochastic process concepts to structural crystallography. In this application, crystallographic groups become orbifolds, crystal structures become Morse functions on orbifolds, and vibrating atoms in a crystal become vector valued Gaussian measures with the Radon-Nikodym property. Intended crystallographic benefits include new methods for visualization of space groups and crystal structures, analysis of the thermal motion patterns seen in ORTEP drawings, and a classification scheme for crystal structures based on their Heegaard splitting properties.

[Crystal structure of SMU.2055 protein from Streptococcus mutans and its small molecule inhibitors design and selection].

PubMed

Xiaodan, Chen; Xiurong, Zhan; Xinyu, Wu; Chunyan, Zhao; Wanghong, Zhao

2015-04-01

The aim of this study is to analyze the three-dimensional crystal structure of SMU.2055 protein, a putative acetyltransferase from the major caries pathogen Streptococcus mutans (S. mutans). The design and selection of the structure-based small molecule inhibitors are also studied. The three-dimensional crystal structure of SMU.2055 protein was obtained by structural genomics research methods of gene cloning and expression, protein purification with Ni²⁺-chelating affinity chromatography, crystal screening, and X-ray diffraction data collection. An inhibitor virtual model matching with its target protein structure was set up using computer-aided drug design methods, virtual screening and fine docking, and Libdock and Autodock procedures. The crystal of SMU.2055 protein was obtained, and its three-dimensional crystal structure was analyzed. This crystal was diffracted to a resolution of 0.23 nm. It belongs to orthorhombic space group C222(1), with unit cell parameters of a = 9.20 nm, b = 9.46 nm, and c = 19.39 nm. The asymmetric unit contained four molecules, with a solvent content of 56.7%. Moreover, five small molecule compounds, whose structure matched with that of the target protein in high degree, were designed and selected. Protein crystallography research of S. mutans SMU.2055 helps to understand the structures and functions of proteins from S. mutans at the atomic level. These five compounds may be considered as effective inhibitors to SMU.2055. The virtual model of small molecule inhibitors we built will lay a foundation to the anticaries research based on the crystal structure of proteins.

Correlation among far-infrared reflection modes, crystal structures and dielectric properties of Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3}–CaTiO{sub 3} ceramics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shi, Feng, E-mail: sf751106@sina.com.cn; Sun, Haiqing; Liu, Hongquan

Highlights: • Crystal symmetry decreases with CT concentration from cubic to hexagonal structure. • Lattice constants as well as the ordered degree change with CT concentration. • Ordered structures turn from 1:1 to 1:2 ordering with change of crystal structures. • There is a correlation between FIR phonon modes and dielectric properties. • There is a correlation between FIR phonon modes and crystal structures. - Abstract: Ba(Zn{sub 1/3}Nb{sub 2/3})O{sub 3} (BZN)–CaTiO{sub 3} (CT) microwave dielectric ceramics were synthesized at 1395 °C for 4 h using conventional solid-state sintering technique with different CT contents. The ceramics were characterized by X-ray diffractionmore » (XRD) and far-infrared reflection (FIR) spectroscopy to evaluate correlations among crystal structures, dielectric properties, and infrared modes. XRD results showed that crystal symmetry decreased with increased CT concentration from cubic to hexagonal structure, and lattice constants and ordered degree changed accordingly. Ordered phases transformed from 1:1 to 1:2 ordered structure with crystal-structure change. FIR results demonstrated that two new IR active modes appeared at 300 cm{sup −1}, and another new mode appeared at 600 cm{sup −1} for the x ≥ 0.60 sample, which agreed with the change in crystal structures as confirmed by XRD results. Correlations between FIR modes and dielectric properties were established.« less

Synthesis, Crystal Chemistry, and Physical Properties of Ternary Intermetallic Compounds An2T2X( An=Pu, Am; X=ln, Sn; T=Co, Ir, Ni, Pd, Pt, Rh)

NASA Astrophysics Data System (ADS)

Pereira, L. C. J.; Wastin, F.; Winand, J. M.; Kanellakopoulos, B.; Rebizant, J.; Spirlet, J. C.; Almeida, M.

1997-11-01

The synthesis, structural, and physical characterization of nine new ternary intermetallic compounds belonging to the isostructural An2T2Xfamily with the transuranium Pu and Am elements, namely, Pu 2Ni 2In, Pu 2Pd 2In, Pu 2Pt 2In, Pu 2Rh 2In, Pu 2Ni 2Sn, Pu 2Pd 2Sn, Pu 2Pt 2Sn, Am 2Ni 2Sn, and Am 2Pd 2Sn, are reported. From these compounds only Pu 2Rh 2In, Am 2Ni 2Sn, and Am 2Pd 2Sn melt incongruently. All of these compounds crystallize in a tetragonal U 3Si 2-type structure, with the space group P4/ mbm, ( Z=2) as most of the U and Np 2-2-1 compounds already found. In this structure, Anatoms occupy the 4 h( x1, x1+0.5, 0.5), Tthe 4 g( x2, x2+0.5, 0), and Xthe 2 a(0, 0, 0) positions. The average values of x1and x2are, respectively, 0.17 and 0.37. Single-crystal X-ray data were refined to R/ RW=0.045/0.066, 0.043/0.072, 0.066/0.080, 0.070/0.098, 0.029/0.048, 0.055/0.080, 0.073/0.096, 0.048/0.086, 0.048/0.065 for Pu 2Ni 2In, Pu 2Pd 2In, Pu 2Pt 2In, Pu 2Rh 2In, Pu 2Ni 2Sn, Pu 2Pd 2Sn, Pu 2Pt 2Sn, Am 2Ni 2Sn, and Am 2Pd 2Sn, respectively, for seven variables. The variation of the lattice parameters and the range of stability of the 2-2-1 phase are discussed in terms of the substitution of different An(actinide), T(transition metal), and X( p-electron) elements in their crystal structure. The possible role of spin fluctuations in the low-temperature behavior of the Pu samples is indicated by magnetic and electrical resistivity measurements.

Precision mechanical structure of an ultra-high-resolution spectrometer for inelastic X-ray scattering instrument

DOEpatents

Shu, Deming; Shvydko, Yuri; Stoupin, Stanislav A.; Khachatryan, Ruben; Goetze, Kurt A.; Roberts, Timothy

2015-04-14

A method and an ultrahigh-resolution spectrometer including a precision mechanical structure for positioning inelastic X-ray scattering optics are provided. The spectrometer includes an X-ray monochromator and an X-ray analyzer, each including X-ray optics of a collimating (C) crystal, a pair of dispersing (D) element crystals, anomalous transmission filter (F) and a wavelength (W) selector crystal. A respective precision mechanical structure is provided with the X-ray monochromator and the X-ray analyzer. The precision mechanical structure includes a base plate, such as an aluminum base plate; positioning stages for D-crystal alignment; positioning stages with an incline sensor for C/F/W-crystal alignment, and the positioning stages including flexure-based high-stiffness structure.

Structure and magnetic properties of low-temperature phase Mn-Bi nanosheets with ultra-high coercivity and significant anisotropy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liu, Rongming, E-mail: rmliu@iphy.ac.cn, E-mail: shenbg@iphy.ac.cn; Zhang, Ming; Niu, E

2014-05-07

The microstructure, crystal structure, and magnetic properties of low-temperature phase (LTP) Mn-Bi nanosheets, prepared by surfactant assistant high-energy ball milling (SA-HEBM) with oleylamine and oleic acid as the surfactant, were examined with scanning electron microscopy, X-ray diffraction, and vibrating sample magnetometer, respectively. Effect of ball-milling time on the coercivity of LTP Mn-Bi nanosheets was systematically investigated. Results show that the high energy ball milling time from tens of minutes to several hours results in the coercivity increase of Mn-Bi powders and peak values of 14.3 kOe around 10 h. LTP Mn-Bi nanosheets are characterized by an average thickness of tensmore » of nanometers, an average diameter of ∼1.5 μm, and possess a relatively large aspect ratio, an ultra-high room temperature coercivity of 22.3 kOe, a significant geometrical and magnetic anisotropy, and a strong (00l) crystal texture. Magnetization and demagnetization behaviors reveal that wall pinning is the dominant coercivity mechanism in these LTP Mn-Bi nanosheets. The ultrafine grain refinement introduced by the SA-HEBM process contribute to the ultra-high coercivity of LTP Mn-Bi nanosheets and a large number of defects put a powerful pinning effect on the magnetic domain movement, simultaneously. Further magnetic measurement at 437 K shows that a high coercivity of 17.8 kOe and a strong positive temperature coefficient of coercivity existed in the bonded permanent magnet made by LTP Mn-Bi nanosheets.« less

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B]pyridine-3-carbonitrile

NASA Astrophysics Data System (ADS)

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K.

2016-05-01

The novel organic material C20H21ClN2O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P21/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å3 and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. The structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.

Structural properties and defects of GaN crystals grown at ultra-high pressures: A molecular dynamics simulation

NASA Astrophysics Data System (ADS)

Gao, Tinghong; Li, Yidan; Xie, Quan; Tian, Zean; Chen, Qian; Liang, Yongchao; Ren, Lei; Hu, Xuechen

2018-01-01

The growth of GaN crystals at different pressures was studied by molecular dynamics simulation employing the Stillinger-Weber potential, and their structural properties and defects were characterized using the radial distribution function, the Voronoi polyhedron index method, and a suitable visualization technology. Crystal structures formed at 0, 1, 5, 10, and 20 GPa featured an overwhelming number of <4 0 0 0> Voronoi polyhedra, whereas amorphous structures comprising numerous disordered polyhedra were produced at 50 GPa. During quenching, coherent twin boundaries were easily formed between zinc-blende and wurtzite crystal structures in GaN. Notably, point defects usually appeared at low pressure, whereas dislocations were observed at high pressure, since the simultaneous growth of two crystal grains with different crystal orientations and their boundary expansion was hindered in the latter case, resulting in the formation of a dislocation between these grains.

Discovering H-bonding rules in crystals with inductive logic programming.

PubMed

Ando, Howard Y; Dehaspe, Luc; Luyten, Walter; Van Craenenbroeck, Elke; Vandecasteele, Henk; Van Meervelt, Luc

2006-01-01

In the domain of crystal engineering, various schemes have been proposed for the classification of hydrogen bonding (H-bonding) patterns observed in 3D crystal structures. In this study, the aim is to complement these schemes with rules that predict H-bonding in crystals from 2D structural information only. Modern computational power and the advances in inductive logic programming (ILP) can now provide computational chemistry with the opportunity for extracting structure-specific rules from large databases that can be incorporated into expert systems. ILP technology is here applied to H-bonding in crystals to develop a self-extracting expert system utilizing data in the Cambridge Structural Database of small molecule crystal structures. A clear increase in performance was observed when the ILP system DMax was allowed to refer to the local structural environment of the possible H-bond donor/acceptor pairs. This ability distinguishes ILP from more traditional approaches that build rules on the basis of global molecular properties.

Study on sensing property of one-dimensional ring mirror-defect photonic crystal

NASA Astrophysics Data System (ADS)

Chen, Ying; Luo, Pei; Cao, Huiying; Zhao, Zhiyong; Zhu, Qiguang

2018-02-01

Based on the photon localization and the photonic bandgap characteristics of photonic crystals (PCs), one-dimensional (1D) ring mirror-defect photonic crystal structure is proposed. Due to the introduction of mirror structure, a defect cavity is formed in the center of the photonic crystal, and then the resonant transmission peak can be obtained in the bandgap of transmission spectrum. The transfer matrix method is used to establish the relationship model between the resonant transmission peak and the structure parameters of the photonic crystals. Using the rectangular air gate photonic crystal structure, the dynamic monitoring of the detected gas sample parameters can be achieved from the shift of the resonant transmission peak. The simulation results show that the Q-value can attain to 1739.48 and the sensitivity can attain to 1642 nm ṡ RIU-1, which demonstrates the effectiveness of the sensing structure. The structure can provide certain theoretical reference for air pollution monitoring and gas component analysis.

Development and photoelectric properties of In/p-Ag{sub 3}AsS{sub 3} surface-barrier structures

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rud', V. Yu., E-mail: rudvas@spbstu.ru; Rud', Yu. V.; Terukov, E. I.

2010-08-15

Homogeneous p-Ag{sub 3}AsS{sub 3} bulk single crystals with rhombic structure have been grown by planar crystallization from melts with atomic composition corresponding to this ternary compound. Photosensitive surface-barrier structures based on the interface between the surface of these crystals and thin films of pure indium are fabricated for the first time. The photosensitivity of fabricated structures is studied in natural and linearly polarized light. Photosensitivity spectra of In/p-Ag{sub 3}AsS{sub 3} structures are measured for the first time and used to determine the nature and energy of interband transitions in p-Ag{sub 3}AsS{sub 3} crystals. The phenomenon of natural photopleochroism is studiedmore » for surface-barrier structures grown on oriented p-Ag{sub 3}AsS{sub 3} single crystals. It is concluded that Ag{sub 3}AsS{sub 3} single crystals can be used in photoconverters of natural and linearly polarized light.« less

Generation of crystal structures using known crystal structures as analogues

PubMed Central

Cole, Jason C.; Groom, Colin R.; Read, Murray G.; Giangreco, Ilenia; McCabe, Patrick; Reilly, Anthony M.; Shields, Gregory P.

2016-01-01

This analysis attempts to answer the question of whether similar molecules crystallize in a similar manner. An analysis of structures in the Cambridge Structural Database shows that the answer is yes – sometimes they do, particularly for single-component structures. However, one does need to define what we mean by similar in both cases. Building on this observation we then demonstrate how this correlation between shape similarity and packing similarity can be used to generate potential lattices for molecules with no known crystal structure. Simple intermolecular interaction potentials can be used to minimize these potential lattices. Finally we discuss the many limitations of this approach. PMID:27484374

Microgravity protein crystallization

PubMed Central

McPherson, Alexander; DeLucas, Lawrence James

2015-01-01

Over the past 20 years a variety of technological advances in X-ray crystallography have shortened the time required to determine the structures of large macromolecules (i.e., proteins and nucleic acids) from several years to several weeks or days. However, one of the remaining challenges is the ability to produce diffraction-quality crystals suitable for a detailed structural analysis. Although the development of automated crystallization systems combined with protein engineering (site-directed mutagenesis to enhance protein solubility and crystallization) have improved crystallization success rates, there remain hundreds of proteins that either cannot be crystallized or yield crystals of insufficient quality to support X-ray structure determination. In an attempt to address this bottleneck, an international group of scientists has explored use of a microgravity environment to crystallize macromolecules. This paper summarizes the history of this international initiative along with a description of some of the flight hardware systems and crystallization results. PMID:28725714

Ultratight crystal packing of a 10 kDa protein

DOE Office of Scientific and Technical Information (OSTI.GOV)

Trillo-Muyo, Sergio; Jasilionis, Andrius; Domagalski, Marcin J.

2013-03-01

The crystal structure of the C-terminal domain of a putative U32 peptidase from G. thermoleovorans is reported; it is one of the most tightly packed protein structures reported to date. While small organic molecules generally crystallize forming tightly packed lattices with little solvent content, proteins form air-sensitive high-solvent-content crystals. Here, the crystallization and full structure analysis of a novel recombinant 10 kDa protein corresponding to the C-terminal domain of a putative U32 peptidase are reported. The orthorhombic crystal contained only 24.5% solvent and is therefore among the most tightly packed protein lattices ever reported.

A Two-Tailed Phosphopeptide Crystallizes to Form a Lamellar Structure.

PubMed

Pellach, Michal; Mondal, Sudipta; Harlos, Karl; Mance, Deni; Baldus, Marc; Gazit, Ehud; Shimon, Linda J W

2017-03-13

The crystal structure of a designed phospholipid-inspired amphiphilic phosphopeptide at 0.8 Å resolution is presented. The phosphorylated β-hairpin peptide crystallizes to form a lamellar structure that is stabilized by intra- and intermolecular hydrogen bonding, including an extended β-sheet structure, as well as aromatic interactions. This first reported crystal structure of a two-tailed peptidic bilayer reveals similarities in thickness to a typical phospholipid bilayer. However, water molecules interact with the phosphopeptide in the hydrophilic region of the lattice. Additionally, solid-state NMR was used to demonstrate correlation between the crystal structure and supramolecular nanostructures. The phosphopeptide was shown to self-assemble into semi-elliptical nanosheets, and solid-state NMR provides insight into the self-assembly mechanisms. This work brings a new dimension to the structural study of biomimetic amphiphilic peptides with determination of molecular organization at the atomic level. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab initio study of structural and mechanical property of solid molecular hydrogens

NASA Astrophysics Data System (ADS)

Ye, Yingting; Yang, Li; Yang, Tianle; Nie, Jinlan; Peng, Shuming; Long, Xinggui; Zu, Xiaotao; Du, Jincheng

2015-06-01

Ab initio calculations based on density functional theory (DFT) were performed to investigate the structural and the elastic properties of solid molecular hydrogens (H2). The influence of molecular axes of H2 on structural relative stabilities of hexagonal close-packed (hcp) and face-centered cubic (fcc) structured hydrogen molecular crystals were systematically investigated. Our results indicate that for hcp structures, disordered hydrogen molecule structure is more stable, while for fcc structures, Pa3 hydrogen molecular crystal is most stable. The cohesive energy of fcc H2 crystal was found to be lower than hcp. The mechanical properties of fcc and hcp hydrogen molecular crystals were obtained, with results consistent with previous theoretical calculations. In addition, the effects of zero point energy (ZPE) and van der Waals (vdW) correction on the cohesive energy and the stability of hydrogen molecular crystals were systematically studied and discussed.

Stochastic generation of complex crystal structures combining group and graph theory with application to carbon

NASA Astrophysics Data System (ADS)

Shi, Xizhi; He, Chaoyu; Pickard, Chris J.; Tang, Chao; Zhong, Jianxin

2018-01-01

A method is introduced to stochastically generate crystal structures with defined structural characteristics. Reasonable quotient graphs for symmetric crystals are constructed using a random strategy combined with space group and graph theory. Our algorithm enables the search for large-size and complex crystal structures with a specified connectivity, such as threefold sp2 carbons, fourfold sp3 carbons, as well as mixed sp2-sp3 carbons. To demonstrate the method, we randomly construct initial structures adhering to space groups from 75 to 230 and a range of lattice constants, and we identify 281 new sp3 carbon crystals. First-principles optimization of these structures show that most of them are dynamically and mechanically stable and are energetically comparable to those previously proposed. Some of the new structures can be considered as candidates to explain the experimental cold compression of graphite.

Theoretical exploration of various lithium peroxide crystal structures in a Li-air battery

DOE PAGES

Lau, Kah; Qiu, Dantong; Luo, Xiangyi; ...

2015-01-14

We describe a series of metastable Li₂O₂ crystal structures involving different orientations and displacements of the O₂²⁻ peroxy ions based on the known Li₂O₂ crystal structure. Within the vicinity of the chemical potential ΔG ~ 0.20 eV/Li from the thermodynamic ground state of the Li₂O₂ crystal structure (i.e., Föppl structure), all of these newly found metastable Li₂O₂ crystal structures are found to be insulating and high-k materials, and they have a common unique signature of an O₂²⁻ O-O vibration mode (ω ~ 799–865 cm⁻¹), which is in the range of that commonly observed in Li-air battery experiments, regardless of themore » random O₂²⁻ orientations and the symmetry in the crystal lattice. From XRD patterns analysis, the commercially available Li₂O₂ powder is confirmed to be the thermodynamic ground state Föppl-like structure. However, for Li₂O₂ compounds that are grown electrochemically under the environment of Li-O₂ cells, we found that the XRD patterns alone are not sufficient for structural identification of these metastable Li₂O₂ crystalline phases due to the poor crystallinity of the sample. In addition, the commonly known Raman signal of O₂²⁻ vibration mode is also found to be insufficient to validate the possible existence of these newly predicted Li₂O₂ crystal structures, as all of them similarly share the similar O₂²⁻ vibration mode. However considering that the discharge voltage in most Li-O₂ cells are typically several tenths of an eV below the thermodynamic equilibrium for the formation of ground state Föppl structure, the formation of these metastable Li₂O₂ crystal structures appears to be thermodynamically feasible.« less

Crystal Structure and Crystal Chemistry of Some Common REE Minerals and Nanpingite

NASA Astrophysics Data System (ADS)

Ni, Yunxiang

1995-01-01

Part I. Crystal structure and crystal chemistry of fluorocarbonate minerals. The crystal structure of bastnasite-(Ce) have been solved in P-62c and refined to R = 0.018. The structure is composed of (001) (CeF) layers interspersed with (CO_3) layers in a 1:1 ratio. The Ce atom is coordinated in rm CeO_6F_3 polyhedra. The atomic arrangement of synchysite-(Ce) has been solved and refined to R = 0.036 with a monoclinic space group C2/c. It possesses a (001) layer structure, with layers of (Ca) and (CeF) separated by layers of carbonate groups. The layers stack in a manner analogous to C2/c muscovite. Polytypism similar to the micas may exist in synchysite. The crystal structures of cordylite-(Ce) have been solved in P6 _3/mmc and refined to R = 0.023. The structure and chemical formula are different from those deduced by Oftedal. The formula is rm MBaCe_2(CO _3)_4F, where M is rm Na^+, Ca^{2+}_{1/2 }+ O_{1/2}, or any solution. The presence of (NaF) layer in the structure is the key difference from the Oftedal's structure. This redefinition of the chemical formula and crystal structure of cordylite will be proposed to IMA-CNMMN. Part II. Crystal structure and crystal chemistry of monazite-xenotime series. Monazite is monoclinic, P2 _1/n, and xenotime is isostructural with zircon (I4_1/amd). Both atomic arrangements are based on (001) chains of intervening phosphate tetrahedra and RE polyhedra, with a REO_8 polyhedron in xenotime that accommodates HRE (Tb - Lu) and a REO_9 polyhedron in monazite that preferentially incorporates LRE (La - Gd). As the structure "transforms" from xenotime to monazite, the crystallographic properties are comparable along the (001) chains, with structural adjustments of 2.2 A along (010) to accommodate the different size RE atoms. Part III. Crystal structure of nanpingite-2M _2, the Cs end-member of muscovite. The crystal structure of nanpingite has been refined to R = 0.058. Compared to K^+ in muscovite, the largest interlayer Cs^+ in nanpingite increases (001) separation between adjacent 2:1 layers, but has little effect on the dimensions in (001). The existence of rare 2M_2 polytype in nanpingite is attributed to this large layer separation, which minimizes the repulsion of the superimposed (along (001)) basal oxygens in neighboring tetrahedral layers.

Inorganic Crystal Structure Database (ICSD) and Standardized Data and Crystal Chemical Characterization of Inorganic Structure Types (TYPIX)—Two Tools for Inorganic Chemists and Crystallographers

PubMed Central

Fluck, Ekkehard

1996-01-01

The two databases ICSD and TYPIX are described. ICSD is a comprehensive compilation of crystal structure data of inorganic compounds (about 39 000 entries). TYPIX contains 3600 critically evaluated data sets representative of structure types formed by inorganic compounds. PMID:27805158

Crystal structure of a birefringent andradite-grossular from Crowsnest Pass, Alberta, Canada

DOE Office of Scientific and Technical Information (OSTI.GOV)

Antao, Sytle M.; Klincker, Allison M.

2014-02-20

The structure of a birefringent andradite–grossular sample was refined using single-crystal X-ray diffraction (SCD) and synchrotron high-resolution powder X-ray diffraction (HRPXRD) data. Electron-microprobe results indicate a homogeneous composition of {Ca 2.88Mn 2+ 0.06Mg 0.04Fe 2+ 0.03} Σ3[Fe 3+ 1.29Al 0.49Ti 4+ 0.17Fe 2+ 0.06] Σ2(Si 2.89Al 0.11) Σ3O 12. The Rietveld refinement reduced χ 2 = 1.384 and overall R (F 2) = 0.0315. The HRPXRD data show that the sample contains three phases. For phase-1, the weight %, unit-cell parameter (Å), distances (Å), and site occupancy factor (sof) are 62.85(7)%, a = 12.000 06(2), average = 2.4196, Fe–O =more » 1.9882(5), Si–O = 1.6542(6) Å, Ca(sof) = 0.970(2), Fe(sof) = 0.763(1), and Si(sof) = 0.954(2). The corresponding data for phase-2 are 19.14(9)%, a = 12.049 51(2), average = 2.427, Fe–O = 1.999(1), Si–O = 1.665(1) Å, Ca(sof) = 0.928(4), Fe(sof) = 0.825(3), and Si(sof) = 0.964(4). The corresponding data for phase-3 are 18.01(9)%, a = 12.019 68(3), average = 2.424, Fe–O = 1.992(2), Si–O = 1.658(2) Å, Ca(sof) = 0.896(5), Fe(sof) = 0.754(4), and Si(sof) = 0.936(5). The fine-scale coexistence of the three phases causes strain that arises from the unit-cell and bond distances differences, and gives rise to strain-induced birefringence. The results from the SCD are similar to the dominant phase-1 obtained by the HRPXRD, but the SCD misses the minor phases.« less

Effect of Co doping, capping agent and optical-structural studies of ZnO:Co2+ nanoparticles

NASA Astrophysics Data System (ADS)

Taheri Otaqsara, S. M.

2011-08-01

Co2+ doped ZnO nanoparticles (NPs) using PEG as a capping agent were prepared by colloidal wet-chemical method. The structure, morphology and characteristics of as-prepared samples were investigated. X-ray diffraction patterns studies revealed wurtzite crystal phase. STM-TEM micrographs show a spherical shape and nearly well distribution with an average particle size of ~15-20 nm. UV-VIS spectra show the presence of exciton peak at 349 nm which can be effectively tuned versus cobalt doping and PEG concentration. PL studies were done under the excitation of 347 nm, which exhibited a UV (~386 nm) and visible (blue-orange) emission peak because of free-exciton recombination and oxygen vacancy.

Morphology-controllable of Sn doped ZnO nanorods prepared by spray pyrolysis for transparent electrode application

NASA Astrophysics Data System (ADS)

Hameed, M. Shahul; Princice, J. Joseph; Babu, N. Ramesh; Zahirullah, S. Syed; Deshmukh, Sampat G.; Arunachalam, A.

2018-05-01

Transparent conductive Sn doped ZnO nanorods have been deposited at various doping level by spray pyrolysis technique on glass substrate. The structural, surface morphological and optical properties of these films have been investigated with the help of X-ray diffraction (XRD), scanning electron microscope (SEM), atomic force microscope (AFM) and UV-Vis spectrophotometer respectively. XRD patterns revealed a successful high quality growth of single crystal ZnO nanorods with hexagonal wurtzite structure having (002) preferred orientation. The scanning electron microscope (SEM) image of the prepared films exposed the uniform distribution of Sn doped ZnO nanorod shaped grains. All these films were highly transparent in the visible region with average transmittance of 90%.

Modeling phosphorus removal and recovery from anaerobic digester supernatant through struvite crystallization in a fluidized bed reactor.

PubMed

Rahaman, Md Saifur; Mavinic, Donald S; Meikleham, Alexandra; Ellis, Naoko

2014-03-15

The cost associated with the disposal of phosphate-rich sludge, the stringent regulations to limit phosphate discharge into aquatic environments, and resource shortages resulting from limited phosphorus rock reserves, have diverted attention to phosphorus recovery in the form of struvite (MAP: MgNH4PO4·6H2O) crystals, which can essentially be used as a slow release fertilizer. Fluidized-bed crystallization is one of the most efficient unit processes used in struvite crystallization from wastewater. In this study, a comprehensive mathematical model, incorporating solution thermodynamics, struvite precipitation kinetics and reactor hydrodynamics, was developed to illustrate phosphorus depletion through struvite crystal growth in a continuous, fluidized-bed crystallizer. A thermodynamic equilibrium model for struvite precipitation was linked to the fluidized-bed reactor model. While the equilibrium model provided information on supersaturation generation, the reactor model captured the dynamic behavior of the crystal growth processes, as well as the effect of the reactor hydrodynamics on the overall process performance. The model was then used for performance evaluation of the reactor, in terms of removal efficiencies of struvite constituent species (Mg, NH4 and PO4), and the average product crystal sizes. The model also determined the variation of species concentration of struvite within the crystal bed height. The species concentrations at two extreme ends (inlet and outlet) were used to evaluate the reactor performance. The model predictions provided a reasonably good fit with the experimental results for PO4-P, NH4-N and Mg removals. Predicated average crystal sizes also matched fairly well with the experimental observations. Therefore, this model can be used as a tool for performance evaluation and process optimization of struvite crystallization in a fluidized-bed reactor. Crown Copyright © 2013. Published by Elsevier Ltd. All rights reserved.

Reduction of glycine particle size by impinging jet crystallization.

PubMed

Tari, Tímea; Fekete, Zoltán; Szabó-Révész, Piroska; Aigner, Zoltán

2015-01-15

The parameters of crystallization processes determine the habit and particle size distribution of the products. A narrow particle size distribution and a small average particle size are crucial for the bioavailability of poorly water-soluble pharmacons. Thus, particle size reduction is often required during crystallization processes. Impinging jet crystallization is a method that results in a product with a reduced particle size due to the homogeneous and high degree of supersaturation at the impingement point. In this work, the applicability of the impinging jet technique as a new approach in crystallization was investigated for the antisolvent crystallization of glycine. A factorial design was applied to choose the relevant crystallization factors. The results were analysed by means of a statistical program. The particle size distribution of the crystallized products was investigated with a laser diffraction particle size analyser. The roundness and morphology were determined with the use of a light microscopic image analysis system and a scanning electron microscope. Polymorphism was characterized by differential scanning calorimetry and powder X-ray diffraction. Headspace gas chromatography was utilized to determine the residual solvent content. Impinging jet crystallization proved to reduce the particle size of glycine. The particle size distribution was appropriate, and the average particle size was an order of magnitude smaller (d(0.5)=8-35 μm) than that achieved with conventional crystallization (d(0.5)=82-680 μm). The polymorphic forms of the products were influenced by the solvent ratio. The quantity of residual solvent in the crystallized products was in compliance with the requirements of the International Conference on Harmonization. Copyright © 2014 Elsevier B.V. All rights reserved.

Recent advances and progress in photonic crystal-based gas sensors

NASA Astrophysics Data System (ADS)

Goyal, Amit Kumar; Sankar Dutta, Hemant; Pal, Suchandan

2017-05-01

This review covers the recent progress made in the photonic crystal-based sensing technology for gas sensing applications. Photonic crystal-based sensing has tremendous potential because of its obvious advantages in sensitivity, stability, miniaturisation, portability, online use, remote monitoring etc. Several 1D and 2D photonic crystal structures including photonic crystal waveguides and cavities for gas sensing applications have been discussed in this review. For each kind of photonic crystal structure, the novelty, measurement principle and their respective gas sensing properties are presented. The reported works and the corresponding results predict the possibility to realize a commercially viable miniaturized and highly sensitive photonic crystal-based optical gas sensor having flexibility in the structure of ultra-compact size with excellent sensing properties.

Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

PubMed

Ding, Haibo; Zhu, Cun; Tian, Lei; Liu, Cihui; Fu, Guangbin; Shang, Luoran; Gu, Zhongze

2017-04-05

In this work, we demonstrate the fabrication of photonic crystal patterns with controllable morphologies and structural colors utilizing electrohydrodynamic jet (E-jet) printing with colloidal crystal inks. The final shape of photonic crystal units is controlled by the applied voltage signal and wettability of the substrate. Optical properties of the structural color patterns are tuned by the self-assembly of the silica nanoparticle building blocks. Using this direct printing technique, it is feasible to print customized functional patterns composed of photonic crystal dots or photonic crystal lines according to relevant printing mode and predesigned tracks. This is the first report for E-jet printing with colloidal crystal inks. Our results exhibit promising applications in displays, biosensors, and other functional devices.

One-dimensional nanoferroic rods; synthesis and characterization

NASA Astrophysics Data System (ADS)

Ahmed, M. A.; Seddik, U.; Okasha, N.; Imam, N. G.

2015-11-01

One-dimensional nanoferroic rods of BaTiO3 were synthesized by improved citrate auto-combustion technology using tetrabutyl titanate. X-ray diffraction (XRD), scanning electron microscopy (SEM), energy-dispersive X-ray (EDX), transmission electron microscopy (TEM), atomic force microscopy (AFM) and Fourier transform infrared spectroscopy (FTIR) have been used to characterize the prepared sample. The results indicated that the crystal structure of BaTiO3 is tetragonal phase with an average crystallite size of 47 nm. SEM image gives a cauliflower-like morphology of the agglomerated nanorods. The stoichiometry of the chemical composition of the BaTiO3 ceramic was confirmed by EDX. TEM micrograph exhibited that BaTiO3 nanoparticles have rod-like shape with an average length of 120 nm and width of 43 nm. AFM was used to investigate the surface topography and its roughness. The topography image in 3D showed that the BaTiO3 particles have a rod shape with an average particle size of 116 nm which in agreement with 3D TEM result.

A Smoluchowski model of crystallization dynamics of small colloidal clusters

NASA Astrophysics Data System (ADS)

Beltran-Villegas, Daniel J.; Sehgal, Ray M.; Maroudas, Dimitrios; Ford, David M.; Bevan, Michael A.

2011-10-01

We investigate the dynamics of colloidal crystallization in a 32-particle system at a fixed value of interparticle depletion attraction that produces coexisting fluid and solid phases. Free energy landscapes (FELs) and diffusivity landscapes (DLs) are obtained as coefficients of 1D Smoluchowski equations using as order parameters either the radius of gyration or the average crystallinity. FELs and DLs are estimated by fitting the Smoluchowski equations to Brownian dynamics (BD) simulations using either linear fits to locally initiated trajectories or global fits to unbiased trajectories using Bayesian inference. The resulting FELs are compared to Monte Carlo Umbrella Sampling results. The accuracy of the FELs and DLs for modeling colloidal crystallization dynamics is evaluated by comparing mean first-passage times from BD simulations with analytical predictions using the FEL and DL models. While the 1D models accurately capture dynamics near the free energy minimum fluid and crystal configurations, predictions near the transition region are not quantitatively accurate. A preliminary investigation of ensemble averaged 2D order parameter trajectories suggests that 2D models are required to capture crystallization dynamics in the transition region.

Rare-earth metal gallium silicides via the gallium self-flux method. Synthesis, crystal structures, and magnetic properties of RE(Ga 1–xSi x)₂ (RE=Y, La–Nd, Sm, Gd–Yb, Lu)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Darone, Gregory M.; Hmiel, Benjamin; Zhang, Jiliang

Fifteen ternary rare-earth metal gallium silicides have been synthesized using molten Ga as a molten flux. They have been structurally characterized by single-crystal and powder X-ray diffraction to form with three different structures—the early to mid-late rare-earth metals RE=La–Nd, Sm, Gd–Ho, Yb and Y form compounds with empirical formulae RE(Ga xSi 1–x)₂ (0.38≤x≤0.63), which crystallize with the tetragonal α-ThSi₂ structure type (space group I4₁/amd, No. 141; Pearson symbol tI12). The compounds of the late rare-earth crystallize with the orthorhombic α-GdSi₂ structure type (space group Imma, No. 74; Pearson symbol oI12), with refined empirical formula REGa xSi 2–x–y (RE=Ho, Er, Tm;more » 0.33≤x≤0.40, 0.10≤y≤0.18). LuGa₀.₃₂₍₁₎Si₁.₄₃₍₁₎ crystallizes with the orthorhombic YbMn₀.₁₇Si₁.₈₃ structure type (space group Cmcm, No. 63; Pearson symbol oC24). Structural trends are reviewed and analyzed; the magnetic susceptibilities of the grown single-crystals are presented. - Graphical abstract: This article details the exploration of the RE–Ga–Si ternary system with the aim to systematically investigate the structural “boundaries” between the α-ThSi₂ and α-GdSi₂-type structures, and studies of the magnetic properties of the newly synthesized single-crystalline materials. Highlights: • Light rare-earth gallium silicides crystallize in α-ThSi₂ structure type. • Heavy rare-earth gallium silicides crystallize in α-GdSi₂ structure type. • LuGaSi crystallizes in a defect variant of the YbMn₀.₁₇Si₁.₈₃ structure type.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

DOE PAGES

Shtukenberg, Alexander G.; Zhu, Qiang; Carter, Damien J.; ...

2017-05-15

Coumarin, a simple, commodity chemical isolated from beans in 1820, has, to date, only yielded one solid state structure. Here, we report a rich polymorphism of coumarin grown from the melt. Four new metastable forms were identified and their crystal structures were solved using a combination of computational crystal structure prediction algorithms and X-ray powder diffraction. With five crystal structures, coumarin has become one of the few rigid molecules showing extensive polymorphism at ambient conditions. We demonstrate the crucial role of advanced electronic structure calculations including many-body dispersion effects for accurate ranking of the stability of coumarin polymorphs and themore » need to account for anharmonic vibrational contributions to their free energy. As such, coumarin is a model system for studying weak intermolecular interactions, crystallization mechanisms, and kinetic effects.« less

Crystal structure, spectral, thermal and dielectric studies of a new zinc benzoate single crystal

NASA Astrophysics Data System (ADS)

Bijini, B. R.; Prasanna, S.; Deepa, M.; Nair, C. M. K.; Rajendra Babu, K.

2012-11-01

Single crystals of zinc benzoate with a novel structure were grown in gel media. Sodium metasilicate of gel density 1.04 g/cc at pH 6 was employed to yield transparent single crystals. The crystal structure of the compound was ascertained by single crystal X-ray diffractometry. It was noted that the crystal belongs to monoclinic system with space group P21/c with unit cell parameters a = 10.669(1) Å, b = 12.995(5) Å, c = 19.119(3) Å, and β = 94.926(3)°. The crystal was seen to possess a linear polymeric structure along b-axis; with no presence of coordinated or lattice water. CHN analysis established the stoichiometric composition of the crystal. The existence of functional groups present in the single crystal system was confirmed by FT-IR studies. The thermal characteristic of the sample was analysed by TGA-DTA techniques, and the sample was found to be thermally stable up to 280 °C. The kinetic and thermodynamic parameters were also determined. UV-Vis spectroscopy corroborated the transparency of the crystal and revealed the optical band gap to be 4 eV. Dielectric studies showed decrease in the dielectric constant of the sample with increase in frequency.

Construction of nanostructures for selective lithium ion conduction using self-assembled molecular arrays in supramolecular solids

NASA Astrophysics Data System (ADS)

Moriya, Makoto

2017-12-01

In the development of innovative molecule-based materials, the identification of the structural features in supramolecular solids and the understanding of the correlation between structure and function are important factors. The author investigated the development of supramolecular solid electrolytes by constructing ion conduction paths using a supramolecular hierarchical structure in molecular crystals because the ion conduction path is an attractive key structure due to its ability to generate solid-state ion diffusivity. The obtained molecular crystals exhibited selective lithium ion diffusion via conduction paths consisting of lithium bis(trifluoromethanesulfonyl)amide (LiTFSA) and small molecules such as ether or amine compounds. In the present review, the correlation between the crystal structure and ion conductivity of the obtained molecular crystals is addressed based on the systematic structural control of the ionic conduction paths through the modification of the component molecules. The relationship between the crystal structure and ion conductivity of the molecular crystals provides a guideline for the development of solid electrolytes based on supramolecular solids exhibiting rapid and selective lithium ion conduction.

Probing the crystal structure landscape by doping: 4-bromo, 4-chloro and 4-methylcinnamic acids.

PubMed

Desiraju, Gautam R; Chakraborty, Shaunak; Joseph, Sumy

2018-06-11

Accessing the data points in the crystal structure landscape of a molecule is a challenging task, either experimentally or computationally. We have charted the crystal structure landscape of 4-bromocinnamic acid (4BCA) experimentally and computationally: experimental doping is achieved with 4-methylcinnamic acid (4MCA) to obtain new crystal structures; computational doping is performed with 4-chlorocinnamic acid (4CCA) as a model system, because of the difficulties associated in parameterizing the Br-atom. The landscape of 4CCA is explored experimentally in turn, also by doping it with 4MCA, and is found to bear a close resemblance to the landscape of 4BCA, justifying the ready miscibility of these two halogenated cinnamic acids to form solid solutions without any change in crystal structure. In effect, 4MCA, 4CCA and 4BCA form a commutable group of crystal structures, which may be realized experimentally or computationally, and constitute the landscape. Unlike the results obtained by Kitaigorodskii and others, all but two of the multiple solid solutions obtained in the methyl-doping experiments take structures that are different from the hitherto observed crystal forms of the parent compounds. Even granted that the latter might be inherently polymorphic, this unusual observation provokes the suggestion that solid solution formation may be used to probe the crystal structure landscape. The influence of pi...pi interactions, weak hydrogen bonds and halogen bonds in directing the formation of these new structures is also seen. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Understanding the atomic-level Green-Kubo stress correlation function for a liquid through phonons in a model crystal

NASA Astrophysics Data System (ADS)

Levashov, V. A.

2014-11-01

In order to gain insight into the connection between the vibrational dynamics and the atomic-level Green-Kubo stress correlation function in liquids, we consider this connection in a model crystal instead. Of course, vibrational dynamics in liquids and crystals are quite different and it is not expected that the results obtained on a model crystal should be valid for liquids. However, these considerations provide a benchmark to which the results of the previous molecular dynamics simulations can be compared. Thus, assuming that vibrations are plane waves, we derive analytical expressions for the atomic-level stress correlation functions in the classical limit and analyze them. These results provide, in particular, a recipe for analysis of the atomic-level stress correlation functions in Fourier space and extraction of the wave-vector and frequency-dependent information. We also evaluate the energies of the atomic-level stresses. The energies obtained are significantly smaller than the energies previously determined in molecular dynamics simulations of several model liquids. This result suggests that the average energies of the atomic-level stresses in liquids and glasses are largely determined by the structural disorder. We discuss this result in the context of equipartition of the atomic-level stress energies. Analysis of the previously published data suggests that it is possible to speak about configurational and vibrational contributions to the average energies of the atomic-level stresses in a glass state. However, this separation in a liquid state is problematic. We also introduce and briefly consider the atomic-level transverse current correlation function. Finally, we address the broadening of the peaks in the pair distribution function with increase of distance. We find that the peaks' broadening (by ≈40 % ) occurs due to the transverse vibrational modes, while contribution from the longitudinal modes does not change with distance.

Diamond Raman laser emitting at 1194, 1419, and 597 nm

NASA Astrophysics Data System (ADS)

Pashinin, V. P.; Ralchenko, V. G.; Bolshakov, A. P.; Ashkinazi, E. E.; Konov, V. I.

2018-03-01

A Raman laser based on a synthetic diamond crystal pumped by nanosecond pulses of a 1030-nm Yb : YAG laser and emitting in the IR region at the first and second Stokes wavelengths of 1194 and 1419 nm, respectively, was developed. The conversion efficiency was 34% with a slope efficiency of 50% and an average power of 1.1 W at a wavelength of 1194 nm; the average power at 1419 nm was 0.52 W. Frequency doubling of the first Stokes component in a nonlinear BBO crystal resulted in orange (597.3 nm) radiation with a pulse energy of 0.15 mJ, an average power of 0.22 W, and a maximum efficiency of 20%.

Functional materials discovery using energy-structure-function maps

NASA Astrophysics Data System (ADS)

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A.; Chong, Samantha Y.; Slater, Benjamin J.; McMahon, David P.; Bonillo, Baltasar; Stackhouse, Chloe J.; Stephenson, Andrew; Kane, Christopher M.; Clowes, Rob; Hasell, Tom; Cooper, Andrew I.; Day, Graeme M.

2017-03-01

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Functional materials discovery using energy-structure-function maps.

PubMed

Pulido, Angeles; Chen, Linjiang; Kaczorowski, Tomasz; Holden, Daniel; Little, Marc A; Chong, Samantha Y; Slater, Benjamin J; McMahon, David P; Bonillo, Baltasar; Stackhouse, Chloe J; Stephenson, Andrew; Kane, Christopher M; Clowes, Rob; Hasell, Tom; Cooper, Andrew I; Day, Graeme M

2017-03-30

Molecular crystals cannot be designed in the same manner as macroscopic objects, because they do not assemble according to simple, intuitive rules. Their structures result from the balance of many weak interactions, rather than from the strong and predictable bonding patterns found in metal-organic frameworks and covalent organic frameworks. Hence, design strategies that assume a topology or other structural blueprint will often fail. Here we combine computational crystal structure prediction and property prediction to build energy-structure-function maps that describe the possible structures and properties that are available to a candidate molecule. Using these maps, we identify a highly porous solid, which has the lowest density reported for a molecular crystal so far. Both the structure of the crystal and its physical properties, such as methane storage capacity and guest-molecule selectivity, are predicted using the molecular structure as the only input. More generally, energy-structure-function maps could be used to guide the experimental discovery of materials with any target function that can be calculated from predicted crystal structures, such as electronic structure or mechanical properties.

Alignment of crystal orientations of the multi-domain photonic crystals in Parides sesostris wing scales

PubMed Central

Yoshioka, S.; Fujita, H.; Kinoshita, S.; Matsuhana, B.

2014-01-01

It is known that the wing scales of the emerald-patched cattleheart butterfly, Parides sesostris, contain gyroid-type photonic crystals, which produce a green structural colour. However, the photonic crystal is not a single crystal that spreads over the entire scale, but it is separated into many small domains with different crystal orientations. As a photonic crystal generally has band gaps at different frequencies depending on the direction of light propagation, it seems mysterious that the scale is observed to be uniformly green under an optical microscope despite the multi-domain structure. In this study, we have carefully investigated the structure of the wing scale and discovered that the crystal orientations of different domains are not perfectly random, but there is a preferred crystal orientation that is aligned along the surface normal of the scale. This finding suggests that there is an additional factor during the developmental process of the microstructure that regulates the crystal orientation. PMID:24352678

Crystal-to-Crystal Transition of Ultrasoft Colloids under Shear

NASA Astrophysics Data System (ADS)

Ruiz-Franco, J.; Marakis, J.; Gnan, N.; Kohlbrecher, J.; Gauthier, M.; Lettinga, M. P.; Vlassopoulos, D.; Zaccarelli, E.

2018-02-01

Ultrasoft colloids typically do not spontaneously crystallize, but rather vitrify, at high concentrations. Combining in situ rheo-small-angle-neutron-scattering experiments and numerical simulations we show that shear facilitates crystallization of colloidal star polymers in the vicinity of their glass transition. With increasing shear rate well beyond rheological yielding, a transition is found from an initial bcc-dominated structure to an fcc-dominated one. This crystal-to-crystal transition is not accompanied by intermediate melting but occurs via a sudden reorganization of the crystal structure. Our results provide a new avenue to tailor colloidal crystallization and the crystal-to-crystal transition at the molecular level by coupling softness and shear.

Crystal growth, structure analysis and characterisation of 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid single crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sankari, R. Siva, E-mail: sivasankari.sh@act.edu.in; Perumal, Rajesh Narayana

2014-04-24

Single crystal of dielectric material 2 - (1, 3 - dioxoisoindolin - 2 - yl) acetic acid has been grown by slow evaporation solution growth method. The grown crystal was harvested in 25 days. The crystal structure was analyzed by Single crystal X - ray diffraction. UV-vis-NIR analysis was performed to examine the optical property of the grown crystal. The thermal property of the grown crystal was studied by thermogravimetric analysis (TGA) and differential thermal analysis (DTA). The dielectric measurements were carried out and the dielectric constant was calculated and plotted at all frequencies.

Transport modes during crystal growth in a centrifuge

NASA Technical Reports Server (NTRS)

Arnold, William A.; Wilcox, William R.; Carlson, Frederick; Chait, Arnon; Regel', Liia L.

1992-01-01

Flow modes arising under average acceleration in centrifugal crystal growth, the gradient of acceleration, and the Coriolis force are investigated using a fully nonlinear three-dimensional numerical model for a centrifugal crystal growth experiment. The analysis focuses on an examination of the quasi-steady state flow modes. The importance of the gradient acceleration is determined by the value of a new nondimensional number, Ad.

X-ray structure investigation of some substituted indoles, and the x-ray crystal of 1,1'-bishomocubane

DOE Office of Scientific and Technical Information (OSTI.GOV)

Quarles, William G.

1970-05-01

The crystal structures of 5-methoxytryptamine, melatonin, and the p-bromobenzoate of 1,1'-bishomocubane have been solved by x-ray diffraction methods. A computer program for the trial and error solution of crystal structures is also described here.

Two Crystallographic Laboratory and Computational Exercises for Undergraduates.

ERIC Educational Resources Information Center

Lessinger, Leslie

1988-01-01

Describes two introductory exercises designed to teach the fundamental ideas and methods of crystallography, and to convey some important features of inorganic and organic crystal structures to students in an advanced laboratory course. Exercises include "The Crystal Structure of NiO" and "The Crystal Structure of Beta-Fumaric Acid." (CW)

MD simulations of ligand-bound and ligand-free aptamer: molecular level insights into the binding and switching mechanism of the add A-riboswitch.

PubMed

Sharma, Monika; Bulusu, Gopalakrishnan; Mitra, Abhijit

2009-09-01

Riboswitches are structural cis-acting genetic regulatory elements in 5' UTRs of mRNAs, consisting of an aptamer domain that regulates the behavior of an expression platform in response to its recognition of, and binding to, specific ligands. While our understanding of the ligand-bound structure of the aptamer domain of the adenine riboswitches is based on crystal structure data and is well characterized, understanding of the structure and dynamics of the ligand-free aptamer is limited to indirect inferences from physicochemical probing experiments. Here we report the results of 15-nsec-long explicit-solvent molecular dynamics simulations of the add A-riboswitch crystal structure (1Y26), both in the adenine-bound (CLOSED) state and in the adenine-free (OPEN) state. Root-mean-square deviation, root-mean-square fluctuation, dynamic cross-correlation, and backbone torsion angle analyses are carried out on the two trajectories. These, along with solvent accessible surface area analysis of the two average structures, are benchmarked against available experimental data and are shown to constitute the basis for obtaining reliable insights into the molecular level details of the binding and switching mechanism. Our analysis reveals the interaction network responsible for, and conformational changes associated with, the communication between the binding pocket and the expression platform. It further highlights the significance of a, hitherto unreported, noncanonical W:H trans base pairing between A73 and A24, in the OPEN state, and also helps us to propose a possibly crucial role of U51 in the context of ligand binding and ligand discrimination.

Transition to collapsed tetragonal phase in CaFe 2As 2 single crystals as seen by 57Fe Mössbauer spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bud'ko, Sergey L.; Ma, Xiaoming; Tomić, Milan

Temperature dependent measurements of 57Fe Mössbauer spectra on CaFe 2As 2 single crystals in the tetragonal and collapsed tetragonal phases are reported. Clear features in the temperature dependencies of the isomer shift, relative spectra area, and quadrupole splitting are observed at the transition from the tetragonal to the collapsed tetragonal phase. From the temperature dependent isomer shift and spectral area data, an average stiffening of the phonon modes in the collapsed tetragonal phase is inferred. The quadrupole splitting increases by ~25% on cooling from room temperature to ~100 K in the tetragonal phase and is only weakly temperature dependent atmore » low temperatures in the collapsed tetragonal phase, in agreement with the anisotropic thermal expansion in this material. In order to gain microscopic insight about these measurements, we perform ab initio density functional theory calculations of the electric field gradient and the electron density of CaFe 2As 2 in both phases. By comparing the experimental data with the calculations we are able to fully characterize the crystal structure of the samples in the collapsed-tetragonal phase through determination of the As z coordinate. Furthermore, based on the obtained temperature dependent structural data we are able to propose charge saturation of the Fe-As bond region as the mechanism behind the stabilization of the collapsed-tetragonal phase at ambient pressure.« less

Dislocation Multiplication in the Early Stage of Deformation in Mo Single Crystals

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hsiung, L.; Lassila, D.H.

Initial dislocation structure in annealed high-purity Mo single crystals and deformation substructure in a crystal subjected to 1% compression have been examined and studied using transmission electron microscopy (TEM) techniques in order to investigate dislocation multiplication mechanisms in the early stage of plastic deformation. The initial dislocation density is in a range of 10{sup 6} {approx} 10{sup 7} cm{sup -2}, and the dislocation structure is found to contain many grown-in superjogs along dislocation lines. The dislocation density increases to a range of 10{sup 8} {approx} 10{sup 9} cm{sup -2}, and the average jog height is also found to increase aftermore » compressing for a total strain of 1%. It is proposed that the preexisting jogged screw dislocations can act as (multiple) dislocation multiplication sources when deformed under quasi-static conditions. The jog height can increase by stress-induced jog coalescence, which takes place via the lateral migration (drift) of superjogs driven by unbalanced line-tension partials acting on link segments of unequal lengths. The coalescence of superjogs results in an increase of both link length and jog height. Applied shear stress begins to push each link segment to precede dislocation multiplication when link length and jog height are greater than critical lengths. This ''dynamic'' dislocation multiplication source is suggested to be crucial for the dislocation multiplication in the early stage of plastic deformation in Mo.« less

Effects of cyclic structure inhibitors on the morphology and growth of tetrahydrofuran hydrate crystals

NASA Astrophysics Data System (ADS)

Li, Sijia; Wang, Yanhong; Lang, Xuemei; Fan, Shuanshi

2013-08-01

Morphology and growth of hydrate crystals with cyclic structure inhibitors at a hydrate-liquid interface were directly observed through a microscopic manipulating apparatus. Tetrahydrofuran (THF) hydrate was employed as an objective. The effects of four kind of cyclic structure inhibitors, polyvinylpyrrolidone (PVP), poly(N-vinyl-2-pyrrolidone-co-2-vinyl pyridine) (PVPP), poly(2-vinyl pyridine-co-N-vinylcaprolactam) (PVPC) and poly(N-vinylcaprolactam) (PVCap), were investigated. Morphological patterns between each hydrate crystal growth from hydrate-liquid interface into droplet were found differ significantly. Lamellar structure growth of hydrate crystal was observed without inhibitor, while with PVP was featheriness-like, PVPP was like long dendritic crystal, PVPC was Mimosa pudica leaf-like and PVCap was like weeds. The growth rate of hydrate crystal without inhibitor was 0.00498 mm3/s, while with PVPP, PVPC and PVCap, were 0.00339 mm3/s, 0.00350 mm3/s, 0.00386 mm3/s and 0.00426 mm3/s, respectively. Cyclic structure inhibitors can decrease the growth rate, degree of reduction in growth rate of hydrate crystals decrease with the increase of cylinder number.

Therapeutic Antibody Engineering To Improve Viscosity and Phase Separation Guided by Crystal Structure.

PubMed

Chow, Chi-Kin; Allan, Barrett W; Chai, Qing; Atwell, Shane; Lu, Jirong

2016-03-07

Antibodies at high concentrations often reveal unanticipated biophysical properties suboptimal for therapeutic development. The purpose of this work was to explore the use of point mutations based on crystal structure information to improve antibody physical properties such as viscosity and phase separation (LLPS) at high concentrations. An IgG4 monoclonal antibody (Mab4) that exhibited high viscosity and phase separation at high concentration was used as a model system. Guided by the crystal structure, four CDR point mutants were made to evaluate the role of hydrophobic and charge interactions on solution behavior. Surprisingly and unpredictably, two of the charge mutants, R33G and N35E, showed a reduction in viscosity and a lower propensity to form LLPS at high concentration compared to the wild-type (WT), while a third charge mutant S28K showed an increased propensity to form LLPS compared to the WT. A fourth mutant, F102H, had reduced hydrophobicity, but unchanged viscosity and phase separation behavior. We further evaluated the correlation of various biophysical measurements including second virial coefficient (A2), interaction parameter (kD), weight-average molecular weight (WAMW), and hydrodynamic diameters (DH), at relatively low protein concentration (4 to 15 mg/mL) to physical properties, such as viscosity and liquid-liquid phase separation (LLPS), at high concentration. Surprisingly, kD measured using dynamic light scattering (DLS) at low antibody concentration correlated better with viscosity and phase separation than did A2 for Mab4. Our results suggest that the high viscosity and phase separation observed at high concentration for Mab4 are mainly driven by charge and not hydrophobicity.

Synthesis, XRD crystal structure, spectroscopic characterization (FT-IR, 1H and 13C NMR), DFT studies, chemical reactivity and bond dissociation energy studies using molecular dynamics simulations and evaluation of antimicrobial and antioxidant activities of a novel chalcone derivative, (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Zainuri, D. Alwani; Arshad, Suhana; Khalib, N. Che; Razak, I. Abdul; Pillai, Renjith Raveendran; Sulaiman, S. Fariza; Hashim, N. Shafiqah; Ooi, K. Leong; Armaković, Stevan; Armaković, Sanja J.; Panicker, C. Yohannan; Van Alsenoy, C.

2017-01-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-iodophenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The compound crystallizes in the monoclinic system with P21/c space group with the unit cell parameters of a = 16.147 (2) Å, b = 14.270 (2) Å, c = 5.9058 (9) Å, β = 92.577 (3)° and Z = 4. The molecular geometry obtained from X-Ray structure determination was optimized by Density Functional Theory (DFT) using B3LYP/6-31G+(d, p)/Lanl2dz(f) method in the ground state. The IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. In order to investigate local reactivity properties of the title molecule, we have conducted DFT calculations of average local ionization energy surface and Fukui functions which were mapped to the electron density surface. In order to predict the open air stability and possible degradation properties, within DFT approach, we have also calculated bond dissociation energies. 1H and 13C NMR spectra were recorded and chemical shifts were calculated theoretically and compared with the experimental values. In addition, in vitro antimicrobial results show that the title compound has great potential of antibacterial activity against Staphylococcus aureus, Staphylococcus epidermidis and Micrococcus luteus bacteria and antifungal activity against Candida albicans in comparison to some reported chalcone derivatives. Antioxidant studies revealed the highest metal chelating activity of this compound.

Bridgman growth of large-aperture yttrium calcium oxyborate crystal

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wu, Anhua, E-mail: wuanhua@mail.sic.ac.cn; Jiang, Linwen; Qian, Guoxing

2012-09-15

Highlights: ► YCOB is a novel non-linear optical crystal possessing good thermal, mechanical and nonlinear optical properties. ► Large size crystal growth is key technology question for YCOB crystal. ► YCOB crystals 3 in. in diameter were grown with modified vertical Bridgman method. ► It is a more effective growth method to obtain large size and high quality YCOB crystal. -- Abstract: Large-aperture yttrium calcium oxyborate YCa{sub 4}O(BO{sub 3}){sub 3} (YCOB) crystals with 3 in. in diameter were grown with modified vertical Bridgman method, and the large crystal plate (63 mm × 68 mm × 20 mm) was harvested formore » high-average power frequency conversion system. The crack, facet growth and spiral growth can be effectively controlled in the as-grown crystal, and Bridgman method displays more effective in obtain large size and high quality YCOB crystal plate than Czochralski technique.« less

Phenytoin crystal growth rates in the presence of phosphate and chloride ions

NASA Astrophysics Data System (ADS)

Zipp, G. L.; Rodríguez-Hornedo, N.

1992-09-01

Phenytoin crystal growth kinetics have been measured as a function of supersaturation in pH 2.2 phosphoric acid and pH 2.2 hydrochloric acid solutions. Two different methods were used for the kinetic analysis. The first involved a zone-sensing device which provided an analysis of the distribution of crystals in a batch crystallizer. Crystal growth rates were calculated from the increase in the size of the distribution with time. In the second method, growth rates were evaluated from the change in size with time of individual crystals observed under an inverted microscope. The results from each method compare favorably. The use of both techniques provides an excellent opportunity to exploit the strengths of each: an average growth rate from a population of crystals from batch crystallization and insight into the effect of growth on the morphology of the crystals from the individual crystal measurements.

Polarizability of acetanilide and RDX in the crystal: effect of molecular geometry

NASA Astrophysics Data System (ADS)

Tsiaousis, D.; Munn, R. W.; Smith, P. J.; Popelier, P. L. A.

2004-10-01

Density-functional theory with the B3LYP functional at the 6-311++G** level is used to calculate the dipole moment and the static polarizability for acetanilide and 1,3,5-trinitro-1,3,5-triazacyclohexane (RDX) in their in-crystal structures. For acetanilide the dipole moment is 2{1}/{2}% larger than for the gas-phase structure and for RDX (where there is a gross geometry change) it is 15% larger. The polarizability for the in-crystal structure is smaller than for the gas-phase structure by 3% for both species, whereas the in-crystal effective optical polarizability is larger than the gas-phase static polarizability for both crystals. Hence, effects in addition to the molecular geometry change in the crystal must be considered in order to interpret the effective polarizability completely.

Synthesis, XRD crystal structure, spectroscopic characterization, local reactive properties using DFT and molecular dynamics simulations and molecular docking study of (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one

NASA Astrophysics Data System (ADS)

Arshad, Suhana; Raveendran Pillai, Renjith; Zainuri, Dian Alwani; Khalib, Nuridayanti Che; Razak, Ibrahim Abdul; Armaković, Stevan; Armaković, Sanja J.; Renjith, Rishikesh; Panicker, C. Yohannan; Van Alsenoy, C.

2017-06-01

In the present study, the title compound named as (E)-1-(4-bromophenyl)-3-(4-(trifluoromethoxy)phenyl)prop-2-en-1-one was synthesized and structurally characterized by single-crystal X-ray diffraction. The FT-IR spectrum was recorded and interpreted in details with the aid of Density Functional Theory (DFT) calculations and Potential Energy Distribution (PED) analysis. Average local ionization energies (ALIE) and Fukui functions have been used as quantum-molecular descriptors to locate the molecule sites that could be of importance from the aspect of reactivity. Degradation properties have been assessed by calculations of bond dissociation energies (BDE) for hydrogen abstraction and the rest of the single acyclic bonds, while molecular dynamics (MD) simulations were used in order to calculate radial distribution functions and determine the atoms with significant interactions with water. In order to understand how the title molecule inhibits and hence increases the catalytic efficiency of MOA-B enzyme, molecular docking study was performed to fit the title compound into the binding site of MOA-B enzyme.

Broadband and omnidirectional light harvesting enhancement in photovoltaic devices with aperiodic TiO2 nanotube photonic crystal

NASA Astrophysics Data System (ADS)

Guo, Min; Su, Haijun; Zhang, Jun; Liu, Lin; Fu, Nianqing; Yong, Zehui; Huang, Haitao; Xie, Keyu

2017-03-01

Design of more effective broadband light-trapping elements to improve the light harvesting efficiency under both normal and tilted light for solar cells and other photonic devices is highly desirable. Herein we present a theoretical analysis on the optical properties of a novel TiO2 nanotube aperiodic photonic crystal (NT APC) following an aperiodic sequences and its photocurrent enhancement effect for dye-sensitized solar cells (DSSCs) under various incidence angles. It is found that, compared to regular PC, the designed TiO2 NT APC owns broader reflection region and a desired omnidirectional reflection (ODR) bandgaps, leading to considerable and stable photocurrent enhancement under both normal and oblique light. The effects of the structural parameters of the TiO2 NT APC, including the average lattice constant and the common sequence difference, on the optical properties, ODR bandgaps and absorption magnification of the integrated DSSCs are investigated in detail. Moreover, the angular dependence of photocurrent enhancement and angular compensation effect of such TiO2 NT APCs are also provided to offer a guidance on the optimum structural parameters design under different engineering application conditions.

Block Copolymer Micelles for Photonic Fluids and Crystals.

PubMed

Poutanen, Mikko; Guidetti, Giulia; Gröschel, Tina I; Borisov, Oleg V; Vignolini, Silvia; Ikkala, Olli; Gröschel, Andre H

2018-04-24

Block copolymer micelles (BCMs) are self-assembled nanoparticles in solution with a collapsed core and a brush-like stabilizing corona typically in the size range of tens of nanometers. Despite being widely studied in various fields of science and technology, their ability to form structural colors at visible wavelength has not received attention, mainly due to the stringent length requirements of photonic lattices. Here, we describe the precision assembly of BCMs with superstretched corona, yet with narrow size distribution to qualify as building blocks for tunable and reversible micellar photonic fluids (MPFs) and micellar photonic crystals (MPCs). The BCMs form free-flowing MPFs with an average interparticle distance of 150-300 nm as defined by electrosteric repulsion arising from the highly charged and stretched corona. Under quiescent conditions, millimeter-sized MPCs with classical FCC lattice grow within the photonic fluid-medium upon refinement of the positional order of the BCMs. We discuss the generic properties of MPCs with special emphasis on surprisingly narrow reflected wavelengths with full width at half-maximum (fwhm) as small as 1 nm. We expect this concept to open a generic and facile way for self-assembled tunable micellar photonic structures.

Total Scattering and Pair Distribution Function Analysis in Modelling Disorder in PZN

DOE Office of Scientific and Technical Information (OSTI.GOV)

Whitfield, Ross E.; Goossens, Darren J; Welberry, T. R.

2016-01-01

The ability of the pair distribution function (PDF) analysis of total scattering (TS) from a powder to determine the local ordering in ferroelectric PZN (PbZn 1/3Nb 2/3O 3) has been explored by comparison with a model established using single-crystal diffuse scattering (SCDS). While X-ray PDF analysis is discussed, the focus is on neutron diffraction results because of the greater extent of the data and the sensitivity of the neutron to oxygen atoms, the behaviour of which is important in PZN. The PDF was shown to be sensitive to many effects not apparent in the average crystal structure, including variations inmore » the B-site—O separation distances and the fact that (110) Pb 2+ displacements are most likely. A qualitative comparison between SCDS and the PDF shows that some features apparent in SCDS were not apparent in the PDF. These tended to pertain to short-range correlations in the structure, rather than to interatomic separations. For example, in SCDS the short-range alternation of the B-site cations was quite apparent in diffuse scattering at (½ ½ ½), whereas it was not apparent in the PDF.« less

From atoms to steps: The microscopic origins of crystal evolution

NASA Astrophysics Data System (ADS)

Patrone, Paul N.; Einstein, T. L.; Margetis, Dionisios

2014-07-01

The Burton-Cabrera-Frank (BCF) theory of crystal growth has been successful in describing a wide range of phenomena in surface physics. Typical crystal surfaces are slightly misoriented with respect to a facet plane; thus, the BCF theory views such systems as composed of staircase-like structures of steps separating terraces. Adsorbed atoms (adatoms), which are represented by a continuous density, diffuse on terraces, and steps move by absorbing or emitting these adatoms. Here we shed light on the microscopic origins of the BCF theory by deriving a simple, one-dimensional (1D) version of the theory from an atomistic, kinetic restricted solid-on-solid (KRSOS) model without external material deposition. We define the time-dependent adatom density and step position as appropriate ensemble averages in the KRSOS model, thereby exposing the non-equilibrium statistical mechanics origins of the BCF theory. Our analysis reveals that the BCF theory is valid in a low adatom-density regime, much in the same way that an ideal gas approximation applies to dilute gasses. We find conditions under which the surface remains in a low-density regime and discuss the microscopic origin of corrections to the BCF model.

Amplified Emission and Field-Effect Transistor Characteristics of One-Dimensionally Structured 2,5-Bis(4-biphenylyl)thiophene Crystals.

PubMed

Hashimoto, Kazumasa; Sasaki, Fumio; Hotta, Shu; Yanagi, Hisao

2016-04-01

One-dimensional (1D) structures of 2,5-bis(4-biphenylyl)thiophene (BP1T) crystals are fabricated for light amplification and field-effect transistor (FET) measurements. A strip-shaped 1D structure (10 µm width) made by photolitography of a vapor-deposited polycrystalline film shows amplified spontaneous emission and lasing oscillations under optical pumping. An FET fabricated with this 1D structure exhibits hole-conduction with a mobility of µh = 8.0 x 10(-3) cm2/Vs. Another 1 D-structured FET is fabricated with epitaxially grown needle-like crystals of BP1T. This needle-crystal FET exhibits higher mobility of µh = 0.34 cm2/Vs. This improved hole mobility is attributed to the single-crystal channel of epitaxial needles while the grain boudaries in the polycrystalline 1 D-structure decrease the carrier transport.

Average crystal structure(s) of the embedded meta stable η‧-phase in the Al-Mg-Zn system

NASA Astrophysics Data System (ADS)

Bøvik Larsen, Helge; Thorkildsen, Gunnar; Natland, Sølvi; Pattison, Philip

2014-05-01

Meta stable embedded nano-sized ?-particles within a single grain extracted from an alloy having the nominal composition ? have been examined with X-ray diffraction. By applying the orientational and metric relationships that exist between the hexagonal unit cell of the ?-particles and the cubic unit cell of the Al-matrix, it has been proven possible to directly collect diffracted intensity data from the ?-particle ensemble. This has been done using synchrotron radiation and a ?-diffractometer having a scintillator point detector setup. The approach has resulted in improved data quality compared to previous experiments. The interpretation of the data set, based on a combination of Patterson syntheses, direct methods and geometrical restraints, yielded two possible average structural representations: one Al-rich with the approximate stoichiometric composition ? and one Al-depleted with approximate stoichiometric composition ?. Both structures are realized in the same space group, ?, and are most probably superimposed in the crystalline system examined. The geometries are discussed within the atomic environment approach where icosahedral or near-icosahedral configurations are encountered. Comparison with previous published models and the equilibrium structure reveals a main difference related to the distribution of the Zn-sites in the unit cell. A possible transformation path is also suggested. Various aspects and challenges regarding data collection, data reduction and data quality are specifically addressed.

Realization of a complementary medium using dielectric photonic crystals.

PubMed

Xu, Tao; Fang, Anan; Jia, Ziyuan; Ji, Liyu; Hang, Zhi Hong

2017-12-01

By exploiting the scaling invariance of photonic band diagrams, a complementary photonic crystal slab structure is realized by stacking two uniformly scaled double-zero-index dielectric photonic crystal slabs together. The space cancellation effect in complementary photonic crystals is demonstrated in both numerical simulations and microwave experiments. The refractive index dispersion of double-zero-index dielectric photonic crystal is experimentally measured. Using pure dielectrics, our photonic crystal structure will be an ideal platform to explore various intriguing properties related to a complementary medium.

High-pressure investigations of yttrium(III) oxoarsenate(V): Crystal structure and luminescence properties of Eu3+-doped scheelite-type Y[AsO4] from xenotime-type precursors

NASA Astrophysics Data System (ADS)

Ledderboge, Florian; Nowak, Jan; Massonne, Hans-Joachim; Förg, Katharina; Höppe, Henning A.; Schleid, Thomas

2018-07-01

Colourless, water- and air-stable single crystals of yttrium(III) oxoarsenate(V) Y[AsO4] in the xenotime-type crystal structure were prepared by the reaction of yttrium sesquioxide (Y2O3) dissolved in aqueous nitric acid (13%) with a solution of arsenic(V) oxide hydrate (As2O5·3H2O) and subsequent neutralization with 1 M caustic soda. Y[AsO4] crystallizes tetragonally in the space group I41/amd with the lattice parameters a = 704.63(6) and c = 628.94(5) pm for Z = 4 and is isotypic to the minerals xenotime RE[PO4] (RE: mainly Y and Yb) and chernovite RE[AsO4] (RE: mainly Y and Ce). This xenotime-type yttrium compound was used as precursor in a high-pressure experiment (20 kbar) at 700 °C to create a new tetragonal modification of Y[AsO4]. It shows the scheelite-type structure (space group: I41/a) with the lattice parameters a = 498.23(4) and c = 1120.71(9) pm for Z = 4, named after the mineral scheelite (Ca[WO4]). Both tetragonal structures are characterized by only one crystallographically unique position for each of the Y3+, As5+ and O2- ions with distances of d(Y-O) = 232 and 241 pm (C.N. = 8) as well as d(As-O) = 169 pm (C.N. = 4) in the case of the scheelite-type structure. The xenotime-type compound shows an unexpected slight decrease in average bond lengths for the yttrium to oxygen (d(Y-O) = 230 and 241 pm, C.N. = 8) as well as for the arsenic to oxygen distances (d(As-O) = 168 pm, C.N. = 4), accompanied by a drastic density increase from Dx = 4.85 (xenotime type) to Dx = 5.44 g • cm-3 (scheelite type). Luminescence spectroscopic measurements of the Eu3+-doped Y[AsO4] samples, obtained in experiments at similar conditions as for the pure compounds, show a bright, reddish lighting for the scheelite type, which does not occur for the xenotime type of yttrium(III) oxoarsenate(V).

Imaging and engineering the nanoscale-domain structure of a Sr0.61Ba0.39Nb2O6 crystal using a scanning force microscope

NASA Astrophysics Data System (ADS)

Terabe, K.; Takekawa, S.; Nakamura, M.; Kitamura, K.; Higuchi, S.; Gotoh, Y.; Gruverman, A.

2002-09-01

We have investigated the ferroelectric domain structure formed in a Sr0.61Ba0.39Nb2O6 single crystal by cooling the crystal through the Curie point. Imaging the etched surface structure using a scanning force microscope (SFM) in both the topographic mode and the piezoresponse mode revealed that a multidomain structure of nanoscale islandlike domains was formed. The islandlike domains could be inverted by applying an appropriate voltage using a conductive SFM tip. Furthermore, a nanoscale periodically inverted-domain structure was artificially fabricated using the crystal which underwent poling treatment.

Morphological Evolution of Vertically Standing Molybdenum Disulfide Nanosheets by Chemical Vapor Deposition.

PubMed

Zhang, Song; Liu, Jiajia; Ruiz, Karla Hernandez; Tu, Rong; Yang, Meijun; Li, Qizhong; Shi, Ji; Li, Haiwen; Zhang, Lianmeng; Goto, Takashi

2018-04-20

In this study, we demonstrated the chemical vapor deposition (CVD) of vertically standing molybdenum disulfide (MoS₂) nanosheets, with an unconventional combination of molybdenum hexacarbonyl (Mo(CO)₆) and 1,2-ethanedithiol (C₂H₆S₂) as the novel kind of Mo and S precursors respectively. The effect of the distance between the precursor’s outlet and substrates (denoted as d ) on the growth characteristics of MoS₂, including surface morphology and nanosheet structure, was investigated. Meanwhile, the relationship between the structure characteristics of MoS₂ nanosheets and their catalytic performance for hydrogen evolution reaction (HER) was elucidated. The formation of vertically standing nanosheets was analyzed and verified by means of an extrusion growth model. The crystallinity, average length, and average depth between peak and valley ( R z) of MoS₂ nanosheets differed depending on the spatial location of the substrate. Good crystalized MoS₂ nanosheets grown at d = 5.5 cm with the largest average length of 440 nm, and the highest R z of 162 nm contributed to a better HER performance, with a respective Tafel slope and exchange current density of 138.9 mV/decade, and 22.6 μA/cm² for raw data (127.8 mV/decade and 19.3 μA/cm² for iR-corrected data).

Crystallization of PTP Domains.

PubMed

Levy, Colin; Adams, James; Tabernero, Lydia

2016-01-01

Protein crystallography is the most powerful method to obtain atomic resolution information on the three-dimensional structure of proteins. An essential step towards determining the crystallographic structure of a protein is to produce good quality crystals from a concentrated sample of purified protein. These crystals are then used to obtain X-ray diffraction data necessary to determine the 3D structure by direct phasing or molecular replacement if the model of a homologous protein is available. Here, we describe the main approaches and techniques to obtain suitable crystals for X-ray diffraction. We include tools and guidance on how to evaluate and design the protein construct, how to prepare Se-methionine derivatized protein, how to assess the stability and quality of the sample, and how to crystallize and prepare crystals for diffraction experiments. While general strategies for protein crystallization are summarized, specific examples of the application of these strategies to the crystallization of PTP domains are discussed.

The control of ice crystal growth and effect on porous structure of konjac glucomannan-based aerogels.

PubMed

Ni, Xuewen; Ke, Fan; Xiao, Man; Wu, Kao; Kuang, Ying; Corke, Harold; Jiang, Fatang

2016-11-01

Konjac glucomannan (KGM)-based aerogels were prepared using a combination of sol-gel and freeze-drying methods. Preparation conditions were chosen to control ice crystal growth and aerogel structure formation. The ice crystals formed during pre-freezing were observed by low temperature polarizing microscopy, and images of aerogel pores were obtained by scanning electron microscopy. The size of ice crystals were calculated and size distribution maps were drawn, and similarly for aerogel pores. Results showed that ice crystal growth and aerogel pore sizes may be controlled by varying pre-freezing temperatures, KGM concentration and glyceryl monostearate concentration. The impact of pre-freezing temperatures on ice crystal growth was explained as combining ice crystal growth rate with nucleation rate, while the impacts of KGM and glyceryl monostearate concentration on ice crystal growth were interpreted based on their influences on sol network structure. Copyright © 2016 Elsevier B.V. All rights reserved.

Investigation of selected structural parameters in Fe 95Si 5 amorphous alloy during crystallization process

NASA Astrophysics Data System (ADS)

Fronczyk, Adam

2007-04-01

In this study, we report on a crystallization behavior of the Fe 95Si 5 metallic glasses using a differential scanning cabrimetry (DSC), and X-ray diffraction. The paper presents the results of experimental investigation of Fe 95Si 5 amorphous alloy, subjected to the crystallizing process by the isothermal annealing. The objective of the experiment was to determine changes in the structural parameters during crystallization process of the examined alloy. Crystalline diameter and the lattice constant of the crystallizing phase were used as parameters to evaluate structural changes in material.

A historical perspective on protein crystallization from 1840 to the present day.

PubMed

Giegé, Richard

2013-12-01

Protein crystallization has been known since 1840 and can prove to be straightforward but, in most cases, it constitutes a real bottleneck. This stimulated the birth of the biocrystallogenesis field with both 'practical' and 'basic' science aims. In the early years of biochemistry, crystallization was a tool for the preparation of biological substances. Today, biocrystallogenesis aims to provide efficient methods for crystal fabrication and a means to optimize crystal quality for X-ray crystallography. The historical development of crystallization methods for structural biology occurred first in conjunction with that of biochemical and genetic methods for macromolecule production, then with the development of structure determination methodologies and, recently, with routine access to synchrotron X-ray sources. Previously, the identification of conditions that sustain crystal growth occurred mostly empirically but, in recent decades, this has moved progressively towards more rationality as a result of a deeper understanding of the physical chemistry of protein crystal growth and the use of idea-driven screening and high-throughput procedures. Protein and nucleic acid engineering procedures to facilitate crystallization, as well as crystallization methods in gelled-media or by counter-diffusion, represent recent important achievements, although the underlying concepts are old. The new nanotechnologies have brought a significant improvement in the practice of protein crystallization. Today, the increasing number of crystal structures deposited in the Protein Data Bank could mean that crystallization is no longer a bottleneck. This is not the case, however, because structural biology projects always become more challenging and thereby require adapted methods to enable the growth of the appropriate crystals, notably macromolecular assemblages. © 2013 FEBS.

Large Area Cd0.9Zn0.1Te Pixelated Detector: Fabrication and Characterization

NASA Astrophysics Data System (ADS)

Chaudhuri, Sandeep K.; Nguyen, Khai; Pak, Rahmi O.; Matei, Liviu; Buliga, Vladimir; Groza, Michael; Burger, Arnold; Mandal, Krishna C.

2014-04-01

Cd0.9Zn0.1Te (CZT) based pixelated radiation detectors have been fabricated and characterized for gamma ray detection. Large area CZT single crystals has been grown using a tellurium solvent method. A 10 ×10 guarded pixelated detector has been fabricated on a 19.5 ×19.5 ×5 mm3 crystal cut out from the grown ingot. The pixel dimensions were 1.3 ×1.3 mm2 and were pitched at 1.8 mm. A guard grid was used to reduce interpixel/inter-electrode leakage. The crystal was characterized in planar configuration using electrical, optical and optoelectronic methods prior to the fabrication of pixelated geometry. Current-voltage (I-V) measurements revealed a leakage current of 27 nA at an operating bias voltage of 1000 V and a resistivity of 3.1 ×1010 Ω-cm. Infrared transmission imaging revealed an average tellurium inclusion/precipitate size less than 8 μm. Pockels measurement has revealed a near-uniform depth-wise distribution of the internal electric field. The mobility-lifetime product in this crystal was calculated to be 6.2 ×10 - 3 cm2/V using alpha ray spectroscopic method. Gamma spectroscopy using a 137Cs source on the pixelated structure showed fully resolved 662 keV gamma peaks for all the pixels, with percentage resolution (FWHM) as high as 1.8%.

Kinetic products in coordination networks: ab initio X-ray powder diffraction analysis.

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

Porous coordination networks are materials that maintain their crystal structure as molecular "guests" enter and exit their pores. They are of great research interest with applications in areas such as catalysis, gas adsorption, proton conductivity, and drug release. As with zeolite preparation, the kinetic states in coordination network preparation play a crucial role in determining the final products. Controlling the kinetic state during self-assembly of coordination networks is a fundamental aspect of developing further functionalization of this class of materials. However, unlike for zeolites, there are few structural studies reporting the kinetic products made during self-assembly of coordination networks. Synthetic routes that produce the necessary selectivity are complex. The structural knowledge obtained from X-ray crystallography has been crucial for developing rational strategies for design of organic-inorganic hybrid networks. However, despite the explosive progress in the solid-state study of coordination networks during the last 15 years, researchers still do not understand many chemical reaction processes because of the difficulties in growing single crystals suitable for X-ray diffraction: Fast precipitation can lead to kinetic (metastable) products, but in microcrystalline form, unsuitable for single crystal X-ray analysis. X-ray powder diffraction (XRPD) routinely is used to check phase purity, crystallinity, and to monitor the stability of frameworks upon guest removal/inclusion under various conditions, but rarely is used for structure elucidation. Recent advances in structure determination of microcrystalline solids from ab initio XRPD have allowed three-dimensional structure determination when single crystals are not available. Thus, ab initio XRPD structure determination is becoming a powerful method for structure determination of microcrystalline solids, including porous coordination networks. Because of the great interest across scientific disciplines in coordination networks, especially porous coordination networks, the ability to determine crystal structures when the crystals are not suitable for single crystal X-ray analysis is of paramount importance. In this Account, we report the potential of kinetic control to synthesize new coordination networks and we describe ab initio XRPD structure determination to characterize these networks' crystal structures. We describe our recent work on selective instant synthesis to yield kinetically controlled porous coordination networks. We demonstrate that instant synthesis can selectively produce metastable networks that are not possible to synthesize by conventional solution chemistry. Using kinetic products, we provide mechanistic insights into thermally induced (573-723 K) (i.e., annealing method) structural transformations in porous coordination networks as well as examples of guest exchange/inclusion reactions. Finally, we describe a memory effect that allows the transfer of structural information from kinetic precursor structures to thermally stable structures through amorphous intermediate phases. We believe that ab initio XRPD structure determination will soon be used to investigate chemical processes that lead intrinsically to microcrystalline solids, which up to now have not been fully understood due to the unavailability of single crystals. For example, only recently have researchers used single-crystal X-ray diffraction to elucidate crystal-to-crystal chemical reactions taking place in the crystalline scaffold of coordination networks. The potential of ab initio X-ray powder diffraction analysis goes beyond single-crystal-to-single-crystal processes, potentially allowing members of this field to study intriguing in situ reactions, such as reactions within pores.

Some Lower Valence Vanadium Fluorides: Their Crystal Distortions, Domain Structures, Modulated Structures, Ferrimagnetism, and Composition Dependence.

ERIC Educational Resources Information Center

Hong, Y. S.; And Others

1980-01-01

Describes some contemporary concepts unique to the structure of advanced solids, i.e., their crystal distortions, domain structures, modulated structures, ferrimagnetism, and composition dependence. (Author/CS)

High-resolution 2-D Bragg diffraction reveal heterogeneous domain transformation behavior in a bulk relaxor ferroelectric

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pramanick, Abhijit, E-mail: apramani@cityu.edu.hk; Stoica, Alexandru D.; An, Ke

2016-08-29

In-situ measurement of fine-structure of neutron Bragg diffraction peaks from a relaxor single-crystal using a time-of-flight instrument reveals highly heterogeneous mesoscale domain transformation behavior under applied electric fields. It is observed that only ∼25% of domains undergo reorientation or phase transition contributing to large average strains, while at least 40% remain invariant and exhibit microstrains. Such insights could be central for designing new relaxor materials with better performance and longevity. The current experimental technique can also be applied to resolve complex mesoscale phenomena in other functional materials.

High-resolution 2-D Bragg diffraction reveal heterogeneous domain transformation behavior in a bulk relaxor ferroelectric

DOE PAGES

Pramanick, Abhijit; Stoica, Alexandru D.; An, Ke

2016-09-02

In-situ measurement of fine-structure of neutron Bragg diffraction peaks from a relaxor single-crystal using a time-of-flight instrument reveals highly heterogeneous mesoscale domain transformation behavior under applied electric fields. We observed that only 25% of domains undergo reorienta- tion or phase transition contributing to large average strains, while at least 40% remain invariant and exhibit microstrains. Such insights could be central for designing new relaxor materials with better performance and longevity. The current experimental technique can also be applied to resolve com- plex mesoscale phenomena in other functional materials.

Silver nanoparticles added PVDF/ZnO nanocomposites: Synthesis and characterization

NASA Astrophysics Data System (ADS)

Singh, Utpal; Kumari, Niraj; Jha, Anal K.; Chandra, K. P.; Kolte, Jayant; Kulkarni, A. R.; Prasad, K.

2018-05-01

Silver and zinc oxide nanoparticles were prepared using citric acid method. The formations and crystal structures were ascertained from the X-ray diffraction data and the average crystallite size was estimated using Williamson-Hall approach. The hybrid combinations of Ag and ZnO nanoparticles were utilized to prepare PVDF/ZnO(90/10)-Ag nanocomposites (with Ag as filler: 0.5, 1 and 1.5%) using melt-mixing technique. Cole-Cole analysis suggested the dielectric relaxation in this system to be of non-Debye type. Also, addition of Ag nanoparticles enabled long-range conductivity in PVDF/ZnO nanocomposite.

Structural and optical properties of nano-sized K3Nd(PO4)2:Yb3+ orthophosphate.

PubMed

Mizer, D; Macalik, L; Tomaszewski, P E; Lisiecki, R; Godlewska, P; Matraszek, A; Szczygieł, I; Zawadzki, M; Hanuza, J

2009-09-01

Nanocrystals of tripotassium neodymium bis-phosphate(V) doped with ytterbium ions, K3Nd(PO4)2: Yb3+, were synthesized by Pechini method. The obtained grains, having an average size of about 40 nm, were characterised by X-ray, electron microscopic, electron absorption, luminescence and IR studies. Moreover, fluorescence decay studies were carried out at room temperature. The energy transfer from the Nd3+ to Yb3+ was described and discussed. The results were compared to those of the K3Nd(PO4)2 bulk crystal.

Aperiodic crystals and beyond.

PubMed

Grimm, Uwe

2015-06-01

Crystals are paradigms of ordered structures. While order was once seen as synonymous with lattice periodic arrangements, the discoveries of incommensurate crystals and quasicrystals led to a more general perception of crystalline order, encompassing both periodic and aperiodic crystals. The current definition of crystals rests on their essentially point-like diffraction. Considering a number of recently investigated toy systems, with particular emphasis on non-crystalline ordered structures, the limits of the current definition are explored.

Structuring β-Ga2O3 photonic crystal photocatalyst for efficient degradation of organic pollutants.

PubMed

Li, Xiaofang; Zhen, Xiuzheng; Meng, Sugang; Xian, Jiangjun; Shao, Yu; Fu, Xianzhi; Li, Danzhen

2013-09-03

Coupling photocatalysts with photonic crystals structure is based on the unique property of photonic crystals in confining, controlling, and manipulating the incident photons. This combination enhances the light absorption in photocatalysts and thus greatly improves their photocatalytic performance. In this study, Ga2O3 photonic crystals with well-arranged skeleton structures were prepared via a dip-coating infiltration method. The positions of the electronic band absorption for Ga2O3 photonic crystals could be made to locate on the red edge, on the blue edge, and away from the edge of their photonic band gaps by changing the pore sizes of the samples, respectively. Particularly, the electronic band absorption of the Ga2O3 photonic crystal with a pore size of 135 nm was enhanced more than other samples by making it locate on the red edge of its photonic band gap, which was confirmed by the higher instantaneous photocurrent and photocatalytic activity for the degradation of various organic pollutants under ultraviolet light irradiation. Furthermore, the degradation mechanism over Ga2O3 photonic crystals was discussed. The design of Ga2O3 photonic crystals presents a prospective application of photonic crystals in photocatalysis to address light harvesting and quantum efficiency problems through manipulating photons or constructing photonic crystal structure as groundwork.

New Directions in Biotechnology

NASA Technical Reports Server (NTRS)

2003-01-01

The macromolecule crystallization program within NASA is undergoing considerable pressure, particularly budgetary pressure. While it has shown some successes, they have not lived up to the expectations of others, and technological advances may rapidly overtake the natural advantages offered by crystallization in microgravity. Concomitant with the microgravity effort has been a research program to study the macromolecule crystallization process. It was believed that a better understanding of the process would lead to growth of improved crystals for X-ray diffraction studies. The results of the various research efforts have been impressive in improving our understanding of macromolecule crystallization, but have not led to any improved structures. Macromolecule crystallization for structure determination is "one of", the job being unique for every protein and finished once a structure is obtained. However, the knowledge gained is not lost, but instead lays the foundation for developments in new areas of biotechnology and nanotechnology. In this it is highly analogous to studies into small molecule crystallization, the results of which have led to our present day microelectronics-based society. We are conducting preliminary experiments into areas such as designed macromolecule crystals, macromolecule-inorganic hybrid structures, and macromolecule-based nanotechnology. In addition, our protein crystallization studies are now being directed more towards industrial and new approaches to membrane protein crystallization.

Synthesis, crystal structure, thermal and nonlinear optical properties of new metal-organic single crystal: Tetrabromo (piperazinium) zincate (II) (TBPZ)

NASA Astrophysics Data System (ADS)

Boopathi, K.; Babu, S. Moorthy; Ramasamy, P.

2018-04-01

Tetrabromo (piperazinium) zincate, a new metal-organic crystal has been synthesized and its single crystal grown by slow evaporation method. The grown crystal has characterized by structural, spectral, thermal, linear and nonlinear optical properties. Single crystal X-ray diffractions study reveals that grown crystal belongs to orthorhombic crystal system with space group P212121. The presence of functional groups is identified by FT-IR spectral analysis. Thermal stability of the crystal was ascertained by TG-DTA measurement. The second order harmonic generation efficiency was measured using Kurtz and Perry technique and it was found to be 1.5 times that of KDP.

Dynamic and magneto-optic properties of bent-core liquid crystals

NASA Astrophysics Data System (ADS)

Salili, Seyyed Muhammad

In this work, we describe dynamic behavior of free-standing bent-core liquid crystal filaments under dilative and axial compressive stresses in the B7 phase. We found that such filaments demonstrate very complex structures depending on the filament's temperature relative to the isotropic phase, initial filament thickness, and velocity at which the filament is pulled or compressed. We also present our experimental methods, results and analysis of the rupture and recoil properties of several bent-core liquid crystal filaments, anticipating that they may serve as a model system for complex biological fibers. After that, we systematically describe rheological measurements for dimeric liquid crystal compounds. We studied the shear-induced alignment properties, measured the viscoelastic properties as a function of temperature, shear rate, stress and frequency, and compared the results with the rheological properties of conventional chiral nematic and smectic phases. Then we present results of chiral nematic liquid crystals composed of flexible dimer molecules subject to large DC magnetic fields between 0 and 31T. We observe that these fields lead to selective reflection of light depending on temperature and magnetic field. The band of reflected wavelengths can be tuned from ultraviolet to beyond the IR-C band. A similar effect induced by electric fields has been presented previously, and was explained by a field-induced oblique-heliconical director deformation in accordance with early theoretical predictions. Finally, we report an unprecedented magnetic field-induced shifts of the isotropic-nematic phase transition temperature observed in liquid crystal dimers where two rigid linear mesogens are linked by flexible chains of either even- or odd-numbered hydrocarbon groups. This effect is explained in terms of quenching of the thermal fluctuations and decrease of the average bend angle of molecules in the odd-numbered dimers.

Atomic density functional and diagram of structures in the phase field crystal model

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ankudinov, V. E., E-mail: vladimir@ankudinov.org; Galenko, P. K.; Kropotin, N. V.

2016-02-15

The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of cylindricalmore » tubes. The method developed here is employed for constructing the diagram for the homogeneous liquid phase and the body-centered iron lattice. The expression for the free energy is derived analytically from density functional theory. The specific features of approximating the phase field crystal model are compared with the approximations and conclusions of the weak crystallization and 2D melting theories.« less

Synthesis and structural study of 4-(2-chlorophenyl)-2-ethoxy-5,6,7,8,9,10-hexahydrocycloocta[B] pyridine-3-carbonitrile

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fathima, K. Saiadali; Vasumathi, M.; Anitha, K., E-mail: singlecrystalxrd@gmail.com

2016-05-23

The novel organic material C{sub 20}H{sub 21}ClN{sub 2}O was synthesized by One-Pot synthesis method and the single crystals were grown by slow evaporation solution growth technique. The crystal structure was elucidated by subjecting the grown crystals to the single crystal x-ray diffraction analysis and was refined by full matrix least-squares method to R=0.039 for 2746 reflections. Crystal system of the grown crystal was found to be monoclinic with the space group P2{sub 1}/a and a=9.196(4) Å, b=13.449(4) Å, c=14.818(4) Å, β= 101.542(3)°, V=1795.6(11) Å{sup 3} and Z=4. In this crystal structure, cyclooctanone prefers to reside in a chair-boat conformation. Themore » structure is stabilized by attractive molecular force such as CH/π interaction called hydrophobic interaction.« less

Analysis of synthetic diamond single crystals by X-ray topography and double-crystal diffractometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Prokhorov, I. A., E-mail: igor.prokhorov@mail.ru; Ralchenko, V. G.; Bolshakov, A. P.

2013-12-15

Structural features of diamond single crystals synthesized under high pressure and homoepitaxial films grown by chemical vapor deposition (CVD) have been analyzed by double-crystal X-ray diffractometry and topography. The conditions of a diffraction analysis of diamond crystals using Ge monochromators have been optimized. The main structural defects (dislocations, stacking faults, growth striations, second-phase inclusions, etc.) formed during crystal growth have been revealed. The nitrogen concentration in high-pressure/high-temperature (HPHT) diamond substrates is estimated based on X-ray diffraction data. The formation of dislocation bundles at the film-substrate interface in the epitaxial structures has been revealed by plane-wave topography; these dislocations are likelymore » due to the relaxation of elastic macroscopic stresses caused by the lattice mismatch between the substrate and film. The critical thicknesses of plastic relaxation onset in CVD diamond films are calculated. The experimental techniques for studying the real diamond structure in optimizing crystal-growth technology are proven to be highly efficient.« less

In situ study of the growth and degradation processes in tetragonal lysozyme crystals on a silicon substrate by high-resolution X-ray diffractometry

NASA Astrophysics Data System (ADS)

Kovalchuk, M. V.; Prosekov, P. A.; Marchenkova, M. A.; Blagov, A. E.; D'yakova, Yu. A.; Tereshchenko, E. Yu.; Pisarevskii, Yu. V.; Kondratev, O. A.

2014-09-01

The results of an in situ study of the growth of tetragonal lysozyme crystals by high-resolution X-ray diffractometry are considered. The crystals are grown by the sitting-drop method on crystalline silicon substrates of different types: both on smooth substrates and substrates with artificial surface-relief structures using graphoepitaxy. The crystals are grown in a special hermetically closed crystallization cell, which enables one to obtain images with an optical microscope and perform in situ X-ray diffraction studies in the course of crystal growth. Measurements for lysozyme crystals were carried out in different stages of the crystallization process, including crystal nucleation and growth, developed crystals, the degradation of the crystal structure, and complete destruction.

Towards the Structure Determination of a Modulated Protein Crystal: The Semicrystalline State of Profilin:Actin

NASA Technical Reports Server (NTRS)

Borgstahl, G.; Lovelace, J.; Snell, E. H.; Bellamy, H.

2003-01-01

One of the remaining challenges to structural biology is the solution of modulated structures. While small molecule crystallographers have championed this type of structure, to date, no modulated macromolecular structures have been determined. Modulation of the molecular structures within the crystal can produce satellite reflections or a superlattice of reflections in reciprocal space. We have developed the data collection methods and strategies that are needed to collect and analyze these data. If the macromolecule's crystal lattice is composed of physiologically relevant packing contacts, structural changes induced under physiological conditions can cause distortion relevant to the function and biophysical processes of the molecule making up the crystal. By careful measurement of the distortion, and the corresponding three-dimensional structure of the distorted molecule, we will visualize the motion and mechanism of the biological macromolecule(s). We have measured the modulated diffraction pattern produced by the semicrystalline state of profilin:actin crystals using highly parallel and highly monochromatic synchrotron radiation coupled with fine phi slicing (0.001-0.010 degrees) for structure determination. These crystals present these crystals present a unique opportunity to address an important question in structural biology. The modulation is believed to be due to the formation of actin helical filaments from the actin beta ribbon upon the pH-induced dissociation of profilin. To date, the filamentous state of actin has resisted crystallization and no detailed structures are available. The semicrystalline state profilin:actin crystals provides a unique opportunity to understand the many conformational states of actin. This knowledge is essential for understanding the dynamics underlying shape changes and motility of eukaryotic cells. Many essential processes, such as cytokinesis, phagocytosis, and cellular migration depend upon the capacity of the actin microfilament system to be restructured in a controlled manner via polymerization, depolymerization, severing, cross-linking, and anchorage. The structure the semicrystalline state of profilin:actin will challenge and validate current models of muscle contraction and cell motility. The methodology and theory under development will be easily extendable to other systems.