3-D Structure of Molecules of Biological Significance

ERIC Educational Resources Information Center

Bennett, Alice S.; Schwenk, Karl

1974-01-01

Describes how to use the distinctive properties of osazone formation in conjunction with molecular model construction to demonstrate the relationship between the three-dimensional structures of simple sugars and the shapes of crystals they form. (BR)

Molecular complexes of alprazolam with carboxylic acids, boric acid, boronic acids, and phenols. Evaluation of supramolecular heterosynthons mediated by a triazole ring.

PubMed

Varughese, Sunil; Azim, Yasser; Desiraju, Gautam R

2010-09-01

A series of molecular complexes, both co-crystals and salts, of a triazole drug-alprazolam-with carboxylic acids, boric acid, boronic acids, and phenols have been analyzed with respect to heterosynthons present in the crystal structures. In all cases, the triazole ring behaves as an efficient hydrogen bond acceptor with the acidic coformers. The hydrogen bond patterns exhibited with aromatic carboxylic acids were found to depend on the nature and position of the substituents. Being a strong acid, 2,6-dihydroxybenzoic acid forms a salt with alprazolam. With aliphatic dicarboxylic acids alprazolam forms hydrates and the water molecules play a central role in synthon formation and crystal packing. The triazole ring makes two distinct heterosynthons in the molecular complex with boric acid. Boronic acids and phenols form consistent hydrogen bond patterns, and these are seemingly independent of the substitutional effects. Boronic acids form noncentrosymmetric cyclic synthons, while phenols form O--H...N hydrogen bonds with the triazole ring.

Charge Transport and Phase Behavior of Imidazolium-Based Ionic Liquid Crystals from Fully Atomistic Simulations

PubMed Central

2018-01-01

Ionic liquid crystals occupy an intriguing middle ground between room-temperature ionic liquids and mesostructured liquid crystals. Here, we examine a non-polarizable, fully atomistic model of the 1-alkyl-3-methylimidazolium nitrate family using molecular dynamics in the constant pressure–constant temperature ensemble. These materials exhibit a distinct “smectic” liquid phase, characterized by layers formed by the molecules, which separate the ionic and aliphatic moieties. In particular, we discuss the implications this layering may have for electrolyte applications. PMID:29301305

Crystallization and preliminary X-ray crystallographic analysis of a carbonyl reductase from Candida parapsilosis

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

Zhang, Rongzhen; Xu, Yan, E-mail: biosean@yahoo.com.cn; Sun, Ying

2008-04-01

A novel short-chain NADPH-dependent (S)-1-phenyl-1,2-ethanediol dehydrogenase (SCR) has been crystallized. A novel short-chain NADPH-dependent (S)-1-phenyl-1,2-ethanediol dehydrogenase (SCR) has been crystallized. Two distinct but related crystal forms of SCR were obtained using the hanging-drop vapour-diffusion method and a reservoir solution consisting of 18%(w/v) polyethylene glycol 2000 monomethyl ether and 8%(v/v) 2-propanol as the precipitant. The crystals were rhomboid in shape with average dimensions of 0.3 × 0.3 × 0.4 mm and diffracted to a resolution of 2.7–3.0 Å. The crystal forms both belong to space group P2{sub 1}2{sub 1}2{sub 1} and have unit-cell parameters a = 104.7, b = 142.8, cmore » = 151.8 Å and a = 101.1, b = 146.0, c = 159.8 Å. The calculated values of V{sub M}, rotation-function and translation-function solutions and consideration of potential crystal packing suggest that there are eight protein subunits per asymmetric unit.« less

Crystallization of multiple forms of bovine seminal ribonuclease in the liganded and unliganded state

NASA Astrophysics Data System (ADS)

Sica, F.; Adinolfi, S.; Berisio, R.; De Lorenzo, C.; Mazzarella, L.; Piccoli, R.; Vitagliano, L.; Zagari, A.

1999-01-01

Bovine seminal ribonuclease (BS-RNase) is an intriguing homodimeric enzyme which exists as two conformational isomers, characterized by distinct catalytic and biological properties, referred to as M×M and M=M. Reduction of inter-chain disulfide bridges produces a stable monomeric derivative (M) which is still active. This paper reports the screening and optimization of crystallization conditions for growing single diffraction-quality crystals for the various BS-RNase forms. The crystallization trials were performed using both the vapor diffusion and microbatch methods. The M×M dimer was crystallized in the free form from polyethylene glycol (PEG) 4000 at pH 8.5 and as a complex with the substrate analog uridylyl(2'- 5')guanosine (UpG) from an unbuffered ammonium sulfate (AS) solution. These two crystal types diffract X-rays to 2.5 and 1.9 Å resolution, respectively. Two different crystal types were obtained both for the M=M dimer and for the monomeric derivative. (M=M)a crystals, grown from PEG 4000 (8% w/v) at pH 5.6, diffract X-rays to 4.0 Å. At higher PEG concentration (15% w/v) a different crystal type was obtained, (M=M)b, which showed a better diffraction limit (2.5 Å). For the monomer, type (M)a and (M)b crystals, diffracting X-rays to 2.5 Å resolution, were obtained from AS at pH 6.5 and from PEG 4000 at pH 8.5, respectively. A comparison with previously crystallized forms of the dimer M×M and its complexes with uridylyl(2'-5')adenosine and 2'-deoxycytidylyl(3'-5')-2'-deoxyadenosine is also presented. The three-dimensional structure analysis of (M×M)·UpG and (M=M)b is in progress.

Complex and hierarchical micelle architectures from diblock copolymers using living, crystallization-driven polymerizations.

PubMed

Gädt, Torben; Ieong, Nga Sze; Cambridge, Graeme; Winnik, Mitchell A; Manners, Ian

2009-02-01

Block copolymers consist of two or more chemically distinct polymer segments, or blocks, connected by a covalent link. In a selective solvent for one of the blocks, core-corona micelle structures are formed. We demonstrate that living polymerizations driven by the epitaxial crystallization of a core-forming metalloblock represent a synthetic tool that can be used to generate complex and hierarchical micelle architectures from diblock copolymers. The use of platelet micelles as initiators enables the formation of scarf-like architectures in which cylindrical micelle tassels of controlled length are grown from specific crystal faces. A similar process enables the fabrication of brushes of cylindrical micelles on a crystalline homopolymer substrate. Living polymerizations driven by heteroepitaxial growth can also be accomplished and are illustrated by the formation of tri- and pentablock and scarf architectures with cylinder-cylinder and platelet-cylinder connections, respectively, that involve different core-forming metalloblocks.

Interlaced crystals having a perfect Bravais lattice and complex chemical order revealed by real-space crystallography

DOE PAGES

Shen, Xiao; Hernandez-Pagan, Emil; Zhou, Wu; ...

2014-11-14

The search for optimal thermoelectric materials aims for structures in which the crystalline order is disrupted to lower the thermal conductivity without degradation of the electron conductivity. Here we report the synthesis and characterization of ternary nanoparticles (two cations and one anion) that exhibit a new form of crystal-line order: an uninterrupted, perfect, global Bravais lattice, in which the two cations exhibit a wide array of distinct ordering patterns within the cation sublattice, form-ing interlaced domains and phases. Partitioning into domains and phases is not unique; the corresponding boundaries have no structural defects or strain and entail no energy cost.more » We call this form of crystalline order “interlaced crystals” and present the example of hexagonal-CuInS 2. Interlacing is possible in multi-cation tetrahedral-ly-bonded compound with an average of two electrons per bond. Interlacing has min-imal effect on electronic properties, but should strongly reduce phonon transport, making interlaced crystals attractive for thermoelectric applications.« less

Chromite in komatiites: 3D morphologies with implications for crystallization mechanisms

NASA Astrophysics Data System (ADS)

Godel, Bélinda; Barnes, Stephen J.; Gürer, Derya; Austin, Peter; Fiorentini, Marco L.

2013-01-01

High-resolution X-ray computed tomography has been carried out on a suite of komatiite samples representing a range of volcanic facies, chromite contents and degrees of alteration and metamorphism, to reveal the wide range of sizes, shapes and degrees of clustering that chromite grains display as a function of cooling history. Dendrites are spectacularly skeletal chromite grains formed during very rapid crystallization of supercooled melt in spinifex zones close to flow tops. At slower cooling rates in the interiors of thick flows, chromite forms predominantly euhedral grains. Large clusters (up to a dozen of grains) are characteristic of liquidus chromite, whereas fine dustings of mostly individual ~20-μm grains form by in situ crystallization from trapped intercumulus liquid. Chromite in coarse-grained olivine cumulates from komatiitic dunite bodies occurs in two forms: as clusters or chains of euhedral crystals, developing into "chicken-wire" texture where chromite is present in supra-cotectic proportions; and as strongly dendritic, semi-poikilitic grains. These dendritic grains are likely to have formed by rapid crescumulate growth from magma that was close to its liquidus temperature but supersaturated with chromite. In some cases, this process seems to have been favoured by nucleation of chromite on the margins of sulphide liquid blebs. This texture is a good evidence for the predominantly cumulus origin of oikocrysts and in situ origin of heteradcumulate textures. Our 3D textural analysis confirms that the morphology of chromite crystals is a distinctive indicator of crystallization environment even in highly altered rocks.

Loop-driven conformational transition between the alternative and collapsed form of prethrombin-2: targeted molecular dynamics study.

PubMed

Wu, Sangwook

2017-01-01

Two distinct crystal structures of prethrombin-2, the alternative and collapsed forms, are elucidated by X-ray crystallogrphy. We analyzed the conformational transition from the alternative to the collapsed form employing targeted molecular dynamics (TMD) simulation. Despite small RMSD difference in the two X-ray crystal structures, some hydrophobic residues (W60d, W148, W215, and F227) show a significant difference between the two conformations. TMD simulation shows that the four hydrophobic residues undergo concerted movement from dimer to trimer transition via tetramer state in the conformational change from the alternative to the collapsed form. We reveal that the concerted movement of the four hydrophobic residues is controlled by movement of specific loop regions behind. In this paper, we propose a sequential scenario for the conformational transition from the alternative form to the collapsed form, which is partially supported by the mutant W148A simulation.

Core drilling through the ross ice shelf (antarctica) confirmed Basal freezing.

PubMed

Zotikov, I A; Zagorodnov, V S; Raikovsky, J V

1980-03-28

New techniques that have been used to obtain a continuous ice core through the whole 416-meter thickness of the Ross Ice Shelf at Camp J-9 have demonstrated that the bottom 6 meters of the ice shelf consists of sea ice. The rate of basal freezing that is forming this ice is estimated by different methods to be 2 centimeters of ice per year. The sea ice is composed of large vertical crystals, which form the waffle-like lower boundary of the shelf. A distinct alignment of the crystals throughout the sea ice layer suggests the presence of persistent long-term currents beneath the ice shelf.

An approach to crystallizing proteins by metal-mediated synthetic symmetrization

PubMed Central

Laganowsky, Arthur; Zhao, Minglei; Soriaga, Angela B; Sawaya, Michael R; Cascio, Duilio; Yeates, Todd O

2011-01-01

Combining the concepts of synthetic symmetrization with the approach of engineering metal-binding sites, we have developed a new crystallization methodology termed metal-mediated synthetic symmetrization. In this method, pairs of histidine or cysteine mutations are introduced on the surface of target proteins, generating crystal lattice contacts or oligomeric assemblies upon coordination with metal. Metal-mediated synthetic symmetrization greatly expands the packing and oligomeric assembly possibilities of target proteins, thereby increasing the chances of growing diffraction-quality crystals. To demonstrate this method, we designed various T4 lysozyme (T4L) and maltose-binding protein (MBP) mutants and cocrystallized them with one of three metal ions: copper (Cu2+), nickel (Ni2+), or zinc (Zn2+). The approach resulted in 16 new crystal structures—eight for T4L and eight for MBP—displaying a variety of oligomeric assemblies and packing modes, representing in total 13 new and distinct crystal forms for these proteins. We discuss the potential utility of the method for crystallizing target proteins of unknown structure by engineering in pairs of histidine or cysteine residues. As an alternate strategy, we propose that the varied crystallization-prone forms of T4L or MBP engineered in this work could be used as crystallization chaperones, by fusing them genetically to target proteins of interest. PMID:21898649

Giant Plagioclase "Mosaicrysts" and Other Textures in the Steens Basalt, Columbia River Flood Basalt Province

NASA Astrophysics Data System (ADS)

Grunder, A.; Moore, N. E.; Bohrson, W. A.

2015-12-01

The Steens Basalts (~16.7 Ma), the oldest and most mafic stage of Columbia River flood basalt volcanism, are known for lavas with conspicuous giant plagioclase laths (2 - 5 cm in diameter). Such flows are intercalated with ones that are nearly aphyric or that bear plagioclase (plag) phenocrysts of 0.5-2 cm. Addition textures are distinctive radial, snowflake plag clusters and sandwich glomerocrysts of plag, with olivine trapped between laths. These clusters and glomerocrysts are typically 1, but as large as 3 cm in diameter. Plag composition of all textural types is limited (An76-60). Plag dominates the phenocryst mode; rare flows, mainly low in the section, have olivine > plag and phenocrystic clinopyroxene occurs rarely, and mainly high in the section. Unlike the flows, dikes have few phenocrysts; giant laths are rare and the snowflake texture has not been observed. Giant plag laths are euhedral and make up a few percent to more than 50% of the rock. Many plag megacrysts are made of several plag crystals that form a mosaic, where the constituent crystals are crystallographically distinct and are overgrown with feldspar to make the crystal euhedral. We describe these composite megacrysts as "mosaicrysts". We are exploring magmatic conditions that would trigger oversaturation to spawn rapid growth yielding clusters and overgrowths that form mosaicrysts. Giant plagioclase basalts (so-called GPB) are also described for the Deccan and Emeishan flood basalt provinces attesting to similar magmatic processes. Plag laths typically define strong flow foliation at the flow base, have a swirled distribution in the flow core, and are sparse in the top. Some particularly crystal-rich flows (or sills) have an abrupt transition to a crystal-poor upper few decimeters of the several-m- thick flow. We interpret the crystal-poor top to be the expelled melt from crystal accumulation in the flow, which locally reinjects and is entrained in lower crystal mush.

Antimalarials inhibit hematin crystallization by unique drug–surface site interactions

PubMed Central

Olafson, Katy N.; Nguyen, Tam Q.; Rimer, Jeffrey D.; Vekilov, Peter G.

2017-01-01

In malaria pathophysiology, divergent hypotheses on the inhibition of hematin crystallization posit that drugs act either by the sequestration of soluble hematin or their interaction with crystal surfaces. We use physiologically relevant, time-resolved in situ surface observations and show that quinoline antimalarials inhibit β-hematin crystal surfaces by three distinct modes of action: step pinning, kink blocking, and step bunch induction. Detailed experimental evidence of kink blocking validates classical theory and demonstrates that this mechanism is not the most effective inhibition pathway. Quinolines also form various complexes with soluble hematin, but complexation is insufficient to suppress heme detoxification and is a poor indicator of drug specificity. Collectively, our findings reveal the significance of drug–crystal interactions and open avenues for rationally designing antimalarial compounds. PMID:28559329

Multiple chiral topological states in liquid crystals from unstructured light beams

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

Loussert, Charles; Brasselet, Etienne, E-mail: e.brasselet@loma.u-bordeaux1.fr

2014-02-03

It is shown experimentally that unstructured light beams can generate a wealth of distinct metastable defect structures in thin films of chiral liquid crystals. Various kinds of individual chiral topological states are obtained as well as dimers and trimers, which correspond to the entanglement of several topological unit cells. Self-assembled nested assemblies of several metastable particle-like topological states can also be formed. Finally, we propose and experimentally demonstrate an opto-electrical approach to generate tailor-made architectures.

Interfacial free energy controlling glass-forming ability of Cu-Zr alloys.

PubMed

Kang, Dong-Hee; Zhang, Hao; Yoo, Hanbyeol; Lee, Hyun Hwi; Lee, Sooheyong; Lee, Geun Woo; Lou, Hongbo; Wang, Xiaodong; Cao, Qingping; Zhang, Dongxian; Jiang, Jianzhong

2014-06-04

Glass is a freezing phase of a deeply supercooled liquid. Despite its simple definition, the origin of glass forming ability (GFA) is still ambiguous, even for binary Cu-Zr alloys. Here, we directly study the stability of the supercooled Cu-Zr liquids where we find that Cu64Zr36 at a supercooled temperature shows deeper undercoolability and longer persistence than other neighbouring compositions with an equivalent driving Gibbs free energy. This observation implies that the GFA of the Cu-Zr alloys is significantly affected by crystal-liquid interfacial free energy. In particular, the crystal-liquid interfacial free energy of Cu64Zr36 in our measurement was higher than that of other neighbouring liquids and, coincidently a molecular dynamics simulation reveals a larger glass-glass interfacial energy value at this composition, which reflects more distinct configuration difference between liquid and crystal phase. The present results demonstrate that the higher crystal-liquid interfacial free energy is a prerequisite of good GFA of the Cu-Zr alloys.

A Capped Dipeptide Which Simultaneously Exhibits Gelation and Crystallization Behavior.

PubMed

Martin, Adam D; Wojciechowski, Jonathan P; Bhadbhade, Mohan M; Thordarson, Pall

2016-03-08

Short peptides capped at their N-terminus are often highly efficient gelators, yet notoriously difficult to crystallize. This is due to strong unidirectional interactions within fibers, resulting in structure propagation only along one direction. Here, we synthesize the N-capped dipeptide, benzimidazole-diphenylalanine, which forms both hydrogels and single crystals. Even more remarkably, we show using atomic force microscopy the coexistence of these two distinct phases. We then use powder X-ray diffraction to investigate whether the single crystal structure can be extrapolated to the molecular arrangement within the hydrogel. The results suggest parallel β-sheet arrangement as the dominant structural motif, challenging existing models for gelation of short peptides, and providing new directions for the future rational design of short peptide gelators.

Heterogeneous nucleation in a glass-forming alloy

NASA Astrophysics Data System (ADS)

Wall, J. J.; Liu, C. T.; Rhim, W.-K.; Li, J. J. Z.; Liaw, P. K.; Choo, H.; Johnson, W. L.

2008-06-01

Nucleation in the undercooled liquid state in the bulk metallic glass-forming composition Zr52.5Cu17.9Ni14.6Al10Ti5 (VIT-105), produced using high purity (PA) and commercial purity (CA) raw materials was investigated using electrostatic levitation and ex situ neutron diffraction. The CA material was observed to have a lower density than the PA sample and crystallized at relatively shallow undercooling. The densities of the samples at temperatures above the solidus showed an oxygen-dependent hysteresis associated with the state change, indicating the presence of oxygen-stabilized intermetallics. The PA alloy exhibited three distinct crystallization modes dependent on the thermal history of the melt, one of which showed a net volume expansion.

Influence of crystal habit on trimethoprim suspension formulation.

PubMed

Tiwary, A K; Panpalia, G M

1999-02-01

The role of crystal habit in influencing the physical stability and pharmacokinetics of trimethoprim suspensions was examined. Different habits for trimethoprim (TMP) were obtained by recrystallizing the commercial sample (PD) utilizing solvent-change precipitation method. Four distinct habits (microscopic observation) belonging to the same polymorphic state (DSC studies) were selected for studies. Preformulation and formulation studies were carried out on suspension dosage forms containing these crystals. The freshly prepared suspensions were also evaluated for their pharmacokinetic behaviour on healthy human volunteers using a cross over study. Variation of crystallization conditions produces different habits of TMP. Among the different crystal habits exhibiting same polymorphic state, the most anisometric crystal showed best physical stability in terms of sedimentation volume and redispersibility. However, habit did not significantly affect the extent of TMP excreted in urine. Modification of surface morphology without significantly altering the polymorphic state can be utilized for improving physical stability of TMP suspensions. However, the pharmacokinetic profile remains unaltered.

Myelography Iodinated Contrast Media. 2. Conformational Versatility of Iopamidol in the Solid State.

PubMed

Bellich, Barbara; Di Fonzo, Silvia; Tavagnacco, Letizia; Paolantoni, Marco; Masciovecchio, Claudio; Bertolotti, Federica; Giannini, Giovanna; De Zorzi, Rita; Geremia, Silvano; Maiocchi, Alessandro; Uggeri, Fulvio; Masciocchi, Norberto; Cesàro, Attilio

2017-02-06

The phenomenon of polymorphism is of great relevance in pharmaceutics, since different polymorphs have different physicochemical properties, e.g., solubility, hence, bioavailability. Coupling diffractometric and spectroscopic experiments with thermodynamic analysis and computational work opens to a methodological approach which provides information on both structure and dynamics in the solid as well as in solution. The present work reports on the conformational changes in crystalline iopamidol, which is characterized by atropisomerism, a phenomenon that influences both the solution properties and the distinct crystal phases. The conformation of iopamidol is discussed for three different crystal phases. In the anhydrous and monohydrate crystal forms, iopamidol molecules display a syn conformation of the long branches stemming out from the triiodobenzene ring, while in the pentahydrate phase the anti conformation is found. IR and Raman spectroscopic studies carried out on the three crystal forms, jointly with quantum chemical computations, revealed that the markedly different spectral features can be specifically attributed to the different molecular conformations. Our results on the conformational versatility of iopamidol in different crystalline phases, linking structural and spectroscopic evidence for the solution state and the solid forms, provide a definite protocol for grasping the signals that can be taken as conformational markers. This is the first step for understanding the crystallization mechanism occurring in supersaturated solution of iopamidol molecules.

Light driven mesoscale assembly of a coordination polymeric gelator into flowers and stars with distinct properties.

PubMed

Mukhopadhyay, Rahul Dev; Praveen, Vakayil K; Hazra, Arpan; Maji, Tapas Kumar; Ajayaghosh, Ayyappanpillai

2015-11-13

Control over the self-assembly process of porous organic-inorganic hybrids often leads to unprecedented polymorphism and properties. Herein we demonstrate how light can be a powerful tool to intervene in the kinetically controlled mesoscale self-assembly of a coordination polymeric gelator. Ultraviolet light induced coordination modulation via photoisomerisation of an azobenzene based dicarboxylate linker followed by aggregation mediated crystal growth resulted in two distinct morphological forms (flowers and stars), which show subtle differences in their physical properties.

Purification, crystallization and preliminary X-ray diffraction analysis of the carbohydrate-binding region of the Streptococcus gordonii adhesin GspB

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

Pyburn, Tasia M.; Yankovskaya, Victoria; Bensing, Barbara A.

2012-07-11

The carbohydrate-binding region of the bacterial adhesin GspB from Streptococcus gordonii strain M99 (GspB{sub BR}) was expressed in Escherichia coli and purified using affinity and size-exclusion chromatography. Separate sparse-matrix screening of GspB{sub BR} buffered in either 20 mM Tris pH 7.4 or 20 mM HEPES pH 7.5 resulted in different crystallographic behavior such that different precipitants, salts and additives supported crystallization of GspB{sub BR} in each buffer. While both sets of conditions supported crystal growth in space group P2{sub 1}2{sub 1}2{sub 1}, the crystals had distinct unit-cell parameters of a = 33.3, b = 86.7, c = 117.9 {angstrom} formore » crystal form 1 and a = 34.6, b = 98.3, c = 99.0 {angstrom} for crystal form 2. Additive screening improved the crystals grown in both conditions such that diffraction extended to beyond 2 {angstrom} resolution. A complete data set has been collected to 1.3 {angstrom} resolution with an overall R{sub merge} value of 0.04 and an R{sub merge} value of 0.33 in the highest resolution shell.« less

Crystallization characteristics of iron-rich glass ceramics prepared from nickel slag and blast furnace slag

NASA Astrophysics Data System (ADS)

Wang, Zhong-Jie; Ni, Wen; Li, Ke-Qing; Huang, Xiao-Yan; Zhu, Li-Ping

2011-08-01

The crystallization process of iron-rich glass-ceramics prepared from the mixture of nickel slag (NS) and blast furnace slag (BFS) with a small amount of quartz sand was investigated. A modified melting method which was more energy-saving than the traditional methods was used to control the crystallization process. The results show that the iron-rich system has much lower melting temperature, glass transition temperature ( T g), and glass crystallization temperature ( T c), which can result in a further energy-saving process. The results also show that the system has a quick but controllable crystallization process with its peak crystallization temperature at 918°C. The crystallization of augite crystals begins from the edge of the sample and invades into the whole sample. The crystallization process can be completed in a few minutes. A distinct boundary between the crystallized part and the non-crystallized part exists during the process. In the non-crystallized part showing a black colour, some sphere-shaped augite crystals already exist in the glass matrix before samples are heated to T c. In the crystallized part showing a khaki colour, a compact structure is formed by augite crystals.

Possible Mechanisms for Turbofan Engine Ice Crystal Icing at High Altitude

NASA Technical Reports Server (NTRS)

Tsao, Jen-Ching; Struk, Peter M.; Oliver, Michael

2014-01-01

A thermodynamic model is presented to describe possible mechanisms of ice formation on unheated surfaces inside a turbofan engine compression system from fully glaciated ice crystal clouds often formed at high altitude near deep convective weather systems. It is shown from the analysis that generally there could be two distinct types of ice formation: (1) when the "surface freezing fraction" is in the range of 0 to 1, dominated by the freezing of water melt from fully or partially melted ice crystals, the ice structure is formed from accretion with strong adhesion to the surface, and (2) when the "surface melting fraction" is the range of 0 to 1, dominated by the further melting of ice crystals, the ice structure is formed from accumulation of un-melted ice crystals with relatively weak bonding to the surface. The model captures important qualitative trends of the fundamental ice-crystal icing phenomenon reported earlier1,2 from the research collaboration work by NASA and the National Research Council (NRC) of Canada. Further, preliminary analysis of test data from the 2013 full scale turbofan engine ice crystal icing test3 conducted in the NASA Glenn Propulsion Systems Laboratory (PSL) has also suggested that (1) both types of ice formation occurred during the test, and (2) the model has captured some important qualitative trend of turning on (or off) the ice crystal ice formation process in the tested engine low pressure compressor (LPC) targeted area under different icing conditions that ultimately would lead to (or suppress) an engine core roll back (RB) event.

Possible Mechanisms for Turbofan Engine Ice Crystal Icing at High Altitude

NASA Technical Reports Server (NTRS)

Tsao, Jen-Ching; Struk, Peter M.; Oliver, Michael J.

2016-01-01

A thermodynamic model is presented to describe possible mechanisms of ice formation on unheated surfaces inside a turbofan engine compression system from fully glaciated ice crystal clouds often formed at high altitude near deep convective weather systems. It is shown from the analysis that generally there could be two distinct types of ice formation: (1) when the "surface freezing fraction" is in the range of 0 to 1, dominated by the freezing of water melt from fully or partially melted ice crystals, the ice structure is formed from accretion with strong adhesion to the surface, and (2) when the "surface melting fraction" is the range of 0 to 1, dominated by the further melting of ice crystals, the ice structure is formed from accumulation of un-melted ice crystals with relatively weak bonding to the surface. The model captures important qualitative trends of the fundamental ice-crystal icing phenomenon reported earlier (Refs. 1 and 2) from the research collaboration work by NASA and the National Research Council (NRC) of Canada. Further, preliminary analysis of test data from the 2013 full scale turbofan engine ice crystal icing test (Ref. 3) conducted in the NASA Glenn Propulsion Systems Laboratory (PSL) has also suggested that (1) both types of ice formation occurred during the test, and (2) the model has captured some important qualitative trend of turning on (or off) the ice crystal ice formation process in the tested engine low pressure compressor (LPC) targeted area under different icing conditions that ultimately would lead to (or suppress) an engine core roll back (RB) event.

Continuous structural evolution of calcium carbonate particles: a unifying model of copolymer-mediated crystallization.

PubMed

Kulak, Alex N; Iddon, Peter; Li, Yuting; Armes, Steven P; Cölfen, Helmut; Paris, Oskar; Wilson, Rory M; Meldrum, Fiona C

2007-03-28

Two double-hydrophilic block copolymers, each comprising a nonionic block and an anionic block comprising pendent aromatic sulfonate groups, were used as additives to modify the crystallization of CaCO3. Marked morphological changes in the CaCO3 particles were observed depending on the reaction conditions used. A poly(ethylene oxide)-b-poly(sodium 4-styrenesulfonate) diblock copolymer was particularly versatile in effecting a morphological change in calcite particles, and a continuous structural transition in the product particles from polycrystalline to mesocrystal to single crystal was observed with variation in the calcium concentration. The existence of this structural sequence provides unique insight into the mechanism of polymer-mediated crystallization. We propose that it reflects continuity in the crystallization mechanism itself, spanning the limits from nonoriented aggregation of nanoparticles to classical ion-by-ion growth. The various pathways to polycrystalline, mesocrystal, and single-crystal particles, which had previously been considered to be distinct, therefore all form part of a unifying crystallization framework based on the aggregation of precursor subunits.

Cirrus clouds as seen by the CALIPSO satellite and ECHAM-HAM global climate model

NASA Astrophysics Data System (ADS)

Gasparini, Blaz; Meyer, Angela; Neubauer, David; Münch, Steffen; Lohmann, Ulrike

2017-04-01

Ice clouds impact the planetary energy balance and upper tropospheric water vapour transport and are therefore relevant for climate. In this study ice clouds at temperatures below -40°C simulated by the ECHAM-HAM global climate model are compared to CALIPSO/CALIOP satellite data. The model reproduces well the mean occurrence of ice clouds, while the ice water path, ice crystal radius, cloud optical depth and extinction are overestimated in terms of annual means and temperature dependent frequency histograms. Two distinct types of cirrus clouds are found: in-situ formed cirrus dominating at temperatures below -60°C and liquid-origin cirrus, dominating at temperatures warmer than -55°C. The latter form in anvils of deep convective clouds or by glaciation of mixed-phase clouds. They are associated with ice water contents of up to 0.1 g m-3 and extinctions of up to 0.1 km-1, while the in-situ formed cirrus are optically thinner and contain at least an order of magnitude less ice. The ice cloud properties do not differ significantly between the southern and the northern hemisphere. In-situ formed ice clouds are further divided into homogeneously and heterogeneously nucleated ones. The simulated liquid-origin ice crystals mainly form in convective outflow in large number concentrations, similar to in-situ homogeneously nucleated ice crystals. On the contrary, heterogeneously nucleated ice crystals are associated with smaller number concentrations. However, ice crystal aggregation and depositional growth smooth the differences between several formation mechanisms making the attribution to a specific ice nucleation mechanism challenging.

Collective Transport Properties of Driven Skyrmions with Random Disorder

NASA Astrophysics Data System (ADS)

Reichhardt, C.; Ray, D.; Reichhardt, C. J. Olson

2015-05-01

We use particle-based simulations to examine the static and driven collective phases of Skyrmions interacting with random quenched disorder. We show that nondissipative effects due to the Magnus term reduce the depinning threshold and strongly affect the Skyrmion motion and the nature of the dynamic phases. The quenched disorder causes the Hall angle to become drive dependent in the moving Skyrmion phase, while different flow regimes produce distinct signatures in the transport curves. For weak disorder, the Skyrmions form a pinned crystal and depin elastically, while for strong disorder the system forms a pinned amorphous state that depins plastically. At high drives the Skyrmions can dynamically reorder into a moving crystal, with the onset of reordering determined by the strength of the Magnus term.

Conformational dimorphism of isochroman-1-ones in the solid state

NASA Astrophysics Data System (ADS)

Babjaková, Eva; Hanulíková, Barbora; Dastychová, Lenka; Kuřitka, Ivo; Nečas, Marek; Vícha, Robert

2014-12-01

Isochroman-1-one derivatives, which are relatives of coumarins, display a broad spectrum of biological activity; therefore, these derivatives attract the attention of chemists. A series of new isochroman-1-ones were prepared by the reaction of benzyl-derived Grignard reagents with acyl chlorides. All of the prepared compounds were characterized using single-crystal X-ray diffraction as well as FT-IR, NMR and MS techniques. Single crystal X-ray diffraction analysis revealed that the isochromanones can adopt two distinct conformations in the solid state. For one of the compounds, two polymorphs with unique forms crystallized separately under different temperatures. The packing of all of the examined crystals is stabilized via weak intramolecular C-H⋯π and/or C-H⋯O interactions. Although the closed conformer was predominantly found in the actual crystals, the open conformer is thermochemically more stable for all of the examined compounds according to DFT calculations.

Phormidium phycoerythrin forms hexamers in crystals: a crystallographic study

PubMed Central

Sonani, Ravi Raghav; Sharma, Mahima; Gupta, Gagan Deep; Kumar, Vinay; Madamwar, Datta

2015-01-01

The crystallographic analysis of a marine cyanobacterium (Phormidium sp. A09DM) phycoerythrin (PE) that shows distinct sequence features compared with known PE structures from cyanobacteria and red algae is reported. Phormidium PE was crystallized using the sitting-drop vapour-diffusion method with ammonium sulfate as a precipitant. Diffraction data were collected on the protein crystallography beamline at the Indus-2 synchrotron. The crystals diffracted to about 2.1 Å resolution at 100 K. The crystals, with an apparent hexagonal morphology, belonged to space group P1, with unit-cell parameters a = 108.3, b = 108.4 Å, c = 116.6 Å, α = 78.94, β = 82.50, γ = 60.34°. The molecular-replacement solution confirmed the presence of 12 αβ monomers in the P1 cell. The Phormidium PE elutes as an (αβ)3 trimer of αβ monomers from a molecular-sieve column and exists as [(αβ)3]2 hexamers in the crystal lattice. Unlike red algal PE proteins, the hexamers of Phormidium PE do not form higher-order structures in the crystals. The existence of only one characteristic visual absorption band at 564 nm suggests the presence of phycoerythrobilin chromophores, and the absence of any other types of bilins, in the Phormidium PE assembly. PMID:26249689

Expression, purification, crystallization and preliminary X-ray diffraction analysis of the VP8* sialic acid-binding domain of porcine rotavirus strain OSU

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

Zhang, Yang-De, E-mail: zhangyd1960@yahoo.com.cn; Li, Hao; Liu, Hui

2007-02-01

Porcine rotavirus strain OSU VP8* domain has been expressed, purified and crystallized. X-ray diffraction data from different crystal forms of the VP8* domain have been collected to 2.65 and 2.2 Å resolution, respectively. The rotavirus outer capsid spike protein VP4 is utilized in the process of rotavirus attachment to and membrane penetration of host cells. VP4 is cleaved by trypsin into two domains: VP8* and VP5*. The VP8* domain is implicated in initial interaction with sialic acid-containing cell-surface carbohydrates and triggers subsequent virus invasion. The VP8* domain from porcine OSU rotavirus was cloned and expressed in Escherichia coli. Different crystalmore » forms (orthorhombic P2{sub 1}2{sub 1}2{sub 1} and tetragonal P4{sub 1}2{sub 1}2) were harvested from two distinct crystallization conditions. Diffraction data have been collected to 2.65 and 2.2 Å resolution and the VP8*{sub 65–224} structure was determined by molecular replacement.« less

Excitations Partition into Two Distinct Populations in Bulk Perovskites

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

Wang, Lili; Brawand, Nicholas P.; Vörös, Márton

2018-01-09

Organolead halide perovskites convert optical excitations to charge carriers with remarkable efficiency in optoelectronic devices. Previous research predominantly documents dynamics in perovskite thin films; however, extensive disorder in this platform may obscure the observed carrier dynamics. Here, carrier dynamics in perovskite single-domain single crystals is examined by performing transient absorption spectroscopy in a transmissive geometry. Two distinct sets of carrier populations that coexist at the same radiation fluence, but display different decay dynamics, are observed: one dominated by second-order recombination and the other by third-order recombination. Based on ab initio simulations, this observation is found to be most consistent withmore » the hypothesis that free carriers and localized carriers coexist due to polaron formation. The calculations suggest that polarons will form in both CH3NH3PbBr3 and CH3NH3PbI3 crystals, but that they are more pronounced in CH3NH3PbBr3. Single-crystal CH3NH3PbBr3 could represent the key to understanding the impact of polarons on the transport properties of perovskite optoelectronic devices.« less

Fluorescence Approaches to Growing Macromolecule Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc; Forsythe, Elizabeth; Achari, Aniruddha

2006-01-01

Trace fluorescent labeling, typically < 1%, can be a powerful aid in macromolecule crystallization. Precipitation concentrates a solute, and crystals are the most densely packed solid form. The more densely packed the fluorescing material, the more brightly the emission from it, and thus fluorescence intensity of a solid phase is a good indication of whether one has crystals or not. The more brightly fluorescing crystalline phase is easily distinguishable, even when embedded in an amorphous precipitate. This approach conveys several distinct advantages: one can see what the protein is doing in response to the imposed conditions, and distinguishing between amorphous and microcrystalline precipitated phases are considerably simpler. The higher fluorescence intensity of the crystalline phase led us to test if we could derive crystallization conditions from screen outcomes which had no obvious crystalline material, but simply "bright spots" in the precipitated phase. Preliminary results show that the presence of these bright spots, not observable under white light, is indeed a good indicator of potential crystallization conditions.

Distortion of Local Atomic Structures in Amorphous Ge-Sb-Te Phase Change Materials

NASA Astrophysics Data System (ADS)

Hirata, A.; Ichitsubo, T.; Guan, P. F.; Fujita, T.; Chen, M. W.

2018-05-01

The local atomic structures of amorphous Ge-Sb-Te phase-change materials have yet to be clarified and the rapid crystal-amorphous phase change resulting in distinct optical contrast is not well understood. We report the direct observation of local atomic structures in amorphous Ge2Sb2Te5 using "local" reverse Monte Carlo modeling dedicated to an angstrom-beam electron diffraction analysis. The results corroborated the existence of local structures with rocksalt crystal-like topology that were greatly distorted compared to the crystal symmetry. This distortion resulted in the breaking of ideal octahedral atomic environments, thereby forming local disordered structures that basically satisfied the overall amorphous structure factor. The crystal-like distorted octahedral structures could be the main building blocks in the formation of the overall amorphous structure of Ge-Sb-Te.

Linking Crystal Populations to Dynamic States: Crystal Dissolution and Growth During an Open-System Event

NASA Astrophysics Data System (ADS)

Bergantz, G. W.; Schleicher, J.; Burgisser, A.

2016-12-01

The identification of shared characteristics in zoned crystals has motivated the definition of crystal populations. These populations reflect the simultaneous transport of crystals, heat and composition during open-system events. An obstacle to interpreting the emergence of a population is the absence of a way to correlate specific dynamic conditions with the characteristic attributes of a population. By combining a boundary-layer diffusion controlled model for crystal growth/dissolution with discrete-element magma dynamics simulations of crystal-bearing magmas, the creation of populations can be simulated. We have implemented a method that decomposes the chemical potential into the thermal and compositional contributions to crystal dissolution/growth. This allows for the explicit treatment of thermal inertia and thermal-compositional decoupling as fluid circulation stirs the system during an open-system event. We have identified three distinct dynamic states producing crystal populations. They are based on the volume fraction of crystals. In a mushy system, thermal and compositional states are tightly linked as the volume involved in the mixing is constrained by the so-called mixing bowl (Bergantz et al., 2015). The mixing bowl volume is a function of the visco-plastic response of the mush and the intrusion width, not by the progressive entrainment of the new intrusion as commonly assumed. Crystal dissolution is the dominate response to input of more primitive magma. At the other endmember, under very dilute conditions, thermal and compositional conditions can become decoupled, and the in-coming magma forms a double-diffusive low-Re jet. This can allow for both dissolution and growth as crystals circulate widely into an increasingly stratified system. A middle range of crystal concentration produces a very complex feedback, as sedimenting crystals form fingers and chains that interact with the incoming magma, break-up the entrainment with chaotic stirring and add a second length scale to the mixing. It simultaneously forms a small mixing bowl in the pile of crystals sedimenting at the base. This can produce very complex populations even in a simple open-system event. Bergantz et al., 2015, Open-system dynamics and mixing in magma mushes, Nature Geosci., DOI: 10.1038/NGEO2534

Mt. Etna plumbing system revealed by combined textural, compositional, and thermobarometric studies in clinopyroxenes

NASA Astrophysics Data System (ADS)

Giacomoni, P. P.; Coltorti, M.; Bryce, J. G.; Fahnestock, M. F.; Guitreau, M.

2016-04-01

Coupled textural and in situ geochemical studies of clinopyroxene (cpx) phenocrysts, from both historical and recent eruptions of Mt. Etna volcano, provide a means to investigate the processes occurring in the deepest portion of the feeding system (>10 km depth). Five distinct textures were recognized: (1) normal oscillatory zoning, (2) normal zoning with Fe-rich rim, (3) sieve-textured core, (4) reverse oscillatory zoning, and (5) dusty rim. Electron microprobe analyses indicate an almost constant diopside-augite composition, with a slight enrichment in the enstatite for more recent erupted cpx. Core-to-rim compositional profiles, performed along the cpx, reveal distinct compositional characteristics. Normal oscillatory zoning is often characterized by a sharp increase in FeO (Δ ~ 2 wt%) accompanied by a drop in Al2O3 on the outermost 30 μm. Reverse oscillatory zoning, by contrast, exhibits a drop in FeO, Al2O3 (Δ ~ 2 wt%), and a remarkable crystal rim increase in MgO (up to 5 wt%). Similar compositional changes are evident in dusty-textured rims, which are characterized by dissolution edges and overgrowth containing glass pockets and channels. No significant compositional variations have been observed across crystals with sieve-textured cores. Trace element concentrations show enrichments in Sr, La, Zr, and REE, together with a decreasing La/Yb ratio (from ~7 to ~4) in rims of normally zoned crystals. Cpx with reverse zoning and dusty rims has low Sr, La, Zr, and REE contents toward crystal rims. Thermometers and barometers, based on equilibrium cpx-melt pairs, suggest that cpx cores start nucleating at 720 MPa, with the majority of them forming between 600 and 400 MPa but continuing to crystallize until very shallow depths (<100 MPa). Normal oscillatory-zoned phenocrysts surrounded by rims form at pressures shallower than 400 MPa, while reverse zoning and dusty rims occur between 400 and 500 MPa. Coupled petrologic and thermobarometric studies on both clinopyroxenes and plagioclases, associated with detailed textural and in situ geochemical analyses, are promising tools to reconstruct the entire magma ascent path beneath open-system volcanoes. At Mt. Etna, two distinct processes could account for the observed textures: Fe-rich rims in normal oscillatory-zoned crystals can be related to decompression-induced crystallization, while reverse zoning and dusty rims can be produced by mixing with a more basic magma at 400-500 MPa (i.e., ~10 km). Textural features are not restricted to a particular evolutionary phase of the volcano, which suggest that the deep feeding system has not changed significantly since the first alkaline volcanic phase.

Two conformational states of the membrane-associated Bacillus thuringiensis Cry4Ba {delta}-endotoxin complex revealed by electron crystallography: Implications for toxin-pore formation

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

Ounjai, Puey; Laboratory of Molecular Biophysics and Structural Biochemistry, Institute of Molecular Biology and Genetics, Mahidol University, Salaya Campus, Nakornpathom 73170; Unger, Vinzenz M.

The insecticidal nature of Cry {delta}-endotoxins produced by Bacillus thuringiensis is generally believed to be caused by their ability to form lytic pores in the midgut cell membrane of susceptible insect larvae. Here we have analyzed membrane-associated structures of the 65-kDa dipteran-active Cry4Ba toxin by electron crystallography. The membrane-associated toxin complex was crystallized in the presence of DMPC via detergent dialysis. Depending upon the charge of the adsorbed surface, 2D crystals of the oligomeric toxin complex have been captured in two distinct conformations. The projection maps of those crystals have been generated at 17 A resolution. Both complexes appeared tomore » be trimeric; as in one crystal form, its projection structure revealed a symmetrical pinwheel-like shape with virtually no depression in the middle of the complex. The other form revealed a propeller-like conformation displaying an obvious hole in the center region, presumably representing the toxin-induced pore. These crystallographic data thus demonstrate for the first time that the 65-kDa activated Cry4Ba toxin in association with lipid membranes could exist in at least two different trimeric conformations, conceivably implying the closed and open states of the pore.« less

In vitro degradation of ZnO flowered coated Zn-Mg alloys in simulated physiological conditions.

PubMed

Alves, Marta M; Prosek, Tomas; Santos, Catarina F; Montemor, Maria F

2017-01-01

Flowered coatings composed by ZnO crystals were successfully electrodeposited on Zn-Mg alloys. The distinct coatings morphologies were found to be dependent upon the solid interfaces distribution, with the smaller number of bigger flowers (ø 46μm) obtained on Zn-Mg alloy containing 1wt.% Mg (Zn-1Mg) contrasting with the higher number of smaller flowers (ø 38μm) achieved on Zn-Mg alloy with 2wt.% Mg (Zn-2Mg). To assess the in vitro behaviour of these novel resorbable materials, a detailed evaluation of the degradation behaviour, in simulated physiological conditions, was performed by electrochemical impedance spectroscopy (EIS). The opposite behaviours observed in the corrosion resistances resulted in the build-up of distinct corrosion layers. The products forming these layers, preferentially detected at the flowers, were identified and their spatial distribution disclosed by EDS and Raman spectroscopy techniques. The presence of smithsonite, simonkolleite, hydrozincite, skorpionite and hydroxyapatite were assigned to both corrosion layers. However the distinct spatial distributions depicted may impact the biocompatibility of these resorbable materials, with the bone analogue compounds (hydroxyapatite and skorpionite) depicted in-between the ZnO crystals and on the top corrosion layer of Zn-1Mg flowers clearly contrasting with the hindered layer formed at the interface of the substrate with the flowers on Zn-2Mg. Copyright © 2016 Elsevier B.V. All rights reserved.

Transformation mechanism of amorphous calcium carbonate into calcite in the sea urchin larval spicule.

PubMed

Politi, Yael; Metzler, Rebecca A; Abrecht, Mike; Gilbert, Benjamin; Wilt, Fred H; Sagi, Irit; Addadi, Lia; Weiner, Steve; Gilbert, P U P A; Gilbert, Pupa

2008-11-11

Sea urchin larval spicules transform amorphous calcium carbonate (ACC) into calcite single crystals. The mechanism of transformation is enigmatic: the transforming spicule displays both amorphous and crystalline properties, with no defined crystallization front. Here, we use X-ray photoelectron emission spectromicroscopy with probing size of 40-200 nm. We resolve 3 distinct mineral phases: An initial short-lived, presumably hydrated ACC phase, followed by an intermediate transient form of ACC, and finally the biogenic crystalline calcite phase. The amorphous and crystalline phases are juxtaposed, often appearing in adjacent sites at a scale of tens of nanometers. We propose that the amorphous-crystal transformation propagates in a tortuous path through preexisting 40- to 100-nm amorphous units, via a secondary nucleation mechanism.

Heterogeneous nucleation in a glass-forming alloy

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

Wall, J. J.; Liu, Chain T; Rhim, W. K.

Nucleation in the undercooled liquid state in the bulk metallic glass-forming composition Zr{sub 52.5}Cu{sub 17.9}Ni{sub 14.6}Al{sub 10}Ti{sub 5} (VIT-105), produced using high purity (PA) and commercial purity (CA) raw materials was investigated using electrostatic levitation and ex situ neutron diffraction. The CA material was observed to have a lower density than the PA sample and crystallized at relatively shallow undercooling. The densities of the samples at temperatures above the solidus showed an oxygen-dependent hysteresis associated with the state change, indicating the presence of oxygen-stabilized intermetallics. The PA alloy exhibited three distinct crystallization modes dependent on the thermal history of themore » melt, one of which showed a net volume expansion.« less

Fragment-based screen against HIV protease.

PubMed

Perryman, Alexander L; Zhang, Qing; Soutter, Holly H; Rosenfeld, Robin; McRee, Duncan E; Olson, Arthur J; Elder, John E; Stout, C David

2010-03-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 A resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the 'exo site' adjacent to the Gly(16)Gly(17)Gln(18)loop where the amide of Gly(17)is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys(14)and Leu(63). Another fragment, indole-6-carboxylic acid, binds on the 'outside/top of the flap' via hydrophobic contacts with Trp(42), Pro(44), Met(46), and Lys(55), a hydrogen bond with Val(56), and a salt-bridge with Arg(57). 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target.

Fragment-Based Screen against HIV Protease

PubMed Central

Perryman, A. L.; Zhang, Q.; Soutter, H. H.; Rosenfeld, R.; McRee, D. E.; Olson, A. J.; Elder, J. E.; Stout, C. D.

2009-01-01

We have employed a fragment-based screen against wild-type (NL4-3) HIV protease (PR) using the Active Sight fragment library and X-ray crystallography. The experiments reveal two new binding sites for small molecules. PR was co-crystallized with fragments, or crystals were soaked in fragment solutions, using five crystal forms, and 378 data sets were collected to 2.3-1.3 Å resolution. Fragment binding induces a distinct conformation and specific crystal form of TL-3 inhibited PR during co-crystallization. One fragment, 2-methylcyclohexanol, binds in the ‘exo site’ adjacent to the Gly16Gly17Gln18 loop where the amide of Gly17 is a specific hydrogen bond donor, and hydrophobic contacts occur with the side chains of Lys14 and Leu63. Another fragment, indole-6-carboxylic acid, binds on the ‘outside/top of the flap’ via hydrophobic contacts with Trp42, Pro44, Met46, and Lys55, a hydrogen bond with Val56, and a salt-bridge with Arg57. 2-acetyl-benzothiophene also binds at this site. This study is the first fragment-based crystallographic screen against HIV PR, and the first time that fragments were screened against an inhibitor-bound drug target to search for compounds that both bind to novel sites and stabilize the inhibited conformation of the target. PMID:20659109

Characterization of two polymorphs of salmeterol xinafoate crystallized from supercritical fluids.

PubMed

Tong, H H; Shekunov, B Y; York, P; Chow, A H

2001-06-01

To characterize two polymorphs of salmeterol xinafoate (SX-I and SX-II) produced by supercritical fluid crystallization. SX-I and SX-II were crystallized as fine powders using Solution Enhanced Dispersion by Supercritical Fluids (SEDS). The two polymorphs and a reference micronized SX sample (MSX) were characterized using powder X-ray diffractometry (PXRD), Fourier transform infrared spectroscopy (FTIR), differential scanning calorimetry (DSC), thermogravimetric analysis (TGA), aqueous solubility (and dissolution) determination at 5-40 degrees C, BET adsorption analysis, and inverse gas chromatography (IGC). Compared with SX-I, SX-II exhibited a lower enthalpy of fusion, a higher equilibrium solubility, a higher intrinsic dissolution rate, a lower enthalpy of solution (based on van't Hoff solubility plots), and a different FTIR spectrum (reflecting differences in intermolecular hydrogen bonding). Solubility ratio plot yielded a transition temperature (-99 degrees C) below the melting points of both polymorphs. MSX showed essentially the same crystal form as SX-I (confirmed by PXRD and FTIR), but a distinctly different thermal behaviour. Mild trituration of SX-I afforded a similar DSC profile to MSX while prolonged grinding of SX-I gave rise to an endotherm at -109 degrees C, corresponding to solid-solid transition of SX-I to SX-II. Surface analysis of MSX, SX-I, and SX-II by IGC revealed significant differences in surface free energy in terms of both dispersive (nonpolar) interactions and specific (polar) acid-base properties. The SEDS-processed SX-I and SX-II display high polymorphic purity and distinctly different physical and surface properties. The polymorphs are related enantiotropically with SX-I being the thermodynamically stable form at room temperature.

Form follows function: morphological diversification and alternative trapping strategies in carnivorous Nepenthes pitcher plants.

PubMed

Bauer, Ulrike; Clemente, C J; Renner, T; Federle, W

2012-01-01

Carnivorous plants of the genus Nepenthes have evolved a striking diversity of pitcher traps that rely on specialized slippery surfaces for prey capture. With a comparative study of trap morphology, we show that Nepenthes pitcher plants have evolved specific adaptations for the use of either one of two distinct trapping mechanisms: slippery wax crystals on the inner pitcher wall and 'insect aquaplaning' on the wet upper rim (peristome). Species without wax crystals had wider peristomes with a longer inward slope. Ancestral state reconstructions identified wax crystal layers and narrow, symmetrical peristomes as ancestral, indicating that wax crystals have been reduced or lost multiple times independently. Our results complement recent reports of nutrient source specializations in Nepenthes and suggest that these specializations may have driven speciation and rapid diversification in this genus. © 2011 The Authors. Journal of Evolutionary Biology © 2011 European Society For Evolutionary Biology.

Self-assembly modes of glycyrrhetinic acid esters in view of the crystal packing of related triterpene molecules.

PubMed

Langer, Dominik; Wicher, Barbara; Szczołko, Wojciech; Gdaniec, Maria; Tykarska, Ewa

2016-08-01

The crystal structures of three ester derivatives of glycyrrhetinic acid (GE) are reported. X-ray crystallography revealed that despite differences in the size of the ester substituents (ethyl, isopropyl and 2-morpholinoethyl) the scheme of molecular self-assembly is similar in all three cases but differs significantly from that observed in other known GE esters. According to our analysis, the two basic patterns of self-assembly of GE esters observed in their unsolvated crystals correspond to two distinct orientations of the ester groups relative to the triterpene backbone. Moreover, comparison of the self-assembly modes of GE esters in their unsolvated forms with the supramolecular organization of GE and carbenoxolone in their solvated crystals revealed that ester substituents replace solvent molecules hydrogen bonded to the COOH group at the triterpene skeleton, resulting in similar packing arrangements of these compounds.

The mechanism of color change in the neon tetra fish: a light-induced tunable photonic crystal array.

PubMed

Gur, Dvir; Palmer, Benjamin A; Leshem, Ben; Oron, Dan; Fratzl, Peter; Weiner, Steve; Addadi, Lia

2015-10-12

The fresh water fish neon tetra has the ability to change the structural color of its lateral stripe in response to a change in the light conditions, from blue-green in the light-adapted state to indigo in the dark-adapted state. The colors are produced by constructive interference of light reflected from stacks of intracellular guanine crystals, forming tunable photonic crystal arrays. We have used micro X-ray diffraction to track in time distinct diffraction spots corresponding to individual crystal arrays within a single cell during the color change. We demonstrate that reversible variations in crystal tilt within individual arrays are responsible for the light-induced color variations. These results settle a long-standing debate between the two proposed models, the "Venetian blinds" model and the "accordion" model. The insight gained from this biogenic light-induced photonic tunable system may provide inspiration for the design of artificial optical tunable systems. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Crystal structure of 4,4′-(disulfanediyl)dibutanoic acid–4,4′-bipyridine (1/1)

PubMed Central

Atria, Ana María; Garland, Maria Teresa; Baggio, Ricardo

2014-01-01

4,4′-(Disulfanediyl)dibutanoic acid (dtba) and 4,4′-bipyridine (4,4′-bpy) crystallize in an 1:1 ratio, leading to the title co-crystal with composition C8H14O4S2·C10H8N2. A distinctive feature of the crystal structure is the geometry of the dtba moiety, which appears to be stretched [with a 9.98 (1) Å span between outermost carbons] and acts as an hydrogen-bonding connector, forming linear chains along [-211] with the 4,4′-bpy moiety by way of O—H⋯N hydrogen bonds and C—H⋯O interactions. The influence of the mol­ecular shape on the hydrogen-bonding pattern is analysed by comparing the title compound and two other 4,4′-bpy co-crystals with closely related mol­ecules of similar formulation but different geometry, showing the way in which this correlates with the packing arrangement. PMID:25309167

Solid-state NMR study of various mono- and divalent cation forms of the natural zeolite natrolite.

PubMed

Park, Min Bum; Vicente, Aurélie; Fernandez, Christian; Hong, Suk Bong

2013-05-28

Here we present the one-dimensional (29)Si and (27)Al MAS NMR and two-dimensional (27)Al MQMAS and DQF-STMAS NMR spectra of the monovalent (Na(+), K(+), Rb(+), Cs(+) and NH4(+)) and divalent (Ca(2+), Sr(2+) and Ba(2+)) cation forms of the natural zeolite natrolite (framework type NAT) with complete Si-Al ordering over the crystallographically distinct tetrahedral sites and with the same hydration state (hydrated, partially dehydrated or fully dehydrated). In the case of monovalent cation-exchanged natrolites, the differences in their crystal symmetry evidenced by (29)Si MAS NMR were found to be in good agreement with those determined by crystallographic analyses. However, (27)Al DQF-STMAS NMR spectroscopy shows the presence of two distinct Al sites in dehydrated K-NAT, Rb-NAT and NH4-NAT, suggesting that their actual crystal symmetry is lower than the reported one (i.e., orthorhombic Fdd2). The MAS NMR results also show that the space group of hydrated Ca-NAT is lower than that (monoclinic F1d1) of hydrated scolecite, the natural calcium counterpart of natrolite, which is also the case with hydrated Sr-NAT and Ba-NAT. We believe that the unexpected diversity in the crystal symmetry of natrolite caused by exchange of various mono- and divalent ions, as well as by dehydration, may be inherently due to the high framework flexibility of this natural zeolite.

Kinetics and thermodynamics of the interchange of the morpheein forms of human porphobilinogen synthase.

PubMed

Selwood, Trevor; Tang, Lei; Lawrence, Sarah H; Anokhina, Yana; Jaffe, Eileen K

2008-03-11

A morpheein is a homo-oligomeric protein that can adopt different nonadditive quaternary assemblies (morpheein forms) with different functionalities. The human porphobilinogen synthase (PBGS) morpheein forms are a high activity octamer, a low activity hexamer, and two structurally distinct dimer conformations. Conversion between hexamer and octamer involves dissociation to dimers, conformational change at the dimer level, followed by association to the alternate assembly. The current work promotes an alternative and novel view of the physiologically relevant dimeric structures, which are derived from the crystal structures, but are distinct from the asymmetric units of their crystal forms. Using a well characterized heteromeric system (WT+F12L; Tang, L. et al. (2005) J. Biol. Chem. 280, 15786-15793), extensive study of the human PBGS morpheein reequilibration process now reveals that the intervening dimers do not dissociate to monomers. The morpheein equilibria of wild type (WT) human PBGS are found to respond to changes in pH, PBGS concentration, and substrate turnover. Notably, the WT enzyme is predominantly an octamer at neutral pH, but increasing pH results in substantial conversion to lower order oligomers. Most significantly, the free energy of activation for the conversion of WT+F12L human PBGS heterohexamers to hetero-octamers is determined to be the same as that for the catalytic conversion of substrate to product by the octamer, remarkably suggesting a common rate-limiting step for both processes, which is postulated to be the opening/closing of the active site lid.

Grotthuss Transport of Iodide in EMIM/I3 Ionic Crystal.

PubMed

McDaniel, Jesse G; Yethiraj, Arun

2018-01-11

Highly ionic environments can mediate unusual chemical reactions that would otherwise be considered impossible based on chemical intuition. For example, the formation of a chemical bond between two iodide anions to form a divalent polyiodide anion is seemingly prohibited due to Coulombic repulsion. Using ab initio molecular dynamics simulations, we show that in the 1-ethyl-3-methylimidazolium (EMIM)/I 3 ionic crystal, the reactive formation of divalent and even trivalent polyiodide anions occurs with extremely small energetic barriers, due to the electrostatic field of the ionic lattice. A practical consequence of this anomalous reactivity is that iodide anions are efficiently transported within the crystal through a "Grotthuss-exchange" mechanism involving bond-breaking and forming events. We characterize two distinct transport pathways, involving both I 4 2- and I 7 3- intermediates, with fast transport of iodide resulting from the release of an I - anion on the opposite side of the intermediate species from the initial bond formation. The ordered cation arrangement in the crystal provides the necessary electrostatic screening for close approach of anions, suggesting a new counterintuitive approach to obtain high ionic conductivity. This new design principle could be used to develop better solid-state electrolytes for batteries, fuel cells, and supercapacitors.

Origins of hydration differences in homochiral and racemic crystals of aspartic acid.

PubMed

Juliano, Thomas R; Korter, Timothy M

2015-02-26

The propensity for crystalline hydrates of organic molecules to form is related to the strength of the interactions between molecules, including the chiral composition of the molecular solids. Specifically, homochiral versus racemic crystalline samples can exhibit distinct differences in their ability to form energetically stable hydrates. The focus of the current study is a comparison of the crystal structures and intermolecular forces found in solid-state L-aspartic acid, DL-aspartic acid, and L-aspartic acid monohydrate. The absence of experimental evidence for the DL-aspartic acid monohydrate is considered here in terms of the enhanced thermodynamic stability of the DL-aspartic acid anhydrate crystal as compared to the L-aspartic acid anhydrate as revealed through solid-state density functional theory calculations and terahertz spectroscopic measurements. The results indicate that anhydrous DL-aspartic acid is the more stable solid, not due to intermolecular forces alone but also due to the improved conformations of the molecules within the racemic solid. Hemihydrated and monohydrated forms of DL-aspartic acid have been computationally evaluated, and in each case, the hydrates produce destabilized aspartic acid conformations that prevent DL-aspartic acid hydrate formation from occurring.

Transformation mechanism of amorphous calcium carbonate into calcite in the sea urchin larval spicule

PubMed Central

Politi, Yael; Metzler, Rebecca A.; Abrecht, Mike; Gilbert, Benjamin; Wilt, Fred H.; Sagi, Irit; Addadi, Lia; Weiner, Steve; Gilbert, P. U. P. A.

2008-01-01

Sea urchin larval spicules transform amorphous calcium carbonate (ACC) into calcite single crystals. The mechanism of transformation is enigmatic: the transforming spicule displays both amorphous and crystalline properties, with no defined crystallization front. Here, we use X-ray photoelectron emission spectromicroscopy with probing size of 40–200 nm. We resolve 3 distinct mineral phases: An initial short-lived, presumably hydrated ACC phase, followed by an intermediate transient form of ACC, and finally the biogenic crystalline calcite phase. The amorphous and crystalline phases are juxtaposed, often appearing in adjacent sites at a scale of tens of nanometers. We propose that the amorphous-crystal transformation propagates in a tortuous path through preexisting 40- to 100-nm amorphous units, via a secondary nucleation mechanism. PMID:18987314

Thermal profiles, crystallization behaviors and microstructure of diacylglycerol-enriched palm oil blends with diacylglycerol-enriched palm olein.

PubMed

Xu, Yayuan; Zhao, Xiaoqing; Wang, Qiang; Peng, Zhen; Dong, Cao

2016-07-01

To elucidate the possible interaction mechanisms between DAG-enriched oils, this study investigated how mixtures of DAG-enriched palm-based oils influenced the phase behavior, thermal properties, crystallization behaviors and the microstructure in binary fat blends. DAG-enriched palm oil (PO-DAGE) was blended with DAG-enriched palm olein (POL-DAGE) in various percentages (0%, 10%, 30%, 50%, 70%, 90%, 100%). Based on the observation of iso-solid diagram and phase diagram, the binary mixture of PO-DAGE/POL-DAGE showed a better compatibility in comparison with their corresponding original blends. DSC thermal profiles exhibited that the melting and crystallization properties of PO-DAGE/POL-DAGE were distinctively different from corresponding original blends. Crystallization kinetics revealed that PO-DAGE/POL-DAGE blends displayed a rather high crystallization rate and exhibited no spherulitic crystal growth. From the results of polarized light micrographs, PO-DAGE/POL-DAGE blends showed more dense structure with very small needle-like crystals than PO/POL. X-ray diffraction evaluation revealed when POL-DAGE was added in high contents to PO-DAGE, above 30%, β-polymorph dominated, and the mount of β' forms crystals was decreasing. Copyright © 2016 Elsevier Ltd. All rights reserved.

Percolation of isotopically heterogeneous interstitial melts in the crystal mush of the Rum layered intrusion, NW Scotland

NASA Astrophysics Data System (ADS)

O'Driscoll, B.; Hepworth, L. N.; Daly, J. S.; Gertisser, R.; Emeleus, C. H.

2017-12-01

The cumulate stratigraphy of layered intrusions offers a means of interrogating the replenishment and solidification histories of mafic magma chambers. Cumulates comprise cumulus minerals, which accumulate to form a silicate framework, and intercumulus minerals, which represent melt crystallised within the crystal mush. This fundamental textural distinction lies at the heart of cumulus theory and underpins some of the classic models of crystal-liquid differentiation that are based on layered intrusions. In order to shed further light on the importance of postcumulus processes in layered intrusions, and to demonstrate that crystal mushes may behave as open-systems during the crystallisation of cumulates, we investigated mineral-scale textural and geochemical heterogeneity in Unit 10 of the 60 Ma Rum layered intrusion. Numerous ( 1 mm thick) Cr-spinel seams occur throughout the 65 m Unit 10 peridotite stratigraphy. Unusually, intercumulus plagioclase and clinopyroxene crystals in the peridotite several centimetres above and below these seams exhibit complex optical and major element zoning. Sampling of individual intra-crystal zones in these phases was carried out using a New Wave Micromill, for analysis of their 87Sr/86Sr compositions to be measured on unspiked samples by TIMS. Both minerals reveal intra-crystalline isotopic heterogeneity. The maximum range (with 2σ uncertainties) of 87Sr/86Sr in the Unit 10 plagioclase is 0.704026±17-0.704591±8 and in clinopyroxene is 0.703533±23-0.704517±17. Within a single, oscillatory-zoned plagioclase, three discrete zones yield 87Sr/86Sr values of 0.704337±20, 0.704095±20 and 0.704052±11. A complex patchily-zoned clinopyroxene yields a 87Sr/86Sr range of 0.703533±23-0.703894±23. The new data demonstrate that multiple generations of isotopically distinct melts percolated through the Unit 10 crystal mush, suggesting solidification from cumulates that underwent repeated cycles of resorption and recrystallisation at the postcumulus stage. The cumulate products of layered intrusions may therefore form from magma addition within the crystal mush, and such a process might be especially relevant for precious metal enrichment, given the association between isotopic disequilibrium and the locations of Cr-spinel seams observed here.

HicAB toxin-antitoxin complex from Escherichia coli: expression and crystallization.

PubMed

Yang, Jingsi; Xu, Bingshuang; Gao, Zengqiang; Zhou, Ke; Liu, Peng; Dong, Yuhui; Zhang, Jianjun; Liu, Quansheng

2017-09-01

Toxin-antitoxin (TA) systems are widespread in both bacteria and archaea, where they enable cells to adapt to environmental cues. TA systems play crucial roles in various cellular processes, such as programmed cell death, cell growth, persistence and virulence. Here, two distinct forms of the type II toxin-antitoxin complex HicAB were identified and characterized in Escherichia coli K-12, and both were successfully overexpressed and purified. The two proposed forms, HicAB L and HicAB S , differed in the presence or absence of a seven-amino-acid segment at the N-terminus in the antitoxin HicB. The short form HicAB S readily crystallized under the conditions 0.1 M Tris-HCl pH 8.0, 20%(w/v) PEG 6000, 0.2 M ammonium sulfate. The HicAB S crystal diffracted and data were collected to 2.5 Å resolution. The crystal belonged to space group I222 or I2 1 2 1 2 1 , with unit-cell parameters a = 67.04, b = 66.31, c = 120.78 Å. Matthews coefficient calculation suggested the presence of two molecules each of HicA and HicB S in the asymmetric unit, with a solvent content of 55.28% and a Matthews coefficient (V M ) of 2.75 Å 3  Da -1 .

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

Heaslet, H.; Rosenfeld, R.; Giffin, M.

The crystal structures of wild-type HIV protease (HIV PR) in the absence of substrate or inhibitor in two related crystal forms at 1.4 and 2.15 {angstrom} resolution are reported. In one crystal form HIV PR adopts an 'open' conformation with a 7.7 {angstrom} separation between the tips of the flaps in the homodimer. In the other crystal form the tips of the flaps are 'curled' towards the 80s loop, forming contacts across the local twofold axis. The 2.3 {angstrom} resolution crystal structure of a sixfold mutant of HIV PR in the absence of substrate or inhibitor is also reported. Themore » mutant HIV PR, which evolved in response to treatment with the potent inhibitor TL-3, contains six point mutations relative to the wild-type enzyme (L24I, M46I, F53L, L63P, V77I, V82A). In this structure the flaps also adopt a 'curled' conformation, but are separated and not in contact. Comparison of the apo structures to those with TL-3 bound demonstrates the extent of conformational change induced by inhibitor binding, which includes reorganization of the packing between twofold-related flaps. Further comparison with six other apo HIV PR structures reveals that the 'open' and 'curled' conformations define two distinct families in HIV PR. These conformational states include hinge motion of residues at either end of the flaps, opening and closing the entire {beta}-loop, and translational motion of the flap normal to the dimer twofold axis and relative to the 80s loop. The alternate conformations also entail changes in the {beta}-turn at the tip of the flap. These observations provide insight into the plasticity of the flap domains, the nature of their motions and their critical role in binding substrates and inhibitors.« less

Crystal structure of dUTP pyrophosphatase from feline immunodeficiency virus.

PubMed Central

Prasad, G. S.; Stura, E. A.; McRee, D. E.; Laco, G. S.; Hasselkus-Light, C.; Elder, J. H.; Stout, C. D.

1996-01-01

We have determined the crystal structure of dUTP pyrophosphatase (dUTPase) from feline immunodeficiency virus (FIV) at 1.9 A resolution. The structure has been solved by the multiple isomorphous replacement (MIR) method using a P6(3) crystal form. The results show that the enzyme is a trimer of 14.3 kDa subunits with marked structural similarity to E. coli dUTPase. In both enzymes the C-terminal strand of an anti-parallel beta-barrel participates in the beta-sheet of an adjacent subunit to form an interdigitated, biologically functional trimer. In the P6(3) crystal form one trimer packs on the 6(3) screw-axis and another on the threefold axis so that there are two independent monomers per asymmetric unit. A Mg2+ ion is coordinated by three asparate residues on the threefold axis of each trimer. Alignment of 17 viral, prokaryotic, and eukaryotic dUTPase sequences reveals five conserved motifs. Four of these map onto the interface between pairs of subunits, defining a putative active site region; the fifth resides in the C-terminal 16 residues, which is disordered in the crystals. Conserved motifs from all three subunits are required to create a given active site. With respect to viral protein expression, it is particularly interesting that the gene for dUTPase (DU) resides in the middle of the Pol gene, the enzyme cassette of the retroviral genome. Other enzymes encoded in the Pol polyprotein, including protease (PR), reverse transcriptase (RT), and most likely integrase (IN), are dimeric enzymes, which implies that the stoichiometry of expression of active trimeric dUTPase is distinct from the other Pol-encoded enzymes. Additionally, due to structural constraints, it is unlikely that dUTPase can attain an active form prior to cleavage from the polyprotein. PMID:8976551

Crystal structure of a small heat-shock protein from Xylella fastidiosa reveals a distinct high-order structure.

PubMed

Fonseca, Emanuella Maria Barreto; Scorsato, Valéria; Dos Santos, Marcelo Leite; Júnior, Atilio Tomazini; Tada, Susely Ferraz Siqueira; Dos Santos, Clelton Aparecido; de Toledo, Marcelo Augusto Szymanski; de Souza, Anete Pereira; Polikarpov, Igor; Aparicio, Ricardo

2017-04-01

Citrus variegated chlorosis is a disease that attacks economically important citrus plantations and is caused by the plant-pathogenic bacterium Xylella fastidiosa. In this work, the structure of a small heat-shock protein from X. fastidiosa (XfsHSP17.9) is reported. The high-order structures of small heat-shock proteins from other organisms are arranged in the forms of double-disc, hollow-sphere or spherical assemblies. Unexpectedly, the structure reported here reveals a high-order architecture forming a nearly square cavity.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

PubMed Central

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A.; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W.; Ke, Jiyuan; Eileen Tan, M. H.; Zhang, Chenghai; Moeller, Arne; West, Graham M.; Pascal, Bruce; Van Eps, Ned; Caro, Lydia N.; Vishnivetskiy, Sergey A.; Lee, Regina J.; Suino-Powell, Kelly M.; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J.; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A.; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N.; Spence, John C. H.; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P.; Katritch, Vsevolod; Gurevich, Vsevolod V.; Griffin, Patrick R.; Hubbell, Wayne L.; Stevens, Raymond C.; Cherezov, Vadim; Melcher, Karsten; Xu, H. Eric

2015-01-01

G protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signaling to numerous G protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly, in which rhodopsin uses distinct structural elements, including TM7 and Helix 8 to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotation between the N- and C- domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signaling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology. PMID:26200343

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

DOE PAGES

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang; ...

2015-07-22

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser.

PubMed

Kang, Yanyong; Zhou, X Edward; Gao, Xiang; He, Yuanzheng; Liu, Wei; Ishchenko, Andrii; Barty, Anton; White, Thomas A; Yefanov, Oleksandr; Han, Gye Won; Xu, Qingping; de Waal, Parker W; Ke, Jiyuan; Tan, M H Eileen; Zhang, Chenghai; Moeller, Arne; West, Graham M; Pascal, Bruce D; Van Eps, Ned; Caro, Lydia N; Vishnivetskiy, Sergey A; Lee, Regina J; Suino-Powell, Kelly M; Gu, Xin; Pal, Kuntal; Ma, Jinming; Zhi, Xiaoyong; Boutet, Sébastien; Williams, Garth J; Messerschmidt, Marc; Gati, Cornelius; Zatsepin, Nadia A; Wang, Dingjie; James, Daniel; Basu, Shibom; Roy-Chowdhury, Shatabdi; Conrad, Chelsie E; Coe, Jesse; Liu, Haiguang; Lisova, Stella; Kupitz, Christopher; Grotjohann, Ingo; Fromme, Raimund; Jiang, Yi; Tan, Minjia; Yang, Huaiyu; Li, Jun; Wang, Meitian; Zheng, Zhong; Li, Dianfan; Howe, Nicole; Zhao, Yingming; Standfuss, Jörg; Diederichs, Kay; Dong, Yuhui; Potter, Clinton S; Carragher, Bridget; Caffrey, Martin; Jiang, Hualiang; Chapman, Henry N; Spence, John C H; Fromme, Petra; Weierstall, Uwe; Ernst, Oliver P; Katritch, Vsevolod; Gurevich, Vsevolod V; Griffin, Patrick R; Hubbell, Wayne L; Stevens, Raymond C; Cherezov, Vadim; Melcher, Karsten; Xu, H Eric

2015-07-30

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ∼20° rotation between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. This structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.

Crystal structure of rhodopsin bound to arrestin by femtosecond X-ray laser

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

Kang, Yanyong; Zhou, X. Edward; Gao, Xiang

G-protein-coupled receptors (GPCRs) signal primarily through G proteins or arrestins. Arrestin binding to GPCRs blocks G protein interaction and redirects signalling to numerous G-protein-independent pathways. Here we report the crystal structure of a constitutively active form of human rhodopsin bound to a pre-activated form of the mouse visual arrestin, determined by serial femtosecond X-ray laser crystallography. Together with extensive biochemical and mutagenesis data, the structure reveals an overall architecture of the rhodopsin-arrestin assembly in which rhodopsin uses distinct structural elements, including transmembrane helix 7 and helix 8, to recruit arrestin. Correspondingly, arrestin adopts the pre-activated conformation, with a ~20° rotationmore » between the amino and carboxy domains, which opens up a cleft in arrestin to accommodate a short helix formed by the second intracellular loop of rhodopsin. In conclusion, this structure provides a basis for understanding GPCR-mediated arrestin-biased signalling and demonstrates the power of X-ray lasers for advancing the frontiers of structural biology.« less

Heterogeneous pumice populations in the 2.08-Ma Cerro Galán Ignimbrite: Implications for magma recharge and ascent preceding a large-volume silicic eruption

USGS Publications Warehouse

Wright, Heather M.; Folkes, Christopher B.; Cas, Ray A.F.; Cashman, Katharine V.

2011-01-01

Triggering mechanisms of large silicic eruptions remain a critical unsolved problem. We address this question for the ~2.08-Ma caldera-forming eruption of Cerro Galán volcano, Argentina, which produced distinct pumice populations of two colors: grey (5%) and white (95%) that we believe may hold clues to the onset of eruptive activity. We demonstrate that the color variations correspond to both textural and compositional variations between the clast types. Both pumice types have bulk compositions of high-K, high-silica dacite to low-silica rhyolite, but there are sufficient compositional differences (e.g., ~150 ppm lower Ba at equivalent SiO2 content and 0.03 wt.% higher TiO2 in white pumice than grey) to suggest that the two pumice populations are not related by simple fractionation. Trace element concentrations in crystals mimic bulk variations between clast types, with grey pumice containing elevated Ba, Cu, Pb, and Zn concentrations in both bulk samples (average Cu, Pb, and Zn concentrations are 27, 35, and 82 in grey pumice vs. 11, 19, and 60 in white pumice) and biotite phenocrysts and white pumice showing elevated Li concentrations in biotite and plagioclase phenocrysts. White and grey clasts are also texturally distinct: White pumice clasts contain abundant phenocrysts (44–57%), lack microlites, and have highly evolved groundmass glass compositions (76.4–79.6 wt.% SiO2), whereas grey pumice clasts contain a lower percentage of phenocrysts/microphenocrysts (35–49%), have abundant microlites, and have less evolved groundmass glass compositions (69.4–73.8 wt.% SiO2). There is also evidence for crystal transfer between magma producing white and grey pumice. Thin highly evolved melt rims surround some fragmental crystals in grey pumice clasts and appear to have come from magma that produced white pumice. Furthermore, based on crystal compositions, white bands within banded pumice contain crystals originating in grey magma. Finally, only grey pumice clasts form breadcrusted surface textures. We interpret these compositional and textural variations to indicate distinct magma batches, where grey pumice originated from an originally deeper, more volatile-rich dacite recharge magma that ascended through and mingled with the volumetrically dominant, more highly crystalline chamber that produced white pumice. Shortly before eruption, the grey pumice magma stalled within shallow fractures, forming a vanguard magma phase whose ascent may have provided a trigger for eruption of the highly crystalline rhyodacite magma. We suggest that in the case of the Cerro Galán eruption, grey pumice provides evidence not only for cryptic silicic recharge in a large caldera system but also a probable trigger for the eruption.

Heterogeneous pumice populations in the 2.08-Ma Cerro Galán Ignimbrite: implications for magma recharge and ascent preceding a large-volume silicic eruption

NASA Astrophysics Data System (ADS)

Wright, Heather M. N.; Folkes, Chris B.; Cas, Raymond A. F.; Cashman, Katharine V.

2011-12-01

Triggering mechanisms of large silicic eruptions remain a critical unsolved problem. We address this question for the ~2.08-Ma caldera-forming eruption of Cerro Galán volcano, Argentina, which produced distinct pumice populations of two colors: grey (5%) and white (95%) that we believe may hold clues to the onset of eruptive activity. We demonstrate that the color variations correspond to both textural and compositional variations between the clast types. Both pumice types have bulk compositions of high-K, high-silica dacite to low-silica rhyolite, but there are sufficient compositional differences (e.g., ~150 ppm lower Ba at equivalent SiO2 content and 0.03 wt.% higher TiO2 in white pumice than grey) to suggest that the two pumice populations are not related by simple fractionation. Trace element concentrations in crystals mimic bulk variations between clast types, with grey pumice containing elevated Ba, Cu, Pb, and Zn concentrations in both bulk samples (average Cu, Pb, and Zn concentrations are 27, 35, and 82 in grey pumice vs. 11, 19, and 60 in white pumice) and biotite phenocrysts and white pumice showing elevated Li concentrations in biotite and plagioclase phenocrysts. White and grey clasts are also texturally distinct: White pumice clasts contain abundant phenocrysts (44-57%), lack microlites, and have highly evolved groundmass glass compositions (76.4-79.6 wt.% SiO2), whereas grey pumice clasts contain a lower percentage of phenocrysts/microphenocrysts (35-49%), have abundant microlites, and have less evolved groundmass glass compositions (69.4-73.8 wt.% SiO2). There is also evidence for crystal transfer between magma producing white and grey pumice. Thin highly evolved melt rims surround some fragmental crystals in grey pumice clasts and appear to have come from magma that produced white pumice. Furthermore, based on crystal compositions, white bands within banded pumice contain crystals originating in grey magma. Finally, only grey pumice clasts form breadcrusted surface textures. We interpret these compositional and textural variations to indicate distinct magma batches, where grey pumice originated from an originally deeper, more volatile-rich dacite recharge magma that ascended through and mingled with the volumetrically dominant, more highly crystalline chamber that produced white pumice. Shortly before eruption, the grey pumice magma stalled within shallow fractures, forming a vanguard magma phase whose ascent may have provided a trigger for eruption of the highly crystalline rhyodacite magma. We suggest that in the case of the Cerro Galán eruption, grey pumice provides evidence not only for cryptic silicic recharge in a large caldera system but also a probable trigger for the eruption.

Crystallization and preliminary crystallographic characterization of LmACR2, an arsenate/antimonate reductase from Leishmania major

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

Bisacchi, Davide; Zhou, Yao; Rosen, Barry P.

2006-10-01

LmACR2 from L. major is the first rhodanese-like enzyme directly involved in the reduction of arsenate and antimonate to be crystallized. Diffraction data have been collected to 1.99 Å resolution using synchrotron X-rays. Arsenic is present in the biosphere owing either to the presence of pesticides and herbicides used in agricultural and industrial activities or to leaching from geological formations. The health effects of prolonged exposure to arsenic can be devastating and may lead to various forms of cancer. Antimony(V), which is chemically very similar to arsenic, is used instead in the treatment of leishmaniasis, an infection caused by themore » protozoan parasite Leishmania sp.; the reduction of pentavalent antimony contained in the drug Pentostam to the active trivalent form arises from the presence in the Leishmania genome of a gene, LmACR2, coding for the protein LmACR2 (14.5 kDa, 127 amino acids) that displays weak but significant sequence similarity to the catalytic domain of Cdc25 phosphatase and to rhodanese enzymes. For structural characterization, LmACR2 was overexpressed, purified to homogeneity and crystallized in a trigonal space group (P321 or P3{sub 1}21/P3{sub 2}21). The protein crystallized in two distinct trigonal crystal forms, with unit-cell parameters a = b = 111.0, c = 86.1 Å and a = b = 111.0, c = 175.6 Å, respectively. At a synchrotron beamline, the diffraction pattern extended to a resolution limit of 1.99 Å.« less

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

Romano, Keith P.; Laine, Jennifer M.; Deveau, Laura M.

Hepatitis C NS3/4A protease is a prime therapeutic target that is responsible for cleaving the viral polyprotein at junctions 3-4A, 4A4B, 4B5A, and 5A5B and two host cell adaptor proteins of the innate immune response, TRIF and MAVS. In this study, NS3/4A crystal structures of both host cell cleavage sites were determined and compared to the crystal structures of viral substrates. Two distinct protease conformations were observed and correlated with substrate specificity: (i) 3-4A, 4A4B, 5A5B, and MAVS, which are processed more efficiently by the protease, form extensive electrostatic networks when in complex with the protease, and (ii) TRIF andmore » 4B5A, which contain polyproline motifs in their full-length sequences, do not form electrostatic networks in their crystal complexes. These findings provide mechanistic insights into NS3/4A substrate recognition, which may assist in a more rational approach to inhibitor design in the face of the rapid acquisition of resistance.« less

Morphological Evolution of Nanocluster Aggregates and Single Crystals in Alkaline Zinc Electrodeposition

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

Desai, D; Turney, DE; Anantharaman, B

2014-04-24

The morphology of Zn electrodeposits is studied on carbon-coated transmission electron microscopy grids. At low over-potentials (eta = -50 mV), the morphology develops by aggregation at two distinct length scales: similar to 5 nm diameter monocrystalline nanoclusters form similar to 50 nm diameter polycrystalline aggregates, and the aggregates form a branched network. Epitaxial (00 (0) over bar2) growth above an overpotential of vertical bar eta(c)vertical bar > 125 mV leads to the formation of hexagonal single crystals up to 2 mu m in diameter. Potentiostatic current transients were used to calculate the nucleation rate from Scharifker et al.'s model. Themore » exp(eta) dependence of the nucleation rates indicates that atomistic nucleation theory explains the nucleation process better than Volmer-Weber theory. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment.« less

The principles of cryostratigraphy

NASA Astrophysics Data System (ADS)

French, Hugh; Shur, Yuri

2010-08-01

Cryostratigraphy adopts concepts from both Russian geocryology and modern sedimentology. Structures formed by the amount and distribution of ice within sediment and rock are termed cryostructures. Typically, layered cryostructures are indicative of syngenetic permafrost while reticulate and irregular cryostructures are indicative of epigenetic permafrost. 'Cryofacies' can be defined according to patterns of sediment characterized by distinct ice lenses and layers, volumetric ice content and ice-crystal size. Cryofacies can be subdivided according to cryostructure. Where a number of cryofacies form a distinctive cryostratigraphic unit, these are termed a 'cryofacies assemblage'. The recognition, if present, of (i) thaw unconformities, (ii) other ice bodies such as vein ice (ice wedges), aggradational ice and thermokarst-cave ('pool') ice, and (iii) ice, sand and gravelly pseudomorphs is also important in determining the nature of the freezing process, the conditions under which frozen sediment accumulates, and the history of permafrost.

Biological influences on modern sulfates: Textures and composition of gypsum deposits from Guerrero Negro, Baja California Sur, Mexico

NASA Astrophysics Data System (ADS)

Vogel, Marilyn B.; Des Marais, David J.; Parenteau, Mary N.; Jahnke, Linda L.; Turk, Kendra A.; Kubo, Michael D. Y.

2010-01-01

Gypsum (CaSO 4·2H 2O) deposits from a range of sedimentary environments at Guerrero Negro, Baja California Sur, Mexico were investigated for microscale texture and composition in order to differentiate features formed under substantial microbial influence from those for which microbial effects were relatively minor or absent. Gypsum deposits were classified according to their sedimentary environment, textures, crystal habit, brine composition and other geochemical factors. The environments studied included subaqueous sediments in anchialine pools and in solar salterns, as well as subsurface sediments of mudflats and saltpans. Gypsum that developed in the apparent absence of biofilms included crystals precipitated in the water column and subsedimentary discs that precipitated from phreatic brines. Subsedimentary gypsum developed in sabkha environments exhibited a sinuous microtexture and poikilitically enclosed detrital particles. Water column precipitates had euhedral prismatic habits and extensive penetrative twinning. Gypsum deposits influenced by biofilms included bottom nucleated crusts and gypsolites developing in anchialine pools and saltern ponds. Gypsum precipitating within benthic biofilms, and in biofilms within subaerial sediment surfaces provided compelling evidence of biological influences on crystal textures and habits. This evidence included irregular, high relief surface textures, accessory minerals (S°, Ca-carbonate, Sr/Ca-sulfate and Mg-hydroxide) and distinctive crystal habits such as equant forms and crystals having distorted prism faces.

Topological Switching and Orbiting Dynamics of Colloidal Spheres Dressed with Chiral Nematic Solitons

PubMed Central

Porenta, T.; Čopar, S.; Ackerman, P. J.; Pandey, M. B.; Varney, M. C. M.; Smalyukh, I. I.; Žumer, S.

2014-01-01

Metastable configurations formed by defects, inclusions, elastic deformations and topological solitons in liquid crystals are a promising choice for building photonic crystals and metamaterials with a potential for new optical applications. Local optical modification of the director or introduction of colloidal inclusions into a moderately chiral nematic liquid crystal confined to a homeotropic cell creates localized multistable chiral solitons. Here we induce solitons that “dress” the dispersed spherical particles treated for tangential degenerate boundary conditions, and perform controlled switching of their state using focused optical beams. Two optically switchable distinct metastable states, toron and hopfion, bound to colloidal spheres into structures with different topological charges are investigated. Their structures are examined using Q-tensor based numerical simulations and compared to the profiles reconstructed from the experiments. A topological explanation of observed multistability is constructed. PMID:25477195

Topological switching and orbiting dynamics of colloidal spheres dressed with chiral nematic solitons.

PubMed

Porenta, T; Copar, S; Ackerman, P J; Pandey, M B; Varney, M C M; Smalyukh, I I; Žumer, S

2014-12-05

Metastable configurations formed by defects, inclusions, elastic deformations and topological solitons in liquid crystals are a promising choice for building photonic crystals and metamaterials with a potential for new optical applications. Local optical modification of the director or introduction of colloidal inclusions into a moderately chiral nematic liquid crystal confined to a homeotropic cell creates localized multistable chiral solitons. Here we induce solitons that "dress" the dispersed spherical particles treated for tangential degenerate boundary conditions, and perform controlled switching of their state using focused optical beams. Two optically switchable distinct metastable states, toron and hopfion, bound to colloidal spheres into structures with different topological charges are investigated. Their structures are examined using Q-tensor based numerical simulations and compared to the profiles reconstructed from the experiments. A topological explanation of observed multistability is constructed.

Topologically protected bound states in photonic parity-time-symmetric crystals.

PubMed

Weimann, S; Kremer, M; Plotnik, Y; Lumer, Y; Nolte, S; Makris, K G; Segev, M; Rechtsman, M C; Szameit, A

2017-04-01

Parity-time (PT)-symmetric crystals are a class of non-Hermitian systems that allow, for example, the existence of modes with real propagation constants, for self-orthogonality of propagating modes, and for uni-directional invisibility at defects. Photonic PT-symmetric systems that also support topological states could be useful for shaping and routing light waves. However, it is currently debated whether topological interface states can exist at all in PT-symmetric systems. Here, we show theoretically and demonstrate experimentally the existence of such states: states that are localized at the interface between two topologically distinct PT-symmetric photonic lattices. We find analytical closed form solutions of topological PT-symmetric interface states, and observe them through fluorescence microscopy in a passive PT-symmetric dimerized photonic lattice. Our results are relevant towards approaches to localize light on the interface between non-Hermitian crystals.

Are there impact-formed zircons in the Hadean record?

NASA Astrophysics Data System (ADS)

Wielicki, M. M.; Lu, X.; Bell, E. A.; Schmitt, A. K.; Harrison, T. M.

2008-12-01

Detrital Hadean zircons from the Jack Hills, Western Australia, show a remarkable cluster of crystallization temperatures at 680±25°C. This is particularly surprising as a simple model relating rock composition and Zr concentration predicts that a very broad spectrum of crystallization temperatures (ca. 650°C to 1000°C) with a median value of 780°C, would result from impact melting of the Earth's surface. Magmatic fractionation would tend to increase the aforementioned values. Given the predicted high rate of impacts during the Hadean, the absence of such a population in the Jack Hills zircons could signal a profound sampling problem, a hint of a history much different than previously supposed, or our lack of understanding of zircon formation due to impact related processes. We have begun to examine the latter issue by investigating the crystallization temperatures of zircons formed in melt sheets preserved in the geologic record. The Sudbury Igneous Complex, formed at 1850±3 Ma within the second largest impact crater on Earth, includes two igneous units termed the Black and Felsic Norites. Examination of zircons from each by SIMS confirms their crystallization age at 1847.3±2.2 Ma and yields Ti-in-zircon temperatures of 720°C and 750°C, respectively. This is consistent with that predicted from zircon saturation systematics. A statistical test indicates that the combined norite population is distinct from the Hadean temperature distribution. Thus the question arises: where are the Hadean zircons expected to have formed at >780°C via impact processes? Similar analysis is being pursued for zircons from the Vredefort Impact Structure, South Africa, which should provide further information on impact-formed zircon temperature spectra.

Structural transitions and guest/host complexing of liquid crystal helical nanofilaments induced by nanoconfinement.

PubMed

Kim, Hanim; Ryu, Seong Ho; Tuchband, Michael; Shin, Tae Joo; Korblova, Eva; Walba, David M; Clark, Noel A; Yoon, Dong Ki

2017-02-01

A lamellar liquid crystal (LC) phase of certain bent-core mesogenic molecules can be grown in a manner that generates a single chiral helical nanofilament in each of the cylindrical nanopores of an anodic aluminum oxide (AAO) membrane. By introducing guest molecules into the resulting composite chiral nanochannels, we explore the structures and functionality of the ordered guest/host LC complex, verifying the smectic-like positional order of the fluidic nematic LC phase, which is obtained by the combination of the LC organization and the nanoporous AAO superstructure. The guest nematic LC 4'- n -pentyl-4-cyanobiphenyl is found to form a distinctive fluid layered ordered LC complex at the nanofilament/guest interface with the host 1,3-phenylene bis[4-(4-nonyloxyphenyliminomethyl)benzoate], where this interface contacts the AAO cylinder wall. Filament growth form is strongly influenced by mixture parameters and pore dimensions.

Structural transitions and guest/host complexing of liquid crystal helical nanofilaments induced by nanoconfinement

PubMed Central

Kim, Hanim; Ryu, Seong Ho; Tuchband, Michael; Shin, Tae Joo; Korblova, Eva; Walba, David M.; Clark, Noel A.; Yoon, Dong Ki

2017-01-01

A lamellar liquid crystal (LC) phase of certain bent-core mesogenic molecules can be grown in a manner that generates a single chiral helical nanofilament in each of the cylindrical nanopores of an anodic aluminum oxide (AAO) membrane. By introducing guest molecules into the resulting composite chiral nanochannels, we explore the structures and functionality of the ordered guest/host LC complex, verifying the smectic-like positional order of the fluidic nematic LC phase, which is obtained by the combination of the LC organization and the nanoporous AAO superstructure. The guest nematic LC 4′-n-pentyl-4-cyanobiphenyl is found to form a distinctive fluid layered ordered LC complex at the nanofilament/guest interface with the host 1,3-phenylene bis[4-(4-nonyloxyphenyliminomethyl)benzoate], where this interface contacts the AAO cylinder wall. Filament growth form is strongly influenced by mixture parameters and pore dimensions. PMID:28246642

Rapakivi texture: An indication of the crystallization of hydrosilicates, II

NASA Astrophysics Data System (ADS)

Elliston, John N.

1985-05-01

Rapakivi granites have puzzled all who have seriously studied them. Typical rapakivi texture is a mixture of variously mantled, non-mantled or partly mantled, concentrically zoned, plastically distorted, fragmented, reaggregated, large and small ovoids. Commonly they are potash feldspar often mantled by, and having a variable content of plagioclase. Some display remarkable sphericity. In form, composition, zoning sequence, and crystallization pattern each ovoid reflects an individual development. Up to five concentric internal plagioclase rims have been observed and some ovoids may be isolated in autoliths and wall-rocks. Anomalies and contradictions arise from any assumption of genesis from a cooling melt. The recorded objective data imply that the "magma" from which rapakivi textures develop had similar diffusive and rheological properties to those of a partly dewatered macromolecular paste or a mixture of gelatinous hydrosilicates. As indicated by deep oil wells this system is found at somewhat elevated temperatures at considerable depths within accumulated sediments. In addition to the very specific diffusive and rheological properties of such partly dewatered sediments, the system has as its major components normal solvated macromolecules of mixed clays, silica gels and hydrous ferromagnesian minerals which are characterised by distinctive particle sizes and geometric shapes (platelets, spheres and rods, respectively). Thixotropic liquefaction and intrusion of such concentrated gelatinous "magma" or sediment paste introduces relative movement between the component macromolecules whereby they can reduce surface energy by interaction to assume a "close-packed" condition and aggregate during laminar flow into macro-accretions comprised essentially of their respective particle shapes. Syneresis of these precursor accretions desorbs ions, including the small montmorillonite particles behaving as a colloidal electrolyte. These diffuse from the illitic cores to form a montmorillonite-rich rim which it is suggested crystallizes together with the illitic cores to form mantled or polymantled feldspar ovoids. Crystallization of the rapakivi massif is associated with strong temperature rise stemming from exothermic crystallization of the close-packed metastable colloids. This follows the development of the characteristic texture. The rounded and rimmed precursor accretions are formed during earlier lower-temperature episodes of thixotropic liquefaction which are isothermal. The fluidity is an earlier event. There is high temperature dependent on the rate of water loss but no molten stage. Forty-six typical features of rapakivi texture are described and illustrated, each of which is directly attributable to specific interactions in an alternately dynamic and static colloidal system. Individual correlation between each observed distinctive feature of the rapakivi texture and the well-documented physico-chemical process is complete. For sediment-derived granites, therefore, the rapakivi texture can confidently be assumed to be an indication of the crystallization of their sedimentary hydrosilicate precursors.

Crystal morphology variation in inkjet-printed organic materials

NASA Astrophysics Data System (ADS)

Ihnen, Andrew C.; Petrock, Anne M.; Chou, Tsengming; Samuels, Phillip J.; Fuchs, Brian E.; Lee, Woo Y.

2011-11-01

The recent commercialization of piezoelectric-based drop-on-demand inkjet printers provides an additive processing platform for producing and micropatterning organic crystal structures. We report an inkjet printing approach where macro- and nano-scale energetic composites composed of cyclotrimethylenetrinitramine (RDX) crystals dispersed in a cellulose acetate butyrate (CAB) matrix are produced by direct phase transformation from organic solvent-based all-liquid inks. The characterization of printed composites illustrates distinct morphological changes dependent on ink deposition parameters. When 10 pL ink droplets rapidly formed a liquid pool, a coffee ring structure containing dendritic RDX crystals was produced. By increasing the substrate temperature, and consequently the evaporation rate of the pooled ink, the coffee ring structure was mitigated and shorter dendrites from up to ∼1 to 0.2 mm with closer arm spacing from ∼15 to 1 μm were produced. When the nucleation and growth of RDX and CAB were confined within the evaporating droplets, a granular structure containing nanoscale RDX crystals was produced. The results suggest that evaporation rate and microfluidic droplet confinement can effectively be used to tailor the morphology of inkjet-printed energetic composites.

Nonlinear waveguide optics and photonic crystal fibers.

PubMed

Knight, J C; Skryabin, D V

2007-11-12

Focus Serial: Frontiers of Nonlinear Optics

Crystal Structure of the Oligomeric Form of Lassa Virus Matrix Protein Z.

PubMed

Hastie, Kathryn M; Zandonatti, Michelle; Liu, Tong; Li, Sheng; Woods, Virgil L; Saphire, Erica Ollmann

2016-05-01

The arenavirus matrix protein Z is highly multifunctional and occurs in both monomeric and oligomeric forms. The crystal structure of a dodecamer of Z from Lassa virus, presented here, illustrates a ring-like structure with a highly basic center. Mutagenesis demonstrates that the dimeric interface within the dodecamer and a Lys-Trp-Lys triad at the center of the ring are important for oligomerization. This structure provides an additional template to explore the many functions of Z. The arenavirus Lassa virus causes hundreds of thousands of infections each year, many of which develop into fatal hemorrhagic fever. The arenavirus matrix protein Z is multifunctional, with at least four distinct roles. Z exists in both monomeric and oligomeric forms, each of which likely serves a specific function in the viral life cycle. Here we present the dodecameric form of Lassa virus Z and demonstrate that Z forms a "wreath" with a highly basic center. This structure and that of monomeric Z now provide a pair of critical templates by which the multiple roles of Z in the viral life cycle may be interpreted. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Mutual interaction between high and low stereo-regularity components for crystallization and melting behaviors of polypropylene blend fibers

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

Kawai, Kouya; Takarada, Wataru; Kikutani, Takeshi, E-mail: kikutani.t.aa@m.titech.ac.jp

Crystallization and melting behaviors of blend fibers of two types of polypropylene (PP), i.e. high stereo-regularity/high molecular weight PP (HPP) and low stereo-regularity/low molecular weight PP (LPP), was investigated. Blend fibers consisting of various HPP/LPP compositions were prepared through the melt spinning process. Differential scanning calorimetry (DSC), temperature modulated DSC (TMDSC) and wide-angle X-ray diffraction (WAXD) analysis were applied for clarifying the crystallization and melting behaviors of individual components. In the DSC measurement of blend fibers with high LPP composition, continuous endothermic heat was detected between the melting peaks of LPP at around 40 °C and that of HPP atmore » around 160 °C. Such endothermic heat was more distinct for the blend fibers with higher LPP composition indicating that the melting of LPP in the heating process was hindered because of the presence of HPP crystals. On the other hand, heat of crystallization was detected at around 90 °C in the case of blend fibers with LPP content of 30 to 70 wt%, indicating that the crystallization of HPP component was taking place during the heating of as-spun blend fibers in the DSC measurement. Through the TMDSC analysis, re-organization of the crystalline structure through the simultaneous melting and re-crystallization was detected in the cases of HPP and blend fibers, whereas re-crystallization was not detected during the melting of LPP fibers. In the WAXD analysis during the heating of fibers, amount of a-form crystal was almost constant up to the melting in the case of single component HPP fibers, whereas there was a distinct increase of the intensity of crystalline reflections from around 100 °C, right after the melting of LPP in the case of blend fibers. These results suggested that the crystallization of HPP in the spinning process as well as during the conditioning process after spinning was hindered by the presence of LPP.« less

Influence of crystal characteristics on the shock sensitivities of cyclotrimethylene trinitramine, cyclotetramethylene tetranitramine, and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetra-cyclo[5,5,0,03,1105,9]dodecane immersed in liquid

NASA Astrophysics Data System (ADS)

Li, Hongzhen; Xu, Rong; Kang, Bing; Li, Jinshan; Zhou, Xiaoqing; Zhang, Chaoyang; Nie, Fude

2013-05-01

The shock sensitivities of differently qualified cyclotrimethylene trinitramine (RDX), cyclotetramethylene tetranitramine(HMX), and 2,4,6,8,10,12-hexanitro-2,4,6,8,10,12-hexaazatetra-cyclo[5,5,0,03,1105,9]dodecane (CL-20) immersed in liquid were determined by the large-scale gap tests, for systemic discussion on the influences of crystal characteristics on them. As a result, it shows that (1) the immersion of crystals in liquid leads to an obvious sensitivity decrease; (2) for all three explosives, their shock sensitivities are lowered with increasing their crystal apparent densities or decreasing their particle sizes, and almost not affected by particle morphologies; (3) the crystal twins are readily formed for HMX and the most distinct factor influencing its shock sensitivities; (4) it is found that the crystal apparent density affects most obviously the shock sensitivities for RDX and CL-20; and (5) CL-20, HMX, and RDX are less and less sensitive to shock, suggesting chemical components are also a determining factor.

Analysis of Phase Separation in Czochralski Grown Single Crystal Ilmenite

NASA Technical Reports Server (NTRS)

Wilkins, R.; Powell, Kirk St. A.; Loregnard, Kieron R.; Lin, Sy-Chyi; Muthusami, Jayakumar; Zhou, Feng; Pandey, R. K.; Brown, Geoff; Hawley, M. E.

1998-01-01

Ilmenite (FeTiOs) is a wide bandgap semiconductor with an energy gap of 2.58 eV. Ilmenite has properties suited for radiation tolerant applications, as well as a variety of other electronic applications. Single crystal ilmenite has been grown from the melt using the Czochralski method. Growth conditions have a profound effect on the microstructure of the samples. Here we present data from a variety of analytical techniques which indicate that some grown crystals exhibit distinct phase separation during growth. This phase separation is apparent for both post-growth annealed and unannealed samples. Under optical microscopy, there appear two distinct areas forming a matrix with an array of dots on order of 5 pm diameter. While appearing bright in the optical micrograph, atomic force microscope (AFM) shows the dots to be shallow pits on the surface. Magnetic force microscope (MFM) shows the dots to be magnetic. Phase identification via electron microprobe analysis (EMPA) indicates two major phases in the unannealed samples and four in the annealed samples, where the dots appear to be almost pure iron. This is consistent with micrographs taken with a scanning probe microscope used in the magnetic force mode. Samples that do not exhibit the phase separation have little or no discernible magnetic structure detectable by the MFM.

Structure symmetry determination and magnetic evolution in Sr 2Ir 1–xRh xO 4

DOE PAGES

Ye, Feng; Wang, Xiaoping; Hoffmann, Christina; ...

2015-11-23

We use single-crystal neutron diffraction to determine the crystal structure symmetry and to study the magnetic evolution in the rhodium doped iridates Sr 2Ir 1–xRh xO 4 (0 ≤ x ≤ 0.16). Throughout this doping range, the crystal structure retains a tetragonal symmetry (space group I4 1/a) with two distinct magnetic Ir sites in the unit cell forming staggered IrO 6 rotation. Upon Rh doping, the magnetic order is suppressed and the magnetic moment of Ir4+ is reduced from 0.21 μ B/Ir for x = 0 to 0.18 μ B/Ir for x = 0.12. As a result, the magnetic structuremore » at x = 0.12 is different from that of the parent compound while the moments remain in the basal plane.« less

Tailored hierarchical micelle architectures using living crystallization-driven self-assembly in two dimensions

NASA Astrophysics Data System (ADS)

Hudson, Zachary M.; Boott, Charlotte E.; Robinson, Matthew E.; Rupar, Paul A.; Winnik, Mitchell A.; Manners, Ian

2014-10-01

Recent advances in the self-assembly of block copolymers have enabled the precise fabrication of hierarchical nanostructures using low-cost solution-phase protocols. However, the preparation of well-defined and complex planar nanostructures in which the size is controlled in two dimensions (2D) has remained a challenge. Using a series of platelet-forming block copolymers, we have demonstrated through quantitative experiments that the living crystallization-driven self-assembly (CDSA) approach can be extended to growth in 2D. We used 2D CDSA to prepare uniform lenticular platelet micelles of controlled size and to construct precisely concentric lenticular micelles composed of spatially distinct functional regions, as well as complex structures analogous to nanoscale single- and double-headed arrows and spears. These methods represent a route to hierarchical nanostructures that can be tailored in 2D, with potential applications as diverse as liquid crystals, diagnostic technology and composite reinforcement.

Temperature and acidity effects on WO{sub 3} nanostructures and gas-sensing properties of WO{sub 3} nanoplates

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

Zhang, Huili; Liu, Zhifang; Yang, Jiaqin

2014-09-15

Graphical abstract: Generally, large acid quantity and high temperature are beneficial to the formation of anhydrous WO3, but the acidity effect on the crystal phase is weaker than that of temperature. Large acid quantity is found helpful to the oriented growth of tungsten oxides, forming a nanoplate-like product. - Highlights: • Large acid quantity is propitious to the oriented growth of a WO{sub 3} nanoplate. • Effect of acid quantity on crystal phases of products is weaker than that of temperature. • One step hydrothermal synthesis of WO{sub 3} is facile and can be easily scaled up. • A WO{submore » 3} nanoplate shows a fast response and distinct sensing selectivity to acetone gas. - Abstract: WO{sub 3} nanostructures were successfully synthesized by a facile hydrothermal method using Na{sub 2}WO{sub 4}·2H{sub 2}O and HNO{sub 3} as raw materials. They are characterized by X-ray diffraction (XRD), scanning electron microscope (SEM) and transmission electron microscope (TEM). The specific surface area was obtained from N{sub 2} adsorption–desorption isotherm. The effects of the amount of HNO{sub 3}, hydrothermal temperature and reaction time on the crystal phases and morphologies of the WO{sub 3} nanostructures were investigated in detail, and the reaction mechanism was discussed. Large amount of acid is found for the first time to be helpful to the oriented growth of tungsten oxides, forming nanoplate-like products, while hydrothermal temperature has more influence on the crystal phase of the product. Gas-sensing properties of the series of as-prepared WO{sub 3} nanoplates were tested by means of acetone, ethanol, formaldehyde and ammonia. One of the WO{sub 3} nanoplates with high specific surface area and high crystallinity displays high sensitivity, fast response and distinct sensing selectivity to acetone gas.« less

The "Sticky Patch" Model of Crystallization and Modification of Proteins for Enhanced Crystallizability.

PubMed

Derewenda, Zygmunt S; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e., crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure, and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular "sticky patch" model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer "sticky patches" which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the "sticky patch" model. We discuss state-of-the-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis.

The solvent component of macromolecular crystals

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

Weichenberger, Christian X.; Afonine, Pavel V.; Kantardjieff, Katherine

2015-04-30

On average, the mother liquor or solvent and its constituents occupy about 50% of a macromolecular crystal. Ordered as well as disordered solvent components need to be accurately accounted for in modelling and refinement, often with considerable complexity. The mother liquor from which a biomolecular crystal is grown will contain water, buffer molecules, native ligands and cofactors, crystallization precipitants and additives, various metal ions, and often small-molecule ligands or inhibitors. On average, about half the volume of a biomolecular crystal consists of this mother liquor, whose components form the disordered bulk solvent. Its scattering contributions can be exploited in initialmore » phasing and must be included in crystal structure refinement as a bulk-solvent model. Concomitantly, distinct electron density originating from ordered solvent components must be correctly identified and represented as part of the atomic crystal structure model. Herein, are reviewed (i) probabilistic bulk-solvent content estimates, (ii) the use of bulk-solvent density modification in phase improvement, (iii) bulk-solvent models and refinement of bulk-solvent contributions and (iv) modelling and validation of ordered solvent constituents. A brief summary is provided of current tools for bulk-solvent analysis and refinement, as well as of modelling, refinement and analysis of ordered solvent components, including small-molecule ligands.« less

Rational Design of Charge-Transfer Interactions in Halogen-Bonded Co-crystals toward Versatile Solid-State Optoelectronics.

PubMed

Zhu, Weigang; Zheng, Renhui; Zhen, Yonggang; Yu, Zhenyi; Dong, Huanli; Fu, Hongbing; Shi, Qiang; Hu, Wenping

2015-09-02

Charge-transfer (CT) interactions between donor (D) and acceptor (A) groups, as well as CT exciton dynamics, play important roles in optoelectronic devices, such as organic solar cells, photodetectors, and light-emitting sources, which are not yet well understood. In this contribution, the self-assembly behavior, molecular stacking structure, CT interactions, density functional theory (DFT) calculations, and corresponding physicochemical properties of two similar halogen-bonded co-crystals are comprehensively investigated and compared, to construct an "assembly-structure-CT-property" relationship. Bpe-IFB wire-like crystals (where Bpe = 1,2-bis(4-pyridyl)ethylene and IFB = 1,3,5-trifluoro-2,4,6-triiodobenzene), packed in a segregated stacking form with CT ground and excited states, are measured to be quasi-one-dimensional (1D) semiconductors and show strong violet-blue photoluminescence (PL) from the lowest CT1 excitons (ΦPL = 26.1%), which can be confined and propagate oppositely along the 1D axial direction. In comparison, Bpe-F4DIB block-like crystals (F4DIB = 1,4-diiodotetrafluorobenzene), packed in a mixed stacking form without CT interactions, are determined to be insulators and exhibit unique white light emission and two-dimensional optical waveguide property. Surprisingly, it seems that the intrinsic spectroscopic states of Bpe and F4DIB do not change after co-crystallization, which is also confirmed by theoretical calculations, thus offering a new design principle for white light emitting materials. More importantly, we show that the CT interactions in co-crystals are related to their molecular packing and can be triggered or suppressed by crystal engineering, which eventually leads to distinct optoelectronic properties. These results help us to rationally control the CT interactions in organic D-A systems by tuning the molecular stacking, toward the development of a fantastic "optoelectronic world".

Magmatic interactions as recorded in plagioclase phenocrysts of Chaos Crags, Lassen Volcanic Center, California

USGS Publications Warehouse

Tepley, F. J.; Davidson, J.P.; Clynne, M.A.

1999-01-01

The silicic lava domes of Chaos Crags in Lassen Volcanic National Park contain a suite of variably quenched, hybrid basaltic andesite magmatic inclusions. The inclusions represent thorough mixing between rhyodacite and basalt recharge liquids accompanied by some mechanical disaggregation of the inclusions resulting in crystals mixing into the rhyodacite host preserved by quenching on dome emplacement. 87Sr/86Sr ratios (~0.7037-0.7038) of the inclusions are distinctly lower than those of the host rhyodacite (~0.704-0.7041), which are used to fingerprint the origin of mineral components and to monitor the mixing and mingling process. Chemical, isotopic, and textural characteristics indicate that the inclusions are hybrid magmas formed from the mixing and undercooling of recharge basaltic magma with rhyodacitic magma. All the host magma phenocrysts (biotite, plagioclase, hornblende and quartz crystals) also occur in the inclusions, where they are rimmed by reaction products. Compositional and strontium isotopic data from cores of unresorbed plagioclase crystals in the host rhyodacite, partially resorbed plagioclase crystals enclosed within basaltic andesite inclusions, and partially resorbed plagioclase crystals in the rhyodacitic host are all similar. Rim 87Sr/86Sr ratios of the partially resorbed plagioclase crystals in both inclusions and host are lower and close to those of the whole-rock hybrid basaltic andesite values. This observation indicates that some crystals originally crystallized in the silicic host, were partially resorbed and subsequently overgrown in the hybrid basaltic andesite magma, and then some of these partially resorbed plagioclase crystals were recycled back into the host rhyodacite. Textural evidence, in the form of sieve zones and major dissolution boundaries of the resorbed plagioclase crystals, indicates immersion of crystals into a hotter, more calcic magma. The occurrence of partially resorbed plagioclase together with plagioclase microlites and olivine crystals reflects disaggregation of inclusions and mingling of this material into the silicic host. These processes are commonplace in some orogenic magma systems and may be elucidated by isotopic microsampling and analysis of the plagioclases crystallizing from them.

Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives

PubMed Central

2014-01-01

Background Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. Results The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by 1HNMR, 13CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Conclusions Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation R 2 2 8 , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation R238, R228 and R238. PMID:24887234

Investigation of supramolecular synthons and structural characterisation of aminopyridine-carboxylic acid derivatives.

PubMed

Hemamalini, Madhukar; Loh, Wan-Sin; Quah, Ching Kheng; Fun, Hoong-Kun

2014-01-01

Co-crystal is a structurally homogeneous crystalline material that contains two or more neutral building blocks that are present in definite stoichiometric amounts. The main advantage of co-crystals is their ability to generate a variety of solid forms of a drug that have distinct physicochemical properties from the solid co-crystal components. In the present investigation, five co-crystals containing 2-amino-6-chloropyridine (AMPY) moiety were synthesized and characterized. The crystal structure of 2-amino-6-chloropyridine (AMPY) (I), and the robustness of pyridine-acid supramolecular synthon were discussed in four stoichiometry co-crystals of AMPY…BA (II), AMPY…2ABA (III), AMPY…3CLBA (IV) and AMPY…4NBA (V). The abbreviated designations used are benzoic acid (BA), 2-aminobenzoic acid (2ABA), 3-chlorobenzoic acid (3CLBA) and 4-nitrobenzoic acid (4NBA). All the crystalline materials have been characterized by (1)HNMR, (13)CNMR, IR, photoluminescence, TEM analysis and X-ray diffraction. The supramolecular assembly of each co-crystal is analyzed and discussed. Extensive N---H · · · N/N---H · · · O/O---H · · · N hydrogen bonds are found in (I-V), featuring different supramolecular synthons. In the crystal structure, for compound (I), the 2-amino-6-chloropyridine molecules are linked together into centrosymmetric dimers by hydrogen bonds to form homosynthon, whereas for compounds (II-V), the carboxylic group of the respective acids (benzoic acid, 2-aminobenzoic acid, 3-chlorobenzoic acid and 4-nitrobenzoic acid) interacts with pyridine molecule in a linear fashion through a pair of N---H · · · O and O---H · · · N hydrogen bonds, generating cyclic hydrogen-bonded motifs with the graph-set notation [Formula: see text] , to form heterosynthon. In compound (II), another intermolecular N---H · · · O hydrogen bonds further link these heterosynthons into zig-zag chains. Whereas in compounds (IV) and (V), these heterosynthons are centrosymmetrically paired via N---H · · · O hydrogen bonds and each forms a complementary DADA [D = donor and A = acceptor] array of quadruple hydrogen bonds, with graph-set notation [Formula: see text], [Formula: see text] and [Formula: see text].

Conformational flexibility in the flap domains of ligand-free HIV protease.

PubMed

Heaslet, Holly; Rosenfeld, Robin; Giffin, Mike; Lin, Ying Chuan; Tam, Karen; Torbett, Bruce E; Elder, John H; McRee, Duncan E; Stout, C David

2007-08-01

The crystal structures of wild-type HIV protease (HIV PR) in the absence of substrate or inhibitor in two related crystal forms at 1.4 and 2.15 A resolution are reported. In one crystal form HIV PR adopts an 'open' conformation with a 7.7 A separation between the tips of the flaps in the homodimer. In the other crystal form the tips of the flaps are 'curled' towards the 80s loop, forming contacts across the local twofold axis. The 2.3 A resolution crystal structure of a sixfold mutant of HIV PR in the absence of substrate or inhibitor is also reported. The mutant HIV PR, which evolved in response to treatment with the potent inhibitor TL-3, contains six point mutations relative to the wild-type enzyme (L24I, M46I, F53L, L63P, V77I, V82A). In this structure the flaps also adopt a 'curled' conformation, but are separated and not in contact. Comparison of the apo structures to those with TL-3 bound demonstrates the extent of conformational change induced by inhibitor binding, which includes reorganization of the packing between twofold-related flaps. Further comparison with six other apo HIV PR structures reveals that the 'open' and 'curled' conformations define two distinct families in HIV PR. These conformational states include hinge motion of residues at either end of the flaps, opening and closing the entire beta-loop, and translational motion of the flap normal to the dimer twofold axis and relative to the 80s loop. The alternate conformations also entail changes in the beta-turn at the tip of the flap. These observations provide insight into the plasticity of the flap domains, the nature of their motions and their critical role in binding substrates and inhibitors.

Trace element chemistry of zircons from oceanic crust: A method for distinguishing detrital zircon provenance

USGS Publications Warehouse

Grimes, Craig B.; John, Barbara E.; Kelemen, P.B.; Mazdab, F.K.; Wooden, J.L.; Cheadle, Michael J.; Hanghoj, K.; Schwartz, J.J.

2007-01-01

We present newly acquired trace element compositions for more than 300 zircon grains in 36 gabbros formed at the slow-spreading Mid-Atlantic and Southwest Indian Ridges. Rare earth element patterns for zircon from modern oceanic crust completely overlap with those for zircon crystallized in continental granitoids. However, plots of U versus Yb and U/Yb versus Hf or Y discriminate zircons crystallized in oceanic crust from continental zircon, and provide a relatively robust method for distinguishing zircons from these environments. Approximately 80% of the modern ocean crust zircons are distinct from the field defined by more than 1700 continental zircons from Archean and Phanerozoic samples. These discrimination diagrams provide a new tool for fingerprinting ocean crust zircons derived from reservoirs like that of modern mid-ocean ridge basalt (MORB) in both modern and ancient detrital zircon populations. Hadean detrital zircons previously reported from the Acasta Gneiss, Canada, and the Narryer Gneiss terrane, Western Australia, plot in the continental granitoid field, supporting hypotheses that at least some Hadean detrital zircons crystallized in continental crust forming magmas and not from a reservoir like modern MORB. ?? 2007 The Geological Society of America.

Crystal structure of tetra­wickmanite, Mn2+Sn4+(OH)6

PubMed Central

Lafuente, Barbara; Yang, Hexiong; Downs, Robert T.

2015-01-01

The crystal structure of tetra­wickmanite, ideally Mn2+Sn4+(OH)6 [mangan­ese(II) tin(IV) hexa­hydroxide], has been determined based on single-crystal X-ray diffraction data collected from a natural sample from Långban, Sweden. Tetra­wickmanite belongs to the octa­hedral-framework group of hydroxide-perovskite minerals, described by the general formula BB’(OH)6 with a perovskite derivative structure. The structure differs from that of an ABO3 perovskite in that the A site is empty while each O atom is bonded to an H atom. The perovskite B-type cations split into ordered B and B′ sites, which are occupied by Mn2+ and Sn4+, respectively. Tetra­wickmanite exhibits tetra­gonal symmetry and is topologically similar to its cubic polymorph, wickmanite. The tetra­wickmanite structure is characterized by a framework of alternating corner-linked [Mn2+(OH)6] and [Sn4+(OH)6] octa­hedra, both with point-group symmetry -1. Four of the five distinct H atoms in the structure are statistically disordered. The vacant A site is in a cavity in the centre of a distorted cube formed by eight octa­hedra at the corners. However, the hydrogen-atom positions and their hydrogen bonds are not equivalent in every cavity, resulting in two distinct environments. One of the cavities contains a ring of four hydrogen bonds, similar to that found in wickmanite, while the other cavity is more distorted and forms crankshaft-type chains of hydrogen bonds, as previously proposed for tetra­gonal stottite, Fe2+Ge4+(OH)6. PMID:25878828

Crystal structure of low-molecular-weight protein tyrosine phosphatase from Mycobacterium tuberculosis at 1.9-A resolution.

PubMed

Madhurantakam, Chaithanya; Rajakumara, Eerappa; Mazumdar, Pooja Anjali; Saha, Baisakhee; Mitra, Devrani; Wiker, Harald G; Sankaranarayanan, Rajan; Das, Amit Kumar

2005-03-01

The low-molecular-weight protein tyrosine phosphatase (LMWPTPase) belongs to a distinctive class of phosphotyrosine phosphatases widely distributed among prokaryotes and eukaryotes. We report here the crystal structure of LMWPTPase of microbial origin, the first of its kind from Mycobacterium tuberculosis. The structure was determined to be two crystal forms at 1.9- and 2.5-A resolutions. These structural forms are compared with those of the LMWPTPases of eukaryotes. Though the overall structure resembles that of the eukaryotic LMWPTPases, there are significant changes around the active site and the protein tyrosine phosphatase (PTP) loop. The variable loop forming the wall of the crevice leading to the active site is conformationally unchanged from that of mammalian LMWPTPase; however, differences are observed in the residues involved, suggesting that they have a role in influencing different substrate specificities. The single amino acid substitution (Leu12Thr [underlined below]) in the consensus sequence of the PTP loop, CTGNICRS, has a major role in the stabilization of the PTP loop, unlike what occurs in mammalian LMWPTPases. A chloride ion and a glycerol molecule were modeled in the active site where the chloride ion interacts in a manner similar to that of phosphate with the main chain nitrogens of the PTP loop. This structural study, in addition to identifying specific mycobacterial features, may also form the basis for exploring the mechanism of the substrate specificities of bacterial LMWPTPases.

In situ observations of a high-pressure phase of H2O ice

USGS Publications Warehouse

Chou, I.-Ming; Blank, J.G.; Goncharov, A.F.; Mao, Ho-kwang; Hemley, R.J.

1998-01-01

A previously unknown solid phase of H2O has been identified by its peculiar growth patterns, distinct pressure-temperature melting relations, and vibrational Raman spectra. Morphologies of ice crystals and their pressure-temperature melting relations were directly observed in a hydrothermal diamond-anvil cell for H2O bulk densities between 1203 and 1257 kilograms per cubic meter at temperatures between -10??and 50??C. Under these conditions, four different ice forms were observed to melt: two stable phases, ice V and ice VI, and two metastable phases, ice IV and the new ice phase. The Raman spectra and crystal morphology are consistent with a disordered anisotropic structure with some similarities to ice VI.

Persistent hydrogen bonding in polymorphic crystal structures.

PubMed

Galek, Peter T A; Fábián, László; Allen, Frank H

2009-02-01

The significance of hydrogen bonding and its variability in polymorphic crystal structures is explored using new automated structural analysis methods. The concept of a chemically equivalent hydrogen bond is defined, which may be identified in pairs of structures, revealing those types of bonds that may persist, or not, in moving from one polymorphic form to another. Their frequency and nature are investigated in 882 polymorphic structures from the Cambridge Structural Database. A new method to compare conformations of equivalent molecules is introduced and applied to derive distinct subsets of conformational and packing polymorphs. The roles of chemical functionality and hydrogen-bond geometry in persistent interactions are systematically explored. Detailed structural comparisons reveal a large majority of persistent hydrogen bonds that are energetically crucial to structural stability.

Crystal Structure of the Ubiquitin-associated (UBA) Domain of p62 and Its Interaction with Ubiquitin*

PubMed Central

Isogai, Shin; Morimoto, Daichi; Arita, Kyohei; Unzai, Satoru; Tenno, Takeshi; Hasegawa, Jun; Sou, Yu-shin; Komatsu, Masaaki; Tanaka, Keiji; Shirakawa, Masahiro; Tochio, Hidehito

2011-01-01

p62/SQSTM1/A170 is a multimodular protein that is found in ubiquitin-positive inclusions associated with neurodegenerative diseases. Recent findings indicate that p62 mediates the interaction between ubiquitinated proteins and autophagosomes, leading these proteins to be degraded via the autophagy-lysosomal pathway. This ubiquitin-mediated selective autophagy is thought to begin with recognition of the ubiquitinated proteins by the C-terminal ubiquitin-associated (UBA) domain of p62. We present here the crystal structure of the UBA domain of mouse p62 and the solution structure of its ubiquitin-bound form. The p62 UBA domain adopts a novel dimeric structure in crystals, which is distinctive from those of other UBA domains. NMR analyses reveal that in solution the domain exists in equilibrium between the dimer and monomer forms, and binding ubiquitin shifts the equilibrium toward the monomer to form a 1:1 complex between the UBA domain and ubiquitin. The dimer-to-monomer transition is associated with a structural change of the very C-terminal end of the p62 UBA domain, although the UBA fold itself is essentially maintained. Our data illustrate that dimerization and ubiquitin binding of the p62 UBA domain are incompatible with each other. These observations reveal an autoinhibitory mechanism in the p62 UBA domain and suggest that autoinhibition plays a role in the function of p62. PMID:21715324

Amorphous calcium carbonate particles form coral skeletons

NASA Astrophysics Data System (ADS)

Mass, Tali; Giuffre, Anthony J.; Sun, Chang-Yu; Stifler, Cayla A.; Frazier, Matthew J.; Neder, Maayan; Tamura, Nobumichi; Stan, Camelia V.; Marcus, Matthew A.; Gilbert, Pupa U. P. A.

2017-09-01

Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed “vital effects,” that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO3). We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO2 increases, such as the Paleocene-Eocene Thermal Maximum that occurred 56 Mya.

Amorphous calcium carbonate particles form coral skeletons.

PubMed

Mass, Tali; Giuffre, Anthony J; Sun, Chang-Yu; Stifler, Cayla A; Frazier, Matthew J; Neder, Maayan; Tamura, Nobumichi; Stan, Camelia V; Marcus, Matthew A; Gilbert, Pupa U P A

2017-09-12

Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed "vital effects," that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO 3 ). We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO 2 increases, such as the Paleocene-Eocene Thermal Maximum that occurred 56 Mya.

Amorphous calcium carbonate particles form coral skeletons

PubMed Central

Mass, Tali; Giuffre, Anthony J.; Sun, Chang-Yu; Stifler, Cayla A.; Frazier, Matthew J.; Neder, Maayan; Tamura, Nobumichi; Stan, Camelia V.; Marcus, Matthew A.

2017-01-01

Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed “vital effects,” that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO3). We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO2 increases, such as the Paleocene–Eocene Thermal Maximum that occurred 56 Mya. PMID:28847944

Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals

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

Welberry, T.R.; Chan, E.J.; Goossens, D.J.

Polymorphism occurs when the same molecular compound can crystallize in more than one distinct crystal structure. Its study is a field of great interest and activity. This is largely driven by its importance in the pharmaceutical industry, but polymorphism is also an issue in the pigments, dyes, and explosives industries. The polymorph formed by a compound generally exerts a strong influence on its solid-state properties. The polymorphic form of a drug molecule may affect the ease of manufacture and processing, shelf life, and most significantly the rate of uptake of the molecule by the human body. They can even varymore » in toxicity; one polymorph may be safe, while a second may be toxic. In this review of recently published work, we show how diffuse scattering experiments coupled with Monte Carlo (MC) computer modeling can aid in the understanding of polymorphism. Examples of the two common pharmaceuticals, benzocaine and aspirin, both of which are bimorphic, at ambient temperatures, are discussed.« less

Diffuse Scattering as an Aid to the Understanding of Polymorphism in Pharmaceuticals

NASA Astrophysics Data System (ADS)

Welberry, T. R.; Chan, E. J.; Goossens, D. J.; Heerdegen, A. P.

2012-05-01

Polymorphism occurs when the same molecular compound can crystallize in more than one distinct crystal structure. Its study is a field of great interest and activity. This is largely driven by its importance in the pharmaceutical industry, but polymorphism is also an issue in the pigments, dyes, and explosives industries. The polymorph formed by a compound generally exerts a strong influence on its solid-state properties. The polymorphic form of a drug molecule may affect the ease of manufacture and processing, shelf life, and most significantly the rate of uptake of the molecule by the human body. They can even vary in toxicity; one polymorph may be safe, while a second may be toxic. In this review of recently published work, we show how diffuse scattering experiments coupled with Monte Carlo (MC) computer modeling can aid in the understanding of polymorphism. Examples of the two common pharmaceuticals, benzocaine and aspirin, both of which are bimorphic, at ambient temperatures, are discussed.

The ‘Sticky Patch’ Model of Crystallization and Modification of Proteins for Enhanced Crystallizability

PubMed Central

Derewenda, Zygmunt S.; Godzik, Adam

2017-01-01

Crystallization of macromolecules has long been perceived as a stochastic process, which cannot be predicted or controlled. This is consistent with another popular notion that the interactions of molecules within the crystal, i.e. crystal contacts, are essentially random and devoid of specific physicochemical features. In contrast, functionally relevant surfaces, such as oligomerization interfaces and specific protein-protein interaction sites, are under evolutionary pressures so their amino acid composition, structure and topology are distinct. However, current theoretical and experimental studies are significantly changing our understanding of the nature of crystallization. The increasingly popular ‘sticky patch’ model, derived from soft matter physics, describes crystallization as a process driven by interactions between select, specific surface patches, with properties thermodynamically favorable for cohesive interactions. Independent support for this model comes from various sources including structural studies and bioinformatics. Proteins that are recalcitrant to crystallization can be modified for enhanced crystallizability through chemical or mutational modification of their surface to effectively engineer ‘sticky patches’ which would drive crystallization. Here, we discuss the current state of knowledge of the relationship between the microscopic properties of the target macromolecule and its crystallizability, focusing on the ‘sticky patch’ model. We discuss state-of-art in silico methods that evaluate the propensity of a given target protein to form crystals based on these relationships, with the objective to design of variants with modified molecular surface properties and enhanced crystallization propensity. We illustrate this discussion with specific cases where these approaches allowed to generate crystals suitable for structural analysis. PMID:28573570

A crystal structure of the bifunctional antibiotic simocyclinone D8, bound to DNA gyrase.

PubMed

Edwards, Marcus J; Flatman, Ruth H; Mitchenall, Lesley A; Stevenson, Clare E M; Le, Tung B K; Clarke, Thomas A; McKay, Adam R; Fiedler, Hans-Peter; Buttner, Mark J; Lawson, David M; Maxwell, Anthony

2009-12-04

Simocyclinones are bifunctional antibiotics that inhibit bacterial DNA gyrase by preventing DNA binding to the enzyme. We report the crystal structure of the complex formed between the N-terminal domain of the Escherichia coli gyrase A subunit and simocyclinone D8, revealing two binding pockets that separately accommodate the aminocoumarin and polyketide moieties of the antibiotic. These are close to, but distinct from, the quinolone-binding site, consistent with our observations that several mutations in this region confer resistance to both agents. Biochemical studies show that the individual moieties of simocyclinone D8 are comparatively weak inhibitors of gyrase relative to the parent compound, but their combination generates a more potent inhibitor. Our results should facilitate the design of drug molecules that target these unexploited binding pockets.

Crystal structure of iron(III) perchlorate nona­hydrate

PubMed Central

Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

2014-01-01

Since the discovery of perchlorate salts on Mars and the known occurrence of ferric salts in the regolith, there is a distinct possibility that the title compound could form on the surface of Mars. [Fe(H2O)6](ClO4)3·3H2O was crystallized from aqueous solutions at low temperatures according to the solid–liquid phase diagram. It consists of Fe(H2O)6 octa­hedra (point group symmetry -3.) and perchlorate anions (point group symmetry .2) as well as non-coordinating water mol­ecules, as part of a second hydrogen-bonded coordination sphere around the cation. The perchlorate appears to be slightly disordered, with major–minor component occupancies of 0.773 (9):0.227 (9). PMID:25552970

Controllable Modular Growth of Hierarchical MOF-on-MOF Architectures.

PubMed

Gu, Yifan; Wu, Yi-Nan; Li, Liangchun; Chen, Wei; Li, Fengting; Kitagawa, Susumu

2017-12-04

Fabrication of hybrid MOF-on-MOF heteroarchitectures can create novel and multifunctional platforms to achieve desired properties. However, only MOFs with similar crystallographic parameters can be hybridized by the classical epitaxial growth method (EGM), which largely suppressed its applications. A general strategy, called internal extended growth method (IEGM), is demonstrated for the feasible assembly of MOFs with distinct crystallographic parameters in an MOF matrix. Various MOFs with diverse functions could be introduced in a modular MOF matrix to form 3D core-satellite pluralistic hybrid system. The number of different MOF crystals interspersed could be varied on demand. More importantly, the different MOF crystals distributed in individual domains could be used to further incorporate functional units or enhance target functions. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental evidence of low-density liquid water upon rapid decompression

PubMed Central

Lin, Chuanlong; Smith, Jesse S.; Sinogeikin, Stanislav V.; Shen, Guoyin

2018-01-01

Water is an extraordinary liquid, having a number of anomalous properties which become strongly enhanced in the supercooled region. Due to rapid crystallization of supercooled water, there exists a region that has been experimentally inaccessible for studying deeply supercooled bulk water. Using a rapid decompression technique integrated with in situ X-ray diffraction, we show that a high-pressure ice phase transforms to a low-density noncrystalline (LDN) form upon rapid release of pressure at temperatures of 140–165 K. The LDN subsequently crystallizes into ice-Ic through a diffusion-controlled process. Together with the change in crystallization rate with temperature, the experimental evidence indicates that the LDN is a low-density liquid (LDL). The measured X-ray diffraction data show that the LDL is tetrahedrally coordinated with the tetrahedral network fully developed and clearly linked to low-density amorphous ices. On the other hand, there is a distinct difference in structure between the LDL and supercooled water or liquid water in terms of the tetrahedral order parameter. PMID:29440411

Pressure evolution of electrical transport in the 3D topological insulator (Bi,Sb) 2 (Se,Te) 3

DOE PAGES

Jeffries, J. R.; Butch, N. P.; Vohra, Y. K.; ...

2015-03-18

The group V-VI compounds|like Bi 2Se 3, Sb 2Te 3, or Bi 2Te 3|have been widely studied in recent years for their bulk topological properties. The high-Z members of this series form with the same crystal structure, and are therefore amenable to isostructural substitution studies. It is possible to tune the Bi-Sb and Te-Se ratios such that the material exhibits insulating behavior, thus providing an excellent platform for understanding how a topological insulator evolves with applied pressure. We report our observations of the pressure-dependent electrical transport and crystal structure of a pseudobinary (Bi,Sb) 2(Te,Se) 3 compound. Similar to some ofmore » its sister compounds, the (Bi,Sb) 2(Te,Se) 3 pseudobinary compound undergoes multiple, pressure-induced phase transformations that result in metallization, the onset of a close-packed crystal structure, and the development of distinct superconducting phases.« less

The crystal structure of the C45S mutant of annelid Arenicola marina peroxiredoxin 6 supports its assignment to the mechanistically typical 2-Cys subfamily without any formation of toroid-shaped decamers

PubMed Central

Smeets, Aude; Loumaye, Eléonore; Clippe, André; Rees, Jean-François; Knoops, Bernard; Declercq, Jean-Paul

2008-01-01

The peroxiredoxins (PRDXs) define a superfamily of thiol-dependent peroxidases able to reduce hydrogen peroxide, alkyl hydroperoxides, and peroxynitrite. Besides their cytoprotective antioxidant function, PRDXs have been implicated in redox signaling and chaperone activity, the latter depending on the formation of decameric high-molecular-weight structures. PRDXs have been mechanistically divided into three major subfamilies, namely typical 2-Cys, atypical 2-Cys, and 1-Cys PRDXs, based on the number and position of cysteines involved in the catalysis. We report the structure of the C45S mutant of annelid worm Arenicola marina PRDX6 in three different crystal forms determined at 1.6, 2.0, and 2.4 Å resolution. Although A. marina PRDX6 was cloned during the search of annelid homologs of mammalian 1-Cys PRDX6s, the crystal structures support its assignment to the mechanistically typical 2-Cys PRDX subfamily. The protein is composed of two distinct domains: a C-terminal domain and an N-terminal domain exhibiting a thioredoxin fold. The subunits are associated in dimers compatible with the formation of intersubunit disulfide bonds between the peroxidatic and the resolving cysteine residues in the wild-type enzyme. The packing of two crystal forms is very similar, with pairs of dimers associated as tetramers. The toroid-shaped decamers formed by dimer association and observed in most typical 2-Cys PRDXs is not present. Thus, A. marina PRDX6 presents structural features of typical 2-Cys PRDXs without any formation of toroid-shaped decamers, suggesting that it should function more like a cytoprotective antioxidant enzyme or a modulator of peroxide-dependent cell signaling rather than a molecular chaperone. PMID:18359859

Conformational Changes and Substrate Recognition in Pseudomonas aeruginosa d-Arginine Dehydrogenase

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

Fu, Guoxing; Yuan, Hongling; Li, Congran

2010-11-15

DADH catalyzes the flavin-dependent oxidative deamination of D-amino acids to the corresponding {alpha}-keto acids and ammonia. Here we report the first X-ray crystal structures of DADH at 1.06 {angstrom} resolution and its complexes with iminoarginine (DADH{sub red}/iminoarginine) and iminohistidine (DADH{sub red}/iminohistidine) at 1.30 {angstrom} resolution. The DADH crystal structure comprises an unliganded conformation and a product-bound conformation, which is almost identical to the DADH{sub red}/iminoarginine crystal structure. The active site of DADH was partially occupied with iminoarginine product (30% occupancy) that interacts with Tyr53 in the minor conformation of a surface loop. This flexible loop forms an 'active site lid',more » similar to those seen in other enzymes, and may play an essential role in substrate recognition. The guanidinium side chain of iminoarginine forms a hydrogen bond interaction with the hydroxyl of Thr50 and an ionic interaction with Glu87. In the structure of DADH in complex with iminohistidine, two alternate conformations were observed for iminohistidine where the imidazole groups formed hydrogen bond interactions with the side chains of His48 and Thr50 and either Glu87 or Gln336. The different interactions and very distinct binding modes observed for iminoarginine and iminohistidine are consistent with the 1000-fold difference in k{sub cat}/K{sub m} values for D-arginine and D-histidine. Comparison of the kinetic data for the activity of DADH on different D-amino acids and the crystal structures in complex with iminoarginine and iminohistidine establishes that this enzyme is characterized by relatively broad substrate specificity, being able to oxidize positively charged and large hydrophobic D-amino acids bound within a flask-like cavity.« less

Specificity Rendering ‘Hot-Spots’ for Aurora Kinase Inhibitor Design: The Role of Non-Covalent Interactions and Conformational Transitions

PubMed Central

Badrinarayan, Preethi; Sastry, G. Narahari

2014-01-01

The present study examines the conformational transitions occurring among the major structural motifs of Aurora kinase (AK) concomitant with the DFG-flip and deciphers the role of non-covalent interactions in rendering specificity. Multiple sequence alignment, docking and structural analysis of a repertoire of 56 crystal structures of AK from Protein Data Bank (PDB) has been carried out. The crystal structures were systematically categorized based on the conformational disposition of the DFG-loop [in (DI) 42, out (DO) 5 and out-up (DOU) 9], G-loop [extended (GE) 53 and folded (GF) 3] and αC-helix [in (CI) 42 and out (CO) 14]. The overlapping subsets on categorization show the inter-dependency among structural motifs. Therefore, the four distinct possibilities a) 2W1C (DI, CI, GE) b) 3E5A (DI, CI, GF) c) 3DJ6 (DI, CO, GF) d) 3UNZ (DOU, CO, GF) along with their co-crystals and apo-forms were subjected to molecular dynamics simulations of 40 ns each to evaluate the variations of individual residues and their impact on forming interactions. The non-covalent interactions formed by the 157 AK co-crystals with different regions of the binding site were initially studied with the docked complexes and structure interaction fingerprints. The frequency of the most prominent interactions was gauged in the AK inhibitors from PDB and the four representative conformations during 40 ns. Based on this study, seven major non-covalent interactions and their complementary sites in AK capable of rendering specificity have been prioritized for the design of different classes of inhibitors. PMID:25485544

The crystal structure of xanthine oxidoreductase during catalysis: Implications for reaction mechanism and enzyme inhibition

PubMed Central

Okamoto, Ken; Matsumoto, Koji; Hille, Russ; Eger, Bryan T.; Pai, Emil F.; Nishino, Takeshi

2004-01-01

Molybdenum is widely distributed in biology and is usually found as a mononuclear metal center in the active sites of many enzymes catalyzing oxygen atom transfer. The molybdenum hydroxylases are distinct from other biological systems catalyzing hydroxylation reactions in that the oxygen atom incorporated into the product is derived from water rather than molecular oxygen. Here, we present the crystal structure of the key intermediate in the hydroxylation reaction of xanthine oxidoreductase with a slow substrate, in which the carbon–oxygen bond of the product is formed, yet the product remains complexed to the molybdenum. This intermediate displays a stable broad charge–transfer band at ≈640 nm. The crystal structure of the complex indicates that the catalytically labile Mo—OH oxygen has formed a bond with a carbon atom of the substrate. In addition, the Mo⋕S group of the oxidized enzyme has become protonated to afford Mo—SH on reduction of the molybdenum center. In contrast to previous assignments, we find this last ligand at an equatorial position in the square-pyramidal metal coordination sphere, not the apical position. A water molecule usually seen in the active site of the enzyme is absent in the present structure, which probably accounts for the stability of this intermediate toward ligand displacement by hydroxide. PMID:15148401

Mineral Biomarkers in Martian Meteorite Allan Hills 84001?

NASA Technical Reports Server (NTRS)

Thomas-Keprta, K. L.; Bazylinski, D. A.; Wentworth, S. J.; McKay, D. S.; Golden, D. C.; Gibson, E. K., Jr.; Romanek, C. S.

1998-01-01

The occurrence of fine-grained magnetite in the Fe-rich rims surrounding carbonate globules in the martian meteorite ALH84001, originally described in , have been proposed as fossil remains of primitive martian organisms. Here we report observations on size and shape distributions of magnetites from ALH84001 and compare them to biogenic and inorganic magnetite crystals of terrestrial origin. While some magnetite morphology is not unequivocally diagnostic for its biogenicity, such as cubodial forms of magnetite, which are common in inorganically formed magnetites, other morphologies of magnetite (parallel-epiped or elongated prismatic and arrowhead forms) are more likely signatures of biogenic activity. Some ALH 84001 magnetite particles described below have unique morphology and length-to-width ratios that are indistinguishable from a variety of terrestrial biogenic magnetite and distinct from all known inorganic forms of magnetite.

What Can Crystal Size Distributions and Olivine Compositions Tell Us About Magma Solidification Processes in Kilauea Iki Lava Lake, Hawaii?

NASA Astrophysics Data System (ADS)

Vinet, N.; Higgins, M. D.

2009-12-01

Lava lakes offer the opportunity to investigate magma solidification and can be considered as a proxy for small magma chambers or layered intrusions. Here we present data from Kilauea Iki Lava Lake, which formed during the near-summit 1959 picritic eruption of Kilauea Volcano, Hawaii. Microprobe geochemical analyses and crystal size distributions (CSDs) of olivine were determined from three eruption scoria samples, and 34 drill core samples taken from 1967 to 1988. The data provide valuable information on the dynamics and timescales of the intra-lake solidification processes, along with origin of, and temporal constraints on, the distinct olivine populations. Based on their core and rim forsterite (Fo) content, three distinct olivine populations were distinguished: (1) a high-Fo population (Fo85-88); (2) an intermediate-Fo population (Fo77-81); and (3) a low-Fo population (Fo72-76). Groups 1 and 2 both have deformed and undeformed crystals indicating that they formed partly within Kilauea plumbing system before the eruption. The second group seems to be associated with the ‘vertical olivine-rich bodies’ (VORBs) of Helz (1980). These structures raise magma from the lower part of the lake; hence they may have a contrasting composition maintained from the initial filling of the lake. The third population may be the result of rejuvenation within the lake during its cooling. Although the shape of the olivine CSDs is fairly uniform, we note significant variations that allow the recognition and quantification of multiple solidification processes. Our data display evidence of minor accumulation occurring by settling modified by convection currents. The concave-up curvature of at least half of the CSDs is strong evidence for mixing of magmas or crystal populations. The turndown at smallest sizes of the CSD, particularly present for samples at the edge of the lake, is thought to be the result of coarsening. Our CSD and crystal chemistry data suggest that the early populations and their related magmas underwent several solidification processes at depth, such as minor growth, coarsening, aggregation and deformation, plus settling and mixing maybe, no matter the order of appearance. The CSD analysis also yields estimates of the crystal residence time for different olivine populations, which are not necessarily the same as those defined using the olivine composition. For a growth rate of 10-9 mm/s, the range of residence times is 2-30 years. The CSDs can be segmented into three main groups: (a) a minor 2-4 yr-old population of smaller, rejuvenated crystals; (b) a dominant 10-18 yr-old population of intermediate-sized crystals; and (c) a 20-30 yr-old population of larger, coarsened, and often deformed crystals. Although the focus is here on volcanic rocks, our work gives a new perspective on the solidification of basic magma that can gain valuable insights into the overall understanding of mafic layered intrusions. References: Helz (1980), Bull. Volc. 43 (4): 675-701

A photoluminescence, thermoluminescence and electron paramagnetic resonance study of EFG grown europium doped lithium fluoride (LiF) crystals

NASA Astrophysics Data System (ADS)

Seth, Pooja; Swati, G.; Haranath, D.; Rao, S. M. D.; Aggarwal, Shruti

2018-07-01

Europium (Eu) doped LiF crystals have been grown by the Edge-defined film fed growth (EFG) technique. The designing and installation of the furnace used for the growth of the crystals have been discussed in detail. In the present study, Eu (Eu2O3) has been doped in LiF in different concentration (0.02-0.2 wt %). X-ray diffractometry (XRD) and Energy Dispersive X-ray (EDX) spectroscopy confirms the incorporation of Eu in LiF. The influence of Eu on LiF has been investigated through photoluminescence (PL), thermoluminescence (TL) and electron paramagnetic resonance (EPR) in as-grown and annealed crystals. PL emission spectra shows the presence of both Eu3+ and Eu2+ form in the as-grown crystals which is confirmed by EPR results. Whereas, in annealed crystals, Eu is present predominantly as Eu2+ form. This suggests that growing crystals at high temperature (∼900 °C) in argon gas atmosphere through EFG technique favours the reduction of Eu3+ → Eu2+. This reduction phenomenon has been explained on the basis of charge compensation model. TL study of the LiF: Eu (0.02-0.2 wt %) crystals has been done after irradiation with Co60 gamma rays. In this study, it has been observed that the TL intensity as well as glow curve structure of LiF: Eu crystals are a strong function of Eu concentration. The maximum TL is observed at Eu concentration of 0.05 wt% at which a well defined glow curve structure with a prominent peak at 185 °C and a small peak at 253 °C. Beyond this concentration (0.05 wt %), TL intensity decreases due to aggregation of defects in the host. The peak at 185 °C in LiF: Eu (0.05 wt %) is certainly due to the presence of Eu2+ associated defects which is also supported by the PL spectra. It has been observed that Eu doping have a key role in creation of more defect levels which lead to the increased number of electron and hole traps. Further, trapping parameters are analysed using glow curve deconvolution method to have an insight study of TL phenomena. Further, TL glow curve structure of as-grown and annealed crystal are distinct which may be attributed to the nature of defect traps formed inside the LiF.

Trapping a 96° domain rotation in two distinct conformations by engineered disulfide bridges

PubMed Central

Schultz-Heienbrok, Robert; Maier, Timm; Sträter, Norbert

2004-01-01

Engineering disulfide bridges is a common technique to lock a protein movement in a defined conformational state. We have designed two double mutants of Escherichia coli 5′-nucleotidase to trap the enzyme in both an open (S228C, P513C) and a closed (P90C, L424C) conformation by the formation of disulfide bridges. The mutant proteins have been expressed, purified, and crystallized, to structurally characterize the designed variants. The S228C, P513C is a double mutant crystallized in two different crystal forms with three independent conformers, which differ from each other by a rotation of up to 12° of the C-terminal domain with respect to the N-terminal domain. This finding, as well as an analysis of the domain motion in the crystal, indicates that the enzyme still exhibits considerable residual domain flexibility. In the double mutant that was designed to trap the enzyme in the closed conformation, the structure analysis reveals an unexpected intermediate conformation along the 96° rotation trajectory between the open and closed enzyme forms. A comparison of the five independent conformers analyzed in this study shows that the domain movement of the variant enzymes is characterized by a sliding movement of the residues of the domain interface along the interface, which is in contrast to a classical closure motion where the residues of the domain interface move perpendicular to the interface. PMID:15215524

A High-Resolution Crystal Structure of a Psychrohalophilic α–Carbonic Anhydrase from Photobacterium profundum Reveals a Unique Dimer Interface

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

Somalinga, Vijayakumar; Buhrman, Greg; Arun, Ashikha

Bacterial α–carbonic anhydrases (α-CA) are zinc containing metalloenzymes that catalyze the rapid interconversion of CO2 to bicarbonate and a proton. We report the first crystal structure of a pyschrohalophilic α–CA from a deep-sea bacterium, Photobacterium profundum. Size exclusion chromatography of the purified P. profundum α–CA (PprCA) reveals that the protein is a heterogeneous mix of monomers and dimers. Furthermore, an “in-gel” carbonic anhydrase activity assay, also known as protonography, revealed two distinct bands corresponding to monomeric and dimeric forms of PprCA that are catalytically active. The crystal structure of PprCA was determined in its native form and reveals a highlymore » conserved “knot-topology” that is characteristic of α–CA’s. Similar to other bacterial α–CA’s, PprCA also crystallized as a dimer. Furthermore, dimer interface analysis revealed the presence of a chloride ion (Cl-) in the interface which is unique to PprCA and has not been observed in any other α–CA’s characterized so far. Molecular dynamics simulation and chloride ion occupancy analysis shows 100% occupancy for the Cl- ion in the dimer interface. Zinc coordinating triple histidine residues, substrate binding hydrophobic patch residues, and the hydrophilic proton wire residues are highly conserved in PprCA and are identical to other well-studied α–CA’s.« less

Effect of cyclophosphamide on the solid form of mannitol during lyophilization.

PubMed

Patel, Krupaliben; Munjal, Bhushan; Bansal, Arvind K

2017-04-01

Mannitol is a commonly used bulking agent in lyophilized formulations. It can crystallize into multiple solid forms during lyophilization thereby exhibiting phase heterogeneity and variability in product performance. In this manuscript, we studied the effect of cyclophosphamide (CPA), an anticancer drug, on the solid form of mannitol during lyophilization from aqueous solutions. Freeze-concentration studies were performed in the DSC while lyophilization was performed in a lab scale freeze dryer. DSC experiments revealed two-stage crystallization of mannitol (1.5% w/v) during freeze-concentration, evident as two distinct exothermic events (at -18.2°C and -30°C) in the cooling curve. This was complemented by two eutectic melting endotherms in the subsequent heating curve. Addition of CPA (4.0% w/v) completely inhibited the exotherm at -18.2°C, but enhanced the enthalpy of exotherm at -30°C by five folds. Likewise, only one eutectic melting endotherm was observed in the subsequent heating curve. Lyophilization of the solution containing only mannitol, yielded a mixture of β- (major) and δ- (minor) polymorphs of mannitol. However, in the presence of CPA, only δ-polymorph was observed in the lyophilized sample. This selective favoring of the metastable δ-polymorph over the stable β-polymorph, was explained by altered freezing kinetics of the solution in presence of CPA. The study provides mechanistic insights into solute crystallization behaviour during lyophilization of multi-component systems. Copyright © 2017. Published by Elsevier B.V.

Crystals: animal, vegetable or mineral?

PubMed Central

Hyde, Stephen T.

2015-01-01

The morphologies of biological materials, from body shapes to membranes within cells, are typically curvaceous and flexible, in contrast to the angular, facetted shapes of inorganic matter. An alternative dichotomy has it that biomolecules typically assemble into aperiodic structures in vivo, in contrast to inorganic crystals. This paper explores the evolution of our understanding of structures across the spectrum of materials, from living to inanimate, driven by those naive beliefs, with particular focus on the development of crystallography in materials science and biology. The idea that there is a clear distinction between these two classes of matter has waxed and waned in popularity through past centuries. Our current understanding, driven largely by detailed exploration of biomolecular structures at the sub-cellular level initiated by Bernal and Astbury in the 1930s, and more recent explorations of sterile soft matter, makes it clear that this is a false dichotomy. For example, liquid crystals and other soft materials are common to both living and inanimate materials. The older picture of disjoint universes of forms is better understood as a continuum of forms, with significant overlap and common features unifying biological and inorganic matter. In addition to the philosophical relevance of this perspective, there are important ramifications for science. For example, the debates surrounding extra-terrestrial life, the oldest terrestrial fossils and consequent dating of the emergence of life on the Earth rests to some degree on prejudices inferred from the supposed dichotomy between life-forms and the rest. PMID:26464788

Crystals: animal, vegetable or mineral?

PubMed

Hyde, Stephen T

2015-08-06

The morphologies of biological materials, from body shapes to membranes within cells, are typically curvaceous and flexible, in contrast to the angular, facetted shapes of inorganic matter. An alternative dichotomy has it that biomolecules typically assemble into aperiodic structures in vivo, in contrast to inorganic crystals. This paper explores the evolution of our understanding of structures across the spectrum of materials, from living to inanimate, driven by those naive beliefs, with particular focus on the development of crystallography in materials science and biology. The idea that there is a clear distinction between these two classes of matter has waxed and waned in popularity through past centuries. Our current understanding, driven largely by detailed exploration of biomolecular structures at the sub-cellular level initiated by Bernal and Astbury in the 1930s, and more recent explorations of sterile soft matter, makes it clear that this is a false dichotomy. For example, liquid crystals and other soft materials are common to both living and inanimate materials. The older picture of disjoint universes of forms is better understood as a continuum of forms, with significant overlap and common features unifying biological and inorganic matter. In addition to the philosophical relevance of this perspective, there are important ramifications for science. For example, the debates surrounding extra-terrestrial life, the oldest terrestrial fossils and consequent dating of the emergence of life on the Earth rests to some degree on prejudices inferred from the supposed dichotomy between life-forms and the rest.

Crystallization of probucol from solution and the glassy state.

PubMed

Kawakami, Kohsaku; Ohba, Chie

2017-01-30

Crystallization of probucol (PBL) from both solution and glassy solid state was investigated. In the crystallization study from solution, six solvents and three methods, i.e., evaporation, addition of a poor solvent, and cooling on ice, were used to obtain various crystal forms. In addition to common two crystal forms (forms I and II), two further forms (forms III and cyclohexane-solvate) were found in this study, and their thermodynamic relationships were determined. Forms I and II are likely to be enantiotropically related with thermodynamic transition temperature below 5°C. Isothermal crystallization studies revealed that PBL glass initially crystallized into form III between 25 and 50°C, and then transformed to form I. The isothermal crystallization appears to be a powerful option to find uncommon crystal forms. The crystallization of PBL was identified to be pressure controlled, thus the physical stability of PBL glass is higher than that of typical compounds. Copyright © 2016 Elsevier B.V. All rights reserved.

AUthigenic feldspar as an indicator of paleo-rock/water interactions in Permian carbonates of the Northern Calcareous Alps, Austria

USGS Publications Warehouse

Spotl, C.; Kralik, M.; Kunk, Michael J.

1996-01-01

Dolostones interbedded with Upper Permian evaporites at the base of the Northern Calcareous Alps contain abundant authigenic K-feldspar. Two petrographically, structurally, and isotopically distinct generations of K-feldspar can be distinguished: crystals composed of an inclusion-rich core and a clear rim, and optically unzoned, transparent crystals. Both feldspar types have essentially identical K-feldspar end-member compositions with ??? 99.5 mole % Or component. Low oxygen isotope ratios (+16.1??? to +18.1??? SMOW) suggest precipitation from 18O-enriched, saline fluids at temperatures in excess of ??? 140??C. 40Ar/39Ar plateau-age spectra of five samples range from 145 ?? 1 to 144 ?? 1 Ma (Early Berriasian) and suggest that both types of feldspar were formed within an interval that did not exceed ??? 2 m.y. Rb/Sr model ages range from 152 to 140 Ma, assuming that the burial diagenetic regime was buffered with respect to strontium by the associated marine Permian evaporites. Authigenic K-feldspar records two distinct events of hot brine flow, most likely triggered by tectonic movements (detachment) and by an increase in the subsurface temperature in response to thrust loading.

Atomistic model of the spider silk nanostructure

NASA Astrophysics Data System (ADS)

Keten, Sinan; Buehler, Markus J.

2010-04-01

Spider silk is an ultrastrong and extensible self-assembling biopolymer that outperforms the mechanical characteristics of many synthetic materials including steel. Here we report atomic-level structures that represent aggregates of MaSp1 proteins from the N. Clavipes silk sequence based on a bottom-up computational approach using replica exchange molecular dynamics. We discover that poly-alanine regions predominantly form distinct and orderly beta-sheet crystal domains while disorderly structures are formed by poly-glycine repeats, resembling 31-helices. These could be the molecular source of the large semicrystalline fraction observed in silks, and also form the basis of the so-called "prestretched" molecular configuration. Our structures are validated against experimental data based on dihedral angle pair calculations presented in Ramachandran plots, alpha-carbon atomic distances, as well as secondary structure content.

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

Gill, Tobias G.; Fleurence, Antoine; Warner, Ben

We observe a new two-dimensional (2D) silicon crystal, using low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) and it's formed by depositing additional Si atoms onto spontaneously-formed epitaxial silicene on a ZrB 2 thin film. From scanning tunnelling spectroscopy (STS) studies, we find that this atomically-thin layered silicon has distinctly different electronic properties. Angle resolved photoelectron spectroscopy (ARPES) reveals that, in sharp contrast to epitaxial silicene, the layered silicon exhibits significantly enhanced density of states at the Fermi level resulting from newly formed metallic bands. Furthermore, the 2D growth of this material could allow for direct contacting tomore » the silicene surface and demonstrates the dramatic changes in electronic structure that can occur by the addition of even a single monolayer amount of material in 2D systems.« less

Amorphous calcium carbonate particles form coral skeletons

DOE PAGES

Mass, Tali; Giuffre, Anthony J.; Sun, Chang -Yu; ...

2017-08-28

Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed “vital effects,” that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO 3).more » We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO 2 increases, such as the Paleocene–Eocene Thermal Maximum that occurred 56 Mya.« less

Amorphous calcium carbonate particles form coral skeletons

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

Mass, Tali; Giuffre, Anthony J.; Sun, Chang -Yu

Do corals form their skeletons by precipitation from solution or by attachment of amorphous precursor particles as observed in other minerals and biominerals? The classical model assumes precipitation in contrast with observed “vital effects,” that is, deviations from elemental and isotopic compositions at thermodynamic equilibrium. Here, we show direct spectromicroscopy evidence in Stylophora pistillata corals that two amorphous precursors exist, one hydrated and one anhydrous amorphous calcium carbonate (ACC); that these are formed in the tissue as 400-nm particles; and that they attach to the surface of coral skeletons, remain amorphous for hours, and finally, crystallize into aragonite (CaCO 3).more » We show in both coral and synthetic aragonite spherulites that crystal growth by attachment of ACC particles is more than 100 times faster than ion-by-ion growth from solution. Fast growth provides a distinct physiological advantage to corals in the rigors of the reef, a crowded and fiercely competitive ecosystem. Corals are affected by warming-induced bleaching and postmortem dissolution, but the finding here that ACC particles are formed inside tissue may make coral skeleton formation less susceptible to ocean acidification than previously assumed. If this is how other corals form their skeletons, perhaps this is how a few corals survived past CO 2 increases, such as the Paleocene–Eocene Thermal Maximum that occurred 56 Mya.« less

A thermodynamic framework for the study of crystallization in polymers

NASA Astrophysics Data System (ADS)

Rao, I. J.; Rajagopal, K. R.

In this paper, we present a new thermodynamic framework within the context of continuum mechanics, to predict the behavior of crystallizing polymers. The constitutive models that are developed within this thermodynamic setting are able to describe the main features of the crystallization process. The model is capable of capturing the transition from a fluid like behavior to a solid like behavior in a rational manner without appealing to any adhoc transition criterion. The anisotropy of the crystalline phase is built into the model and the specific anisotropy of the crystalline phase depends on the deformation in the melt. These features are incorporated into a recent framework that associates different natural configurations and material symmetries with distinct microstructural features within the body that arise during the process under consideration. Specific models are generated by choosing particular forms for the internal energy, entropy and the rate of dissipation. Equations governing the evolution of the natural configurations and the rate of crystallization are obtained by maximizing the rate of dissipation, subject to appropriate constraints. The initiation criterion, marking the onset of crystallization, arises naturally in this setting in terms of the thermodynamic functions. The model generated within such a framework is used to simulate bi-axial extension of a polymer film that is undergoing crystallization. The predictions of the theory that has been proposed are consistent with the experimental results (see [28] and [7]).

Energy-selective Neutron Imaging for Three-dimensional Non-destructive Probing of Crystalline Structures

NASA Astrophysics Data System (ADS)

Peetermans, S.; Bopp, M.; Vontobel, P.; Lehmann, E. H.

Common neutron imaging uses the full polychromatic neutron beam spectrum to reveal the material distribution in a non-destructive way. Performing it with a reduced energy band, i.e. energy-selective neutron imaging, allows access to local variation in sample crystallographic properties. Two sample categories can be discerned with different energy responses. Polycrystalline materials have an energy-dependent cross-section featuring Bragg edges. Energy-selective neutron imaging can be used to distinguish be- tween crystallographic phases, increase material sensitivity or penetration, improve quantification etc. An example of the latter is shown by the examination of copper discs prior to machining them into linear accelerator cavity structures. The cross-section of single crystals features distinct Bragg peaks. Based on their pattern, one can determine the orientation of the crystal, as in a Laue pattern, but with the tremendous advantage that the operation can be performed for each pixel, yielding crystal orientation maps at high spatial resolution. A wholly different method to investigate such samples is also introduced: neutron diffraction imaging. It is based on projections formed by neutrons diffracted from the crystal lattice out of the direct beam. The position of these projections on the detector gives information on the crystal orientation. The projection itself can be used to reconstruct the crystal shape. A three-dimensional mapping of local Bragg reflectivity or a grain orientation mapping can thus be obtained.

Episodic intrusion, internal differentiation, and hydrothermal alteration of the miocene tatoosh intrusive suite south of Mount Rainier, Washington

USGS Publications Warehouse

du Bray, E.A.; Bacon, C.R.; John, D.A.; Wooden, J.L.; Mazdab, F.K.

2011-01-01

The Miocene Tatoosh intrusive suite south of Mount Rainier is composed of three broadly granodioritic plutons that are manifestations of ancestral Cascades arc magmatism. Tatoosh intrusive suite plutons have individually diagnostic characteristics, including texture, mineralogy, and geochemistry, and apparently lack internal contacts. New ion-microprobe U-Pb zircon ages indicate crystallization of the Stevens pluton ca. 19.2 Ma, Reflection-Pyramid pluton ca. 18.5 Ma, and Nisqually pluton ca. 17.5 Ma. The Stevens pluton includes rare, statistically distinct ca. 20.1 Ma zircon antecrysts. Wide-ranging zircon rare earth element (REE), Hf, U, and Th concentrations suggest late crystallization from variably evolved residual liquids. Zircon Eu/Eu*-Hf covariation is distinct for each of the Reflection-Pyramid, Nisqually, and Stevens plutons. Although most Tatoosh intrusive suite rocks have been affected by weak hydrothermal alteration, and sparse mineralized veins cut some of these rocks, significant base or precious metal mineralization is absent. At the time of shallow emplacement, each of these magma bodies was largely homogeneous in bulk composition and petrographic features, but, prior to final solidification, each of the Tatoosh intrusive suite plutons developed internal compositional variation. Geochemical and petrographic trends within each pluton are most consistent with differential loss of residual melt, possibly represented by late aplite dikes or erupted as rhyolite, from crystal-rich magma. Crystal-rich magma that formed each pluton evidently accumulated in reservoirs below the present level of exposure and then intruded to a shallow depth. Assembled by episodic intrusion, the Tatoosh intrusive suite may be representative of midsized composite plutonic complexes beneath arc volcanoes. ?? 2011 Geological Society of America.

Light driven mesoscale assembly of a coordination polymeric gelator into flowers and stars with distinct properties† †Electronic supplementary information (ESI) available: Text, figures, and tables depicting different synthetic procedures, detailed experimental procedures, characterisation data including FT-IR, microscopic analyses, TGA, EDAX and SAED analyses, pore size distribution. See DOI: 10.1039/c5sc02233a Click here for additional data file.

PubMed Central

Mukhopadhyay, Rahul Dev; Praveen, Vakayil K.; Hazra, Arpan; Maji, Tapas Kumar

2015-01-01

Control over the self-assembly process of porous organic–inorganic hybrids often leads to unprecedented polymorphism and properties. Herein we demonstrate how light can be a powerful tool to intervene in the kinetically controlled mesoscale self-assembly of a coordination polymeric gelator. Ultraviolet light induced coordination modulation via photoisomerisation of an azobenzene based dicarboxylate linker followed by aggregation mediated crystal growth resulted in two distinct morphological forms (flowers and stars), which show subtle differences in their physical properties. PMID:28757961

Silicon Carbide From a Carbon Nodule in the Canyon Diablo Meteorite

NASA Astrophysics Data System (ADS)

Leung, I. S.; Winston, R.

2011-12-01

The Canyon Diablo Meteorite fell in the Arizona desert 50,000 years ago, giving rise to the well-preserved Meteor Crater. Irons of various sizes were scattered around the crater rim and on the surrounding plains. We studied a rusty specimen containing a carbon nodule. We dug out small blocks of sooty carbon by means of a sharp tungsten carbide tip. These carbon materials contain traces of silicon carbide (SiC) and diamond/lonsdaleite. We report here our findigs of two groups of SiC grains. (1) Relatively large crystals, about 80-90 microns in size. Their colors are in shades of blue, green and neutral. One of the grains are composed of a cluster of 3 crystals of the 3C polytype, whereas, 7 other individual crystals are of hexagonal structure. All crystals in this group have dark, rounded resorption rims. (2) Small crystals, about 30-50 microns in size. They are pale blue in color, and they lack dark-colored rims. These two distinct groups probably have different modes of origin. The large crystals seem to be early-formed, but had been reheated or partially melted, as indicated by the bead-like rims. The complexities displayed by these SiC crystals might have resulted from a long residence time in the meteorite while it was still in space. Their origin might be akin to that of SiC occurring in carbonaceous chondrites and interplanetary dust particles.

Thyroxine revisited.

PubMed

Katrusiak, Andrzej; Katrusiak, Anna

2004-12-01

The crystal structure of the common therapeutic agent, the pentahydrated sodium salt of L-thyroxine hormone (3-[4-(4-hydroxy-3,5-diiodophenoxy)-3,5-diiodophenyl]-L-alanine), has been determined and discussed in relation to the drug's stability. The stoichiometry and absolute configuration (-)-C(8)S-[C15H10I4NO4]-.Na+.5H2O have been confirmed. The crystals are built of a three-dimensional supramolecular network with two symmetry-independent L-thyroxine anions, in two distinct conformations not previously reported, linked by strong NH-O hydrogen bonds into dimers. Two independent sodium cations are fivefold and sixfold coordinated. The cations and two independent water molecules not involved in coordinating the Na cations form sheets along the crystallographic (001) planes. The presence of differently coordinated cations and non-coordinating water molecules may be responsible for water transport and loss, for decay of the crystals, and subsequent low stability of the drug. Only a conglomerate could be obtained when racemic sodium thyroxine was crystallized from ethanol and methanol solutions by evaporation, which explains the equal penta-hydration of the sodium salts of enantiomorphic and racemic thyroxine, and the fact that there are no apparent differences in their stability. (c) 2004 Wiley-Liss, Inc. and the American Pharmacists Association

Crystal structure of a c-kit promoter quadruplex reveals the structural role of metal ions and water molecules in maintaining loop conformation.

PubMed

Wei, Dengguo; Parkinson, Gary N; Reszka, Anthony P; Neidle, Stephen

2012-05-01

We report here the 1.62 Å crystal structure of an intramolecular quadruplex DNA formed from a sequence in the promoter region of the c-kit gene. This is the first reported crystal structure of a promoter quadruplex and the first observation of localized magnesium ions in a quadruplex structure. The structure reveals that potassium and magnesium ions have an unexpected yet significant structural role in stabilizing particular quadruplex loops and grooves that is distinct from but in addition to the role of potassium ions in the ion channel at the centre of all quadruplex structures. The analysis also shows how ions cluster together with structured water molecules to stabilize the quadruplex arrangement. This particular quadruplex has been previously studied by NMR methods, and the present X-ray structure is in accord with the earlier topology assignment. However, as well as the observations of potassium and magnesium ions, the crystal structure has revealed a highly significant difference in the dimensions of the large cleft in the structure, which is a plausible target for small molecules. This difference can be understood by the stabilizing role of structured water networks.

The effects of Bacillus thuringiensis Cry6A on the survival, growth, reproduction, locomotion, and behavioral response of Caenorhabditis elegans.

PubMed

Luo, Hui; Xiong, Jing; Zhou, Qiaoni; Xia, Liqiu; Yu, Ziquan

2013-12-01

Several families of crystal proteins from Bacillus thuringiensis exhibit nematicidal activity. Cry5B protein, a pore-forming toxin, has been intensively studied yielding many insights into the mode of action of crystal protein at molecular level and pathogenesis of pore-forming toxins. However, little attention was paid to Cry6A, another representative nematicidal crystal protein. Cry6A shares very low homology with Cry5B at amino acid sequence and probably acts in a distinct pathway from Cry5B and even the other main commercial crystal proteins. In the current study, we comprehensively investigated the nematicidal properties of Cry6Aa2 against the free-living soil nematode Caenorhabditis elegans and examined the physical response of C. elegans to Cry6Aa2 attack. Our results indicate that Cry6Aa2 exhibits high lethal activity to C. elegans and could cause detrimental effects on C. elegans, including obviously suppressed growth, decreased brood size, and even abnormal motility. Meanwhile, our study additionally shows that C. elegans could defend against the Cry6Aa2 toxin harmful threat through behavioral defense responses, such as reduced oral uptake and physical avoidance. In general, this study suggests that Cry6Aa2 possesses diverse nematicidal properties, which strongly indicates that Cry6Aa2 is a promising potential candidate of nematicidal agent. Moreover, this study highlights the importance of behavioral responses in defense of C. elegans for survival and demonstrates the key role of crystal protein in the interaction of B. thuringiensis-C. elegans. These findings could shed light on understanding the interaction of C. elegans with B. thuringiensis and provide a perfect model to study the role of pathogenic factor in the interaction of pathogen-host.

Phase transitions of antibiotic clarithromycin forms I, IV and new form VII crystals.

PubMed

Ito, Masataka; Shiba, Rika; Watanabe, Miteki; Iwao, Yasunori; Itai, Shigeru; Noguchi, Shuji

2018-06-01

Metastable crystal form I of the antibiotic clarithromycin has a pharmaceutically valuable characteristic that its crystalline phase transition can be applied for its sustained release from tablets. The phase transition of form I was investigated in detail by single crystal and powder X-ray analyses, dynamic vapor sorption analysis and thermal analysis. The single crystal structure of form I revealed that form I was not an anhydrate crystal but contained a partially occupied water molecule in the channel-like void space. Dynamic vapor sorption (DVS) analysis demonstrated that form I crystals reversibly sorbed water molecules in two steps when the relative humidity (RH) increased and finally transited to hydrate form IV at 95% RH. DVS analysis also showed that when the RH decreased form IV crystals lost water molecules at 40% RH and transited to the newly identified anhydrate crystal form VII. Form VII reversibly transited to form IV at lower RH than form I, suggesting that form I is more suitable for manufacturing a sustained-release tablet of CAM utilizing the crystalline phase transition. Copyright © 2018 Elsevier B.V. All rights reserved.

Mosaic structure in epitaxial thin films having large lattice mismatch

NASA Astrophysics Data System (ADS)

Srikant, V.; Speck, J. S.; Clarke, D. R.

1997-11-01

Epitaxial films having a large lattice mismatch with their substrate invariably form a mosaic structure of slightly misoriented sub-grains. The mosaic structure is usually characterized by its x-ray rocking curve on a surface normal reflection but this is limited to the out-of-plane component unless off-axis or transmission experiments are performed. A method is presented by which the in-plane component of the mosaic misorientation can be determined from the rocking curves of substrate normal and off-axis reflections. Results are presented for two crystallographically distinct heteroepitaxial systems, ZnO, AlN, and GaN (wurtzite crystal structure) on c-plane sapphire and MgO (rock salt crystal structure) on (001) GaAs. The differences in the mosaic structure of these films are attributed to the crystallographic nature of their lattice dislocations.

Structural discrimination via density functional theory and lattice dynamics: Monoclinic Mg2NiH4

NASA Astrophysics Data System (ADS)

Herbst, J. F.; Hector, L. G., Jr.

2009-04-01

Two distinct crystal structures for the monoclinic, low-temperature phase of Mg2NiH4 , which we designate as LTI and LTII, are available in the published literature. We demonstrate that density functional theory and lattice dynamics can easily identify LTII as the preferable structure at two levels of inquiry. First, enthalpies of formation ΔH calculated using three different forms for the exchange-correlation energy functional are in better agreement with experiment for LTII. Second, the phonon spectrum calculated for LTII contains no anomalies while that for LTI exhibits a variety of soft modes. By analyzing the soft modes in LTI as well as those we find for the known CaMgNiH4 structure with Ca replaced by Mg we derive a crystal structure that closely approximates LTII.

Structure of Mycobacterium tuberculosis phosphopantetheine adenylyltransferase in complex with the feedback inhibitor CoA reveals only one active-site conformation

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

Wubben, T.; Mesecar, A.D.; UIC)

Phosphopantetheine adenylyltransferase (PPAT) catalyzes the penultimate step in the coenzyme A (CoA) biosynthetic pathway, reversibly transferring an adenylyl group from ATP to 4'-phosphopantetheine to form dephosphocoenzyme A (dPCoA). To complement recent biochemical and structural studies on Mycobacterium tuberculosis PPAT (MtPPAT) and to provide further insight into the feedback regulation of MtPPAT by CoA, the X-ray crystal structure of the MtPPAT enzyme in complex with CoA was determined to 2.11 {angstrom} resolution. Unlike previous X-ray crystal structures of PPAT-CoA complexes from other bacteria, which showed two distinct CoA conformations bound to the active site, only one conformation of CoA is observedmore » in the MtPPAT-CoA complex.« less

Sphene-centered ocellar texture as a petrological tool to unveil the mechanism facilitating magma mixing

NASA Astrophysics Data System (ADS)

Gogoi, Bibhuti; Saikia, Ashima; Ahmad, Mansoor

2015-04-01

The sphene-centered ocellar texture is a unique magma mixing feature characterized by leucocratic ocelli of sphene enclosed in a biotite/hornblende-rich matrix (Hibbard, 1991). The ocelli usually consist of plagioclase, K-feldspar and quartz with sphene crystals at its centre. Although geochemical and isotopic data provide concrete evidence for the interaction between two compositionally distinct magmas, the exact processes by which mixing takes place is yet uncertain. So, textural analysis can be used to decipher the behaviour of two disparate magmas during mixing. Presented work is being carried out on the sphene ocelli, occurring in hybrid rocks of the Nimchak Granite Pluton (NGP), to understand its formation while two compositionally different magmas come in contact and try to equilibrate. The NGP is ca. 1 km2in extent which has been extensively intruded by number of mafic dykes exhibiting well preserved magma mixing and mingling structures and textures in the Bathani Volcano-Sedimentary Sequence (BVSS) located on the northern fringe of the Proterozoic Chotanagpur Granite Gneiss Complex (CGGC) of eastern Indian Shield. From petrographic and mineral chemical studies we infer that when basaltic magma intruded the crystallizing granite magma chamber, initially the two compositionally different magmas existed as separate entities. The first interaction that took place between the two phases is diffusion of heat from the relatively hotter mafic magma to the colder felsic one followed by diffusion of elemental components like K and incompatible elements from the felsic to the mafic domain. Once thermal equilibrium was attained between the mafic and felsic melts, the rheological contrasts between the two phases were greatly reduced. This allowed the felsic magma to back-vein into the mafic magma. The influx of back-veined felsic melt into the mafic system disrupted the equilibrium conditions in the mafic domain wherein minerals like amphibole, plagioclase and biotite were crystallizing. This led to the incongruent melting of amphibole and biotite to form liquids of sphene composition. Meanwhile, plagioclase continued to grow in the mafic-turned-hybrid system with a different composition after the advent of felsic melt as indicated by compositional zoning in plagioclase crystals. The newly produced sphene-liquid, owing to its higher affinity for felsic phase than mafic, got incorporated into the back-veining felsic melt forming a distinct liquid of its own. The felsic melt also incorporated crystallizing plagioclase grains in it from the mafic matrix. The mixture of felsic melt, sphene-liquid and plagioclase crystals flowed through the biotite, amphibole and plagioclase dominated matrix towards the low pressure zones to occupy the spherical void spaces left behind by escaping of gases/volatiles forming the sphene ocelli. Hibbard, M.J., 1991. Textural anatomy of twelve magma-mixed granitoid systems. In: Didier, J., Barbarin, B. (Eds.) Enclaves and granite petrology, 431-444.

Crystal Structure of the Complex Between Programmed Death-1 (PD-1) and its Ligand PD-L2

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

Lazar-Molnar,E.; Yan, Q.; Cao, E.

2008-01-01

Programmed death-1 (PD-1) is a member of the CD28/B7 superfamily that delivers negative signals upon interaction with its two ligands, PD-L1 or PD-L2. The high-resolution crystal structure of the complex formed by the complete ectodomains of murine PD-1 and PD-L2 revealed a 1:1 receptor:ligand stoichiometry and displayed a binding interface and overall molecular organization distinct from that observed in the CTLA-4/B7 inhibitory complexes. Furthermore, our structure also provides insights into the association between PD-1 and PD-L1 and highlights differences in the interfaces formed by the two PD-1 ligands (PD-Ls) Mutagenesis studies confirmed the details of the proposed PD-1/PD-L binding interfacesmore » and allowed for the design of a mutant PD-1 receptor with enhanced affinity. These studies define spatial and organizational constraints that control the localization and signaling of PD-1/PD-L complexes within the immunological synapse and provide a basis for manipulating the PD-1 pathways for immunotherapy.« less

Crystal Structure of Dengue Virus Type 1 Envelope Protein in the Postfusion Conformation and Its Implications for Membrane Fusion

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

Nayak, Vinod; Dessau, Moshe; Kucera, Kaury

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the 'pH sensor' that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less

Crystal Structure of Dengue Type 1 Envelope Protein in the Postfusion Conformation and its Implication for Receptor Binding, Membrane Fusion and Antibody Recognition

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

Nayak, V.; Dessau, M; Kucera, K

Dengue virus relies on a conformational change in its envelope protein, E, to fuse the viral lipid membrane with the endosomal membrane and thereby deliver the viral genome into the cytosol. We have determined the crystal structure of a soluble fragment E (sE) of dengue virus type 1 (DEN-1). The protein is in the postfusion conformation even though it was not exposed to a lipid membrane or detergent. At the domain I-domain III interface, 4 polar residues form a tight cluster that is absent in other flaviviral postfusion structures. Two of these residues, His-282 and His-317, are conserved in flavivirusesmore » and are part of the pH sensor that triggers the fusogenic conformational change in E, at the reduced pH of the endosome. In the fusion loop, Phe-108 adopts a distinct conformation, forming additional trimer contacts and filling the bowl-shaped concavity observed at the tip of the DEN-2 sE trimer.« less

Quasi-two-dimensional complex plasma containing spherical particles and their binary agglomerates.

PubMed

Chaudhuri, M; Semenov, I; Nosenko, V; Thomas, H M

2016-05-01

A unique type of quasi-two-dimensional complex plasma system was observed which consisted of monodisperse microspheres and their binary agglomerations (dimers). The particles and their dimers levitated in a plasma sheath at slightly different heights and formed two distinct sublayers. The system did not crystallize and may be characterized as a disordered solid. The dimers were identified based on their characteristic appearance in defocused images, i.e., rotating interference fringe patterns. The in-plane and interplane particle separations exhibit nonmonotonic dependence on the discharge pressure.

Ejection of Coulomb Crystals from a Linear Paul Ion Trap for Ion-Molecule Reaction Studies.

PubMed

Meyer, K A E; Pollum, L L; Petralia, L S; Tauschinsky, A; Rennick, C J; Softley, T P; Heazlewood, B R

2015-12-17

Coulomb crystals are being increasingly employed as a highly localized source of cold ions for the study of ion-molecule chemical reactions. To extend the scope of reactions that can be studied in Coulomb crystals-from simple reactions involving laser-cooled atomic ions, to more complex systems where molecular reactants give rise to multiple product channels-sensitive product detection methodologies are required. The use of a digital ion trap (DIT) and a new damped cosine trap (DCT) are described, which facilitate the ejection of Coulomb-crystallized ions onto an external detector for the recording of time-of-flight (TOF) mass spectra. This enables the examination of reaction dynamics and kinetics between Coulomb-crystallized ions and neutral molecules: ionic products are typically cotrapped, thus ejecting the crystal onto an external detector reveals the masses, identities, and quantities of all ionic species at a selected point in the reaction. Two reaction systems are examined: the reaction of Ca(+) with deuterated isotopologues of water, and the charge exchange between cotrapped Xe(+) with deuterated isotopologues of ammonia. These reactions are examples of two distinct types of experiment, the first involving direct reaction of the laser-cooled ions, and the second involving reaction of sympathetically-cooled heavy ions to form a mixture of light product ions. Extensive simulations are conducted to interpret experimental results and calculate optimal operating parameters, facilitating a comparison between the DIT and DCT approaches. The simulations also demonstrate a correlation between crystal shape and image shape on the detector, suggesting a possible means for determining crystal geometry for nonfluorescing ions.

The assessment of pore connectivity in hierarchical zeolites using positron annihilation lifetime spectroscopy: instrumental and morphological aspects.

PubMed

Zubiaga, Asier; Warringham, Robbie; Boltz, Marilyne; Cooke, David; Crivelli, Paolo; Gidley, David; Pérez-Ramírez, Javier; Mitchell, Sharon

2016-04-07

Recent studies demonstrated the power of positron annihilation lifetime spectroscopy (PALS) to characterise the connectivity and corresponding effectiveness of hierarchical pore networks in zeolites. This was based on the fractional escape of ortho-positronium (Ps), formed within the micropore framework, to vacuum. To further develop this technique, here we assess the impact of the positron implantation energy and of the zeolite crystal size and the particle morphology. Conventional measurements using fast positrons and beam measurements applying moderated positrons both readily distinguish purely microporous ZSM-5 zeolites comprised of single crystals or crystal aggregates. Unlike beam measurements, however, conventional measurements fail to discriminate model hierarchical zeolites with open or constricted mesopore architectures. Several steps are taken to rationalise these observations. The dominant contribution of Ps diffusion to the PALS response is confirmed by capping the external surface of the zeolite crystals with tetraethylorthosilicate, which greatly enhances the sensitivity to the micropore network. A one-dimensional model is constructed to predict the out-diffusion of Ps from a zeolite crystal, which is validated experimentally by comparing coffin-shaped single crystals of varying size. Calculation of the trends expected on the application of fast or moderated positrons indicates that the distinctions in the initial distribution of Ps at the crystal level cannot explain the limited sensitivity of the former to the mesopore architecture. Instead, we propose that the greater penetration of fast positrons within the sample increases the probability of Ps re-entry from intercrystalline voids into mesopores connected with the external surface of zeolite crystals, thereby reducing their fractional escape.

Flow Fields of the 3.5 Ga Komati Formation, South Africa: Geochemical, Stratigraphic, and Temporal relationships between Massive, Vesicular, and Spinifex flows

NASA Astrophysics Data System (ADS)

Dann, J. C.

2007-12-01

A challenge of Archean volcanology is to reconstruct submarine flow fields by mapping and analyzing vertically dipping sequences of lavas. Some flow fields are bound by sediments and/or seafloor alteration that mark clear gaps in volcanism. Flow fields in the Lower Komati Fm are defined by alternating layers of komatiite (26% MgO) and komatiitic basalt (15% MgO). Five komatiite flow fields (100-200m thick) repeat the same stratigraphic zoning of spinifex overlying massive komatiite, and each flow field has a distinct Al2O3/CaO, a ratio unaffected by olivine fractionation, consistent with the contention that each komatiite flow field represents a distinct batch of mantle melting. Although massive and spinifex komatiite form distinct stratigraphic units on a map scale, detailed outcrop mapping reveals that the change in flow type represents a transition within a single flow field. In one type of transition, thin massive flows alternate with spinifex flow lobes of a compound flow unit. In another, a vesicular flow along the boundary links the underlying massive komatiite and overlying spinifex flows in time. The vesicular flow has alternating spinifex and vesicular layers that form a distinctive crust above a thick massive interior. Locally, this crust is tilted, intruded by massive komatiite from the interior, and overlain by a thick breccia including a spinifex flow broken into blocks and rotated like dominoes by the tilting. These outcrop relations indicate that spinifex flow lobes were starting to flow over the vesicular flow before it had undergone differential inflation, a temporal link between the lower massive and upper spinifex komatiites consistent with their belonging to the same flow field. The transition in flow type may reflect 1) an overlap of proximal and distal facies of komatiite flows as eruption rates waned and/or 2) thermal maturation prior to eruption. Early, cooler, crystal-rich, massive lava, flowing out as thick sheet flows, was replaced by hotter, crystal-poor, less degassed lava, flowing out as spinifex flows.

Petrology of the Western Highland Province: Ancient crust formation at the Apollo 14 site

NASA Astrophysics Data System (ADS)

Shervais, John W.; McGee, James J.

1999-03-01

Plutonic rocks found at the Apollo 14 site comprise four lithologic suites: the magnesian suite, the alkali suite, evolved lithologies, and the ferroan anorthosite suite (FAN). Rocks of the magnesian suite include troctolite, anorthosite, norite, dunite, and harzburgite; they are characterized by plagioclase ~An95 and mafic minerals with mg#s 82-92. Alkali suite rocks and evolved rocks generally have plagioclase ~An90 to ~An40, and mafic minerals with mg#s 82-40. Lithologies include anorthosite, norite, quartz monzodiorite, granite, and felsite. Ferroan anorthosites have plagioclase ~An96 and mafic minerals with mg#s 45-70. Whole rock geochemical data show that most magnesian suite samples and all alkali anorthosites are cumulates with little or no trapped liquid component. Norites may contain significant trapped liquid component, and some alkali norites may represent cumulate-enriched, near-liquid compositions, similar to KREEP basalt 15386. Evolved lithologies include evolved partial cumulates related to alkali suite fractionation (quartz monzodiorite), immiscible melts derived from these evolved magmas (granites), and impact melts of preexisting granite (felsite). Plots of whole rock mg# versus whole rock Ca/(Ca+Na+K) show a distinct gap between rocks of the magnesian suite and rocks of the alkali suite, suggesting either distinct parent magmas or distinct physical processes of formation. Chondrite-normalized rare earth element (REE) patterns show that rocks of both the magnesian suite and alkali suite have similar ranges, despite the large difference in major element chemistry. Current models for the origin of the magnesian suite call for a komatiitic parent magma derived from early magma ocean cumulates; these melts must assimilate plagiophile elements to form troctolites at low pressures and must assimilate a highly enriched KREEP component so that the resulting mixture has REE concentrations similar to high-K KREEP. There are as yet no plausible scenarios that can explain these unusual requirements. We propose that partial melting of a primitive lunar interior and buffering of these melts by ultramagnesian early magma ocean cumulates provides a more reasonable pathway to form magnesian troctolites. Alkali anorthosites and norites formed by crystallization of a parent magma with major element compositions similar to KREEP basalt 15386. If the parent magma of the alkali suite and evolved rocks is related to the magnesian suite, then that magma must have evolved through combined assimilation-fractional crystallization processes to form the alkali suite cumulates.

Physicochemical and crystal structure analyses of the antidiabetic agent troglitazone.

PubMed

Kobayashi, Katsuhiro; Fukuhara, Hiroshi; Hata, Tadashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

2003-07-01

The antidiabetic agent troglitazone has two asymmetric carbons located at the chroman ring and the thiazolidine ring and is produced as a mixture of equal amounts of four optical isomers, 2R-5S, 2S-5R, 2R-5R, and 2S-5S. The crystalline powdered drug substance consists of two diastereomer pairs, 2R-5R/2S-5S and 2R-5S/2S-5R. There are many types of crystals obtained from various crystallization conditions. The X-ray structure analysis and the physicochemical analyses of troglitazone were performed. The solvated crystals of the 2R-5R/2S-5S pair were crystallized from several solutions: methanol, ethanol, acetonitrile, and dichloromethane. The ratio of solvent and troglitazone was 1 : 2 (L1/2-form). The monohydrate crystals were obtained from aqueous acetone solution (L1-form). On the other hand, only an anhydrate crystal of the 2R-5S/2S-5R pair was crystallized from various solutions (H0-form). The dihydrous mixed crystal (MA2-form) was obtained from a mixture of the two diastereomer pairs of 2R-5R/2S-5S and 2R-5S/2S-5R in equal amounts by the slow evaporation of aqueous acetone solution. The crystal structure of the MA2-form is similar to the H0-form. When the MA2 crystal was kept under low humidity, it was converted into the dehydrated form (MA0-form) with retention of the single crystal form. The structure of the MA0-form is isomorphous to the H0-form. The MA2-form was converted into the MA0-form and vice versa with retention of the single crystal under low and high humidity, respectively. The crystallization and storage conditions of the drug substances were successfully analyzed.

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

Jones, B.; Renault, R.W.

Platy calcite crystals, which have their c axis parallel to their shortest length axis, are common components of travertine deposits found around some hot springs in the Kenya Rift Valley. They are composite crystals formed of numerous paper-thin subcrystals. Individual plates allowed to grow without obstruction develop a hexagonal motif. The Kenyan crystals typically form in hot (>75 C) waters that have a low Ca content (<10 mg/l), a high CO{sub 2} content, and a high rate of CO{sub 2} degassing. At Chemurkeu, aggregates of numerous small platy crystals collectively form lattice crystals that superficially resemble ray crystals. The wallsmore » of the lattice crystals are formed of large platy crystals that have their long and intermediate length axes aligned parallel to the plane of the long axis of the lattice crystal. Internally, the lattice crystals are formed of small platy calcite crystals arranged in a boxlike pattern that creates the appearance of a lattice when viewed in thin section. Lattice crystals are highly porous, with each pore being enclosed by platy crystals. At Lorusio, travertines are mainly formed of pseudodentrites that are constructed by numerous small platy crystals attached to a main stem which is a large platy crystal that commonly curves along its long axis. The pseudodentrites are the main construction blocks in ledges and lilypads that form in the vent pool and spring outflow channels, where the water is too hot for microbes other than hyperthermophiles. The platy calcite crystals in the Kenyan travertines are morphologically similar to platy calcite crystals that form as scale in pipes in the geothermal fields of New Zealand and hydrothermal angel wing calcite from the La Fe mine in Mexico. Comparison of the Kenyan and New Zealand crystals indicates that platy calcite crystals form from waters with a low Ca{sup 2+} content and a high CO{sub 3}/Ca ratio due to rapid rates of CO{sub 2} degassing.« less

Plateau-Rayleigh Crystal Growth of Nanowire Heterostructures: Strain-Modified Surface Chemistry and Morphological Control in One, Two, and Three Dimensions.

PubMed

Day, Robert W; Mankin, Max N; Lieber, Charles M

2016-04-13

One-dimensional (1D) structures offer unique opportunities for materials synthesis since crystal phases and morphologies that are difficult or impossible to achieve in macroscopic crystals can be synthesized as 1D nanowires (NWs). Recently, we demonstrated one such phenomenon unique to growth on a 1D substrate, termed Plateau-Rayleigh (P-R) crystal growth, where periodic shells develop along a NW core to form diameter-modulated NW homostructures with tunable morphologies. Here we report a novel extension of the P-R crystal growth concept with the synthesis of heterostructures in which Ge (Si) is deposited on Si (Ge) 1D cores to generate complex NW morphologies in 1, 2, or 3D. Depositing Ge on 50 nm Si cores with a constant GeH4 pressure yields a single set of periodic shells, while sequential variation of GeH4 pressure can yield multimodulated 1D NWs with two distinct sets of shell periodicities. P-R crystal growth on 30 nm cores also produces 2D loop structures, where Ge (Si) shells lie primarily on the outside (inside) of a highly curved Si (Ge) core. Systematic investigation of shell morphology as a function of growth time indicates that Ge shells grow in length along positive curvature Si cores faster than along straight Si cores by an order of magnitude. Short Ge deposition times reveal that shells develop on opposite sides of 50 and 100 nm Si cores to form straight 1D morphologies but that shells develop on the same side of 20 nm cores to produce 2D loop and 3D spring structures. These results suggest that strain mediates the formation of 2 and 3D morphologies by altering the NW's surface chemistry and that surface diffusion of heteroatoms on flexible freestanding 1D substrates can facilitate this strain-mediated mechanism.

Growth and dislocation studies of β-HMX.

PubMed

Gallagher, Hugh G; Sherwood, John N; Vrcelj, Ranko M

2014-01-01

The defect structure of organic materials is important as it plays a major role in their crystal growth properties. It also can play a subcritical role in "hot-spot" detonation processes of energetics and one such energetic is cyclotetramethylene-tetranitramine, in the commonly used beta form (β-HMX). The as-grown crystals grown by evaporation from acetone show prismatic, tabular and columnar habits, all with {011}, {110}, (010) and (101) faces. Etching on (010) surfaces revealed three different types of etch pits, two of which could be identified with either pure screw or pure edge dislocations, the third is shown to be an artifact of the twinning process that this material undergoes. Examination of the {011} and {110} surfaces show only one type of etch pit on each surface; however their natural asymmetry precludes the easy identification of their Burgers vector or dislocation type. Etching of cleaved {011} surfaces demonstrates that the etch pits can be associated with line dislocations. All dislocations appear randomly on the crystal surfaces and do not form alignments characteristic of mechanical deformation by dislocation slip. Crystals of β-HMX grown from acetone show good morphological agreement with that predicted by modelling, with three distinct crystal habits observed depending upon the supersaturation of the growth solution. Prismatic habit was favoured at low supersaturation, while tabular and columnar crystals were predominant at higher super saturations. The twin plane in β-HMX was identified as a (101) reflection plane. The low plasticity of β-HMX is shown by the lack of etch pit alignments corresponding to mechanically induced dislocation arrays. On untwinned {010} faces, two types of dislocations exist, pure edge dislocations with b = [010] and pure screw dislocations with b = [010]. On twinned (010) faces, a third dislocation type exists and it is proposed that these pits are associated with pure screw dislocations with b = [010]. Graphical abstractEtch pits on the twinned (010) face of β-HMX.

Competition between monomeric and dimeric crystals in schematic models for globular proteins.

PubMed

Fusco, Diana; Charbonneau, Patrick

2014-07-17

Advances in experimental techniques and in theoretical models have improved our understanding of protein crystallization. However, they have also left open questions regarding the protein phase behavior and self-assembly kinetics, such as why (nearly) identical crystallization conditions can sometimes result in the formation of different crystal forms. Here, we develop a patchy particle model with competing sets of patches that provides a microscopic explanation of this phenomenon. We identify different regimes in which one or two crystal forms can coexist with a low-density fluid. Using analytical approximations, we extend our findings to different crystal phases, providing a general framework for treating protein crystallization when multiple crystal forms compete. Our results also suggest different experimental routes for targeting a specific crystal form, and for reducing the dynamical competition between the two forms, thus facilitating protein crystal assembly.

Geometrical criteria for characterizing open and closed states of WPD-loop in PTP1B

NASA Astrophysics Data System (ADS)

Shinde, Ranajit Nivrutti; Elizabeth Sobhia, M.

2012-06-01

Distinctive movement of WPD-loop occurs during the catalysis of phosphotyrosine by protein tyrosine phosphatase 1B (PTP1B). This loop is in the "open" state in apo-form whereas it is catalytically competent in the "closed" state. During the closure of this loop, unique hydrogen bond interactions are formed between different residues of the PTP1B. Present study examines such interactions from the available 118 crystal structures of PTP1B. It gives insights into the five novel hydrogen bonds essentially formed in the "closed" loop structures. Additionally, the study provides distance ranges between the atoms involved in the hydrogen bonds. This information can be used as a geometrical criterion in the characterization of conformational state of the WPD-loop especially in the molecular dynamics simulations.

Structural Studies of Geosmin Synthase, a Bifunctional Sesquiterpene Synthase with Alpha-Alpha Domain Architecture that Catalyzes a Unique Cyclization-Fragmentation Reaction Sequence

PubMed Central

Harris, Golda G.; Lombardi, Patrick M.; Pemberton, Travis A.; Matsui, Tsutomu; Weiss, Thomas M.; Cole, Kathryn E.; Köksal, Mustafa; Murphy, Frank V.; Vedula, L. Sangeetha; Chou, Wayne K.W.; Cane, David E.; Christianson, David W.

2015-01-01

Geosmin synthase from Streptomyces coelicolor (ScGS) catalyzes an unusual, metal-dependent terpenoid cyclization and fragmentation reaction sequence. Two distinct active sites are required for catalysis: the N-terminal domain catalyzes the ionization and cyclization of farnesyl diphosphate to form germacradienol and inorganic pyrophosphate (PPi), and the C-terminal domain catalyzes the protonation, cyclization, and fragmentation of germacradienol to form geosmin and acetone through a retro-Prins reaction. A unique αα domain architecture is predicted for ScGS based on amino acid sequence: each domain contains the metal-binding motifs typical of a class I terpenoid cyclase, and each domain requires Mg2+ for catalysis. Here, we report the X-ray crystal structure of the unliganded N-terminal domain of ScGS and the structure of its complex with 3 Mg2+ ions and alendronate. These structures highlight conformational changes required for active site closure and catalysis. Although neither full-length ScGS nor constructs of the C-terminal domain could be crystallized, homology models of the C-terminal domain were constructed based on ~36% sequence identity with the N-terminal domain. Small-angle X-ray scattering experiments yield low resolution molecular envelopes into which the N-terminal domain crystal structure and the C-terminal domain homology model were fit, suggesting possible αα domain architectures as frameworks for bifunctional catalysis. PMID:26598179

Resolving the Chemically Discrete Structure of Synthetic Borophene Polymorphs.

PubMed

Campbell, Gavin P; Mannix, Andrew J; Emery, Jonathan D; Lee, Tien-Lin; Guisinger, Nathan P; Hersam, Mark C; Bedzyk, Michael J

2018-05-09

Atomically thin two-dimensional (2D) materials exhibit superlative properties dictated by their intralayer atomic structure, which is typically derived from a limited number of thermodynamically stable bulk layered crystals (e.g., graphene from graphite). The growth of entirely synthetic 2D crystals, those with no corresponding bulk allotrope, would circumvent this dependence upon bulk thermodynamics and substantially expand the phase space available for structure-property engineering of 2D materials. However, it remains unclear if synthetic 2D materials can exist as structurally and chemically distinct layers anchored by van der Waals (vdW) forces, as opposed to strongly bound adlayers. Here, we show that atomically thin sheets of boron (i.e., borophene) grown on the Ag(111) surface exhibit a vdW-like structure without a corresponding bulk allotrope. Using X-ray standing wave-excited X-ray photoelectron spectroscopy, the positions of boron in multiple chemical states are resolved with sub-angström spatial resolution, revealing that the borophene forms a single planar layer that is 2.4 Å above the unreconstructed Ag surface. Moreover, our results reveal that multiple borophene phases exhibit these characteristics, denoting a unique form of polymorphism consistent with recent predictions. This observation of synthetic borophene as chemically discrete from the growth substrate suggests that it is possible to engineer a much wider variety of 2D materials than those accessible through bulk layered crystal structures.

Noncovalent Polymerization of Mesogens Crystallizes Lysozyme: Correlation between Nonamphiphilic Lyotropic Liquid Crystal Phase and Protein Crystal Formation

PubMed Central

Simon, Karen A.; Shetye, Gauri S.; Englich, Ulrich; Wu, Lei; Luk, Yan-Yeung

2011-01-01

Crystallization of proteins is important for fundamental studies and biopharmaceutical development but remains largely an empirical science. Here, we report the use of organic salts that can form a class of unusual non-amphiphilic lyotropic liquid crystals to crystallize the protein lysozyme. Certain non-amphiphilic organic molecules with fused aromatic rings and two charges can assemble into stable thread-like noncovalent polymers that may further form liquid crystal phases in water, traditionally termed chromonic liquid crystals. Using five of these mesogenic molecules as additives to induce protein crystallization, we discover that molecules that can form liquid crystal phases in water are highly effective at inducing the crystal formation of lysozyme, even at concentrations significantly lower than that required for forming liquid crystal phases. This result reveals an example of inducing protein crystallization by the molecular assembly of the additives, and is consistent with a new mechanism by which the strong hydration of an assembly process provides a gradual means to compete for the water molecules to enable solvated proteins to form crystals. PMID:21786812

Crystallography of waxes - an electron diffraction study of refined and natural products

NASA Astrophysics Data System (ADS)

Dorset, Douglas L.

1997-02-01

The crystal structure of four waxes has been investigated by electron crystallography. Two of these waxes, including a refined petroleum product (Gulfwax) and a material from lignite (montan wax), form well ordered crystals and their structure could be solved quantitatively from the observed 0022-3727/30/3/018/img1 diffraction patterns. As also found previously for simpler binary n-paraffin solid solutions, the average structure resembles that of a pure paraffin (e.g. n-0022-3727/30/3/018/img2) but with a Gaussian distribution of atomic occupancies near the chain ends to account for the statistical distribution of chain lengths within a lamella. Two other waxes from living organisms, South African bee honeycomb and the leaves of the Brazilian carnauba palm, are much less ordered, even though they share the same methylene subcell packing of the most crystalline parts of the previous materials. It appears that these waxes cannot fully separate into distinct lamellae, perhaps due to the presence of very long `tie' molecules, and are therefore `frustrated' crystal structures.

Uraniferous bitumen nodules in the Talvivaara Ni-Zn-Cu-Co deposit (Finland): influence of metamorphism on uranium mineralization in black shales

NASA Astrophysics Data System (ADS)

Lecomte, Andreï; Cathelineau, Michel; Deloule, Etienne; Brouand, Marc; Peiffert, Chantal; Loukola-Ruskeeniemi, Kirsti; Pohjolainen, Esa; Lahtinen, Hannu

2014-04-01

In the central part of the Fennoscandian Shield, the Talvivaara Ni-Zn-Cu-Co deposit, hosted by Palaeoproterozoic metamorphosed black schists, contains low uranium concentrations ranging from 10 to 30 ppm. The Talvivaara black schists were deposited 2.0-1.9 Ga ago and underwent subsequent metamorphism during the 1.9-1.79 Ga Svecofennian orogeny. Anhedral uraninite crystals rimmed by bitumen constitute the main host of uranium. U-Pb secondary ion mass spectrometry dating indicates that uraninite crystals were formed between 1,878 ± 17 and 1,871 ± 43 Ma, during peak metamorphism. Rare earth element patterns and high Th content (average 6.38 wt%) in disseminated uraninite crystals indicate that U was concentrated during high temperature metamorphism (>400 °C). The formation of bitumen rims around uraninite may be explained by two distinct scenarios: (a) a transport of U coincident with the migration of hydrocarbons or (b) post-metamorphic formation of bitumen rims, through radiolytic polymerization of gaseous hydrocarbons at the contact with uraninite.

Influence of chain topology on polymer crystallization: poly(ethylene oxide) (PEO) rings vs. linear chains.

PubMed

Zardalidis, George; Mars, Julian; Allgaier, Jürgen; Mezger, Markus; Richter, Dieter; Floudas, George

2016-10-04

The absence of entanglements, the more compact structure and the faster diffusion in melts of cyclic poly(ethylene oxide) (PEO) chains have consequences on their crystallization behavior at the lamellar and spherulitic length scales. Rings with molecular weight below the entanglement molecular weight (M < M e ), attain the equilibrium configuration composed from twice-folded chains with a lamellar periodicity that is half of the corresponding linear chains. Rings with M > M e undergo distinct step-like conformational changes to a crystalline lamellar with the equilibrium configuration. Rings melt from this configuration in the absence of crystal thickening in sharp contrast to linear chains. In general, rings more easily attain their extended equilibrium configuration due to strained segments and the absence of entanglements. In addition, rings have a higher equilibrium melting temperature. At the level of the spherulitic superstructure, growth rates are much faster for rings reflecting the faster diffusion and more compact structure. With respect to the segmental dynamics in their semi-crystalline state, ring PEOs with a steepness index of ∼34 form some of the "strongest" glasses.

The Crystal Structure of Coxsackievirus A21 and Its Interaction with ICAM-1

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

Xiao, Chuan; Bator-Kelly, Carol M.; Rieder, Elizabeth

2010-11-30

CVA21 and polioviruses both belong to the Enterovirus genus in the family of Picornaviridae, whereas rhinoviruses form a distinct picornavirus genus. Nevertheless, CVA21 and the major group of human rhinoviruses recognize intercellular adhesion molecule-1 (ICAM-1) as their cellular receptor, whereas polioviruses use poliovirus receptor. The crystal structure of CVA21 has been determined to 3.2 {angstrom} resolution. Its structure has greater similarity to poliovirus structures than to other known picornavirus structures. Cryo-electron microscopy (cryo-EM) was used to determine an 8.0 {angstrom} resolution structure of CVA21 complexed with an ICAM-1 variant, ICAM-1{sup Kilifi}. The cryo-EM map was fitted with the crystal structuresmore » of ICAM-1 and CVA21. Significant differences in the structure of CVA21 with respect to the poliovirus structures account for the inability of ICAM-1 to bind polioviruses. The interface between CVA21 and ICAM-1 has shape and electrostatic complementarity with many residues being conserved among those CVAs that bind ICAM-1.« less

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

Wang, Lili; Brawand, Nicholas P.; Vörös, Márton

Organolead halide perovskites convert optical excitations to charge carriers with remarkable efficiency in optoelectronic devices. Previous research predominantly documents dynamics in perovskite thin films; however, extensive disorder in this platform may obscure the observed carrier dynamics. Here, carrier dynamics in perovskite single-domain single crystals is examined by performing transient absorption spectroscopy in a transmissive geometry. Two distinct sets of carrier populations that coexist at the same radiation fluence, but display different decay dynamics, are observed: one dominated by second-order recombination and the other by third-order recombination. Based on ab initio simulations, this observation is found to be most consistent withmore » the hypothesis that free carriers and localized carriers coexist due to polaron formation. The calculations suggest that polarons will form in both CH3NH3PbBr3 and CH3NH3PbI3 crystals, but that they are more pronounced in CH3NH3PbBr3. Single-crystal CH3NH3PbBr3 could represent the key to understanding the impact of polarons on the transport properties of perovskite optoelectronic devices.« less

Anisotropic antiferromagnetic order in the spin-orbit coupled trigonal-lattice Ca2Sr2IrO6

NASA Astrophysics Data System (ADS)

Sheng, Jieming; Ye, Feng; Hoffmann, Christina; Cooper, Valentino R.; Okamoto, Satoshi; Terzic, Jasminka; Zheng, Hao; Zhao, Hengdi; Cao, G.

2018-06-01

We used single-crystal x-ray and neutron diffraction to investigate the crystal and magnetic structures of trigonal lattice iridate Ca2Sr2IrO6 . The crystal structure is determined to be R 3 ¯ with two distinct Ir sites. The system exhibits long-range antiferromagnetic order below TN=13.1 K. The magnetic wave vector is identified as (0,0.5,1) with ferromagnetic coupling along the a axis and antiferromagnetic correlation along the b axis. Spins align dominantly within the basal plane along the [1,2,0] direction and tilt 34∘ toward the c axis. The ordered moment is 0.66(3) μB/Ir, larger than other iridates where iridium ions form corner- or edge-sharing IrO6 octahedral networks. The tilting angle is reduced to ≈19∘ when a magnetic field of 4.9 T is applied along the c axis. Density functional theory calculations confirm that the experimentally determined magnetic configuration is the most probable ground state with an insulating gap ˜0.5 eV.

Liquid Crystal Enabled Early Stage Detection of Beta Amyloid Formation on Lipid Monolayers

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

Sadati, Monirosadat; Apik, Aslin Izmitli; Armas-Perez, Julio C.

2015-09-09

Liquid crystals (LCs) can serve as sensitive reporters of interfacial events, and this property has been used for sensing of synthetic or biological toxins. Here it is demonstrated that LCs can distinguish distinct molecular motifs and exhibit a specific response to beta-sheet structures. That property is used to detect the formation of highly toxic protofibrils involved in neurodegenerative diseases, where it is crucial to develop methods that probe the early-stage aggregation of amyloidogenic peptides in the vicinity of biological membranes. In the proposed method, the amyloid fibrils formed at the lipid-decorated LC interface can change the orientation of LCs andmore » form elongated and branched structures that are amplified by the mesogenic medium; however, nonamyloidogenic peptides form ellipsoidal domains of tilted LCs. Moreover, a theoretical and computational analysis is used to reveal the underlying structure of the LC, thereby providing a detailed molecular-level view of the interactions and mechanisms responsible for such motifs. The corresponding signatures can be detected at nanomolar concentrations of peptide by polarized light microscopy and much earlier than the ones that can be identified by fluorescence-based techniques. As such, it offers the potential for early diagnoses of neurodegenerative diseases and for facile testing of inhibitors of amyloid formation.« less

Do All X-ray Structures of Protein-Ligand Complexes Represent Functional States? EPOR, a Case Study.

PubMed

Corbett, Michael S P; Mark, Alan E; Poger, David

2017-02-28

Based on differences between the x-ray crystal structures of ligand-bound and unbound forms, the activation of the erythropoietin receptor (EPOR) was initially proposed to involve a cross-action scissorlike motion. However, the validity of the motions involved in the scissorlike model has been recently challenged. Here, atomistic molecular dynamics simulations are used to examine the structure of the extracellular domain of the EPOR dimer in the presence and absence of erythropoietin and a series of agonistic or antagonistic mimetic peptides free in solution. The simulations suggest that in the absence of crystal packing effects, the EPOR chains in the different dimers adopt very similar conformations with no clear distinction between the agonist and antagonist-bound complexes. This questions whether the available x-ray crystal structures of EPOR truly represent active or inactive conformations. The study demonstrates the difficulty in using such structures to infer a mechanism of action, especially in the case of membrane receptors where just part of the structure has been considered in addition to potential confounding effects that arise from the comparison of structures in a crystal as opposed to a membrane environment. The work highlights the danger of assigning functional significance to small differences between structures of proteins bound to different ligands in a crystal environment without consideration of the effects of the crystal lattice and thermal motion. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

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

Self-organisation of semi-flexible rod-like particles

NASA Astrophysics Data System (ADS)

de Braaf, Bart; Oshima Menegon, Mariana; Paquay, Stefan; van der Schoot, Paul

2017-12-01

We report on a comprehensive computer simulation study of the liquid-crystal phase behaviour of purely repulsive, semi-flexible rod-like particles. For the four aspect ratios we consider, the particles form five distinct phases depending on their packing fraction and bending flexibility: the isotropic, nematic, smectic A, smectic B, and crystal phase. Upon increasing the particle bending flexibility, the various phase transitions shift to larger packing fractions. Increasing the aspect ratio achieves the opposite effect. We find two different ways in which the layer thickness of the particles in the smectic A phase may respond to an increase in concentration. The layer thickness may either decrease or increase depending on the aspect ratio and flexibility. For the smectic B and the crystalline phases, increasing the concentration always decreases the layer thickness. Finally, we find that the layer spacing jumps to a larger value on transitioning from the smectic A phase to the smectic B phase.

Crystal structure of a designed, thermostable, heterotrimeric coiled coil.

PubMed Central

Nautiyal, S.; Alber, T.

1999-01-01

Electrostatic interactions are often critical for determining the specificity of protein-protein complexes. To study the role of electrostatic interactions for assembly of helical bundles, we previously designed a thermostable, heterotrimeric coiled coil, ABC, in which charged residues were employed to drive preferential association of three distinct, 34-residue helices. To investigate the basis for heterotrimer specificity, we have used multiwavelength anomalous diffraction (MAD) analysis to determine the 1.8 A resolution crystal structure of ABC. The structure shows that ABC forms a heterotrimeric coiled coil with the intended arrangement of parallel chains. Over half of the ion pairs engineered to restrict helix associations were apparent in the experimental electron density map. As seen in other trimeric coiled coils, ABC displays acute knobs-into-holes packing and a buried anion coordinated by core polar amino acids. These interactions validate the design strategy and illustrate how packing and polar contacts determine structural uniqueness. PMID:10210186

A Supramolecular Ice Growth Inhibitor.

PubMed

Drori, Ran; Li, Chao; Hu, Chunhua; Raiteri, Paolo; Rohl, Andrew L; Ward, Michael D; Kahr, Bart

2016-10-12

Safranine O, a synthetic dye, was found to inhibit growth of ice at millimolar concentrations with an activity comparable to that of highly evolved antifreeze glycoproteins. Safranine inhibits growth of ice crystals along the crystallographic a-axis, resulting in bipyramidal needles extended along the <0001> directions as well as and plane-specific thermal hysteresis (TH) activity. The interaction of safranine with ice is reversible, distinct from the previously reported behavior of antifreeze proteins. Spectroscopy and molecular dynamics indicate that safranine forms aggregates in aqueous solution at micromolar concentrations. Metadynamics simulations and aggregation theory suggested that as many as 30 safranine molecules were preorganized in stacks at the concentrations where ice growth inhibition was observed. The simulations and single-crystal X-ray structure of safranine revealed regularly spaced amino and methyl substituents in the aggregates, akin to the ice-binding site of antifreeze proteins. Collectively, these observations suggest an unusual link between supramolecular assemblies of small molecules and functional proteins.

The N-terminal domain of GluR6-subtype glutamate receptor ion channels

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

Kumar, Janesh; Schuck, Peter; Jin, Rongsheng

2009-09-25

The amino-terminal domain (ATD) of glutamate receptor ion channels, which controls their selective assembly into AMPA, kainate and NMDA receptor subtypes, is also the site of action of NMDA receptor allosteric modulators. Here we report the crystal structure of the ATD from the kainate receptor GluR6. The ATD forms dimers in solution at micromolar protein concentrations and crystallizes as a dimer. Unexpectedly, each subunit adopts an intermediate extent of domain closure compared to the apo and ligand-bound complexes of LIVBP and G protein-coupled glutamate receptors (mGluRs), and the dimer assembly has a markedly different conformation from that found in mGluRs.more » This conformation is stabilized by contacts between large hydrophobic patches in the R2 domain that are absent in NMDA receptors, suggesting that the ATDs of individual glutamate receptor ion channels have evolved into functionally distinct families.« less

Light rare earth element systematics as a tool for investigating the petrogenesis of phoscorite-carbonatite associations, as exemplified by the Phalaborwa Complex, South Africa

NASA Astrophysics Data System (ADS)

Milani, Lorenzo; Bolhar, Robert; Frei, Dirk; Harlov, Daniel E.; Samuel, Vinod O.

2017-12-01

In-situ trace element analyses of fluorapatite, calcite, dolomite, olivine, and phlogopite have been undertaken on representative phoscorite and carbonatite rocks of the Palaeoproterozoic Phalaborwa Complex. Textural and compositional characterization reveals uniformity of fluorapatite and calcite among most of the intrusions, and seems to favor a common genetic origin for the phoscorite-carbonatite association. Representing major repositories for rare earth elements (REE), fluorapatite and calcite exhibit tightly correlated light REE (LREE) abundances, suggesting that partitioning of LREE into these rock forming minerals was principally controlled by simple igneous differentiation. However, light rare earth element distribution in apatite and calcite cannot be adequately explained by equilibrium and fractional crystallization and instead favors a complex crystallization history involving mixing of compositionally distinct magma batches, in agreement with previously reported mineral isotope variability that requires open-system behaviour.

Structure of the measles virus hemagglutinin bound to its cellular receptor SLAM.

PubMed

Hashiguchi, Takao; Ose, Toyoyuki; Kubota, Marie; Maita, Nobuo; Kamishikiryo, Jun; Maenaka, Katsumi; Yanagi, Yusuke

2011-02-01

Measles virus, a major cause of childhood morbidity and mortality worldwide, predominantly infects immune cells using signaling lymphocyte activation molecule (SLAM) as a cellular receptor. Here we present crystal structures of measles virus hemagglutinin (MV-H), the receptor-binding glycoprotein, in complex with SLAM. The MV-H head domain binds to a β-sheet of the membrane-distal ectodomain of SLAM using the side of its β-propeller fold. This is distinct from attachment proteins of other paramyxoviruses that bind receptors using the top of their β-propeller. The structure provides templates for antiviral drug design, an explanation for the effectiveness of the measles virus vaccine, and a model of the homophilic SLAM-SLAM interaction involved in immune modulations. Notably, the crystal structures obtained show two forms of the MV-H-SLAM tetrameric assembly (dimer of dimers), which may have implications for the mechanism of fusion triggering.

Preliminary crystallographic studies of four crystal forms of serum albumin

NASA Technical Reports Server (NTRS)

Carter, D. C.; Chang, B.; Ho, J. X.; Keeling, K.; Krishnasami, Z.

1994-01-01

Several crystal forms of serum albumin suitable for three-dimensional structure determination have been grown. These forms include crystals of recombinant and wild-type human serum albumin, baboon serum albumin, and canine serum albumin. The intrinsic limits of X-ray diffraction for these crystals are in the range 0.28-0.22 nm. Two of the crystal forms produced from human and canine albumin include incorporated long-chain fatty acids. Molecular replacement experiments have been successfully conducted on each crystal form using the previously determined atomic coordinates of human serum albumin illustrating the conserved tertiary structure.

Crystal Cargo Characterization: Unravelling Granite Petrogenesis through Combined MicroXRF Imaging and In-situ Analyses.

NASA Astrophysics Data System (ADS)

McLeod, C. L.; Brown, K.; Brydon, R.; Haley, M.; Hill, T.; Shaulis, B.; Tronnes, R. G.

2017-12-01

Advances in the capabilities of microanalysis over the past several decades have promoted a redefinition of traditional petrological terminology. This has allowed a more accurate evaluation of a samples petrogenetic history. For example, the term "phenocryst", specifically describes crystals that grew from the liquid that solidified into the groundmass. Evolving from this idea is the term xenocryst, referring to crystals that did not originate in the magma but were gathered by it, and antecrysts, which crystallized from a progenitor of the magma that solidified into the groundmass. Through identification of a magmas different, and distinct, crystal populations, the petrogenetic history of a magmatic rock can therefore be unraveled. This approach has been widely applied to terrestrial volcanic systems throughout the past several decades. This study presents results from a combined microimaging and in-situ microanalytical investigation of granitic magmas crystal cargoes in order to unravel how granitic batholiths are constructed. 27 lithological units from two granite batholiths in the Oslo Rift, Norway form the basis of this investigation. Micro X-Ray Fluorescence (µXRF) mapping of major elements and selected trace elements is used in order to chemically map each granitic unit, identify any characteristic growth zoning, and compare the crystal cargoes of the different units. Major and trace elemental abundances of the major phases (feldspars, biotite, amphibole) and minor phases (apatite and titanite) are to be quantified through electron microprobe analysis (EPMA) and laser ablation inductively coupled plasma mass spectrometry (LA-ICPMS) respectively. Through chemically fingerprinting the crystal cargoes of these Oslo Rift granitic magmas, the open vs. closed nature of granitic, intrusive, magmatic systems will be investigated. Within the context of the Oslo Rift, this study also offers an opportunity to evaluate the processes inherent to granitoid magmatism during continental rifting.

Crystallization and X-ray diffraction of crystals formed in water-plasticized amorphous lactose.

PubMed

Jouppila, K; Kansikas, J; Roos, Y H

1998-01-01

Effects of storage time and relative humidity on crystallization and crystal forms produced from amorphous lactose were investigated. Crystallization was observed from time-dependent loss of sorbed water and increasing intensities of peaks in X-ray diffraction patterns. The rate of crystallization increased with increasing storage relative humidity. Lactose crystallized mainly as alpha-lactose monohydrate and anhydrous crystals with alpha- and beta-lactose in a molar ratio of 5:3. The results suggested that the crystal form was defined by the early nucleation process. The crystallization data are important in modeling of crystallization phenomena and prediction of stability of lactose-containing food and pharmaceutical materials.

Tautomerism and isomerism in some antitrichinellosis active benzimidazoles: Morphological study in polarized light, quantum chemical computations

NASA Astrophysics Data System (ADS)

Anichina, Kameliya; Mavrova, Anelia; Yancheva, Denitsa; Tsenov, Jordan; Dimitrov, Rasho

2017-12-01

The morphology of the crystal structure of some antitrichinellosis active benzimidazole derivatives including (1H-benzimidazol-2-ylthio)acetic acids, [1,3]thiazolo[3,2-a]benzimidazol-3(2H)-ones, 1H-benzimidazol-2-ylthioacetylpiperazines and starting 2-mercapto benzimidazoles, was studied by the use of Polarized Light Microscopy (PLM). Characterization of the crystal phase was complimented by Differential scanning calorimetry analysis (DSC) and spectroscopic data. DFT computations were performed in order to investigate the prototropic tautomerism and the geometry of the molecule of the synthesized compounds. One distinct type of crystal structure for each one of 5 or 6-methyl-(1H-benzimidazol-2-ylthio)acetic acid 6 was observed by PLM - dendritic and needle-shaped formations. Compound 14, containing a methyl substituent in the benzimidazole ring crystallized also into two phases; while for the unsubstituted compound 13 a separation of phases does not take place. The influence of the both solvents - chloroform and ethanol on the phase separation and the formation of the crystalline structure of compound 14 was investigated. The morphological study showed that the cyclization of 6 in the presence of acetic anhydride in pyridine medium led to a mixture of 6-methyl-[1,3]tiazolo[3,2-a]benzimidazol-3(2H)-one (10a) and 7-methyl-[1,3]thiazolo[3,2-a]-benzimidazole-3(2H)-one (10b), which crystallized in the form of fibrils and spherulites respectively. It was found that a difference in the crystal structures of substituted and unsubstituted benzimidazol-2-thiones, respectively benzimidazol-2-thiol derivatives exists, which may be due not only to the thiol-thione tautomerism but to the prototropic properties of the hydrogen atom in first position of the ring. The calculation results indicated that the thione form is more stable than the thiol tautomer by 51-55 kJ mol-1. But at the same time ΔG for the two thiol tautomers is below 0.5 kJ mol-1. In solid phase the 5(6)-substituted-1H-benzimidazol-2-thiols crystallized in two different crystal structures while the unsubstituted 1H-benzimidazol-2-thiol possess one type of crystal structure.

Testing the Origins of Basalt Fragments fro Apollo 16

NASA Technical Reports Server (NTRS)

Donohue, P. H.; Stevens, R. E.; Neal, C. R.; Zeigler, R. A.

2013-01-01

Several 2-4 mm regolith fragments of basalt from the Apollo 16 site were recently described by [1]. These included a high-Ti vitrophyric basalts (60603,10-16) and one very-low-titanium (VLT) crystalline basalt (65703,9-13). As Apollo 16 was the only highlands sample return mission distant from the maria, identification of basaltic samples at the site indicates input from remote sites via impact processes [1]. However, distinguishing between impact melt and pristine basalt can be notoriously difficult and requires significant sample material [2-6]. The crystal stratigraphy method utilizes essentially non-destructive methods to make these distinctions [7,8]. Crystal stratigraphy combines quantitative petrography in the form of crystal size distributions (CSDs) coupled with mineral geochemistry to reveal the petrogenetic history of samples. The classic CSD plot of crystal size versus population density can reveal insights on growth/cooling rates, residence times, and magma history which in turn can be used to evaluate basaltic vs impact melt origin [7-9]. Electron microprobe (EMP) and laser ablation (LA)-ICP-MS analyses of mineral phases complement textural investigations. Trace element variations document subtle changes occurring during the formation of the samples, and are key in the interpretation and preservation of this rare lunar sample collection.

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

J Cai; B Hsiao; R Gross

Poly({omega}-pentadecalactone) (PPDL), a model polymer in the poly({omega}-hydroxyl fatty acids) family, is a new biopolymer with monomer synthesized by yeast-catalyzed {omega}-hydroxylation of fatty acids. In this study, deformation-induced structural changes in two PPDL samples with different molecular weights were studied by in situ wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) techniques. The high molecular weight PPDL (PPDL-high) sample exhibited notable strain hardening, while the low molecular weight PPDL (PPDL-low) sample did not. The behavior can be explained by the entanglement density concept. The evolution of crystallinity (from WAXD) as a function of strain could be divided into fourmore » distinct regions, but their respective mechanisms differ slightly in each sample. During stretching, a mesomorphic phase formed in both samples, bridging between the amorphous and strain-induced crystal phases. The SAXS data verified the effect of molecular weight (or the entanglement density) on the deformation-induced structure of PPDL. The parameters of chain orientation factor (f) calculated from the orthorhombic crystal cell as well as the nonorthorhombic crystal cell proposed by Wilchinsky were used to follow the orientation process during stretching of PPDLs. It was found that the different molecular entanglement network (i.e., PPDL-low versus PPDL-high) led to different crystal orientation behavior, especially in the low strain range.« less

Structural basis for antibody recognition in the receptor-binding domains of toxins A and B from Clostridium difficile.

PubMed

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N; Klassen, John S; Ng, Kenneth K S

2014-01-24

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents.

Structural Basis for Antibody Recognition in the Receptor-binding Domains of Toxins A and B from Clostridium difficile*

PubMed Central

Murase, Tomohiko; Eugenio, Luiz; Schorr, Melissa; Hussack, Greg; Tanha, Jamshid; Kitova, Elena N.; Klassen, John S.; Ng, Kenneth K. S.

2014-01-01

Clostridium difficile infection is a serious and highly prevalent nosocomial disease in which the two large, Rho-glucosylating toxins TcdA and TcdB are the main virulence factors. We report for the first time crystal structures revealing how neutralizing and non-neutralizing single-domain antibodies (sdAbs) recognize the receptor-binding domains (RBDs) of TcdA and TcdB. Surprisingly, the complexes formed by two neutralizing antibodies recognizing TcdA do not show direct interference with the previously identified carbohydrate-binding sites, suggesting that neutralization of toxin activity may be mediated by mechanisms distinct from steric blockage of receptor binding. A camelid sdAb complex also reveals the molecular structure of the TcdB RBD for the first time, facilitating the crystallization of a strongly negatively charged protein fragment that has resisted previous attempts at crystallization and structure determination. Electrospray ionization mass spectrometry measurements confirm the stoichiometries of sdAbs observed in the crystal structures. These studies indicate how key epitopes in the RBDs from TcdA and TcdB are recognized by sdAbs, providing molecular insights into toxin structure and function and providing for the first time a basis for the design of highly specific toxin-specific therapeutic and diagnostic agents. PMID:24311789

Live Imaging and Heating of Confined RDX and HMX Crystals Until Reaction Using the Dual Windowed Test Vehicle

NASA Astrophysics Data System (ADS)

Stennett, Chris; Cook, Malcolm; Cheese, Philip; Wood, Andrew; White, Nathan; Reeves, Tom

2017-06-01

A high fidelity live camera feed recording RDX and HMX crystals, measuring 1 mm thick and 15 mm in diameter, decomposing while heavily confined and subjected to various heating rates until a reaction occurs has been analysed. Video records reveal unexpected behaviour in both RDX and HMX crystals prior to ignition. Three distinct stages can be observed: phase changes and melting; slow, flameless decomposition with production of gaseous intermediates; and finally burning with a luminous flame of the gaseous intermediates. Tests with pure RDX and HMX crystals reveal pockets of gaseous materials forming above the molten and bubbling nitramine, before a flame appears at one side then burns inwards in an apparent conductive manner at a few metres per second. This causes the remaining bubbling nitramine to be compressed. Violent reaction appears to occur via a bubble collapse mechanism. The violence of this event is dependent on the loss of confinement; if it fails in the first or second phase the reaction is less violent than if the third phase is reached. The third phase burning reaction has associated pressure waves, which is presumed oscillation of the flame front, leading to wave interactions, pressure spikes and ultimately a violent reaction.

Programming Hierarchical Self-Assembly of Patchy Particles into Colloidal Crystals via Colloidal Molecules.

PubMed

Morphew, Daniel; Shaw, James; Avins, Christopher; Chakrabarti, Dwaipayan

2018-03-27

Colloidal self-assembly is a promising bottom-up route to a wide variety of three-dimensional structures, from clusters to crystals. Programming hierarchical self-assembly of colloidal building blocks, which can give rise to structures ordered at multiple levels to rival biological complexity, poses a multiscale design problem. Here we explore a generic design principle that exploits a hierarchy of interaction strengths and employ this design principle in computer simulations to demonstrate the hierarchical self-assembly of triblock patchy colloidal particles into two distinct colloidal crystals. We obtain cubic diamond and body-centered cubic crystals via distinct clusters of uniform size and shape, namely, tetrahedra and octahedra, respectively. Such a conceptual design framework has the potential to reliably encode hierarchical self-assembly of colloidal particles into a high level of sophistication. Moreover, the design framework underpins a bottom-up route to cubic diamond colloidal crystals, which have remained elusive despite being much sought after for their attractive photonic applications.

In situ major and trace element analysis of amphiboles in quartz monzodiorite porphyry from the Tonglvshan Cu-Fe (Au) deposit, Hubei Province, China: insights into magma evolution and related mineralization

NASA Astrophysics Data System (ADS)

Duan, Deng-Fei; Jiang, Shao-Yong

2017-05-01

The Tonglvshan deposit is the largest Cu-Fe (Au) skarn deposit in the Edong district, which is located in the westernmost part of the Middle and Lower Yangtze River metallogenic belt, China. In this study, we performed a detailed in situ analysis of major and trace elements in amphiboles from the ore-related Tonglvshan quartz monzodiorite porphyry using electron microprobe (EMPA) analysis and laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Two distinct populations of amphiboles, which can be distinguished by their aluminum content, are found in the quartz monzodiorite porphyry. The low-aluminum (Low-Al) amphiboles are subhedral or anhedral and formed at 46.3-73.5 MPa and 713-763 °C. In contrast, the high-aluminum (High-Al) amphiboles are euhedral and formed at 88-165 MPa and 778-854 °C. Some euhedral amphiboles are partially or completely replaced by Low-Al amphibole. The compositions of parental melts in equilibrium with the High-Al amphibole ( Melt 1) and Low-Al amphibole ( Melt 2) were computed by applying solid/liquid partition coefficients. This modeling shows that magma in equilibrium with High-Al amphibole ( Melt 1) underwent 40% fractional crystallization of amphibole, plagioclase and apatite at a depth of 5 km to evolve to magma in equilibrium with Low-Al amphibole ( Melt 2). Copper enrichment occurred in the magma after undergoing fractional crystallization. The magma had a high oxygen fugacity, increasing from NNO + 1 ( Melt 1) through NNO + 2 to HM ( Melt 2), which could have prevented the loss of Cu (and possibly Au) to sulfide minerals during crystallization. Finally, the evolved magma intruded to shallower depths, where it presumably exsolved aqueous ore-forming fluids. Therefore, the large Cu-Fe-Au reserves of the Tonglvshan deposit can likely be attributed to a combination of controlling factors, including high oxygen fugacity, fractional crystallization, fluid exsolution, and a shallow emplacement depth.

Thermal oxidation of single crystal aluminum antimonide and materials having the same

DOEpatents

Sherohman, John William; Yee, Jick Hong; Coombs, III, Arthur William; Wu, Kuang Jen J.

2012-12-25

In one embodiment, a method for forming a non-conductive crystalline oxide layer on an AlSb crystal includes heat treating an AlSb crystal in a partial vacuum atmosphere at a temperature conducive for air adsorbed molecules to desorb, surface molecule groups to decompose, and elemental Sb to evaporate from a surface of the AlSb crystal and exposing the AlSb crystal to an atmosphere comprising oxygen to form a crystalline oxide layer on the surface of the AlSb crystal. In another embodiment, a method for forming a non-conductive crystalline oxide layer on an AlSb crystal includes heat treating an AlSb crystal in a non-oxidizing atmosphere at a temperature conducive for decomposition of an amorphous oxidized surface layer and evaporation of elemental Sb from the AlSb crystal surface and forming stable oxides of Al and Sb from residual surface oxygen to form a crystalline oxide layer on the surface of the AlSb crystal.

Structure of polyhydroxyalkanoate (PHA) synthase PhaC from Chromobacterium sp. USM2, producing biodegradable plastics.

PubMed

Chek, Min Fey; Kim, Sun-Yong; Mori, Tomoyuki; Arsad, Hasni; Samian, Mohammed Razip; Sudesh, Kumar; Hakoshima, Toshio

2017-07-13

Polyhydroxyalkanoate (PHA) is a promising candidate for use as an alternative bioplastic to replace petroleum-based plastics. Our understanding of PHA synthase PhaC is poor due to the paucity of available three-dimensional structural information. Here we present a high-resolution crystal structure of the catalytic domain of PhaC from Chromobacterium sp. USM2, PhaC Cs -CAT. The structure shows that PhaC Cs -CAT forms an α/β hydrolase fold comprising α/β core and CAP subdomains. The active site containing Cys291, Asp447 and His477 is located at the bottom of the cavity, which is filled with water molecules and is covered by the partly disordered CAP subdomain. We designated our structure as the closed form, which is distinct from the recently reported catalytic domain from Cupriavidus necator (PhaC Cn -CAT). Structural comparison showed PhaC Cn -CAT adopting a partially open form maintaining a narrow substrate access channel to the active site, but no product egress. PhaC Cs -CAT forms a face-to-face dimer mediated by the CAP subdomains. This arrangement of the dimer is also distinct from that of the PhaC Cn -CAT dimer. These findings suggest that the CAP subdomain should undergo a conformational change during catalytic activity that involves rearrangement of the dimer to facilitate substrate entry and product formation and egress from the active site.

Effect of local structures on crystallization in deeply undercooled metallic glass-forming liquids

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

Jiang, S. Q.; Li, M. Z., E-mail: maozhili@ruc.edu.cn; Wu, Z. W.

2016-04-21

The crystallization mechanism in deeply undercooled ZrCu metallic glass-forming liquids was investigated via molecular dynamics simulations. It was found that the crystallization process is mainly controlled by the growth of crystal nuclei formed by the BCC-like atomic clusters, consistent with experimental speculations. The crystallization rate is found to relate to the number of growing crystal nuclei in the crystallization process. The crystallization rate in systems with more crystal nuclei is significantly hindered by the larger surface fractions of crystal nuclei and their different crystalline orientations. It is further revealed that in the crystallization in deeply undercooled regions, the BCC-like crystalmore » nuclei are formed from the inside of the precursors formed by the FCC-like atomic clusters, and growing at the expense of the precursors. Meanwhile, the precursors are expanding at the expense of the outside atomic clusters. This process is consistent with the so-called Ostwald step rule. The atomic structures of metallic glasses are found to have significant impact on the subsequent crystallization process. In the Zr{sub 85}Cu{sub 15} system, the stronger spatial correlation of Cu atoms could hinder the crystallization processes in deeply undercooled regions.« less

An Investigation into the Polymorphism and Crystallization of Levetiracetam and the Stability of its Solid Form.

PubMed

Xu, Kailin; Xiong, Xinnuo; Guo, Liuqi; Wang, Lili; Li, Shanshan; Tang, Peixiao; Yan, Jin; Wu, Di; Li, Hui

2015-12-01

Levetiracetam (LEV) crystals were prepared using different solvents at different temperatures. The LEV crystals were systematically characterized by X-ray powder diffraction (XRPD) and morphological analysis. The results indicated that many kinds of crystal habits exist in a solid form of LEV. To investigate the effects of LEV concentration, crystallization temperature, and crystallization type on crystallization and solid phase transformation of LEV, multiple methods were performed for LEV aqueous solution to determine if a new solid form exists in solid-state LEV. However, XRPD data demonstrate that the LEV solid forms possess same spatial arrangements that are similar to the original solid form. This result indicates that the LEV concentration, crystallization temperature, and crystallization type in aqueous solution have no influence on the crystallization and solid phase transformation of LEV. Moreover, crystallization by sublimation, melt cooling, and quench cooling, as well as mechanical effect, did not result in the formation of new LEV solid state. During melt cooling, the transformation of solid form LEV is a direct process from melting amorphous phase to the original LEV crystal phase, and the conversion rate is very quick. In addition, stability investigation manifested that LEV solid state is very stable under various conditions. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Metallic atomically-thin layered silicon epitaxially grown on silicene/ZrB 2

DOE PAGES

Gill, Tobias G.; Fleurence, Antoine; Warner, Ben; ...

2017-02-17

We observe a new two-dimensional (2D) silicon crystal, using low energy electron diffraction (LEED) and scanning tunnelling microscopy (STM) and it's formed by depositing additional Si atoms onto spontaneously-formed epitaxial silicene on a ZrB 2 thin film. From scanning tunnelling spectroscopy (STS) studies, we find that this atomically-thin layered silicon has distinctly different electronic properties. Angle resolved photoelectron spectroscopy (ARPES) reveals that, in sharp contrast to epitaxial silicene, the layered silicon exhibits significantly enhanced density of states at the Fermi level resulting from newly formed metallic bands. Furthermore, the 2D growth of this material could allow for direct contacting tomore » the silicene surface and demonstrates the dramatic changes in electronic structure that can occur by the addition of even a single monolayer amount of material in 2D systems.« less

Discrete dipole approximation models of chrystalline forsterite: Applications to cometary crystalline silicates

NASA Astrophysics Data System (ADS)

Lindsay, Sean Stephen

The shape, size, and composition of crystalline silicates observed in comet comae and external proto-planetary disks are indicative of the formation and evolution of the dust grains during the processes of planetary formation. In this dissertation, I present the 3 -- 40 mum absorption efficiencies( Qabs) of irregularly shaped forsterite crystals computed with the discrete dipole approximation (DDA) code DDSCAT developed by Draine and Flatau and run on the NASA Advanced Supercomputing facility Pleiades. An investigation of grain shapes ranging from spheroidal to irregular indicate that the strong spectral features from forsterite are sensitive to grain shape and are potentially degenerate with the effects of crystal solid state composition (Mg-content). The 10, 11, 18, 23, and 33.5 mum features are found to be the most crystal shape sensitive and should be avoided in determining Mg-content. The distinct spectral features for the three shape classes are connected with crystal formation environment using a condensation experiment by (Kobatake et al., 2008). The condensation experiment demonstrates that condensed forsterite crystal shapes are dependent on the condensation environmental temperature. I generate DDSCAT target analog shapes to the condensed crystal shapes. These analog shapes are represented by the three shape classes: 1) equant, 2) a, c-columns, and 3) b-shortened platelets. Each of these shape classes exhibit distinct spectral features that can be used to interpret grain shape characteristics from 8 --- 40 mum spectroscopy of astronomical objects containing crystalline silicates. Synthetic spectral energy distributions (SEDs) of the coma of Hale-Bopp at rh = 2.8 AU are generated by thermally modeling the flux contributions of 5 mineral species present in comets. The synthetic SEDs are constrained using a chi2- minimization technique. The mineral species are amorphous carbon, amorphous pyroxene, amorphous olivine, crystalline enstatite, and crystalline forsterite. Using the DDSCAT computed absorption efficiencies for a large variety of forsterite crystal shapes, which are computed for 66 grain sizes between 0.1 -- 5.0 mum, the flux contribution of irregularly shaped forsterite is computed. The forsterite flux contribution is then summed with the amorphous and crystalline enstatite contributions to generate the total synthetic SED. The DDSCAT forsterite grain shape synthetic SEDs reveal that the crystalline silicates in the coma of Hale-Bopp are irregular in shape with two distinct shape characteristics related to specific formation mechanisms: 1) equant grains with sharp ( ≲ 90°) angles between the faces, edges, and vertices that formed as high temperature condensates in the inner 1 -- 3 AU radial region of the Solar System's protoplanetary disk; and 2) c-shortened platelet shapes that likely formed from collisional processing of the crystals. The 8 -- 40 mum silicate spectral features of Hale-Bopp's coma are compared to the silicate spectral features of the comae of 17P/Holmes during 2007 outburst and 9P/Tempel 1 during the Deep Impact experiment to show that the silicate features with crystalline resonances are remarkably similar. The similarity in silicate spectral features suggests that the grain populations in the comae of these comets are similar in shape, size, and compositon. However, Hale-Bopp is a nearly isotropic comet (NIC) that dynamically came from the Oort cloud, and 17P and 9P are ecliptic comets (ECs) that dynamically came from the Scattered Disk. The different dynamical source regions yet similar silicate (amorphous and crystalline) grain populations suggest that ECs and NICs innately have similar grains and that the typically weaker silicate features of ECs are an effect of the surface grains becoming compacted with numerous perihelion passages. Hence, the differences in silicate between ECs and NICs are the result of grain structure and not grain composition. (Abstract shortened by UMI.)

Influence of pH and method of crystallization on the solid physical form of indomethacin.

PubMed

Dubbini, Alessandra; Censi, Roberta; Martena, Valentina; Hoti, Ela; Ricciutelli, Massimo; Malaj, Ledjan; Di Martino, Piera

2014-10-01

The purpose of this study was to investigate the effect of pH and method of crystallization on the solid physical form of indomethacin (IDM). IDM, a non steroidal anti-inflammatory drug poorly soluble in water, underwent two different crystallization methods: crystallization by solvent evaporation under reduced pressure at 50.0°C (method A), and crystallization by cooling of solution from 50.0 to 5.0°C (method B). In both cases, several aqueous ethanolic solutions of IDM of different pHs were prepared. pHs were adjusted by adding acidic solutions (HCl 2M) or alkali (NaOH or NH4OH 2M) to an aqueous ethanolic solution of IDM. Thus, several batches were recovered after crystallization. The chemical stability of IDM was verified through (1)H NMR and mass spectroscopy (FIA-ESI-MS), that revealed that IDM degraded in strong alkali media (pH ≥ 12). Crystals obtained under different crystallization conditions at pHs of 1.0, 4.5, 7.0, 8.0, 10.0 and chemically stable were thus characterized for crystal habit by scanning electron microscopy, for thermal behaviour by differential scanning calorimetry, and thermogravimetry, and for solid state by X-ray powder diffractometry. Under the Method A, IDM always crystallized into pure metastable alpha form when solutions were acidified or alkalized respectively with HCl and NH4OH. On the contrary, in presence of NaOH, IDM crystallized under a mixture of alpha and sodium trihydrate form, because the presence of the sodium counter ion orientates the crystallization towards the formation of the trihydrate salt. Under the method B, at pH of 1.0, IDM crystallized under the alpha form; at pH 4.5, IDM crystallized under the form alpha in presence of some nuclei of gamma form; at pH 7.0, 8.0, and 10.0 for NH4OH, IDM crystallized under the most stable polymorph gamma form, whereas in presence of NaOH, a mix of alpha, and salt forms was formed whatever the pH of the solution. Copyright © 2014 Elsevier B.V. All rights reserved.

Microfocus diffraction from different regions of a protein crystal: structural variations and unit-cell polymorphism

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

Thompson, Michael C.; Cascio, Duilio; Yeates, Todd O.

Real macromolecular crystals can be non-ideal in a myriad of ways. This often creates challenges for structure determination, while also offering opportunities for greater insight into the crystalline state and the dynamic behavior of macromolecules. To evaluate whether different parts of a single crystal of a dynamic protein, EutL, might be informative about crystal and protein polymorphism, a microfocus X-ray synchrotron beam was used to collect a series of 18 separate data sets from non-overlapping regions of the same crystal specimen. A principal component analysis (PCA) approach was employed to compare the structure factors and unit cells across the datamore » sets, and it was found that the 18 data sets separated into two distinct groups, with largeRvalues (in the 40% range) and significant unit-cell variations between the members of the two groups. This categorization mapped the different data-set types to distinct regions of the crystal specimen. Atomic models of EutL were then refined against two different data sets obtained by separately merging data from the two distinct groups. A comparison of the two resulting models revealed minor but discernable differences in certain segments of the protein structure, and regions of higher deviation were found to correlate with regions where larger dynamic motions were predicted to occur by normal-mode molecular-dynamics simulations. The findings emphasize that large spatially dependent variations may be present across individual macromolecular crystals. This information can be uncovered by simultaneous analysis of multiple partial data sets and can be exploited to reveal new insights about protein dynamics, while also improving the accuracy of the structure-factor data ultimately obtained in X-ray diffraction experiments.« less

Effect of Multiple Alloying Elements on the Glass-Forming Ability, Thermal Stability, and Crystallization Behavior of Zr-Based Alloys

NASA Astrophysics Data System (ADS)

Bazlov, A. I.; Tsarkov, A. A.; Ketov, S. V.; Suryanarayana, C.; Louzguine-Luzgin, D. V.

2018-02-01

Effect of multiple alloying elements on the glass-forming ability, thermal stability, and crystallization behavior of Zr-based glass-forming alloys were studied in the present work. We investigated the effect of complete or partial substitution of Ti and Ni with similar early and late transition metals, respectively, on the glass-forming ability and crystallization behavior of the Zr50Ti10Cu20Ni10Al10 alloy. Poor correlation was observed between different parameters indicating the glass-forming ability and the critical size of the obtained glassy samples. Importance of the width of the crystallization interval is emphasized. The kinetics of primary crystallization, i.e., the rate of nucleation and rate of growth of the nuclei of primary crystals is very different from that of the eutectic alloys. Thus, it is difficult to estimate the glass-forming ability only on the basis of the empirical parameters not taking into account the crystallization behavior and the crystallization interval.

Optical-analog-to-digital conversion based on successive-like approximations in octagonal-shape photonic crystal ring resonators

NASA Astrophysics Data System (ADS)

Tavousi, A.; Mansouri-Birjandi, M. A.

2018-02-01

Implementing intensity-dependent Kerr-like nonlinearity in octagonal-shape photonic crystal ring resonators (OSPCRRs), a new class of optical analog-to-digital converters (ADCs) with low power consumption is presented. Due to its size dependent refractive index, Silicon (Si) nanocrystal is used as nonlinear medium in the proposed ADC. Coding system of optical ADC is based on successive-like approximations which requires only one quantization level to represent each single bit, despite of conventional ADCs that require at least two distinct levels for each bit. Each is representing bit of optical ADC is formed by vertically alignment of double rings of OSPCRRs (DR-OSPCRR) and cascading m number of DR-OSPCRR, forms an m bit ADC. Investigating different parameters of DR-OSPCRR such as refractive indices of rings, lattice refractive index, and coupling coefficients of waveguide-to-ring and ring-to-ring, the ADC's threshold power is tuned. Increasing the number of bits of ADC, increases the overall power consumption of ADC. One can arrange to have any number of bits for this ADC, as long as the power levels are treated carefully. Finite difference time domain (FDTD) in-house codes were used to evaluate the ADC's effectiveness.

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

Yan, Wupeng; Stone, Everett; Zhang, Yan Jessie

Enzyme therapeutics that can degrade l-methionine (l-Met) are of great interest as numerous malignancies are exquisitely sensitive to l-Met depletion. To exhaust the pool of methionine in human serum, we previously engineered an l-Met-degrading enzyme based on the human cystathionine-γ-lyase scaffold (hCGL-NLV) to circumvent immunogenicity and stability issues observed in the preclinical application of bacterially derived methionine-γ-lyases. To gain further insights into the structure–activity relationships governing the chemistry of the hCGL-NLV lead molecule, we undertook a biophysical characterization campaign that captured crystal structures (2.2 Å) of hCGL-NLV with distinct reaction intermediates, including internal aldimine, substrate-bound, gem-diamine, and external aldimine forms.more » Curiously, an alternate form of hCGL-NLV that crystallized under higher-salt conditions revealed a locally unfolded active site, correlating with inhibition of activity as a function of ionic strength. Subsequent mutational and kinetic experiments pinpointed that a salt bridge between the phosphate of the essential cofactor pyridoxal 5'-phosphate (PLP) and residue R62 plays an important role in catalyzing β- and γ-eliminations. Our study suggests that solvent ions such as NaCl disrupt electrostatic interactions between R62 and PLP, decreasing catalytic efficiency.« less

Enrichment of Non-Terrestrial L-Proteinogenic Amino Acids by Aqueous Alteration on the Tagish Lake Meteorite Parent Body

NASA Technical Reports Server (NTRS)

Glavin, Daniel P.; Elsila, Jamie E.; Burton, Aaron S.; Callahan, Michael P.; Dworkin, Jason P.; Herd, Christopher D. K.

2012-01-01

The distribution and isotopic and enantiomeric compositions of amino acids found in three distinct fragments of the Tagish Lake C2-type carbonaceous chondrite were investigated via liquid chromatography fluorescence detection time-of-flight mass spectrometry and gas chromatography isotope ratio mass spectrometry. Large L-enantiomeric excesses (L(sub ee) approx. 43 to 59%) of the a-hydrogen aspartic and glutamic amino acids were measured in Tagish Lake, whereas alanine, another alpha-hydrogen protein amino acid, was found to be nearly racemic (D approx. L) using both techniques. Carbon isotope measurements of D- and L-aspartic acid and D- and L-alanine in Tagish Lake fall well outside of the terrestrial range and indicate that the measured aspartic acid enantioenrichment is indigenous to the meteorite. Alternate explanations for the Lexcesses of aspartic acid such as interference from other compounds present in the sample, analytical biases, or terrestrial amino acid contamination were investigated and rejected. These results can be explained by differences in the solid-solution phase behavior of aspartic acid, which can form conglomerate enantiopure solids during crystallization, and alanine, which can only form racemic crystals.

Re-awakening Magmatic Systems: The Mechanics of an Open-system Event

NASA Astrophysics Data System (ADS)

Bergantz, George; Burgisser, Alain; Schleicher, Jillian

2016-04-01

The re-awakening of magmatic systems requires new magma input, which often induces mixing with a resident magma existing as a crystal-rich mush. This is expressed by complex phenocryst populations, many of which preserve evidence of multiple episodes of recycling. The unlocking and mobilization of these resident mushes conditions the progress of re-awakening, however their processes are poorly understood. Crystal-rich but mobile systems, dominated by their granular mechanics, are not satisfactorily explained from either fluid or solid-like models. We will present a generalizing framework for describing the mechanics of crystal-rich mushes based on the notion of force chains. Force chains arise from crystal-crystal contacts and describe the highly non-uniform way that stress is transmitted in a crystal-rich mush. Using CFD-DEM simulations that resolve crystal-scale mechanics, we will show how the populations of crystal mush force chains and their spatial fabric change during an open-system event. We will show how the various forms of dissipation, such as: fluid drag, particle-fluid drag, particle normal and shear lubrication, and contact friction, jointly contribute to the processes of magma mush unlocking, mobilization and fabric formation. We will also describe non-intuitive constitutive behavior such as non-local and non-affine deformation as well as complex, rheological transitions from continuous to discontinuous shear thickening as a function of the dimensionless shear rate. One implication of this is that many of the commonly-invoked postulates about magma behavior such as lock-up at a critical crystallinity and suspension rheology, are better understood from a micro-physical (crystal-scale) perspective as a combination of far-field geometrical controls, local frictional thickening and shear jamming, each with distinct time scales. This kind of crystal-based unifying framework can simultaneously recover diverse processes such as strain-localization, shear-induced dilatency, and help to identify the volumes of resident magma re-mobilized during magma system re-awakening.

Microscopic studies of polycrystalline nanoparticle growth in free space

NASA Astrophysics Data System (ADS)

Mohan, A.; Kaiser, M.; Verheijen, M. A.; Schropp, R. E. I.; Rath, J. K.

2017-06-01

We have extensively studied by multiple microscopic techniques the growth and crystallization of silicon nanoparticles in pulsed SiH4/Ar plasmas. We observe that the crystallinity of the particles can be tuned from amorphous to crystalline by altering the plasma ON time, tON. Three phases can be identified as a function of tON. Microscopic studies reveal that, in the initial gas phase (phase I) single particles of polycrystalline nature are formed which according to our hypothesis grow out of a single nucleus. The individual crystallites of the polycrystalline particles become bigger crystalline regions which marks the onset of cauliflower shaped particles (phase II). At longer tON (phase III) distinct cauliflower particles are formed by the growth of these crystalline regions by local epitaxy.

Using thermally stimulated current (TSC) to investigate disorder in micronized drug substance produced at different milling energies.

PubMed

Forcino, Rachel; Brum, Jeffrey; Galop, Marc; Sun, Yan

2010-10-01

To investigate the use of thermally stimulated current (TSC) to characterize disorder resulting from micronization of a crystalline drug substance. Samples processed at different milling energies are characterized, and annealing studied. Molecular mobility in micronized drug substance was studied using TSC and compared to results from differential scanning calorimetry (DSC). The micronized drug substance TSC spectra are compared to crystalline and amorphous references. TSC shows distinct relaxation modes for micronized material in comparison to a single weak exotherm observed with DSC. Molecular mobility modes are unique for micronized material compared to the amorphous reference indicating physically distinct disorder compared to phase-separated amorphous material. Signals are ascribed as arising from crystal defects. TSC differentiates material processed at different milling energies showing reasonable correlation between the AUC of the α-relaxation and micronization energy. The annealing process of crystal defects in micronized drug appears to proceed differently for α and β relaxations. TSC proves sensitive to the crystal defects in the micronized drug substance studied here. The technique is able to differentiate distinct types of disorder and can be used to characterize noncrystalline regions arising from milling processes which are physically distinct from amorphous material.

In situ creation of reactive polymer nanoparticles and resulting polymer layers formed at the interfaces of liquid crystals (Conference Presentation)

NASA Astrophysics Data System (ADS)

Kang, Shin-Woong; Kundu, Sudarshan; Park, Heung-Shik; Oh, Keun Chan; Lyu, Jae Jin

2017-02-01

We report the in situ creation of reactive polymer nanoparticles and resulting polymer networks formed at the interfaces of liquid crystals. It is known that polymerization-induced phase separation proceeds in two distinct regimes depending on the concentration of monomer. For a high monomer concentration, phase separation occurs mainly through the spinodal decomposition process, consequently resulting in interpenetrating polymer networks. For a dilute system, however, the phase separation mainly proceeds and completes in the binodal decomposition regime. The system resembles the aggregation process of colloidal particle. In this case, the reaction kinetics is limited by the reaction between in situ created polymer aggregates and hence the network morphologies are greatly influenced by the diffusion of reactive polymer particles. The thin polymer layers localized at the surface of substrate are inevitably observed and can be comprehended by the interfacial adsorption and further cross-linking reaction of reactive polymer aggregates at the interface. This process provides a direct perception on understanding polymer stabilized liquid crystals accomplished by the interfacial polymer layer. The detailed study has been performed for an extremely dilute condition (below 0.5 wt%) by employing systematic experimental approaches. Creation and growth of polymer nanoparticles have been measured by particle size analyzer. The interfacial localization of polymer aggregates and resulting interfacial layer formation with a tens of nanometer scale have been exploited at various interfaces such as liquid-solid, liquid-liquid, and liquid-gas interfaces. The resulting interfacial layers have been characterized by using fuorescent confocal microscope and field emission scanning electron microscope. The detailed processes of the polymer stabilized vertically aligned liquid crystals will be discussed in support of the reported study.

Flow-Directed Crystallization for Printed Electronics.

PubMed

Qu, Ge; Kwok, Justin J; Diao, Ying

2016-12-20

The solution printability of organic semiconductors (OSCs) represents a distinct advantage for materials processing, enabling low-cost, high-throughput, and energy-efficient manufacturing with new form factors that are flexible, stretchable, and transparent. While the electronic performance of OSCs is not comparable to that of crystalline silicon, the solution processability of OSCs allows them to complement silicon by tackling challenging aspects for conventional photolithography, such as large-area electronics manufacturing. Despite this, controlling the highly nonequilibrium morphology evolution during OSC printing remains a challenge, hindering the achievement of high electronic device performance and the elucidation of structure-property relationships. Many elegant morphological control methodologies have been developed in recent years including molecular design and novel processing approaches, but few have utilized fluid flow to control morphology in OSC thin films. In this Account, we discuss flow-directed crystallization as an effective strategy for controlling the crystallization kinetics during printing of small molecule and polymer semiconductors. Introducing the concept of flow-directed crystallization to the field of printed electronics is inspired by recent advances in pharmaceutical manufacturing and flow processing of flexible-chain polymers. Although flow-induced crystallization is well studied in these areas, previous findings may not apply directly to the field of printed electronics where the molecular structures (i.e., rigid π-conjugated backbone decorated with flexible side chains) and the intermolecular interactions (i.e., π-π interactions, quadrupole interactions) of OSCs differ substantially from those of pharmaceuticals or flexible-chain polymers. Another critical difference is the important role of solvent evaporation in open systems, which defines the flow characteristics and determines the crystallization kinetics and pathways. In other words, flow-induced crystallization is intimately coupled with the mass transport processes driven by solvent evaporation during printing. In this Account, we will highlight these distinctions of flow-directed crystallization for printed electronics. In the context of solution printing of OSCs, the key issue that flow-directed crystallization addresses is the kinetics mismatch between crystallization and various transport processes during printing. We show that engineering fluid flows can tune the kinetics of OSC crystallization by expediting the nucleation and crystal growth processes, significantly enhancing thin film morphology and device performance. For small molecule semiconductors, nucleation can be enhanced and patterned by directing the evaporative flux via contact line engineering, and defective crystal growth can be alleviated by enhancing mass transport to yield significantly improved coherence length and reduced grain boundaries. For conjugated polymers, extensional and shear flow can expedite nucleation through flow-induced conformation change, facilitating the control of microphase separation, degree of crystallinity, domain alignment, and percolation. Although the nascent concept of flow-directed solution printing has not yet been widely adopted in the field of printed electronics, we anticipate that it can serve as a platform technology in the near future for improving device performance and for systematically tuning thin film morphology to construct structure-property relationships. From a fundamental perspective, it is imperative to develop a better understanding of the effects of fluid flow and mass transport on OSC crystallization as these processes are ubiquitous across all solution processing techniques and can critically impact charge transport properties.

Multiphase inclusions in plagioclase from anorthosites in the Stillwater Complex, Montana: implications for the origin of the anorthosites

USGS Publications Warehouse

Loferski, P.J.; Arculus, R.J.

1993-01-01

Multiphase inclusions, consisting of clinopyroxene+ilmenite+apatite, occur within cumulus plagioclase grains from anorthosites in the Stillwater Complex, Montana, and in other rocks from the Middle Banded series of the intrusion. The textures and constant modal mineralogy of the inclusions indicate that they were incorporated in the plagioclase as liquid droplets that later crystallized rather than as solid aggregates. Their unusual assemblage, including a distinctive manganiferous ilmenite and the presence of baddeleyite (ZrO2), indicates formation from an unusual liquid. A process involving silicater liquid immiscibility is proposed, whereby small globules of a liquid enriched in Mg, Fe, Ca, Ti, P, REE, Zr and Mn exsolved from the main liquid that gave rise to the anorthosites, became trapped in the plagioclase, and later crystallized to form the inclusions. The immiscibility could have occurred locally within compositional boundaries around crystallizing plagioclase grains or it could have occurred pervasively throughout the liquid. It is proposed that the two immiscible liquids were analogous, n terms of their melt structures, to immiscible liquid pairs reported in the literature both in experiments and in natural basalts. For the previously reported pairs, immiscibility is between a highly polymerized liquid, typically granitic in composition, and a depolymerized liquid, typically ferrobasaltic in composition. In the case of the anorthosites, the depolymerized liquid is represented by the inclusions, and the other liquid was a highly polymerized aluminosilicate melt with a high normative plagioclase content from which the bulk of the anorthosites crystallized. Crystallization of the anorthosites from this highly polymerized liquid accounts for various distinctive textural and chemical features of the anorthosites compared to other rocks in the Stillwater Complex. A lack of correlation between P contents and chondrite-normalized rare earth element (REE) ratios of plagioclase separates indicates that the amount of apatite in the inclusions is too low to affect the REE signature of the plagioclase separates. Nevertheless, workers should use caution when attempting REE modelling studies of cumulates having low REE contents, because apatite-bearing inclusions can potentially cause problems. ?? 1993 Springer-Verlag.

Over-Expression, Purification and Crystallization of Human Dihydrolipoamide Dehydrogenase

NASA Technical Reports Server (NTRS)

Hong, Y. S.; Ciszak, Ewa; Patel, Mulchand

2000-01-01

Dehydrolipoamide dehydrogenase (E3; dihydrolipoan-tide:NAD+ oxidoreductase, EC 1.8.1.4) is a common catalytic component found in pyruvate dehydrogenase complex, alpha-ketoglutarate dehydrogenase complex, and branched-chain cc-keto acid dehydrogenase complex. E3 is also a component (referred to as L protein) of the glycine cleavage system in bacterial metabolism (2). Active E3 forms a homodimer with four distinctive subdomain structures (FAD binding, NAD+ binding, central and interface domains) with non-covalently but tightly bound FAD in the holoenzyme. Deduced amino acids from cloned full-length human E3 gene showed a total of 509 amino acids with a leader sequence (N-terminal 35 amino acids) that is excised (mature form) during transportation of expressed E3 into mitochondria membrane. So far, three-dimensional structure of human E3 has not been reported. Our effort to achieve the elucidation of the X-ray crystal structure of human E3 will be presented. Recombinant pPROEX-1 expression vector (from GIBCO BRL Life Technologies) having the human E3 gene without leader sequence was constructed by Polymerase Chain Reaction (PCR) and subsequent ligation, and cloned in E.coli XL1-Blue by transformation. Since pPROEX-1 vector has an internal His-tag (six histidine peptide) located at the upstream region of a multicloning site, one-step affinity purification of E3 using nickelnitriloacetic acid (Ni-NTA) agarose resin, which has a strong affinity to His-tag, was feasible. Also a seven-amino-acid spacer peptide and a recombinant tobacco etch virus protease recognition site (seven amino acids peptide) found between His-tag and first amino acid of expressed E3 facilitated the cleavage of His-tag from E3 after the affinity purification. By IPTG induction, ca. 15 mg of human E3 (mature form) was obtained from 1L LB culture with overnight incubation at 25C. Over 98% of purity of E3 from one-step Ni-NTA agarose affinity purification was confirmed by SDS-PAGE analysis. For crystallization, E3 samples were prepared with and without His-tag. To minimize the aggregation of E3, apo- and holo- forms of E3s were tested, as well as a mutated E3. Dynamic light scattering measurements revealed that the E3 preparations without His-tag and substrate are highly monodispersive with regard to homodimers. Consequent crystallization trials of this E3 preparation led to single crystals of E3 grown by the vapor diffusion method. Crystals were obtained within a few days from solution containing poly (ethylene glycol) monomethyl ether 5000 as a precipitant. Autoindexing and integration of the X-ray diffraction data showed that E3 crystals belong to an orthorhombic system with unit cell parameters a-- 123. 1, b= 165.3 and c=214.3A. Further optimization of protein preparation and crystallization experiments for the structural determination will be discussed.

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

Bolotin, B. M., E-mail: bolotin70@yandex.ru; Mikhlina, Ya. A.; Arkhipova, S. A.

The crystal and molecular structures of two crystal forms (pale yellow form 1 and yellow form 2) of N-[2-(4-oxo-4H-benzo[d][1,3]oxazin-2-yl)phenyl]naphthalene-2-sulfonamide (Orlyum White 520T), which is an organic luminophore with an anomalously high Stokes shift, were determined. Crystal 2 is a solvate with para-xylene. Crystal 1 is a solvent-free form. The molecular geometry in crystal 1 differs from that in 2 only in the orientation of the SO{sub 2}Ar substituent. The bond-length distribution in the planar moiety of the molecule in crystal 1 is virtually identical to that in 2, but the bonds in the NH-SO{sub 2}Ar-bearing benzene ring in crystal 1more » are systematically longer than the corresponding bonds in crystal 2. This fact can be attributed to the crystal-packing effects. In 2 the molecules form stacked dimers with {pi}-stacking interactions between two planar conjugated tricyclic systems. The charge transfer in this system accounts for the intensification of the color of these crystals and the observed difference in the optical properties of 1 and 2.« less

Characterization of bacteria isolated from palaeoproterozoic metasediments for sequestration of carbon dioxide and formation of calcium carbonate.

PubMed

Srivastava, Shaili; Bharti, Randhir K; Thakur, Indu Shekhar

2015-01-01

Bacterial community of palaeoproterozoic metasediments was enriched in the chemostat in the presence of different concentrations of NaHCO3. Six bacterial isolates were isolated from the chemostat on nutrient agar plates on the basis of distinct morphology. Denaturing gradient gel electrophoresis (DGGE) proved the presence of six operational taxonomic units (OTUs) at 50 and 100 mM NaHCO3. The OTU was reduced to three and one at enrichment concentration of 150 and 200 mM NaHCO3 respectively. These six isolates were tested for sequestration of carbon dioxide by (14)C metabolic labeling of NaH(14)CO3. Among the six isolates, one of the bacterium showed better potency to fix radiolabeled NaH(14)CO3. The isolate (ISTD04) was identified as Serratia sp. by 16S ribosomal RNA (16S rRNA) sequence analysis and was found to be same as the DGGE OTU sequence at 200-mM NaHCO3 concentration. The bacterium was tested for product formation in form of calcite crystals in presence of 5 % CO2. Scanning electron microscopy (SEM) of product formed by the bacterium revealed defined faceted rhombohedral structure which resembled calcite and vaterite phases of the crystal. Formation of calcium carbonate crystals was further confirmed by Fourier transform infrared (FTIR) spectroscopy as carbonate group showing strong vibration at 1,456 cm(-1). Major calcite phase diffraction peaks were determined by X-ray diffraction (XRD) analysis, and energy-dispersive X-ray (EDX) analysis showed the presence of CaO (72 %) and carbon (18 %). Bacterium use bicarbonate as carbon source for their growth as well as by-product formation in form of calcite shows carbon circulation and storage.

Photonic band gap templating using optical interference lithography

NASA Astrophysics Data System (ADS)

Chan, Timothy Y. M.; Toader, Ovidiu; John, Sajeev

2005-04-01

We describe the properties of three families of inversion-symmetric, large photonic band-gap (PBG) template architectures defined by iso-intensity surfaces in four beam laser interference patterns. These templates can be fabricated by optical interference (holographic) lithography in a suitable polymer photo-resist. PBG materials can be synthesized from these templates using two stages of infiltration and inversion, first with silica and second with silicon. By considering point and space group symmetries to produce laser interference patterns with the smallest possible irreducible Brillouin zones, we obtain laser beam intensities, directions, and polarizations which generate a diamond-like (fcc) crystal, a novel body-centered cubic (bcc) architecture, and a simple-cubic (sc) structure. We obtain laser beam parameters that maximize the intensity contrasts of the interference patterns. This optimizes the robustness of the holographic lithography to inhomogeneity in the polymer photo-resist. When the optimized iso-intensity surface defines a silicon to air boundary (dielectric contrast of 11.9 to 1), the fcc, bcc, and sc crystals have PBG to center frequency ratios of 25%, 21%, and 11%, respectively. A full PBG forms for the diamond-like crystal when the refractive index contrast exceeds 1.97 to 1. We illustrate a noninversion symmetric PBG architecture that interpolates between a simple fcc structure and a diamond network structure. This crystal exhibits two distinct and complete photonic band gaps. We also describe a generalized class of tetragonal photonic crystals that interpolate between and extrapolate beyond the diamond-like crystal and the optimized bcc crystal. We demonstrate the extent to which the resulting PBG materials are robust against perturbations to the laser beam amplitudes and polarizations, and template inhomogeneity. The body centered cubic structure exhibits the maximum robustness overall.

Quantitative determination of the mineral distribution in different collagen zones of calcifying tendon using high voltage electron microscopic tomography

NASA Technical Reports Server (NTRS)

McEwen, B. F.; Song, M. J.; Landis, W. J.

1991-01-01

High voltage electron microscopic tomography was used to make the first quantitative determination of the distribution of mineral between different regions of collagen fibrils undergoing early calcification in normal leg tendons of the domestic turkey, Meleagris gallopavo. The tomographic 3-D reconstruction was computed from a tilt series of 61 different views spanning an angular range of +/- 60 degrees in 2 degrees intervals. Successive applications of an interactive computer operation were used to mask the collagen banding pattern of either hole or overlap zones into separate versions of the reconstruction. In such 3-D volumes, regions specified by the mask retained their original image density while the remaining volume was set to background levels. This approach was also applied to the mineral crystals present in the same volumes to yield versions of the 3-D reconstructions that were masked for both the crystal mass and the respective collagen zones. Density profiles from these volumes contained a distinct peak corresponding only to the crystal mass. A comparison of the integrated density of this peak from each profile established that 64% of the crystals observed were located in the collagen hole zones and 36% were found in the overlap zones. If no changes in crystal stability occur once crystals are formed, this result suggests the possibilities that nucleation of mineral is preferentially and initially associated with the hole zones, nucleation occurs more frequently in the hole zones, the rate of crystal growth is more rapid in the hole zones, or a combination of these alternatives. All lead to the conclusion that the overall accumulation of mineral mass is predominant in the collagen hole zones compared to overlap zones during early collagen fibril calcification.

Crystal Growth Texture in Light Vein at Garden City

NASA Image and Video Library

2015-11-11

This view from the Mars Hand Lens Imager (MAHLI) on the arm of NASA's Curiosity Mars rover shows texture within a light-toned vein at a site called "Garden City" on lower Mount Sharp. The area shown is roughly 0.9 inch (2.2 centimeters) wide. It was taken during the 946th Martian day, or sol, of Curiosity's work on Mars (April 4, 2015). Differences in textures of light-toned veins in the Garden City complex of crisscrossing mineral veins are clues that these veins may result from distinct fluid events. This vein's texture shows indications of crystal growth, suggesting that crystallization may have exerted a force for opening the fracture filled by the vein. Different examples are at PIA19926 and PIA19927. Mineral veins often form where fluids move through fractured rocks, depositing minerals in the fractures and affecting chemistry of the surrounding rock. At Garden City, the veins have been more resistant to erosion than the surrounding host rock. The fluid movement through fractures at Garden City occurred later than wet environmental conditions in which the host rock formed, before it hardened and cracked. Malin Space Science Systems, San Diego, built and operates MAHLI. NASA's Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, manages the Mars Science Laboratory Project for the NASA Science Mission Directorate, Washington. JPL designed and built the project's Curiosity rover. http://photojournal.jpl.nasa.gov/catalog/PIA19925

Crystalline Organic Pigment-Based Field-Effect Transistors.

PubMed

Zhang, Haichang; Deng, Ruonan; Wang, Jing; Li, Xiang; Chen, Yu-Ming; Liu, Kewei; Taubert, Clinton J; Cheng, Stephen Z D; Zhu, Yu

2017-07-05

Three conjugated pigment molecules with fused hydrogen bonds, 3,7-diphenylpyrrolo[2,3-f]indole-2,6(1H,5H)-dione (BDP), (E)-6,6'-dibromo-[3,3'-biindolinylidene]-2,2'-dione (IIDG), and 3,6-di(thiophen-2-yl)-2,5-dihydropyrrolo-[3,4-c]pyrrole-1,4-dione (TDPP), were studied in this work. The insoluble pigment molecules were functionalized with tert-butoxylcarbonyl (t-Boc) groups to form soluble pigment precursors (BDP-Boc, IIDG-Boc, and TDPP-Boc) with latent hydrogen bonding. The single crystals of soluble pigment precursors were obtained. Upon simple thermal annealing, the t-Boc groups were removed and the soluble pigment precursor molecules with latent hydrogen bonding were converted into the original pigment molecules with fused hydrogen bonding. Structural analysis indicated that the highly crystalline soluble precursors were directly converted into highly crystalline insoluble pigments, which are usually only achievable by gas-phase routes like physical vapor transport. The distinct crystal structure after the thermal annealing treatment suggests that fused hydrogen bonding is pivotal for the rearrangement of molecules to form a new crystal in solid state, which leads to over 2 orders of magnitude enhancement in charge mobility in organic field-effect transistor (OFET) devices. This work demonstrated that crystalline OFET devices with insoluble pigment molecules can be fabricated by their soluble precursors. The results indicated that a variety of commercially available conjugated pigments could be potential active materials for high-performance OFETs.

Injection of Light Material into an Older Dark Vein

NASA Image and Video Library

2015-11-11

Light material emplaced within darker vein material is seen in this view of a mineral vein at the "Garden City" site on lower Mount Sharp, Mars. The Mars Hand Lens Imager (MAHLI) on the arm of NASA's Curiosity Mars Rover took the image on April 4, 2015, during the 946th Martian day, or sol, of Curiosity's work on Mars. The area shown is roughly 0.4 inch (1 centimeter) wide. Differences in textures of light-toned veins in the Garden City complex of crisscrossing mineral veins are clues that these veins may result from distinct fluid events. This example shows where injection of light material into a prior dark vein suggests high fluid pressure. Differences in textures of light-toned veins in the Garden City complex of crisscrossing mineral veins are clues that these veins may result from distinct fluid events. This vein's texture shows indications of crystal growth, suggesting that crystallization may have exerted a force for opening the fracture filled by the vein. Different examples are at PIA19925 and PIA19927. Mineral veins often form where fluids move through fractured rocks, depositing minerals in the fractures and affecting chemistry of the surrounding rock. At Garden City, the veins have been more resistant to erosion than the surrounding host rock. The fluid movement through fractures at Garden City occurred later than wet environmental conditions in which the host rock formed, before it hardened and cracked. Malin Space Science Systems, San Diego, built and operates MAHLI. NASA's Jet Propulsion Laboratory, a division of the California Institute of Technology in Pasadena, manages the Mars Science Laboratory Project for the NASA Science Mission Directorate, Washington. JPL designed and built the project's Curiosity rover. http://photojournal.jpl.nasa.gov/catalog/PIA19926

Nanogeochronology of discordant zircon measured by atom probe microscopy of Pb-enriched dislocation loops

PubMed Central

Peterman, Emily M.; Reddy, Steven M.; Saxey, David W.; Snoeyenbos, David R.; Rickard, William D. A.; Fougerouse, Denis; Kylander-Clark, Andrew R. C.

2016-01-01

Isotopic discordance is a common feature in zircon that can lead to an erroneous age determination, and it is attributed to the mobilization and escape of radiogenic Pb during its post-crystallization geological evolution. The degree of isotopic discordance measured at analytical scales of ~10 μm often differs among adjacent analysis locations, indicating heterogeneous distributions of Pb at shorter length scales. We use atom probe microscopy to establish the nature of these sites and the mechanisms by which they form. We show that the nanoscale distribution of Pb in a ~2.1 billion year old discordant zircon that was metamorphosed c. 150 million years ago is defined by two distinct Pb reservoirs. Despite overall Pb loss during peak metamorphic conditions, the atom probe data indicate that a component of radiogenic Pb was trapped in 10-nm dislocation loops that formed during the annealing of radiation damage associated with the metamorphic event. A second Pb component, found outside the dislocation loops, represents homogeneous accumulation of radiogenic Pb in the zircon matrix after metamorphism. The 207Pb/206Pb ratios measured from eight dislocation loops are equivalent within uncertainty and yield an age consistent with the original crystallization age of the zircon, as determined by laser ablation spot analysis. Our results provide a specific mechanism for the trapping and retention of radiogenic Pb during metamorphism and confirm that isotopic discordance in this zircon is characterized by discrete nanoscale reservoirs of Pb that record different isotopic compositions and yield age data consistent with distinct geological events. These data may provide a framework for interpreting discordance in zircon as the heterogeneous distribution of discrete radiogenic Pb populations, each yielding geologically meaningful ages. PMID:27617295

Structural Basis for the Interconversion of Maltodextrins by MalQ, the Amylomaltase of Escherichia coli*

PubMed Central

Weiss, Simon C.; Skerra, Arne; Schiefner, André

2015-01-01

Amylomaltase MalQ is essential for the metabolism of maltose and maltodextrins in Escherichia coli. It catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. To elucidate the molecular basis of transglycosylation by MalQ, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine-glucose-acarbose, at resolutions down to 2.1 Å. MalQ represents the first example of a mesophilic bacterial amylomaltase with known structure and exhibits an N-terminal extension of about 140 residues, in contrast with previously described thermophilic enzymes. This moiety seems unique to amylomaltases from Enterobacteriaceae and folds into two distinct subdomains that associate with different parts of the catalytic core. Intriguingly, the three MalQ crystal structures appear to correspond to distinct states of this enzyme, revealing considerable conformational changes during the catalytic cycle. In particular, the inhibitor complex highlights the requirement of both a 3-OH group and a 4-OH group (or α1–4-glycosidic bond) at the acceptor subsite +1 for the catalytically competent orientation of the acid/base catalyst Glu-496. Using an HPLC-based MalQ enzyme assay, we could demonstrate that the equilibrium concentration of maltodextrin products depends on the length of the initial substrate; with increasing numbers of glycosidic bonds, less glucose is formed. Thus, both structural and enzymatic data are consistent with the extremely low hydrolysis rates observed for amylomaltases and underline the importance of MalQ for the metabolism of maltodextrins in E. coli. PMID:26139606

Precipitation of ikaite crystals in Antarctic marine sediments: implications from pore water geochemistry

NASA Astrophysics Data System (ADS)

Lu, Z.; Kennedy, H.; Rickaby, R. E.; Georg, B.; Shaw, S.; Lennie, A.; Pancost, R. D.

2008-12-01

Ikaite is a calcium carbonate hexahydrate (CaCO3•6H20) considered to be stable only at low temperatures. It has been found in form of tufa tower at locations where alkaline water mixes with water masses enriched in calcium (e.g. Ikka Fjord, Mono Lake). Large euhedral single crystals of ikaite were also recovered in marine sediments, associated with organic matter degradation, anaerobic oxidation of methane (AOM) and sulfate reduction. The hydration water in the ikaite crystals were demonstrated to record the oxygen isotope composition of the water from which they precipitated. Such a characteristic may allow using ikaite to reconstruct the ice volume in the past. For this purpose, the controls on its precipitation in the sediment column need to be investigated which is the main goal of this study. U.S. Antarctica Program cruise NBP0703 collected two cores with ikaite crystals at Antarctica Peninsula (Bransfield Strait and Firth of Tay). We determined major cation/anion concentrations, dissolved inorganic carbon (DIC) and δ13C composition of DIC in the pore waters in these two cores. Strong organic matter degradation or AOM in both cores results in quick consumption of sulfate in shallow part of the cores (SMT at around 3m).Rapid build-up of DIC is accompanied by the sharp decrease of dissolved calcium in the top 5m. Large variations were observed in δ13CDIC values (-20‰ to +13‰). The δ13C of ikaite in two cores were distinctive from each other (-19‰ and +4‰) corresponding to the DIC pools at different depths. The down core saturation state of the ikaite was modeled in PHREEQC based on the pore water chemistry, and the results are consistent with carbon isotope data, suggesting that these large crystals very likely formed within a narrow depth interval and a short time period (given high sedimentation rates of 0.5-1 cm/yr in this area).

A complex magma reservoir system for a large volume intra- to extra-caldera ignimbrite: Mineralogical and chemical architecture of the VEI8, Permian Ora ignimbrite (Italy)

NASA Astrophysics Data System (ADS)

Willcock, M. A. W.; Bargossi, G. M.; Weinberg, R. F.; Gasparotto, G.; Cas, R. A. F.; Giordano, G.; Marocchi, M.

2015-11-01

Intra-caldera settings record a wealth of information on caldera-forming processes, yet field study is rarely possible due to lack of access and exposure. The Permian Ora Formation, Italy, preserves > 1000 m of vertical section through its intra-caldera succession. This provides an excellent opportunity to detail its mineralogical and geochemical architecture and gain understanding of the eruption evolution and insight into the pre-eruptive magma system. Detailed juvenile clast phenocryst and matrix crystal fragment point count and image analysis data, coupled with bulk-rock chemistry and single mineral compositional data, show that the Ora ignimbrite succession is rhyolitic (72.5-77.7% SiO2), crystal-rich (~ 25-57%; average 43%) and has a constant main mineral population (volcanic quartz + sanidine + plagioclase + biotite). Although a seemingly homogeneous ignimbrite succession, important subtle but detectable lateral and vertical variations in modal mineralogy and bulk-rock major and trace elements are identified here. The Ora Formation is comprised of multiple lithofacies, dominated by four densely welded ignimbrite lithofacies. They are crystal-rich, typically lithic-poor (< 2%), and juvenile clast-bearing (average 20%). The ignimbrite lithofacies are distinguished by variation in crystal fragment size and abundance and total lithic content. The intra-caldera stratigraphic architecture shows both localised and some large-scale lithofacies correlation, however, it does not conform to a 'layer-cake' stratigraphy. The intra-caldera succession is divided into two depo-centres: Southern and Northern, with proximal extra-caldera deposits preserved to the south and north of the system. The Southern and Northern intra-caldera ignimbrite successions are discriminated by variations in total biotite crystal abundance. Detailed mineralogical and chemical data records decreases across the caldera system from south to north in biotite phenocrysts in the groundmass of juvenile clasts (average 12-2%), matrix biotite (average 7.5-2%) and plagioclase crystal fragments (average 18-6%), and total crystal fragment abundance in the matrix (average 47-37%); a biotite compositional change to iron-rich (0.57-0.78 Fe); and bulk-rock element decreases in Fe2O3, MgO, P2O5, Ce, Hf, V, La and Zr, and increases in SiO2, Y and Nb, with TiO2. Together, the changes enable subtle distinction of the Southern and Northern successions, indicating that the Northern deposits are more evolved. Furthermore, the data reveals discrimination within the Northern succession, with the northwestern extra-caldera fine-crystal-rich lithofacies, having a distinct texture, componentry and composition. The componentry variation, mineralogical and chemical ranges identified here are consistent with an eruption from a heterogeneous magma system. Our results suggest that the Ora magma was likely stored in multiple chambers within a genetically related magma reservoir network. The mineralogical and chemical architecture together with stratigraphic relationships, enable interpretation of eruption sequence. Caldera eruption is proposed to have commenced in the south and progressed to the north, forming the two pene-contemporaneous caldera depressions. Moreover, this data illustrates heterogeneity and local zonation from base-to-top of the main intra-caldera and extra-caldera successions. These variations together with crystal fragment size variations between ignimbrite lithofacies support the hypothesis of a multi-vent eruption process, incremental caldera in-filling by subtly compositionally different pyroclastic flow pulses, and a lower intensity eruption style (Willcock et al., 2013, 2014).

Photonic time crystals.

PubMed

Zeng, Lunwu; Xu, Jin; Wang, Chengen; Zhang, Jianhua; Zhao, Yuting; Zeng, Jing; Song, Runxia

2017-12-07

When space (time) translation symmetry is spontaneously broken, the space crystal (time crystal) forms; when permittivity and permeability periodically vary with space (time), the photonic crystal (photonic time crystal) forms. We proposed the concept of photonic time crystal and rewritten the Maxwell's equations. Utilizing Finite Difference Time Domain (FDTD) method, we simulated electromagnetic wave propagation in photonic time crystal and photonic space-time crystal, the simulation results show that more intensive scatter fields can obtained in photonic time crystal and photonic space-time crystal.

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

Kish, Kevin; McDonnell, Patricia A.; Goldfarb, Valentina

Protein tyrosine phosphatase {gamma} is a membrane-bound receptor and is designated RPTP{gamma}. RPTP{gamma} and two mutants, RPTP{gamma}(V948I, S970T) and RPTP{gamma}(C858S, S970T), were recombinantly expressed and purified for X-ray crystallographic studies. The purified enzymes were crystallized using the hanging-drop vapor-diffusion method. Crystallographic data were obtained from several different crystal forms in the absence and the presence of inhibitor. In this paper, a description is given of how three different crystal forms were obtained that were used with various ligands. An orthorhombic crystal form and a trigonal crystal form were obtained both with and without ligand, and a monoclinic crystal form wasmore » only obtained in the presence of a particularly elaborated inhibitor.« less

The crystal structures of the tri-functional Chloroflexus aurantiacus and bi-functional Rhodobacter sphaeroides malyl-CoA lyases and comparison with CitE-like superfamily enzymes and malate synthases.

PubMed

Zarzycki, Jan; Kerfeld, Cheryl A

2013-11-09

Malyl-CoA lyase (MCL) is a promiscuous carbon-carbon bond lyase that catalyzes the reversible cleavage of structurally related Coenzyme A (CoA) thioesters. This enzyme plays a crucial, multifunctional role in the 3-hydroxypropionate bi-cycle for autotrophic CO2 fixation in Chloroflexus aurantiacus. A second, phylogenetically distinct MCL from Rhodobacter sphaeroides is involved in the ethylmalonyl-CoA pathway for acetate assimilation. Both MCLs belong to the large superfamily of CitE-like enzymes, which includes the name-giving β-subunit of citrate lyase (CitE), malyl-CoA thioesterases and other enzymes of unknown physiological function. The CitE-like enzyme superfamily also bears sequence and structural resemblance to the malate synthases. All of these different enzymes share highly conserved catalytic residues, although they catalyze distinctly different reactions: C-C bond formation and cleavage, thioester hydrolysis, or both (the malate synthases). Here we report the first crystal structures of MCLs from two different phylogenetic subgroups in apo- and substrate-bound forms. Both the C. aurantiacus and the R. sphaeroides MCL contain elaborations on the canonical β8/α8 TIM barrel fold and form hexameric assemblies. Upon ligand binding, changes in the C-terminal domains of the MCLs result in closing of the active site, with the C-terminal domain of one monomer forming a lid over and contributing side chains to the active site of the adjacent monomer. The distinctive features of the two MCL subgroups were compared to known structures of other CitE-like superfamily enzymes and to malate synthases, providing insight into the structural subtleties that underlie the functional versatility of these enzymes. Although the C. aurantiacus and the R. sphaeroides MCLs have divergent primary structures (~37% identical), their tertiary and quaternary structures are very similar. It can be assumed that the C-C bond formation catalyzed by the MCLs occurs as proposed for malate synthases. However, a comparison of the two MCL structures with known malate synthases raised the question why the MCLs are not also able to hydrolyze CoA thioester bonds. Our results suggest the previously proposed reaction mechanism for malate synthases may be incomplete or not entirely correct. Further studies involving site-directed mutagenesis based on these structures may be required to solve this puzzling question.

Lattice Rotation Patterns and Strain Gradient Effects in Face-Centered-Cubic Single Crystals Under Spherical Indentation

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

Gao, Y. F.; Larson, B. C.; Lee, J. H.

Strain gradient effects are commonly modeled as the origin of the size dependence of material strength, such as the dependence of indentation hardness on contact depth and spherical indenter radius. However, studies on the microstructural comparisons of experiments and theories are limited. First, we have extended a strain gradient Mises-plasticity model to its crystal plasticity version and implemented a finite element method to simulate the load-displacement response and the lattice rotation field of Cu single crystals under spherical indentation. The strain gradient simulations demonstrate that the forming of distinct sectors of positive and negative angles in the lattice rotation fieldmore » is governed primarily by the slip geometry and crystallographic orientations, depending only weakly on strain gradient effects, although hardness depends strongly on strain gradients. Second, the lattice rotation simulations are compared quantitatively with micron resolution, three-dimensional X-ray microscopy (3DXM) measurements of the lattice rotation fields under 100mN force, 100 mu m radius spherical indentations in < 111 >, < 110 >, and < 001 > oriented Cu single crystals. Third, noting the limitation of continuum strain gradient crystal plasticity models, two-dimensional discrete dislocation simulation results suggest that the hardness in the nanocontact regime is governed synergistically by a combination of strain gradients and source-limited plasticity. However, the lattice rotation field in the discrete dislocation simulations is found to be insensitive to these two factors but to depend critically on dislocation obstacle densities and strengths.« less

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

DOE PAGES

McGuire, Michael A.; Clark, Genevieve; KC, Santosh; ...

2017-06-19

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

Magnetic behavior and spin-lattice coupling in cleavable van der Waals layered CrCl 3 crystals

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

McGuire, Michael A.; Clark, Genevieve; KC, Santosh

CrCl 3 is a layered insulator that undergoes a crystallographic phase transition below room temperature and orders antiferromagnetically at low temperature. Weak van der Waals bonding between the layers and ferromagnetic in-plane magnetic order make it a promising material for obtaining atomically thin magnets and creating van der Waals heterostructures. In this work we have grown crystals of CrCl 3, revisited the structural and thermodynamic properties of the bulk material, and explored mechanical exfoliation of the crystals. We find two distinct anomalies in the heat capacity at 14 and 17 K confirming that the magnetic order develops in two stagesmore » on cooling, with ferromagnetic correlations forming before long-range antiferromagnetic order develops between them. This scenario is supported by magnetization data. A magnetic phase diagram is constructed from the heat capacity and magnetization results. We also find an anomaly in the magnetic susceptibility at the crystallographic phase transition, indicating some coupling between the magnetism and the lattice. First-principles calculations accounting for van der Waals interactions also indicate spin-lattice coupling, and find multiple nearly degenerate crystallographic and magnetic structures consistent with the experimental observations. Lastly, we demonstrate that monolayer and few-layer CrCl 3 specimens can be produced from the bulk crystals by exfoliation, providing a path for the study of heterostructures and magnetism in ultrathin crystals down to the monolayer limit.« less

Heterologous expression, refolding and functional characterization of two antifreeze proteins from Fragilariopsis cylindrus (Bacillariophyceae).

PubMed

Uhlig, Christiane; Kabisch, Johannes; Palm, Gottfried J; Valentin, Klaus; Schweder, Thomas; Krell, Andreas

2011-12-01

Antifreeze proteins (AFPs) provide protection for organisms subjected to the presence of ice crystals. The psychrophilic diatom Fragilariopsis cylindrus which is frequently found in polar sea ice carries a multitude of AFP isoforms. In this study we report the heterologous expression of two antifreeze protein isoforms from F. cylindrus in Escherichia coli. Refolding from inclusion bodies produced proteins functionally active with respect to crystal deformation, recrystallization inhibition and thermal hysteresis. We observed a reduction of activity in the presence of the pelB leader peptide in comparison with the GS-linked SUMO-tag. Activity was positively correlated to protein concentration and buffer salinity. Thermal hysteresis and crystal deformation habit suggest the affiliation of the proteins to the hyperactive group of AFPs. One isoform, carrying a signal peptide for secretion, produced a thermal hysteresis up to 1.53°C±0.53°C and ice crystals of hexagonal bipyramidal shape. The second isoform, which has a long preceding N-terminal sequence of unknown function, produced thermal hysteresis of up to 2.34°C±0.25°C. Ice crystals grew in form of a hexagonal column in presence of this protein. The different sequences preceding the ice binding domain point to distinct localizations of the proteins inside or outside the cell. We thus propose that AFPs have different functions in vivo, also reflected in their specific TH capability. Copyright © 2011 Elsevier Inc. All rights reserved.

Crystal residence times from trace element zoning in plagioclase reveal changes in magma transfer dynamics at Mt. Etna during the last 400 years

NASA Astrophysics Data System (ADS)

Viccaro, Marco; Barca, Donatella; Bohrson, Wendy A.; D'Oriano, Claudia; Giuffrida, Marisa; Nicotra, Eugenio; Pitcher, Bradley W.

2016-04-01

Trace element zoning in plagioclase of selected alkaline lavas from the historic (1607-1892 AD) and recent (1983-2013 AD) activity of Mt. Etna volcano has been used to explore the possible role that volcano-tectonics exert on magma transfer dynamics. The observed textural characteristics of crystals include near-equilibrium textures (i.e., oscillatory zoning) and textures with variable extent of disequilibrium (patchy zoning, coarse sieve textures and dissolved cores). Historic crystals exhibit lower K concentrations at lower anorthite contents, a feature in agreement with the general more potassic character of the recent lavas if compared to the historic products. Historic plagioclases have statistically higher Ba and lower Sr concentrations than the recent crystals, which result in different Sr/Ba ratios for the two suites of plagioclase. Variations in the anorthite content along core-to-rim profiles obtained on crystals with different types of textures for both the historic and recent eruptive periods were evaluated particularly versus Sr/Ba. At comparable average An contents, crystals characterized by oscillatory zoning, which are representative of near-equilibrium crystallization from the magma, display distinct Sr/Ba ratios. We suggest that these features are primarily related to recharge of a new, geochemically-distinct magma into the storage and transport system of the volcano. In addition to distinct trace element and textural characteristics of plagioclase, Sr diffusion modeling for plagioclase suggests that residence times are generally shorter for crystals found in recently erupted lavas (25-77 years, average 43 years) compared to those of the historic products (43-163 years, average 99 years). Shorter residences times correlate with gradual increases in eruption volume and eruption frequency rates through time. We attribute these features to an increasing influence, since the 17th century, of extensional tectonic structures within the upper 10 km of the Etnean crust, which have promoted shorter residence times and higher eruption frequency.

Growth and defects of explosives crystals

NASA Astrophysics Data System (ADS)

Cady, H. H.

Large single crystals of PETN, RDX, and TNT can be grown easily from evaporating ethyl acetate solutions. The crystals all share a similar type of defect that may not be commonly recognized. The defect generates conical faces, ideally mosaic crystals, and may account for the 'polymorphs' of TNT and detonator grades of PETN. TATB crystals manufactured by the amination of trichlorotrinitrobenzene in dry toluene entrain two forms of ammonium chloride. One of these forms causes 'worm holes' in the TATB crystals that may be the reason for its unusually low failure diameters. Strained HMX crystals form mechanical twins that can spontaneously revert back to the untwinned form when the straining force is removed. Large strains or temperatures above 100 C lock in the mechanical twins.

Phototrophic microbes form endolithic biofilms in ikaite tufa columns (SW Greenland).

PubMed

Trampe, Erik; Castenholz, Richard W; Larsen, Jens E N; Kühl, Michael

2017-11-01

Marine tufa-columns, formed by the hydrated carbonate mineral ikaite, present a unique alkaline microbial habitat only found in Ikka Fjord (SW-Greenland). The outermost parts of the ikaite columns exhibit a multitude of physico-chemical gradients, and the porous ikaite is colonized by endolithic phototrophic biofilms serving as a substrate for grazing epifauna, where scraping by sea urchins affects overall column-topography. We present a detailed study of the optical microenvironment, spatial organization, and photosynthetic activity of endolithic phototrophs within the porous ikaite crystal matrix. Cyanobacteria and diatoms formed distinctly coloured zones and were closely associated with ikaite-crystals via excretion of exopolymers. Scalar-irradiance measurements showed strong attenuation of visible light (400-700 nm), where only ∼1% of incident irradiance remained at 20 mm depth. Transmission spectra showed in vivo absorption signatures of diatom and cyanobacterial photopigments, which were confirmed by HPLC-analysis. Variable-chlorophyll-fluorescence-imaging showed active photosynthesis with high-light acclimation in the outer diatom layer, and low-light acclimation in the underlying cyanobacterial part. Phototrophs in ikaite thus thrive in polymer-bound endolithic biofilms in a complex gradient microhabitat experiencing constant slow percolation of highly alkaline phosphate-enriched spring water mixing with cold seawater at the tufa-column-apex. We discuss the potential role of these biofilms in ikaite column formation. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Effect of surfactants or a water soluble polymer on the crystal transition of clarithromycin during a wet granulation process.

PubMed

Nozawa, Kenji; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2015-11-10

To generate products containing a stable form of clarithromycin (CAM) (form II) regardless of the initial crystal form of CAM or type of granulation solvent, the effects of five surfactants, or a water-soluble polymer (macrogol 400) were determined on the crystal transition of CAM. The metastable form (form I) was kneaded with water, after adding surfactants, or a water-soluble polymer. Form II was also kneaded with ethanol, after adding the same additives. The resulting samples were analyzed by powder X-ray diffraction. Form I was completely converted to form II by a wet granulation using water with additives bearing polyoxyethylene chains such as polysorbate 80 (PS80), polyoxyl 40 stearate or macrogol 400. The granulation of the form II using ethanol with these additives did not result in a crystal transition to form I. Furthermore, CAM tablets were manufactured using granules with PS80, and these crystal forms and dissolution behaviors were investigated. As a result, the wet granulation of CAM with PS80 gave CAM tablets containing only form II and PS80 did not have any adverse effects on tablet characteristics. Therefore, these data suggests that the crystal form of CAM can be controlled to be form II using a wet granulation process with additives bearing polyoxyethylene chains regardless of the initial crystal form of CAM or type of granulation solvent. Copyright © 2015 Elsevier B.V. All rights reserved.

Insect-cell expression, crystallization and X-ray data collection of the bradyzoite-specific antigen BSR4 from Toxoplasma gondii

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

Grujic, Ognjen; Grigg, Michael E.; Boulanger, Martin J., E-mail: mboulang@uvic.ca

2008-05-01

Preliminary X-ray diffraction studies of the bradyzoite-specific surface antigen BSR4 from T. gondii are described. Toxoplasma gondii is an important global pathogen that infects nearly one third of the world’s adult population. A family of developmentally expressed structurally related surface-glycoprotein adhesins (SRSs) mediate attachment to and are utilized for entry into host cells. The latent bradyzoite form of T. gondii persists for the life of the host and expresses a distinct family of SRS proteins, of which the bradyzoite-specific antigen BSR4 is a prototypical member. Structural studies of BSR4 were initiated by first recombinantly expressing BSR4 in insect cells, whichmore » was followed by crystallization and preliminary X-ray data collection to 1.95 Å resolution. Data processing showed that BSR4 crystallized with one molecule in the asymmetric unit of the P4{sub 1}2{sub 1}2 or P4{sub 3}2{sub 1}2 space group, with a solvent content of 60% and a corresponding Matthews coefficient of 2.98 Å{sup 3} Da{sup −1}.« less

Crystallization and crystal manipulation of a steric chaperone in complex with its lipase substrate

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

Pauwels, Kris, E-mail: krpauwel@vub.ac.be; Loris, Remy; Vandenbussche, Guy

2005-08-01

Crystals of the lipase of B. glumae in complex with its specific foldase were obtained in two forms. Crystallization, crystal manipulation and preliminary X-ray diffraction analysis are described. Bacterial lipases that are secreted via the type II secretion pathway require a lipase-specific foldase in order to obtain their native and biologically active conformation in the periplasmic space. The lipase–foldase complex from Burkholderia glumae (319 and 333 residues, respectively) was crystallized in two crystal forms. One crystal form belongs to space group P3{sub 1}21 (P3{sub 2}21), with unit-cell parameters a = b = 122.3, c = 98.2 Å. A procedure ismore » presented which improved the diffraction of these crystals from ∼5 to 2.95 Å. For the second crystal form, which belonged to space group C2 with unit-cell parameters a = 183.0, b = 75.7, c = 116.6 Å, X-ray data were collected to 1.85 Å.« less

Characterization of the multilayered shell of a limpet, Lottia kogamogai (Mollusca: Patellogastropoda), using SEM-EBSD and FIB-TEM techniques.

PubMed

Suzuki, Michio; Kameda, Jun; Sasaki, Takenori; Saruwatari, Kazuko; Nagasawa, Hiromichi; Kogure, Toshihiro

2010-08-01

The microstructure and its crystallographic aspect of the shell of a limpet, Lottiakogamogai, have been investigated, as the first step to clarify the mechanism of shell formation in limpet. The shell consists of five distinct layers stacked along the shell thickness direction. Transmission electron microscopy (TEM) with the focused ion beam (FIB) sample preparation technique was primarily adopted, as well as scanning electron microscopy (SEM) with electron back-scattered diffraction (EBSD). The five layers were termed as M+3, M+2, M+1, M, M-1 from the outside to the inside in previous works, where M means myostracum. The outmost M+3 layer consists of calcite with a "mosaic" structure; granular submicron sub-grains with small-angle grain boundaries often accompanying dislocation arrays. M+2 layer consists of flat prismatic aragonite crystals with a leaf-like cross section, stacked obliquely to the shell surface. It looks that the prismatic crystals are surrounded by organic sheets, forming a compartment structure. M+1 and M-1 layers adopt a crossed lamellar structure consisting of aragonite flat prisms with rectangular cross section. M layer has a prismatic structure of aragonite perpendicular to the shell surface and with irregular shaped cross sections. Distinct organic sheets were not observed between the crystals in M+1, M and M-1 layers. The {110} twins are common in all aragonite M+2, M+1, M and M-1 layers, with the twin boundaries parallel to the prisms. These results for the microstructure of each layer should be considered in the discussion of the formation mechanism of the limpet shell structure. Copyright 2010 Elsevier Inc. All rights reserved.

40Ar/39Ar geochronology and geochemistry of the Central Saurashtra mafic dyke swarm: insights into magmatic evolution, magma transport, and dyke-flow relationships in the northwestern Deccan Traps

NASA Astrophysics Data System (ADS)

Cucciniello, Ciro; Demonterova, Elena I.; Sheth, Hetu; Pande, Kanchan; Vijayan, Anjali

2015-05-01

The Central Saurashtra mafic dyke swarm in the northwestern Deccan Traps contains a few picrites, several subalkalic basalts and basaltic andesites, and an andesite. We have obtained precise 40Ar/39Ar ages of 65.6 ± 0.2 Ma, 66.6 ± 0.3, and 62.4 ± 0.3 Ma (2σ errors) for three of the dykes, indicating the emplacement of the swarm over several million years. Mineral chemical and whole-rock major and trace element and Sr-Nd isotopic data show that fractional crystallization and crystal accumulation were important processes. Except for two dykes (with ɛNd t values of -8.2 and -12.3), the magmas were only moderately contaminated by continental crust. The late-emplaced (62.4 Ma) basalt dyke has compositional characteristics (low La/Sm and Th/Nb, high ɛNd t of +4.3) suggesting little or no crustal contamination. Most dykes are low-Ti and a few high-Ti, and these contrasting Ti types cannot be produced by fractional crystallization processes but require distinct parental magmas. Some dykes are compositionally homogeneous over tens of kilometers, whereas others are heterogeneous, partly because they were formed by multiple magma injections. The combined field and geochemical data establish the Sardhar dyke as ≥62 km long and the longest in Saurashtra, but this and the other Central Saurasthra dykes cannot have fed any of the hitherto studied lava-flow sequences in Saurashtra, given their very distinct Sr-Nd isotopic compositions. As observed previously, high-Ti lavas and dykes only outcrop east-northeast of a line joining Rajkot and Palitana, probably because of underlying enriched mantle at ~65 Ma.

New Form Discovery for the Analgesics Flurbiprofen and Sulindac Facilitated by Polymer-Induced Heteronucleation

PubMed Central

GRZESIAK, ADAM L.; MATZGER, ADAM J.

2008-01-01

The selection and discovery of new crystalline forms is a longstanding issue in solid-state chemistry of critical importance because of the effect molecular packing arrangement exerts on materials properties. Polymer-induced heteronucleation has recently been developed as a powerful approach to discover and control the production of crystal modifications based on the insoluble polymer heteronucleant added to the crystallization solution. The selective nucleation and discovery of new crystal forms of the well-studied pharmaceuticals flurbiprofen (FBP) and sulindac (SUL) has been achieved utilizing this approach. For the first time, FBP form III was produced in bulk quantities and its crystal structure was also determined. Furthermore, a novel 3:2 FBP:H2O phase was discovered that nucleates selectively from only a few polymers. Crystallization of SUL in the presence of insoluble polymers facilitated the growth of form I single crystals suitable for structure determination. Additionally, a new SUL polymorph (form IV) was discovered by this method. The crystal forms of FBP and SUL are characterized by Raman and FTIR spectroscopies, X-ray diffraction, and differential scanning calorimetry. PMID:17567888

Multicolor fluorescence enhancement from a photonics crystal surface

NASA Astrophysics Data System (ADS)

Pokhriyal, A.; Lu, M.; Huang, C. S.; Schulz, S.; Cunningham, B. T.

2010-09-01

A photonic crystal substrate exhibiting resonant enhancement of multiple fluorophores has been demonstrated. The device, fabricated uniformly from plastic materials over a ˜3×5 in.2 surface area by nanoreplica molding, utilizes two distinct resonant modes to enhance electric field stimulation of a dye excited by a λ =632.8 nm laser (cyanine-5) and a dye excited by a λ =532 nm laser (cyanine-3). Resonant coupling of the laser excitation to the photonic crystal surface is obtained for each wavelength at a distinct incident angle. Compared to detection of a dye-labeled protein on an ordinary glass surface, the photonic crystal surface exhibited a 32× increase in fluorescent signal intensity for cyanine-5 conjugated streptavidin labeling, while a 25× increase was obtained for cyanine-3 conjugated streptavidin labeling. The photonic crystal is capable of amplifying the output of any fluorescent dye with an excitation wavelength in the 532 nm<λ<633 nm range by selection of an appropriate incident angle. The device is designed for biological assays that utilize multiple fluorescent dyes within a single imaged area, such as gene expression microarrays.

Multicolor fluorescence enhancement from a photonics crystal surface

PubMed Central

Pokhriyal, A.; Lu, M.; Huang, C. S.; Schulz, S.; Cunningham, B. T.

2010-01-01

A photonic crystal substrate exhibiting resonant enhancement of multiple fluorophores has been demonstrated. The device, fabricated uniformly from plastic materials over a ∼3×5 in.2 surface area by nanoreplica molding, utilizes two distinct resonant modes to enhance electric field stimulation of a dye excited by a λ=632.8 nm laser (cyanine-5) and a dye excited by a λ=532 nm laser (cyanine-3). Resonant coupling of the laser excitation to the photonic crystal surface is obtained for each wavelength at a distinct incident angle. Compared to detection of a dye-labeled protein on an ordinary glass surface, the photonic crystal surface exhibited a 32× increase in fluorescent signal intensity for cyanine-5 conjugated streptavidin labeling, while a 25× increase was obtained for cyanine-3 conjugated streptavidin labeling. The photonic crystal is capable of amplifying the output of any fluorescent dye with an excitation wavelength in the 532 nm<λ<633 nm range by selection of an appropriate incident angle. The device is designed for biological assays that utilize multiple fluorescent dyes within a single imaged area, such as gene expression microarrays. PMID:20957067

Structure of the heterotrimeric complex that regulates type III secretion needle formation

PubMed Central

Quinaud, Manuelle; Plé, Sophie; Job, Viviana; Contreras-Martel, Carlos; Simorre, Jean-Pierre; Attree, Ina; Dessen, Andréa

2007-01-01

Type III secretion systems (T3SS), found in several Gram-negative pathogens, are nanomachines involved in the transport of virulence effectors directly into the cytoplasm of target cells. T3SS are essentially composed of basal membrane-embedded ring-like structures and a hollow needle formed by a single polymerized protein. Within the bacterial cytoplasm, the T3SS needle protein requires two distinct chaperones for stabilization before its secretion, without which the entire T3SS is nonfunctional. The 2.0-Å x-ray crystal structure of the PscE-PscF55–85-PscG heterotrimeric complex from Pseudomonas aeruginosa reveals that the C terminus of the needle protein PscF is engulfed within the hydrophobic groove of the tetratricopeptide-like molecule PscG, indicating that the macromolecular scaffold necessary to stabilize the T3SS needle is totally distinct from chaperoned complexes between pilus- or flagellum-forming molecules. Disruption of specific PscG–PscF interactions leads to impairment of bacterial cytotoxicity toward macrophages, indicating that this essential heterotrimer, which possesses homologs in a wide variety of pathogens, is a unique attractive target for the development of novel antibacterials. PMID:17470796

Trace elements in magnetite as petrogenetic indicators

NASA Astrophysics Data System (ADS)

Dare, Sarah A. S.; Barnes, Sarah-Jane; Beaudoin, Georges; Méric, Julien; Boutroy, Emilie; Potvin-Doucet, Christophe

2014-10-01

We have characterized the distribution of 25 trace elements in magnetite (Mg, Al, Si, P, Ca, Sc, Ti, V, Cr, Mn, Co, Ni, Cu, Zn, Ga, Ge, Y, Zr, Nb, Mo, Sn, Hf, Ta, W, and Pb), using laser ablation ICP-MS and electron microprobe, from a variety of magmatic and hydrothermal ore-forming environments and compared them with data from the literature. We propose a new multielement diagram, normalized to bulk continental crust, designed to emphasize the partitioning behavior of trace elements between magnetite, the melt/fluid, and co-crystallizing phases. The normalized pattern of magnetite reflects the composition of the melt/fluid, which in both magmatic and hydrothermal systems varies with temperature. Thus, it is possible to distinguish magnetite formed at different degrees of crystal fractionation in both silicate and sulfide melts. The crystallization of ilmenite or sulfide before magnetite is recorded as a marked depletion in Ti or Cu, respectively. The chemical signature of hydrothermal magnetite is distinct being depleted in elements that are relatively immobile during alteration and commonly enriched in elements that are highly incompatible into magnetite (e.g., Si and Ca). Magnetite formed from low-temperature fluids has the lowest overall abundance of trace elements due to their lower solubility. Chemical zonation of magnetite is rare but occurs in some hydrothermal deposits where laser mapping reveals oscillatory zoning, which records the changing conditions and composition of the fluid during magnetite growth. This new way of plotting all 25 trace elements on 1 diagram, normalized to bulk continental crust and elements in order of compatibility into magnetite, provides a tool to help understand the processes that control partitioning of a full suit of trace elements in magnetite and aid discrimination of magnetite formed in different environments. It has applications in both petrogenetic and provenance studies, such as in the exploration of ore deposits and in sedimentology.

Solid-state characterization of mefenamic acid.

PubMed

Panchagnula, Ramesh; Sundaramurthy, Prakash; Pillai, Omathanu; Agrawal, Shrutidevi; Raj, Yasvanth Ashok

2004-04-01

The purpose of this study was to characterize mefenamic acid (MA) from commercial samples and samples crystallized from different solvents. Various techniques used for characterization included microscopy (hot stage microscopy, scanning electron microscopy), intrinsic dissolution rate, differential scanning calorimetry (DSC), Fourier transform infrared (FTIR) spectroscopy and powder X-ray diffractometry (pXRD). The commercial samples varied in their crystal habit, thermal behavior, and intrinsic dissolution rate. It was found that the commercial samples were polymorphic Form I, which converted to Form II on heating in a DSC pan. Similarly, compression in an intrinsic dissolution rate (IDR) press resulted in the conversion of Form I to Form II. On the other hand, the samples recrystallized from different solvents under varying conditions yielded different crystal habits. Stirring and degree of supersaturation significantly influenced the crystal habit in all the solvents used in the study. Samples crystallized from ethanol and tetrahydrofuran yielded Form I, which behaved similarly to the commercial samples (M1 and M3). Recrystallization from ethyl acetate at a fast cooling rate yielded Form I, which on melting crystallized to Form II. The form I crystallized from ethyl acetate by fast cooling converted partially to form II on storing at ambient conditions. Forms I and II of MA were enantiotropically related. The results demonstrate the variable material characteristics of the commercial samples of MA and the influence of the crystallizing conditions on the formation of the polymorphs. Copyright 2004 Wiley-Liss, Inc. and the American Pharmacists Association.

Synthesis and Structural Features of [4,4'-Diisopropoxyester-2,2'-bipyridine], [Dichloro(4,4'-diisopropoxyester-2,2'-bi-pyridine)-platinum(ii)] and Its Dichloromethane Solvated Pseudo-Polymorph: Versatile Supramolecular Interactions

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

Browning, Charles; Nesterov, Vladimir N.; Wang, Xiaoping

We report that the organic ligand 4,4'-diisopropoxyester-2,2'-bipyridine, C 18H 20N 2O 4 (1), crystallizes in the triclinic crystal system P-1 and the molecule occupies a special position in the unit cell. In the crystal, molecules form stacks with partial overlapping of the pyridine rings. The Pt(II) dichloro complex of 1 crystallizes from a mixture of ethanol/hexane and from dichloromethane to form orange and yellow crystals, respectively. The orange non-solvated crystals of the (bipyridine)(dichloro)platinum(II) complex C 18H 20N 2O 4PtCl 2 (2) crystallize in the triclinic crystal system P-1 as well with two independent molecules in the unit cell. In themore » crystal packing, molecules form two types of dimers with Pt1 ··· Pt1A and Pt2···Pt2A distances of 3.478 and 5.186 angstrom respectively. The yellow crystals, as a solvated pseudo-polymorph C 18H 20N 2O 4PtCl 2·1.5 CH 2Cl 2 (3) also crystallize in the triclinic crystal system P-1 with two independent molecules in the unit cell. In the crystal packing, molecules form Pt2 ···Pt1 ···Pt1A ···Pt2A intermolecular contacts with alternating distances 3.501 and 3.431 angstrom, respectively, forming infinite chains. Graphical Abstract The dichloro(bipyridine)platinum complex, dichloro(4,4'-diisopropoxyester-2,2'-bipyridine)platinum(II), forms single crystals as a stable non-solvated form and a solvated polymorph with dramatically different supramolecular structure and short contacts.« less

Synthesis and Structural Features of [4,4'-Diisopropoxyester-2,2'-bipyridine], [Dichloro(4,4'-diisopropoxyester-2,2'-bi-pyridine)-platinum(ii)] and Its Dichloromethane Solvated Pseudo-Polymorph: Versatile Supramolecular Interactions

DOE PAGES

Browning, Charles; Nesterov, Vladimir N.; Wang, Xiaoping; ...

2015-06-03

We report that the organic ligand 4,4'-diisopropoxyester-2,2'-bipyridine, C 18H 20N 2O 4 (1), crystallizes in the triclinic crystal system P-1 and the molecule occupies a special position in the unit cell. In the crystal, molecules form stacks with partial overlapping of the pyridine rings. The Pt(II) dichloro complex of 1 crystallizes from a mixture of ethanol/hexane and from dichloromethane to form orange and yellow crystals, respectively. The orange non-solvated crystals of the (bipyridine)(dichloro)platinum(II) complex C 18H 20N 2O 4PtCl 2 (2) crystallize in the triclinic crystal system P-1 as well with two independent molecules in the unit cell. In themore » crystal packing, molecules form two types of dimers with Pt1 ··· Pt1A and Pt2···Pt2A distances of 3.478 and 5.186 angstrom respectively. The yellow crystals, as a solvated pseudo-polymorph C 18H 20N 2O 4PtCl 2·1.5 CH 2Cl 2 (3) also crystallize in the triclinic crystal system P-1 with two independent molecules in the unit cell. In the crystal packing, molecules form Pt2 ···Pt1 ···Pt1A ···Pt2A intermolecular contacts with alternating distances 3.501 and 3.431 angstrom, respectively, forming infinite chains. Graphical Abstract The dichloro(bipyridine)platinum complex, dichloro(4,4'-diisopropoxyester-2,2'-bipyridine)platinum(II), forms single crystals as a stable non-solvated form and a solvated polymorph with dramatically different supramolecular structure and short contacts.« less

Solubility behavior of lamivudine crystal forms in recrystallization solvents.

PubMed

Jozwiakowski, M J; Nguyen, N A; Sisco, J M; Spancake, C W

1996-02-01

Lamivudine can be obtained as acicular crystals (form I, 0.2 hydrate) from water or methanol and as bipyramidal crystals (form II, nonsolvated) from many nonaqueous solvents. Form II is thermodynamically favored in the solid state (higher melting point and greater density than form I) at ambient relative humidities. Solubility measurements on both forms versus solvent and temperature was used to determine whether entropy or enthalpy was the driving force for solubility. Solution calorimetry data indicated that form I is favored (less soluble) in all solvents studied on the basis of enthalpy alone. In higher alcohols and other organic solvents, form I has a larger entropy of solution than form II, which compensates for the enthalpic factors and results in physical stability for form II in these systems. The metastable crystal form solubility at 25 degrees C was estimated to be 1.2-2.3 times as high as the equilibrium solubility of the stable form, depending on the temperature, solvent, and crystal form. Binary solvent studies showed that > 18-20% water must be present in ethanol to convert the excess solid to form I at equilibrium.

In-Situ Atomic Force Microscope Imaging of Calcite Etch Pit Morphology Changes in Undersaturated and 1-Hydroxyethylidene-1,1-diphosphonic Acid Poisoned Solutions

PubMed Central

Britt, David W.

2012-01-01

Morphology changes in etch pits formed on the (1014) cleavage plane of calcite were induced by varying the ratio of [Ca2+] to [CO32−] in the bulk solution as well as through the addition of the crystal poison 1-hydroxyethylidene-1,1-diphosphonic acid (HEDP). Three distinct morphologies were noted: symmetric rhombic, asymmetric rhombic, and triangular with a rough curved hypotenuse. The latter represents a transient morphology which is only observed during the actual dissolution process, while the former morphologies persist after dissolution is halted. PMID:25125794

Self-organization of a periodic structure between amorphous and crystalline phases in a GeTe thin film induced by femtosecond laser pulse amorphization

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

Katsumata, Y.; Morita, T.; Morimoto, Y.

A self-organized fringe pattern in a single amorphous mark of a GeTe thin film was formed by multiple femtosecond pulse amorphization. Micro Raman measurement indicates that the fringe is a periodic alternation between crystalline and amorphous phases. The period of the fringe is smaller than the irradiation wavelength and the direction is parallel to the polarization direction. Snapshot observation revealed that the fringe pattern manifests itself via a complex but coherent process, which is attributed to crystallization properties unique to a nonthermally amorphized phase and the distinct optical contrast between crystalline and amorphous phases.

[Cognitive capacity in advanced age: initial results of the Berlin Aging Study].

PubMed

Lindenberger, U; Baltes, P B

1995-01-01

This study reports data on intellectual functioning in old and very old age from the Berlin Aging Study (N = 516; age range = 70-103 years; mean age = 85 years). A psychometric battery of 14 tests was used to assess five cognitive abilities: reasoning, memory, and perceptual speed from the broad fluid-mechanical as well as knowledge and fluency from the broad crystallized-pragmatic domains. Cognitive abilities had a negative linear relationship with age, with more pronounced age-based reductions in fluid-mechanical than crystallized-pragmatic abilities. At the same time, ability intercorrelations formed a highly positive manifold, and did not follow the fluid-crystallized distinction. Interindividual variability was of about equal magnitude across the entire age range studied. There was, however, no evidence for substantial sex differences. As to origins of individual differences, indicators of sensory and sensorimotor functioning were more powerful predictors of intellectual functioning than cultural-biographical variables, and the two sets of predictors were, consistent with theoretical expectations, differentially related to measures of fluid-mechanical (perceptual speed) and crystallized pragmatic (knowledge) functioning. Results, in general indicative of sizeable and general losses with age, are consistent with the view that aging-induced biological influences are a prominent source of individual differences in intellectual functioning in old and very old age. Longitudinal follow-ups are underway to examine the role of cohort effects, selective mortality, and interindividual differences in change trajectories.

Crystallization of Na2O-SiO2 gel and glass

NASA Technical Reports Server (NTRS)

Neilson, G. F.; Weinberg, M. C.

1984-01-01

The crystallization behavior of a 19 wt pct soda silica gel and gel-derived glass was compared to that of the ordinary glass of the same composition. Both bulk and ground glass samples were utilized. X-ray diffraction measurements were made to identify the crystalline phases and gauge the extent of crystallization. It was found that the gel crystallized in a distinctive manner, while the gel glass behavior was not qualitatively different from that of the ordinary glass.

Relationship Between Equilibrium Forms of Lysozyme Crystals and Precipitant Anions

NASA Technical Reports Server (NTRS)

Nadarajah, Arunan

1996-01-01

Molecular forces, such as electrostatic, hydrophobic, van der Waals and steric forces, are known to be important in determining protein interactions. These forces are affected by the solution conditions and changing the pH, temperature or the ionic strength of the solution can sharply affect protein interactions. Several investigations of protein crystallization have shown that this process is also strongly dependent on solution conditions. As the ionic strength of the solution is increased, the initially soluble protein may either crystallize or form an amorphous precipitate at high ionic strengths. Studies done on the model protein hen egg white lysozyme have shown that different crystal forms can be easily and reproducibly obtained, depending primarily on the anion used to desolubilize the protein. In this study we employ pyranine to probe the effect of various anions on the water structure. Additionally, lysozyme crystallization was carried out at these conditions and the crystal form was determined by X-ray crystallography. The goal of the study was to understand the physico-chemical basis for the effect of changing the anion concentration on the equilibrium form of lysozyme crystals. It will also verify the hypothesis that the anions, by altering the bulk water structure in the crystallizing solutions, alter the surface energy of the between the crystal faces and the solution and, consequently, the equilibrium form of the crystals.

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.

Effects of storage time and temperature on pH, specific gravity, and crystal formation in urine samples from dogs and cats.

PubMed

Albasan, Hasan; Lulich, Jody P; Osborne, Carl A; Lekcharoensuk, Chalermpol; Ulrich, Lisa K; Carpenter, Kathleen A

2003-01-15

To determine effects of storage temperature and time on pH and specific gravity of and number and size of crystals in urine samples from dogs and cats. Randomized complete block design. 31 dogs and 8 cats. Aliquots of each urine sample were analyzed within 60 minutes of collection or after storage at room or refrigeration temperatures (20 vs 6 degrees C [68 vs 43 degrees F]) for 6 or 24 hours. Crystals formed in samples from 11 of 39 (28%) animals. Calcium oxalate (CaOx) crystals formed in vitro in samples from 1 cat and 8 dogs. Magnesium ammonium phosphate (MAP) crystals formed in vitro in samples from 2 dogs. Compared with aliquots stored at room temperature, refrigeration increased the number and size of crystals that formed in vitro; however, the increase in number and size of MAP crystals in stored urine samples was not significant. Increased storage time and decreased storage temperature were associated with a significant increase in number of CaOx crystals formed. Greater numbers of crystals formed in urine aliquots stored for 24 hours than in aliquots stored for 6 hours. Storage time and temperature did not have a significant effect on pH or specific gravity. Urine samples should be analyzed within 60 minutes of collection to minimize temperature- and time-dependent effects on in vitro crystal formation. Presence of crystals observed in stored samples should be validated by reevaluation of fresh urine.

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

A New Protein Architecture for Processing Alkylation Damaged DNA: The Crystal Structure of DNA Glycosylase AlkD

PubMed Central

Rubinson, Emily H.; Metz, Audrey H.; O'Quin, Jami; Eichman, Brandt F.

2013-01-01

Summary DNA glycosylases safeguard the genome by locating and excising chemically modified bases from DNA. AlkD is a recently discovered bacterial DNA glycosylase that removes positively charged methylpurines from DNA, and was predicted to adopt a protein fold distinct from other DNA repair proteins. The crystal structure of Bacillus cereus AlkD presented here shows that the protein is composed exclusively of helical HEAT-like repeats, which form a solenoid perfectly shaped to accommodate a DNA duplex on the concave surface. Structural analysis of the variant HEAT repeats in AlkD provides a rationale for how this protein scaffolding motif has been modified to bind DNA. We report 7mG excision and DNA binding activities of AlkD mutants, along with a comparison of alkylpurine DNA glycosylase structures. Together, these data provide important insight into the requirements for alkylation repair within DNA and suggest that AlkD utilizes a novel strategy to manipulate DNA in its search for alkylpurine bases. PMID:18585735

The Crystal Structure of the Drosophila Germline Inducer Oskar Identifies Two Domains with Distinct Vasa Helicase- and RNA-Binding Activities.

PubMed

Jeske, Mandy; Bordi, Matteo; Glatt, Sebastian; Müller, Sandra; Rybin, Vladimir; Müller, Christoph W; Ephrussi, Anne

2015-07-28

In many animals, the germ plasm segregates germline from soma during early development. Oskar protein is known for its ability to induce germ plasm formation and germ cells in Drosophila. However, the molecular basis of germ plasm formation remains unclear. Here, we show that Oskar is an RNA-binding protein in vivo, crosslinking to nanos, polar granule component, and germ cell-less mRNAs, each of which has a role in germline formation. Furthermore, we present high-resolution crystal structures of the two Oskar domains. RNA-binding maps in vitro to the C-terminal domain, which shows structural similarity to SGNH hydrolases. The highly conserved N-terminal LOTUS domain forms dimers and mediates Oskar interaction with the germline-specific RNA helicase Vasa in vitro. Our findings suggest a dual function of Oskar in RNA and Vasa binding, providing molecular clues to its germ plasm function. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

Microscopic approach of the crystallization of tripalmitin and tristearin by microscopy.

PubMed

Silva, Roberta Claro da; Martini Soares, Fabiana Andrea Schafer De; Maruyama, Jéssica Mayumi; Dagostinho, Natália Roque; Silva, Ylana Adami; Ract, Juliana Neves Rodrigues; Gioielli, Luiz Antonio

2016-06-01

The crystallization behavior of lipids has important implications in industrial processing of food products, whose physical characteristics depend largely on crystallized fats. The study of the crystallization behavior and polymorphism of a pure lipid system is of great scientific importance as a means of gaining an understanding of the phenomena involved, serving as basic knowledge to help guide the addition or removal of these compounds in different raw materials. The crystallization behavior and polymorphism of pure tripalmitin (PPP) and tristearin (SSS) were investigated by Polarized Light Microscopy (PLM) and Differential Scanning Calorimetry (DSC) under different crystallization conditions. The polymorphic forms (β' and β) of PPP and SSS exhibited different morphologies depending on how they were obtained, either from α form recrystallization or from isotropic melt. Crystallization in the β form was faster in SSS than in PPP, indicating that the process occurs faster in TAGs composed of longer fatty acid chains. Both β' and β polymorphic forms were obtained from α form recrystallization, albeit with predominance of the β form. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Characterization and evaluation of miconazole salts and cocrystals for improved physicochemical properties.

PubMed

Tsutsumi, Shunichirou; Iida, Motoo; Tada, Norio; Kojima, Takashi; Ikeda, Yukihiro; Moriwaki, Toshiya; Higashi, Kenjirou; Moribe, Kunikazu; Yamamoto, Keiji

2011-12-15

Miconazole salts and cocrystals were studied to improve the physicochemical properties of miconazole. Maleate, hemifumarate, and hemisuccinate were prepared and characterized by powder X-ray diffractometry, differential scanning calorimetry, and single crystal X-ray diffractometry. The intrinsic dissolution rate and stability of each miconazole crystal form were compared to those of freebase and nitrate to evaluate the optimal crystal form. Crystal structure analysis indicated that maleate was a salt formed by proton transfer from the acid to the imidazole group of miconazole. Hemifumarate and hemisuccinate were determined to be cocrystals formed by hydrogen bonding between the acids and the base in their crystal lattices. Intrinsic dissolution tests showed that the formation of salts and cocrystals improved the dissolution rate of miconazole. Stability tests of preliminary formulations prepared with each crystal form indicated that maleate and hemifumarate were unstable at 80°C and generated a specific degraded product, i.e., a Michael adduct, between miconazole and the acids. Hemisuccinate had a superior intrinsic dissolution rate and stability, and is thus considered a promising crystal form of miconazole. Copyright © 2011 Elsevier B.V. All rights reserved.

Calciphytoliths (calcium oxalate crystals) analysis for the identification of decayed tea plants (Camellia sinensis L.).

PubMed

Zhang, Jianping; Lu, Houyuan; Huang, Linpei

2014-10-24

The history of tea is poorly known, mainly due to the questionable identification of decayed tea plants in archaeological samples. This paper attempts to test the utility of calciphytoliths (calcium oxalate crystals) for the identification of tea in archaeological samples. It provides the first survey of the macropatterns of calciphytoliths in several species of Theaceae and common non-Theaceae plants. Crystals were extracted from 45 samples of tea, Theaceae and common non-Theaceae plants, and detected microscopically between crossed polarizers. In tea plants, druse and trichome base are the most distinctive crystals. Druses have the smallest diameter (11.65 ± 3.64 μm), and trichome bases have four distinctive straight and regular cracks, similar to a regular extinction cross. The results provide morphological criteria for distinguishing tea from other plants, specifically the presence of identifiable druses together with calcified trichome bases. The implications are significant for understanding the history of tea and plant exploitation, especially for plants for which the preservation of macrofossils is poor.

Amorphous photonic crystals with only short-range order.

PubMed

Shi, Lei; Zhang, Yafeng; Dong, Biqin; Zhan, Tianrong; Liu, Xiaohan; Zi, Jian

2013-10-04

Distinct from conventional photonic crystals with both short- and long-range order, amorphous photonic crystals that possess only short-range order show interesting optical responses owing to their unique structural features. Amorphous photonic crystals exhibit unique light scattering and transport, which lead to a variety of interesting phenomena such as isotropic photonic bandgaps or pseudogaps, noniridescent structural colors, and light localization. Recent experimental and theoretical advances in the study of amorphous photonic crystals are summarized, focusing on their unique optical properties, artificial fabrication, bionspiration, and potential applications. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Magmatic processes that generated the rhyolite of Glass Mountain, Medicine Lake volcano, N. California

USGS Publications Warehouse

Grove, T.L.; Donnelly-Nolan, J. M.; Housh, T.

1997-01-01

Glass Mountain consists of a 1 km3, compositionally zoned rhyolite to dacite glass flow containing magmatic inclusions and xenoliths of underlying shallow crust. Mixing of magmas produced by fractional crystallization of andesite and crustal melting generated the rhyolite of Glass Mountain. Melting experiments were carried out on basaltic andesite and andesite magmatic inclusions at 100, 150 and 200 MPa, H2O-saturated with oxygen fugacity controlled at the nickel-nickel oxide buffer to provide evidence of the role of fractional crystallization in the origin of the rhyolite of Glass Mountain. Isotopic evidence indicates that the crustal component assimilated at Glass Mountain constitutes at least 55 to 60% of the mass of erupted rhyolite. A large volume of mafic andesite (2 to 2.5 km3) periodically replenished the magma reservoir(s) beneath Glass Mountain, underwent extensive fractional crystallization and provided the heat necessary to melt the crust. The crystalline residues of fractionation as well as residual liquids expelled from the cumulate residues are preserved as magmatic inclusions and indicate that this fractionation process occurred at two distinct depths. The presence and composition of amphibole in magmatic inclusions preserve evidence for crystallization of the andesite at pressures of at least 200 MPa (6 km depth) under near H2O-saturated conditions. Mineralogical evidence preserved in olivine-plagioclase and olivine-plagioclase-high-Ca clinopyroxene-bearing magmatic inclusions indicates that crystallization under near H2O-saturated conditions also occurred at pressures of 100 MPa (3 km depth) or less. Petrologic, isotopic and geochemical evidence indicate that the andesite underwent fractional crystallization to form the differentiated melts but had no chemical interaction with the melted crustal component. Heat released by the fractionation process was responsible for heating and melting the crust.

On the Hydrogranular Dynamics of Magmatic Gravity Currents

NASA Astrophysics Data System (ADS)

McIntire, M. Z.; Bergantz, G. W.; Schleicher, J.; Burgisser, A.

2016-12-01

Magmatic processes are generally governed by multi-phase interactions of silicate liquid, crystals, and bubbles. However, the modes of dissipation and the manner that stress is transmitted are poorly understood. We use a model of a simple but widely applicable gravity current as a means to exemplify the hydrogranular dynamics in crystal-rich magmas. Viscous and lubrication forces are of special interest because they have a dual role in dispersal and mixing in a crystal-rich gravity current. For example, lubrication forces provide an initial apparent yield strength by inducing a negative pore pressure as crystals move apart. However, once the gravity current is underway, lubrication forces reduce the dissipation due to collision and frictional contact.The gravity current is initiated by a combination of toppling and sliding along a well-defined granular fault. This produces three distinct regimes: a quasi-static base, an overlying particle hump that translates in a quasi-plastic fashion by grain-passing and rolling until the angle of repose is reached, and a viscous particle current. The current initially forms a leading vortex at the head, but the loss of crystals by sedimentation-assisted granular capture by an upward growing particle front drains energy from the flow. The vortex is soon abandoned, but persists in the reservoir as a fossil feature of orphaned crystals in a smear of previous intercumulate fluid. The kinetic energy of the most active crystals decays in a dual fashion, initially linearly, then parabolically with a near symmetrical increase and loss of kinetic energy.There is very little entrainment and mixing between intercumulate and reservoir fluids from magmatic gravity currents. Only a thin seam of reservoir melt is captured by the base of the flow as it descends across the floor. Hence magmatic gravity currents, while producing modest amounts of crystal sorting, are not effective agents of mixing as lubrication and viscous forces inhibit interpenetration of reservoir fluid.

Is it Possible to have the Similar Unit Cell in Crystals of Different form from the same Macromolecule? (A Case Study of Ribosome Crystals)

NASA Technical Reports Server (NTRS)

Karpova, E. A.; Rose, M. Franklin (Technical Monitor)

2000-01-01

Three different types of ribosome crystals were grown by the vapor diffusion technique in hanging drops as described in (1,2). The ribosome is a large asymmetric RNA-protein complex (2.3 million Da), which is protein syntheses machinery of the cell. In this poster we would like to discuss the features of ribosome crystallization. Ribosomes were purified from the thermophilic bacteria Thermus thermophilus by centrifugation (3). Three types of crystals (needle, flat tetragonal and tetragonal-like pyramid) can be grown from the same solution; furthermore, in the same drop using 10-15% 2-methyl-2,4- pentanediol as a precipitant. The crystals appeared in 5-48 hours. The crystals were stable and can co-exist in solution over long period of time. The kinetics of appearance of different crystal forms was different: first the needle crystals were grown, then the tetragonal, and finally the tetragonal pyramids. Later studies of the process of ribosome crystal growth depending on supersaturation showed that low supersaturation results in the appearance of tetragonal plates or tetragonal-like pyramids. An electron microscopy study, together with computer modeling, has shown that crystals of different forms have a high probability of having the same unit cell parameters. According to these experiments the following conclusion can be dranvn: the level of supersaturation of the macromolecule in a crystallizing solution is one of the major factors for forming three-dimensional crystals convenient for X-rays diffraction analysis. From the same macromolecule solution, crystals of different forms can be grown at approximately the same conditions by varying the concentration of macromolecule in the solution. Ion-macromolecule and water-macromolecule interactions, apparently, play the main role in the formation of the unit cell of the crystals.

Crystallization and preliminary crystallographic analysis of the Clostridium perfringens enterotoxin

PubMed Central

Briggs, David C.; Smedley, James G.; McClane, Bruce A.; Basak, Ajit K.

2010-01-01

Clostridium perfringens is a Gram-positive anaerobic species of bacterium that is notable for its ability to produce a plethora of toxins, including membrane-active toxins (α-toxins), pore-forming toxins (∊-toxins) and binary toxins (ι-toxins). Here, the crystallization of the full-length wild-type C. perfringens enterotoxin is reported, which is the causative agent of the second most prevalent food-borne illness in the United States and has been implicated in many other gastrointestinal pathologies. Several crystal forms were obtained. However, only two of these optimized crystal forms (I and II) were useable for X-ray diffraction data collection. The form I crystals diffracted to d min = 2.7 Å and belonged to space group C2, while the form II crystals diffracted to d min = 4 Å and belonged to space group P213. PMID:20606275

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

Jones, B.; Renaut, R.W.

Skeletal crystals are hollow crystals that develop because their outer walls grow before their cores. The presence of skeletal crystals of calcite (three types--trigonal prisms, hexagonal prisms, and plates) and trona in hot (> 90 C) spring deposits in New Zealand (Waikite Springs and Ohaaki Pool) and Kenya (Lorusio hot springs) shows that they can form in natural sedimentary regimes. Analysis of samples from these deposits shows that this crystal morphology develops under disequilibrium conditions that are unrelated to a specific environmental or diagenetic setting. Skeletal crystals transform into solid crystals when subsequent precipitation fills their hollow cores. In somemore » cases, this may involve precipitation of crystalline material that has a sieve-like texture. In other examples, the skeletal crystal provides a framework upon which other materials can be precipitated. Walls in the skeletal trigonal calcite prisms from Waikite Springs are formed of subcrystals that mimic the shape of the parent crystal. Similarly, plate-like skeletal crystals from Lorusio are formed of densely packed subcrystals that are < 0.5 {micro}m long. Conversely, the walls of the skeletal hexagonal calcite crystals from Ohaaki Pool and the skeletal trona crystals from Lorusio are not formed of subcrystals. Recognition of skeletal crystals is important because they represent growth that follows the reverse pattern of normal growth. Failure to recognize that crystal growth followed the skeletal motif may lead to false interpretations concerning the growth of a crystal.« less

Nucleation and growth in alkaline zinc electrodeposition An Experimental and Theoretical study

NASA Astrophysics Data System (ADS)

Desai, Divyaraj

The current work seeks to investigate the nucleation and growth of zinc electrodeposition in alkaline electrolyte, which is of commercial interest to alkaline zinc batteries for energy storage. The morphology of zinc growth places a severe limitation on the typical cycle life of such batteries. The formation of mossy zinc leads to a progressive deterioration of battery performance while zinc dendrites are responsible for sudden catastrophic battery failure. The problems are identified as the nucleation-controlled formation of mossy zinc and the transport-limited formation of dendritic zinc. Consequently, this thesis work seeks to investigate and accurately simulate the conditions under which such morphologies are formed. The nucleation and early-stage growth of Zn electrodeposits is studied on carbon-coated TEM grids. At low overpotentials, the morphology develops by aggregation at two distinct length scales: ~5 nm diameter monocrystalline nanoclusters form ~50nm diameter polycrystalline aggregates, and second, the aggregates form a branched network. Epitaxial (0002) growth above a critical overpotential leads to the formation of hexagonal single-crystals. A kinetic model is provided using the rate equations of vapor solidification to simulate the evolution of the different morphologies. On solving these equations, we show that aggregation is attributed to cluster impingement and cluster diffusion while single-crystal formation is attributed to direct attachment. The formation of dendritic zinc is investigated using in-operando transmission X-ray microscopy which is a unique technique for imaging metal electrodeposits. The nucleation density of zinc nuclei is lowered using polyaniline films to cover the active nucleation sites. The effect of overpotential is investigated and the morphology shows beautiful in-operando formation of symmetric zinc crystals. A linear perturbation model was developed to predict the growth and formation of these crystals to first-order accuracy. Existing phase-field models of solidification and electrodeposition are used to simulate the growth and formation of individual zinc crystals. The driving force for solidification models (i.e. supersaturation) is reinterpreted in terms of overpotential under the assumption of a conductive electrolyte. The final morphologies are astonishingly similar to those observed in dynamical experiments. Further, the phase-field models obey the predictions of the linear perturbation analysis, which gives good credibility to the phase-field approach to simulate electrodeposition processes.

Discrimination of Two Aspects of Cognitive-Social Intelligence from Academic Intelligence.

ERIC Educational Resources Information Center

Jones, Karen; Day, Jeanne D.

1997-01-01

A multitrait-multimethod study collected measures of social-cognitive flexibility, crystallized social knowledge, and academic problem solving from 169 high school seniors. Results support a division of social-cognitive intelligence into declarative and procedural social knowledge (crystallized) and flexible knowledge application as distinct from…

Aggressive versus Nonaggressive Antisocial Behavior: Distinctive Etiological Moderation by Age

ERIC Educational Resources Information Center

Burt, S. Alexandra; Neiderhiser, Jenae M.

2009-01-01

Research has supported the existence of distinct behavioral patterns, demographic correlates, and etiologic mechanisms for aggressive (AGG) versus nonaggressive but delinquent (DEL) antisocial behavior. Though behavioral genetic studies have the potential to further crystallize these dimensions, inconsistent results have limited their…

Viral assembly of oriented quantum dot nanowires

NASA Astrophysics Data System (ADS)

Mao, Chuanbin; Flynn, Christine E.; Hayhurst, Andrew; Sweeney, Rozamond; Qi, Jifa; Georgiou, George; Iverson, Brent; Belcher, Angela M.

2003-06-01

The highly organized structure of M13 bacteriophage was used as an evolved biological template for the nucleation and orientation of semiconductor nanowires. To create this organized template, peptides were selected by using a pIII phage display library for their ability to nucleate ZnS or CdS nanocrystals. The successful peptides were expressed as pVIII fusion proteins into the crystalline capsid of the virus. The engineered viruses were exposed to semiconductor precursor solutions, and the resultant nanocrystals that were templated along the viruses to form nanowires were extensively characterized by using high-resolution analytical electron microscopy and photoluminescence. ZnS nanocrystals were well crystallized on the viral capsid in a hexagonal wurtzite or a cubic zinc blende structure, depending on the peptide expressed on the viral capsid. Electron diffraction patterns showed single-crystal type behavior from a polynanocrystalline area of the nanowire formed, suggesting that the nanocrystals on the virus were preferentially oriented with their [001] perpendicular to the viral surface. Peptides that specifically directed CdS nanocrystal growth were also engineered into the viral capsid to create wurtzite CdS virus-based nanowires. Lastly, heterostructured nucleation was achieved with a dual-peptide virus engineered to express two distinct peptides within the same viral capsid. This work represents a genetically controlled biological synthesis route to a semiconductor nanoscale heterostructure.

Viral assembly of oriented quantum dot nanowires.

PubMed

Mao, Chuanbin; Flynn, Christine E; Hayhurst, Andrew; Sweeney, Rozamond; Qi, Jifa; Georgiou, George; Iverson, Brent; Belcher, Angela M

2003-06-10

The highly organized structure of M13 bacteriophage was used as an evolved biological template for the nucleation and orientation of semiconductor nanowires. To create this organized template, peptides were selected by using a pIII phage display library for their ability to nucleate ZnS or CdS nanocrystals. The successful peptides were expressed as pVIII fusion proteins into the crystalline capsid of the virus. The engineered viruses were exposed to semiconductor precursor solutions, and the resultant nanocrystals that were templated along the viruses to form nanowires were extensively characterized by using high-resolution analytical electron microscopy and photoluminescence. ZnS nanocrystals were well crystallized on the viral capsid in a hexagonal wurtzite or a cubic zinc blende structure, depending on the peptide expressed on the viral capsid. Electron diffraction patterns showed single-crystal type behavior from a polynanocrystalline area of the nanowire formed, suggesting that the nanocrystals on the virus were preferentially oriented with their [001] perpendicular to the viral surface. Peptides that specifically directed CdS nanocrystal growth were also engineered into the viral capsid to create wurtzite CdS virus-based nanowires. Lastly, heterostructured nucleation was achieved with a dual-peptide virus engineered to express two distinct peptides within the same viral capsid. This work represents a genetically controlled biological synthesis route to a semiconductor nanoscale heterostructure.

Novel organogels for topical delivery of naproxen: design, physicochemical characteristics and in vitro drug permeation.

PubMed

Osmałek, Tomasz; Milanowski, Bartłomiej; Froelich, Anna; Górska, Sylwia; Białas, Wojciech; Szybowicz, Mirosław; Kapela, Marcin

2017-06-01

Taking into account possible irritation of the skin upon contact with naproxen (NPX) crystals and lower bioavailability after administration of the suspended or ionized drug, the aim of the work was to design and characterize novel and easy-to-formulate gels with the entirely dissolved drug in the acidic form. The formulations contained ethanol, SynperonicTMPE/L 62 and Arlasolve® DMI or Transcutol®. Carbopol®940 was used as the thickener. The properties of organogels were compared with six market products. The rheological measurements included steady flow experiments and oscillatory analysis. The texture profile analysis was conducted to calculate the mechanistic parameters. The in vitro permeation studies were performed on SOTAX CE 7 smart apparatus with the application of Strat-M artificial membranes. The obtained organogels fulfilled the requirements for topical products in terms of consistency, uniformity, stability, drug dissolution and permeation. The permeation studies revealed distinct differences among the commercial hydrogels according to permeation coefficients (k P ), drug flux (J ss ) and average cumulative amount of NPX per area after 12 h (Q 12h ). The presented work clearly shows that the organogels can be proposed as an alternative for commercial products where NPX occurs in the form of crystals.

Studies of Magmatic Inclusions in the Basaltic Martian Meteorites Shergotty, Zagami, EETA 79001 and QUE 94201

NASA Technical Reports Server (NTRS)

Harvey, Ralph P.; McKay, Gordon A.

1997-01-01

Currently there are 12 meteorites thought by planetary scientists to be martian samples, delivered to the Earth after violent impacts on that planet's surface. Of these 12 specimens, 4 are basaltic: Shergotty, Zagami, EETA 79001 and QUE 94201. Basalts are particularly important rocks to planetary geologists- they are the most common rocks found on the surfaces of the terrestrial planets, representing volcanic activity of their parent worlds. In addition, because they are generated by partial melting of the mantle and/or lower crust, they can serve as guide posts to the composition and internal processes of a planet. Consequently these four meteorites can serve as 'ground-truth' representatives of the predominant volcanic surface rocks of Mars, and offer researchers a glimpse of the magmatic history of that planet. Unfortunately, unraveling the parentage of a basaltic rock is not always straightforward. While many basalts are simple, unaltered partial melts of the mantle, others have undergone secondary processes which change the original parental chemistry, such as assimilation of other crustal rocks, mixing with other magmas, accumulation, re-equilibration between mineral species after crystallization, loss of late-stage magmatic fluids and alteration by metamorphic or metasomatic processes. Fortunately, magmatic inclusions can trap the evolving magmatic liquid, isolating it from many of these secondary processes and offering a direct look at the magma during different stages of development. These inclusions form when major or minor phases grow skeletally, surrounding small amounts of the parental magma within pockets in the growing crystal. The inclusion as a whole (usually consisting of glass with enclosed crystals) continues to represent the composition of the parental magma at the time the melt pocket closed, even when the rock as a whole evolves under changing conditions. The four basaltic martian meteorites contain several distinct generations of melt inclusions; those found within early-forming pigeonite, intermediate and late-forming Ti, Fe-oxides and sulfides, and intermediate to late-forming phosphates. In this summer' s study we have made a detailed study of all of the various forms of inclusions found within the 4 basaltic martian meteorites listed above. Glasses and minerals within the inclusions were analyzed using the Camera SX-100 Electron Microprobe in Building 31. The mineralogy and textural context of the inclusions will then be used to explore the crystallization history of these specimens, and to investigate any differences in crystallization history or parental magma compositions between these rocks. In this manner, the magmatic inclusions provide a road map backwards toward the 'parental' compositions for the basaltic martian meteorites and provide significant insight into the igneous processes found within the crust of Mars.

Recovering and recycling uranium used for production of molybdenum-99

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

Reilly, Sean Douglas; May, Iain; Copping, Roy

A processes for recycling uranium that has been used for the production of molybdenum-99 involves irradiating a solution of uranium suitable for forming fission products including molybdenum-99, conditioning the irradiated solution to one suitable for inducing the formation of crystals of uranyl nitrate hydrates, then forming the crystals and a supernatant and then separating the crystals from the supernatant, thus using the crystals as a source of uranium for recycle. Molybdenum-99 is recovered from the supernatant using an adsorbent such as alumina. Another process involves irradiation of a solid target comprising uranium, forming an acidic solution from the irradiated targetmore » suitable for inducing the formation of crystals of uranyl nitrate hydrates, then forming the crystals and a supernatant and then separating the crystals from the supernatant, thus using the crystals as a source of uranium for recycle. Molybdenum-99 is recovered from the supernatant using an adsorbent such as alumina.« less

Caught in the Act: 1.5 Å Resolution Crystal Structures of the HIV-1 Protease and the I54V Mutant Reveal a Tetrahedral Reaction Intermediate

PubMed Central

Kovalevsky, Andrey Y.; Chumanevich, Alexander A.; Liu, Fengling; Louis, John M.; Weber, Irene T.

2008-01-01

HIV-1 protease (PR) is the target for several important antiviral drugs used in AIDS therapy. The drugs bind inside the active-site cavity of PR where normally the viral poly-protein substrate is bound and hydrolyzed. We report two high resolution crystal structures of wild-type PR (PRWT) and the multi-drug resistant variant with the I54V mutation (PRI54V) in complex with a peptide at 1.46 Å and 1.50 Å resolution, respectively. The peptide forms a gem-diol tetrahedral reaction intermediate (TI) in the crystal structures. Distinctive interactions are observed for the TI binding in the active site cavity of PRWT and PRI54V. The mutant PRI54V /TI complex has lost water-mediated hydrogen bond interactions with the amides of Ile 50 and 50′ in the flap. Hence, the structures provide insight into the mechanism of drug resistance arising from this mutation. The structures also illustrate an intermediate state in the hydrolysis reaction. One of the gem-diol hydroxide groups in the PRWT complex forms a very short (2.3 Å) hydrogen bond with the outer carboxylate oxygen of Asp25. Quantum chemical calculations based on this TI structure are consistent with protonation of the inner carboxylate oxygen of Asp25′, in contrast to several theoretical studies. These TI complexes and quantum calculations are discussed in relation to the chemical mechanism of the peptide bond hydrolysis catalyzed by PR. PMID:18052235

Growth, Characterization and Applications of Beta-Barium Borate and Related Crystals

DTIC Science & Technology

1993-10-31

Crystal symmetry determines the form of the second order polarization tensor. The second order polarizability tensor is defined by the piezoelectric...cold finger. A temperature oscillation technique1 I was used to limit the number of nuclei formed . These experiments typically yielded thin crystal...statistically sampled to determine the optimal seeding orientation. % was reasoned that the large crystal plates were formed from nucleii which had a favorable

Influence of moisture on the crystal forms of niclosamide obtained from acetone and ethyl acetate.

PubMed

Manek, Rahul V; Kolling, William M

2004-03-04

The purpose of this study was to elucidate the formation of crystal hydrates of niclosamide and to delineate the effect of relative humidity on the crystal forms obtained from acetone and ethyl acetate. Recrystallization of niclosamide was performed in the presence and absence of moisture. Two hydrates and their corresponding anhydrates were isolated. The hydrates obtained by the process of recrystallization from acetone (Form I) and that obtained from ethyl acetate (Form II) were classified based on differences in their dehydration profile, crystal structure, shape, and morphology. Crystals obtained in the absence of moisture were unstable, and when exposed to the laboratory atmosphere transformed to their corresponding hydrates. Differential scanning calorimetry thermograms indicate that Form I changes to an anhydrate at temperatures below 100 degrees C, while Form II dehydrates in a stepwise manner above 140 degrees C. This finding was further confirmed by thermogravimetric analysis. Dehydration of Form II was accompanied by a loss of structural integrity, demonstrating that water molecules play an important role in maintaining its crystal structure. Form I, Form II, and the anhydrate of Form II showed no significant moisture sorption over the entire range of relative humidity. Although the anhydrate of Form I did not show any moisture uptake at low humidity, it converted to the monohydrate at elevated relative humidity (>95%). All forms could be interconverted depending on the solvent and humidity conditions.

Nanoliter microfluidic hybrid method for simultaneous screening and optimization validated with crystallization of membrane proteins

PubMed Central

Li, Liang; Mustafi, Debarshi; Fu, Qiang; Tereshko, Valentina; Chen, Delai L.; Tice, Joshua D.; Ismagilov, Rustem F.

2006-01-01

High-throughput screening and optimization experiments are critical to a number of fields, including chemistry and structural and molecular biology. The separation of these two steps may introduce false negatives and a time delay between initial screening and subsequent optimization. Although a hybrid method combining both steps may address these problems, miniaturization is required to minimize sample consumption. This article reports a “hybrid” droplet-based microfluidic approach that combines the steps of screening and optimization into one simple experiment and uses nanoliter-sized plugs to minimize sample consumption. Many distinct reagents were sequentially introduced as ≈140-nl plugs into a microfluidic device and combined with a substrate and a diluting buffer. Tests were conducted in ≈10-nl plugs containing different concentrations of a reagent. Methods were developed to form plugs of controlled concentrations, index concentrations, and incubate thousands of plugs inexpensively and without evaporation. To validate the hybrid method and demonstrate its applicability to challenging problems, crystallization of model membrane proteins and handling of solutions of detergents and viscous precipitants were demonstrated. By using 10 μl of protein solution, ≈1,300 crystallization trials were set up within 20 min by one researcher. This method was compatible with growth, manipulation, and extraction of high-quality crystals of membrane proteins, demonstrated by obtaining high-resolution diffraction images and solving a crystal structure. This robust method requires inexpensive equipment and supplies, should be especially suitable for use in individual laboratories, and could find applications in a number of areas that require chemical, biochemical, and biological screening and optimization. PMID:17159147

The Crystal Stratigraphy of Ontong Java Plateau Plagioclase Pegacrysts: New Insights into the Evolution of LIP Magmas.

NASA Astrophysics Data System (ADS)

Neal, C. R.; Kinman, W. S.

2003-12-01

The Ontong Java Plateau (OJP) is the world's largest LIP made up of 2 isotopically distinct lava types that comprise the Singgalo and Kwaimbaita formations (Tejada et al., 2002, J.Pet 43:449). Some Kwaimbaita basaltic flows contain plagioclase-rich cumulate xenoliths. As plagioclase is stable over a range of magmatic conditions, microanalysis of this phase allows the evolution of the parent magma(s) to be constrained (cf. Davidson & Tepley, 1997, Science 275:826). This crystal stratigraphy approach has been applied to cm-size plagioclase megacrysts from three basaltic units (5B, 6, and 7) recovered at ODP Leg 192 Site 1183. Core-to-rim trace element variations were quantified by LA-ICP-MS, major elements by EPMA, and compositional backscatter SEM imaging was used to investigate the subtle compositional zoning and textural features within the plagioclases. All 5 OJP megacrysts sampled show little core-to-rim anorthite variation (82 mol % An +/- 5%); An-rich plagioclase crystals are resistant to re-equilibration and are more likely to retain magmatic trace element signatures (Blundy & Wood, 1991, GCA 55:193). The Unit 7 (oldest) plagioclase contains a relatively Sr, Ga, REE, and Ti poor core bounded by a resorption surface and a relatively Sr, Ga, REE, and Ti rich zone suggesting this crystal was exposed to 2 compositionally distinct magmas. The Unit 6 plagioclase contains a relatively Sr, Ga, REE, and Ti poor core with increasing abundances toward the rim, consistent with evolution through fractional crystallization. This megacryst also contains a distinct resorption surface bounded by a core-like Sr, REE, and Ti poor zone. The three Unit 5B plagioclases display core-to-rim Sr and Ba increases with little core-to-rim REE and Ga variations. The uppermost Unit 5B crystal (youngest) exhibits a core-to-rim decrease in Ti, while the lower 2 crystals display the opposite relationship. We suggest the textural and trace element variations seen in OJP plagioclase megacrysts are again evidence of magma mixing. Reconstructed liquids suggest at least two distinct mixing end members: an enriched end member, similar to Singgalo-type lavas, and a depleted end member, similar to Kwaimbaita type lavas. As the Singgalo- and Kwaimbaita-type basalts are isotopically distinct (I(Sr) = 0.7041 and 0.7038, resp.), Sr isotope determinations of the different plagioclase zones through microdrilling is planned for the near future to test this hypothesis. If correct, it suggests that both the Kwaimbaita and Singgalo sources were active at the same time, which is in contrast to the stratigraphy determined by whole-rock compositions.

Purification, crystallization and preliminary X-ray diffraction analysis of aspartate semialdehyde dehydrogenase (Rv3708c) from Mycobacterium tuberculosis

PubMed Central

Vyas, Rajan; Kumar, Vijay; Panjikar, Santosh; Karthikeyan, Subramanian; Kishan, K. V. Radha; Tewari, Rupinder; Weiss, Manfred S.

2008-01-01

Aspartate semialdehyde dehydrogenase from Mycobacterium tuberculosis (Asd, ASADH, Rv3708c), which is the second enzyme in the lysine/homoserine-biosynthetic pathways, has been expressed heterologously in Escherichia coli. The enzyme was purified using affinity and gel-filtration chromatographic techniques and crystallized in two different crystal forms. Preliminary diffraction data analysis suggested the presence of up to four monomers in the asymmetric unit of the orthorhombic crystal form A and of one or two monomers in the cubic crystal form B. PMID:18323599

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.

Solid-state properties and crystallization behavior of PHA-739521 polymorphs.

PubMed

Sun, Changquan Calvin

2006-08-17

PHA-739521 is an experimental compound that exhibits polymorphism. The two anhydrous crystal forms, I and II, are characterized using powder X-ray diffractometry, thermal analyses, moisture sorption gravimetry. Both Forms I and II are non-hygroscopic and are stable to compaction pressure. The melting temperature is about 152 degrees C for Form I and 168 degrees C for Form II. Forms I and II are enantiotropically related where Form I is more stable below a transition temperature of approximately 70 degrees C. Crystallization behavior of this compound from solutions and during heating is also studied. Information obtained is used to design an appropriate crystallization process to successfully manufacture desired polymorph at large scale.

Method of making macrocrystalline or single crystal semiconductor material

NASA Technical Reports Server (NTRS)

Shlichta, P. J. (Inventor); Holliday, R. J. (Inventor)

1986-01-01

A macrocrystalline or single crystal semiconductive material is formed from a primary substrate including a single crystal or several very large crystals of a relatively low melting material. This primary substrate is deposited on a base such as steel or ceramic, and it may be formed from such metals as zinc, cadmium, germanium, aluminum, tin, lead, copper, brass, magnesium silicide, or magnesium stannide. These materials generally have a melting point below about 1000 C and form on the base crystals the size of fingernails or greater. The primary substrate has an epitaxial relationship with a subsequently applied layer of material, and because of this epitaxial relationship, the material deposited on the primary substrate will have essentially the same crystal size as the crystals in the primary substrate. If required, successive layers are formed, each of a material which has an epitaxial relationship with the previously deposited layer, until a layer is formed which has an epitaxial relationship with the semiconductive material. This layer is referred to as the epitaxial substrate, and its crystals serve as sites for the growth of large crystals of semiconductive material. The primary substrate is passivated to remove or otherwise convert it into a stable or nonreactive state prior to deposition of the seconductive material.

A method for in Vivo radiolabeling Bacillus thuringiensis native δ-endotoxin crystals

Treesearch

C. Noah Koller; Leah S. Bauer; Robert M. Hollingworth

1995-01-01

The entomocidal CryIIIA δ-endotoxin protein of Bacillus thuringiensis var. tenebrionis is distinctive in chemistry and host range. In contrast to other δ-endotoxins, the CryIIIA parasporal crystals are toxic within the acidic midgut environment of several coleopteran species, particularly those in the family...

Photonic crystal devices formed by a charged-particle beam

DOEpatents

Lin, Shawn-Yu; Koops, Hans W. P.

2000-01-01

A photonic crystal device and method. The photonic crystal device comprises a substrate with at least one photonic crystal formed thereon by a charged-particle beam deposition method. Each photonic crystal comprises a plurality of spaced elements having a composition different from the substrate, and may further include one or more impurity elements substituted for spaced elements. Embodiments of the present invention may be provided as electromagnetic wave filters, polarizers, resonators, sources, mirrors, beam directors and antennas for use at wavelengths in the range from about 0.2 to 200 microns or longer. Additionally, photonic crystal devices may be provided with one or more electromagnetic waveguides adjacent to a photonic crystal for forming integrated electromagnetic circuits for use at optical, infrared, or millimeter-wave frequencies.

Effects of Melt Processing on Evolution of Structure in PEEK

NASA Technical Reports Server (NTRS)

Georgiev, Georgi; Dai, Patrick Shuanghua; Oyebode, Elizabeth; Cebe, Peggy; Capel, Malcolm

1999-01-01

We report on the effects of melt processing temperature on structure formation in Poly(ether-ether-ketone), PEEK. Real time Small Angle X-ray Scattering, SAXS, and thermal analysis are used to follow the melting behavior after various stages of processing. Assignment of peaks to structural entities within the material, the relative perfection of the crystals, and the possibility of their reorganization, are all influenced by the melt processing history. With the advent of high intensity synchrotron sources of X-radiation, polymer scientists gain a research tool which, when used along with thermal analysis, provides additional structural information about the crystals during growth and subsequent melting. PEEK is an engineering thermoplastic polymer with a very high glass transition temperature (145 C) and crystal melting point (337 C). PEEK has been the subject of recent studies by X-ray scattering in which melt and cold crystallization were followed in real-time. X-ray scattering and thermal studies have been used to address the formation of dual endothermic response which has been variously ascribed to lamellar insertion, dual crystal populations, or melting followed by re-crystallization. Another important issue is whether all of the amorphous phase is located in interlamellar regions, or alternatively whether some is located in "pockets" away from the crystalline lamellar stacks. The interpretation of scattering from lamellar stacks varies depending upon whether such amorphous pockets are formed. Some groups believe all of the amorphous phase is interlamellar. This leads to selection of a smaller thickness for the crystals. Other groups suggest that most amorphous phase is not interlamellar, and this leads to the suggestion that the crystal thickness is larger than the amorphous layer within the stacks. To investigate these ideas, we used SAXS and Differential Scanning Calorimetry to compare results of single and dual stage melt crystallization of PEEK using a treatment scheme involving annealing/crystallization at T(sub a1) followed by annealing at T(sub a2) where either T(sub a1) < T(sub a2) or T(sub a1) > T(sub a2). We proposed a model to explain multiple melting endotherms in PPS, treated according to one or two-stage melt or cold crystallization. Key features of this model are that multiple endotherms: (1) are due to reorganization/recrystallization after cold crystallization; and, (2) are dominated by crystal morphology after melt crystallization at high T. In other words, multiple distinct crystal populations are formed by the latter treatment, leading to observation of multiple melting. PEEK 45OG pellets (ICI Americas) were the starting material for this study. Films were compression molded at 400 C, then quenched to ice water. Samples were heated to 375 C in a Mettler FP80 hot stage and held for three min. to erase crystal seeds before cooling them to T(sub a1) = 280 C . Samples were held at T(sub a2) for a period of time, then immediately heated to 360 C. In the second treatment samples were held at T(sub a1) = 31 C for different crystallization times t(sub c) then cooled to 295 C and held 15 min. In situ (SAXS) experiments were performed at the Brookhaven National Synchrotron Light Source with the sample located inside the Mettler hot stage. The system was equipped with a two-dimensional position sensitive detector. The sample to detector distance was 172.7 cm and the X-ray wavelength was 1.54 Angstroms. SAXS data were taken continuously during the isothermal periods and during the heating to 360 C at 5 C/min. Each SAXS scan was collected for 30 sec. Since the samples were isotropic, circular integration was used to increase the signal to noise ratio. After dual stage melt crystallization with T(sub a1) < T(sub a2) the lower melting endotherm arises from holding at T(sub a1). During cooling a broad distribution of crystals forms, and the low-melting tail is perfected during T(sub al). Heating to T(sub a2) melts these imperfect crystals and allows others with greater average long spacing to form in their place. After dual stage crystallization with T(sub a1) > T(sub a2), the amount of space remaining for additional growth at T(sub a2) depends upon the holding time at T(sub a1). The long period of crystals formed at T(sub a2) is smaller than that formed at T(sub a1) due to growth in a now-restricted geometry. Perfection of crystals is seen as an increase of the intensity of the population scattering at higher s, while the intensity of the population scattering at lower s stays constant. During heating from below to above the minor endotherm, we see rapid decrease of the intensity of the X-ray scattering corresponding to the population of crystals scattering in the shoulder. Another important observation is that after the sample is annealed at 295 C, the shoulder intensity is restored once again. The population scattering at higher s remains longer before it disappears in the sample treated to the second stage of melt crystallization, compared to the sample crystallized with a single stage. This could be interpreted as an effect of continued perfection of the less perfect population, which is also reflected in the increased melting temperature of the smaller endotherm as the holding time at 295 C increases. In the corresponding DSC scans we see a shift in the area and the peak temperature of the lower melting endotherm with an increase of the annealing time.

2-tert-Butylamino-4-chloro-6-ethylamino-1,3,5-triazine: a structure with Z' = 4 containing two different molecular conformations and two independent chains of hydrogen-bonded R(2)2(8) rings.

PubMed

Quesada, Antonio; Fontecha, Maria A; López, Maria V; Low, John N; Glidewell, Christopher

2008-08-01

The title compound (trivial name terbutylazine), C(9)H(16)ClN(5), (I), crystallizes with Z' = 4 in the space group Pca2(1), and equal numbers of molecules adopt two different conformations for the ethylamine groups. The four independent molecules form two approximately enantiomorphic pairs. Eight independent N-H...N hydrogen bonds link the molecules into two independent chains of R(2)(2)(8) rings, in which the arrangement of the alkylamine substituents in the independent molecules precludes any further crystallographic symmetry. The significance of this study lies in its finding of two distinct molecular conformations within the structure and two distinct ways in which the molecules are organized into hydrogen-bonded chains, and in its comparison of the hydrogen-bonded structure of (I) with those of analogous 1,3,5-triazines and pyrimidines.

Distinct ice patterns on solid surfaces with various wettabilities

PubMed Central

Liu, Jie; Zhu, Chongqin; Liu, Kai; Jiang, Ying; Song, Yanlin; Francisco, Joseph S.; Zeng, Xiao Cheng; Wang, Jianjun

2017-01-01

No relationship has been established between surface wettability and ice growth patterns, although ice often forms on top of solid surfaces. Here, we report experimental observations obtained using a process specially designed to avoid the influence of nucleation and describe the wettability-dependent ice morphology on solid surfaces under atmospheric conditions and the discovery of two growth modes of ice crystals: along-surface and off-surface growth modes. Using atomistic molecular dynamics simulation analysis, we show that these distinct ice growth phenomena are attributable to the presence (or absence) of bilayer ice on solid surfaces with different wettability; that is, the formation of bilayer ice on hydrophilic surface can dictate the along-surface growth mode due to the structural match between the bilayer hexagonal ice and the basal face of hexagonal ice (ice Ih), thereby promoting rapid growth of nonbasal faces along the hydrophilic surface. The dramatically different growth patterns of ice on solid surfaces are of crucial relevance to ice repellency surfaces. PMID:29073045

Distinct ice patterns on solid surfaces with various wettabilities.

PubMed

Liu, Jie; Zhu, Chongqin; Liu, Kai; Jiang, Ying; Song, Yanlin; Francisco, Joseph S; Zeng, Xiao Cheng; Wang, Jianjun

2017-10-24

No relationship has been established between surface wettability and ice growth patterns, although ice often forms on top of solid surfaces. Here, we report experimental observations obtained using a process specially designed to avoid the influence of nucleation and describe the wettability-dependent ice morphology on solid surfaces under atmospheric conditions and the discovery of two growth modes of ice crystals: along-surface and off-surface growth modes. Using atomistic molecular dynamics simulation analysis, we show that these distinct ice growth phenomena are attributable to the presence (or absence) of bilayer ice on solid surfaces with different wettability; that is, the formation of bilayer ice on hydrophilic surface can dictate the along-surface growth mode due to the structural match between the bilayer hexagonal ice and the basal face of hexagonal ice (ice I h ), thereby promoting rapid growth of nonbasal faces along the hydrophilic surface. The dramatically different growth patterns of ice on solid surfaces are of crucial relevance to ice repellency surfaces. Published under the PNAS license.

Crystallization and preliminary crystallographic analysis of latent, active and recombinantly expressed aurone synthase, a polyphenol oxidase, from Coreopsis grandiflora

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

Molitor, Christian; Mauracher, Stephan Gerhard; Rompel, Annette, E-mail: annette.rompel@univie.ac.at

2015-05-22

Latent and active aurone synthase purified from petals of C. grandiflora (cgAUS1) were crystallized. The crystal quality of recombinantly expressed latent cgAUS1 was significantly improved by co-crystallization with the polyoxotungstate Na{sub 6}[TeW{sub 6}O{sub 24}] within the liquid–liquid phase-separation zone. Aurone synthase (AUS), a member of a novel group of plant polyphenol oxidases (PPOs), catalyzes the oxidative conversion of chalcones to aurones. Two active cgAUS1 (41.6 kDa) forms that differed in the level of phosphorylation or sulfation as well as the latent precursor form (58.9 kDa) were purified from the petals of Coreopsis grandiflora. The differing active cgAUS1 forms and themore » latent cgAUS1 as well as recombinantly expressed latent cgAUS1 were crystallized, resulting in six different crystal forms. The active forms crystallized in space groups P2{sub 1}2{sub 1}2{sub 1} and P12{sub 1}1 and diffracted to ∼1.65 Å resolution. Co-crystallization of active cgAUS1 with 1,4-resorcinol led to crystals belonging to space group P3{sub 1}21. The crystals of latent cgAUS1 belonged to space group P12{sub 1}1 and diffracted to 2.50 Å resolution. Co-crystallization of recombinantly expressed pro-AUS with the hexatungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}] within the liquid–liquid phase separation zone significantly improved the quality of the crystals compared with crystals obtained without hexatungstotellurate(VI)« less

Two-stage magnetic orientation of uric acid crystals as gout initiators

NASA Astrophysics Data System (ADS)

Takeuchi, Y.; Miyashita, Y.; Mizukawa, Y.; Iwasaka, M.

2014-01-01

The present study focuses on the magnetic behavior of uric acid crystals, which are responsible for gout. Under a sub-Tesla (T)-level magnetic field, rotational motion of the crystals, which were caused by diamagnetic torque, was observed. We used horizontal magnetic fields with a maximum magnitude of 500 mT generated by an electromagnet to observe the magnetic orientation of the uric acid microcrystals by a microscope. The uric acid crystals showed a perpendicular magnetic field orientation with a minimum threshold of 130 mT. We speculate that the distinct diamagnetic anisotropy in the uric acid crystals resulted in their rotational responses.

Polymorph selection: the role of nucleation, crystal growth and molecular modeling.

PubMed

Erdemir, Deniz; Lee, Alfred Y; Myerson, Allan S

2007-11-01

Solution crystallization is an important separation and purification process used in the chemical, pharmaceutical and food industries. The quality of a crystalline product is generally judged by four main criteria: purity, crystal habit, particle size and solid form. Consistent production of the desired polymorph is crucial as the unanticipated emergence of a different crystal form may have severe consequences. Thus, the selection of a solid-state form for a crystalline product is vital and is ultimately based on knowledge of the properties of the other polymorphs. This review discusses the role of nucleation, crystal growth and molecular modeling on polymorphism in molecular crystals. Examples are presented demonstrating how the first two factors can govern the appearance of a particular crystalline form, and how the latter factor can be used as a tool for understanding polymorphism.

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

Aoki, Ken-ichi; Tanaka, Nobutada, E-mail: ntanaka@pharm.showa-u.ac.jp; Ishikura, Shuhei

Pig heart carbonyl reductase has been crystallized in the presence of NADPH. Diffraction data have been collected using synchrotron radiation. Pig heart carbonyl reductase (PHCR), which belongs to the short-chain dehydrogenase/reductase (SDR) family, has been crystallized by the hanging-drop vapour-diffusion method. Two crystal forms (I and II) have been obtained in the presence of NADPH. Form I crystals belong to the tetragonal space group P4{sub 2}, with unit-cell parameters a = b = 109.61, c = 94.31 Å, and diffract to 1.5 Å resolution. Form II crystals belong to the tetragonal space group P4{sub 1}2{sub 1}2, with unit-cell parameters amore » = b = 120.10, c = 147.00 Å, and diffract to 2.2 Å resolution. Both crystal forms are suitable for X-ray structure analysis at high resolution.« less

Screening and Characterization of Hydrate Forms of T-3256336, a Novel Inhibitor of Apoptosis (IAP) Protein Antagonist.

PubMed

Takeuchi, Shoko; Kojima, Takashi; Hashimoto, Kentaro; Saito, Bunnai; Sumi, Hiroyuki; Ishikawa, Tomoyasu; Ikeda, Yukihiro

2015-01-01

Different crystal packing of hydrates from anhydrate crystals leads to different physical properties, such as solubility and stability. Investigation of the potential of varied hydrate formation, and understanding the stability in an anhydrous/hydrate system, are crucial to prevent an undesired transition during the manufacturing process and storage. Only one anhydrous form of T-3256336, a novel inhibitor of apoptosis (IAP) protein antagonist, was discovered during synthesis, and no hydrate form has been identified. In this study, we conducted hydrate screening such as dynamic water vapor sorption/desorption (DVS), and the slurry experiment, and characterized the solid-state properties of anhydrous/hydrate forms to determine the most desirable crystalline form for development. New hydrate forms, both mono-hydrate and hemi-hydrate forms, were discovered as a result of this hydrate screening. The characterization of two new hydrate forms was conducted, and the anhydrous form was determined to be the most desirable development form of T-3256336 in terms of solid-state stability. In addition, the stability of the anhydrous form was investigated using the water content and temperature controlled slurry experiment to obtain the desirable crystal form in the crystallization process. The water content regions of the stable phase of the desired form, the anhydrous form, were identified for the cooling crystallization process.

Spectators Control Selectivity in Surface Chemistry: Acrolein Partial Hydrogenation Over Pd

PubMed Central

2015-01-01

We present a mechanistic study on selective hydrogenation of acrolein over model Pd surfaces—both single crystal Pd(111) and Pd nanoparticles supported on a model oxide support. We show for the first time that selective hydrogenation of the C=O bond in acrolein to form an unsaturated alcohol is possible over Pd(111) with nearly 100% selectivity. However, this process requires a very distinct modification of the Pd(111) surface with an overlayer of oxopropyl spectator species that are formed from acrolein during the initial stages of reaction and turn the metal surface selective toward propenol formation. By applying pulsed multimolecular beam experiments and in situ infrared reflection–absorption spectroscopy, we identified the chemical nature of the spectator and the reactive surface intermediate (propenoxy species) and experimentally followed the simultaneous evolution of the reactive intermediate on the surface and formation of the product in the gas phase. PMID:26481220

From molecular salt to pseudo CAB cocrystal: Expanding solid-state landscape of carboxylic acids based on charge-assisted COOH⋯COO- hydrogen bonds

NASA Astrophysics Data System (ADS)

Lou, Benyong; Perumalla, Sathyanarayana Reddy; Sun, Changquan Calvin

2015-11-01

Using three carboxylic acids, we show that the COOH⋯COO- synthon is robust for directing the cocrystallization between a carboxylic acid and a carboxylate of either the same or a chemically different molecule to form a CAB or pseudo CAB cocrystal, respectively. For a given carboxylic acid and a counterion, only one salt could be prepared. However, additional one CAB cocrystals and two pseudo CAB cocrystals could be prepared based on the COOH⋯COO- synthon. The same synthon has the potential to enable the preparation of additional molecular pseudo CAB cocrystals using other chemically distinct carboxylic acids. This significantly increased number of solid forms highlights the values of charge-assisted synthons, such as COOH⋯COO-, in crystal engineering for expanding the range of material properties of a given molecule for optimum performance in product design.

Structure of the uncleaved ectodomain of the paramyxovirus (hPIV3) fusion protein

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

Yin, Hsien-Sheng; Paterson, Reay G.; Wen, Xiaolin

2010-03-08

Class I viral fusion proteins share common mechanistic and structural features but little sequence similarity. Structural insights into the protein conformational changes associated with membrane fusion are based largely on studies of the influenza virus hemagglutinin in pre- and postfusion conformations. Here, we present the crystal structure of the secreted, uncleaved ectodomain of the paramyxovirus, human parainfluenza virus 3 fusion (F) protein, a member of the class I viral fusion protein group. The secreted human parainfluenza virus 3 F forms a trimer with distinct head, neck, and stalk regions. Unexpectedly, the structure reveals a six-helix bundle associated with the postfusionmore » form of F, suggesting that the anchor-minus ectodomain adopts a conformation largely similar to the postfusion state. The transmembrane anchor domains of F may therefore profoundly influence the folding energetics that establish and maintain a metastable, prefusion state.« less

Molecular mechanisms for protein-encoded inheritance

PubMed Central

Wiltzius, Jed J. W.; Landau, Meytal; Nelson, Rebecca; Sawaya, Michael R.; Apostol, Marcin I.; Goldschmidt, Lukasz; Soriaga, Angela B.; Cascio, Duilio; Rajashankar, Kanagalaghatta; Eisenberg, David

2013-01-01

Strains are phenotypic variants, encoded by nucleic acid sequences in chromosomal inheritance and by protein “conformations” in prion inheritance and transmission. But how is a protein “conformation” stable enough to endure transmission between cells or organisms? Here new polymorphic crystal structures of segments of prion and other amyloid proteins offer structural mechanisms for prion strains. In packing polymorphism, prion strains are encoded by alternative packings (polymorphs) of β-sheets formed by the same segment of a protein; in a second mechanism, segmental polymorphism, prion strains are encoded by distinct β-sheets built from different segments of a protein. Both forms of polymorphism can produce enduring “conformations,” capable of encoding strains. These molecular mechanisms for transfer of information into prion strains share features with the familiar mechanism for transfer of information by nucleic acid inheritance, including sequence specificity and recognition by non-covalent bonds. PMID:19684598

Temperature dependent evolution of wrinkled single-crystal silicon ribbons on shape memory polymers.

PubMed

Wang, Yu; Yu, Kai; Qi, H Jerry; Xiao, Jianliang

2017-10-25

Shape memory polymers (SMPs) can remember two or more distinct shapes, and thus can have a lot of potential applications. This paper presents combined experimental and theoretical studies on the wrinkling of single-crystal Si ribbons on SMPs and the temperature dependent evolution. Using the shape memory effect of heat responsive SMPs, this study provides a method to build wavy forms of single-crystal silicon thin films on top of SMP substrates. Silicon ribbons obtained from a Si-on-insulator (SOI) wafer are released and transferred onto the surface of programmed SMPs. Then such bilayer systems are recovered at different temperatures, yielding well-defined, wavy profiles of Si ribbons. The wavy profiles are shown to evolve with time, and the evolution behavior strongly depends on the recovery temperature. At relatively low recovery temperatures, both wrinkle wavelength and amplitude increase with time as evolution progresses. Finite element analysis (FEA) accounting for the thermomechanical behavior of SMPs is conducted to study the wrinkling of Si ribbons on SMPs, which shows good agreement with experiment. Merging of wrinkles is observed in FEA, which could explain the increase of wrinkle wavelength observed in the experiment. This study can have important implications for smart stretchable electronics, wrinkling mechanics, stimuli-responsive surface engineering, and advanced manufacturing.

Bioinspired fabrication of hierarchically structured, pH-tunable photonic crystals with unique transition.

PubMed

Yang, Qingqing; Zhu, Shenmin; Peng, Wenhong; Yin, Chao; Wang, Wanlin; Gu, Jiajun; Zhang, Wang; Ma, Jun; Deng, Tao; Feng, Chuanliang; Zhang, Di

2013-06-25

We herein report a new class of photonic crystals with hierarchical structures, which are of color tunability over pH. The materials were fabricated through the deposition of polymethylacrylic acid (PMAA) onto a Morpho butterfly wing template by using a surface bonding and polymerization route. The amine groups of chitosan in Morpho butterfly wings provide reaction sites for the MAA monomer, resulting in hydrogen bonding between the template and MAA. Subsequent polymerization results in PMAA layers coating homogenously on the hierarchical photonic structures of the biotemplate. The pH-induced color change was detected by reflectance spectra as well as optical observation. A distinct U transition with pH was observed, demonstrating PMAA content-dependent properties. The appearance of the unique U transition results from electrostatic interaction between the -NH3(+) of chitosan and the -COO(-) groups of PMAA formed, leading to a special blue-shifted point at the pH value of the U transition, and the ionization of the two functional groups in the alkali and acid environment separately, resulting in a red shift. This work sets up a strategy for the design and fabrication of tunable photonic crystals with hierarchical structures, which provides a route for combining functional polymers with biotemplates for wide potential use in many fields.

THE CRYSTALLIZATION AND SEROLOGICAL DIFFERENTIATION OF A STREPTOCOCCAL PROTEINASE AND ITS PRECURSOR

PubMed Central

Elliott, S. D.

1950-01-01

Grown in dialysate broth at a pH between 5.5 and 6.5, some strains of group A streptococci elaborate the precursor of a proteolytic enzyme. Within this range of hydrogen concentration the precursor is also produced when the streptococci are suspended in a peptone dialysate containing glucose and incubated at 37°C. The precursor does not appear to be produced at a neutral or alkaline reaction. Methods are described whereby the precursor and proteinase have been isolated in crystalline form. The precursor crystallizes from half-saturated ammonium sulfate at pH 8.0 and a temperature of 22°C. or higher; the proteinase crystallizes from 0.15 saturated ammonium sulfate at pH 8.0 but does so most readily at refrigerator temperature. The degree of purification achieved by these procedures is discussed. The activity of purified preparations of the precursor and of proteinase has been tested against α-benzoyl-l-arginineamide and, with this as a substrate, the conversion of precursor to proteinase by autocatalysis or by trypsin has been confirmed. Immunological experiments are described, the results of which provide evidence of the distinct antigenic specificity of the precursor and proteinase; the conversion of precursor to proteinase has been followed by means of serological tests. PMID:15436931

Mechanochemical synthesis of N-salicylidene­aniline: thermosalient effect of polymorphic crystals

PubMed Central

Mittapalli, Sudhir; Sravanakumar Perumalla, D.

2017-01-01

Polymorphs of the dichloro derivative of N-salicylideneaniline exhibit mechanical responses such as jumping (Forms I and III) and exploding (Form II) in its three polymorphs. The molecules are connected via the amide N—H⋯O dimer synthon and C—Cl⋯O halogen bond in the three crystal structures. A fourth high-temperature Form IV was confirmed by variable-temperature single-crystal X-ray diffraction at 180°C. The behaviour of jumping exhibited by the polymorphic crystals of Forms I and III is due to the layered sheet morphology and the transmission of thermal stress in a single direction, compared with the corrugated sheet structure of Form II such that heat dissipation is more isotropic causing blasting. The role of weak C—Cl⋯O interactions in the thermal response of molecular crystals is discussed. PMID:28512571

Monomer structure of a hyperthermophilic β-glucosidase mutant forming a dodecameric structure in the crystal form

PubMed Central

Nakabayashi, Makoto; Kataoka, Misumi; Watanabe, Masahiro; Ishikawa, Kazuhiko

2014-01-01

One of the β-glucosidases from Pyrococcus furiosus (BGLPf) is found to be a hyperthermophilic tetrameric enzyme that can degrade cellooligosaccharides. Recently, the crystal structures of the tetrameric and dimeric forms were solved. Here, a new monomeric form of BGLPf was constructed by removing the C-terminal region of the enzyme and its crystal structure was solved at a resolution of 2.8 Å in space group P1. It was discovered that the mutant enzyme forms a unique dodecameric structure consisting of two hexameric rings in the asymmetric unit of the crystal. Under biological conditions, the mutant enzyme forms a monomer. This result helps explain how BGLPf has attained its oligomeric structure and thermostability. PMID:25005077

Spinodal decomposition of the gamma-phase upon quenching in the Ti-Al-Nb ternary

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

Rios, Orlando; Ebrahimi, Fereshteh

2010-01-01

The {gamma}-TiAl with L1{sub 0} crystal structure shows extensive solubility for Nb at elevated temperatures. Recently (Rios et al., Acta materialia 2009; 57:6243), we have demonstrated that the high-Nb {gamma}-TiAl phase becomes unstable upon rapid cooling into a nano-scale two-phase microstructure. In this paper, using detailed compositional and microstructural analyses, we have demonstrated that this phase goes through a spinodal decomposition that results in the compositionally distinct phases identified as a lower-Nb {gamma}-phase and the h-phase, which is rich in Nb and forms by the ordering of this element in the {gamma}-phase.

N-(L-2-aminopentanoyl)-L-phenylalanine dihydrate, a hydrophobic dipeptide with a nonproteinogenic residue.

PubMed

Görbitz, Carl Henrik; Yadav, Vitthal N

2013-09-01

The title dipeptide, better known as L-norvalyl-L-phenylalanine {systematic name: (S)-2-[(S)-2-aminopentanamido]-3-phenylpropanoic acid dihydrate}, C14H20N2O3·2H2O, has a nonproteinogenic N-terminal residue. In the solid state, it takes on a molecular conformation typical for one of the three classes of nanoporous dipeptides, but like two related compounds with a hydrophobic N-terminal residue and a C-terminal L-phenylalanine, it fails to form channels or pores. Instead, the crystal structure is divided into distinct hydrophobic and hydrophilic layers, the latter encompassing cocrystallized water molecules connecting the charged N- and C-terminal groups.

Modeling Episodic Ephemeral Brine Lake Evaporation and Salt Crystallization on the Bonneville Salt Flats, Utah

NASA Astrophysics Data System (ADS)

Liu, T.; Harman, C. J.; Kipnis, E. L.; Bowen, B. B.

2017-12-01

Public concern about apparent reductions in the areal extent of the Bonneville Salt Flat (BSF) and perceived changes in inundation frequency has motivated renewed interest in the hydrologic and geochemical behavior of this salt playa. In this study, we develop a numerical modeling framework to simulate the relationship between hydrometeorologic variability, brine evaporation and salt crystallization processes on BSF. The BSF, locates in Utah, is the remnant of paleo-lake Bonneville, and is capped by up to 1 meter of salt deposition over a 100 km2 area. The BSF has two distinct hydrologic periods each year: a winter wet periods with standing surface brine and the summer dry periods when the brine is evaporated, exposing the surface salt crust. We develop a lumped non-linear dynamical models coupling conservation expressions from water, dissolved salt and thermal energy to investigate the seasonal and diurnal behavior of brine during the transition from standing brine to exposed salt at BSF. The lumped dynamic models capture important nonlinear and kinetic effects introduced by the high ionic concentration of the brine, including the pronounced effect of the depressed water activity coefficient on evaporation. The salt crystallization and dissolution rate is modeled as a kinetic process linearly proportional to the degree of supersaturation of brine. The model generates predictions of the brine temperature and the solute and solvent masses controlled by diurnal net radiation input and aerodynamic forcing. Two distinct mechanisms emerge as potential controls on salt production and dissolution: (1) evapo-concentration and (2) changes in solubility related to changes in brine temperature. Although the evaporation of water is responsible for ultimate disappearance of the brine each season ,variation in solubility is found to be the dominant control on diurnal cycles of salt precipitation and dissolution in the BSF case. Most salt is crystallized during nighttime, but the long-term salt production is driven by the seasonal evapo-concentration. Moreover, we find that the timing of the brine temperature fluctuations and salt production lags the diurnal net radiation input. The key controls on the magnitudes of these effects and phase lags are determined by analytical periodic analysis of linearized forms of the model.

Composition and automated crystal orientation mapping of rapid solidification products in hypoeutectic Al-4 at.%Cu alloys

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

Zweiacker, K. W.; Liu, Can; Gordillo, M. A.

Rmore » apid solidification can produce metastable phases and unusual microstructure modifications in multi-component alloys during additive manufacturing or laser beam welding. Composition and phase mapping by transmission electron microscopy have been used in this paper to characterize the morphologically distinct zones developing in hypoeutectic Al-4 at.% Cu alloy after pulsed laser melting for different crystal growth rate regimes. Deviations of the compositions of the alloy phases from equilibrium predictions and unique orientation relationships between the solidification transformation products have been determined. Specifically, for the columnar growth zone at solidification rates of 0.8 m s - 1 < v < v a = 1.8 m s - 1 , two distinct orientation relationships were established between the concomitantly forming non-equilibrium phases, supersaturated α-Al solid solution and the discontinuously distributed α-Al 2Cu-based θ'-phase, which can be described as {110} θ ∥ {001} α, [001] θ ∥ [110] α and {001} θ ∥ {001} α, [100] θ ∥ [100] α. These orientation relationships permit formation of coherent interphase interfaces with low interfacial free energy. Finally, this endows a kinetic advantage to the thermodynamically less stable θ'-Al 2Cu phase relative to the more stable equilibrium θ-Al 2Cu phase during formation of the morphologically modified eutectic of the columnar growth zone grains, since repeated nucleation is required to establish the discontinuous distribution of θ'-Al 2Cu phase.« less

Composition and automated crystal orientation mapping of rapid solidification products in hypoeutectic Al-4 at.%Cu alloys

DOE PAGES

Zweiacker, K. W.; Liu, Can; Gordillo, M. A.; ...

2017-12-05

Rmore » apid solidification can produce metastable phases and unusual microstructure modifications in multi-component alloys during additive manufacturing or laser beam welding. Composition and phase mapping by transmission electron microscopy have been used in this paper to characterize the morphologically distinct zones developing in hypoeutectic Al-4 at.% Cu alloy after pulsed laser melting for different crystal growth rate regimes. Deviations of the compositions of the alloy phases from equilibrium predictions and unique orientation relationships between the solidification transformation products have been determined. Specifically, for the columnar growth zone at solidification rates of 0.8 m s - 1 < v < v a = 1.8 m s - 1 , two distinct orientation relationships were established between the concomitantly forming non-equilibrium phases, supersaturated α-Al solid solution and the discontinuously distributed α-Al 2Cu-based θ'-phase, which can be described as {110} θ ∥ {001} α, [001] θ ∥ [110] α and {001} θ ∥ {001} α, [100] θ ∥ [100] α. These orientation relationships permit formation of coherent interphase interfaces with low interfacial free energy. Finally, this endows a kinetic advantage to the thermodynamically less stable θ'-Al 2Cu phase relative to the more stable equilibrium θ-Al 2Cu phase during formation of the morphologically modified eutectic of the columnar growth zone grains, since repeated nucleation is required to establish the discontinuous distribution of θ'-Al 2Cu phase.« less

Disequilibrium growth of olivine in mafic magmas revealed by phosphorus zoning patterns of olivine from mafic-ultramafic intrusions

NASA Astrophysics Data System (ADS)

Xing, Chang-Ming; Wang, Christina Yan; Tan, Wei

2017-12-01

Olivine from mafic-ultramafic intrusions rarely displays growth zoning in major and some minor elements, such as Fe, Mg and Ni, due to fast diffusion of these elements at high temperatures. These elements in olivine are thus not useful in deciphering magma chamber processes, such as magma convection, multiple injection and mixing. High-resolution X-ray elemental intensity mapping reveals distinct P zoning patterns of olivine from two mafic-ultramafic intrusions in SW China. Polyhedral olivine grains from lherzolite and dunite of the Abulangdang intrusion show P-rich dendrites similar to those observed in volcanic rocks. Rounded olivine grains from net-textured Fe-Ti oxide ores of the Baima layered intrusion have irregular P-rich patches/bands crosscut and interlocked by P-poor olivine domains. P-rich patches/bands contain 250 to 612 ppm P, much higher than P-poor olivine domains with 123 to 230 ppm P. In electron backscattered diffraction (EBSD) maps, P-rich patches/bands within a single olivine grain have the same crystallographic orientation, indicating that they were remnants of the same crystal. Thus, both P-rich patches/bands and P-poor olivine domains in the same grain show a disequilibrium texture and clearly record two-stage growth. The P-rich patches/bands are likely the remnants of a polyhedral olivine crystal that formed in the first stage, whereas the P-poor olivine domains containing rounded Ti-rich magnetite and Fe-rich melt inclusions may have formed from an Fe-rich ambient melt in the second stage. The complex P zoning of olivine can be attributed to the dissolution of early polyhedral olivine and re-precipitation from the Fe-rich ambient melt. The early polyhedral olivine was in chemical disequilibrium with the ambient melt that may have been developed by silicate liquid immiscibility in a crystal mush. Our study implies that olivine crystals in igneous cumulates with an equilibrium appearance may have experienced disequilibrium growth processes during slow cooling. Therefore, the crystallization sequence of mafic magmas based on textural relationships should be treated with caution.

Structural Evidence for Regulation and Specificity of Flaviviral Proteases and Evolution of the Flaviviridae Fold

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

Aleshin,A.; Shiryaev, S.; Strongin, A.

2007-01-01

Pathogenic members of the flavivirus family, including West Nile Virus (WNV) and Dengue Virus (DV), are growing global threats for which there are no specific treatments. The two-component flaviviral enzyme NS2B-NS3 cleaves the viral polyprotein precursor within the host cell, a process that is required for viral replication. Here, we report the crystal structure of WNV NS2B-NS3pro both in a substrate-free form and in complex with the trypsin inhibitor aprotinin/BPTI. We show that aprotinin binds in a substrate-mimetic fashion in which the productive conformation of the protease is fully formed, providing evidence for an 'induced fit' mechanism of catalysis andmore » allowing us to rationalize the distinct substrate specificities of WNV and DV proteases. We also show that the NS2B cofactor of WNV can adopt two very distinct conformations and that this is likely to be a general feature of flaviviral proteases, providing further opportunities for regulation. Finally, by comparing the flaviviral proteases with the more distantly related Hepatitis C virus, we provide insights into the evolution of the Flaviviridae fold. Our work should expedite the design of protease inhibitors to treat a range of flaviviral infections.« less

Calciphytoliths (calcium oxalate crystals) analysis for the identification of decayed tea plants (Camellia sinensis L.)

PubMed Central

Zhang, Jianping; Lu, Houyuan; Huang, Linpei

2014-01-01

The history of tea is poorly known, mainly due to the questionable identification of decayed tea plants in archaeological samples. This paper attempts to test the utility of calciphytoliths (calcium oxalate crystals) for the identification of tea in archaeological samples. It provides the first survey of the macropatterns of calciphytoliths in several species of Theaceae and common non-Theaceae plants. Crystals were extracted from 45 samples of tea, Theaceae and common non-Theaceae plants, and detected microscopically between crossed polarizers. In tea plants, druse and trichome base are the most distinctive crystals. Druses have the smallest diameter (11.65 ± 3.64 μm), and trichome bases have four distinctive straight and regular cracks, similar to a regular extinction cross. The results provide morphological criteria for distinguishing tea from other plants, specifically the presence of identifiable druses together with calcified trichome bases. The implications are significant for understanding the history of tea and plant exploitation, especially for plants for which the preservation of macrofossils is poor. PMID:25342006

3-D X-ray tomography of diamondiferous mantle eclogite xenoliths, Siberia: A review

NASA Astrophysics Data System (ADS)

Howarth, Geoffrey H.; Sobolev, Nikolay V.; Pernet-Fisher, John F.; Ketcham, Richard A.; Maisano, Jessica A.; Pokhilenko, Lyudmila N.; Taylor, Dawn; Taylor, Lawrence A.

2015-04-01

Diamonds form over billions of years, hundreds of kilometers beneath the Earth's surface, and in combination with inclusions trapped within, provide important constraints on the evolution of the mantle over geological time. Diamonds are generally studied as individual crystals sourced from highly explosive kimberlite pipes, which entrain and subsequently disaggregate mantle fragments (xenoliths) en route to the surface. This has resulted in a general absence of robust textural descriptions of diamonds relative to their hosting mantle protolith. The textural associations of diamonds within their mantle host rocks are reviewed here on the basis of a compilation of X-ray tomographic data for 17 diamondiferous eclogite xenoliths from Siberian kimberlites. This review represents a comprehensive description of diamonds relative to their host silicates. The lack of such descriptions in previous studies is largely due to the rarity of these xenoliths, the difficulty in preparing petrographic thin sections containing diamonds, and their high-monetary value. High-resolution computed X-ray tomography (HRCXT) produces up to 1200 sequential 2-D slices through individual xenoliths, each of which represents a 'pseudo thin-section' with a resolution on the order of 5-20 μm. The improved resolution of X-ray imaging in recent studies allows for the identification of not only primary minerals, but metasomatic minerals assemblages, including: 'spongy' textured clinopyroxene, phlogopite/K-richterite, and hercynitic spinel, allowing for the delineation of distinct metasomatic pathways through the xenoliths and their relationship to diamonds. Diamonds are observed in three distinct textural settings, potentially representing several temporally distinct diamond growth events, these setting includes: (1) diamonds completely enclosed in garnet; (2) diamonds associated with highly embayed silicate grain boundaries; and (3) diamonds contained within distinct metasomatic 'plumbing-systems'. Diamonds observed completely enclosed in garnets suggest an early diamond-forming event prior to major re-crystallization and eclogite formation during subduction. The occurrence of diamond in association with embayed garnets suggests that diamond grew at the expense of the hosting silicate protolith. In addition, the spatial relationships of diamonds with metasomatic pathways, which are generally interpreted to result from late-stage proto-kimberlitic fluid percolation, indicate a period of diamond growth occurring close to, but prior to, the time of kimberlite emplacement. Furthermore, the paragenesis of sulfides within eclogite xenoliths are described using 3-D models for entire xenoliths volumes, providing important constraints of the timing of sulfide mobilization within the mantle. Three-D animations created using X-ray tomography data for ten of the xenoliths can be viewed at the following link: http://eps.utk.edu/faculty/taylor/tomography.php

Effect of supersaturation on L-glutamic acid polymorphs under droplet-based microchannels

NASA Astrophysics Data System (ADS)

Jiang, Nan; Wang, Zhanzhong; Dang, Leping; Wei, Hongyuan

2016-07-01

Supersaturation is an important controlling factor for crystallization process and polymorphism. Droplet-based microchannels and conventional crystallization were used to investigate polymorphs of L-gluatamic acid in this work. The results illustrate that it is easy to realize the accurate and rapid control of the crystallization temperature in the droplets, which is especially beneficial to heat and mass transfer during crystallization. It is also noted that higher degree of supersaturation favors the nucleation of α crystal form, while lower degree of supersaturation favors the nucleation of β crystal form under droplet-based microchannels for L-gluatamic acid. In addition, there is a different nucleation behavior to be found under droplet-based microchannels both for the β form and α form of L-glutamic acid. This new finding can provide important insight into the development and design of investigation meanings for drug polymorph.

Crystallization, X-ray diffraction analysis and SIRAS/molecular-replacenent phasing of three crystal forms of Anabaena sensory rhodopsin transducer

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

Vogeley, Lutz; Luecke, Hartmut, E-mail: hudel@uci.edu

2006-04-01

Crystals of Anabaena sensory rhodopsin transducer, the transducer for the cyanobacterial photosensor Anabaena sensory rhodopsin, obtained in the space groups P4, C2 and P2{sub 1}2{sub 1}2{sub 1} diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for these crystal forms were obtained by SIRAS phasing using an iodide quick-soak derivative (P4) and molecular replacement (C2 and P2{sub 1}2{sub 1}2{sub 1}). Anabaena sensory rhodopsin transducer (ASRT) is a 14.7 kDa soluble signaling protein associated with the membrane-embedded light receptor Anabaena sensory rhodopsin (ASR) from Anabaena sp., a freshwater cyanobacterium. Crystals of ASRT were obtained in three different space groups, P4, C2more » and P2{sub 1}2{sub 1}2{sub 1}, which diffract to 1.8, 2.1 and 2.0 Å, respectively. Phases for one of these crystal forms (P4) were obtained by SIRAS phasing using an iodide quick-soak derivative and a partial model was built. Phases for the remaining crystal forms were obtained by molecular replacement using the partial model from the P4 crystal form.« less

The structure of and origin of nodular chromite from the Troodos ophiolite, Cyprus, revealed using high-resolution X-ray computed tomography and electron backscatter diffraction

NASA Astrophysics Data System (ADS)

Prichard, H. M.; Barnes, S. J.; Godel, B.; Reddy, S. M.; Vukmanovic, Z.; Halfpenny, A.; Neary, C. R.; Fisher, P. C.

2015-03-01

Nodular chromite is a characteristic feature of ophiolitic podiform chromitite and there has been much debate about how it forms. Nodular chromite from the Troodos ophiolite in Cyprus is unusual in that it contains skeletal crystals enclosed within the centres of the nodules and interstitial to them. 3D imaging and electron backscatter diffraction have shown that the skeletal crystals within the nodules are single crystals that are surrounded by a rim of polycrystalline chromite. 3D analysis reveals that the skeletal crystals are partially or completely formed cage or hopper structures elongated along the < 111 > axis. The rim is composed of a patchwork of chromite grains that are truncated on the outer edge of the rim. The skeletal crystals formed first from a magma supersaturated in chromite and silicate minerals crystallised from melt trapped between the chromite skeletal crystal blades as they grew. The formation of skeletal crystals was followed by a crystallisation event which formed a silicate-poor rim of chromite grains around the skeletal crystals. These crystals show a weak preferred orientation related to the orientation of the core skeletal crystal implying that they formed by nucleation and growth on this core, and did not form by random mechanical aggregation. Patches of equilibrium adcumulate textures within the rim attest to in situ development of such textures. The nodules were subsequently exposed to chromite undersaturated magma resulting in dissolution, recorded by truncated grain boundaries in the rim and a smooth outer surface to the nodule. None of these stages of formation require a turbulent magma. Lastly the nodules impinged on each other causing local deformation at points of contact.

Symmetrical polyhedra (simple crystal forms) as orbits of noncrystallographic point symmetry groups

NASA Astrophysics Data System (ADS)

Ovsetsina, T. I.; Chuprunov, E. V.

2017-09-01

Simple crystal forms are analyzed as the orbits of noncrystallographic point symmetry groups on a set of smooth or structured ("hatched") planes of crystal space. Polyhedra with symmetrically equivalent faces, obtained using noncrystallographic point symmetry groups, are considered. All possible versions of simple forms for all noncrystallographic groups are listed in a unified table.

Biogenic twinned crystals exhibiting unique morphological symmetry

NASA Astrophysics Data System (ADS)

Hirsch, Anna; Gur, Dvir; Palmer, Ben; Addadi, Lia; Leiserowitz, Leslie; Kronik, Leeor

Guanine crystals are widely used in nature as components of multilayer reflectors. Organisms control the size, morphology, and arrangement of these crystals, to obtain a variety of optical ''devices''. The reflection systems found in the lens of the scallop eye and in the copepod cuticle are unique in that the multilayered reflectors are tiled together to form a contiguous packed array. In the former, square crystals are tiled to form a reflecting mirror. In the latter, hexagonal crystals are closely packed to produce brilliant colors. Based on electron diffraction, morphology considerations, and density functional theory, these crystals were shown to possess similar monoclinic crystal symmetry, which we have previously identified as different from that of synthetic anhydrous guanine. However, the crystals are different in that multiple twinning about the {012} and the {011} crystallographic planes results in square and hexagonal morphology, respectively. This is a unique example where controlled twinning is used as a strategy to form a morphology with higher symmetry than that of the underlying crystal, allowing for tilling that facilitates optical functionality.

Real-time molecular scale observation of crystal formation.

PubMed

Schreiber, Roy E; Houben, Lothar; Wolf, Sharon G; Leitus, Gregory; Lang, Zhong-Ling; Carbó, Jorge J; Poblet, Josep M; Neumann, Ronny

2017-04-01

How molecules in solution form crystal nuclei, which then grow into large crystals, is a poorly understood phenomenon. The classical mechanism of homogeneous crystal nucleation proceeds via the spontaneous random aggregation of species from liquid or solution. However, a non-classical mechanism suggests the formation of an amorphous dense phase that reorders to form stable crystal nuclei. So far it has remained an experimental challenge to observe the formation of crystal nuclei from five to thirty molecules. Here, using polyoxometallates, we show that the formation of small crystal nuclei is observable by cryogenic transmission electron microscopy. We observe both classical and non-classical nucleation processes, depending on the identity of the cation present. The experiments verify theoretical studies that suggest non-classical nucleation is the lower of the two energy pathways. The arrangement in just a seven-molecule proto-crystal matches the order found by X-ray diffraction of a single bulk crystal, which demonstrates that the same structure was formed in each case.

CUMULATE ROCKS ASSOCIATED WITH CARBONATE ASSIMILATION, HORTAVÆR COMPLEX, NORTH-CENTRAL NORWAY

NASA Astrophysics Data System (ADS)

Barnes, C. G.; Prestvik, T.; Li, Y.

2009-12-01

The Hortavær igneous complex intruded high-grade metamorphic rocks of the Caledonian Helgeland Nappe Complex at ca. 466 Ma. The complex is an unusual mafic-silicic layered intrusion (MASLI) because the principal felsic rock type is syenite and because the syenite formed in situ rather than by deep-seated partial melting of crustal rocks. Magma differentiation in the complex was by assimilation, primarily of calc-silicate rocks and melts with contributions from marble and semi-pelites, plus fractional crystallization. The effect of assimilation of calcite-rich rocks was to enhance stability of fassaitic clinopyroxene at the expense of olivine, which resulted in alkali-rich residual melts and lowering of silica activity. This combination of MASLI-style emplacement and carbonate assimilation produced three types of cumulate rocks: (1) Syenitic cumulates formed by liquid-crystal separation. As sheets of mafic magma were loaded on crystal-rich syenitic magma, residual liquid was expelled, penetrating the overlying mafic sheets in flame structures, and leaving a cumulate syenite. (2) Reaction cumulates. Carbonate assimilation, illustrated by a simple assimilation reaction: olivine + calcite + melt = clinopyroxene + CO2 resulted in cpx-rich cumulates such as clinopyroxenite, gabbro, and mela-monzodiorite, many of which contain igneous calcite. (3) Magmatic skarns. Calc-silicate host rocks underwent partial melting during assimilation, yielding a Ca-rich melt as the principal assimilated material and permitting extensive reaction with surrounding magma to form Kspar + cpx + garnet-rich ‘cumulate’ rocks. Cumulate types (2) and (3) do not reflect traditional views of cumulate rocks but instead result from a series of melt-present discontinuous (peritectic) reactions and partial melting of calc-silicate xenoliths. In the Hortavær complex, such cumulates are evident because of the distinctive peritectic cumulate assemblages. It is unclear whether assimilation of ‘normal’ silicate rocks results in peritectic assemblages, or whether they could be identified as such if they exist.

Growth of silicon carbide crystals on a seed while pulling silicon crystals from a melt

NASA Technical Reports Server (NTRS)

Ciszek, T. F.; Schwuttke, G. H. (Inventor)

1979-01-01

A saturated solution of silicon and an element such as carbon having a segregation coefficient less than unity is formed by placing a solid piece of carbon in a body of molten silicon having a temperature differential decreasing toward the surface. A silicon carbide seed crystal is disposed on a holder beneath the surface of the molten silicon. As a rod or ribbon of silicon is slowly pulled from the melt, a supersaturated solution of carbon in silicon is formed in the vicinity of the seed crystal. Excess carbon is emitted from the solution in the form of silicon carbide which crystallizes on the seed crystal held in the cool region of the melt.

Morphology and solubility of multiple crystal forms of Taka-amylase A

NASA Astrophysics Data System (ADS)

Ninomiya, Kumiko; Yamamoto, Tenyu; Oheda, Tadashi; Sato, Kiyotaka; Sazaki, Gen; Matsuura, Yoshiki

2001-01-01

An α-amylase originating from a mold Aspergillus oryzae, Taka-amylase A (Mr of 52 kDa, pI of 3.8), has been purified to an electrophoretically single band grade. Crystallization behaviors were investigated using ammonium sulfate and polyethleneglycol 8000 as precipitants. The variations in the morphology of the crystals obtained with changing crystallization parameters are described. Five apparently different crystal forms were obtained, and their morphology and crystallographic data have been determined. Solubility values of four typical forms were measured using a Michelson-type two-beam interferometer. The results of these experiments showed that this protein can be a potentially interesting and useful model for crystal growth study with a gram-amount availability of pure protein sample.

Shaped nanocrystal particles and methods for making the same

DOEpatents

Alivisatos, A Paul [Oakland, CA; Scher, Erik C [Menlo Park, CA; Manna, Liberato [Berkeley, CA

2011-11-22

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped nanocrystal particles and methods for making the same

DOEpatents

Alivisatos, A. Paul; Scher, Erik C; Manna, Liberato

2013-12-17

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped nanocrystal particles and methods for working the same

DOEpatents

Alivisatos, A. Paul; Sher, Eric C.; Manna, Liberato

2007-12-25

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

Shaped Nonocrystal Particles And Methods For Making The Same

DOEpatents

Alivisatos, A. Paul; Scher, Erik C.; Manna, Liberato

2005-02-15

Shaped nanocrystal particles and methods for making shaped nanocrystal particles are disclosed. One embodiment includes a method for forming a branched, nanocrystal particle. It includes (a) forming a core having a first crystal structure in a solution, (b) forming a first arm extending from the core having a second crystal structure in the solution, and (c) forming a second arm extending from the core having the second crystal structure in the solution.

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

Crystallization and preliminary crystallographic analysis of an aminoglycoside kinase from Legionella pneumophila

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

Lemke, Christopher T.; Hwang, Jiyoung; Xiong, Bing

2005-06-01

Two crystal forms of the antibiotic resistance enzyme APH(9)-Ia from L. pneumophila are reported. 9-Aminoglycoside phosphotransferase type Ia [APH(9)-Ia] is a resistance factor in Legionella pneuemophila, the causative agent of legionnaires’ disease. It is responsible for providing intrinsic resistance to the antibiotic spectinomycin. APH(9)-Ia phosphorylates one of the hydroxyl moieties of spectinomycin in an ATP-dependent manner, abolishing the antibiotic properties of this drug. Here, the crystallization and preliminary X-ray studies of this enzyme in two crystal forms is reported. One of the these crystal forms provides diffraction data to a resolution of 1.7 Å.

Reactions of atomic oxygen with the chlorate ion and the perchlorate ion

NASA Astrophysics Data System (ADS)

Anan'ev, Vladimir; Miklin, Mikhail; Kriger, Ludmila

2014-06-01

The reactions of the chlorate ion with atomic oxygen formed under photolysis of the nitrate ion introduced to potassium chlorate crystal by co-crystallization were studied by optical and infrared absorption spectroscopy. The perchlorate ion was found to form in solids as product of addition reaction of singlet atomic oxygen, formed under dissociation of the peroxynitrite ion - the product of isomerization of the excited nitrate ion. Triplet atomic oxygen does not react with the chlorate ion. The atomic oxygen formed under photolysis of the nitrate ion introduced to potassium perchlorate crystal by co-crystallization does not react with the perchlorate ion.

Defect-mediated phonon dynamics in TaS2 and WSe2

PubMed Central

Cremons, Daniel R.; Plemmons, Dayne A.; Flannigan, David J.

2017-01-01

We report correlative crystallographic and morphological studies of defect-dependent phonon dynamics in single flakes of 1T-TaS2 and 2H-WSe2 using selected-area diffraction and bright-field imaging in an ultrafast electron microscope. In both materials, we observe in-plane speed-of-sound acoustic-phonon wave trains, the dynamics of which (i.e., emergence, propagation, and interference) are strongly dependent upon discrete interfacial features (e.g., vacuum/crystal and crystal/crystal interfaces). In TaS2, we observe cross-propagating in-plane acoustic-phonon wave trains of differing frequencies that undergo coherent interference approximately 200 ps after initial emergence from distinct interfacial regions. With ultrafast bright-field imaging, the properties of the interfering wave trains are observed to correspond to the beat frequency of the individual oscillations, while intensity oscillations of Bragg spots generated from selected areas within the region of interest match well with the real-space dynamics. In WSe2, distinct acoustic-phonon dynamics are observed emanating and propagating away from structurally dissimilar morphological discontinuities (vacuum/crystal interface and crystal terrace), and results of ultrafast selected-area diffraction reveal thickness-dependent phonon frequencies. The overall observed dynamics are well-described using finite element analysis and time-dependent linear-elastic continuum mechanics. PMID:28503630

Intermolecular Vibrations of Hydrophobic Amino Acids

NASA Astrophysics Data System (ADS)

Williams, Michael Roy Casselman

Hydrophobic amino acids interact with their chemical environment through a combination of electrostatic, hydrogen bonding, dipole, induced dipole, and dispersion forces. These interactions all have their own characteristic energy scale and distance dependence. The low-frequency (0.1-5 THz, 5-150 cm-1) vibrational modes of amino acids in the solid state are a direct indicator of the interactions between the molecules, which include interactions between an amino acid functional group and its surroundings. This information is central to understanding the dynamics and morphology of proteins. The alpha-carbon is a chiral center for all of the hydrophobic amino acids, meaning that they exist in two forms, traditionally referred to as L- and D-enantiomers. This nomenclature indicates which direction the molecule rotates plane-polarized visible light (levorotory and dextrorotory). Chiral a-amino acids in proteins are exclusively the L-variety In the solid state, the crystal lattice of the pure L-enantiomer is the mirror image of the D-enantiomer crystal lattice. These solids are energetically identical. Enantiomers also have identical spectroscopic properties except when the measurement is polarization sensitive. A mixture of equal amounts D- and L-amino acid enantiomers can crystallize into a racemic (DL-) structure that is different from that of the pure enantiomers. Whether a solution of both enantiomers will crystallize into a racemic form or spontaneously resolve into a mixture of separate D- and L-crystals largely depends on the interactions between molecules available in the various possible configurations. This is an active area of research. Low-frequency vibrations with intermolecular character are very sensitive to changes in lattice geometry, and consequently the vibrational spectra of racemic crystals are usually quite distinct from the spectra of the crystals of the corresponding pure enantiomers in the far-infrared (far-IR). THz time-domain spectroscopy (THz-TDS) was used to measure the absorption spectra of low-frequency vibrational modes for a variety of hydrophobic amino acids in the solid (polycrystalline) state. The THz-TDS technique uses ultrafast (<50 fs) pulses of light from a visible/near-IR laser to generate single-cycle pulses of THz (far-IR) light. Pulses from the ultrafast laser are also used to coherently gate a THz detector, allowing phase-sensitive measurements of the THz electric field. In some cases, Raman scattering spectra of some of the polycrystalline hydrophobic amino acid samples were measured as well, in this case using an Ar+ laser and a triple monochromator to detect signals at the low Raman-shift values corresponding to the far-IR. THz-TDS was used to measure the low-frequency vibrational absorption spectra of pure L- and pure D-valine crystals as well as the racemic cocrystal, DL-valine. As expected, the Land D-valine THz-TDS absorption spectra are identical to one another (they are enantiomorphous crystals) but very different from the spectrum of DL-valine. In the process of these experiments, it was discovered that it was possible to prepare two distinct polymorphs (different crystalline arrangements) of DL-valine by varying the conditions under which stock material was recrystallized. Once crystallized in a particular form, both polymorphs remained (meta)stable at all temperatures investigated (from 80 K to room temperature), i.e., no phase transformation was observed. The THz-TDS and Raman spectra of the two polymorphs of DL-valine were measured. In addition, THz-TDS and Raman spectra of DL-leucine were measured; this substance has a crystal structure closely analagous to one of the DL-valine polymorphs. The temperature-dependence of the THz-TDS spectrum of each material was also measured. At lower temperatures, it is generally expected that intermolecular vibration frequencies increase (blueshift) due to a shrinking unit cell (effectively squeezing the oscillator potential into a smaller space). While most peaks were indeed observed to blueshift as the sample was cooled, the temperature dependence of the peak position and intensity varied significantly for different modes: while some peaks were hardly affected by the decreasing temperature, others sharpened and/or blueshifted appreciably. Theoretical modeling of intermolecular vibrations in hydrophobic amino acids is challenging because the van der Waals dispersion interactions between the molecules are not accounted for in standard density functional theory (DFT). However, recent advances in theory have made it possible to incorporate these non-local electron correlation forces within the framework of DFT. In addition to carrying out these calculations, methods for comparing results from different theoretical models were devised and evaluated. Perhaps most significantly, a new approach was developed to allow for concise description and easy comparison of vibrational modes that involve complicated mixtures of inter- and intramolecular displacements.

The nature of the mineral component of bone and the mechanism of calcification.

PubMed

Glimcher, M J

1987-01-01

From the physical chemical standpoint, the formation of a solid phase of Ca-P in bone represents a phase transformation, a process exemplified by the formation of ice from water. Considering the structural complexity and abundance of highly organized macromolecules in the cells and extracellular tissue spaces of mineralized tissues generally and in bone particularly, it is inconceivable that this phase transformation occurs by homogeneous nucleation, i.e., without the active participation of an organic component acting as a nucleator. This is almost surely true in biologic mineralization in general. Electron micrographs and low-angle neutron and X-ray diffraction studies clearly show that calcification of collagen fibrils occurs in an extremely intimate and highly organized fashion: initiation of crystal formation within the collagen fibrils in the hole zone region, with the long axes (c-axis) of the crystals aligned roughly parallel to the long axis of the fibril within which they are located. Crystals are initially formed in hole zone regions within individual fibrils separated by unmineralized regions. Calcification is initiated in spatially distinct nucleation sites. This indicates that such regions within a single, undirectional fibril represents independent sites for heterogeneous nucleation. Clearly, sites where mineralization is initiated in adjacent collagen fibrils are even further separated, emphasizing even more clearly that the process of progressive calcification of the collagen fibrils and therefore of the tissue is characterized principally by the presence of increasing numbers of independent nucleation sites within additional hole zone regions of the collagen fibrils. The increase in the mass of Ca-P apatite accrues principally by multiplication of more crystals, mostly by secondary nucleation from the crystals initially deposited in the hole zone region. Very little additional growth of the crystals occurs with time, the additional increase in mineral mass being principally the result of increase in the number of crystals (multiplication), not size of the crystals (crystal growth). The crystals within the collagen fibers grow in number and possibly in size to extend into the overlap zone of the collagen fibrils ("pores") so that all of the available space within the fibrils, which has possibly expanded in volume from its uncalcified level, is eventually occupied by the mineral crystals. It must be recognized that the calcification of separate tissue components and compartments (collagen, mitochondria, matrix vesicles) must be an independent physical chemical event.(ABSTRACT TRUNCATED AT 400 WORDS)

The use of trimethylamine N-oxide as a primary precipitating agent and related methylamine osmolytes as cryoprotective agents for macromolecular crystallography

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

Marshall, Haley; Venkat, Murugappan; Hti Lar Seng, Nang San

2012-01-01

The stabilizing osmolyte trimethylamine N-oxide (TMAO) is shown to be an efficient primary precipitant for protein crystal growth. In addition to TMAO, two other methylamine osmolytes, sarcosine and betaine, are shown to be effective cryoprotective agents for protein crystal cooling. Both crystallization and cryoprotection are often bottlenecks for high-resolution X-ray structure determination of macromolecules. Methylamine osmolytes are known stabilizers of protein structure. One such osmolyte, trimethylamine N-oxide (TMAO), has seen occasional use as an additive to improve macromolecular crystal quality and has recently been shown to be an effective cryoprotective agent for low-temperature data collection. Here, TMAO and the relatedmore » osmolytes sarcosine and betaine are investigated as primary precipitating agents for protein crystal growth. Crystallization experiments were undertaken with 14 proteins. Using TMAO, seven proteins crystallized in a total of 13 crystal forms, including a new tetragonal crystal form of trypsin. The crystals diffracted well, and eight of the 13 crystal forms could be effectively cryocooled as grown with TMAO as an in situ cryoprotective agent. Sarcosine and betaine produced crystals of four and two of the 14 proteins, respectively. In addition to TMAO, sarcosine and betaine were effective post-crystallization cryoprotective agents for two different crystal forms of thermolysin. Precipitation reactions of TMAO with several transition-metal ions (Fe{sup 3+}, Co{sup 2+}, Cu{sup 2+} and Zn{sup 2+}) did not occur with sarcosine or betaine and were inhibited for TMAO at lower pH. Structures of proteins from TMAO-grown crystals and from crystals soaked in TMAO, sarcosine or betaine were determined, showing osmolyte binding in five of the 12 crystals tested. When an osmolyte was shown to bind, it did so near the protein surface, interacting with water molecules, side chains and backbone atoms, often at crystal contacts.« less

Crystal Growth Inhibitors for the Prevention of L-Cystine Kidney Stones Through Molecular Design

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

Rimer, Jeffrey D.; An, Zhihua; Zhu, Zina

2010-11-12

Crystallization of L-cystine is a critical step in the pathogenesis of cystine kidney stones. Treatments for this disease are somewhat effective but often lead to adverse side effects. Real-time in situ atomic force microscopy (AFM) reveals that L-cystine dimethylester (L-CDME) and L-cystine methylester (L-CME) dramatically reduce the growth velocity of the six symmetry-equivalent {l_brace}100{r_brace} steps because of specific binding at the crystal surface, which frustrates the attachment of L-cystine molecules. L-CDME and L-CME produce L-cystine crystals with different habits that reveal distinct binding modes at the crystal surfaces. The AFM observations are mirrored by reduced crystal yield and crystal sizemore » in the presence of L-CDME and L-CME, collectively suggesting a new pathway to the prevention of L-cystine stones by rational design of crystal growth inhibitors.« less

A flow-free droplet-based device for high throughput polymorphic crystallization.

PubMed

Yang, Shih-Mo; Zhang, Dapeng; Chen, Wang; Chen, Shih-Chi

2015-06-21

Crystallization is one of the most crucial steps in the process of pharmaceutical formulation. In recent years, emulsion-based platforms have been developed and broadly adopted to generate high quality products. However, these conventional approaches such as stirring are still limited in several aspects, e.g., unstable crystallization conditions and broad size distribution; besides, only simple crystal forms can be produced. In this paper, we present a new flow-free droplet-based formation process for producing highly controlled crystallization with two examples: (1) NaCl crystallization reveals the ability to package saturated solution into nanoliter droplets, and (2) glycine crystallization demonstrates the ability to produce polymorphic crystallization forms by controlling the droplet size and temperature. In our process, the saturated solution automatically fills the microwell array powered by degassed bulk PDMS. A critical oil covering step is then introduced to isolate the saturated solution and control the water dissolution rate. Utilizing surface tension, the solution is uniformly packaged in the form of thousands of isolating droplets at the bottom of each microwell of 50-300 μm diameter. After water dissolution, individual crystal structures are automatically formed inside the microwell array. This approach facilitates the study of different glycine growth processes: α-form generated inside the droplets and γ-form generated at the edge of the droplets. With precise temperature control over nanoliter-sized droplets, the growth of ellipsoidal crystalline agglomerates of glycine was achieved for the first time. Optical and SEM images illustrate that the ellipsoidal agglomerates consist of 2-5 μm glycine clusters with inner spiral structures of ~35 μm screw pitch. Lastly, the size distribution of spherical crystalline agglomerates (SAs) produced from microwells of different sizes was measured to have a coefficient variation (CV) of less than 5%, showing crystal sizes can be precisely controlled by microwell sizes with high uniformity. This new method can be used to reliably fabricate monodispersed crystals for pharmaceutical applications.

Characterization of two distinctly different mineral-related proteins from the teeth of the Camarodont sea urchin Lytechinus variegatus: Specificity of function with relation to mineralization

NASA Astrophysics Data System (ADS)

Veis, A.; Alvares, K.; Dixit, S. N.; Robach, J. S.; Stock, S. R.

2009-06-01

The majority of the mineral phase of the Lytechinus variegatus tooth is comprised of magnesium containing calcite crystal elements, collectively arranged so that they appear as a single crystal under polarized light, as well as under X-ray or electron irradiation. However, the crystal elements are small, and in spite of the common alignment of their crystal axes, are not the same size or shape in different parts of the tooth. The toughness of the tooth structure arises from the fact that it is a composite in which the crystals are coated with surface layers of organic matter that probably act to inhibit crack formation and elongation. In the growth region the organic components represent a greater part of the tooth structure. In the most heavily mineralized adoral region the primary plates fuse with inter-plate pillars. Using Scanning Electron Microscopy; TOF-SIMS mapping of the characteristic amino acids of the mineral related proteins; and isolation and characterization of the mineral-protected protein we report that the late-forming inter-plate pillars had more than a three-fold greater Mg content than the primary plates. Furthermore, the aspartic acid content of the mineralrelated protein was highest in the high Mg pillars whereas the mineral-protected protein of the primary plates was richer in glutamic acid content.These results suggest that the Asp-rich protein(s) is important for formation of the late developing inter-plate pillars that fuse the primary plates and increase the stiffness of the most mature tooth segment. Supported by NIDCR Grant DE R01-01374 to AV.

Crystal Structures of Apo and Liganded 4-Oxalocrotonate Decarboxylase Uncover a Structural Basis for the Metal-Assisted Decarboxylation of a Vinylogous β-Keto Acid.

PubMed

Guimarães, Samuel L; Coitinho, Juliana B; Costa, Débora M A; Araújo, Simara S; Whitman, Christian P; Nagem, Ronaldo A P

2016-05-10

The enzymes in the catechol meta-fission pathway have been studied for more than 50 years in several species of bacteria capable of degrading a number of aromatic compounds. In a related pathway, naphthalene, a toxic polycyclic aromatic hydrocarbon, is fully degraded to intermediates of the tricarboxylic acid cycle by the soil bacteria Pseudomonas putida G7. In this organism, the 83 kb NAH7 plasmid carries several genes involved in this biotransformation process. One enzyme in this route, NahK, a 4-oxalocrotonate decarboxylase (4-OD), converts 2-oxo-3-hexenedioate to 2-hydroxy-2,4-pentadienoate using Mg(2+) as a cofactor. Efforts to study how 4-OD catalyzes this decarboxylation have been hampered because 4-OD is present in a complex with vinylpyruvate hydratase (VPH), which is the next enzyme in the same pathway. For the first time, a monomeric, stable, and active 4-OD has been expressed and purified in the absence of VPH. Crystal structures for NahK in the apo form and bonded with five substrate analogues were obtained using two distinct crystallization conditions. Analysis of the crystal structures implicates a lid domain in substrate binding and suggests roles for specific residues in a proposed reaction mechanism. In addition, we assign a possible function for the NahK N-terminal domain, which differs from most of the other members of the fumarylacetoacetate hydrolase superfamily. Although the structural basis for metal-dependent β-keto acid decarboxylases has been reported, this is the first structural report for that of a vinylogous β-keto acid decarboxylase and the first crystal structure of a 4-OD.

X-ray sensing materials stability: influence of ambient storage temperature on essential thermal properties of undoped vitreous selenium

NASA Astrophysics Data System (ADS)

Tonchev, D.; Mani, H.; Belev, G.; Kostova, I.; Kasap, S.

2014-12-01

Amorphous selenium (a-Se) is currently used in x-ray image detectors as an x-ray photoconductor. Normally a-Se films used in device applications are fabricated by the evaporation of vitreous bulk material loaded into boats in a typical vacuum deposition system. The resistance against crystallization is an important factor in both film and bulk forms of a-Se. Previous work has indicted that the resistance to crystallization is surprisingly more pronounced around 35 °C [1]. In this work we have therefore examined the essential thermal properties of vitreous selenium (99.999%) samples that have been stored at different temperatures. The thermal characterization experiments involved a series of DSC (Differential Scanning Calorimetry) measurements in which have monitored the glass transition and melting endotherms, and the crystallization exotherm in heating-cooling-heating scans. In DSC experiments, a sample would be heated to a temperature above the melting temperature, equilibrated, then cooled at a fixed rate down to 20 °C, then equilibrated and finally scanned again under a heating schedule. The samples were isothermally stored at temperatures corresponding to 18, 35 and 55 °C. The thermal analysis results show that there are distinct differences in the thermal properties. We have examined the stability in terms of the difference in the crystallization onset temperature (Tc) and the onset of glass transition temperature (Tg). We also examined the Hruby coefficient (Kgl) of these samples, that is Kgl = (Tc - Tg)/(Tm - Tc) where Tc is the crystallization onset temperature and Tm is the melting onset temperature. We have found Kgl to depend on the storage temperature. Surprisingly, we observed that the Hruby coefficient is actually larger at 35 °C compared to the values at 18 and 55 °C.

Phase relations in KxFe2-ySe2 and the structure of superconducting KxFe2Se2 via high-resolution synchrotron diffraction

NASA Astrophysics Data System (ADS)

Shoemaker, Daniel P.; Chung, Duck Young; Claus, Helmut; Francisco, Melanie C.; Avci, Sevda; Llobet, Anna; Kanatzidis, Mercouri G.

2012-11-01

Superconductivity in iron selenides has experienced a rapid growth, but not without major inconsistencies in the reported properties. For alkali-intercalated iron selenides, even the structure of the superconducting phase is a subject of debate, in part because the onset of superconductivity is affected much more delicately by stoichiometry and preparation than in cuprate or pnictide superconductors. If high-quality, pure, superconducting intercalated iron selenides are ever to be made, the intertwined physics and chemistry must be explained by systematic studies of how these materials form and by and identifying the many coexisting phases. To that end, we prepared pure K2Fe4Se5 powder and superconductors in the KxFe2-ySe2 system, and examined differences in their structures by high-resolution synchrotron and single-crystal x-ray diffraction. We found four distinct phases: semiconducting K2Fe4Se5, a metallic superconducting phase KxFe2Se2 with x ranging from 0.38 to 0.58, the phase KFe1.6Se2 with full K occupancy and no Fe vacancy ordering, and a oxidized phase K0.51(5)Fe0.70(2)Se that forms the PbClF structure upon exposure to moisture. We find that the vacancy-ordered phase K2Fe4Se5 does not become superconducting by doping, but the distinct iron-rich minority phase KxFe2Se2 precipitates from single crystals upon cooling from above the vacancy ordering temperature. This coexistence of separate metallic and semiconducting phases explains a broad maximum in resistivity around 100 K. Further studies to understand the solubility of excess Fe in the KxFe2-ySe2 structure will shed light on the maximum fraction of superconducting KxFe2Se2 that can be obtained by solid state synthesis.

Crystal Growth of ZnSe and Related Ternary Compound Semiconductors by Vapor Transport

NASA Technical Reports Server (NTRS)

Su, Ching-Hua; Brebrick, Robert F.; Volz, Martin P.; Burger, Arnold; Dudley, Michael; Matyi, Richard J.; Ramachandran, Narayanan; Sha, Yi-Gao; Volz, Martin P.; Shih, Hung-Dah

2001-01-01

Crystal growth by vapor transport has several distinct advantages over melt growth techniques. Among various potential benefits from material processing in reduced gravity the followings two are considered to be related to crystal growth by vapor transport: (1) elimination of the crystal weight and its influence on the defect formation and (2) reduction of natural buoyancy-driven convective flows arising from thermally and/ or solutally induced density gradient in fluids. The previous results on vapor crystal growth of semiconductors showed the improvements in surface morphology, crystalline quality, electrical properties and dopant distribution of the crystals grown in reduced gravity as compared to the crystals grown on Earth. But the mechanisms, which are responsible for the improvements and cause the gravitational effects on the complicated and coupled processes of vapor mass transport and growth kinetics, are not well understood.

Electron crystallographic analysis of two-dimensional streptavidin crystals coordinated to metal-chelated lipid monolayers.

PubMed Central

Frey, W; Brink, J; Schief, W R; Chiu, W; Vogel, V

1998-01-01

Coordination of individual histidine residues located on a protein surface to metal-chelated lipid monolayers is a potentially general method for crystallizing proteins in two dimensions. It was shown recently by Brewster angle microscopy (BAM) that the model protein streptavidin binds via its surface histidines to Cu-DOIDA lipid monolayers, and aggregates into regularly shaped domains that have the appearance of crystals. We have used electron microscopy to confirm that the domains are indeed crystalline with lattice parameters similar to those of the same protein crystallized beneath biotinylated lipid monolayers. Although BAM demonstrates that the two-dimensional protein crystals grown via metal chelation are distinct from the biotin-bound crystals in both microscopic shape and thermodynamic behavior, the two crystal types show similar density projections and the same plane group symmetry. PMID:9591691

Emission behaviors of unsymmetrical 1,3-diaryl-β-diketones: A model perfectly disclosing the effect of molecular conformation on luminescence of organic solids

NASA Astrophysics Data System (ADS)

Cheng, Xiao; Li, Feng; Han, Shenghua; Zhang, Yufei; Jiao, Chuanjun; Wei, Jinbei; Ye, Kaiqi; Wang, Yue; Zhang, Hongyu

2015-03-01

A series of unsymmetrical 1,3-diaryl-β-diketones 1-6 displaying molecular conformation-dependent fluorescence quantum yields have been synthesized. Crystals with planar molecular conformation such as 1, 2, 3 and 4 are highly fluorescent (φf: 39-53%), and the one holding slightly twisted conformation (5) is moderately luminescent (φf = 17%), while crystal 6 possessing heavily bent structure is completely nonluminous (φf ~ 0). The distinct fluorescence efficiencies are ascribed to their different molecular conformations, since all the crystals hold the same crystal system, space group and crystal packing structures. Additionally, the fluorescent crystals 1-5 display low threshold amplified spontaneous emission (ASE) with small full widths at half-maximum (FWHM: 3-7 nm), indicating their potential as candidates for organic crystal lasing devices.

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.

Polymorphism of Alprazolam (Xanax): a review of its crystalline phases and identification, crystallographic characterization, and crystal structure of a new polymorph (form III).

PubMed

de Armas, Héctor Novoa; Peeters, Oswald M; Van den Mooter, Guy; Blaton, Norbert

2007-05-01

A new polymorphic form of Alprazolam (Xanax), 8-chloro-1-methyl-6-phenyl-4H-[1,2,4]triazolo-[4,3-alpha][1,4]benzodiazepine, C(17)H(13)ClN(4), has been investigated by means of X-ray powder diffraction (XRPD), single crystal X-ray diffraction, and differential scanning calorimetry (DSC). This polymorphic form (form III) was obtained during DSC experiments after the exothermic recrystallization of the melt of form I. The crystal unit cell dimensions for form III were determined from diffractometer methods. The monoclinic unit cell found for this polymorph using XRPD after indexing the powder diffractogram was confirmed by the cell parameters obtained from single crystal X-ray diffractometry on a crystal isolated from the DSC pans. The single crystal unit cell parameters are: a = 28.929(9), b = 13.844(8), c = 7.361(3) angstroms, beta = 92.82(3) degrees , V = 2944(2) angstroms(3), Z = 8, space group P2(1) (No.4), Dx = 1.393 Mg/m(3). The structure obtained from single crystal X-ray diffraction was used as initial model for Rietveld refinement on the powder diffraction data of form III. The temperature phase transformations of alprazolam were also studied using high temperature XRPD. A review of the different phases available in the Powder Diffraction File (PDF) database for this drug is described bringing some clarification and corrections. (c) 2007 Wiley-Liss, Inc. and the American Pharmacists Association.

Crystal-contact engineering to obtain a crystal form of the Kelch domain of human Keap1 suitable for ligand-soaking experiments.

PubMed

Hörer, Stefan; Reinert, Dirk; Ostmann, Katja; Hoevels, Yvette; Nar, Herbert

2013-06-01

Keap1 is a substrate adaptor protein for a Cul3-dependent ubiquitin ligase complex and plays an important role in the cellular response to oxidative stress. It binds Nrf2 with its Kelch domain and thus triggers the ubiquitinylation and degradation of Nrf2. Oxidative stress prevents the degradation of Nrf2 and leads to the activation of cytoprotective genes. Therefore, Keap1 is an attractive drug target in inflammatory diseases. The support of a medicinal chemistry effort by structural research requires a robust crystallization system in which the crystals are preferably suited for performing soaking experiments. This facilitates the generation of protein-ligand complexes in a routine and high-throughput manner. The structure of human Keap1 has been described previously. In this crystal form, however, the binding site for Nrf2 was blocked by a crystal contact. This interaction was analysed and mutations were introduced to disrupt this crystal contact. One double mutation (E540A/E542A) crystallized in a new crystal form in which the binding site for Nrf2 was not blocked and was accessible to small-molecule ligands. The crystal structures of the apo form of the mutated Keap1 Kelch domain (1.98 Å resolution) and of the complex with an Nrf2-derived peptide obtained by soaking (2.20 Å resolution) are reported.

Suppressed Release of Clarithromycin from Tablets by Crystalline Phase Transition of Metastable Polymorph Form I.

PubMed

Fujiki, Sadahiro; Watanabe, Narumi; Iwao, Yasunori; Noguchi, Shuji; Mizoguchi, Midori; Iwamura, Takeru; Itai, Shigeru

2015-08-01

The pharmaceutical properties of clarithromycin (CAM) tablets containing the metastable form I of crystalline CAM were investigated. Although the dissolution rate of form I was higher than that of stable form II, the release of CAM from form I tablet was delayed. Disintegration test and liquid penetration test showed that the disintegration of the tablet delayed because of the slow penetration of an external solution into form I tablet. Investigation by scanning electron microscopy revealed that the surface of form I tablet was covered with fine needle-shaped crystals following an exposure to the external solution. These crystals were identified as form IV crystals by powder X-ray diffraction. The phenomenon that CAM releases from tablet was inhibited by fine crystals spontaneously formed on the tablet surface could be applied to the design of sustained-release formulation systems with high CAM contents by minimizing the amount of functional excipients. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

Crystal water as the mol-ecular glue for obtaining different co-crystal ratios: the case of gallic acid tris-caffeine hexa-hydrate.

PubMed

Vella-Zarb, L; Baisch, U

2018-04-01

The crystal structure of the hexa-hydrate co-crystal of gallic acid and caffeine, C 7 H 6 O 5 ·3C 8 H 10 N 4 O 2 ·6H 2 O or GAL3CAF·6H 2 O , is a remarkable example of the importance of hydrate water acting as structural glue to facilitate the crystallization of two components of different stoichiometries and thus to compensate an imbalance of hydrogen-bond donors and acceptors. The water mol-ecules provide the additional hydrogen bonds required to form a crystalline solid. Whereas the majority of hydrogen bonds forming the inter-molecular network between gallic acid and caffeine are formed by crystal water, only one direct classical hydrogen bond between two mol-ecules is formed between the carb-oxy-lic oxygen of gallic acid and the carbonyl oxygen of caffeine with d ( D ⋯ A ) = 2.672 (2) Å. All other hydrogen bonds either involve crystal water or utilize protonated carbon atoms as donors.

Crystallization and preliminary X-ray analysis of a protease inhibitor from the latex of Carica papaya

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

Azarkan, Mohamed; Garcia-Pino, Abel; Dibiani, Rachid

2006-12-01

The Kunitz-type trypsin/chymotrypsin inhibitor isolated from C. papaya latex has been crystallized using the hanging-drop vapour-diffusion method. Two different crystal forms are observed, diffracting to 2.6 and 1.7 Å. A Kunitz-type protease inhibitor purified from the latex of green papaya (Carica papaya) fruits was crystallized in the presence and absence of divalent metal ions. Crystal form I, which is devoid of divalent cations, diffracts to a resolution of 2.6 Å and belongs to space group P3{sub 1} or P3{sub 2}. This crystal form is a merohedral twin with two molecules in the asymmetric unit and unit-cell parameters a = bmore » = 74.70, c = 78.97 Å. Crystal form II, which was grown in the presence of Co{sup 2+}, diffracts to a resolution of 1.7 Å and belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 44.26, b = 81.99, c = 140.89 Å.« less

Crystal structure of a chimaeric bacterial glutamate dehydrogenase

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

Oliveira, Tânia; Sharkey, Michael A.; Engel, Paul C.

2016-05-23

Glutamate dehydrogenases (EC 1.4.1.2–4) catalyse the oxidative deamination of L-glutamate to α-ketoglutarate using NAD(P) +as a cofactor. The bacterial enzymes are hexameric, arranged with 32 symmetry, and each polypeptide consists of an N-terminal substrate-binding segment (domain I) followed by a C-terminal cofactor-binding segment (domain II). The catalytic reaction takes place in the cleft formed at the junction of the two domains. Distinct signature sequences in the nucleotide-binding domain have been linked to the binding of NAD +versusNADP +, but they are not unambiguous predictors of cofactor preference. In the absence of substrate, the two domains move apart as rigid bodies,more » as shown by the apo structure of glutamate dehydrogenase fromClostridium symbiosum. Here, the crystal structure of a chimaeric clostridial/Escherichia colienzyme has been determined in the apo state. The enzyme is fully functional and reveals possible determinants of interdomain flexibility at a hinge region following the pivot helix. The enzyme retains the preference for NADP +cofactor from the parentE. colidomain II, although there are subtle differences in catalytic activity.« less

Crystal structures of the M 1 and M 4 muscarinic acetylcholine receptors

DOE PAGES

Thal, David M.; Sun, Bingfa; Feng, Dan; ...

2016-03-09

Muscarinic M1–M5 acetylcholine receptors are G-protein-coupled receptors that regulate many vital functions of the central and peripheral nervous systems. In particular, the M1 and M4 receptor subtypes have emerged as attractive drug targets for treatments of neurological disorders, such as Alzheimer’s disease and schizophrenia, but the high conservation of the acetylcholine-binding pocket has spurred current research into targeting allosteric sites on these receptors. In this paper, we report the crystal structures of the M1 and M4 muscarinic receptors bound to the inverse agonist, tiotropium. Comparison of these structures with each other, as well as with the previously reported M2 andmore » M3 receptor structures, reveals differences in the orthosteric and allosteric binding sites that contribute to a role in drug selectivity at this important receptor family. Finally, we also report identification of a cluster of residues that form a network linking the orthosteric and allosteric sites of the M4 receptor, which provides new insight into how allosteric modulation may be transmitted between the two spatially distinct domains.« less

Crystal structures of the M 1 and M 4 muscarinic acetylcholine receptors

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

Thal, David M.; Sun, Bingfa; Feng, Dan

Muscarinic M1–M5 acetylcholine receptors are G-protein-coupled receptors that regulate many vital functions of the central and peripheral nervous systems. In particular, the M1 and M4 receptor subtypes have emerged as attractive drug targets for treatments of neurological disorders, such as Alzheimer’s disease and schizophrenia, but the high conservation of the acetylcholine-binding pocket has spurred current research into targeting allosteric sites on these receptors. In this paper, we report the crystal structures of the M1 and M4 muscarinic receptors bound to the inverse agonist, tiotropium. Comparison of these structures with each other, as well as with the previously reported M2 andmore » M3 receptor structures, reveals differences in the orthosteric and allosteric binding sites that contribute to a role in drug selectivity at this important receptor family. Finally, we also report identification of a cluster of residues that form a network linking the orthosteric and allosteric sites of the M4 receptor, which provides new insight into how allosteric modulation may be transmitted between the two spatially distinct domains.« less

Crystal Structure of Bicc1 SAM Polymer and Mapping of Interactions between the Ciliopathy-Associated Proteins Bicc1, ANKS3, and ANKS6.

PubMed

Rothé, Benjamin; Leettola, Catherine N; Leal-Esteban, Lucia; Cascio, Duilio; Fortier, Simon; Isenschmid, Manuela; Bowie, James U; Constam, Daniel B

2018-02-06

Head-to-tail polymers of sterile alpha motifs (SAM) can scaffold large macromolecular complexes. Several SAM-domain proteins that bind each other are mutated in patients with cystic kidneys or laterality defects, including the Ankyrin (ANK) and SAM domain-containing proteins ANKS6 and ANKS3, and the RNA-binding protein Bicc1. To address how their interactions are regulated, we first determined a high-resolution crystal structure of a Bicc1-SAM polymer, revealing a canonical SAM polymer with a high degree of flexibility in the subunit interface orientations. We further mapped interactions between full-length and distinct domains of Bicc1, ANKS3, and ANKS6. Neither ANKS3 nor ANKS6 alone formed macroscopic homopolymers in vivo. However, ANKS3 recruited ANKS6 to Bicc1, and the three proteins together cooperatively generated giant macromolecular complexes. Thus, the giant assemblies are shaped by SAM domains, their flanking sequences, and SAM-independent protein-protein and protein-mRNA interactions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Petrology, geochemistry and LA-ICP-MS U-Pb geochronology of Paleoproterozoic basement rocks in Bangladesh: An evaluation of calc-alkaline magmatism and implication for Columbia supercontinent amalgamation

NASA Astrophysics Data System (ADS)

Hossain, Ismail; Tsunogae, Toshiaki; Tsutsumi, Yukiyasu; Takahashi, Kazuki

2018-05-01

The Paleoproterozoic (1.7 Ga) basement rocks from Maddhapara, Bangladesh show a large range of chemical variations (e.g. SiO2 = 50.7-74.7%) and include diorite, quartz diorite, monzodiorite, quartz monzonite and granite. The pluton overall displays metaluminous, calc-alkaline orogenic suite; mostly I-type suites formed within subduction-related magmatism. The observed major elements show general trends for fractional crystallization. Trace element contents also indicate the possibility of a fractionation or assimilation; explain the entire variation from diorite to monzonite, even granite. The pluton may have evolved the unique chemical features by a process that included partial melting of calc-alkaline lithologies and mixing of mantle-derived magmas, followed by fractional crystallization, and by assimilation of country rocks. The pluton shows evidence of crystal fractionation involving largely plagioclase, amphibole and possibly biotite. Some of the fractionated magmas may have mixed with more potassic melts from distinct parts of the continental lithosphere to produce granites and/or pegmatites. New geochronological results of granitic pegmatite (1722 ± 10 Ma) are indisputably consistent with diorite and tonalite and those data showing credible geochronological sequence (i.e., diorite - tonalite - granitic pegmatite). Identical Paleoproterozoic age (1.7 Ga) with distinctive magmatism of the Maddhapara basement rocks have agreeable relationship with the CITZ, India. The consistent magmatism is also common in the Transamazonian of South America, Trans-Hudson orogeny in North America, Bohemian Massif and the Svecofennian, Poland, have identified the sequential growth of the continent through the amalgamation of juvenile terrains, succeeded by a major collisional orogeny. Such Paleoproterozoic subduction-related orogens in Australia have similar counterparts in Antarctica and other part of the world. These types of Paleoproterozoic magmatism dominantly contributed to assemble, amalgamation and breakup of the enormous Columbia supercontinent.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.

PubMed

Bruhn, Jessica F; Kirchdoerfer, Robert N; Urata, Sarah M; Li, Sheng; Tickle, Ian J; Bricogne, Gérard; Saphire, Erica Ollmann

2017-01-15

Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (genera Marburgvirus and Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. Marburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics. Copyright © 2017 American Society for Microbiology.

Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

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

Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.

ABSTRACT Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOVmore » VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV. IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics.« less

Observation of two distinct negative trions in tungsten disulfide monolayers

NASA Astrophysics Data System (ADS)

Boulesbaa, Abdelaziz; Huang, Bing; Wang, Kai; Lin, Ming-Wei; Mahjouri-Samani, Masoud; Rouleau, Christopher; Xiao, Kai; Yoon, Mina; Sumpter, Bobby; Puretzky, Alexander; Geohegan, David

2015-09-01

Ultrafast pump-probe spectroscopy of two-dimensional tungsten disulfide monolayers (2 D W S2) grown on sapphire substrates revealed two transient absorption spectral peaks that are attributed to distinct negative trions at ˜2.02 eV (T1) and ˜1.98 eV (T2) . The dynamics measurements indicate that trion formation by the probe is enabled by photodoped 2D WS2 crystals with electrons remaining after trapping of holes from excitons or free electron-hole pairs at defect sites in the crystal or on the substrate. Dynamics of the characteristic absorption bands of excitons XA and XB at ˜2.03 and ˜2.40 eV , respectively, were separately monitored and compared to the photoinduced absorption features. Selective excitation of the lowest exciton level XA using λpump<2.4 eV forms only trion T1, implying that the electron remaining from dissociation of exciton XA is involved in the creation of this trion with a binding energy ˜10 meV with respect to XA. The absorption peak corresponding to trion T2 appears when λpump<2.4 eV , which is just sufficient to excite exciton XB. The dynamics of trion T2 formation are found to correlate with the disappearance of the bleach of the XB exciton, indicating the involvement of holes participating in the bleach dynamics of exciton XB. Static electrical-doping photoabsorption measurements confirm the presence of an induced absorption peak similar to that of T2. Since the proposed trion formation process here involves exciton dissociation through hole trapping by defects in the 2D crystal or substrate, this discovery highlights the strong role of defects in defining optical and electrical properties of 2D metal chalcogenides, which is relevant to a broad spectrum of basic science and technological applications.

Effect of method of crystallization on the IV-III and IV-II polymorphic transitions of ammonium nitrate.

PubMed

Vargeese, Anuj A; Joshi, Satyawati S; Krishnamurthy, V N

2009-01-15

A study has been undertaken on the effect of crystallization method on the IV<-->III transition of ammonium nitrate (AN). AN is crystallized in three different ways, viz. recrystallization, evaporative crystallization and melt crystallization. When the samples were crystallized from saturated aqueous solution, ideal crystals were formed, which behaved differently from the crystals formed from the other methods. The DTA examination of the crystals showed that the crystals have different transition behaviour. The moisture uptake of the samples determined were found to have influenced by the mode of crystallization. The samples were further analyzed by powder X-ray diffraction (XRD) and scanning electron microscopy (SEM). The present study showed that the parameters like thermal history, number of previous transformations and moisture content have a very negligible influence on the IV<-->III transition of AN as compared to the method of crystallization.

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

Structure analysis of the global metabolic regulator Crc from Pseudomonas aeruginosa.

PubMed

Wei, Yong; Zhang, Heng; Gao, Zeng-Qiang; Xu, Jian-Hua; Liu, Quan-Sheng; Dong, Yu-Hui

2013-01-01

The global metabolic regulator catabolite repression control (Crc) has recently been found to modulate the susceptibility to antibiotics and virulence in the opportunistic pathogen Pseudomonas aeruginosa and been suggested as a nonlethal target for novel antimicrobials. In P. aeruginosa, Crc couples with the CA motifs from the small RNA CrcZ to form a post-transcriptional regulator system and is removed from the 5'-end of the target mRNAs. In this study, we first reported the crystal structure of Crc from P. aeruginosa refined to 2.20 Å. The structure showed that it consists of two halves with similar overall topology and there are 11 β strands surrounded by 13 helices, forming a four-layered α/β-sandwich. The circular dichroism spectroscopy revealed that it is thermostable in solution and shares similar characteristics to that in crystal. Comprehensive structural analysis and comparison with the homologies of Crc showed high similarity with several known nucleases and consequently may be classified into a member exodeoxyribonuclease III. However, it shows distinct substrate specificity (RNA as the preferred substrate) compared to these DNA endonucleases. Structural comparisons also revealed potential RNA recognition and binding region mainly consisting of five flexible loops. Our structure study provided the basis for the future application of Crc as a target to develop new antibiotics. Copyright © 2012 International Union of Biochemistry and Molecular Biology, Inc.

Three-dimensional crystals of ribosomes and their subunits from eu- and archaebacteria.

PubMed

Glotz, C; Müssig, J; Gewitz, H S; Makowski, I; Arad, T; Yonath, A; Wittmann, H G

1987-11-01

Ordered three-dimensional crystals of 70S ribosomes as well as of 30S and 50S ribosomal subunits from various bacteria (E. coli, Bacillus stearothermophilus, Thermus thermophilus and Halobacterium marismortui) have been grown by vapour diffusion in hanging drops using mono- and polyalcohols. A new compact crystal form of 50S subunits has been obtained, and it is suitable for crystallographic studies at medium resolution. In addition, from one crystal form large crystals could be grown in X-ray capillaries. In all cases the crystals were obtained from functionally active ribosomal particles, and the particles from dissolved crystals retained their integrity and biological activity.

Location of Bromide Ions in Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Lim, Kap; Nadarajah, Arunan; Forsythe, Elizabeth L.; Pusey, Marc L.

1998-01-01

Anions have been shown to play a dominant role in the crystallization of chicken egg white lysozyme from salt solutions. Previous studies employing X-ray crystallography had found one chloride ion binding site in the tetragonal crystal form of the protein and four nitrate ion binding sites in the monoclinic form. In this study the anion positions in the tetragonal form were determined from the difference Fourier map obtained from lysozyme crystal grown in bromide and chloride solutions. Five possible anion binding sites were found in this manner. Some of these sites were in pockets containing basic residues while others were near neutral, but polar, residues. The sole chloride ion binding site found in previous studies was confirmed, while four of these sites corresponded to four binding sites found for nitrate ions in monoclinic crystals. The study suggests that most of the anion binding sites in lysozyme remain unchanged, even when different anions and different crystal forms of lysozyme are employed.

Locations of Bromide Ions in Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Lim, Kap; Nadarajah, Arunan; Forsythe, Elizabeth L.; Pusey, Marc L.

1998-01-01

Anions have been shown to play a dominant role in the crystallization of chicken egg-white lysozyme from salt solutions. Previous studies employing X-ray crystallography have found one chloride ion binding site in the tetragonal crystal form of the protein and four nitrate ion binding sites in the monoclinic form. In this study the anion positions in the tetragonal form were determined from the difference Fourier map obtained from lysozyme crystals grown in bromide and chloride solutions. Five possible anion-binding sites were found in this manner. Some of these sites were in pockets containing basic residues while others were near neutral, but polar, residues. The sole chloride ion binding site found in previous studies was confirmed, while four further sites were found which corresponded to the four binding sites found for nitrate ions in monoclinic crystals. The study suggests that most of the anion-binding sites in lysozyme remain unchanged even when different anions and different crystal forms of lysozyme are employed.

Process for Forming a High Temperature Single Crystal Canted Spring

NASA Technical Reports Server (NTRS)

DeMange, Jeffrey J (Inventor); Ritzert, Frank J (Inventor); Nathal, Michael V (Inventor); Dunlap, Patrick H (Inventor); Steinetz, Bruce M (Inventor)

2017-01-01

A process for forming a high temperature single crystal canted spring is provided. In one embodiment, the process includes fabricating configurations of a rapid prototype spring to fabricate a sacrificial mold pattern to create a ceramic mold and casting a canted coiled spring to form at least one canted coil spring configuration based on the ceramic mold. The high temperature single crystal canted spring is formed from a nickel-based alloy containing rhenium using the at least one coil spring configuration.

In situ 3D topographic and shape analysis by synchrotron radiation X-ray microtomography for crystal form identification in polymorphic mixtures

PubMed Central

Yin, Xian-Zhen; Xiao, Ti-Qiao; Nangia, Ashwini; Yang, Shuo; Lu, Xiao-Long; Li, Hai-Yan; Shao, Qun; He, You; York, Peter; Zhang, Ji-Wen

2016-01-01

Polymorphism denotes the existence of more than one crystal structure of a substance, and great practical and theoretical interest for the chemical and pharmaceutical industries. In many cases, it is challenging to produce a pure crystal form and establish a sensitive detection method for the identification of crystal form in a mixture of polymorphs. In this study, an accurate and sensitive method based on synchrotron radiation X-ray computed microtomography (SR-μCT) was devised to identify the polymorphs of clopidogrel bisulphate (CLP). After 3D reconstruction, crystal particles were extracted and dozens of structural parameters were calculated. Whilst, the particle shapes of the two crystal forms were all irregular, the surface of CLP II was found to be rougher than CLP I. In order to classify the crystal form based on the quantitative morphological property of particles, Volume Bias Percentage based on Surface Smoothing (VBP) was defined and a new method based on VBP was successfully developed, with a total matching rate of 99.91% for 4544 particles and a lowest detectable limit of 1%. More important for the mixtures in solid pharmaceutical formulations, the interference of excipients can be avoided, a feature cannot achieved by other available analytical methods. PMID:27097672

Highly robust crystalsome via directed polymer crystallization at curved liquid/liquid interface

PubMed Central

Wang, Wenda; Qi, Hao; Zhou, Tian; Mei, Shan; Han, Lin; Higuchi, Takeshi; Jinnai, Hiroshi; Li, Christopher Y.

2016-01-01

Lipids and amphiphilic block copolymers spontaneously self-assemble in water to form a plethora of micelles and vesicles. They are typically fluidic in nature and often mechanically weak for applications such as drug delivery and gene therapeutics. Mechanical properties of polymeric materials could be improved by forming crystalline structures. However, most of the self-assembled micelles and vesicles have curved surfaces and precisely tuning crystallization within a nanoscale curved space is challenging, as the curved geometry is incommensurate with crystals having three-dimensional translational symmetry. Herein, we report using a miniemulsion crystallization method to grow nanosized, polymer single-crystal-like capsules. We coin the name crystalsome to describe this unique structure, because they are formed by polymer lamellar crystals and their structure mimics liposomes and polymersomes. Using poly(L-lactic acid) (PLLA) as the model polymer, we show that curved water/p-xylene interface formed by the miniemulsion process can guide the growth of PLLA single crystals. Crystalsomes with the size ranging from ∼148 nm to over 1 μm have been formed. Atomic force microscopy measurement demonstrate a two to three orders of magnitude increase in bending modulus compared with conventional polymersomes. We envisage that this novel structure could shed light on investigating spherical crystallography and drug delivery. PMID:26837260

Magma feeding system of Kutcharo and Mashu calderas, Hokkaido, Japan: Evidence of a common basaltic magma evolving into two distinct rock series

NASA Astrophysics Data System (ADS)

Miyagi, I.; Itoh, J.; Nguyen, H.

2009-12-01

Kutcharo and its adjacent Mashu volcanoes are located in NE Hokkaido, about 150 km west of the Kurile trench. The latest major activity of Kutcharo was 35 thousand years ago (termed KP I) produced about 50 km3 D.R.E, Mashu meanwhile became active after KP I. To understand the magma feeding system of adjoining but distinct Kutcharo (medium-K) and Mashu (low-K) volcanoes, we examined major and trace element, and Sr, Nd, and Pb isotopic compositions of whole rocks. We also studied phenocryst chemical zoning and chemical compositions of melt inclusions in phenocryst. The chemical results of melt inclusions show no distinction between medium- and low-K as being recognized in bulk rock chemistry of the volcanoes. Instead, the results form a smooth trend between low-K rock series and high-K rhyolitic melt end-member (as high as 5 wt. % K2O). There is no significant difference Sr, Nd and Pb isotopes between basalt and rhyolite suggesting genetic relationship. Moreover, the trace element distribution patterns show enrichment increasing gradually from the basalt to rhyolite via andesite indicating fractional crystallization evolution. Chemical zoning in plagioclase phenocryst in KP I (An 80-40) suggest that basaltic magma injected repeatedly into a voluminous felsic magma chamber of Kutcharo volcano. Chemical compositions of olivine phenocryst show that Kutcharo (Fo 86) was hotter as compared to Mashu (Fo 75). Application of MELTS program (Ghiorso and Sack, 1995) on composition of the basaltic melt end-member suggests that crystallization or subsequent re-melting of the basalt may produce medium- to high-K rhyolite melt, and mixing of the rhyolite with basalt may form the observed medium-K Kutcharo and low-K Mashu rock series. It is estimated that total volume of the basaltic magma supplied intermittently beneath the volcanoes was several folds to 10 times larger than the erupted rhyolite magma. And that the basalt injection may be more intensive beneath Kutcharo, leading to the formation of a thermal structure that has a peak at Kutcharo and lowers gradually toward Mashu. The thermal structure may explain the observed difference in erupted volumes and rock series between two volcanoes. This research project has been conducted under the research contract with Nuclear and Industrial Safety Agency (NISA).

Effect of milling conditions on solid-state amorphization of glipizide, and characterization and stability of solid forms.

PubMed

Xu, Kailin; Xiong, Xinnuo; Zhai, Yuanming; Wang, Lili; Li, Shanshan; Yan, Jin; Wu, Di; Ma, Xiaoli; Li, Hui

2016-09-10

In this study, the amorphization of glipizide was systematically investigated through high-energy ball milling at different temperatures. The results of solid-state amorphization through milling indicated that glipizide underwent direct crystal-to-glass transformation at 15 and 25°C and crystal-to-glass-to-crystal conversion at 35°C; hence, milling time and temperature had significant effects on the amorphization of glipizide, which should be effectively controlled to obtain totally amorphous glipizide. Solid forms of glipizide were detailedly characterized through analyses of X-ray powder diffraction, morphology, thermal curves, vibrational spectra, and solid-state nuclear magnetic resonance. The physical stability of solid forms was investigated under different levels of relative humidity (RH) at 25°C. Forms I and III are kinetically stable and do not form any new solid-state forms at various RH levels. By contrast, Form II is kinetically unstable, undergoing direct glass-to-crystal transformation when RH levels higher than 32.8%. Therefore, stability investigation indicated that Form II should be stored under relatively dry conditions to prevent rapid crystallization. High temperatures can also induce the solid-state transformation of Form II; the conversion rate increased with increasing temperature. Copyright © 2016 Elsevier B.V. All rights reserved.

Unusual Nonterrestrial L-proteinogenic Amino Acid excesses in the Tagish Lake Meteorite

NASA Technical Reports Server (NTRS)

Glavin, Daniel P.; Elsila, Jamie E.; Burton, Aaron S.; Callahan, Michael P.; Dworkin, Jason P.; Hilts, Robert W.; Herd, D. K.

2012-01-01

The distribution and isotopic and enantiomeric compositions of amino acids found in three distinct fragments of the Tagish Lake C2-type carbonaceous chondrite were investigated via liquid chromatography with fluorescence detection and time-of-flight mass spectrometry and gas chromatography isotope ratio mass spectrometry. Large L-enantiomeric excesses (L(sub ee) approximately 43-59%) of the alpha-hydrogen aspartic and glutamic amino acids were measured in Tagish Lake, whereas alanine, another alpha hydrogen protein amino acid, was found to be nearly racemic (D much approximately L) using both techniques. Carbon isotope measurements of D- and L-aspartic acid and 1)- and L-alanine in Tagish Lake fall well outside of the terrestrial range and indicate that the measured aspartic acid enantioenrichment is indigenous to the meteorite. Alternate explanations for the L-excesses of aspartic acid such as interference from other compounds present in the sample, analytical biases, or terrestrial amino acid contamination were investigated and rejected. These results can be explained by differences in the solid-solution phase behavior of aspartic acid, which can form conglomerate enantiopure solids during crystallization, and alanine, which can only form racemic crystals. Amplification of a small initial L-enantiomer excess during aqueous alteration on the meteorite parent body could have led to the large L-enrichments observed for aspartic acid and other conglomerate amino acids in Tagish Lake. The detection of non terrestrial L-proteinogenic amino acid excesses in the Tagish Lake meteorite provides support for the hypothesis that significant enantiomeric enrichments for some amino acids could form by abiotic processes prior to the emergence of life.

Effect of water on self-assembled tubules in β-sitosterol + γ-oryzanol-based organogels

NASA Astrophysics Data System (ADS)

den Adel, Ruud; Heussen, Patricia C. M.; Bot, Arjen

2010-10-01

Mixtures of β-sitosterol and γ-oryzanol form a network in triglyceride oil that may serve as an alternative to the network of small crystallites of triglycerides occurring in regular oil structuring. The present x-ray diffraction study investigates the relation between the crystal forms of the individual compounds and the mixture in oil, water and emulsion. β-Sitosterol and γ-oryzanol form normal crystals in oil, in water, or in emulsions. The crystals are sensitive to the presence of water. The mixture of β-sitosterol + γ-oryzanol forms crystals in water and emulsions that can be traced back to the crystals of the pure compounds. Only in oil, a completely different structure emerges in the mixture of β-sitosterol + γ-oryzanol, which bears no relation to the structures that are formed by both individual compounds, and which can be identified as a self-assembled tubule (diameter 7.2±0.1 nm, wall thickness 0.8±0.2 nm).

Crystallization of Chicken Egg White Lysozyme from Sulfate Salts

NASA Technical Reports Server (NTRS)

Forsythe, Elizabeth; Pusey, Marc

1998-01-01

It has been "known" that chicken egg white lysozyme does not crystallize from sulfate, particularly ammonium sulfate, salts, but instead gives amorphous precipitates. This has been the basis of several studies using lysozyme comparing macromolecule crystal nucleation and amorphous precipitation. Recently Ries-Kautt et al (Acta Cryst D50, (1994) 366) have shown that purified isoionic CEWL could be crystallized from low concentrations of sulfate at basic pH, and we subsequently showed that in fact CEWL could be purified in both the tetragonal and orthorhombic forms using ammonium sulfate over the pH range 4.0 to 7.8 (Acta Cryst D53, (1997) 795). We have now extended these observations to include a range of common sulfate salts, specifically sodium, potassium, rubidium, magnesium, and manganese sulfates. In all cases but the manganese sulfates both the familiar tetragonal and orthorhombic forms were obtained, with unit cell dimensions close to those known for the "classic" sodium chloride crystallized forms. Manganese sulfate has only yielded orthorhombic crystals to date. All crystallizations were carried out using low (typically less than or equal to 6 M) salt and high (greater than approximately 90 mg/ml) protein concentrations. As with ammonium sulfate, the tetragonal - orthorhombic phase shift appears to be a function of both the temperature and the protein concentration, with higher temperatures and concentrations favoring the orthorhombic and lower the tetragonal form. The phase change range is somewhat reduced for the sulfate salts, depending upon conditions being typically between approximately 15 - 20 C. Both the magnesium and manganese sulfates gave crystals at salt concentrations over 0.6 M as well, with magnesium sulfate giving a very slowly nucleating and growing hexagonal form. A triclinic crystal form, characterized by aggressively small crystals (typically 0.1 mm in size) has been occasionally obtained from ammonium sulfate. Finally, preliminary spot solubility determinations have suggested that in some cases the solubility increases with increasing salt concentrations.

Constraining Cometary Crystal Shapes from IR Spectral Features

NASA Technical Reports Server (NTRS)

Wooden, Diane H.; Lindsay, Sean; Harker, David E.; Kelley, Michael S. P.; Woodward, Charles E.; Murphy, James Richard

2013-01-01

A major challenge in deriving the silicate mineralogy of comets is ascertaining how the anisotropic nature of forsterite crystals affects the spectral features' wavelength, relative intensity, and asymmetry. Forsterite features are identified in cometary comae near 10, 11.05-11.2, 16, 19, 23.5, 27.5 and 33 microns [1-10], so accurate models for forsterite's absorption efficiency (Qabs) are a primary requirement to compute IR spectral energy distributions (SEDs, lambdaF lambda vs. lambda) and constrain the silicate mineralogy of comets. Forsterite is an anisotropic crystal, with three crystallographic axes with distinct indices of refraction for the a-, b-, and c-axis. The shape of a forsterite crystal significantly affects its spectral features [13-16]. We need models that account for crystal shape. The IR absorption efficiencies of forsterite are computed using the discrete dipole approximation (DDA) code DDSCAT [11,12]. Starting from a fiducial crystal shape of a cube, we systematically elongate/reduce one of the crystallographic axes. Also, we elongate/reduce one axis while the lengths of the other two axes are slightly asymmetric (0.8:1.2). The most significant grain shape characteristic that affects the crystalline spectral features is the relative lengths of the crystallographic axes. The second significant grain shape characteristic is breaking the symmetry of all three axes [17]. Synthetic spectral energy distributions using seven crystal shape classes [17] are fit to the observed SED of comet C/1995 O1 (Hale-Bopp). The Hale-Bopp crystalline residual better matches equant, b-platelets, c-platelets, and b-columns spectral shape classes, while a-platelets, a-columns and c-columns worsen the spectral fits. Forsterite condensation and partial evaporation experiments demonstrate that environmental temperature and grain shape are connected [18-20]. Thus, grain shape is a potential probe for protoplanetary disk temperatures where the cometary crystalline forsterite formed. The forsterite crystal shapes (equant, b-platelets, c-platelets, b-columns - excluding a- and c-columns) derived from our modeling [17] of comet Hale- Bopp, compared to laboratory synthesis experiments [18], suggests that these crystals are high temperature condensates. By observing and modeling the crystalline features in comet ISON, we may constrain forsterite crystal shape(s) and link to their formation temperature(s) and environment(s).

Four crystal forms of a Bence-Jones protein

PubMed Central

Makino, Debora L.; Henschen-Edman, Agnes H.; McPherson, Alexander

2005-01-01

Four crystal forms have been grown and characterized by X-ray diffraction of a Bence-Jones protein collected from the urine of a multiple myeloma patient more than 40 years ago. Closely related tetragonal and orthorhombic forms belonging to space groups P43212 and P212121, with unit-cell parameters a = b = 68.7, c = 182.1 and a = 67.7, b = 69.4, c = 87.3 Å, diffract to 1.5 and 1.9 Å, respectively. Two closely related trigonal forms, both belonging to space group P3121 with unit-cell parameters a = b = 154.3 Å but differing by a doubling of the c axis, one 46.9 Å and the other 94.0 Å, diffract to 2.9 and 2.6 Å resolution, respectively. The trigonal crystal of short c-axis length shows a positive indication of twinning. The trigonal crystal of longer c axis, which appeared only after eight months of incubation at room temperature, is likely to be composed of proteolytically degraded molecules and unlike the other crystal forms contains two entire Bence-Jones dimers in the asymmetric unit. This latter crystal form may shed some light on the formation of fibrils common to certain storage diseases. PMID:16508097

Purification, crystallization and preliminary crystallographic study of low oxygen-affinity haemoglobin from cat (Felis silvestris catus) in two different crystal forms.

PubMed

Balasubramanian, M; Moorthy, Pon Sathya; Neelagandan, K; Ponnuswamy, M N

2009-03-01

Haemoglobin is a metalloprotein which plays a major role in the transportation of oxygen from the lungs to tissues and of carbon dioxide back to the lungs. The present work reports the preliminary crystallographic study of low oxygen-affinity haemoglobin from cat in different crystal forms. Cat blood was collected, purified by anion-exchange chromatography and crystallized in two different conditions by the hanging-drop vapour-diffusion method under unbuffered low-salt and buffered high-salt concentrations using PEG 3350 as a precipitant. Intensity data were collected using MAR345 and MAR345dtb image-plate detector systems. Cat haemoglobin crystallizes in monoclinic and orthorhombic crystal forms with one and two whole biological molecules (alpha(2)beta(2)), respectively, in the asymmetric unit.

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.

Production of a Pyrrole Antibiotic by a Marine Bacterium1

PubMed Central

Burkholder, Paul R.; Pfister, Robert M.; Leitz, Frederick H.

1966-01-01

Evidence is presented for the isolation and identification of bacteria able to synthesize an unusual antibiotic containing five bromine atoms per molecule. The identification and taxonomic position of these bacteria was made by use of a computer in conjunction with traditional methods. These microorganisms and closely related strains have been isolated on various occasions from tropical water in the vicinity of Puerto Rico. One bacterium, a pseudomonad, has been given the name Pseudomonas bromoutilis because of its distinctive capability. The antibiotic has been extracted, purified, and obtained in crystal form, and its structure has been determined. Although clinical tests of its properties were not encouraging, it may be of significant value and interest from an ecological standpoint. Images Fig. 1 PMID:4380876

Observation of solid–solid transitions in 3D crystals of colloidal superballs

PubMed Central

Meijer, Janne-Mieke; Pal, Antara; Ouhajji, Samia; Lekkerkerker, Henk N. W.; Philipse, Albert P.; Petukhov, Andrei V.

2017-01-01

Self-organization in anisotropic colloidal suspensions leads to a fascinating range of crystal and liquid crystal phases induced by shape alone. Simulations predict the phase behaviour of a plethora of shapes while experimental realization often lags behind. Here, we present the experimental phase behaviour of superball particles with a shape in between that of a sphere and a cube. In particular, we observe the formation of a plastic crystal phase with translational order and orientational disorder, and the subsequent transformation into rhombohedral crystals. Moreover, we uncover that the phase behaviour is richer than predicted, as we find two distinct rhombohedral crystals with different stacking variants, namely hollow-site and bridge-site stacking. In addition, for slightly softer interactions we observe a solid–solid transition between the two. Our investigation brings us one step closer to ultimately controlling the experimental self-assembly of superballs into functional materials, such as photonic crystals. PMID:28186101

Engineering calcium oxalate crystal formation in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Many plants accumulate crystals of calcium oxalate. Just how these crystals form remains unknown. To gain insight into the mechanisms regulating calcium oxalate crystal formation, a crystal engineering approach was initiated utilizing the non-crystal accumulating plant, Arabidopsis. The success of t...

Relationship of Open-Circuit Voltage to CdTe Hole Concentration and Lifetime

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

Duenow, Joel N.; Burst, James M.; Albin, David S.

We investigate the correlation of bulk CdTe and CdZnTe material properties with experimental open-circuit voltage (Voc) through fabrication and characterization of diverse single-crystal solar cells with different dopants. Several distinct crystal types reach Voc >900 mV. Correlations are in general agreement with Voc limits modeled from bulk minority-carrier lifetime and hole concentration.

The role of cocrystals in pharmaceutical science.

PubMed

Shan, Ning; Zaworotko, Michael J

2008-05-01

Pharmaceutical cocrystals, a subset of a long known but little-studied class of compounds, represent an emerging class of crystal forms in the context of pharmaceutical science. They are attractive to pharmaceutical scientists because they can significantly diversify the number of crystal forms that exist for a particular active pharmaceutical ingredient (API), and they can lead to improvements in physical properties of clinical relevance. In this article we address pharmaceutical cocrystals from the perspective of design (crystal engineering) and present a series of case studies that demonstrate how they can enhance the solubility, bioavailability, and/or stability of API crystal forms.

Probing the limits of metal plasticity with molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Zepeda-Ruiz, Luis A.; Stukowski, Alexander; Oppelstrup, Tomas; Bulatov, Vasily V.

2017-10-01

Ordinarily, the strength and plasticity properties of a metal are defined by dislocations--line defects in the crystal lattice whose motion results in material slippage along lattice planes. Dislocation dynamics models are usually used as mesoscale proxies for true atomistic dynamics, which are computationally expensive to perform routinely. However, atomistic simulations accurately capture every possible mechanism of material response, resolving every ``jiggle and wiggle'' of atomic motion, whereas dislocation dynamics models do not. Here we present fully dynamic atomistic simulations of bulk single-crystal plasticity in the body-centred-cubic metal tantalum. Our goal is to quantify the conditions under which the limits of dislocation-mediated plasticity are reached and to understand what happens to the metal beyond any such limit. In our simulations, the metal is compressed at ultrahigh strain rates along its [001] crystal axis under conditions of constant pressure, temperature and strain rate. To address the complexity of crystal plasticity processes on the length scales (85-340 nm) and timescales (1 ns-1μs) that we examine, we use recently developed methods of in situ computational microscopy to recast the enormous amount of transient trajectory data generated in our simulations into a form that can be analysed by a human. Our simulations predict that, on reaching certain limiting conditions of strain, dislocations alone can no longer relieve mechanical loads; instead, another mechanism, known as deformation twinning (the sudden re-orientation of the crystal lattice), takes over as the dominant mode of dynamic response. Below this limit, the metal assumes a strain-path-independent steady state of plastic flow in which the flow stress and the dislocation density remain constant as long as the conditions of straining thereafter remain unchanged. In this distinct state, tantalum flows like a viscous fluid while retaining its crystal lattice and remaining a strong and stiff metal.

Fabrication of single crystal architecture in Sb-S-I glass: Transition from dot to line

DOE PAGES

Savytskii, Dmytro; Dierolf, Volkmar; Tamura, Nobumichi; ...

2017-12-08

We have investigated the occurrence of the sometimes observed grain boundaries, as initial seed is extended to form line in laser-fabricated single-crystal architecture in glass (SCAG). In particular, for Sb 2S 3 SCAG in Sb-S-I glass as a model system, grain boundaries are formed during the transition from laser-written initial seed dot to crystal line. Such grain boundaries during the growth of Sb 2S 3 crystals occur in 16SbI 3-84Sb 2S 3glass, whereas they are absent in Sb 2S 3 glass. We correlate this difference in tendency to form multiple grains with the relative glass forming ability i.e. the dynamicsmore » of nucleation and crystal growth as determined by differential scanning calorimetry (DSC). On the basis of this understanding, methods to minimize the appearance of grain boundaries in the transition region are suggested.« less

Fabrication of single crystal architecture in Sb-S-I glass: Transition from dot to line

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

Savytskii, Dmytro; Dierolf, Volkmar; Tamura, Nobumichi

We have investigated the occurrence of the sometimes observed grain boundaries, as initial seed is extended to form line in laser-fabricated single-crystal architecture in glass (SCAG). In particular, for Sb 2S 3 SCAG in Sb-S-I glass as a model system, grain boundaries are formed during the transition from laser-written initial seed dot to crystal line. Such grain boundaries during the growth of Sb 2S 3 crystals occur in 16SbI 3-84Sb 2S 3glass, whereas they are absent in Sb 2S 3 glass. We correlate this difference in tendency to form multiple grains with the relative glass forming ability i.e. the dynamicsmore » of nucleation and crystal growth as determined by differential scanning calorimetry (DSC). On the basis of this understanding, methods to minimize the appearance of grain boundaries in the transition region are suggested.« less

Methods for synthesizing microporous crystals and microporous crystal membranes

DOEpatents

Dutta, Prabir; Severance, Michael; Sun, Chenhu

2017-02-07

A method of making a microporous crystal material, comprising: a. forming a mixture comprising NaOH, water, and one or more of an aluminum source, a silicon source, and a phosphate source, whereupon the mixture forms a gel; b. heating the gel for a first time period, whereupon a first volume of water is removed from the gel and micoroporous crystal nuclei form, the nuclei having a framework; and c.(if a membrane is to be formed) applying the gel to a solid support seeded with microporous crystals having a framework that is the same as the framework of the nuclei; d. heating the gel for a second time period. during which a second volume of water is added to the gel; wherein the rate of addition of the second volume of water is between about 0.5 and about 2.0 fold the rate of removal of the first volume of water.

Polymorphs and polymorphic cocrystals of temozolomide.

PubMed

Babu, N Jagadeesh; Reddy, L Sreenivas; Aitipamula, Srinivasulu; Nangia, Ashwini

2008-07-07

Crystal polymorphism in the antitumor drug temozolomide (TMZ), cocrystals of TMZ with 4,4'-bipyridine-N,N'-dioxide (BPNO), and solid-state stability were studied. Apart from a known X-ray crystal structure of TMZ (form 1), two new crystalline modifications, forms 2 and 3, were obtained during attempted cocrystallization with carbamazepine and 3-hydroxypyridine-N-oxide. Conformers A and B of the drug molecule are stabilized by intramolecular amide N--HN(imidazole) and N--HN(tetrazine) interactions. The stable conformer A is present in forms 1 and 2, whereas both conformers crystallized in form 3. Preparation of polymorphic cocrystals I and II (TMZBPNO 1:0.5 and 2:1) were optimized by using solution crystallization and grinding methods. The metastable nature of polymorph 2 and cocrystal II is ascribed to unused hydrogen-bond donors/acceptors in the crystal structure. The intramolecularly bonded amide N-H donor in the less stable structure makes additional intermolecular bonds with the tetrazine C==O group and the imidazole N atom in stable polymorph 1 and cocrystal I, respectively. All available hydrogen-bond donors and acceptors are used to make intermolecular hydrogen bonds in the stable crystalline form. Synthon polymorphism and crystal stability are discussed in terms of hydrogen-bond reorganization.

Crystallization and preliminary X-ray diffraction studies of delta-toxin from Clostridium perfringens.

PubMed

Huyet, Jessica; Gilbert, Maryse; Popoff, Michel R; Basak, Ajit

2011-03-01

Clostridium perfringens is a Gram-positive anaerobic bacterium that is responsible for a wide range of diseases in humans and both wild and domesticated animals, including birds. C. perfringens is notable for its ability to produce a plethora of toxins, e.g. phospholipases C (alpha-toxin), pore-forming toxins (epsilon-toxin, beta-toxin and enterotoxin) and binary toxins (iota-toxin). Based on alpha-, beta-, epsilon- and iota-toxin production, the bacterium is classified into five different toxinotypes (A-E). Delta-toxin, which is a 32.6 kDa protein with 290 amino acids, is one of three haemolysins released by type C and possibly by type B strains of C. perfringens. This toxin is immunogenic and lytic to erythrocytes from the even-toed ungulates sheep, goats and pigs, and is cytotoxic to other cell types such as rabbit macrophages, human monocytes and blood platelets from goats, rabbits, guinea pigs and humans. The recombinant delta-toxin has been cloned, expressed, purified and crystallized in two different crystal forms by the hanging-drop vapour-diffusion method. Of these two different crystal forms, only the form II crystal diffracted to atomic resolution (dmin=2.4 Å), while the form I crystal diffracted to only 15 Å resolution. The form II crystals belonged to space group P2(1)2(1)2, with one molecule in the crystallographic asymmetric unit and unit-cell parameters a=49.66, b=58.48, c=112.93 Å.

Distinguishing polymorphs of the semiconducting pigment copper phthalocyanine by solid-state NMR and Raman spectroscopy.

PubMed

Shaibat, Medhat A; Casabianca, Leah B; Siberio-Pérez, Diana Y; Matzger, Adam J; Ishii, Yoshitaka

2010-04-08

Cu(II)(phthalocyanine) (CuPc) is broadly utilized as an archetypal molecular semiconductor and is the most widely used blue printing pigment. CuPc crystallizes in six different forms; the chemical and physical properties are substantially modulated by its molecular packing among these polymorphs. Despite the growing importance of this system, spectroscopic identification of different polymorphs for CuPc has posed difficulties. This study presents the first example of spectroscopic distinction of alpha- and beta-forms of CuPc, the most widely used polymorphs, by solid-state NMR (SSNMR) and Raman spectroscopy. (13)C high-resolution SSNMR spectra of alpha- and beta-CuPc using very-fast magic angle spinning (VFMAS) at 20 kHz show that hyperfine shifts sensitively reflect polymorphs of CuPc. The experimental results were confirmed by ab initio chemical shift calculations. (13)C and (1)H SSNMR relaxation times of alpha- and beta-CuPc under VFMAS also showed marked differences, presumably because of the difference in electronic spin correlation times in the two forms. Raman spectroscopy also provided another reliable method of differentiation between the two polymorphs.

Plate tectonics of virus shell assembly and reorganization in phage φ8, a distant relative of mammalian reoviruses.

PubMed

El Omari, Kamel; Sutton, Geoff; Ravantti, Janne J; Zhang, Hanwen; Walter, Thomas S; Grimes, Jonathan M; Bamford, Dennis H; Stuart, David I; Mancini, Erika J

2013-08-06

The hallmark of a virus is its capsid, which harbors the viral genome and is formed from protein subunits, which assemble following precise geometric rules. dsRNA viruses use an unusual protein multiplicity (120 copies) to form their closed capsids. We have determined the atomic structure of the capsid protein (P1) from the dsRNA cystovirus Φ8. In the crystal P1 forms pentamers, very similar in shape to facets of empty procapsids, suggesting an unexpected assembly pathway that proceeds via a pentameric intermediate. Unlike the elongated proteins used by dsRNA mammalian reoviruses, P1 has a compact trapezoid-like shape and a distinct arrangement in the shell, with two near-identical conformers in nonequivalent structural environments. Nevertheless, structural similarity with the analogous protein from the mammalian viruses suggests a common ancestor. The unusual shape of the molecule may facilitate dramatic capsid expansion during phage maturation, allowing P1 to switch interaction interfaces to provide capsid plasticity. Copyright © 2013 The Authors. Published by Elsevier Inc. All rights reserved.

Saturated fatty acids and fatty acid esters promote the polymorphic transition of clarithromycin metastable form I crystal.

PubMed

Watanabe, Miteki; Mizoguchi, Midori; Aoki, Hajime; Iwao, Yasunori; Noguchi, Shuji; Itai, Shigeru

2016-10-15

The phase transition of active pharmaceutical ingredients should be taken into account during manufacturing, processing- and storage, because different crystal forms lead to different physical properties of formulations. The phase transition of clarithromycin (CAM) metastable form I to stable form II was investigated on heating with additives such as fatty acids or fatty acid esters. Differential scanning calorimetry analyses revealed that when form I was heated with additives, the phase transition temperature of form I decreased close to the melting points of the additives. Powder X-ray diffraction analyses indicated the tentative presence of a non-crystalline component during the transition of form I to form II on heating with additives. These observations implied that CAM form I dissolved in the melted additives on heating and the dissolved CAM crystallized to form II. Reduction of transition temperatures in the presence of additives were also observed for the crystals of nifedipine form B and carbamazepine form III. These results suggested that the phenomena can be widely applicable for simultaneous crystalline phase transition and granulation using binder additives. Copyright © 2016 Elsevier B.V. All rights reserved.

Phase behavior and crystal structure of 3-(1-naphthyloxy)- and 3-(4-indolyloxy)-propane-1,2-diol, synthetic precursors of chiral drugs propranolol and pindolol

NASA Astrophysics Data System (ADS)

Bredikhin, Alexander A.; Gubaidullin, Aidar T.; Bredikhina, Zemfira A.; Fayzullin, Robert R.; Samigullina, Aida I.; Zakharychev, Dmitry V.

2013-08-01

Valuable precursors of popular chiral drugs propranolol and pindolol, 3-(1-naphthyloxy)-propane-1,2-diol 3 and 3-(4-indolyloxy)-propane-1,2-diol 4 were investigated by IR spectroscopy, DSC, and X-ray diffraction methods. Both compounds, crystallizing from enantiopure feed material, form "guaifenesin-like" crystal packing in which the classic H-bonded bilayers, framed in both sides by hydrophobic fragments of the molecules, acts as the basic crystal-forming motif. Diol 4 prone to spontaneous resolution and conserves its packing pattern crystallizing from racemate. Under the same conditions, diol 3 forms weakly stable solid racemic compound. Some reasons for such a behavior are identified and discussed.

Improving the dissolution and bioavailability of 6-mercaptopurine via co-crystallization with isonicotinamide.

PubMed

Wang, Jian-Rong; Yu, Xueping; Zhou, Chun; Lin, Yunfei; Chen, Chen; Pan, Guoyu; Mei, Xuefeng

2015-03-01

6-Mercaptopurine (6-MP) is a clinically important antitumor drug. The commercially available form was provided as monohydrate and belongs to BCS class II category. Co-crystallization screening by reaction crystallization method (RCM) and monitored by powder X-ray diffraction led to the discovery of a new co-crystal formed between 6-MP and isonicotinamide (co-crystal 1). Co-crystal 1 was thoroughly characterized by X-ray diffraction, FT-IR and Raman spectroscopy, and thermal analysis. Noticeably, the in vitro and in vivo studies revealed that co-crystal 1 possesses improved dissolution rate and superior bioavailability on animal model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Engineering p-n junctions and bandgap tuning of InSe nanolayers by controlled oxidation

NASA Astrophysics Data System (ADS)

Balakrishnan, Nilanthy; Kudrynskyi, Zakhar R.; Smith, Emily F.; Fay, Michael W.; Makarovsky, Oleg; Kovalyuk, Zakhar D.; Eaves, Laurence; Beton, Peter H.; Patanè, Amalia

2017-06-01

Exploitation of two-dimensional (2D) van der Waals (vdW) crystals can be hindered by the deterioration of the crystal surface over time due to oxidation. On the other hand, the existence of a stable oxide at room temperature can offer prospects for several applications. Here we report on the chemical reactivity of γ-InSe, a recent addition to the family of 2D vdW crystals. We demonstrate that, unlike other 2D materials, InSe nanolayers can be chemically stable under ambient conditions. However, both thermal- and photo-annealing in air induces the oxidation of the InSe surface, which converts a few surface layers of InSe into In2O3, thus forming an InSe/In2O3 heterostructure with distinct and interesting electronic properties. The oxidation can be activated in selected areas of the flake by laser writing or prevented by capping the InSe surface with an exfoliated flake of hexagonal boron nitride. We exploit the controlled oxidation of p-InSe to fabricate p-InSe/n-In2O3 junction diodes with room temperature electroluminescence and spectral response from the near-infrared to the visible and near-ultraviolet ranges. These findings reveal the limits and potential of thermal- and photo-oxidation of InSe in future technologies.

Minor Elements in Nakhlite Pyroxenes: Does Cr Record Changes in REDOX Conditions during Crystallization?

NASA Technical Reports Server (NTRS)

McKay, G.; Schwandt, C.; Le, L.; Mikouchi, T.

2007-01-01

Nakhlites are olivine-bearing clinopyroxene cumulates. Based on petrographic characteristics, they may be divided into groups that cooled at different rates and may have been formed at different depths in a single flow. The order of cooling rate from slowest to fastest is NWA998

Present and future of membrane protein structure determination by electron crystallography.

PubMed

Ubarretxena-Belandia, Iban; Stokes, David L

2010-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This chapter describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. Copyright © 2010 Elsevier Inc. All rights reserved.

Present and future of membrane protein structure determination by electron crystallography

PubMed Central

Ubarretxena-Belandia, Iban; Stokes, David L.

2011-01-01

Membrane proteins are critical to cell physiology, playing roles in signaling, trafficking, transport, adhesion, and recognition. Despite their relative abundance in the proteome and their prevalence as targets of therapeutic drugs, structural information about membrane proteins is in short supply. This review describes the use of electron crystallography as a tool for determining membrane protein structures. Electron crystallography offers distinct advantages relative to the alternatives of X-ray crystallography and NMR spectroscopy. Namely, membrane proteins are placed in their native membranous environment, which is likely to favor a native conformation and allow changes in conformation in response to physiological ligands. Nevertheless, there are significant logistical challenges in finding appropriate conditions for inducing membrane proteins to form two-dimensional arrays within the membrane and in using electron cryo-microscopy to collect the data required for structure determination. A number of developments are described for high-throughput screening of crystallization trials and for automated imaging of crystals with the electron microscope. These tools are critical for exploring the necessary range of factors governing the crystallization process. There have also been recent software developments to facilitate the process of structure determination. However, further innovations in the algorithms used for processing images and electron diffraction are necessary to improve throughput and to make electron crystallography truly viable as a method for determining atomic structures of membrane proteins. PMID:21115172

Structure of a new crystal form of human Hsp70 ATPase domain.

PubMed

Osipiuk, J; Walsh, M A; Freeman, B C; Morimoto, R I; Joachimiak, A

1999-05-01

Hsp70 proteins are highly conserved proteins induced by heat shock and other stress conditions. An ATP-binding domain of human Hsp70 protein has been crystallized in two major morphological forms at pH 7.0 in the presence of PEG 8000 and CaCl2. Both crystal forms belong to the orthorhombic space group P212121, but show no resemblance in unit-cell parameters. Analysis of the crystal structures for both forms shows a 1-2 A shift of one of the subdomains of the protein. This conformational change could reflect a 'natural' flexibility of the protein which might be relevant to ATP binding and may facilitate the interaction of other proteins with Hsp70 protein.

Acoustic Dirac degeneracy and topological phase transitions realized by rotating scatterers

NASA Astrophysics Data System (ADS)

Wen, Xinhua; Qiu, Chunyin; Lu, Jiuyang; He, Hailong; Ke, Manzhu; Liu, Zhengyou

2018-03-01

The artificial crystals for classical waves provide a good platform to explore the topological physics proposed originally in condensed matter systems. In this paper, acoustic Dirac degeneracy is realized by simply rotating the scatterers in sonic crystals, where the degeneracy is induced accidentally by modulating the scattering strength among the scatterers during the rotation process. This gives a flexible way to create a topological phase transition in acoustic systems. Edge states are further observed along the interface separating the two topologically distinct gapped sonic crystals.

Defect dynamics in active nematics

PubMed Central

Giomi, Luca; Bowick, Mark J; Mishra, Prashant; Sknepnek, Rastko; Cristina Marchetti, M

2014-01-01

Topological defects are distinctive signatures of liquid crystals. They profoundly affect the viscoelastic behaviour of the fluid by constraining the orientational structure in a way that inevitably requires global changes not achievable with any set of local deformations. In active nematic liquid crystals, topological defects not only dictate the global structure of the director, but also act as local sources of motion, behaving as self-propelled particles. In this article, we present a detailed analytical and numerical study of the mechanics of topological defects in active nematic liquid crystals. PMID:25332389

Initial stage of nucleation-mediated crystallization of a supercooled melt

NASA Astrophysics Data System (ADS)

Chernov, A. A.; Pil'nik, A. A.; Islamov, D. R.

2016-09-01

The kinetic model of nucleation-mediated crystallization of a supercooled melt is presented in this work. It correctly takes into account the change in supercooling of the initial phase in the process of formation and evolution of a new phase. The model makes it possible to find the characteristic time of the process, time course of the crystal phase volume, solidified material microstructure. The distinctive feature of the model is the use of the "forbidden" zones in the volume where the formation of new nucleation centers is suppressed.

Morphological Diversity in Crystal Growth of l-Ascorbic Acid Dissolved in Methanol

NASA Astrophysics Data System (ADS)

Ito, Miho; Izui, Machiko; Yamazaki, Yoshihiro; Matsushita, Mitsugu

2003-06-01

Morphological diagram with respect to crystal growth of l-ascorbic acid (C6H8O6; so-called vitamin C) from methanol solution on a flat glass dish is presented. Varying humidity and initial concentration of l-ascorbic acid in methanol solution, the following three distinct kinds of growing patterns have been observed: homogeneous disk, concentric ring and dendrite. In addition, in higher concentration clearly faceted small single crystals grow in any humidity less than 90%. Crossovers from one pattern to another were observed, too.

Crystal Structure of the C-terminal Region of Streptococcus mutans Antigen I/II and Characterization of Salivary Agglutinin Adherence Domains

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

Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Crowley, Paula J.

2012-05-29

The Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein that adheres to salivary components and extracellular matrix molecules. Here we report the 2.5 {angstrom} resolution crystal structure of the complete C-terminal region of AgI/II. The C-terminal region is comprised of three major domains: C{sub 1}, C{sub 2}, and C{sub 3}. Each domain adopts a DE-variant IgG fold, with two {beta}-sheets whose A and F strands are linked through an intramolecular isopeptide bond. The adherence of the C-terminal AgI/II fragments to the putative tooth surface receptor salivary agglutinin (SAG), as monitored by surface plasmon resonance, indicated that the minimalmore » region of binding was contained within the first and second DE-variant-IgG domains (C{sub 1} and C{sub 2}) of the C terminus. The minimal C-terminal region that could inhibit S. mutans adherence to SAG was also confirmed to be within the C{sub 1} and C{sub 2} domains. Competition experiments demonstrated that the C- and N-terminal regions of AgI/II adhere to distinct sites on SAG. A cleft formed at the intersection between these C{sub 1} and C{sub 2} domains bound glucose molecules from the cryo-protectant solution, revealing a putative binding site for its highly glycosylated receptor SAG. Finally, electron microscopy images confirmed the elongated structure of AgI/II and enabled building a composite tertiary model that encompasses its two distinct binding regions.« less

Oxide Scales Formed on NiTi and NiPtTi Shape Memory Alloys

NASA Technical Reports Server (NTRS)

Smialek, James L.; Garg, Anita; Rogers, Richard B.; Noebe, Ronald D.

2011-01-01

Ni-49Ti and Ni-30Pt-50Ti (at.%) shape memory alloys were oxidized isothermally in air over the temperature range of 500 to 900 C. The microstructure, composition, and phase content of the scales were studied by SEM, EDS, XRD, and metallography. Extensive plan view SEM/EDS identified various features of intact or spalled scale surfaces. The outer surface of the scale was a relatively pure TiO2 rutile structure, typified by a distinct highly striated and faceted crystal morphology. Crystal size increased significantly with temperature. Spalled regions exhibited some porosity and less distinct features. More detailed information was obtained by correlation of SEM/EDS studies of 700 C/100 hr cross-sections with XRD analyses of serial or taper-polishing of plan surfaces. Overall, multiple layers exhibited graded mixtures of NiO, TiO2, NiTiO3, Ni(Ti) or Pt(Ni,Ti) metal dispersoids, Ni3Ti or Pt3Ti depletion zones, and substrate, in that order. The NiTi alloy contained a 3 at.% Fe impurity that appeared in embedded localized Fe-Ti-rich oxides, while the NiPtTi alloy contained a 2 v/o dispersion of TiC that appeared in lower layers. The oxidation kinetics of both alloys (in a previous report) indicated parabolic growth and an activation energy (250 kJ/mole) near those reported in other Ti and NiTi studies. This is generally consistent with TiO2 existing as the primary scale constituent, as described here.

The Dimanganese(II) Site of Bacillus subtilis Class Ib Ribonucleotide Reductase

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

Boal, Amie K.; Cotruvo, Jr., Joseph A.; Stubbe, JoAnne

2014-10-02

Class Ib ribonucleotide reductases (RNRs) use a dimanganese-tyrosyl radical cofactor, Mn{sub 2}{sup III}-Y{sm_bullet}, in their homodimeric NrdF ({beta}2) subunit to initiate reduction of ribonucleotides to deoxyribonucleotides. The structure of the Mn{sub 2}{sup II} form of NrdF is an important component in understanding O{sub 2}-mediated formation of the active metallocofactor, a subject of much interest because a unique flavodoxin, NrdI, is required for cofactor assembly. Biochemical studies and sequence alignments suggest that NrdF and NrdI proteins diverge into three phylogenetically distinct groups. The only crystal structure to date of a NrdF with a fully ordered and occupied dimanganese site is thatmore » of Escherichia coli Mn{sub 2}{sup II}-NrdF, prototypical of the enzymes from actinobacteria and proteobacteria. Here we report the 1.9 {angstrom} resolution crystal structure of Bacillus subtilis Mn{sub 2}{sup II}-NrdF, representative of the enzymes from a second group, from Bacillus and Staphylococcus. The structures of the metal clusters in the {beta}2 dimer are distinct from those observed in E. coli Mn{sub 2}{sup II}-NrdF. These differences illustrate the key role that solvent molecules and protein residues in the second coordination sphere of the Mn{sub 2}{sup II} cluster play in determining conformations of carboxylate residues at the metal sites and demonstrate that diverse coordination geometries are capable of serving as starting points for Mn{sub 2}{sup III}-Y{sm_bullet} cofactor assembly in class Ib RNRs.« less

Method For Screening Microcrystallizations For Crystal Formation

DOEpatents

Santarsiero, Bernard D. , Stevens, Raymond C. , Schultz, Peter G. , Jaklevic, Joseph M. , Yegian, Derek T. , Cornell, Earl W. , Nordmeyer, Robert A.

2003-10-07

A method is provided for performing array microcrystallizations to determine suitable crystallization conditions for a molecule, the method comprising: forming an array of microcrystallizations, each microcrystallization comprising a drop comprising a mother liquor solution whose composition varies within the array and a molecule to be crystallized, the drop having a volume of less than 1 microliter; storing the array of microcrystallizations under conditions suitable for molecule crystals to form in the drops in the array; and detecting molecule crystal formation in the drops by taking images of the drops.

Refractory oxide hosts for a high power, broadly tunable laser with high quantum efficiency and method of making same

DOEpatents

Chen, Yok; Gonzalez, Roberto

1986-01-01

Refractory oxide crystals having high-quantum efficiency and high thermal stability for use as broadly tunable laser host materials. The crystals are formed by removing hydrogen from a single crystal of the oxide material to a level below about 10.sup.12 protons per cm.sup.3 and subsequently thermochemically reducing the oxygen content of the crystal to form sufficient oxygen anion vacancies so that short-lived F.sup.+ luminescence is produced when the crystal is optically excited.

Refractory oxide hosts for a high power, broadly tunable laser with high quantum efficiency and method of making same

DOEpatents

Chen, Yok; Gonzalez, R.

1985-07-03

Refractory oxide crystals having high-quantum efficiency and high thermal stability for use as broadly tunable laser host materials. The crystals are formed by removing hydrogen from a single crystal of the oxide material to a level below about 10/sup 12/ protons per cm/sup 3/ and subsequently thermochemically reducing the oxygen content of the crystal to form sufficient oxygen anion vacancies so that short-lived F/sup +/ luminescence is produced when the crystal is optically excited.

Cooperative dynamics in ultrasoft 2D crystals

NASA Astrophysics Data System (ADS)

Sprakel, Joris; van der Meer, Berend; Dijkstra, Marjolein; van der Gucht, Jasper

2015-03-01

The creation, annihilation, and diffusion of defects in crystal lattices play an important role during crystal melting and deformation. Although it is well understood how defects form and react when crystals are subjected to external stresses, it remains unclear how crystals cope with internal stresses. We report a study in which we create a highly localized internal stress, by means of optical tweezing, in a crystal formed from micrometer-sized colloidal spheres and directly observe how the solid reacts using microscopy. We find that, even though the excitation is highly localized, a collective dance of colloidal particles results; these collective modes take the form of closed rings or open-ended strings, depending on the sequence of events which nucleate the rearrangements. Surprisingly, we find from Brownian Dynamics simulations that these cooperative dynamics are thermally-activated modes inherent to the crystal, and can even occur through a single, sufficiently large thermal fluctuation, resulting in the irreversible displacement of 100s of particles from their lattice sites.

Formation of 3D cholesterol crystals from 2D nucleation sites in lipid bilayer membranes: implications for atherosclerosis.

PubMed

Varsano, Neta; Fargion, Iael; Wolf, Sharon G; Leiserowitz, Leslie; Addadi, Lia

2015-02-04

Atherosclerosis is the major precursor of cardiovascular disease. The formation of cholesterol crystals in atherosclerotic plaques is associated with the onset of acute pathology. The cholesterol crystals induce physical injury in the plaque core, promoting cell apoptosis and triggering an increased inflammatory response. Herein we address the question of how cholesterol crystal formation occurs in atherosclerosis. We demonstrate that three-dimensional (3D) cholesterol crystals can undergo directed nucleation from bilayer membranes containing two-dimensional (2D) cholesterol crystalline domains. We studied crystal formation on supported lipid bilayers loaded with exogenous cholesterol and labeled using a monoclonal antibody that specifically recognizes ordered cholesterol arrays. Our findings show that 3D crystals are formed exclusively on the bilayer regions where there are segregated 2D cholesterol crystalline domains and that they form on the domains. This study has potentially significant implications for our understanding of the crucial step in the mechanism by which atherosclerotic lesions form.

Chitosan-Assisted Crystallization and Film Forming of Perovskite Crystals through Biomineralization.

PubMed

Yang, Yang; Sun, Chen; Yip, Hin-Lap; Sun, Runcang; Wang, Xiaohui

2016-03-18

Biomimetic mineralization is a powerful approach for the synthesis of advanced composite materials with hierarchical organization and controlled structure. Herein, chitosan was introduced into a perovskite precursor solution as a biopolymer additive to control the crystallization and to improve the morphology and film-forming properties of a perovskite film by way of biomineralization. The biopolymer additive was able to control the size and morphology of the perovskite crystals and helped to form smooth films. The mechanism of chitosan-mediated nucleation and growth of the perovskite crystals was explored. As a possible application, the chitosan-perovskite composite film was introduced into a planar heterojunction solar cell and increased power conversion efficiency relative to that observed for the pristine perovskite film was achieved. The biomimetic mineralization method proposed in this study provides an alternative way of preparing perovskite crystals with well-controlled morphology and properties and extends the applications of perovskite crystals in photoelectronic fields, including planar-heterojunction solar cells. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Fabrication and characterization of poly(L-lactic acid) gels induced by fibrous complex crystallization with solvents

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

Matsuda, Yasuhiro; Fukatsu, Akinobu; Wang, Yangyang

2014-01-01

Complex crystal induced gelation of poly(L-lactic acid) (PLLA) solutions was studied for a series of solvents, including N,N-dimethylformamide (DMF). By cooling the solutions prepared at elevated temperatures, PLLA gels were produced in solvents that induced complex crystals ( -crystals) with PLLA. Fibrous structure of PLLA in the gel with DMF was observed by polarizing optical microscopy, field emission electron microscopy, and atomic force microscopy. Upon heating, the crystal form of PLLA in the DMF gel changed from -crystal to a-crystal, the major crystal form in common untreated PLLA films, but the morphology and high elastic modulus of the gel remainedmore » until the a-crystal dissolved at higher temperature. In addition, a solvent exchanging method was developed, which allowed PLLA gels to be prepared in other useful solvents that do not induce -crystals without losing the morphology and mechanical properties.« less

Sent packing: protein engineering generates a new crystal form of Pseudomonas aeruginosa DsbA1 with increased catalytic surface accessibility

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

McMahon, Roisin M., E-mail: r.mcmahon1@uq.edu.au; Coinçon, Mathieu; Tay, Stephanie

The crystal structure of a P. aeruginosa DsbA1 variant is more suitable for fragment-based lead discovery efforts to identify inhibitors of this antimicrobial drug target. In the reported structures the active site of the protein can simultaneously bind multiple ligands introduced in the crystallization solution or via soaking. Pseudomonas aeruginosa is an opportunistic human pathogen for which new antimicrobial drug options are urgently sought. P. aeruginosa disulfide-bond protein A1 (PaDsbA1) plays a pivotal role in catalyzing the oxidative folding of multiple virulence proteins and as such holds great promise as a drug target. As part of a fragment-based lead discoverymore » approach to PaDsbA1 inhibitor development, the identification of a crystal form of PaDsbA1 that was more suitable for fragment-soaking experiments was sought. A previously identified crystallization condition for this protein was unsuitable, as in this crystal form of PaDsbA1 the active-site surface loops are engaged in the crystal packing, occluding access to the target site. A single residue involved in crystal-packing interactions was substituted with an amino acid commonly found at this position in closely related enzymes, and this variant was successfully used to generate a new crystal form of PaDsbA1 in which the active-site surface is more accessible for soaking experiments. The PaDsbA1 variant displays identical redox character and in vitro activity to wild-type PaDsbA1 and is structurally highly similar. Two crystal structures of the PaDsbA1 variant were determined in complex with small molecules bound to the protein active site. These small molecules (MES, glycerol and ethylene glycol) were derived from the crystallization or cryoprotectant solutions and provide a proof of principle that the reported crystal form will be amenable to co-crystallization and soaking with small molecules designed to target the protein active-site surface.« less

Impact of interaction range and curvature on crystal growth of particles confined to spherical surfaces.

PubMed

Paquay, Stefan; Both, Gert-Jan; van der Schoot, Paul

2017-07-01

When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the isotropic crystal that forms reaches a critical size, growth continues via the incorporation of defects to alleviate elastic strain. Recently, it was experimentally found that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal. Here we report on computer simulations in which we observe both the formation of ribbons at short interaction ranges and packings that incorporate defects if the interaction is longer-ranged. The ribbons only form above some critical crystal size, below which the nucleus is disk-shaped. We find that the scaling of the critical crystal size differs slightly from the one proposed in the literature, and we argue that this is because the actual morphology transition is caused by the competition between line tension and elastic stress, rather than the competition between chemical potential and elastic stress.

Impact of interaction range and curvature on crystal growth of particles confined to spherical surfaces

NASA Astrophysics Data System (ADS)

Paquay, Stefan; Both, Gert-Jan; van der Schoot, Paul

2017-07-01

When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the isotropic crystal that forms reaches a critical size, growth continues via the incorporation of defects to alleviate elastic strain. Recently, it was experimentally found that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal. Here we report on computer simulations in which we observe both the formation of ribbons at short interaction ranges and packings that incorporate defects if the interaction is longer-ranged. The ribbons only form above some critical crystal size, below which the nucleus is disk-shaped. We find that the scaling of the critical crystal size differs slightly from the one proposed in the literature, and we argue that this is because the actual morphology transition is caused by the competition between line tension and elastic stress, rather than the competition between chemical potential and elastic stress.

Charge Stabilized Crystalline Colloidal Arrays As Templates For Fabrication of Non-Close-Packed Inverted Photonic Crystals

PubMed Central

Bohn, Justin J.; Ben-Moshe, Matti; Tikhonov, Alexander; Qu, Dan; Lamont, Daniel N.

2010-01-01

We developed a straightforward method to form non close-packed highly ordered fcc direct and inverse opal silica photonic crystals. We utilize an electrostatically self assembled crystalline colloidal array (CCA) template formed by monodisperse, highly charged polystyrene particles. We then polymerize a hydrogel around the CCA (PCCA) and condense the silica to form a highly ordered silica impregnated (siPCCA) photonic crystal. Heating at 450 °C removes the organic polymer leaving a silica inverse opal structure. By altering the colloidal particle concentration we independently control the particle spacing and the wall thickness of the inverse opal photonic crystals. This allows us to control the optical dielectric constant modulation in order to optimize the diffraction; the dielectric constant modulation is controlled independently of the photonic crystal periodicity. These fcc photonic crystals are better ordered than typical close-packed photonic crystals because their self assembly utilizes soft electrostatic repulsive potentials. We show that colloidal particle size and charge polydispersity has modest impact on ordering, in contrast to that for close-packed crystals. PMID:20163800

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

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

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less

DNA Base Flipping: A General Mechanism for Writing, Reading, and Erasing DNA Modifications

PubMed Central

Cheng, Xiaodong

2017-01-01

The modification of DNA bases is a classic hallmark of epigenetics. Four forms of modified cytosine—5-methylcytosine, 5-hydroxymethylcytosine, 5-formylcytosine, and 5-carboxylcytosine—have been discovered in eukaryotic DNA. In addition to cytosine carbon-5 modifications, cytosine and adenine methylated in the exocyclic amine—N4-methylcytosine and N6-methyladenine—are other modified DNA bases discovered even earlier. Each modified base can be considered a distinct epigenetic signal with broader biological implications beyond simple chemical changes. Since 1994, crystal structures of proteins and enzymes involved in writing, reading, and erasing modified bases have become available. Here, we present a structural synopsis of writers, readers, and erasers of the modified bases from prokaryotes and eukaryotes. Despite significant differences in structures and functions, they are remarkably similar regarding their engagement in flipping a target base/nucleotide within DNA for specific recognitions and/or reactions. We thus highlight base flipping as a common structural framework broadly applied by distinct classes of proteins and enzymes across phyla for epigenetic regulations of DNA. PMID:27826845

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection.

PubMed

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A; Joyce, M Gordon; Kwon, Young Do; Zhou, Tongqing; Sheng, Zizhang; Zhang, Baoshan; O'Dell, Sijy; McKee, Krisha; Georgiev, Ivelin S; Chuang, Gwo-Yu; Longo, Nancy S; Lynch, Rebecca M; Saunders, Kevin O; Soto, Cinque; Srivatsan, Sanjay; Yang, Yongping; Bailer, Robert T; Louder, Mark K; Mullikin, James C; Connors, Mark; Kwong, Peter D; Mascola, John R; Shapiro, Lawrence

2015-04-23

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of the study period, VRC01-lineage clades showed continuous evolution, with rates of ∼2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization. Copyright © 2015 Elsevier Inc. All rights reserved.

Maturation and Diversity of the VRC01-Antibody Lineage over 15 Years of Chronic HIV-1 Infection

DOE PAGES

Wu, Xueling; Zhang, Zhenhai; Schramm, Chaim A.; ...

2015-04-09

HIV-1-neutralizing antibodies develop in most HIV-1-infected individuals, although highly effective antibodies are generally observed only after years of chronic infection. Here in this paper, we characterize the rate of maturation and extent of diversity for the lineage that produced the broadly neutralizing antibody VRC01 through longitudinal sampling of peripheral B cell transcripts over 15 years and co-crystal structures of lineage members. Next-generation sequencing identified VRC01-lineage transcripts, which encompassed diverse antibodies organized into distinct phylogenetic clades. Prevalent clades maintained characteristic features of antigen recognition, though each evolved binding loops and disulfides that formed distinct recognition surfaces. Over the course of themore » study period, VRC01-lineage clades showed continuous evolution, with rates of ~2 substitutions per 100 nucleotides per year, comparable to that of HIV-1 evolution. This high rate of antibody evolution provides a mechanism by which antibody lineages can achieve extraordinary diversity and, over years of chronic infection, develop effective HIV-1 neutralization.« less

Structural basis of cargo recognitions for class V myosins

PubMed Central

Wei, Zhiyi; Liu, Xiaotian; Yu, Cong; Zhang, Mingjie

2013-01-01

Class V myosins (MyoV), the most studied unconventional myosins, recognize numerous cargos mainly via the motor’s globular tail domain (GTD). Little is known regarding how MyoV-GTD recognizes such a diverse array of cargos specifically. Here, we solved the crystal structures of MyoVa-GTD in its apo-form and in complex with two distinct cargos, melanophilin and Rab interacting lysosomal protein-like 2. The apo-MyoVa-GTD structure indicates that most mutations found in patients with Griscelli syndrome, microvillus inclusion disease, or cancers or in “dilute” rodents likely impair the folding of GTD. The MyoVa-GTD/cargo complex structure reveals two distinct cargo-binding surfaces, one primarily via charge–charge interaction and the other mainly via hydrophobic interactions. Structural and biochemical analysis reveal the specific cargo-binding specificities of various isoforms of mammalian MyoV as well as very different cargo recognition mechanisms of MyoV between yeast and higher eukaryotes. The MyoVa-GTD structures resolved here provide a framework for future functional studies of vertebrate class V myosins. PMID:23798443

Solid-state characterization of nevirapine.

PubMed

Sarkar, Mahua; Perumal, O P; Panchagnula, R

2008-09-01

The purpose of this investigation is to characterize nevirapine from commercial samples and samples crystallized from different solvents under various conditions. The solid-state behavior of nevirapine samples was investigated using a variety of complementary techniques such as microscopy (optical, polarized, hot stage microscopy), differential scanning calorimeter, thermogravimetric analysis, Fourier transform infrared spectroscopy and powder X-ray diffractometry. The commercial samples of nevirapine had the same polymorphic crystalline form with an anhedral crystal habit. Intrinsic dissolution of nevirapine was similar for both the commercial batches. Powder dissolution showed pH dependency, with maximum dissolution in acidic pH and there was no significant effect of particle size. The samples recrystallized from different solvent systems with varying polarity yielded different crystal habits. Stirring and degrees of supersaturation influenced the size and shape of the crystals. The recrystallized samples did not produce any new polymorphic form, but weak solvates with varying crystal habit were produced. Recrystallized samples showed differences in the x-ray diffractograms. However, all the samples had the same internal crystal lattice as revealed from their similar melting points and heat of fusion. The intrinsic dissolution rate of recrystallized samples was lower than the commercial sample. It was found that the compression pressure resulted in desolvation and partial conversion of the crystal form. After compression, the recrystallized samples showed similar x-ray diffractograms to the commercial sample. Amorphous form showed slightly higher aqueous solubility than the commercial crystalline form.

Large single domain 123 material produced by seeding with single crystal rare earth barium copper oxide single crystals

DOEpatents

Todt, V.; Miller, D.J.; Shi, D.; Sengupta, S.

1998-07-07

A method of fabricating bulk YBa{sub 2}Cu{sub 3}O{sub x} where compressed powder oxides and/or carbonates of Y and Ba and Cu present in mole ratios to form YBa{sub 2}Cu{sub 3}O{sub x} are heated in the presence of a Nd{sub 1+x}Ba{sub 2{minus}x}Cu{sub 3}O{sub y} seed crystal to a temperature sufficient to form a liquid phase in the YBa{sub 2}Cu{sub 3}O{sub x} while maintaining the seed crystal solid. The materials are slowly cooled to provide a YBa{sub 2}Cu{sub 3}O{sub x} material having a predetermined number of domains between 1 and 5. Crack-free single domain materials can be formed using either plate shaped seed crystals or cube shaped seed crystals with a pedestal of preferential orientation material. 7 figs.

Large single domain 123 material produced by seeding with single crystal rare earth barium copper oxide single crystals

DOEpatents

Todt, Volker; Miller, Dean J.; Shi, Donglu; Sengupta, Suvankar

1998-01-01

A method of fabricating bulk YBa.sub.2 Cu.sub.3 O.sub.x where compressed powder oxides and/or carbonates of Y and Ba and Cu present in mole ratios to form YBa.sub.2 Cu.sub.3 O.sub.x are heated in the presence of a Nd.sub.1+x Ba.sub.2-x Cu.sub.3 O.sub.y seed crystal to a temperature sufficient to form a liquid phase in the YBa.sub.2 Cu.sub.3 O.sub.x while maintaining the seed crystal solid. The materials are slowly cooled to provide a YBa.sub.2 Cu.sub.3 O.sub.x material having a predetermined number of domains between 1 and 5. Crack-free single domain materials can be formed using either plate shaped seed crystals or cube shaped seed crystals with a pedestal of preferential orientation material.

Growth of zeolite crystals in the microgravity environment of space

NASA Technical Reports Server (NTRS)

Sacco, A., Jr.; Sand, L. B.; Collette, D.; Dieselman, K.; Crowley, J.; Feitelberg, A.

1986-01-01

Zeolites are hydrated, crystalline aluminosilicates with alkali and alkaling earth metals substituted into cation vacancies. Typically zeolite crystals are 3 to 8 microns. Larger cyrstals are desirable. Large zeolite crystals were produced (100 to 200 microns); however, they have taken restrictively long times to grow. It was proposed if the rate of nucleation or in some other way the number of nuclei can be lowered, fewer, larger crystals will be formed. The microgravity environment of space may provide an ideal condition to achieve rapid growth of large zeolite crystals. The objective of the project is to establish if large zeolite crystals can be formed rapidly in space.

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.

Formation of porous crystals via viscoelastic phase separation

NASA Astrophysics Data System (ADS)

Tsurusawa, Hideyo; Russo, John; Leocmach, Mathieu; Tanaka, Hajime

2017-10-01

Viscoelastic phase separation of colloidal suspensions can be interrupted to form gels either by glass transition or by crystallization. With a new confocal microscopy protocol, we follow the entire kinetics of phase separation, from homogeneous phase to different arrested states. For the first time in experiments, our results unveil a novel crystallization pathway to sponge-like porous crystal structures. In the early stages, we show that nucleation requires a structural reorganization of the liquid phase, called stress-driven ageing. Once nucleation starts, we observe that crystallization follows three different routes: direct crystallization of the liquid phase, the Bergeron process, and Ostwald ripening. Nucleation starts inside the reorganized network, but crystals grow past it by direct condensation of the gas phase on their surface, driving liquid evaporation, and producing a network structure different from the original phase separation pattern. We argue that similar crystal-gel states can be formed in monatomic and molecular systems if the liquid phase is slow enough to induce viscoelastic phase separation, but fast enough to prevent immediate vitrification. This provides a novel pathway to form nanoporous crystals of metals and semiconductors without dealloying, which may be important for catalytic, optical, sensing, and filtration applications.

Poly[2,5-bis(3-dodecylthiophen-2-yl)thieno[3,2-b]thiophene] Oligomer Single-Crystal Nanowires from Supercritical Solution and Their Anisotropic Exciton Dynamics.

PubMed

Colella, Nicholas S; Labastide, Joelle A; Cherniawski, Benjamin P; Thompson, Hilary B; Marques, Sarah R; Zhang, Lei; Usluer, Özlem; Watkins, James J; Briseno, Alejandro L; Barnes, Michael D

2017-07-06

Supercritical fluids, exhibiting a combination of liquid-like solvation power and gas-like diffusivity, are a relatively unexplored medium for processing and crystallization of oligomer and polymeric semiconductors whose optoelectronic properties critically depend on the microstructure. Here we report oligomer crystallization from the polymer organic semiconductor, poly[2,5-bis(3-dodecylthiophen-2-yl)thieno[3,2-b]thiophene] (PBTTT) in supercritical hexane, yielding needle-like single crystals up to several microns in length. We characterize the crystals' photophysical properties by time- and polarization-resolved photoluminescence (TPRPL) spectroscopy. These techniques reveal two-dimensional interchromophore coupling facilitated by the high degree of π-stacking order within the crystal. Furthermore, the crystals obtained from supercritical fluid were found to be similar photophysically as the crystallites found in solution-cast thin films and distinct from solution-grown crystals that exhibited spectroscopic signatures indicative of different packing geometries.

The Meaning of "Magma"

NASA Astrophysics Data System (ADS)

Bartley, J. M.; Glazner, A. F.; Coleman, D. S.

2016-12-01

Magma is a fundamental constituent of the Earth, and its properties, origin, evolution, and significance bear on issues ranging from volcanic hazards to planetary evolution. Unfortunately, published usages indicate that the term "magma" means distinctly different things to different people and this can lead to miscommunication among Earth scientists and between scientists and the public. Erupting lava clearly is magma; the question is whether partially molten rock imaged at depth and too crystal-rich to flow should also be called magma. At crystal fractions > 50%, flow can only occur via crystal deformation and solution-reprecipitation. As the solid fraction increases to 90% or more, the material becomes a welded crystal framework with melt in dispersed pores and/or along grain boundaries. Seismic images commonly describe such volumes of a few % melt as magma, yet the rheological differences between melt-rich and melt-poor materials make it vital not to confuse a large rock volume that contains a small melt fraction with melt-rich material. To ensure this, we suggest that "magma" be reserved for melt-rich materials that undergo bulk fluid flow on timescales consonant with volcanic eruptions. Other terms should be used for more crystal-rich and largely immobile partially molten rock (e.g., "crystal mush," "rigid sponge"). The distinction is imprecise but useful. For the press, the public, and even earth scientists who do not study magmatic systems, "magma" conjures up flowing lava; reports of a large "magma" body that contains a few percent melt can engender the mistaken perception of a vast amount of eruptible magma. For researchers, physical processes like crystal settling are commonly invoked to account for features in plutonic rocks, but many such processes are only possible in melt-rich materials.

Investigation of the Influence of Heat Balance Shifts on the Freeze Microstructure and Composition in Aluminum Smelting Bath System: Cryolite-CaF2-AlF3-Al2O3

NASA Astrophysics Data System (ADS)

Liu, Jingjing; Fallah-Mehrjardi, Ata; Shishin, Denis; Jak, Evgueni; Dorreen, Mark; Taylor, Mark

2017-12-01

In an aluminum electrolysis cell, the side ledge forms on side walls to protect it from the corrosive cryolitic bath. In this study, a series of laboratory analogue experiments have been carried out to investigate the microstructure and composition of side ledge (freeze linings) at different heat balance steady states. Three distinct layers are found in the freeze linings formed in the designed Cryolite-CaF2-AlF3-Al2O3 electrolyte system: a closed (columnar) crystalline layer, an open crystalline layer, and a sealing layer. This layered structure changes when the heat balance is shifted between different steady states, by melting or freezing the open crystalline layer. Phase chemistry of the freeze lining is studied in this paper to understand the side ledge formation process upon heat balance shifts. Electron probe X-ray microanalysis (EPMA) is used to characterize the microstructure and compositions of distinct phases existing in the freeze linings, which are identified as cryolite, chiolite, Ca-cryolite, and alumina. A freeze formation mechanism is further developed based on these microstructural/compositional investigations and also thermodynamic calculations through the software—FactSage. It is found that entrapped liquid channels exist in the open crystalline layer, assisting with the mass transfer between solidified crystals and bulk molten bath.

40 Ma of hydrothermal W mineralization during the Variscan orogenic evolution of the French Massif Central revealed by U-Pb dating of wolframite

NASA Astrophysics Data System (ADS)

Harlaux, Matthieu; Romer, Rolf L.; Mercadier, Julien; Morlot, Christophe; Marignac, Christian; Cuney, Michel

2018-01-01

We present U-Pb thermal ionization mass spectrometer (TIMS) ages of wolframite from several granite-related hydrothermal W±Sn deposits in the French Massif Central (FMC) located in the internal zone of the Variscan belt. The studied wolframite samples are characterized by variable U and Pb contents (typically <10 ppm) and show significant variations in their radiogenic Pb isotopic compositions. The obtained U-Pb ages define three distinct geochronological groups related to three contrasting geodynamic settings: (i) Visean to Namurian mineralization (333-327 Ma) coeval with syn-orogenic compression and emplacement of large peraluminous leucogranites (ca. 335-325 Ma), (ii) Namurian to Westphalian mineralization (317-315 Ma) synchronous with the onset of late-orogenic extension and emplacement of syn-tectonic granites (ca. 315-310 Ma) and (iii) Stephanian to Permian mineralization (298-274 Ma) formed during post-orogenic extension contemporaneous with the Permian volcanism in the entire Variscan belt. The youngest ages (276-274 Ma) likely reflect the reopening of the U-Pb isotopic system after wolframite crystallization and may correspond to late hydrothermal alteration (e.g. ferberitization). Our results demonstrate that W(±Sn) mineralization in the FMC formed during at least three distinct hydrothermal events in different tectono-metamorphic settings over a time range of 40 Ma.

Aberrated surface soliton formation in a nonlinear 1D and 2D photonic crystal

PubMed Central

Lysak, Tatiana M.; Trykin, Evgenii M.

2018-01-01

We discuss a novel type of surface soliton—aberrated surface soliton—appearance in a nonlinear one dimensional photonic crystal and a possibility of this surface soliton formation in two dimensional photonic crystal. An aberrated surface soliton possesses a nonlinear distribution of the wavefront. We show that, in one dimensional photonic crystal, the surface soliton is formed at the photonic crystal boundary with the ambient medium. Essentially, that it occupies several layers at the photonic crystal boundary and penetrates into the ambient medium at a distance also equal to several layers, so that one can infer about light energy localization at the lateral surface of the photonic crystal. In the one dimensional case, the surface soliton is formed from an earlier formed soliton that falls along the photonic crystal layers at an angle which differs slightly from the normal to the photonic crystal face. In the two dimensional case, the soliton can appear if an incident Gaussian beam falls on the photonic crystal face. The influence of laser radiation parameters, optical properties of photonic crystal layers and ambient medium on the one dimensional surface soliton formation is investigated. We also discuss the influence of two dimensional photonic crystal configuration on light energy localization near the photonic crystal surface. It is important that aberrated surface solitons can be created at relatively low laser pulse intensity and for close values of alternating layers dielectric permittivity which allows their experimental observation. PMID:29558497

Can computed crystal energy landscapes help understand pharmaceutical solids?

PubMed Central

Price, Sarah L.; Braun, Doris E.; Reutzel-Edens, Susan M.

2017-01-01

Computational crystal structure prediction (CSP) methods can now be applied to the smaller pharmaceutical molecules currently in drug development. We review the recent uses of computed crystal energy landscapes for pharmaceuticals, concentrating on examples where they have been used in collaboration with industrial-style experimental solid form screening. There is a strong complementarity in aiding experiment to find and characterise practically important solid forms and understanding the nature of the solid form landscape. PMID:27067116

DNA-guided nanoparticle assemblies

DOEpatents

Gang, Oleg; Nykypanchuk, Dmytro; Maye, Mathew; van der Lelie, Daniel

2013-07-16

In some embodiments, DNA-capped nanoparticles are used to define a degree of crystalline order in assemblies thereof. In some embodiments, thermodynamically reversible and stable body-centered cubic (bcc) structures, with particles occupying <.about.10% of the unit cell, are formed. Designs and pathways amenable to the crystallization of particle assemblies are identified. In some embodiments, a plasmonic crystal is provided. In some aspects, a method for controlling the properties of particle assemblages is provided. In some embodiments a catalyst is formed from nanoparticles linked by nucleic acid sequences and forming an open crystal structure with catalytically active agents attached to the crystal on its surface or in interstices.

Recrystallization of puerarin using the supercritical fluid antisolvent process

NASA Astrophysics Data System (ADS)

Li, Y.; Yang, D. J.; Zhou, W.; Chen, S. B.; Chen, S. L.

2012-02-01

The purpose of this study was to investigate the influence of supercritical fluid (SCF) processing on the polymorphism of puerarin (Pur), a poorly soluble drug. The gas anti-solvent (GAS) technique was used to crystalize the drug in different conditions. The samples were analyzed by scanning electron microscopy and laser granulometry for changes in the habitus and particle size. The solid state was studied by X-ray powder diffraction (XRPD), differential scanning calorimetry (DSC), Fourier-transform infrared spectroscopy (FT-IR) and melting point determination. Finally, the dissolution and solubility tests were carried out. It was attested that compared with the commercial Pur in Crystal form I, at the optimum and most of conditions, Pur changed into crystal form II with more orderly and pure appearances. At the concentration of 60 mg/ml and at the solvent of methanol, two other new crystal forms (named form III and form IV) were produced. It was demonstrated that the particles mean diameter, size distribution and morphology can be strongly controlled through the manipulation of the process parameters and more importantly, Pur in the new crystal forms, which were not reported before with better physico-chemical properties could be produced by recrystalization by GAS.

The solid state of rebamipide: preparation, characterization, and dissolution.

PubMed

Jeon, Seong Hyeon; Sohn, Young Taek

2016-04-01

Rebamipide is marketed as a peptic ulcer agent under the trade name Mucosta(R). The objective of this work was to investigate the existence of polymorphs and pseudopolymorphs of rebamipide. Two crystal forms of rebamipide were isolated by recrystallization and characterized by differential thermal analysis (DTA), thermogravimetric analysis (TG), powder X-ray diffractometry, infrared spectrometry, and nuclear magnetic resonance. The DTA curve of Form 1 showed one endothermic peak at 305.2 °C, and that of Form 2 showed one endothermic peak at 307.3 °C. The TG curve of Form 1 showed a single weight loss at 305.2 °C, which corresponded to melting. The TG curve of Form 2 also showed a single weight loss at 307.3 °C, which corresponded to melting. The melting point of Form 2 was higher than that of Form 1. In the dissolution studies in pH 6.8 buffer at 37 ± 0.5 °C, the two crystal forms showed no significant differences in dissolution. After 3 months of storage at 0, 52, and 95% RH, the two crystal forms were not transformed. After milling with a Specamill for 2 h, the two crystal forms were not transformed.

Geochemical and isotopic studies of syenites from the Yamato Mountains, East Antarctica: Implications for the origin of syenitic magmas

NASA Astrophysics Data System (ADS)

Zhao, J.-X.; Shiraishi, K.; Ellis, D. J.; Sheraton, J. W.

1995-04-01

Voluminous syenites were intruded during the waning stage of the granulite facies metamorphism in the Yamato Mountains of East Antarctica. The area has been interpreted as part of a Cambrian continental collision zone with regional upper amphibolite to granulite facies metamorphism occurring during ca. 500-660 Ma period. Regardless of minor geochemical variations between different groups, all syenites are characterised by high K 20 + Na 20 (8-12%), K 20/Na 20 (˜2), Sr (800-3500 ppm), Ba (2000-8500 ppm), and comparatively high TiO 2, P 20 5, Zr, and light REES relative to I-type granites. They are significantly higher in Mg number (50-75) compared with typical calc-alkaline suites, igneous charnockites, or A-type granites and define a distinctive trend on an AFM (alkali-FeO tot-MgO) diagram. Their trace element distribution diagrams are characterised by pronounced enrichment in LIL and REES, large negative Nb and Ti anomalies, and no depletion in Sr or Ba relative to the neighbouring elements. In this regard, they closely resemble the ˜500 Ma post-tectonic mela-syenite to alkali basalt dikes widely occurring in East Antarctica. Such geochemical features are distinct from rift- or hotspot-related syenites, which are usually characterised by low K/Na ratios, negative Ba and Sr anomalies, and a lack of negative Nb anomalies. Initial isotopic compositions of the syenites are characterised by relatively low initial ɛNd values (-2.6 to -5.5) and high Sri ratios (0.7057-0.7088). Since the syenites are extremely enriched in Sr and Nd, such isotopic signatures are interpreted as reflecting the nature of the mantle source, rather than significant crystal contamination. Such isotopic signatures are also distinct from those of the rift- or hotspot-related syenites which are thought to be derived from depleted asthenospheric mantle. Considering the distinctive geochemical signatures of the Yamato syenites and their analogy to posttectonic alkaline mafic dikes in Antarctica, it is proposed that the syenites were generated by fractionation and magma mixing (with a crystal melt) of a Si-undersaturated alkali basaltic magma in a lower-crust magma chamber, followed by further crystal fractionation/cumulate-melt unmixing at middle to upper crustal levels (<5 kbars). Tectonically, it is proposed that the syenites were probably formed within the hinterland of the proposed Cambrian continental collision zone, with the parental magma being derived ultimately by partial melting of the metasomatised mantle wedge above the deepest part of the subduction zone. Similar models may also apply to the origin of some post-tectonic alkaline dikes in East Antarctica, with their sources being the continental lithospheric mantle previously modified by subduction-related processes.

Solid state of CG-400549, a novel FabI inhibitor: characterization, dissolution, transformation.

PubMed

Kim, Bo-Yeon; Sohn, Young-Taek

2011-05-01

The polymorphic and pseudopolymorphic forms of CG-400549, a novel FabI inhibitor with potent in vivo activity were prepared and characterized by differential scanning calorimetry (DSC), powder X-ray diffractometry (PXRD) and thermogravimetric analysis (TG). Seven crystal forms of CG-400549, one anhydrate and six solvates, have been isolated by recrystallization and the DSC and PXRD patterns of the seven crystal forms of CG-400549 were different respectively. The dissolution patterns of these seven crystal forms of CG-400549 were studied and they showed significant differences in the dissolution rate. After storage of 1 month at 0% RH (silica gel, 20°C), 52% RH (saturated solution of Na(2)Cr(2)O(7)2H(2)O/20°C) and 95% RH (saturated solution of Na(2)HPO(4)/20°C), all crystal forms were not transformed.

Crystallization over the liquid layer

NASA Astrophysics Data System (ADS)

Bogonosov, K. A.; Maksimovskii, S. N.

2013-04-01

In this article, a new phenomenon of high-speed crystallization of metals in a low-temperature plasma formed as a result of the effect of a short laser pulse is considered. The mechanism of the way the reaction occurs on the surface of the melt formed under the effect of the laser pulse on an amorphous substrate is described. The main factors affecting the crystallization process are described. Primary attention is paid to laminar convection and the latent heat of crystallization.

Crystallization of human estrogenic 17β-hydroxysteroid dehydrogenase under microgravity

NASA Astrophysics Data System (ADS)

Zhu, Dao-Wei; Zhou, Ming; Mao, Ying; Labrie, Fernand; Lin, Sheng-Xiang

1995-11-01

Human 17β-hydroxysteroid dehydrogenase has been crystallized on the ground in the complex form with NADP + and a complete data set of the crystal was primarily collected at 2.9 Å [D.-W. Zhu, X. Lee, R. Breton, D. Ghosh, W. Pangborn, W.L. Duax and S.-X. Lin, J. Mol. Biol. 234 (1993) 242]. To eliminate multiseeding, formation of multicrystals and to obtain higher quality crystals, we carried out the crystallization aboard the Russian MIR space station and crystals were recovered in January, 1994. Crystals of the enzyme were formed in 9 of the total 12 sitting drops in the space mission, in the presence of NADP + or estradiol. This is a first attempt of crystallization of a membrane-associated protein under microgravity in the presence of a detergent. The space experiments showed better results in nucleation number, crystal size and morphology than the ground ones, obtaining crystals diffracting to resolutions between 2.5-2.7 Å. The too early ground mixing has limited a more important improvement of the crystallization.

Magneto-phonon polaritons in two-dimension antiferromagnetic/ion-crystalic photonic crystals

NASA Astrophysics Data System (ADS)

Ta, J. X.; Song, Y. L.; Wang, X. Z.

2012-01-01

Magneto-phonon polaritons in a two-dimension photonic crystal (PC) are discussed. This PC is constructed by embedding a periodical square lattice of ionic-crystal cylinders into an antiferromagnet. The two media are dispersive, with their individual resonant frequencies near each other. We first set up an effective-medium method to obtain the effective magnetic permeability and dielectric permittivity of the PC, followed by the dispersion relations of surface and bulk polaritons. There are a number of new surface polaritons, and two new distinctive bulk polariton bands in which the negative refraction and left-handedness can appear. The numerical calculations are based on the example, FeF2/TlBr PC.

Characteristics of color optical shutter with dye-doped polymer network liquid crystal.

PubMed

Lee, G H; Hwang, K Y; Jang, J E; Jin, Y W; Lee, S Y; Jung, J E

2011-03-01

The optical properties and the theoretical prediction of color optical shutter with dye-doped polymer network liquid crystal (PNLC) were investigated. The view-angle dependence of reflectance according to the bias conditions showed distinctive characteristics, which could be explained from the effects of dye absorption and path length. It was also shown that the thickness dependence of reflectance was strongly influenced by the light-scattering coefficient. Our experimental results matched up well with the theoretical prediction based on the light scattering of liquid crystals in polymer network and the absorption of dichroic dye. This work indicates potential to improve the optical device using dye-doped liquid crystal-polymer composite.

Chiral organosilica particles and their use as inducers of conformational deracemization of liquid crystal phases

NASA Astrophysics Data System (ADS)

Cohen, Orit; Ferris, Andrew J.; Adkins, Raymond; Lemieux, Robert P.; Avnir, David; Gelman, Dmitri; Rosenblatt, Charles

2018-03-01

Chiral organosilica particles of size ∼200 nm were synthesized from an enantio-pure multi-armed chiral D-maltose organosilane precursor in the absence of co-condensation with an achiral monomer. Two distinct experiments were performed to demonstrate the particles' ability to induce conformational deracemization of a host liquid crystal. The first involves an electric field-induced tilt of the liquid crystal director in the deracemized smectic-A phase. The other involves domain wall curvature separating left- and right-handed liquid crystal helical pitch domains imposed by the cells' substrates. The results demonstrate unequivocally that enantio-pure organosilica nanoparticles can be synthesized and can induce chirality in a host.

Supercritical fluid crystallization of griseofulvin: crystal habit modification with a selective growth inhibitor.

PubMed

Jarmer, Daniel J; Lengsfeld, Corinne S; Anseth, Kristi S; Randolph, Theodore W

2005-12-01

Poly (sebacic anhydride) (PSA) was used as a growth inhibitor to selectively modify habit of griseofulvin crystals formed via the Precipitation with a compressed-fluid antisolvent (PCA) process. PSA and griseofulvin were coprecipitated within a PCA injector, which provided efficient mixing between the solution and compressed antisolvent process streams. Griseofulvin crystal habit was modified from acicular to bipyramidal when the mass ratio of PSA/griseofulvin in the solution feed stream was

An RNA-Binding Multimer Specifies Nematode Sperm Fate.

PubMed

Aoki, Scott T; Porter, Douglas F; Prasad, Aman; Wickens, Marvin; Bingman, Craig A; Kimble, Judith

2018-06-26

FOG-3 is a master regulator of sperm fate in Caenorhabditis elegans and homologous to Tob/BTG proteins, which in mammals are monomeric adaptors that recruit enzymes to RNA binding proteins. Here, we determine the FOG-3 crystal structure and in vitro demonstrate that FOG-3 forms dimers that can multimerize. The FOG-3 multimeric structure has a basic surface potential, suggestive of binding nucleic acid. Consistent with that prediction, FOG-3 binds directly to nearly 1,000 RNAs in nematode spermatogenic germ cells. Most binding is to the 3' UTR, and most targets (94%) are oogenic mRNAs, even though assayed in spermatogenic cells. When tethered to a reporter mRNA, FOG-3 represses its expression. Together these findings elucidate the molecular mechanism of sperm fate specification and reveal the evolution of a protein from monomeric to multimeric form with acquisition of a distinct mode of mRNA repression. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

MgCu metallic glass

NASA Astrophysics Data System (ADS)

Durandurdu, Murat

2018-03-01

We generate an amorphous MgCu model using the rapid solidification of the melt through a first-principles molecular dynamics approach within a generalised gradient approximation and reveal, for the first time, its structural features and mechanical properties in details. The liquid and glassy MgCu are found to acquire slightly distinct local structures. Yet in both forms of MgCu, most Cu atoms have a tendency to form the ideal and defective icosahedrons while Mg atoms are arranged in complex configurations. The mean coordination number of Cu and Mg at 300 K is 11.31 and 13.73, respectively. The short-range order of MgCu glass is projected to be different than the known crystalline MgCu and Mg2Cu phases. The mechanical properties of MgCu glass and the CsCl-type MgCu crystal are computed and compared. On the basis of the enthalpy analyses, a possible pressure-induced crystallisation of the MgCu glass into a CsCl-type structure is proposed to occur at around 11 GPa.

Architecture of the pontin/reptin complex, essential in the assembly of several macromolecular complexes

PubMed Central

Torreira, Eva; Jha, Sudhakar; López-Blanco, José R.; Arias-Palomo, Ernesto; Chacón, Pablo; Cañas, Cristina; Ayora, Sylvia; Dutta, Anindya; Llorca, Oscar

2008-01-01

Summary Pontin and reptin belong to the AAA+ family and they are essential for the structural integrity and catalytic activity of several chromatin remodeling complexes. They are also indispensable for the assembly of several ribonucleoprotein complexes, including telomerase. Here, we propose a structural model of the yeast pontin/reptin complex based on a cryo-electron microscopy reconstruction at 13 Å. Pontin/reptin hetero-dodecamers were purified from in vivo assembled complexes forming a double ring. Two rings interact through flexible domains projecting from each hexamer, constituting an atypical asymmetric form of oligomerization. These flexible domains and the AAA+ cores reveal significant conformational changes when compared to the crystal structure of human pontin that generate enlarged channels. This structure of endogenously assembled pontin/reptin complexes is different to previously described structures, suggesting that pontin and reptin could acquire distinct structural states to regulate their broad functions as molecular motors and scaffolds for nucleic acids and proteins. PMID:18940606

Sponge-like nanoporous single crystals of gold

PubMed Central

Khristosov, Maria Koifman; Bloch, Leonid; Burghammer, Manfred; Kauffmann, Yaron; Katsman, Alex; Pokroy, Boaz

2015-01-01

Single crystals in nature often demonstrate fascinating intricate porous morphologies rather than classical faceted surfaces. We attempt to grow such crystals, drawing inspiration from biogenic porous single crystals. Here we show that nanoporous single crystals of gold can be grown with no need for any elaborate fabrication steps. These crystals are found to grow following solidification of a eutectic composition melt that forms as a result of the dewetting of nanometric thin films. We also present a kinetic model that shows how this nano-porous single-crystalline structure can be obtained, and which allows the potential size of the porous single crystal to be predicted. Retaining their single-crystalline nature is due to the fact that the full crystallization process is faster than the average period between two subsequent nucleation events. Our findings clearly demonstrate that it is possible to form single-crystalline nano porous metal crystals in a controlled manner. PMID:26554856

Nematic order-disorder state transition in a liquid crystal analogue formed by oriented and migrating amoeboid cells

NASA Astrophysics Data System (ADS)

Kemkemer, R.; Teichgräber, V.; Schrank-Kaufmann, S.; Kaufmann, D.; Gruler, H.

2000-10-01

In cell culture, liquid crystal analogues are formed by elongated, migrating, and interacting amoeboid cells. An apolar nematic liquid crystal analogue is formed by different cell types like human melanocytes (=pigment cells of the skin), human fibroblasts (=connective tissue cells), human osteoblasts (=bone cells), human adipocytes (=fat cells), etc. The nematic analogue is quite well described by i) a stochastic machine equation responsible for cell orientation and ii) a self-organized extracellular guiding signal, E_2, which is proportional to the orientational order parameter as well as to the cell density. The investigations were mainly made with melanocytes. The transition to an isotropic state analogue can be accomplished either by changing the strength of interaction (e.g. variation of the cell density) or by influencing the cellular machinery by an externally applied signal: i) An isotropic gaseous state analogue is observed at low cell density (ρ < 110melanocytes/mm^2) and a nematic liquid crystal state analogue at higher cell density. ii) The nematic state analogue disappears if the bipolar shaped melanocytes are forced to become a star-like shape (induced by colchicine or staurosporine). The analogy between nematic liquid crystal state analogue formed by elongated, migrating and interacting cells and the nematic liquid crystal phase formed by interacting elongated molecules is discussed.

Crystal Properties and Radiation Effects in Solid Molecular Hydrogens

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

Kozioiziemski, B

2000-09-01

The crystal lattice structure, growth shapes and helium generated by beta-decay of solid deuterium-tritium (D-T) mixtures have been studied. Understanding of these D-T properties is important for predicting and optimizing the target design of the National Ignition Facility (NIF). Raman spectroscopy showed the D-T crystal structure is hexagonal close packed, common to the non-tritiated isotopes. The isotopic mixtures of both tritiated and non-tritiated species broadens the rotational transitions, especially of the lighter species in the mixture. The vibrational frequencies of each isotope is shifted to higher energy in the mixture than the pure components. The J = 1-0 population decreasesmore » exponentially with a 1/e time constant which rapidly increases above 10.5 K for both D{sub 2} and T{sub 2} in D-T. The conversion rate is nearly constant from 5 K to 10 K for both D{sub 2} and T{sub 2} at 7.1 hours and 2.1 hours, respectively. The smoothing of D-T layers by beta decay heating is limited by the crystal surface energy. Deuterium and hydrogen-deuteride crystals were grown at a number of temperatures below the triple point to determine the surface energy and roughening transition. Several distinct crystal shapes were observed on a number of different substrates. The a facet roughens between 0.9 T{sub TP} and T{sub TP}, while the c facet persists up to the melting temperature. This is very different from the behavior of the other rare gas crystals which grow completely rounded above 0.8 T{sub TP}. Helium bubbles formed as a product of the beta decay were observed using optical microscopy and the diffusion of smaller bubbles measured with dynamic light scattering. Bubble diffusion coefficients as high as 2.0 x 10{sup -16} m{sup 2}/s were measured for 10-50 nm bubbles. The bubbles move in response to a thermal gradient, with speeds between 1 {micro}m/hour and 100 {micro}m/hour for thermal gradients and temperatures appropriate to NIF targets.« less

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

Venkadesh, S.; Mandal, P.K.; Gautham, N., E-mail: n_gautham@hotmail.com

Highlights: {yields} This is the first crystal structure of a four-way junction with sticky ends. {yields} Four junction structures bind to each other and form a rhombic cavity. {yields} Each rhombus binds to others to form 'infinite' 2D tiles. {yields} This is an example of bottom-up fabrication of a DNA nano-lattice. -- Abstract: We report here the crystal structure of the partially self-complementary decameric sequence d(CGGCGGCCGC), which self assembles to form a four-way junction with sticky ends. Each junction binds to four others through Watson-Crick base pairing at the sticky ends to form a rhombic structure. The rhombuses bind tomore » each other and form two dimensional tiles. The tiles stack to form the crystal. The crystal diffracted in the space group P1 to a resolution of 2.5 A. The junction has the anti-parallel stacked-X conformation like other junction structures, though the formation of the rhombic net noticeably alters the details of the junction geometry.« less

Development of a New Class of Drugs To Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

ARdbd-DNA crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening operations with... Chiang , Y.T., Sharma, A., Peacock, J.W., Wang, W., Cherkasov, A., Rennie, P.S., Gleave, M.E., and Ong, C.J. (2016) Androgen Receptor transcriptionally

Diagnosing the Internal Architecture of Zeolite Ferrierite

PubMed Central

Schmidt, Joel E.; Hendriks, Frank C.; Lutz, Martin; Post, L. Christiaan; Fu, Donglong

2017-01-01

Abstract Large crystals of zeolite ferrierite (FER) are important model systems for spatially resolved catalysis and diffusion studies, though there is considerable variation in crystal habit depending on the chemical composition and employed synthesis conditions. A synergistic combination of techniques has been applied, including single crystal X‐ray diffraction, high‐temperature in situ confocal fluorescence microscopy, fluorescent probe molecules, wide‐field microscopy and atomic force microscopy to unravel the internal architecture of three distinct FER zeolites. Pyrolyzed template species can be used as markers for the 8‐membered ring direction as they are trapped in the terraced roof of the FER crystals. This happens as the materials grow in a layer‐by‐layer, defect‐free manner normal to the large crystal surface, and leads to a facile method to diagnose the pore system orientation, which avoids tedious single crystal X‐ray diffraction experiments. PMID:28809081

Study of crystallization mechanisms of Fe nanoparticle

NASA Astrophysics Data System (ADS)

Kien, P. H.; Trang, G. T. T.; Hung, P. K.

2017-06-01

In this paper, the nanoparticle (NP) Fe was investigated by means of molecular dynamics simulation. The crystallization mechanism was studied through the time evolution of crystal cluster and potential energies of different atom types. The simulation shows that the NP was crystallized into bcc crystal structure when it was annealed at 900 K for long times. At early stage of the annealing, small nuclei form in different places of NP and dissolve for short times. After long times some nuclei form and gather nearby which create the stable clusters in the core of NP. After that the crystal clusters grow in the direction to cover the core and then to spread into the surface of NP. Analyzing the energies of different type atoms, we found that the crystal growth is originated from specific atomic arrangement in the boundary region of crystal clusters.

Struvite formation and decomposition characteristics for ammonia and phosphorus recovery: A review of magnesium-ammonia-phosphate interactions.

PubMed

Tansel, Berrin; Lunn, Griffin; Monje, Oscar

2018-03-01

Struvite (MgNH 4 PO 4 ·6H 2 O) forms in aqueous systems with high ammonia and phosphate concentrations. However, conditions that result into struvite formation are highly dependent on the ionic compositions, temperature, pH, and ion speciation characteristics. The primary ions involved in struvite formation have complex interactions and can form different crystals depending on the ionic levels, pH and temperature. Struvite as well as struvite analogues (with substitution of monovalent cations for NH 4 + or divalent cations for Mg 2+ ) as well as other crystals can form simultaneously and result in changes in crystal morphology during crystal growth. This review provides the results from experimental and theoretical studies on struvite formation and decomposition studies. Characteristics of NH 4 + or divalent cations for Mg 2+ were evaluated in comparison to monovalent and divalent ions for formation of struvite and its analogues. Struvite crystals forming in wastewater systems are likely to contain crystals other than struvite due to ionic interactions, pH changes, temperature effects and clustering of ions during nucleation and crystal growth. Decomposition of struvite occurs following a series of reactions depending on the rate of heating, temperature and availability of water during heating. Copyright © 2017 Elsevier Ltd. All rights reserved.

The closo-Si{sub 12}C{sub 12} molecule from cluster to crystal: A theoretical prediction

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

Duan, Xiaofeng F., E-mail: xiaofeng.duan@wpafb.af.mil, E-mail: larry.burggraf@us.af.mil; Air Force Institute of Technology, Wright-Patterson Air Force Base, Ohio 45433; Burggraf, Larry W., E-mail: xiaofeng.duan@wpafb.af.mil, E-mail: larry.burggraf@us.af.mil

2016-03-21

The structure of closo-Si{sub 12}C{sub 12} is unique among stable Si{sub n}C{sub m} isomers (n, m > 4) because of its high symmetry, π–π stacking of C{sub 6} rings and unsaturated silicon atoms at symmetrical peripheral positions. Dimerization potential surfaces reveal various dimerization reactions that form between two closo-Si{sub 12}C{sub 12} molecules through Si–Si bonds at unsaturated Si atoms. As a result the closo-Si{sub 12}C{sub 12} molecule is capable of polymerization to form stable 1D polymer chains, 2D crystal layers, and 3D crystals. 2D crystal structures formed by side-side polymerization satisfy eight Si valences on each monomer without large distortionmore » of the monomer structure. 3D crystals are formed by stacking 2D structures in the Z direction, preserving registry of C{sub 6} rings in monomer moiety.« less

Crystallization of the C-terminal domain of the addiction antidote CcdA in complex with its toxin CcdB

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

Buts, Lieven; De Jonge, Natalie; Loris, Remy, E-mail: reloris@vub.ac.be

2005-10-01

The CcdA C-terminal domain was crystallized in complex with CcdB in two crystal forms that diffract to beyond 2.0 Å resolution. CcdA and CcdB are the antidote and toxin of the ccd addiction module of Escherichia coli plasmid F. The CcdA C-terminal domain (CcdA{sub C36}; 36 amino acids) was crystallized in complex with CcdB (dimer of 2 × 101 amino acids) in three different crystal forms, two of which diffract to high resolution. Form II belongs to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 37.6, b = 60.5, c = 83.8 Å and diffracts to 1.8more » Å resolution. Form III belongs to space group P2{sub 1}, with unit-cell parameters a = 41.0, b = 37.9, c = 69.6 Å, β = 96.9°, and diffracts to 1.9 Å resolution.« less

Crystalline structures, thermal properties and crystallizing mechanism of polyamide 6 nanotubes in confined space

NASA Astrophysics Data System (ADS)

Li, Xiaoru; Peng, Zhi; Yang, Chao; Han, Ping; Song, Guojun; Cong, Longliang

2016-09-01

The polyamide 6 (PA6) nanotubes were prepared by infiltrating the anodic aluminum oxide templates with polymer solution. Crystalline regions in the nanotube walls were detected by high-resolution transmission electron microscopy (HRTEM). X-ray diffraction (XRD), Fast Fourier Transform (FFT) and differential scanning calorimetry (DSC) techniques were employed to investigate crystallization, crystal faces and thermodynamics. It was found that the crystals were transformed from α-form in bulk to γ-form in nanotubes. It was made a detailed analysis in this article. Moreover, schematic diagram for the crystallizing mechanism of PA6 nanotubes was given to explain PA6 molecules how to crystallize in the nano-pores.

Drop deployment system for crystal growth apparatus

NASA Technical Reports Server (NTRS)

Rhodes, Percy (Inventor); Snyder, Robert S. (Inventor); Pusey, Marc L. (Inventor)

1990-01-01

A crystal growth apparatus is presented. It utilizes a vapor diffusion method for growing protein crystals, and particularly such an apparatus wherein a ball mixer is used to mix the fluids that form a drop within which crystals are grown. Particular novelty of this invention lies in utilizing a ball mixer to completely mix the precipitate and protein solutions prior to forming the drop. Additional novelty lies in details of construction of the vials, the fluid deployment system, and the fluid storage system of the preferred embodiment.

Influence of temperature on the rhombic shape of paracetamol molecular crystals

NASA Astrophysics Data System (ADS)

Belyaev, A. P.; Rubets, V. P.; Antipov, V. V.

2017-04-01

The method of differential scanning ellipsometry has been used to study the influence of heating on the rhombic shape of paracetamol molecular crystals. Rhombic molecular paracetamol crystals have been synthesized in vacuum from the vapor phase of paracetamol as a result of complex transformation, which includes a second-order transition that gives rise to a pretransition phase. It has been found that these crystals contain monoclinic nuclei, which favor the form I-to-form II polymorphic transformation during heating.

Expression, purification and preliminary X-ray diffraction studies of the transcriptional factor PyrR from Bacillus halodurans

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

Arreola, Rodrigo; Vega-Miranda, Anita; Gómez-Puyou, Armando

The gene-regulation factor PyrR from B. halodurans has been crystallized in two crystal forms. Preliminary crystallographic analysis showed that the protein forms tetramers in both space groups. The PyrR transcriptional regulator is widely distributed in bacteria. This RNA-binding protein is involved in the control of genes involved in pyrimidine biosynthesis, in which uridyl and guanyl nucleotides function as effectors. Here, the crystallization and preliminary X-ray diffraction analysis of two crystal forms of Bacillus halodurans PyrR are reported. One of the forms belongs to the monoclinic space group P2{sub 1} with unit-cell parameters a = 59.7, b = 87.4, c =more » 72.1 Å, β = 104.4°, while the other form belongs to the orthorhombic space group P22{sub 1}2{sub 1} with unit-cell parameters a = 72.7, b = 95.9, c = 177.1 Å. Preliminary X-ray diffraction data analysis and molecular-replacement solution revealed the presence of four and six monomers per asymmetric unit; a crystallographic tetramer is formed in both forms.« less

Saturated Monoglyceride Polymorphism and Gel Formation of Biodiesel Blends

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

Chupka, Gina; Fouts, Lisa; McCormick, Robert

Crystallization or gel formation of normal paraffins in diesel fuel under cold weather conditions leading to fuel filter clogging is a common problem. Cold weather operability of biodiesel (B100) and blends with diesel fuel presents additional complexity because of the presence of saturated monoglycerides (SMGs) and other relatively polar species. Currently, the cloud point measurement (a measure of when the first component crystallizes out of solution) is used to define the lowest temperature at which the fuel can be used without causing cold weather issues. While filter plugging issues have declined, there still remain intermittent unexpected problems above the cloudmore » point for biodiesel blends. Development of a fundamental understanding of how minor components in biodiesel crystallize, gel, and transform is needed in order to prevent these unexpected issues. We have found that SMGs, a low level impurity present in B100 from the production process, can crystallize out of solution and undergo a solvent-mediated polymorphic phase transformation to a more stable, less soluble form. This causes them to persist at temperatures above the cloud point once they have some out of solution. Additionally, we have found that SMGs can cause other more soluble, lower melting point minor components in the B100 to co-crystallize and come out of solution. Monoolein, another minor component from the production process is an unsaturated monoglyceride with a much lower melting point and higher solubility than SMGs. It is able to form a co-crystal with the SMGs and is found together with the SMGs on plugged filters we have analyzed in our laboratory. An observation of isolated crystals in the lab led us to believe that the SMGs may also be forming a gel-like network with components of the B100 and diesel fuel. During filtration experiments, we have noted that in some cases a solid layer of crystals forms and blocks the filter completely, while in other cases this does not occur. Because SMGs are polar and can form layered networks once a sufficient amount of crystals have come out of solution, we recently began investigating the ability of SMGs to form a gel network with fuel components as well as with other minor polar components in the fuel in order to obtain a fundamental understanding of the mechanism of formation. It has been well established that this type of phenomena occurs in sub-sea pipelines where a chief crystallizing component begins to crystallize out of solution. Once a sufficient amount of crystals exists, a volume spanning network of solid crystals can trap liquid crude oil and form a solid-like gel network. We are investigating whether this type of phenomena can occur with SMGs and both fatty acid methyl esters from the B100 and normal paraffins from diesel fuel. Additionally, SMGs are well known to incorporate water into their layered crystal structure. Water is often used to stabilize less stable polymorphic forms of SMGs, therefore water was another minor component of interest. Also of interest is glycerin which has been found on clogged filters in our laboratory.« less

Scanning electron microscope view of iron crystal growing on pyroxene crystal

NASA Technical Reports Server (NTRS)

1972-01-01

A scanning electron microscope photograph of a four-micron size iron crystal growing on a pyroxene crystal (calcium-magnesium-iron silicate) from the Apollo 15 Hadley-Apennino lunar landing site. The well developed crystal faces indicate that the crystal was formed from a hot vapor as the rock was cooling.

Effect of coccolith polysaccharides isolated from the coccolithophorid, Emiliania huxleyi, on calcite crystal formation in in vitro CaCO3 crystallization.

PubMed

Kayano, Keisuke; Saruwatari, Kazuko; Kogure, Toshihiro; Shiraiwa, Yoshihiro

2011-02-01

Marine coccolithophorids (Haptophyceae) produce calcified scales "coccoliths" which are composed of CaCO(3) and coccolith polysaccharides (CP) in the coccolith vesicles. CP was previously reported to be composed of uronic acids and sulfated residues, etc. attached to the polymannose main chain. Although anionic polymers are generally known to play key roles in biomineralization process, there is no experimental data how CP contributes to calcite crystal formation in the coccolithophorids. CP used was isolated from the most abundant coccolithophorid, Emiliania huxleyi. CaCO(3) crystallization experiment was performed on agar template layered onto a plastic plate that was dipped in the CaCO(3) crystallization solution. The typical rhombohedral calcite crystals were formed in the absence of CP. CaCO(3) crystals formed on the naked plastic plate were obviously changed to stick-like shapes when CP was present in the solution. EBSD analysis proved that the crystal is calcite of which c-axis was elongated. CP in the solution stimulated the formation of tabular crystals with flat edge in the agarose gel. SEM and FIB-TEM observations showed that the calcite crystals were formed in the gel. The formation of crystals without flat edge was stimulated when CP was preliminarily added in the gel. These observations suggest that CP has two functions: namely, one is to elongate the calcite crystal along c-axis and another is to induce tabular calcite crystal formation in the agarose gel. Thus, CP may function for the formation of highly elaborate species-specific structures of coccoliths in coccolithophorids.

Crystallization and preliminary X-ray crystallographic analysis of latent isoform PPO4 mushroom (Agaricus bisporus) tyrosinase

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

Mauracher, Stephan Gerhard; Molitor, Christian; Al-Oweini, Rami

Polyphenol oxidase 4 (PPO4) from the natural source A. bisporus was crystallized in its latent precursor form (pro-tyrosinase; Ser2–Thr565) using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a crystallization additive. Tyrosinase exhibits catalytic activity for the ortho-hydroxylation of monophenols to diphenols as well as their subsequent oxidation to quinones. Owing to polymerization of these quinones, brown-coloured high-molecular-weight compounds called melanins are generated. The latent precursor form of polyphenol oxidase 4, one of the six tyrosinase isoforms from Agaricus bisporus, was purified to homogeneity and crystallized. The obtained crystals belonged to space group C121 (two molecules per asymmetric unit)more » and diffracted to 2.78 Å resolution. The protein only formed crystals under low-salt conditions using the 6-tungstotellurate(VI) salt Na{sub 6}[TeW{sub 6}O{sub 24}]·22H{sub 2}O as a co-crystallization agent.« less

Sodium chloride crystallization from thin liquid sheets, thick layers, and sessile drops in microgravity

NASA Astrophysics Data System (ADS)

Fontana, Pietro; Pettit, Donald; Cristoforetti, Samantha

2015-10-01

Crystallization from aqueous sodium chloride solutions as thin liquid sheets, 0.2-0.7 mm thick, with two free surfaces supported by a wire frame, thick liquid layers, 4-6 mm thick, with two free surfaces supported by metal frame, and hemispherical sessile drops, 20-32 mm diameter, supported by a flat polycarbonate surface or an initially flat gelatin film, were carried out under microgravity on the International Space Station (ISS). Different crystal morphologies resulted based on the fluid geometry: tabular hoppers, hopper cubes, circular [111]-oriented crystals, and dendrites. The addition of polyethylene glycol (PEG-3350) inhibited the hopper growth resulting in flat-faced surfaces. In sessile drops, 1-4 mm tabular hopper crystals formed on the free surface and moved to the fixed contact line at the support (polycarbonate or gelatin) self-assembling into a shell. Ring formation created by sessile drop evaporation to dryness was observed but with crystals 100 times larger than particles in terrestrially formed coffee rings. No hopper pyramids formed. By choosing solution geometries offered by microgravity, we found it was possible to selectively grow crystals of preferred morphologies.

Crystallization kinetics and molecular mobility of an amorphous active pharmaceutical ingredient: A case study with Biclotymol.

PubMed

Schammé, Benjamin; Couvrat, Nicolas; Malpeli, Pascal; Delbreilh, Laurent; Dupray, Valérie; Dargent, Éric; Coquerel, Gérard

2015-07-25

The present case study focuses on the crystallization kinetics and molecular mobility of an amorphous mouth and throat drug namely Biclotymol, through differential scanning calorimetry (DSC), temperature resolved X-ray powder diffraction (TR-XRPD) and hot stage microscopy (HSM). Kinetics of crystallization above the glass transition through isothermal and non-isothermal cold crystallization were considered. Avrami model was used for isothermal crystallization process. Non-isothermal cold crystallization was investigated through Augis and Bennett model. Differences between crystallization processes have been ascribed to a site-saturated nucleation mechanism of the metastable form, confirmed by optical microscopy images. Regarding molecular mobility, a feature of molecular dynamics in glass-forming liquids as thermodynamic fragility index m was determined through calorimetric measurements. It turned out to be around m=100, describing Biclotymol as a fragile glass-former for Angell's classification. Relatively long-term stability of amorphous Biclotymol above Tg was analyzed indirectly by calorimetric monitoring to evaluate thermodynamic parameters and crystallization behavior of glassy Biclotymol. Within eight months of storage above Tg (T=Tg+2°C), amorphous Biclotymol does not show a strong inclination to crystallize and forms a relatively stable glass. This case study, involving a multidisciplinary approach, points out the importance of continuing looking for stability predictors. Copyright © 2015 Elsevier B.V. All rights reserved.

The Effect of Additives on the Early Stages of Growth of Calcite Single Crystals

PubMed Central

Freeman, Colin L.; Gong, Xiuqing; Levenstein, Mark A.; Wang, Yunwei; Kulak, Alexander; Anduix‐Canto, Clara; Lee, Phillip A.; Li, Shunbo; Chen, Li; Christenson, Hugo K.

2017-01-01

Abstract As crystallization processes are often rapid, it can be difficult to monitor their growth mechanisms. In this study, we made use of the fact that crystallization proceeds more slowly in small volumes than in bulk solution to investigate the effects of the soluble additives Mg2+ and poly(styrene sulfonate) (PSS) on the early stages of growth of calcite crystals. Using a “Crystal Hotel” microfluidic device to provide well‐defined, nanoliter volumes, we observed that calcite crystals form via an amorphous precursor phase. Surprisingly, the first calcite crystals formed are perfect rhombohedra, and the soluble additives have no influence on the morphology until the crystals reach sizes of 0.1–0.5 μm for Mg2+ and 1–2 μm for PSS. The crystals then continue to grow to develop morphologies characteristic of these additives. These results can be rationalized by considering additive binding to kink sites, which is consistent with crystal growth by a classical mechanism. PMID:28767197

Crystallization of isoelectrically homogeneous cholera toxin

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

Spangler, B.D.; Westbrook, E.M.

1989-02-07

Past difficulty in growing good crystals of cholera toxin has prevented the study of the crystal structure of this important protein. The authors have determined that failure of cholera toxin to crystallize well has been due to its heterogeneity. They have now succeeded in overcoming the problem by isolating a single isoelectric variant of this oligomeric protein (one A subunit and five B subunits). Cholera toxin purified by their procedure readily forms large single crystals. The crystal form has been described previously. They have recorded data from native crystals of cholera toxin to 3.0-{angstrom} resolution with our electronic area detectors.more » With these data, they have found the orientation of a 5-fold symmetry axis within these crystals, perpendicular to the screw dyad of the crystal. They are now determining the crystal structure of cholera toxin by a combination of multiple heavy-atom isomorphous replacement and density modification techniques, making use of rotational 5-fold averaging of the B subunits.« less

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.

Gypsum ground: a new occurrence of gypsum sediment in playas of central Australia

NASA Astrophysics Data System (ADS)

Xiang Yang Chen; Bowler, James M.; Magee, John W.

1991-06-01

There are many playas (dry salt lakes) in arid central Australia (regional rainfall about 250 mm/y and pan evaporation around 3000 mm/y). Highly soluble salts, such as halite, only appear as a thin (several centimetres thick), white, ephemeral efflorescent crust on the dry surface. Gypsum is the major evaporite precipitating both at present and preserved in sediment sequences. One type of gypsum deposit forms a distinctive surface feature, which is here termed "gypsum ground". It consists of a thick (up to 80 cm) gypsum zone which rises from the surrounding smooth white playa surface and is overlain by a heaved brown crust. The gypsum zone, with an average gypsum content above 60%, consists of pure gypsum sublayers and interlayered clastic bands of sandy clay. The gypsum crystals are highly corroded, especially in the direction parallel to the c-axis and on the upper sides where illuviated clay has accumulated in corrosion hollows. Overgrowth parallel to the a- and b-axes is very common, forming highly discoidal habits. These secondary changes (corrosion and overgrowth) are well-developed in the vadose zone and absent from crystals below the long-term watertable (depth around 40 cm). These crystal characteristics indicate a rainwater leaching process. At Lake Amadeus, one of the largest playas (800 km 2) of central Australia, such gypsum ground occupies 16% of the total area. The gypsum ground is interpreted as an alteration of a pre-existing gypsum deposit which probably extended across the whole playa before breaking down, leaving a playa marginal terrace and several terrace islands within the gypsum ground. This pre-existing gypsum deposit, preserved in the residual islands, consists of pure, pale, sand-sized lenticular crystals. It is believed to have been deposited during an episode of high regional watertable, causing active groundwater seepage and more frequent surface brine in the playa. A later fall in watertable, probably resulting from climatic change, caused the degradation of the gypsum deposit by dissolution and leaching processes. The common distribution of the gypsum ground and marginal terraces in the playas of central Australia demonstrates the extent of this hydrologic and climatic history.

Influence of additive L-phenylalanine on stabilization of metastable α-form of L-glutamic acid in cooling crystallization

NASA Astrophysics Data System (ADS)

Quang, Khuu Chau; Nhan, Le Thi Hong; Huyen, Trinh Thi Thanh; Tuan, Nguyen Anh

2017-09-01

The influence of additive amino acid L-phenylalanine on stabilization of metastable α-form of L-glutamic acid was investigated in cooling crystallization. The present study found that the additive L-phenylalanine could be used to stabilize the pure metastable α-form in L-glutamic acid crystallization, where the additive concentration of 0.05-0.1 (g/L) was sufficient to stabilize the 100% wt metastable α-form in solid product at L-glutamic acid concentration of 30-45 (g/L). Additionally, the present results indicated that the adsorption of additive L-phenylalanine on the (001) surface of α-form was more favorable than that of the β-form molecular, so the nucleation sites of stable β-form was occupied by additive molecular, which resulted in inhibition of nucleation and growth of β-form, allowing stabilization of metastable α-form.

The effect of crystal structure on the electromechanical properties of piezoelectric Nylon-11 nanowires.

PubMed

Choi, Yeon Sik; Kim, Sung Kyun; Williams, Findlay; Calahorra, Yonatan; Elliott, James A; Kar-Narayan, Sohini

2018-06-19

Crystal structure is crucial in determining the properties of piezoelectric polymers, particularly at the nanoscale where precise control of the crystalline phase is possible. Here, we investigate the electromechanical properties of three distinct crystalline phases of Nylon-11 nanowires using advanced scanning probe microscopy techniques. Stiff α-phase nanowires exhibited a low piezoelectric response, while relatively soft δ'-phase nanowires displayed an enhanced piezoelectric response.

Recycling, Remobilization, and Eruption of Crystals from the Lassen Volcanic Center

NASA Astrophysics Data System (ADS)

Schrecengost, K.; Cooper, K. M.; Kent, A. J.; Huber, C.; Clynne, M. A.

2016-12-01

The Lassen Volcanic Center recently produced two relatively small dacitic eruptions (0.03 km3 -1.4 km3) with a complex mixing history. Preliminary data for the 1915 Lassen Peak (LP) and the 1103±13 ybp Chaos Crags (CC) eruptions indicate complex mixing between a remobilized crystal mush (hornblende, biotite, sodic plagioclase, quartz) and basalt or basaltic andesite. U-series bulk ages represent crystallization of plagioclase at an average age of either a single event or a mixture of different plagioclase populations that crystallized during distinct crystallization events separated in time. We present 238U-230Th disequilibria for the LP light dacite and black dacite along with three stages (upper pyroclastic flow deposit, Dome B, and Dome F) of the CC eruption. Initial 230Th/232Th activity ratios for the LP plagioclase are higher than the LP host liquid and modeled equilibrium zero-age plagioclase towards the CC host liquid composition. The LP plagioclase data are inconsistent with crystallization from the LP host liquid. Therefore, at least a portion of the plagioclase carried by the LP eruptive products are antecrystic originating from an older and/or isotopically distinct host liquid composition. Moreover, LP bulk plagioclase is consistent with crystallization from the CC host liquid, suggesting that both eruptions are sourced from a similar host reservoir (i.e., crystal mush). Hornblende and biotite from the LP eruption have isotopic ratios that are consistent with zero age crystallization from the LP liquid composition, suggesting that they are younger and originate from a different magma than the plagioclase, with mixing between the magmas prior to eruption. However, it is more likely that hornblende, biotite, and plagioclase with varying average crystal ages were remobilized and erupted from a common crystal mush reservoir during the LP and CC eruptions. These data are consistent with zircon 238U-230Th model ages [1] that emphasize the importance of local, small-scale rejuvenation and mixing within a long-lived magmatic system. Moreover, assuming crystallization from a CC-like liquid compositions, LP bulk plagioclase model ages produce similar ages to those derived from LP and CC zircon (i.e., 17 ka to secular equilibrium). [1] Klemetti and Clynne, PLoS ONE, 9(12): e113157.

Development of a New Class of Drugs to Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

previous rat ARdbd-DNA crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening...to VPC-14449 as a model drug to assist on other related projects. 1. Tam, K., Dalal, K., Hsing, M., Cheng, C.W., Chiang , Y.T., Sharma, A., Peacock

Development of a New Class of Drugs To Inhibit All Forms of Androgen Receptor in Castration Resistant Prostate Cancers

DTIC Science & Technology

2016-10-01

crystals and may represent a new crystal form. Key outcome 2: We have carried out followup crystallization screening operations with the ARdbd protein...related projects. 1. Tam, K., Dalal, K., Hsing, M., Cheng, C.W., Chiang , Y.T., Sharma, A., Peacock, J.W., Wang, W., Cherkasov, A., Rennie, P.S

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System

NASA Astrophysics Data System (ADS)

Rovny, Jared; Blum, Robert L.; Barrett, Sean E.

2018-05-01

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Observation of Discrete-Time-Crystal Signatures in an Ordered Dipolar Many-Body System.

PubMed

Rovny, Jared; Blum, Robert L; Barrett, Sean E

2018-05-04

A discrete time crystal (DTC) is a robust phase of driven systems that breaks the discrete time translation symmetry of the driving Hamiltonian. Recent experiments have observed DTC signatures in two distinct systems. Here we show nuclear magnetic resonance observations of DTC signatures in a third, strikingly different system: an ordered spatial crystal. We use a novel DTC echo experiment to probe the coherence of the driven system. Finally, we show that interactions during the pulse of the DTC sequence contribute to the decay of the signal, complicating attempts to measure the intrinsic lifetime of the DTC.

Measurement of single crystal surface parameters

NASA Technical Reports Server (NTRS)

Swanson, L. W.; Bell, A. E.; Strayer, R. W.

1972-01-01

The sticking coefficient and thermal desorption spectra of Cs from the (110) plane of W was investigated. A sticking coefficient of unity for the monolayer region was measured for T 250 K. Several distinct binding states were observed in the thermal desorption spectrum. Work function and electron reflection measurements were made on the (110) and (100) crystal faces of Mo. Both LEED and Auger were used to determine the orientation and cleanliness of the crystal surfaces. The work function values obtained for the (110) and (100) planes of Mo were 4.92 and 4.18 eV respectively.

Crystal growth in a low gravity environment

NASA Technical Reports Server (NTRS)

Carruthers, J. R.

1977-01-01

Crystal growth in microgravity possesses several distinct technological advantages over earth-bound processes; containerless handling and reduction of density gradient driven as well as sedimentation flows. Experiments performed in space to date have been basically reproductions of processes currently used on earth and the results have clarified our understanding of crystal growth dynamics. In addition, both unresolved problems and areas requiring further study on earth have been identified. Future work in space processing of materials must address these areas of study as soon as possible if the full potential of a space environment to develop new techniques and materials is to be realized.

Helix formation in arrestin accompanies recognition of photoactivated rhodopsin.

PubMed

Feuerstein, Sophie E; Pulvermüller, Alexander; Hartmann, Rudolf; Granzin, Joachim; Stoldt, Matthias; Henklein, Peter; Ernst, Oliver P; Heck, Martin; Willbold, Dieter; Koenig, Bernd W

2009-11-17

Binding of arrestin to photoactivated phosphorylated rhodopsin terminates the amplification of visual signals in photoreceptor cells. Currently, there is no crystal structure of a rhodopsin-arrestin complex available, although structures of unbound rhodopsin and arrestin have been determined. High-affinity receptor binding is dependent on distinct arrestin sites responsible for recognition of rhodopsin activation and phosphorylation. The loop connecting beta-strands V and VI in rod arrestin has been implicated in the recognition of active rhodopsin. We report the structure of receptor-bound arrestin peptide Arr(67-77) mimicking this loop based on solution NMR data. The peptide binds photoactivated rhodopsin in the unphosphorylated and phosphorylated form with similar affinities and stabilizes the metarhodopsin II photointermediate. A largely alpha-helical conformation of the receptor-bound peptide is observed.

Structure and thermodynamic stability of UTa 3 O 10 , a U( v )-bearing compound

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

Guo, Xiaofeng; Lipp, Christian; Tiferet, Eitan

Heating a mixture of uranyl(VI) nitrate and tantalum(V) oxide in the molar ratio of 2 : 3 to 1400 °C resulted in the formation of a new compound, UTa 3O 10. The honey colored to yellow brown crystals of UTa 3O 10 crystallize in an orthorhombic structure with the space group Fddd (no. 70), lattice parameters a = 7.3947(1), b = 12.7599(2), c = 15.8156(2) Å, and Z = 8. Vertex sharing [TaO 6] 7- octahedra of two crystallographically distinct Ta cations form a three dimensional tantalate framework. Within this framework, six membered rings of [TaO 6] 7- octahedra aremore » formed within the (001) plane. The center of these rings is occupied by the uranyl cations [UO 2] +, with an oxidation state of +5 for uranium. The pentavalence of U and Ta was confirmed by X-ray photoelectron spectroscopy and X-ray adsorption spectroscopy. The enthalpy of formation of UTa 3O 10 from Ta 2O 5, β-U 3O 7, and U 3O 8 has been determined to be 13.1 ± 18.1 kJ mol -1 using high temperature oxide melt solution calorimetry with sodium molybdate as the solvent at 700 °C. The close to zero enthalpy of formation of UTa 3O 10 can be explained by closely balanced structural stabilizing and destabilizing factors, which may also apply to other UM 3O 10 compounds.« less

Elongated fibrillar structure of a streptococcal adhesin assembled by the high-affinity association of [alpha]- and PPII-helices

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

Larson, Matthew R.; Rajashankar, Kanagalaghatta R.; Patel, Manisha H.

2010-08-18

Streptococcus mutans antigen I/II (AgI/II) is a cell surface-localized protein adhesin that interacts with salivary components within the salivary pellicle. AgI/II contributes to virulence and has been studied as an immunological and structural target, but a fundamental understanding of its underlying architecture has been lacking. Here we report a high-resolution (1.8 {angstrom}) crystal structure of the A{sub 3}VP{sub 1} fragment of S. mutans AgI/II that demonstrates a unique fibrillar form (155 {angstrom}) through the interaction of two noncontiguous regions in the primary sequence. The A{sub 3} repeat of the alanine-rich domain adopts an extended {alpha}-helix that intertwines with the P{submore » 1} repeat polyproline type II (PPII) helix to form a highly extended stalk-like structure heretofore unseen in prokaryotic or eukaryotic protein structures. Velocity sedimentation studies indicate that full-length AgI/II that contains three A/P repeats extends over 50 nanometers in length. Isothermal titration calorimetry revealed that the high-affinity association between the A{sub 3} and P{sub 1} helices is enthalpically driven. Two distinct binding sites on AgI/II to the host receptor salivary agglutinin (SAG) were identified by surface plasmon resonance (SPR). The current crystal structure reveals that AgI/II family proteins are extended fibrillar structures with the number of alanine- and proline-rich repeats determining their length.« less

Heterobimetallic thiocyanato-bridged coordination polymers based on [Hg(SCN) 4] 2-: Synthesis, crystal structure, magnetic properties and ESR studies

NASA Astrophysics Data System (ADS)

Jian, Fang-Fang; Xiao, Hai-Lian; Liu, Fa Qian

2006-12-01

Three new M/Hg bimetallic thiocyanato-bridged coordination polymers; [Hg(SCN) 4Ni(Im) 3] ∞1, [Hg(SCN) 4Mn(Im) 2] ∞2, and [Hg(SCN) 4Cu(Me-Im) 2 Hg(SCN) 4Cu(Me-Im) 4] ∞3, (Im=imidazole, Me-Im= N-methyl-imidazole), have been synthesized and characterized by means of elemental analysis, ESR, and single-crystal X-ray. X-ray diffraction analysis reveals that these three complexes all form 3D network structure, and their structures all contain a thiocyanato-bridged Hg⋯M⋯Hg chain ( M=Mn, Ni, Cu) in which the metal and mercury centers exhibit different coordination environments. In complex 1, the [Hg(SCN) 4] 2- anion connects three [Ni(Im) 3] 2+ using three SCN ligands giving rise to a 3D structure, and in complex 2, four SCN ligands bridge [Hg(SCN) 4] 2- and [Mn(Im) 2] 2+ to form a 3D structure. The structure of 3 contains two copper atoms with distinct coordination environment; one is coordinated by four N-methyl-imidazole ligands and two axially elongated SCN groups, and another by four SCN groups (two elongated) and two N-methyl-imidazole ligands. The magnetic property of complex 1 has been investigated. The spin state structure in hetermetallic NiHgNi systems of complex 1 is irregular. The ESR spectra results of complex 3 demonstrate Cu 2+ ion lie on octahedral environment.

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

AhYoung, Andrew P.; Lu, Brian; Cascio, Duilio

Membrane contact sites between organelles serve as molecular hubs for the exchange of metabolites and signals. In yeast, the Endoplasmic Reticulum – Mitochondrion Encounter Structure (ERMES) tethers these two organelles likely to facilitate the non-vesicular exchange of essential phospholipids. Present in Fungi and Amoebas but not in Metazoans, ERMES is composed of five distinct subunits; among those, Mdm12, Mmm1 and Mdm34 each contain an SMP domain functioning as a lipid transfer module. We previously showed that the SMP domains of Mdm12 and Mmm1 form a hetero-tetramer. Here we describe our strategy to diversify the number of Mdm12/Mmm1 complexes suited formore » structural studies. We use sequence analysis of orthologues combined to protein engineering of disordered regions to guide the design of protein constructs and expand the repertoire of Mdm12/Mmm1 complexes more likely to crystallize. Using this combinatorial approach we report crystals of Mdm12/Mmm1 ERMES complexes currently diffracting to 4.5 Å resolution and a new structure of Mdm12 solved at 4.1 Å resolution. Our structure reveals a monomeric form of Mdm12 with a conformationally dynamic N-terminal β-strand; it differs from a previously reported homodimeric structure where the N-terminal β strands where swapped to promote dimerization. Based on our electron microscopy data, we propose a refined pseudo-atomic model of the Mdm12/Mmm1 complex that agrees with our crystallographic and small-angle X-ray scattering (SAXS) solution data.« less

Crystal Structure of Neurotropism-Associated Variable Surface Protein 1 (VSP1) of Borrelia Turicatae

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

Lawson,C.; Yung, B.; Barbour, A.

2006-01-01

Vsp surface lipoproteins are serotype-defining antigens of relapsing fever spirochetes that undergo multiphasic antigenic variation to allow bacterial persistence in spite of an immune response. Two isogenic serotypes of Borrelia turicatae strain Oz1 differ in their Vsp sequences and in disease manifestations in infected mice: Vsp1 is associated with the selection of a neurological niche, while Vsp2 is associated with blood and skin infection. We report here crystal structures of the Vsp1 dimer at 2.7 and 2.2 Angstroms. The structures confirm that relapsing fever Vsp proteins share a common helical fold with OspCs of Lyme disease-causing Borrelia. The fold featuresmore » an inner stem formed by highly conserved N and C termini and an outer 'dome' formed by the variable central residues. Both Vsp1 and OspC structures possess small water-filled cavities, or pockets, that are lined largely by variable residues and are thus highly variable in shape. These features appear to signify tolerance of the Vsp-OspC fold for imperfect packing of residues at its antigenic surface. Structural comparison of Vsp1 with a homology model for Vsp2 suggests that observed differences in disease manifestation may arise in part from distinct differences in electrostatic surface properties; additional predicted positively charged surface patches on Vsp2 compared to Vsp1 may be sufficient to explain the relative propensity of Vsp2 to bind to acidic glycosaminoglycans.« less

Proline zwitterion dynamics in solution, glass, and crystalline state.

PubMed

Kapitán, Josef; Baumruk, Vladimír; Kopecký, Vladimír; Pohl, Radek; Bour, Petr

2006-10-18

Raman and Raman optical activity spectra of L- and D-proline zwitterionic (PROZW) forms were recorded for H(2)O and D(2)O solutions in a wide frequency range and analyzed with respect to the motion of the proline ring and rotation of the carbonyl group. The solution spectra were additionally compared to Raman scattering of glass and crystalline powder proline. Solution and glass spectral band broadenings are similar and reveal information about the extent of internal molecular motion. Two distinct but equally populated flexible forms were found in the glass and the solution. The equal population is consistent with NMR data, temperature, and concentration dependencies. The molecular flexibility is reduced significantly in the crystal, however, where only one conformer is present. Consequently, the crystal bands are narrow and exhibit minor frequency shifts. The spectra were interpreted with the aid of density functional theory computations involving both continuum and explicit solvent. A two-dimensional potential energy surface pertaining to the five-member ring puckering coordinates was constructed and used for dynamical averaging of spectral properties. Comparison of the computed and experimental bandwidths suggests that the puckering is strongly correlated with the carbonyl rotation. An averaging over these two motions produces similar results. The interpretation of the Raman experiments with the aid of the simulation techniques also indicates that the environment modulates properties of the hydrophobic part of the molecule indirectly by interacting with the ionic group. Such behavior may be important for the reactivity and biological activity of proline-containing peptides and proteins.

Influence of the Ligand Field on the Slow Relaxation of Magnetization of Unsymmetrical Monomeric Lanthanide Complexes: Synthesis and Theoretical Studies.

PubMed

Upadhyay, Apoorva; Vignesh, Kuduva R; Das, Chinmoy; Singh, Saurabh Kumar; Rajaraman, Gopalan; Shanmugam, Maheswaran

2017-11-20

A series of monomeric lanthanide Schiff base complexes with the molecular formulas [Ce(HL) 3 (NO 3 ) 3 ] (1) and [Ln(HL) 2 (NO 3 ) 3 ], where Ln III = Tb (2), Ho (3), Er (4), and Lu (5), were isolated and characterized by single-crystal X-ray diffraction (XRD). Single-crystal XRD reveals that, except for 1, all complexes possess two crystallographically distinct molecules within the unit cell. Both of these crystallographically distinct molecules possess the same molecular formula, but the orientation of the coordinating ligand distinctly differs from those in complexes 2-5. Alternating-current magnetic susceptibility measurement reveals that complexes 1-3 exhibit slow relaxation of magnetization in the presence of an optimum external magnetic field. In contrast to 1-3, complex 4 shows a blockade of magnetization in the absence of an external magnetic field, a signature characteristic of a single-ion magnet (SIM). The distinct magnetic behavior observed in 4 compared to other complexes is correlated to the suitable ligand field around a prolate Er III ion. Although the ligand field stabilizes an easy axis of anisotropy, quantum tunnelling of magnetization (QTM) is still predominant in 4 because of the low symmetry of the complex. The combination of low symmetry and an unsuitable ligand-field environment in complexes 1-3 triggers faster magnetization relaxation; hence, these complexes exhibit field-induced SIM behavior. In order to understand the electronic structures of complexes 1-4 and the distinct magnetic behavior observed, ab initio calculations were performed. Using the crystal structure of the complexes, magnetic susceptibility data were computed for all of the complexes. The computed susceptibility and magnetization are in good agreement with the experimental magnetic data [χ M T(T) and M(H)] and this offers confidence on the reliability of the extracted parameters. A tentative mechanism of magnetization relaxation observed in these complexes is also discussed in detail.

A co-crystal between benzene and ethane: a potential evaporite material for Saturn’s moon Titan

PubMed Central

Maynard-Casely, Helen E.; Hodyss, Robert; Cable, Morgan L.; Vu, Tuan Hoang; Rahm, Martin

2016-01-01

Using synchrotron X-ray powder diffraction, the structure of a co-crystal between benzene and ethane formed in situ at cryogenic conditions has been determined, and validated using dispersion-corrected density functional theory calculations. The structure comprises a lattice of benzene molecules hosting ethane molecules within channels. Similarity between the intermolecular interactions found in the co-crystal and in pure benzene indicate that the C—H⋯π network of benzene is maintained in the co-crystal, however, this expands to accommodate the guest ethane molecules. The co-crystal has a 3:1 benzene:ethane stoichiometry and is described in the space group with a = 15.977 (1) Å and c = 5.581 (1) Å at 90 K, with a density of 1.067 g cm−3. The conditions under which this co-crystal forms identify it is a potential that forms from evaporation of Saturn’s moon Titan’s lakes, an evaporite material. PMID:27158505

Does Z' equal 1 or 2? Enhanced powder NMR crystallography verification of a disordered room temperature crystal structure of a p38 inhibitor for chronic obstructive pulmonary disease.

PubMed

Widdifield, Cory M; Nilsson Lill, Sten O; Broo, Anders; Lindkvist, Maria; Pettersen, Anna; Svensk Ankarberg, Anna; Aldred, Peter; Schantz, Staffan; Emsley, Lyndon

2017-06-28

The crystal structure of the Form A polymorph of N-cyclopropyl-3-fluoro-4-methyl-5-[3-[[1-[2-[2-(methylamino)ethoxy]phenyl]cyclopropyl]amino]-2-oxo-pyrazin-1-yl]benzamide (i.e., AZD7624), determined using single-crystal X-ray diffraction (scXRD) at 100 K, contains two molecules in the asymmetric unit (Z' = 2) and has regions of local static disorder. This substance has been in phase IIa drug development trials for the treatment of chronic obstructive pulmonary disease, a disease which affects over 300 million people and contributes to nearly 3 million deaths annually. While attempting to verify the crystal structure using nuclear magnetic resonance crystallography (NMRX), we measured 13 C solid-state NMR (SSNMR) spectra at 295 K that appeared consistent with Z' = 1 rather than Z' = 2. To understand this surprising observation, we used multinuclear SSNMR ( 1 H, 13 C, 15 N), gauge-including projector augmented-wave density functional theory (GIPAW DFT) calculations, crystal structure prediction (CSP), and powder XRD (pXRD) to determine the room temperature crystal structure. Due to the large size of AZD7624 (ca. 500 amu, 54 distinct 13 C environments for Z' = 2), static disorder at 100 K, and (as we show) dynamic disorder at ambient temperatures, NMR spectral assignment was a challenge. We introduce a method to enhance confidence in NMR assignments by comparing experimental 13 C isotropic chemical shifts against site-specific DFT-calculated shift distributions established using CSP-generated crystal structures. The assignment and room temperature NMRX structure determination process also included measurements of 13 C shift tensors and the observation of residual dipolar coupling between 13 C and 14 N. CSP generated ca. 90 reasonable candidate structures (Z' = 1 and Z' = 2), which when coupled with GIPAW DFT results, room temperature pXRD, and the assigned SSNMR data, establish Z' = 2 at room temperature. We find that the polymorphic Form A of AZD7624 is maintained at room temperature, although dynamic disorder is present on the NMR timescale. Of the CSP-generated structures, 2 are found to be fully consistent with the SSNMR and pXRD data; within this pair, they are found to be structurally very similar (RMSD 16 = 0.30 Å). We establish that the CSP structure in best agreement with the NMR data possesses the highest degree of structural similarity with the scXRD-determined structure (RMSD 16 = 0.17 Å), and has the lowest DFT-calculated energy amongst all CSP-generated structures with Z' = 2.

Studies of Toxoplasma gondii and Plasmodium falciparum enoyl acyl carrier protein reductase and implications for the development of antiparasitic agents

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

Muench, Stephen P.; Prigge, Sean T.; McLeod, Rima

2007-03-01

The crystal structures of T. gondii and P. falciparum ENR in complex with NAD{sup +} and triclosan and of T. gondii ENR in an apo form have been solved to 2.6, 2.2 and 2.8 Å, respectively. Recent studies have demonstrated that submicromolar concentrations of the biocide triclosan arrest the growth of the apicomplexan parasites Plasmodium falciparum and Toxoplasma gondii and inhibit the activity of the apicomplexan enoyl acyl carrier protein reductase (ENR). The crystal structures of T. gondii and P. falciparum ENR in complex with NAD{sup +} and triclosan and of T. gondii ENR in an apo form have beenmore » solved to 2.6, 2.2 and 2.8 Å, respectively. The structures of T. gondii ENR have revealed that, as in its bacterial and plant homologues, a loop region which flanks the active site becomes ordered upon inhibitor binding, resulting in the slow tight binding of triclosan. In addition, the T. gondii ENR–triclosan complex reveals the folding of a hydrophilic insert common to the apicomplexan family that flanks the substrate-binding domain and is disordered in all other reported apicomplexan ENR structures. Structural comparison of the apicomplexan ENR structures with their bacterial and plant counterparts has revealed that although the active sites of the parasite enzymes are broadly similar to those of their bacterial counterparts, there are a number of important differences within the drug-binding pocket that reduce the packing interactions formed with several inhibitors in the apicomplexan ENR enzymes. Together with other significant structural differences, this provides a possible explanation of the lower affinity of the parasite ENR enzyme family for aminopyridine-based inhibitors, suggesting that an effective antiparasitic agent may well be distinct from equivalent antimicrobials.« less

Mechanism of autophosphorylation of mycobacterial PknB explored by molecular dynamics simulations.

PubMed

Damle, Nikhil P; Mohanty, Debasisa

2014-07-22

Mycobacterial Ser/Thr kinase, PknB, is essential for the growth of the pathogen. Unphosphorylated PknB is catalytically inactive, and its activation requires autophosphorylation of Thr residues on the activation loop. Autophosphorylation can in principle take place via two distinct mechanisms. Intermolecular trans autophosphorylation involves dimerization and phosphorylation of the activation loop of one chain in the catalytic pocket of the other chain. On the other hand, intramolecular cis autophosphorylation involves phosphorylation of the activation loop of the kinases in its own catalytic pocket within a monomer. On the basis of the crystal structure of PknB in the front-to-front dimeric form, it is currently believed that activation of PknB involves trans autophosphorylation. However, because of the lack of coordinates of the activation loop in the crystal structures, atomic details of the conformational changes associated with activation are yet to be deciphered. Therefore, to understand the conformational transitions associated with activation via autophosphorylation, a series of explicit solvent molecular dynamics simulations with a duration of 1 μs have been performed on each of the phosphorylated and nonphosphorylated forms of the PknB catalytic domain in monomeric and dimeric states. Simulations on phosphorylated PknB revealed a differential network of crucial electrostatic and hydrophobic residues that stabilize the phosphorylated form in the active conformation. Interestingly, in our simulations on nonphosphorylated monomers, the activation loop was observed to fold into its own active site, thereby opening the novel possibility of activation through intramolecular cis autophosphorylation. Thus, our simulations suggest that autophosphorylation of PknB might also involve cis initiation followed by trans amplification as reported for other eukaryotic kinases based on recent reaction kinetics studies.

Crystallization of the Nonameric Small Terminase Subunit of Bacteriophage P22

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

A Roy; A Bhardwaj; G Cingolani

2011-12-31

The packaging of viral genomes into preformed empty procapsids is powered by an ATP-dependent genome-translocating motor. This molecular machine is formed by a heterodimer consisting of large terminase (L-terminase) and small terminase (S-terminase) subunits, which is assembled into a complex of unknown stoichiometry, and a dodecameric portal protein. There is considerable confusion in the literature regarding the biologically relevant oligomeric state of terminases, which, like portal proteins, form ring-like structures. The number of subunits in a hollow oligomeric protein defines the internal diameter of the central channel and the ability to fit DNA inside. Thus, knowledge of the exact stoichiometrymore » of terminases is critical to decipher the mechanisms of terminase-dependent DNA translocation. Here, the gene encoding bacteriophage P22 S-terminase in Escherichia coli has been overexpressed and the protein purified under native conditions. In the absence of detergents and/or denaturants that may cause disassembly of the native oligomer and formation of aberrant rings, it was found that P22 S-terminase assembles into a concentration-independent nonamer of {approx}168 kDa. Nonameric S-terminase was crystallized in two different crystal forms at neutral pH. Crystal form I belonged to space group P2{sub 1}2{sub 1}2, with unit-cell parameters a = 144.2, b = 144.2, c = 145.3 {angstrom}, and diffracted to 3.0 {angstrom} resolution. Crystal form II belonged to space group P2{sub 1}, with unit-cell parameters a = 76.48, b = 100.9, c = 89.95 {angstrom}, {beta} = 93.73{sup o}, and diffracted to 1.75 {angstrom} resolution. Preliminary crystallographic analysis of crystal form II confirms that the S-terminase crystals contain a nonamer in the asymmetric unit and are suitable for high-resolution structure determination.« less