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

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

Dechene, Michelle; Wink, Glenna; Smith, Mychal

2010-11-12

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

On the purification and preliminary crystallographic analysis of isoquinoline 1-oxidoreductase from Brevundimonas diminuta 7

PubMed Central

Boer, D. Roeland; Müller, Axel; Fetzner, Susanne; Lowe, David J.; Romão, Maria João

2005-01-01

Isoquinoline 1-oxidoreductase (IOR) from Brevundimonas diminuta is a mononuclear molybdoenzyme of the xanthine-dehydrogenase family of proteins and catalyzes the conversion of isoquinoline to isoquinoline-1-one. Its primary sequence and behaviour, specifically in its substrate specificity and lipophilicity, differ from other members of the family. A crystal structure of the enzyme is expected to provide an explanation for these differences. This paper describes the crystallization and preliminary X-ray diffraction experiments as well as an optimized purification protocol for IOR. Crystallization of IOR was achieved using two different crystallization buffers. Streak-seeding and cross-linking were essential to obtain well diffracting crystals. Suitable cryo-conditions were found and a structure solution was obtained by molecular replacement. However, phases need to be improved in order to obtain a more interpretable electron-density map. PMID:16508115

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

PubMed

Atahan-Evrenk, Sule; Aspuru-Guzik, Alán

2014-01-01

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

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.

Free-falling Crystals: Biological Macromolecular Crystal Growth Studies in Low Earth Orbit

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, E. H.; Pusey, M. L.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

Spacecraft orbiting the earth experience a reduced acceleration environment due to being in a state of continuous free-fall. This state colloquially termed microgravity, has produced improved X-ray diffraction quality crystals of biological macromolecules. Improvements in X-ray diffraction resolution (detail) or signal to noise, provide greater detail in the three-dimensional molecular structure providing information about the molecule, how it works, how to improve its function or how to impede it. Greater molecular detail obtained by crystallization in microgravity, has important implications for structural biology. In this article we examine the theories behind macromolecule crystal quality improvement in microgravity using results obtained from studies with the model protein, chicken egg white lysozyme.

Seeding for sirtuins: microseed matrix seeding to obtain crystals of human Sirt3 and Sirt2 suitable for soaking

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

Rumpf, Tobias; Gerhardt, Stefan; Einsle, Oliver, E-mail: einsle@biochemie.uni-freiburg.de

2015-11-18

In the present study, microseed matrix seeding was successfully applied to obtain a large number of crystals of the human sirtuin isotypes Sirt2 and Sirt3. These crystals appeared predictably in diverse crystallization conditions, diffracted to a higher resolution than reported in the literature and were subsequently used to study the protein–ligand interactions of two indole inhibitors. Sirtuins constitute a family of NAD{sup +}-dependent enzymes that catalyse the cleavage of various acyl groups from the ∊-amino group of lysines. They regulate a series of cellular processes and their misregulation has been implicated in various diseases, making sirtuins attractive drug targets. Tomore » date, only a few sirtuin modulators have been reported that are suitable for cellular research and their development has been hampered by a lack of structural information. In this work, microseed matrix seeding (MMS) was used to obtain crystals of human Sirt3 in its apo form and of human Sirt2 in complex with ADP ribose (ADPR). Crystal formation using MMS was predictable, less error-prone and yielded a higher number of crystals per drop than using conventional crystallization screening methods. The crystals were used to solve the crystal structures of apo Sirt3 and of Sirt2 in complex with ADPR at an improved resolution, as well as the crystal structures of Sirt2 in complex with ADPR and the indoles EX527 and CHIC35. These Sirt2–ADPR–indole complexes unexpectedly contain two indole molecules and provide novel insights into selective Sirt2 inhibition. The MMS approach for Sirt2 and Sirt3 may be used as the basis for structure-based optimization of Sirt2/3 inhibitors in the future.« less

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

PubMed

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

2015-04-01

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

Carboplatin binding to histidine

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

Tanley, Simon W. M.; Diederichs, Kay; Kroon-Batenburg, Loes M. J.

An X-ray crystal structure showing the binding of purely carboplatin to histidine in a model protein has finally been obtained. This required extensive crystallization trials and various novel crystal structure analyses. Carboplatin is a second-generation platinum anticancer agent used for the treatment of a variety of cancers. Previous X-ray crystallographic studies of carboplatin binding to histidine (in hen egg-white lysozyme; HEWL) showed the partial conversion of carboplatin to cisplatin owing to the high NaCl concentration used in the crystallization conditions. HEWL co-crystallizations with carboplatin in NaBr conditions have now been carried out to confirm whether carboplatin converts to the brominemore » form and whether this takes place in a similar way to the partial conversion of carboplatin to cisplatin observed previously in NaCl conditions. Here, it is reported that a partial chemical transformation takes place but to a transplatin form. Thus, to attempt to resolve purely carboplatin binding at histidine, this study utilized co-crystallization of HEWL with carboplatin without NaCl to eliminate the partial chemical conversion of carboplatin. Tetragonal HEWL crystals co-crystallized with carboplatin were successfully obtained in four different conditions, each at a different pH value. The structural results obtained show carboplatin bound to either one or both of the N atoms of His15 of HEWL, and this particular variation was dependent on the concentration of anions in the crystallization mixture and the elapsed time, as well as the pH used. The structural details of the bound carboplatin molecule also differed between them. Overall, the most detailed crystal structure showed the majority of the carboplatin atoms bound to the platinum centre; however, the four-carbon ring structure of the cyclobutanedicarboxylate moiety (CBDC) remained elusive. The potential impact of the results for the administration of carboplatin as an anticancer agent are described.« less

Highly sensitive quartz crystal microbalance based biosensor using Au dendrite structure

NASA Astrophysics Data System (ADS)

Asai, Naoto; Terasawa, Hideaki; Shimizu, Tomohiro; Shingubara, Shoso; Ito, Takeshi

2018-02-01

A Au dendrite structure was obtained by only electroplating under a suitable potential. A blanch like nanostructure was formed along the crystal orientation. In this study, we attempted to fabricate a Au dendrite structure on the electrode of a quartz crystal by electroplating to increase the specific surface area. We estimated the effective surface area by cyclic voltammetry (CV) and monitored the frequency shift induced by antigen-antibody interaction by the quartz crystal microbalance (QCM) method. The dendrite structure with the largest surface area was formed under -0.95 V for 5 min. In the measurement of the antigen-antibody interaction, the frequency shifts of 40, 80, and 110 Hz were obtained with the dendrite structured QCM chips formed at the above potential for 1, 1.5, and 2.0 min, respectively. The sensitivity was improved compared with that QCM chip having a flat surface electrode.

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

σ-Hole and π-Hole Synthon Mimicry in Third-Generation Crystal Engineering: Design of Elastic Crystals.

PubMed

Saha, Subhankar; Desiraju, Gautam R

2017-04-06

Designing elastic crystals is a difficult task and is of relevance in potential applications from materials to biology. Here, multi-step crystal engineering based on σ-hole and π-hole synthon mimicry is performed to obtain binary organic molecular crystals with a high degree of flexibility. A structural model is proposed based only on σ-hole-oriented type-II halogen bonds with their characteristic orthogonal geometry. These σ-hole contacts are then partly replaced by chemically and geometrically similar π-hole synthons to obtain new crystals in the second step. In the final step, all the σ-hole interactions are replaced with π-hole interactions and elastic crystals of non-halogenated compounds are obtained. All the crystals obtained according to our protocols are found to be elastic. When crystals that do not conform to the desired structure type appeared, they were found to be brittle. This underlines the role of orthogonal-type interactions, whether they are of the σ-hole or π-hole type, in achieving elasticity. This is the first report in which π-hole interactions are used for property engineering. This example may illustrate a new generation of crystal engineering in which a particular property is associated more with topological rather than chemical attributes, although the significance of the latter cannot be completely excluded. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improving the Quality of Protein Crystals Using Stirring Crystallization

NASA Astrophysics Data System (ADS)

Adachi, Hiroaki; Matsumura, Hiroyoshi; Niino, Ai; Takano, Kazufumi; Kinoshita, Takayoshi; Warizaya, Masaichi; Inoue, Tsuyoshi; Mori, Yusuke; Sasaki, Takatomo

2004-04-01

Recent reports state that a high magnetic field improves the crystal quality of bovine adenosine deaminase (ADA) with an inhibitor [Kinoshita et al.: Acta Cryst. D59 (2003) 1333]. In this paper, we examine the effect of stirring solution on ADA crystallization using a vapor-diffusion technique with rotary and figure-eight motion shakers. The probability of obtaining high-quality crystals is increased with stirring in a figure-eight pattern. Furthermore, rotary stirring greatly increased the probability of obtaining high-quality crystals, however, nucleation time was also increased. The crystal structure with the inhibitor was determined at a high resolution using a crystal obtained from a stirred solution. These results indicate that stirring with simple equipment is as useful as the high magnetic field technique for protein crystallization.

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.

Cracking a chemical conundrum

NASA Astrophysics Data System (ADS)

Adams, James M.; Ivanov, Alexandre S.; Johnson, Mark R.; Stride, John A.

2004-07-01

An everyday laboratory chemical, hexamethylbenzene (HMB) has assumed an important role in the history of molecular structure and crystallography. It was one of the first organic crystal structures to be solved and provided direct experimental proof for the hypothesis of planarity in aromatic systems. Very soon after this, HMB was found to undergo a phase transition at 117K, resulting in crystal shattering. Since then, many attempts have been made to obtain the low-temperature structure, but none have succeeded until now. Making use of the unique properties of the neutron, we have performed powder diffraction measurements to obtain the low-temperature crystal structure and inelastic measurements to determine the dynamics of the system. These experiments have been augmented by the use of ab initio calculations and molecular modelling to obtain a complete picture of HMB in the solid state.

The amino-terminal structure of human fragile X mental retardation protein obtained using precipitant-immobilized imprinted polymers

NASA Astrophysics Data System (ADS)

Hu, Yufeng; Chen, Zhenhang; Fu, Yanjun; He, Qingzhong; Jiang, Lun; Zheng, Jiangge; Gao, Yina; Mei, Pinchao; Chen, Zhongzhou; Ren, Xueqin

2015-03-01

Flexibility is an intrinsic property of proteins and essential for their biological functions. However, because of structural flexibility, obtaining high-quality crystals of proteins with heterogeneous conformations remain challenging. Here, we show a novel approach to immobilize traditional precipitants onto molecularly imprinted polymers (MIPs) to facilitate protein crystallization, especially for flexible proteins. By applying this method, high-quality crystals of the flexible N-terminus of human fragile X mental retardation protein are obtained, whose absence causes the most common inherited mental retardation. A novel KH domain and an intermolecular disulfide bond are discovered, and several types of dimers are found in solution, thus providing insights into the function of this protein. Furthermore, the precipitant-immobilized MIPs (piMIPs) successfully facilitate flexible protein crystal formation for five model proteins with increased diffraction resolution. This highlights the potential of piMIPs for the crystallization of flexible proteins.

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

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

PubMed

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

2016-02-26

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

Structural investigation of the β-cyclodextrin complexes with chiral bicyclic monoterpenes - Influence of the functionality group on the host-guest stoichiometry

NASA Astrophysics Data System (ADS)

Ceborska, Magdalena

2017-10-01

The crystal structures of the complexes of β-cyclodextrin with (+)- and (-)-camphors are presented. The comparison of the obtained crystal structures with available data for other complexes of β-cyclodextrin with chiral bicyclic monoterpenes (hydrocarbon (+)-fenchene and alcohols: (-)-isopinocampheol, and (+)-, and (-)-borneols) obtained from Cambridge Structural Database (CSD) shows the trend of alcohols to form dimeric complexes of 2:3 stoichiometry, while hydrocarbons and ketones prefer to form 2:2 host-guest inclusion complexes.

Crystal structure of minoxidil at low temperature and polymorph prediction.

PubMed

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

2008-02-01

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

Structural, spectroscopic and DFT study of 4-methoxybenzohydrazide Schiff bases. A new series of polyfunctional ligands.

PubMed

Ferraresi-Curotto, Verónica; Echeverría, Gustavo A; Piro, Oscar E; Pis-Diez, Reinaldo; González-Baró, Ana C

2015-02-25

Five Schiff bases obtained from condensation of 4-methoxybenzohydrazide with related aldehydes, namely o-vanillin, vanillin, 5-bromovanillin, 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde were prepared. A detailed structural and spectroscopic study is reported. The crystal structures of four members of the family were determined and compared with one another. The hydrazones obtained from 5-chlorosalicylaldehyde and 5-bromosalicylaldehyde resulted to be isomorphic to each other. The solid-state structures are stabilized by intra-molecular O-H⋯N interactions in salicylaldehyde derivatives between the O-H moiety from the aldehyde and the hydrazone nitrogen atom. All crystals are further stabilized by inter-molecular H-bonds mediated by the crystallization water molecule. A comparative analysis between experimental and theoretical results is presented. The conformational space was searched and geometries were optimized both in gas phase and including solvent effects. The structure is predicted for the compound for which the crystal structure was not determined. Infrared and electronic spectra were measured and assigned with the help of data obtained from computational methods based on the Density Functional Theory. Copyright © 2014 Elsevier B.V. All rights reserved.

Key structure-activity relationships in the vanadium phosphorus oxide catalyst system

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

Thompson, M.R.; Ebner, J.R.

1990-04-01

The crystal structure of vanadyl pyrophosphate has been redetermined using single crystals obtained from a near solidified melt of a microcrystalline catalyst sample. Crystals that index as vanadyl pyrophosphate obtained from this melt are variable in color. Crystallographic refinement of the single crystal x-ray diffraction data indicates that structural differences among these materials can be described in terms of crystal defects associated with linear disorder of the vanadium atoms. The importance of the disorder is outlined in the context of its effect on the proposed surface topology parallel to (1,0,0). Models of the surface topology simply and intuitively account formore » the non-stoichometric surface atomic P/V ratio exhibited by selective catalysts of this phase. These models also point to the possible role of the excess phosphorus in providing site isolation of reactive centers at the surface. 33 refs., 7 figs.« less

Tackling both the player and the ball: lessons from crystallographic studies on the N-utilization substance B (NusB) from Mycobacterium tuberculosis

NASA Astrophysics Data System (ADS)

Haire, L. F.; Gopal, B.

2001-11-01

The N-utilization substance B (NusB) from Mycobacterium tuberculosis is an important element in a complex assembly of other proteins and ribonucleic acid effecting transcription antitermination in this organism. The cloning and overexpression of the protein in E. coli, followed by the purification, crystallization, and use of selenomethionine samples to obtain phase information by anomalous dispersion techniques, allows us to investigate the fine interplay of sample engineering and modification of crystallization parameters leading to successful structure determination. Knowledge of the crystal structure and the surface properties of the protein allows an analysis of the packing of the NusB dimers in the crystal lattice. This exercise, albeit post facto, helps to demonstrate how biophysical and functional information could help 'rationalize' the course of obtaining protein crystals suitable for structural studies.

A hybrid phononic crystal for roof application.

PubMed

Wan, Qingmian; Shao, Rong

2017-11-01

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

Protein crystallization: Eluding the bottleneck of X-ray crystallography

PubMed Central

Holcomb, Joshua; Spellmon, Nicholas; Zhang, Yingxue; Doughan, Maysaa; Li, Chunying; Yang, Zhe

2017-01-01

To date, X-ray crystallography remains the gold standard for the determination of macromolecular structure and protein substrate interactions. However, the unpredictability of obtaining a protein crystal remains the limiting factor and continues to be the bottleneck in determining protein structures. A vast amount of research has been conducted in order to circumvent this issue with limited success. No single method has proven to guarantee the crystallization of all proteins. However, techniques using antibody fragments, lipids, carrier proteins, and even mutagenesis of crystal contacts have been implemented to increase the odds of obtaining a crystal with adequate diffraction. In addition, we review a new technique using the scaffolding ability of PDZ domains to facilitate nucleation and crystal lattice formation. Although in its infancy, such technology may be a valuable asset and another method in the crystallography toolbox to further the chances of crystallizing problematic proteins. PMID:29051919

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.

Fe-Al alloy single-crystal thin film preparation for basic magnetic measurements

NASA Astrophysics Data System (ADS)

Abe, Tatsuya; Kawai, Tetsuroh; Futamoto, Masaaki; Ohtake, Mitsuru; Inaba, Nobuyuki

2018-04-01

Fe100-xAlx (x = 0, 4, 10, 20, 30 at. %) alloy films of 40 nm thickness are prepared on MgO(001) single-crystal substrates by varying substrate temperature from room temperature to 600 °C. Single-crystal films of (001) orientation with bcc-based disordered A2 structure are obtained for the Al content range of x = 0 - 20 at. %. An ordered phase of DO3 structure is observed in Fe70Al30 films prepared at temperatures higher than 200 °C, whereas (001) oriented single-crystal films of A2 structure are obtained when prepared at room temperature. The film surface profile does not depend much on the film composition, while the surface roughness increases with increasing substrate temperature. Island-like crystals are observed for films prepared at 600°C for all compositions. Difference in lattice spacing measured parallel and perpendicular to the substrate is noted for the single-crystal thin films and it increases with increasing Al content. The lattice strain in single-crystal film is caused possibly to accommodate the lattice mismatch with the MgO substrate. The (001)-oriented single-crystal films with A2 structure show four-fold symmetries in in-plane magnetic anisotropy with the easy magnetization axis A2[100] and the hard magnetization axis A2[110], whereas the films with DO3 ordered structure show almost isotropic magnetic properties.

The Nucleation and Growth of Protein Crystals

NASA Technical Reports Server (NTRS)

Pusey, Marc

2004-01-01

Obtaining crystals of suitable size and high quality continues to be a major bottleneck in macromolecular crystallography. Currently, structural genomics efforts are achieving on average about a 10% success rate in going from purified protein to a deposited crystal structure. Growth of crystals in microgravity was proposed as a means of overcoming size and quality problems, which subsequently led to a major NASA effort in microgravity crystal growth, with the agency also funding research into understanding the process. Studies of the macromolecule crystal nucleation and growth process were carried out in a number of labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. Based upon experimental evidence, as well as simple starting assumptions, we have proposed that crystal nucleation occurs by a series of discrete self assembly steps, which 'set' the underlying crystal symmetry. This talk will review the model developed, and its origins, in our laboratory for how crystals nucleate and grow, and will then present, along with preliminary data, how we propose to use this model to improve the success rate for obtaining crystals from a given protein.

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

PubMed Central

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

2016-01-01

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

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

PubMed

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

2016-04-01

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

Crystal structure of zwitterionic bisimidazolium sulfonates

NASA Astrophysics Data System (ADS)

Kohmoto, Shigeo; Okuyama, Shinpei; Yokota, Nobuyuki; Takahashi, Masahiro; Kishikawa, Keiki; Masu, Hyuma; Azumaya, Isao

2012-05-01

Crystal structures of three zwitterionic bisimidazolium salts 1-3 in which imidazolium sulfonate moieties were connected with aromatic linkers, p-xylylene, 4,4'-dimethylenebiphenyl, and phenylene, respectively, were examined. The latter two were obtained as hydrates. An S-shaped molecular structure in which the sulfonate moiety was placed on the imidazolium ring was observed for 1. A helical array of hydrated water molecules was obtained for 2 while a linear array of hydrated water molecules was observed for 3.

Crystal Structures of the β2-Adrenergic Receptor

NASA Astrophysics Data System (ADS)

Weis, William I.; Rosenbaum, Daniel M.; Rasmussen, Søren G. F.; Choi, Hee-Jung; Thian, Foon Sun; Kobilka, Tong Sun; Yao, Xiao-Jie; Day, Peter W.; Parnot, Charles; Fung, Juan J.; Ratnala, Venkata R. P.; Kobilka, Brian K.; Cherezov, Vadim; Hanson, Michael A.; Kuhn, Peter; Stevens, Raymond C.; Edwards, Patricia C.; Schertler, Gebhard F. X.; Burghammer, Manfred; Sanishvili, Ruslan; Fischetti, Robert F.; Masood, Asna; Rohrer, Daniel K.

G protein coupled receptors (GPCRs) constitute the largest family of membrane proteins in the human genome, and are responsible for the majority of signal transduction events involving hormones and neuro-transmitters across the cell membrane. GPCRs that bind to diffusible ligands have low natural abundance, are relatively unstable in detergents, and display basal G protein activation even in the absence of ligands. To overcome these problems two approaches were taken to obtain crystal structures of the β2-adrenergic receptor (β2AR), a well-characterized GPCR that binds cate-cholamine hormones. The receptor was bound to the partial inverse agonist carazolol and co-crystallized with a Fab made to a three-dimensional epitope formed by the third intracellular loop (ICL3), or by replacement of ICL3 with T4 lysozyme. Small crystals were obtained in lipid bicelles (β2AR-Fab) or lipidic cubic phase (β2AR-T4 lysozyme), and diffraction data were obtained using microfocus technology. The structures provide insights into the basal activity of the receptor, the structural features that enable binding of diffusible ligands, and the coupling between ligand binding and G-protein activation.

Structure of Bacillus halmapalus α-amylase crystallized with and without the substrate analogue acarbose and maltose

PubMed Central

Lyhne-Iversen, Louise; Hobley, Timothy J.; Kaasgaard, Svend G.; Harris, Pernille

2006-01-01

Recombinant Bacillus halmapalus α-amylase (BHA) was studied in two different crystal forms. The first crystal form was obtained by crystallization of BHA at room temperature in the presence of acarbose and maltose; data were collected at cryogenic temperature to a resolution of 1.9 Å. It was found that the crystal belonged to space group P212121, with unit-cell parameters a = 47.0, b = 73.5, c = 151.1 Å. A maltose molecule was observed and found to bind to BHA and previous reports of the binding of a nonasaccharide were confirmed. The second crystal form was obtained by pH-induced crystallization of BHA in a MES–HEPES–boric acid buffer (MHB buffer) at 303 K; the solubility of BHA in MHB has a retrograde temperature dependency and crystallization of BHA was only possible by raising the temperature to at least 298 K. Data were collected at cryogenic temperature to a resolution of 2.0 Å. The crystal belonged to space group P212121, with unit-cell parameters a = 38.6, b = 59.0, c = 209.8 Å. The structure was solved using molecular replacement. The maltose-binding site is described and the two structures are compared. No significant changes were seen in the structure upon binding of the substrates. PMID:16946462

Study of Fluid Flow Control In Protein Crystallization Using Strong Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F.; Ciszak, E.; Curreri, Peter A. (Technical Monitor)

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in 'microgravity', researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined.

Conformational flexibility and packing plausibility of repaglinide polymorphs

NASA Astrophysics Data System (ADS)

Rani, Dimpy; Goyal, Parnika; Chadha, Renu

2018-04-01

The present manuscript highlights the structural insight into the repaglinide polymorphs. The experimental screening for the possible crystal forms were carried out using various solvents, which generated three forms. The crystal structure of Form II and III was determined using PXRD pattern whereas structural analysis of Form I has already been reported. Form I, II and II was found to exist in P212121, PNA21 and P21/c space groups respectively. Conformational analysis was performed to account the conformational flexibility of RPG. The obtained conformers were further utilized to obtain the information about the crystal packing pattern of RPG polymorphs by polymorph prediction module. The lattice energy landscape, depicting the relationship between lattice energy and density of the polymorphs has been obtained for various possible polymorphs. The experimentally isolated polymorphs were successfully fitted into lattice energy landscape.

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

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

Finite element method analysis of band gap and transmission of two-dimensional metallic photonic crystals at terahertz frequencies.

PubMed

Degirmenci, Elif; Landais, Pascal

2013-10-20

Photonic band gap and transmission characteristics of 2D metallic photonic crystals at THz frequencies have been investigated using finite element method (FEM). Photonic crystals composed of metallic rods in air, in square and triangular lattice arrangements, are considered for transverse electric and transverse magnetic polarizations. The modes and band gap characteristics of metallic photonic crystal structure are investigated by solving the eigenvalue problem over a unit cell of the lattice using periodic boundary conditions. A photonic band gap diagram of dielectric photonic crystal in square lattice array is also considered and compared with well-known plane wave expansion results verifying our FEM approach. The photonic band gap designs for both dielectric and metallic photonic crystals are consistent with previous studies obtained by different methods. Perfect match is obtained between photonic band gap diagrams and transmission spectra of corresponding lattice structure.

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

NASA Astrophysics Data System (ADS)

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

2017-12-01

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

7A projection map of the S-layer protein sbpA obtained with trehalose-embedded monolayer crystals.

PubMed

Norville, Julie E; Kelly, Deborah F; Knight, Thomas F; Belcher, Angela M; Walz, Thomas

2007-12-01

Two-dimensional crystallization on lipid monolayers is a versatile tool to obtain structural information of proteins by electron microscopy. An inherent problem with this approach is to prepare samples in a way that preserves the crystalline order of the protein array and produces specimens that are sufficiently flat for high-resolution data collection at high tilt angles. As a test specimen to optimize the preparation of lipid monolayer crystals for electron microscopy imaging, we used the S-layer protein sbpA, a protein with potential for designing arrays of both biological and inorganic materials with engineered properties for a variety of nanotechnology applications. Sugar embedding is currently considered the best method to prepare two-dimensional crystals of membrane proteins reconstituted into lipid bilayers. We found that using a loop to transfer lipid monolayer crystals to an electron microscopy grid followed by embedding in trehalose and quick-freezing in liquid ethane also yielded the highest resolution images for sbpA lipid monolayer crystals. Using images of specimens prepared in this way we could calculate a projection map of sbpA at 7A resolution, one of the highest resolution projection structures obtained with lipid monolayer crystals to date.

Transmission electron microscopy: direct observation of crystal structure in refractory ceramics.

PubMed

Shaw, T M; Thomas, G

1978-11-10

Using high-resolution multibeam interference techniques in the transmission electron microscope, images have been obtained that make possible a real-space structure analysis of a beryllium-silicon-nitrogen compound. The results illustrate the usefulness of lattice imaging in the analysis of local crystal structure in these technologically promising ceramic materials.

Radial wave crystals: radially periodic structures from anisotropic metamaterials for engineering acoustic or electromagnetic waves.

PubMed

Torrent, Daniel; Sánchez-Dehesa, José

2009-08-07

We demonstrate that metamaterials with anisotropic properties can be used to develop a new class of periodic structures that has been named radial wave crystals. They can be sonic or photonic, and wave propagation along the radial directions is obtained through Bloch states like in usual sonic or photonic crystals. The band structure of the proposed structures can be tailored in a large amount to get exciting novel wave phenomena. For example, it is shown that acoustical cavities based on radial sonic crystals can be employed as passive devices for beam forming or dynamically orientated antennas for sound localization.

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

PubMed Central

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; Stellato, Francesco; Chiu, Elaine; Yeh, Shin-Mei; Aquila, Andrew; Basu, Shibom; Bean, Richard; Beyerlein, Kenneth R.; Botha, Sabine; Boutet, Sébastien; DePonte, Daniel P.; Doak, R. Bruce; Fromme, Raimund; Galli, Lorenzo; Grotjohann, Ingo; James, Daniel R.; Kupitz, Christopher; Lomb, Lukas; Messerschmidt, Marc; Nass, Karol; Rendek, Kimberly; Shoeman, Robert L.; Wang, Dingjie; Weierstall, Uwe; White, Thomas A.; Williams, Garth J.; Zatsepin, Nadia A.; Fromme, Petra; Spence, John C. H.; Goldie, Kenneth N.; Jehle, Johannes A.; Metcalf, Peter; Barty, Anton

2017-01-01

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam is often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach. PMID:28202732

Atomic structure of granulin determined from native nanocrystalline granulovirus using an X-ray free-electron laser

DOE PAGES

Gati, Cornelius; Oberthuer, Dominik; Yefanov, Oleksandr; ...

2017-02-15

To understand how molecules function in biological systems, new methods are required to obtain atomic resolution structures from biological material under physiological conditions. Intense femtosecond-duration pulses from X-ray free-electron lasers (XFELs) can outrun most damage processes, vastly increasing the tolerable dose before the specimen is destroyed. This in turn allows structure determination from crystals much smaller and more radiation sensitive than previously considered possible, allowing data collection from room temperature structures and avoiding structural changes due to cooling. Regardless, high-resolution structures obtained from XFEL data mostly use crystals far larger than 1 μm3 in volume, whereas the X-ray beam ismore » often attenuated to protect the detector from damage caused by intense Bragg spots. Here, we describe the 2 Å resolution structure of native nanocrystalline granulovirus occlusion bodies (OBs) that are less than 0.016 μm3 in volume using the full power of the Linac Coherent Light Source (LCLS) and a dose up to 1.3 GGy per crystal. The crystalline shell of granulovirus OBs consists, on average, of about 9,000 unit cells, representing the smallest protein crystals to yield a high-resolution structure by X-ray crystallography to date. The XFEL structure shows little to no evidence of radiation damage and is more complete than a model determined using synchrotron data from recombinantly produced, much larger, cryocooled granulovirus granulin microcrystals. Furthermore, our measurements suggest that it should be possible, under ideal experimental conditions, to obtain data from protein crystals with only 100 unit cells in volume using currently available XFELs and suggest that single-molecule imaging of individual biomolecules could almost be within reach.« less

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.

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

NASA Astrophysics Data System (ADS)

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

2015-06-01

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

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

NASA Astrophysics Data System (ADS)

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

2014-09-01

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

A first principles prediction of the crystal structure of C6Br2ClFH2

NASA Astrophysics Data System (ADS)

Misquitta, Alston J.; Welch, Gareth W. A.; Stone, Anthony J.; Price, Sarah L.

2008-04-01

We have constructed an intermolecular potential for the 1,3-dibromo-2-chloro-5-fluorobenzene molecule from first principles using SAPT(DFT) interaction energy calculations and the Williams-Stone-Misquitta method for obtaining molecular properties in distributed form. This molecule was included in the fourth Blind Test of crystal structure prediction organised by the Cambridge Crystallographic Data Centre. Using our potential, we have predicted the crystal structure of CBrClFH and found the lowest energy solution to be in excellent agreement with the experimentally observed crystal when it was subsequently revealed.

Cytotoxicity of copper(II)-complexes with some S-alkyl derivatives of thiosalicylic acid. Crystal structure of the binuclear copper(II)-complex with S-ethyl derivative of thiosalicylic acid

NASA Astrophysics Data System (ADS)

Nikolić, Miloš V.; Mijajlović, Marina Ž.; Jevtić, Verica V.; Ratković, Zoran R.; Novaković, Slađana B.; Bogdanović, Goran A.; Milovanović, Jelena; Arsenijević, Aleksandar; Stojanović, Bojana; Trifunović, Srećko R.; Radić, Gordana P.

2016-07-01

The spectroscopically predicted structure of the obtained copper(II)-complex with S-ethyl derivative of thiosalicylic acid was confirmed by X-ray structural study and compared to previously reported crystal structure of the Cu complex with S-methyl derivative. Single crystals suitable for X-ray measurements were obtained by slow crystallization from a water solution. Cytotoxic effects of S-alkyl (R = benzyl (L1), methyl (L2), ethyl (L3), propyl (L4) and butyl (L5)) derivatives of thiosalicylic acid and the corresponding binuclear copper(II)-complexes on murine colon carcinoma cell lines, CT26 and CT26.CL25 and human colon carcinoma cell line HCT-116 were reported here. The analysis of cancer cell viability showed that all the tested complexes had low cytotoxic effect on murine colon carcinoma cell lines, but several times higher cytotoxicity on normal human colon carcinoma cells.

Growth Temperature Dependence of Morphology of GaN Single Crystals in the Na-Li-Ca Flux Method

NASA Astrophysics Data System (ADS)

Wu, Xi; Hao, Hangfei; Li, Zhenrong; Fan, Shiji; Xu, Zhuo

2018-02-01

In this paper, the effect of growth temperature on the morphology and transparency of the GaN crystals obtained by the Li-Ca-added Na Flux method was studied. Addition of Li-Ca was attempted to control the growth habit and further improve transparency of GaN crystals. The samples with wurtzite structure of GaN were confirmed by the x-ray powder diffraction analysis. GaN single crystal with maximum size of about 6 mm was grown at 750°C. As the growth temperature was increased from 700°C to 850°C, the morphology of the crystals changed from pyramid to prism, and their surfaces became smooth. It was found that high growth temperature was beneficial to obtain a transparent crystal, but the evaporation of sodium would suppress its further growth. The E 2 (high) mode in the Raman spectra was at 568 cm-1, and the full-width at half-maximum values of this peak for the crystals obtained at 700°C, 750°C, 800°C, and 850°C were 7.5 cm-1, 10.3 cm-1, 4.4 cm-1, and 4.0 cm-1, respectively. It indicates that all the crystals are stress free and the transparent crystal grown at high temperature has high structural quality or low impurity concentrations.

Discovery of a diamond-based photonic crystal structure in beetle scales.

PubMed

Galusha, Jeremy W; Richey, Lauren R; Gardner, John S; Cha, Jennifer N; Bartl, Michael H

2008-05-01

We investigated the photonic crystal structure inside iridescent scales of the weevil Lamprocyphus augustus. By combining a high-resolution structure analysis technique based on sequential focused ion beam milling and scanning electron microscopy imaging with theoretical modeling and photonic band-structure calculations, we discovered a natural three-dimensional photonic structure with a diamond-based crystal lattice operating at visible wavelengths. Moreover, we found that within individual scales, the diamond-based structure is assembled in the form of differently oriented single-crystalline micrometer-sized pixels with only selected lattice planes facing the scales' top surface. A comparison of results obtained from optical microreflectance measurements with photonic band-structure calculations reveals that it is this sophisticated microassembly of the diamond-based crystal lattice that lends Lamprocyphus augustus its macroscopically near angle-independent green coloration.

High-throughput crystallization screening.

PubMed

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

2014-01-01

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

Growing Larger Crystals for Neutron Diffraction

NASA Technical Reports Server (NTRS)

Pusey, Marc

2003-01-01

Obtaining crystals of suitable size and high quality has been a major bottleneck in macromolecular crystallography. With the advent of advanced X-ray sources and methods the question of size has rapidly dwindled, almost to the point where if one can see the crystal then it was big enough. Quality is another issue, and major national and commercial efforts were established to take advantage of the microgravity environment in an effort to obtain higher quality crystals. Studies of the macromolecule crystallization process were carried out in many labs in an effort to understand what affected the resultant crystal quality on Earth, and how microgravity improved the process. While technological improvements are resulting in a diminishing of the minimum crystal size required, neutron diffraction structural studies still require considerably larger crystals, by several orders of magnitude, than X-ray studies. From a crystal growth physics perspective there is no reason why these 'large' crystals cannot be obtained: the question is generally more one of supply than limitations mechanism. This talk will discuss our laboratory s current model for macromolecule crystal growth, with highlights pertaining to the growth of crystals suitable for neutron diffraction studies.

Satellite Tobacco Mosaic Virus Structure

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Crystal growth and electronic structure of low-temperature phase SrMgF{sub 4}

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

Atuchin, Victor V.; Functional Electronics Laboratory, Tomsk State University, Tomsk 634050; Laboratory of Semiconductor and Dielectric Materials, Novosibirsk State University, Novosibirsk 630090

2016-04-15

Using the vertical Bridgman method, the single crystal of low temperature phase SrMgF{sub 4} is obtained. The crystal is in a very good optical quality with the size of 10×7×5 mm{sup 3}. Detailed photoemission spectra of the element core levels are determined by a monochromatic AlKa (1486.6 eV) X-ray source. Moreover, the first-principles calculations are performed to investigate the electronic structure of SrMgF{sub 4}. A good agreement between experimental and calculated results is achieved. It is demonstrated that almost all the electronic orbitals are strongly localized and the hybridization with the others is very small, but the Mg–F bonds covalencymore » is relatively stronger than that of Sr–F bonds. - Graphical abstract: Large size of low-temperature phase SrMgF{sub 4} crystal was obtained (right) and its electronic structure was investigated by X-ray photoelectron spectroscopy and first-principles calculation (left). - Highlights: • Large size single crystal of low-temperature phase SrMgF{sub 4} is obtained. • Electronic structure of SrMgF{sub 4} is measured by X-ray photoelectron spectroscopy. • Partial densities of states are determined by first-principles calculation. • Good agreement between experimental and calculated results is achieved. • Strong ionic characteristics of chemical bonds are exhibited in SrMgF{sub 4}.« less

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

PubMed

Krishnaswamy, Shobhana; Shashidhar, Mysore S

2018-04-06

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

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Crystallization of Proteins from Crude Bovine Rod Outer Segments☆

PubMed Central

Baker, Bo Y.; Gulati, Sahil; Shi, Wuxian; Wang, Benlian; Stewart, Phoebe L.; Palczewski, Krzysztof

2015-01-01

Obtaining protein crystals suitable for X-ray diffraction studies comprises the greatest challenge in the determination of protein crystal structures, especially for membrane proteins and protein complexes. Although high purity has been broadly accepted as one of the most significant requirements for protein crystallization, a recent study of the Escherichia coli proteome showed that many proteins have an inherent propensity to crystallize and do not require a highly homogeneous sample (Totir et al., 2012). As exemplified by RPE65 (Kiser, Golczak, Lodowski, Chance, & Palczewski, 2009), there also are cases of mammalian proteins crystallized from less purified samples. To test whether this phenomenon can be applied more broadly to the study of proteins from higher organisms, we investigated the protein crystallization profile of bovine rod outer segment (ROS) crude extracts. Interestingly, multiple protein crystals readily formed from such extracts, some of them diffracting to high resolution that allowed structural determination. A total of seven proteins were crystallized, one of which was a membrane protein. Successful crystallization of proteins from heterogeneous ROS extracts demonstrates that many mammalian proteins also have an intrinsic propensity to crystallize from complex biological mixtures. By providing an alternative approach to heterologous expression to achieve crystallization, this strategy could be useful for proteins and complexes that are difficult to purify or obtain by recombinant techniques. PMID:25950977

Crystallization of Macromolecules

PubMed Central

Friedmann, David; Messick, Troy; Marmorstein, Ronen

2014-01-01

X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent . Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:22045560

Fluid Physics and Macromolecular Crystal Growth in Microgravity

NASA Technical Reports Server (NTRS)

Pusey, M.; Snell, E.; Judge, R.; Chayen, N.; Boggon, T.; Helliwell, J.; Rose, M. Franklin (Technical Monitor)

2000-01-01

The molecular structure of biological macromolecules is important in understanding how these molecules work and has direct application to rational drug design for new medicines and for the improvement and development of industrial enzymes. In order to obtain the molecular structure, large, well formed, single macromolecule crystals are required. The growth of macromolecule crystals is a difficult task and is often hampered on the ground by fluid flows that result from the interaction of gravity with the crystal growth process. One such effect is the bulk movement of the crystal through the fluid due to sedimentation. A second is buoyancy driven convection close to the crystal surface. On the ground the crystallization process itself induces both of these flows.

Crystallographic analysis of ground and space thermostable T1 lipase crystal obtained via counter diffusion method approach.

PubMed

Mohamad Aris, Sayangku Nor Ariati; Thean Chor, Adam Leow; Mohamad Ali, Mohd Shukuri; Basri, Mahiran; Salleh, Abu Bakar; Raja Abd Rahman, Raja Noor Zaliha

2014-01-01

Three-dimensional structure of thermostable lipase is much sought after nowadays as it is important for industrial application mainly found in the food, detergent, and pharmaceutical sectors. Crystallization utilizing the counter diffusion method in space was performed with the aim to obtain high resolution diffracting crystals with better internal order to improve the accuracy of the structure. Thermostable T1 lipase enzyme has been crystallized in laboratory on earth and also under microgravity condition aboard Progress spacecraft to the ISS in collaboration with JAXA (Japanese Aerospace Exploration Agency). This study is conducted with the aims of improving crystal packing and structure resolution. The diffraction data set for ground grown crystal was collected to 1.3 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.40 Å, b = 80.95 Å, and c = 99.81 Å, whereas the diffraction data set for space grown crystal was collected to 1.1 Å resolution and belonged to monoclinic C2 space group with unit cell parameters a = 117.31 Å, b = 80.85 Å, and c = 99.81 Å. The major difference between the two crystal growth systems is the lack of convection and sedimentation in microgravity environment resulted in the growth of much higher quality crystals of T1 lipase.

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

PubMed

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

2016-11-01

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

Crystallization and preliminary X-ray diffraction analysis of central structure domains from mumps virus F protein

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

Liu, Yueyong; Xu, Yanhui; Zhu, Jieqing

2005-09-01

Single crystals of the central structure domains from mumps virus F protein have been obtained by the hanging-drop vapour-diffusion method. A diffraction data set has been collected to 2.2 Å resolution. Fusion of members of the Paramyxoviridae family involves two glycoproteins: the attachment protein and the fusion protein. Changes in the fusion-protein conformation were caused by binding of the attachment protein to the cellular receptor. In the membrane-fusion process, two highly conserved heptad-repeat (HR) regions, HR1 and HR2, are believed to form a stable six-helix coiled-coil bundle. However, no crystal structure has yet been determined for this state in themore » mumps virus (MuV, a member of the Paramyxoviridae family). In this study, a single-chain protein consisting of two HR regions connected by a flexible amino-acid linker (named 2-Helix) was expressed, purified and crystallized by the hanging-drop vapour-diffusion method. A complete X-ray data set was obtained in-house to 2.2 Å resolution from a single crystal. The crystal belongs to space group C2, with unit-cell parameters a = 161.2, b = 60.8, c = 40.1 Å, β = 98.4°. The crystal structure will help in understanding the molecular mechanism of Paramyxoviridae family membrane fusion.« less

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

Hajian, Hodjat, E-mail: hodjat.hajian@bilkent.edu.tr; Ozbay, Ekmel; Department of Physics, Bilkent University, 06800 Ankara

Certain types of photonic crystals with Dirac cones at the Γ point of their band structure have a zero effective index of refraction at Dirac cone frequency. Here, by an appropriate design of the photonic structure, we obtain a strong coupling between modes around the Dirac cone frequency of an all-dielectric zero-index photonic crystal and the guided ones supported by a photonic crystal waveguide. Consequently, we experimentally demonstrate that the presence of the zero-index photonic crystal at the inner side of the photonic crystal waveguide leads to an enhancement in the transmission of some of the guided waves passing throughmore » this hybrid system. Moreover, those electromagnetic waves extracted from the structure with enhanced transmission exhibit high directional beaming due to the presence of the zero-index photonic crystal at the outer side of the photonic crystal waveguide.« less

Formation of the Structure of a Eutectic Alloy of the Nb - Si System During Directed Crystallization with Liquid-Metal Coolant

NASA Astrophysics Data System (ADS)

Bondarenko, Yu. A.; Echin, A. B.; Kolodyazhnyi, M. Yu.; Surova, V. A.

2017-11-01

Peculiarities of the structure of a refractory eutectic alloy of the Nb - Si system, formed by the method of directed crystallization with liquid-metal coolant, have been studied. Characteristic zones of microstructure of the ingot obtained upon directed crystallization are considered, the alloy composition is analyzed, and volume fractions of phases in the Nb - Si composite are determined.

Growth and characterization of β-Ga2O3 crystals

NASA Astrophysics Data System (ADS)

Nikolaev, V. I.; Maslov, V.; Stepanov, S. I.; Pechnikov, A. I.; Krymov, V.; Nikitina, I. P.; Guzilova, L. I.; Bougrov, V. E.; Romanov, A. E.

2017-01-01

Here we report on the growth and characterization of β-Ga2O3 bulk crystals and polycrystalline layer on different substrates. Bulk β-Ga2O3 crystals were produced by free crystallisation of gallium oxide melt in sapphire crucible. Transparent single crystals measuring up to 8 mm across were obtained. Good structural quality was confirmed by x-ray diffraction rocking curve FWHM values of 46″. Young's modulus, shear modulus and hardness of the β-Ga2O3 crystals were measured by nanoindentation and Vickers microindentation techniques. Polycrystalline β-Ga2O3 films were deposited on silicon and sapphire substrates by sublimation method. It was found that structure and morphology of the films were greatly influenced by the material and orientation of the substrates. The best results were achieved on a-plane sapphire substrates where predominantly (111) oriented films were obtained.

Order and disorder in crystals of hexameric NTPases from dsRNA bacteriophages.

PubMed

Mancini, Erika J; Grimes, Jonathan M; Malby, Robyn; Sutton, Geoffrey C; Kainov, Denis E; Juuti, Jarmo T; Makeyev, Eugene V; Tuma, Roman; Bamford, Dennis H; Stuart, David I

2003-12-01

The packaging of genomic RNA in members of the Cystoviridae is performed by P4, a hexameric protein with NTPase activity. Across family members such as Phi6, Phi8 and Phi13, the P4 proteins show low levels of sequence identity, but presumably have similar atomic structures. Initial structure-determination efforts for P4 from Phi6 and Phi8 were hampered by difficulties in obtaining crystals that gave ordered diffraction. Diffraction from crystals of full-length P4 showed a variety of disorder and anisotropy. Subsequently, crystals of Phi13 P4 were obtained which yielded well ordered diffraction to 1.7 A. Comparison of the packing arrangements of P4 hexamers in different crystal forms and analysis of the disorder provides insights into the flexibility of this family of proteins, which might be an integral part of their biological function.

Salvage of failed protein targets by reductive alkylation.

PubMed

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

2014-01-01

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

Salvage of Failed Protein Targets by Reductive Alkylation

PubMed Central

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

2014-01-01

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

A Maltose-Binding Protein Fusion Construct Yields a Robust Crystallography Platform for MCL1

PubMed Central

Clifton, Matthew C.; Dranow, David M.; Leed, Alison; Fulroth, Ben; Fairman, James W.; Abendroth, Jan; Atkins, Kateri A.; Wallace, Ellen; Fan, Dazhong; Xu, Guoping; Ni, Z. J.; Daniels, Doug; Van Drie, John; Wei, Guo; Burgin, Alex B.; Golub, Todd R.; Hubbard, Brian K.; Serrano-Wu, Michael H.

2015-01-01

Crystallization of a maltose-binding protein MCL1 fusion has yielded a robust crystallography platform that generated the first apo MCL1 crystal structure, as well as five ligand-bound structures. The ability to obtain fragment-bound structures advances structure-based drug design efforts that, despite considerable effort, had previously been intractable by crystallography. In the ligand-independent crystal form we identify inhibitor binding modes not observed in earlier crystallographic systems. This MBP-MCL1 construct dramatically improves the structural understanding of well-validated MCL1 ligands, and will likely catalyze the structure-based optimization of high affinity MCL1 inhibitors. PMID:25909780

Purification, crystallization and initial crystallographic characterization of the Ginkgo biloba 11S seed globulin ginnacin

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

Jin, Tengchuan; Chen, Yu-Wei; Howard, Andrew

2008-07-01

The crystallization of ginnacin, the 11S seed storage protein from G. biloba, is reported. Ginkgo biloba, a well known ‘living fossil’ native to China, is grown worldwide as an ornamental shade plant. Medicinal and nutritional uses of G. biloba in Asia have a long history. However, ginkgo seed proteins have not been well studied at the biochemical and molecular level. In this study, the G. biloba 11S seed storage protein ginnacin was purified by sequential anion-exchange and gel-filtration chromatography. A crystallization screen was performed and well diffracting single crystals were obtained by the vapor-diffusion method. A molecular-replacement structural solution hasmore » been obtained. There are six protomers in an asymmetric unit. Structure refinement is currently in progress.« less

Fingerprinting redox and ligand states in haemprotein crystal structures using resonance Raman spectroscopy.

PubMed

Kekilli, Demet; Dworkowski, Florian S N; Pompidor, Guillaume; Fuchs, Martin R; Andrew, Colin R; Antonyuk, Svetlana; Strange, Richard W; Eady, Robert R; Hasnain, S Samar; Hough, Michael A

2014-05-01

It is crucial to assign the correct redox and ligand states to crystal structures of proteins with an active redox centre to gain valid functional information and prevent the misinterpretation of structures. Single-crystal spectroscopies, particularly when applied in situ at macromolecular crystallography beamlines, allow spectroscopic investigations of redox and ligand states and the identification of reaction intermediates in protein crystals during the collection of structural data. Single-crystal resonance Raman spectroscopy was carried out in combination with macromolecular crystallography on Swiss Light Source beamline X10SA using cytochrome c' from Alcaligenes xylosoxidans. This allowed the fingerprinting and validation of different redox and ligand states, identification of vibrational modes and identification of intermediates together with monitoring of radiation-induced changes. This combined approach provides a powerful tool to obtain complementary data and correctly assign the true oxidation and ligand state(s) in redox-protein crystals.

Single crystal growth and characterization of kagomé-lattice shandites Co3Sn2-xInxS2

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2015-09-01

Single crystals of the shandite-type half metallic ferromagnet Co3Sn2S2, and its In-substituted compounds, Co3Sn2-xInxS2 (0

The crystal structure of the new ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2)

NASA Astrophysics Data System (ADS)

Fedyna, L. O.; Bodak, O. I.; Fedorchuk, A. O.; Tokaychuk, Ya. O.

2005-06-01

New ternary antimonide Dy 3Cu 20+xSb 11-x ( x≈2) was synthesized and its crystal structure was determined by direct methods from X-ray powder diffraction data (diffractometer DRON-3M, Cu Kα-radiation, R=6.99%,R=12.27%,R=11.55%). The compound crystallizes with the own cubic structure type: space group F 4¯ 3m, Pearson code cF272, a=16.6150(2) Å,Z=8. The structure of the Dy 3Cu 20Sb 11-x ( x≈2) can be obtained from the structure type BaHg 11 by doubling of the lattice parameter and subtraction of 16 atoms. The studied structure was compared with the structures of known compounds, which crystallize in the same space group with similar cell parameters.

Design considerations for a Space Shuttle Main Engine turbine blade made of single crystal material

NASA Technical Reports Server (NTRS)

Abdul-Aziz, A.; August, R.; Nagpal, V.

1993-01-01

Nonlinear finite-element structural analyses were performed on the first stage high-pressure fuel turbopump blade of the Space Shuttle Main Engine. The analyses examined the structural response and the dynamic characteristics at typical operating conditions. Single crystal material PWA-1480 was considered for the analyses. Structural response and the blade natural frequencies with respect to the crystal orientation were investigated. The analyses were conducted based on typical test stand engine cycle. Influence of combined thermal, aerodynamic, and centrifugal loadings was considered. Results obtained showed that the single crystal secondary orientation effects on the maximum principal stresses are not highly significant.

Specific features of the structural and magnetic states of a Zn1 - x Ni x Se crystal ( x = 0.0025) at low temperatures

NASA Astrophysics Data System (ADS)

Dubinin, S. F.; Sokolov, V. I.; Parkhomenko, V. D.; Teploukhov, S. G.; Gruzdev, N. B.

2008-12-01

The magnetic state and the structure of a Zn1 - x Ni x Se ( x = 0.0025) bulk crystal were studied at low temperatures. It is revealed that the magnetic and crystal structures below T ≅ 15 K are dependent on the cooling rate of this dilute semiconductor. For example, on fast cooling to 4.2 K, about 10% hexagonal ferromagnetic phase is formed in the crystal. During heating, the phase disappears at T ≅ 15 K. The results obtained are discussed with allowance for the specific features of the Jahn-Teller distortions in this compound.

Yb7Ni4InGe12: a quaternary compound having mixed valent Yb atoms grown from indium flux.

PubMed

Subbarao, Udumula; Jana, Rajkumar; Chondroudi, Maria; Balasubramanian, Mahalingam; Kanatzidis, Mercouri G; Peter, Sebastian C

2015-03-28

The new intermetallic compound Yb7Ni4InGe12 was obtained as large silver needle shaped single crystals from reactive indium flux. Single crystal X-ray diffraction suggests that Yb7Ni4InGe12 crystallizes in the Yb7Co4InGe12 structure type, and tetragonal space group P4/m and lattice constants are a = b = 10.291(2) Å and c = 4.1460(8) Å. The crystal structure of Yb7Ni4InGe12 consists of columnar units of three different types of channels filled with the Yb atoms. The crystal structure of Yb7Ni4InGe12 is closely related to Yb5Ni4Ge10. The effective magnetic moment obtained from the magnetic susceptibility measurements in the temperature range 200-300 K is 3.66μB/Yb suggests mixed/intermediate valence behavior of ytterbium atoms. X-ray absorption near edge spectroscopy (XANES) confirms that Yb7Ni4InGe12 exhibits mixed valence.

High-quality photonic crystals with a nearly complete band gap obtained by direct inversion of woodpile templates with titanium dioxide.

PubMed

Marichy, Catherine; Muller, Nicolas; Froufe-Pérez, Luis S; Scheffold, Frank

2016-02-25

Photonic crystal materials are based on a periodic modulation of the dielectric constant on length scales comparable to the wavelength of light. These materials can exhibit photonic band gaps; frequency regions for which the propagation of electromagnetic radiation is forbidden due to the depletion of the density of states. In order to exhibit a full band gap, 3D PCs must present a threshold refractive index contrast that depends on the crystal structure. In the case of the so-called woodpile photonic crystals this threshold is comparably low, approximately 1.9 for the direct structure. Therefore direct or inverted woodpiles made of high refractive index materials like silicon, germanium or titanium dioxide are sought after. Here we show that, by combining multiphoton lithography and atomic layer deposition, we can achieve a direct inversion of polymer templates into TiO2 based photonic crystals. The obtained structures show remarkable optical properties in the near-infrared region with almost perfect specular reflectance, a transmission dip close to the detection limit and a Bragg length comparable to the lattice constant.

Ten Good Reasons for the Use of the Tellurium-Centered Anderson-Evans Polyoxotungstate in Protein Crystallography.

PubMed

Bijelic, Aleksandar; Rompel, Annette

2017-06-20

Protein crystallography represents at present the most productive and most widely used method to obtain structural information on target proteins and protein-ligand complexes within the atomic resolution range. The knowledge obtained in this way is essential for understanding the biology, chemistry, and biochemistry of proteins and their functions but also for the development of compounds of high pharmacological and medicinal interest. Here, we address the very central problem in protein crystallography: the unpredictability of the crystallization process. Obtaining protein crystals that diffract to high resolutions represents the essential step to perform any structural study by X-ray crystallography; however, this method still depends basically on trial and error making it a very time- and resource-consuming process. The use of additives is an established process to enable or improve the crystallization of proteins in order to obtain high quality crystals. Therefore, a more universal additive addressing a wider range of proteins is desirable as it would represent a huge advance in protein crystallography and at the same time drastically impact multiple research fields. This in turn could add an overall benefit for the entire society as it profits from the faster development of novel or improved drugs and from a deeper understanding of biological, biochemical, and pharmacological phenomena. With this aim in view, we have tested several compounds belonging to the emerging class of polyoxometalates (POMs) for their suitability as crystallization additives and revealed that the tellurium-centered Anderson-Evans polyoxotungstate [TeW 6 O 24 ] 6- (TEW) was the most suitable POM-archetype. After its first successful application as a crystallization additive, we repeatedly reported on TEW's positive effects on the crystallization behavior of proteins with a particular focus on the protein-TEW interactions. As electrostatic interactions are the main force for TEW binding to proteins, TEW with its highly negative charge addresses in principle all proteins possessing positively charged patches. Furthermore, due to its high structural and chemical diversity, TEW exhibits major advantages over some commonly used crystallization additives. Therefore, we summarized all features of TEW, which are beneficial for protein crystallization, and present ten good reasons to promote the use of TEW in protein crystallography as a powerful additive. Our results demonstrate that TEW is a compound that is, in many respects, predestined as a crystallization additive. We assume that many crystallographers and especially researchers, who are not experts in this field but willing to crystallize their structurally unknown target protein, could benefit from the use of TEW as it is able to promote both the crystallization process itself and the subsequent structure elucidation by providing valuable anomalous signals, which are helpful for the phasing step.

Ten Good Reasons for the Use of the Tellurium-Centered Anderson–Evans Polyoxotungstate in Protein Crystallography

PubMed Central

2017-01-01

Conspectus Protein crystallography represents at present the most productive and most widely used method to obtain structural information on target proteins and protein–ligand complexes within the atomic resolution range. The knowledge obtained in this way is essential for understanding the biology, chemistry, and biochemistry of proteins and their functions but also for the development of compounds of high pharmacological and medicinal interest. Here, we address the very central problem in protein crystallography: the unpredictability of the crystallization process. Obtaining protein crystals that diffract to high resolutions represents the essential step to perform any structural study by X-ray crystallography; however, this method still depends basically on trial and error making it a very time- and resource-consuming process. The use of additives is an established process to enable or improve the crystallization of proteins in order to obtain high quality crystals. Therefore, a more universal additive addressing a wider range of proteins is desirable as it would represent a huge advance in protein crystallography and at the same time drastically impact multiple research fields. This in turn could add an overall benefit for the entire society as it profits from the faster development of novel or improved drugs and from a deeper understanding of biological, biochemical, and pharmacological phenomena. With this aim in view, we have tested several compounds belonging to the emerging class of polyoxometalates (POMs) for their suitability as crystallization additives and revealed that the tellurium-centered Anderson–Evans polyoxotungstate [TeW6O24]6– (TEW) was the most suitable POM-archetype. After its first successful application as a crystallization additive, we repeatedly reported on TEW’s positive effects on the crystallization behavior of proteins with a particular focus on the protein–TEW interactions. As electrostatic interactions are the main force for TEW binding to proteins, TEW with its highly negative charge addresses in principle all proteins possessing positively charged patches. Furthermore, due to its high structural and chemical diversity, TEW exhibits major advantages over some commonly used crystallization additives. Therefore, we summarized all features of TEW, which are beneficial for protein crystallization, and present ten good reasons to promote the use of TEW in protein crystallography as a powerful additive. Our results demonstrate that TEW is a compound that is, in many respects, predestined as a crystallization additive. We assume that many crystallographers and especially researchers, who are not experts in this field but willing to crystallize their structurally unknown target protein, could benefit from the use of TEW as it is able to promote both the crystallization process itself and the subsequent structure elucidation by providing valuable anomalous signals, which are helpful for the phasing step. PMID:28562014

Purification, characterization and crystallization of the human 80S ribosome

PubMed Central

Khatter, Heena; Myasnikov, Alexander G.; Mastio, Leslie; Billas, Isabelle M. L.; Birck, Catherine; Stella, Stefano; Klaholz, Bruno P.

2014-01-01

Ribosomes are key macromolecular protein synthesis machineries in the cell. Human ribosomes have so far not been studied to atomic resolution because of their particularly complex structure as compared with other eukaryotic or prokaryotic ribosomes, and they are difficult to prepare to high homogeneity, which is a key requisite for high-resolution structural work. We established a purification protocol for human 80S ribosomes isolated from HeLa cells that allows obtaining large quantities of homogenous samples as characterized by biophysical methods using analytical ultracentrifugation and multiangle laser light scattering. Samples prepared under different conditions were characterized by direct single particle imaging using cryo electron microscopy, which helped optimizing the preparation protocol. From a small data set, a 3D reconstruction at subnanometric resolution was obtained showing all prominent structural features of the human ribosome, and revealing a salt concentration dependence of the presence of the exit site tRNA, which we show is critical for obtaining crystals. With these well-characterized samples first human 80S ribosome crystals were obtained from several crystallization conditions in capillaries and sitting drops, which diffract to 26 Å resolution at cryo temperatures and for which the crystallographic parameters were determined, paving the way for future high-resolution work. PMID:24452798

New investigations of the guanine trichloro cuprate(II) complex crystal

NASA Astrophysics Data System (ADS)

Fabijanić, Ivana; Matković-Čalogović, Dubravka; Pilepić, Viktor; Ivanišević, Irena; Mohaček-Grošev, Vlasta; Sanković, Krešimir

2017-01-01

Crystals of the guanine trichloro cuprate(II) complex, (HGua)2[Cu2Cl6]·2H2O (HGua = protonated guanine), were prepared and analysed by spectroscopic (IR, Raman) and computational methods. A new single-crystal X-ray diffraction analysis was conducted to obtain data with lower standard uncertainties than those in the previously published structure. Raman and IR spectroscopy and quantum-mechanical analysis gave us new insight into the vibrational states of the (HGua)2[Cu2Cl6]·2H2O crystal. The vibrational spectra of the crystal were assigned by performing a normal coordinate analysis for a free dimer with a centre of inversion as the only symmetry element. The stretching vibration observed at 279 cm-1 in the infrared spectrum corresponds to the N-Cu bond. The noncovalent interaction (NCI) plots and quantum theory of atoms in molecules (QTAIM) analysis of the electron density obtained from periodic DFT calculations elucidated the interactions that exist within the crystal structure. Closed-shell ionic attractions, as well as weak and medium strength hydrogen bonds, prevailed in the crystal packing.

Growth and structural characterization of single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) obtained by the partial melting technique

NASA Astrophysics Data System (ADS)

Yamaki, K.; Bamba, Y.; Mochiku, T.; Funahashi, S.; Matsushita, Y.; Irie, A.

2018-05-01

In this study, cubic single crystals of the magnetic superconductor Ru1-xSr2-yGd1+yCu2+xO8-δ (RuGd-1212) with typical dimensions of 100-150 μm in length were grown by the partial melting technique. Multiple 00l reflections were first observed by XRD measurements of the bulk RuGd-1212 single crystals. The resistivity of the obtained crystals was roughly estimated to be ∼24-80 mΩ cm and no superconducting transition was observed down to 4.2 K. From the XRD measurements and refinement of the crystal structure, it was apparent that the Ru and Sr sites of the single-crystal RuGd-1212 were partially substituted by Cu and Gd, respectively. Oxygen defects were found to be minor (δ ≈ 0.1). The lattice parameters a and c of the single crystals were found to be larger and smaller, respectively, than those of a polycrystalline sample.

A comparative study of two polymorphs of L-aspartic acid hydrochloride.

PubMed

Benali-Cherif, Rim; Takouachet, Radhwane; Bendeif, El-Eulmi; Benali-Cherif, Nourredine

2014-07-01

Two polymorphs of L-aspartic acid hydrochloride, C4H8NO4(+)·Cl(-), were obtained from the same aqueous solution. Their crystal structures have been determined from single-crystal data collected at 100 K. The crystal structures revealed three- and two-dimensional hydrogen-bonding networks for the triclinic and orthorhombic polymorphs, respectively. The cations and anions are connected to one another via N-H···Cl and O-H···Cl interactions and form alternating cation-anion layer-like structures. The two polymorphs share common structural features; however, the conformations of the L-aspartate cations and the crystal packings are different. Furthermore, the molecular packing of the orthorhombic polymorph contains more interesting interactions which seems to be a favourable factor for more efficient charge transfer within the crystal.

Structure of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) single crystals

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

Makarova, I. P., E-mail: makarova@crys.ras.ru; Grebenev, V. V.; Vasil’ev, I. I.

2016-01-15

Single crystals of Cs{sub 4}(HSO{sub 4}){sub 3}(H{sub 2}PO{sub 4}) are synthesized and studied for the first time. The new compound is found in the course of studies of the phase diagram of the CsHSO{sub 4}–CsH{sub 2}PO{sub 4}–H{sub 2}O triple system. Data on the atomic crystal structure of single-crystalline and powder specimens, as well as on structural phase transitions, are obtained.

Synthesis, crystal structure, NLO and Hirshfeld surface analysis of 1,2,3-triazolyl chalcone single crystal

NASA Astrophysics Data System (ADS)

Shruthi, C.; Ravindrachary, V.; Guruswamy, B.; Lokanath, N. K.; Kumara, Karthik; Goveas, Janet

2018-05-01

Needle shaped brown coloured single crystal of the title compound was grown by slow evaporation technique using methanol as solvent. The grown crystal was characterized using FT-IR, Single crystal XRD, UV-visible and NLO studies. Crystal structure was confirmed by FT-IR study and the functional groups were identified. XRD study reveals that the crystal belongs to orthorhombic crystal system with pnaa space group and the corresponding cell parameters were calculated. UV-visible spectrum shows that the crystal is transparent in the entire visible region and absorption takes place in the UV-range. NLO efficiency of the crystal obtained 0.66 times that of urea was determined by SHG test. The intermolecular interaction and percentage contribution of each individual atom in the crystal lattice was quantized using Hirshfeld surface and 2D finger print analysis.

Purification and Bicelle Crystallization for Structure Determination of the E. coli Outer Membrane Protein TamA.

PubMed

Gruss, Fabian; Hiller, Sebastian; Maier, Timm

2015-01-01

TamA is an Omp85 protein involved in autotransporter assembly in the outer membrane of Escherichia coli. It comprises a C-terminal 16-stranded transmembrane β-barrel as well as three periplasmic POTRA domains, and is a challenging target for structure determination. Here, we present a method for crystal structure determination of TamA, including recombinant expression in E. coli, detergent extraction, chromatographic purification, and bicelle crystallization in combination with seeding. As a result, crystals in space group P21212 are obtained, which diffract to 2.3 Å resolution. This protocol also serves as a template for structure determination of other outer membrane proteins, in particular of the Omp85 family.

Structural coloration of chitosan coated cellulose fabrics by electrostatic self-assembled poly (styrene-methyl methacrylate-acrylic acid) photonic crystals.

PubMed

Yavuz, Gönül; Zille, Andrea; Seventekin, Necdet; Souto, Antonio P

2018-08-01

The structural coloration of a chitosan-coated woven cotton fabric obtained by glutaraldehyde-stabilized deposition of electrostatic self-assembled monodisperse and spherically uniform (250 nm) poly (styrene-methyl methacrylate-acrylic acid) photonic crystal nanospheres (P(St-MMA-AA)) was investigated. Bright iridescent coatings displaying different colors in function of the viewing angle were obtained. The SEM, diffuse reflectance spectroscopy, TGA, DSC and FTIR analyses confirm the presence of structural color and the glutaraldehyde and chitosan ability to provide durable chemical bonding between cotton fabric and photonic crystal (PCs) coating with the highest degradation temperature and the lowest enthalpy. The coatings are characterized by a mixture of face-centered cubic and hexagonal close-packed arrays alternating random packing regions. For the first time a cost-efficient structural coloration with high washing and light fastness using self-assembled P(St-MMA-AA) photonic crystals was successfully developed onto woven cotton fabric using chitosan and/or glutaraldehyde as stabilizing agent opening new strategies for the development of dye-free coloration of textiles. Copyright © 2018 Elsevier Ltd. All rights reserved.

Determination of the X-ray structure of the snake venom protein omwaprin by total chemical synthesis and racemic protein crystallography.

PubMed

Banigan, James R; Mandal, Kalyaneswar; Sawaya, Michael R; Thammavongsa, Vilasak; Hendrickx, Antoni P A; Schneewind, Olaf; Yeates, Todd O; Kent, Stephen B H

2010-10-01

The 50-residue snake venom protein L-omwaprin and its enantiomer D-omwaprin were prepared by total chemical synthesis. Radial diffusion assays were performed against Bacillus megaterium and Bacillus anthracis; both L- and D-omwaprin showed antibacterial activity against B. megaterium. The native protein enantiomer, made of L-amino acids, failed to crystallize readily. However, when a racemic mixture containing equal amounts of L- and D-omwaprin was used, diffraction quality crystals were obtained. The racemic protein sample crystallized in the centrosymmetric space group P2(1)/c and its structure was determined at atomic resolution (1.33 A) by a combination of Patterson and direct methods based on the strong scattering from the sulfur atoms in the eight cysteine residues per protein. Racemic crystallography once again proved to be a valuable method for obtaining crystals of recalcitrant proteins and for determining high-resolution X-ray structures by direct methods.

Impact of Lu/Gd ratio and activator concentration on structure and scintillation properties of LGSO:Ce crystals

NASA Astrophysics Data System (ADS)

Sidletskiy, O.; Bondar, V.; Grinyov, B.; Kurtsev, D.; Baumer, V.; Belikov, K.; Katrunov, K.; Starzhinsky, N.; Tarasenko, O.; Tarasov, V.; Zelenskaya, O.

2010-02-01

We have studied the dependence of structural and scintillation characteristics of Lu 2 xGd 2-2 xSiO 5:Ce (LGSO:Ce) crystals on cation composition. LGSO:Ce crystals at x=0-1 have been obtained by the Czochralski method. We report here a strong correlation between ionic radii of trivalent cations and their distribution between non-equivalent sites in lattice. By choosing the optimal Lu/Gd ratio and Ce concentration we were able to obtain the light output by˜70%, as compared to LSO:Ce crystals, and energy resolution ˜7 at% 662 KeV ( 137Cs); the afterglow level was decreased by 1-3 orders of magnitude as compared to LSO:Ce. We also discuss the possible mechanisms of control on scintillation characteristics of mixed orthosilicates.

Effect of cellulose nanocrystals (CNC) on rheological and mechanical properties and crystallization behavior of PLA/CNC nanocomposites.

PubMed

Kamal, Musa R; Khoshkava, Vahid

2015-06-05

In earlier work, we reported that spray freeze drying of cellulose nanocrystals (CNC) yields porous agglomerate structures. On the other hand, the conventional spray dried CNC (CNCSD) and the freeze dried CNC (CNCFD) produce compact solid structures with very low porosity. As it is rather difficult to obtain direct microscopic evidence of the quality of dispersion of CNC in polymer nanocomposites, it was shown that supporting evidence of the quality and influence of dispersion in a polypropylene (PP)/CNC nanocomposite could be obtained by studying the rheological behavior, mechanical properties and crystallization characteristics of PP/CNC nanocomposites. In an effort to produce a sustainable, fully biosourced, biodegradable nanocomposite, this manuscript presents the results of a study of the rheological, mechanical and crystallization behavior of PLA/CNCSFD nanocomposites obtained by melt processing. The results are analyzed to determine CNC network formation, rheological percolation threshold concentrations, mechanical properties in the rubbery and glassy states, and the effect of CNCSFD on crystalline nucleation and crystallization rates of PLA. These results suggest that the porosity and network structure of CNCSFD agglomerates contribute significantly to good dispersion of CNC in the PLA matrix. Copyright © 2015 Elsevier Ltd. All rights reserved.

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

PubMed Central

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

2014-01-01

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

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

Patil, Vidya, E-mail: vidya.patil@ruparel.edu; Patki, Mugdha, E-mail: mugdha.patki@ruparel.edu

Many nonlinear optical (NLO) crystals have been identified as potential candidates in optical and electro-optical devices. Use of NLO organic crystals is expected in photonic applications. Hence organic nonlinear optical materials have been intensely investigated due to their potentially high nonlinearities, and rapid response in electro-optic effect compared to inorganic NLO materials. There are many methods to grow organic crystals such as vapor growth method, melt growth method and solution growth method. Out of these methods, solution growth method is useful in providing constraint free crystal. Single crystals of Dopamine have been grown by evaporating the solvents from aqueous solution.more » Crystals obtained were of the size of orders of mm. The crystal structure of dopamine was determined using XRD technique. Images of crystals were obtained using FEG SEM Quanta Series under high vacuum and low KV.« less

Learning from oligosaccharide soaks of crystals of an AA13 lytic polysaccharide monooxygenase: crystal packing, ligand binding and active-site disorder.

PubMed

Frandsen, Kristian E H; Poulsen, Jens Christian Navarro; Tovborg, Morten; Johansen, Katja S; Lo Leggio, Leila

2017-01-01

Lytic polysaccharide monooxygenases (LPMOs) are a class of copper-dependent enzymes discovered within the last ten years. They oxidatively cleave polysaccharides (chitin, lignocellulose, hemicellulose and starch-derived), presumably making recalcitrant substrates accessible to glycoside hydrolases. Recently, the first crystal structure of an LPMO-substrate complex was reported, giving insights into the interaction of LPMOs with β-linked substrates (Frandsen et al., 2016). The LPMOs acting on α-linked glycosidic bonds (family AA13) display binding surfaces that are quite different from those of LPMOs that act on β-linked glycosidic bonds (families AA9-AA11), as revealed from the first determined structure (Lo Leggio et al., 2015), and thus presumably the AA13s interact with their substrate in a distinct fashion. Here, several new structures of the same AA13 enzyme, Aspergillus oryzae AA13, are presented. Crystals obtained in the presence of high zinc-ion concentrations were used, as they can be obtained more reproducibly than those used to refine the deposited copper-containing structure. One structure with an ordered zinc-bound active site was solved at 1.65 Å resolution, and three structures from crystals soaked with maltooligosaccharides in solutions devoid of zinc ions were solved at resolutions of up to 1.10 Å. Despite similar unit-cell parameters, small rearrangements in the crystal packing occur when the crystals are depleted of zinc ions, resulting in a more occluded substrate-binding surface. In two of the three structures maltooligosaccharide ligands are bound, but not at the active site. Two of the structures presented show a His-ligand conformation that is incompatible with metal-ion binding. In one of these structures this conformation is the principal one (80% occupancy), giving a rare atomic resolution view of a substantially misfolded enzyme that is presumably rendered inactive.

The structural basis for enhanced silver reflectance in Koi fish scale and skin.

PubMed

Gur, Dvir; Leshem, Ben; Oron, Dan; Weiner, Steve; Addadi, Lia

2014-12-10

Fish have evolved biogenic multilayer reflectors composed of stacks of intracellular anhydrous guanine crystals separated by cytoplasm, to produce the silvery luster of their skin and scales. Here we compare two different variants of the Japanese Koi fish; one of them with enhanced reflectivity. Our aim is to determine how biology modulates reflectivity, and from this to obtain a mechanistic understanding of the structure and properties governing the intensity of silver reflectance. We measured the reflectance of individual scales with a custom-made microscope, and then for each individual scale we characterized the structure of the guanine crystal/cytoplasm layers using high-resolution cryo-SEM. The measured reflectance and the structural-geometrical parameters were used to calculate the reflectance of each scale, and the results were compared to the experimental measurements. We show that enhanced reflectivity is obtained with the same basic guanine crystal/cytoplasm stacks, but the structural arrangement between the stack, inside the stacks, and relative to the scale surface is varied when reflectivity is enhanced. Finally, we propose a model that incorporates the basic building block parameters, the crystal orientation inside the tissue, and the resulting reflectance and explains the mechanistic basis for reflectance enhancement.

Structural characterization of polymorphs and molecular complexes of finasteride

NASA Astrophysics Data System (ADS)

Wawrzycka, Irena; Stȩpniak, Krystyna; Matyjaszczyk, Sławomir; Kozioł, Anna E.; Lis, Tadeusz; Abboud, Khalil A.

1999-01-01

The molecular structure of finasteride, 17 β-( N-tert-butylcarbamoyl)-4-aza-5 α-androst-1-en-3-one, and structures of three related crystalline forms have been determined by X-ray analysis. The rigid steroid skeleton of the molecule adopts a half-chair/chair/chair/half-chair conformation. Two peptide groups, one cyclic (lactam) in the ring A and a second being a part of the substituent at C17, are the main factors influencing intermolecular contacts. Different hydrogen-bond interactions of these hydrophilic groups are observed in the crystal structures. An infinite ribbon of finasteride molecules is formed between lactam groups in the orthorhombic homomolecular crystal ( 1) obtained from an ethanol solution. The linear molecular complex finasteride-acetic acid ( 1a) is connected by hydrogen bonds between the lactam of finasteride and the carboxyl group of acetic acid. The crystallization from an ethyl acetate solution gives a complex structure of bis-finasteride monohydrate ethyl acetate clathrate ( 1b) with guest molecule disordered in channels. Crystals of a second (monoclinic) finasteride polymorph ( 2) were obtained during thermal decomposition of 1a, and sublimation of 1, 1a and 1b. Two polymorphic forms show different IR spectra.

Fluorescent Approaches to High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Forsythe, Elizabeth; Achari, Amiruddha

2005-01-01

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1 %, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. Preliminary experiments show that the presence of the fluorescent probe does not affect the nucleation process or the quality of the X-ray data obtained.

Human 17β-hydroxysteroid dehydrogenase-ligand complexes: crystals of different space groups with various cations and combined seeding and co-crystallization

NASA Astrophysics Data System (ADS)

Zhu, D.-W.; Han, Q.; Qiu, W.; Campbell, R. L.; Xie, B.-X.; Azzi, A.; Lin, S.-X.

1999-01-01

Human estrogenic 17β-hydroxysteroid dehydrogenase (17β-HSD1) is responsible for the synthesis of active estrogens that stimulate the proliferation of breast cancer cells. The enzyme has been crystallized using a Mg 2+/PEG (3500)/β-octyl glucoside system [Zhu et al., J. Mol. Biol. 234 (1993) 242]. The space group of these crystals is C2. Here we report that cations can affect 17β-HSD1 crystallization significantly. In the presence of Mn 2+ instead of Mg 2+, crystals have been obtained in the same space group with similar unit cell dimensions. In the presence of Li + and Na + instead of Mg 2+, the space group has been changed to P2 12 12 1. A whole data set for a crystal of 17ß-HSD1 complex with progesterone grown in the presence of Li + has been collected to 1.95 Å resolution with a synchrotron source. The cell dimensions are a=41.91 Å, b=108.21 Å, c=117.00 Å. The structure has been preliminarily determined by molecular replacement, yielding important information on crystal packing in the presence of different cations. In order to further understand the structure-function relationship of 17β-HSD1, enzyme complexes with several ligands have been crystallized. As the steroids have very low aqueous solubility, we used a combined method of seeding and co-crystallization to obtain crystals of 17β-HSD1 complexed with various ligands. This method provides ideal conditions for growing complex crystals, with ligands such as 20α-hydroxysteroid progesterone, testosterone and 17β-methyl-estradiol-NADP +. Several complex structures have been determined with reliable electronic density of the bound ligands.

Observing the overall rocking motion of a protein in a crystal

NASA Astrophysics Data System (ADS)

Ma, Peixiang; Xue, Yi; Coquelle, Nicolas; Haller, Jens D.; Yuwen, Tairan; Ayala, Isabel; Mikhailovskii, Oleg; Willbold, Dieter; Colletier, Jacques-Philippe; Skrynnikov, Nikolai R.; Schanda, Paul

2015-10-01

The large majority of three-dimensional structures of biological macromolecules have been determined by X-ray diffraction of crystalline samples. High-resolution structure determination crucially depends on the homogeneity of the protein crystal. Overall `rocking' motion of molecules in the crystal is expected to influence diffraction quality, and such motion may therefore affect the process of solving crystal structures. Yet, so far overall molecular motion has not directly been observed in protein crystals, and the timescale of such dynamics remains unclear. Here we use solid-state NMR, X-ray diffraction methods and μs-long molecular dynamics simulations to directly characterize the rigid-body motion of a protein in different crystal forms. For ubiquitin crystals investigated in this study we determine the range of possible correlation times of rocking motion, 0.1-100 μs. The amplitude of rocking varies from one crystal form to another and is correlated with the resolution obtainable in X-ray diffraction experiments.

Discovery of a 2,4-Diamino-7-aminoalkoxy-quinazoline as a Potent and Selective Inhibitor of Histone Lysine Methyltransferase G9a†

PubMed Central

Liu, Feng; Chen, Xin; Allali-Hassani, Abdellah; Quinn, Amy M.; Wasney, Gregory A.; Dong, Aiping; Barsyte, Dalia; Kozieradzki, Ivona; Senisterra, Guillermo; Chau, Irene; Siarheyeva, Alena; Kireev, Dmitri B.; Jadhav, Ajit; Herold, J. Martin; Frye, Stephen V.; Arrowsmith, Cheryl H.; Brown, Peter J.; Simeonov, Anton; Vedadi, Masoud; Jin, Jian

2010-01-01

SAR exploration of the 2,4-diamino-6,7-dimethoxyquinazoline template led to the discovery of 8 (UNC0224) as a potent and selective G9a inhibitor. A high resolution X-ray crystal structure of the G9a-8 complex, the first co-crystal structure of G9a with a small molecule inhibitor, was obtained. The co-crystal structure validated our binding hypothesis and will enable structure-based design of novel inhibitors. 8 is a useful tool for investigating the biology of G9a and its roles in chromatin remodeling. PMID:19891491

Synthesis of rhenium nitride crystals with MoS2 structure

NASA Astrophysics Data System (ADS)

Kawamura, Fumio; Yusa, Hitoshi; Taniguchi, Takashi

2012-06-01

Rhenium nitride (ReN2) crystals were synthesized from a metathesis reaction between ReCl5 and Li3N under high pressure. The reaction was well controlled by the addition of a large amount of NaCl as reaction inhibitor to prevent a violent exothermic reaction. The largest rhenium nitride crystals obtained had a millimeter-order size with a platelet shape. X-ray diffraction analysis revealed that rhenium nitride has MoS2 structure similar to hexagonal rhenium diboride (ReB2) which has recently been investigated as an ultra-hard material. The structure was different from any structures previously predicted for ReN2 by theoretical calculations.

Large Area Stress Distribution in Crystalline Materials Calculated from Lattice Deformation Identified by Electron Backscatter Diffraction

NASA Astrophysics Data System (ADS)

Shao, Yongliang; Zhang, Lei; Hao, Xiaopeng; Wu, Yongzhong; Dai, Yuanbin; Tian, Yuan; Huo, Qin

2014-08-01

We report a method to obtain the stress of crystalline materials directly from lattice deformation by Hooke's law. The lattice deformation was calculated using the crystallographic orientations obtained from electron backscatter diffraction (EBSD) technology. The stress distribution over a large area was obtained efficiently and accurately using this method. Wurtzite structure gallium nitride (GaN) crystal was used as the example of a hexagonal crystal system. With this method, the stress distribution of a GaN crystal was obtained. Raman spectroscopy was used to verify the stress distribution. The cause of the stress distribution found in the GaN crystal was discussed from theoretical analysis and EBSD data. Other properties related to lattice deformation, such as piezoelectricity, can also be analyzed by this novel approach based on EBSD data.

Large area stress distribution in crystalline materials calculated from lattice deformation identified by electron backscatter diffraction.

PubMed

Shao, Yongliang; Zhang, Lei; Hao, Xiaopeng; Wu, Yongzhong; Dai, Yuanbin; Tian, Yuan; Huo, Qin

2014-08-05

We report a method to obtain the stress of crystalline materials directly from lattice deformation by Hooke's law. The lattice deformation was calculated using the crystallographic orientations obtained from electron backscatter diffraction (EBSD) technology. The stress distribution over a large area was obtained efficiently and accurately using this method. Wurtzite structure gallium nitride (GaN) crystal was used as the example of a hexagonal crystal system. With this method, the stress distribution of a GaN crystal was obtained. Raman spectroscopy was used to verify the stress distribution. The cause of the stress distribution found in the GaN crystal was discussed from theoretical analysis and EBSD data. Other properties related to lattice deformation, such as piezoelectricity, can also be analyzed by this novel approach based on EBSD data.

Large Area Stress Distribution in Crystalline Materials Calculated from Lattice Deformation Identified by Electron Backscatter Diffraction

PubMed Central

Shao, Yongliang; Zhang, Lei; Hao, Xiaopeng; Wu, Yongzhong; Dai, Yuanbin; Tian, Yuan; Huo, Qin

2014-01-01

We report a method to obtain the stress of crystalline materials directly from lattice deformation by Hooke's law. The lattice deformation was calculated using the crystallographic orientations obtained from electron backscatter diffraction (EBSD) technology. The stress distribution over a large area was obtained efficiently and accurately using this method. Wurtzite structure gallium nitride (GaN) crystal was used as the example of a hexagonal crystal system. With this method, the stress distribution of a GaN crystal was obtained. Raman spectroscopy was used to verify the stress distribution. The cause of the stress distribution found in the GaN crystal was discussed from theoretical analysis and EBSD data. Other properties related to lattice deformation, such as piezoelectricity, can also be analyzed by this novel approach based on EBSD data. PMID:25091314

Structure of bovine cytochrome c oxidase crystallized at a neutral pH using a fluorinated detergent.

PubMed

Luo, Fangjia; Shinzawa-Itoh, Kyoko; Hagimoto, Kaede; Shimada, Atsuhiro; Shimada, Satoru; Yamashita, Eiki; Yoshikawa, Shinya; Tsukihara, Tomitake

2017-07-01

Cytochrome c oxidase (CcO) couples proton pumping to O 2 reduction. Its enzymatic activity depends sensitively on pH over a wide range. However, owing to difficulty in crystallizing this protein, X-ray structure analyses of bovine CcO aimed at understanding its reaction mechanism have been conducted using crystals prepared at pH 5.7, which is significantly lower than that in the cell. Here, oxidized CcO at pH 7.3 was crystallized using a fluorinated octyl-maltoside derivative, and the structure was determined at 1.77 Å resolution. No structural differences between crystals obtained at the neutral pH and the acidic pH were detected within the molecules. On the other hand, some differences in intermolecular interactions were detected between the two types of crystal. The influence of pH on the molecular surface is likely to contribute to the pH dependency of the aerobic oxidation of ferrocytochrome c.

Purification and crystallization of dengue and West Nile virus NS2B–NS3 complexes

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

D’Arcy, Allan, E-mail: allan.darcy@novartis.com; Chaillet, Maxime; Schiering, Nikolaus

Crystals of dengue serotype 2 and West Nile virus NS2B–NS3 protease complexes have been obtained and the crystals of both diffract to useful resolution. Sample homogeneity was essential for obtaining X-ray-quality crystals of the dengue protease. Controlled proteolysis produced a crystallizable fragment of the apo West Nile virus NS2B–NS3 and crystals were also obtained in the presence of a peptidic inhibitor. Both dengue and West Nile virus infections are an increasing risk to humans, not only in tropical and subtropical areas, but also in North America and parts of Europe. These viral infections are generally transmitted by mosquitoes, but maymore » also be tick-borne. Infection usually results in mild flu-like symptoms, but can also cause encephalitis and fatalities. Approximately 2799 severe West Nile virus cases were reported this year in the United States, resulting in 102 fatalities. With this alarming increase in the number of West Nile virus infections in western countries and the fact that dengue virus already affects millions of people per year in tropical and subtropical climates, there is a real need for effective medicines. A possible therapeutic target to combat these viruses is the protease, which is essential for virus replication. In order to provide structural information to help to guide a lead identification and optimization program, crystallizations of the NS2B–NS3 protease complexes from both dengue and West Nile viruses have been initiated. Crystals that diffract to high resolution, suitable for three-dimensional structure determinations, have been obtained.« less

Crystallization screening test for the whole-cell project on Thermus thermophilus HB8

PubMed Central

Iino, Hitoshi; Naitow, Hisashi; Nakamura, Yuki; Nakagawa, Noriko; Agari, Yoshihiro; Kanagawa, Mayumi; Ebihara, Akio; Shinkai, Akeo; Sugahara, Mitsuaki; Miyano, Masashi; Kamiya, Nobuo; Yokoyama, Shigeyuki; Hirotsu, Ken; Kuramitsu, Seiki

2008-01-01

It was essential for the structural genomics of Thermus thermophilus HB8 to efficiently crystallize a number of proteins. To this end, three conventional robots, an HTS-80 (sitting-drop vapour diffusion), a Crystal Finder (hanging-drop vapour diffusion) and a TERA (modified microbatch) robot, were subjected to a crystallization condition screening test involving 18 proteins from T. thermophilus HB8. In addition, a TOPAZ (microfluidic free-interface diffusion) designed specifically for initial screening was also briefly examined. The number of diffraction-quality crystals and the time of appearance of crystals increased in the order HTS-80, Crystal Finder, TERA. With the HTS-80 and Crystal Finder, the time of appearance was short and the rate of salt crystallization was low. With the TERA, the number of diffraction-quality crystals was high, while the time of appearance was long and the rate of salt crystallization was relatively high. For the protein samples exhibiting low crystallization success rates, there were few crystallization conditions that were common to the robots used. In some cases, the success rate depended greatly on the robot used. The TOPAZ showed the shortest time of appearance and the highest success rate, although the crystals obtained were too small for diffraction studies. These results showed that the combined use of different robots significantly increases the chance of obtaining crystals, especially for proteins exhibiting low crystallization success rates. The structures of 360 of 944 purified proteins have been successfully determined through the combined use of an HTS-80 and a TERA. PMID:18540056

Overview of electron crystallography of membrane proteins: crystallization and screening strategies using negative stain electron microscopy.

PubMed

Nannenga, Brent L; Iadanza, Matthew G; Vollmar, Breanna S; Gonen, Tamir

2013-01-01

Electron cryomicroscopy, or cryoEM, is an emerging technique for studying the three-dimensional structures of proteins and large macromolecular machines. Electron crystallography is a branch of cryoEM in which structures of proteins can be studied at resolutions that rival those achieved by X-ray crystallography. Electron crystallography employs two-dimensional crystals of a membrane protein embedded within a lipid bilayer. The key to a successful electron crystallographic experiment is the crystallization, or reconstitution, of the protein of interest. This unit describes ways in which protein can be expressed, purified, and reconstituted into well-ordered two-dimensional crystals. A protocol is also provided for negative stain electron microscopy as a tool for screening crystallization trials. When large and well-ordered crystals are obtained, the structures of both protein and its surrounding membrane can be determined to atomic resolution.

Crystallography of decahedral and icosahedral particles. I - Geometry of twinning

NASA Technical Reports Server (NTRS)

Yang, C. Y.

1979-01-01

The crystal structure of the tetrahedral twins in multiply-twinned particles with decahedral and icosahedral point group symmetries has been examined and correlated with the face-centered cubic structure. Details on the crystal structure as well as the geometrical relationships among twins in each particle are presented. These crystallographic facts serve as a basis for the interpretation of small particle images obtained with advanced methods of transmission electron microscopy.

Crystal Structure of Cocosin, A Potential Food Allergen from Coconut (Cocos nucifera).

PubMed

Jin, Tengchuan; Wang, Cheng; Zhang, Caiying; Wang, Yang; Chen, Yu-Wei; Guo, Feng; Howard, Andrew; Cao, Min-Jie; Fu, Tong-Jen; McHugh, Tara H; Zhang, Yuzhu

2017-08-30

Coconut (Cocos nucifera) is an important palm tree. Coconut fruit is widely consumed. The most abundant storage protein in coconut fruit is cocosin (a likely food allergen), which belongs to the 11S globulin family. Cocosin was crystallized near a century ago, but its structure remains unknown. By optimizing crystallization conditions and cryoprotectant solutions, we were able to obtain cocosin crystals that diffracted to 1.85 Å. The cocosin gene was cloned from genomic DNA isolated from dry coconut tissue. The protein sequence deduced from the predicted cocosin coding sequence was used to guide model building and structure refinement. The structure of cocosin was determined for the first time, and it revealed a typical 11S globulin feature of a double layer doughnut-shaped hexamer.

Electrical and Structural Characterization of Web Dendrite Crystals

NASA Technical Reports Server (NTRS)

Schwuttke, G. H.; Koliwad, K.; Dumas, K. A.

1985-01-01

Minority carrier lifetime distributions in silicon web dendrites are measured. Emphasis is placed on measuring areal homogeneity of lifetime, show its dependency on structural defects, and its unique change during hot processing. The internal gettering action of defect layers present in web crystals and their relation to minority carrier lifetime distributions is discussed. Minority carrier lifetime maps of web dendrites obtained before and after high temperature heat treatment are compared to similar maps obtained from 100 mm diameter Czochralski silicon wafers. Such maps indicate similar or superior areal homogeneity of minority carrier lifetime in webs.

Study of the spectra of silica colloidal crystals with assembled silver obtained from a photolysis method

NASA Astrophysics Data System (ADS)

Li, Wenjiang; He, Jinglong; He, Sailing

2005-02-01

The colorful artificial 3D silica colloidal crystals (opal) were prepared through self-assembly of silica spheres in the visible frequency range. We directly synthesized nano silver particles in the void of the silica artificial opal film using the photolysis of silver nitrate under UV light, nano silver particles were self-deposited around the surface of silica sphere. The shifts of the stop band of the artificial crystals after exposing different time under UV light were studied. Synthetic silica opal with three-dimensional (3D) structure is potentially useful for the development of diffractive optical devices, micro mechanical systems, and sensory elements because photonic band gaps obtained from self-assembled closely packed periodic structures.

Prediction study of structural, elastic and electronic properties of FeMP (M = Ti, Zr, Hf) compounds

NASA Astrophysics Data System (ADS)

Tanto, A.; Chihi, T.; Ghebouli, M. A.; Reffas, M.; Fatmi, M.; Ghebouli, B.

2018-06-01

First principles calculations are applied in the study of FeMP (M = Ti, Zr, Hf) compounds. We investigate the structural, elastic, mechanical and electronic properties by combining first-principles calculations with the CASTEP approach. For ideal polycrystalline FeMP (M = Ti, Zr, Hf) the shear modulus, Young's modulus, Poisson's ratio, elastic anisotropy indexes, Pugh's criterion, elastic wave velocities and Debye temperature are also calculated from the single crystal elastic constants. The shear anisotropic factors and anisotropy are obtained from the single crystal elastic constants. The Debye temperature is calculated from the average elastic wave velocity obtained from shear and bulk modulus as well as the integration of elastic wave velocities in different directions of the single crystal.

Structural Biology of Proteins of the Multi-enzyme Assembly Human Pyruvate Dehydrogenase Complex

NASA Technical Reports Server (NTRS)

2003-01-01

Objectives and research challenges of this effort include: 1. Need to establish Human Pyruvate Dehydrogenase Complex protein crystals; 2. Need to test value of microgravity for improving crystal quality of Human Pyruvate Dehydrogenase Complex protein crystals; 3. Need to improve flight hardware in order to control and understand the effects of microgravity on crystallization of Human Pyruvate Dehydrogenase Complex proteins; 4. Need to integrate sets of national collaborations with the restricted and specific requirements of flight experiments; 5. Need to establish a highly controlled experiment in microgravity with a rigor not yet obtained; 6. Need to communicate both the rigor of microgravity experiments and the scientific value of results obtained from microgravity experiments to the national community; and 7. Need to advance the understanding of Human Pyruvate Dehydrogenase Complex structures so that scientific and commercial advance is identified for these proteins.

High nitrogen pressure solution growth of GaN

NASA Astrophysics Data System (ADS)

Bockowski, Michal

2014-10-01

Results of GaN growth from gallium solution under high nitrogen pressure are presented. Basic of the high nitrogen pressure solution (HNPS) growth method is described. A new approach of seeded growth, multi-feed seed (MFS) configuration, is demonstrated. The use of two kinds of seeds: free-standing hydride vapor phase epitaxy GaN (HVPE-GaN) obtained from metal organic chemical vapor deposition (MOCVD)-GaN/sapphire templates and free-standing HVPE-GaN obtained from the ammonothermally grown GaN crystals, is shown. Depending on the seeds’ structural quality, the differences in the structural properties of pressure grown material are demonstrated and analyzed. The role and influence of impurities, like oxygen and magnesium, on GaN crystals grown from gallium solution in the MFS configuration is presented. The properties of differently doped GaN crystals are discussed. An application of the pressure grown GaN crystals as substrates for electronic and optoelectronic devices is reported.

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

Crystal structure and vibrational spectra of piperazinium bis(4-hydroxybenzenesulphonate) molecular-ionic crystal

NASA Astrophysics Data System (ADS)

Marchewka, M. K.; Pietraszko, A.

2008-02-01

The piperazinium bis(4-hydroxybenzenesulphonate) crystallizes from water solution at room temperature in P2 1/ c space group of monoclinic system. The crystals are built up of doubly protonated piperazinium cations and ionized 4-hydroxybenzenesulphonate anions that interact through weak hydrogen bonds of O-H⋯O and N-H⋯O type. Mutual orientation of anions is determined by non-conventional hydrogen bonds of C-H⋯π type. Room temperature powder FT IR and FT Raman measurements were carried out. The vibrational spectra are in full agreement with the structure obtained from X-ray crystallography. The big single crystals of the title salt can be grown.

Towards protein-crystal centering using second-harmonic generation (SHG) microscopy

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

Kissick, David J.; Dettmar, Christopher M.; Becker, Michael

2013-05-01

The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals has been explored. The potential of second-harmonic generation (SHG) microscopy for automated crystal centering to guide synchrotron X-ray diffraction of protein crystals was explored. These studies included (i) comparison of microcrystal positions in cryoloops as determined by SHG imaging and by X-ray diffraction rastering and (ii) X-ray structure determinations of selected proteins to investigate the potential for laser-induced damage from SHG imaging. In studies using β{sub 2} adrenergic receptor membrane-protein crystals prepared in lipidic mesophase, the crystal locations identified by SHGmore » images obtained in transmission mode were found to correlate well with the crystal locations identified by raster scanning using an X-ray minibeam. SHG imaging was found to provide about 2 µm spatial resolution and shorter image-acquisition times. The general insensitivity of SHG images to optical scatter enabled the reliable identification of microcrystals within opaque cryocooled lipidic mesophases that were not identified by conventional bright-field imaging. The potential impact of extended exposure of protein crystals to five times a typical imaging dose from an ultrafast laser source was also assessed. Measurements of myoglobin and thaumatin crystals resulted in no statistically significant differences between structures obtained from diffraction data acquired from exposed and unexposed regions of single crystals. Practical constraints for integrating SHG imaging into an active beamline for routine automated crystal centering are discussed.« less

New Directions in Biotechnology

NASA Technical Reports Server (NTRS)

2003-01-01

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

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging.

PubMed

Coughlan, H D; Darmanin, C; Phillips, N W; Hofmann, F; Clark, J N; Harder, R J; Vine, D J; Abbey, B

2015-07-01

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

PubMed Central

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.; Hofmann, F.; Clark, J. N.; Harder, R. J.; Vine, D. J.; Abbey, B.

2015-01-01

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources. PMID:26798804

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

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

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Radiation damage in a micron-sized protein crystal studied via reciprocal space mapping and Bragg coherent diffractive imaging

DOE PAGES

Coughlan, H. D.; Darmanin, C.; Phillips, N. W.; ...

2015-04-29

For laboratory and synchrotron based X-ray sources, radiation damage has posed a significant barrier to obtaining high-resolution structural data from biological macromolecules. The problem is particularly acute for micron-sized crystals where the weaker signal often necessitates the use of higher intensity beams to obtain the relevant data. Here, we employ a combination of techniques, including Bragg coherent diffractive imaging to characterise the radiation induced damage in a micron-sized protein crystal over time. The approach we adopt here could help screen for potential protein crystal candidates for measurement at X-ray free election laser sources.

Self-assembly of nematic liquid crystal elastomer filaments

NASA Astrophysics Data System (ADS)

Wei, Wei-Shao; Xia, Yu; Yang, Shu; Yodh, A. G.

In this work we investigate the self-assembly of nematic liquid crystal polymer (NLCP) filaments and their corresponding cross-linked elastomer structures. Specifically, by fine-tuning surfactant concentration, prepolymer chain length, and temperature within a background aqueous phase we can generate filaments composed of oligomerized LC monomers. Filaments with narrowly dispersed diameters ranging from one hundred nanometers to a few micrometers can be obtained. Using polarization optical microscopy, we show that the nematic LCs within the filaments have an escaped radial structure. After photo-cross-linking, nematic liquid crystal elastomer filaments are obtained with well-maintained directors and smooth surface structure. Since these materials are elastomers, the size and mechanical and optical response of the filaments can be ''tuned'' near the nematic to isotropic phase transition temperature. This work is supported by NSF DMR16-07378, PENN MRSEC Grant DMR11-20901, and NASA Grant NNX08AO0G.

Protein crystal growth in microgravity: Temperature induced large scale crystallization of insulin

NASA Technical Reports Server (NTRS)

Long, Marianna M.; Delucas, Larry J.; Smith, C.; Carson, M.; Moore, K.; Harrington, Michael D.; Pillion, D. J.; Bishop, S. P.; Rosenblum, W. M.; Naumann, R. J.

1994-01-01

One of the major stumbling blocks that prevents rapid structure determination using x-ray crystallography is macro-molecular crystal growth. There are many examples where crystallization takes longer than structure determination. In some cases, it is impossible to grow useful crystals on earth. Recent experiments conducted in conjuction with NASA on various Space Shuttle missions have demonstrated that protein crystals often grow larger and display better internal molecular order than their earth-grown counterparts. This paper reports results from three Shuttle flights using the Protein Crystallization Facility (PCF). The PCF hardware produced large, high-quality insulin crystals by using a temperature change as the sole means to affect protein solubility and thus, crystallization. The facility consists of cylinders/containers with volumes of 500, 200, 100, and 50 ml. Data from the three Shuttle flights demonstrated that larger, higher resolution crystals (as evidenced by x-ray diffraction data) were obtained from the microgravity experiments when compared to earth-grown crystals.

Advanced Structural Analyses by Third Generation Synchrotron Radiation Powder Diffraction

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

Sakata, M.; Aoyagi, S.; Ogura, T.

2007-01-19

Since the advent of the 3rd generation Synchrotron Radiation (SR) sources, such as SPring-8, the capabilities of SR powder diffraction increased greatly not only in an accurate structure refinement but also ab initio structure determination. In this study, advanced structural analyses by 3rd generation SR powder diffraction based on the Large Debye-Scherrer camera installed at BL02B2, SPring-8 is described. Because of high angular resolution and high counting statistics powder data collected at BL02B2, SPring-8, ab initio structure determination can cope with a molecular crystals with 65 atoms including H atoms. For the structure refinements, it is found that a kindmore » of Maximum Entropy Method in which several atoms are omitted in phase calculation become very important to refine structural details of fairy large molecule in a crystal. It should be emphasized that until the unknown structure is refined very precisely, the obtained structure by Genetic Algorithm (GA) or some other ab initio structure determination method using real space structural knowledge, it is not possible to tell whether the structure obtained by the method is correct or not. In order to determine and/or refine crystal structure of rather complicated molecules, we cannot overemphasize the importance of the 3rd generation SR sources.« less

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.

Molecular Dynamics Study on Nucleation Behavior and Lamellar Mergence of Polyethylene Globule Crystallization

NASA Astrophysics Data System (ADS)

Yang, Xiaozhen; Wang, Simiao

2012-02-01

The site order parameter (SOP) has been adopted to analyze various order structure formation and distribution during the crystallization of a multi-chain polyethylene globule simulated by molecular dynamics. We found that the nucleation relies on crystallinity fluctuation with increase of amplitude, and the baby nucleus in the fluctuation suddenly appears with different shape and increasing size. In the growth stage, a number of lamellar mergence was observed and their selective behaviors were suggested to be related to the orientation difference between the merging lamellae. We obtained that SOP distribution of all atoms in the system during crystallization appears with two peaks: one for the amorphous phase and the other for the crystalline phase. Mesomorphic structures with medium orders locate between the two peaks as an order promotion pathway. Obtained data show that the medium order structure fluctuates at the growth front and does not always be available; the medium order structure existing at the front is not always good for developing. It is possibly caused by chain entanglement.

The microdopant effects of surfactant elements on structure-phase transitions during the rapid quenched crystallization of Fe-C-based melts

NASA Astrophysics Data System (ADS)

Polukhin, V. A.; Belyakova, R. M.; Rigmant, L. K.

2008-02-01

The nature of microdopant effects of surfactant Te and H2 reagents on structure-phase transitions in rapidly quenched and crystallized eutectic Fe-C-based melts were studied by experimental and computer methods. On the base of results of statistic-geometrical analysis the new information about the structure changes in multi-scaling systems -from meso- to nano-ones were obtained.

SdsA polymorph isolation and improvement of their crystal quality using nonconventional crystallization techniques

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

De la Mora, Eugenio; Flores-Hernández, Edith; Jakoncic, Jean

SdsA, a sodium dodecyl sulfate hydrolase, from Pseudomonas aeruginosa was crystallized in three different crystal polymorphs and their three-dimensional structure was determined. The different polymorphs present different crystal packing habits. One of the polymorphs suggests the existence of a tetramer, an oligomeric state not observed previously, while the crystal packing of the remaining two polymorphs obstructs the active site entrance but stabilizes flexible regions of the protein. Nonconventional crystallization methods that minimize convection, such as counterdiffusion in polyvinyl alcohol gel coupled with the influence of a 500 MHz (10.2 T) magnetic field, were necessary to isolate the poorest diffracting polymorphmore » and increase its internal order to determine its structure by X-ray diffraction. In conclusion, the results obtained show the effectiveness of nonconventional crystallographic methods to isolate different crystal polymorphs.« less

Unique Crystallization of Fullerenes: Fullerene Flowers

PubMed Central

Kim, Jungah; Park, Chibeom; Song, Intek; Lee, Minkyung; Kim, Hyungki; Choi, Hee Cheul

2016-01-01

Solution-phase crystallization of fullerene molecules strongly depends on the types of solvent and their ratios because solvent molecules are easily included in the crystal lattice and distort its structure. The C70 (solute)–mesitylene (solvent) system yields crystals with various morphologies and structures, such as cubes, tubes, and imperfect rods. Herein, using C60 and C70 dissolved in mesitylene, we present a novel way to grow unique flower-shaped crystals with six symmetric petals. The different solubility of C60 and C70 in mesitylene promotes nucleation of C70 with sixfold symmetry in the early stage, which is followed by co-crystallization of both C60 and C70 molecules, leading to lateral petal growth. Based on the growth mechanism, we obtained more complex fullerene crystals, such as multi-deck flowers and tube-flower complexes, by changing the sequence and parameters of crystallization. PMID:27561446

Fabrication of large binary colloidal crystals with a NaCl structure

PubMed Central

Vermolen, E. C. M.; Kuijk, A.; Filion, L. C.; Hermes, M.; Thijssen, J. H. J.; Dijkstra, M.; van Blaaderen, A.

2009-01-01

Binary colloidal crystals offer great potential for tuning material properties for applications in, for example, photonics, semiconductors and spintronics, because they allow the positioning of particles with quite different characteristics on one lattice. For micrometer-sized colloids, it is believed that gravity and slow crystallization rates hinder the formation of high-quality binary crystals. Here, we present methods for growing binary colloidal crystals with a NaCl structure from relatively heavy, hard-sphere-like, micrometer-sized silica particles by exploring the following external fields: electric, gravitational, and dielectrophoretic fields and a structured surface (colloidal epitaxy). Our simulations show that the free-energy difference between the NaCl and NiAs structures, which differ in their stacking of the hexagonal planes of the larger spheres, is very small (≈0.002 kBT). However, we demonstrate that the fcc stacking of the large spheres, which is crucial for obtaining the pure NaCl structure, can be favored by using a combination of the above-mentioned external fields. In this way, we have successfully fabricated large, 3D, oriented single crystals having a NaCl structure without stacking disorder. PMID:19805259

Structural, electronic and vibrational properties of LaF3 according to density functional theory and Raman spectroscopy

NASA Astrophysics Data System (ADS)

Oreshonkov, A. S.; Roginskii, E. M.; Krylov, A. S.; Ershov, A. A.; Voronov, V. N.

2018-06-01

Crystal structure of LaF3 single crystal is refined in tysonite-type trigonal unit cell P c1 using density functional theory calculations and Raman spectroscopy. It is shown that trigonal structure with P c1 space group is more energy-efficient than hexagonal structure with space group P63 cm. Simulated Raman spectra obtained using LDA approximation is in much better agreement with experimental data than that obtained with PBE and PBEsol functionals of GGA. The calculated frequency value of silent mode B 2 in case of hexagonal structure P63 cm was found to be imaginary (unstable mode), thus the energy surface obtains negative curvature with respect to the corresponding normal coordinates of the mode which leads to instability of the hexagonal structure in harmonic approximation. The A 1g line at 214 cm‑1 in Raman spectra of LaF3 related to the translation of F2 ions along c axis can be connected with F2 ionic conductivity.

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.

Macromolecular Crystallization in Microgravity

NASA Technical Reports Server (NTRS)

Snell, Edward H.; Helliwell, John R.

2004-01-01

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

Temperature insensitive curvature sensor based on cascading photonic crystal fiber

NASA Astrophysics Data System (ADS)

Fu, Guangwei; Li, Yunpu; Fu, Xinghu; Jin, Wa; Bi, Weihong

2018-03-01

A temperature insensitive curvature sensor is proposed based on cascading photonic crystal fiber. Using the arc fusion splicing method, this sensor is fabricated by cascading together a single-mode fiber (SMF), a three layers air holes structure of photonic crystal fiber (3PCF), a five layers air holes structure of photonic crystal fiber (5PCF) and a SMF in turn. So the structure SMF-3PCF-5PCF-SMF can be obtained with a total length of 20 mm. During the process of fabrication, the splicing machine parameters and the length of each optical fiber are adjusted to obtain a high sensitivity curvature sensor. The experimental results show that the curvature sensitivity is -8.40 nm/m-1 in the curvature variation range of 0-1.09 m-1, which also show good linearity. In the range of 30-90 °C, the temperature sensitivity is only about 3.24 pm/°C, indicating that the sensor is not sensitive to temperature. The sensor not only has the advantages of easy fabricating, simple structure, high sensitivity but also can solve the problem of temperature measurement cross sensitivity, so it can be used for different areas including aerospace, large-scale bridge, architectural structure health monitoring and so on.

Advanced Methods of Protein Crystallization.

PubMed

Moreno, Abel

2017-01-01

This chapter provides a review of different advanced methods that help to increase the success rate of a crystallization project, by producing larger and higher quality single crystals for determination of macromolecular structures by crystallographic methods. For this purpose, the chapter is divided into three parts. The first part deals with the fundamentals for understanding the crystallization process through different strategies based on physical and chemical approaches. The second part presents new approaches involved in more sophisticated methods not only for growing protein crystals but also for controlling the size and orientation of crystals through utilization of electromagnetic fields and other advanced techniques. The last section deals with three different aspects: the importance of microgravity, the use of ligands to stabilize proteins, and the use of microfluidics to obtain protein crystals. All these advanced methods will allow the readers to obtain suitable crystalline samples for high-resolution X-ray and neutron crystallography.

Development of an automated large-scale protein-crystallization and monitoring system for high-throughput protein-structure analyses.

PubMed

Hiraki, Masahiko; Kato, Ryuichi; Nagai, Minoru; Satoh, Tadashi; Hirano, Satoshi; Ihara, Kentaro; Kudo, Norio; Nagae, Masamichi; Kobayashi, Masanori; Inoue, Michio; Uejima, Tamami; Oda, Shunichiro; Chavas, Leonard M G; Akutsu, Masato; Yamada, Yusuke; Kawasaki, Masato; Matsugaki, Naohiro; Igarashi, Noriyuki; Suzuki, Mamoru; Wakatsuki, Soichi

2006-09-01

Protein crystallization remains one of the bottlenecks in crystallographic analysis of macromolecules. An automated large-scale protein-crystallization system named PXS has been developed consisting of the following subsystems, which proceed in parallel under unified control software: dispensing precipitants and protein solutions, sealing crystallization plates, carrying robot, incubators, observation system and image-storage server. A sitting-drop crystallization plate specialized for PXS has also been designed and developed. PXS can set up 7680 drops for vapour diffusion per hour, which includes time for replenishing supplies such as disposable tips and crystallization plates. Images of the crystallization drops are automatically recorded according to a preprogrammed schedule and can be viewed by users remotely using web-based browser software. A number of protein crystals were successfully produced and several protein structures could be determined directly from crystals grown by PXS. In other cases, X-ray quality crystals were obtained by further optimization by manual screening based on the conditions found by PXS.

Artificial crystals with 3d metal and palladium particles subjected to high-temperature heat treatment

NASA Astrophysics Data System (ADS)

Rinkevich, A. B.; Nemytova, O. V.; Perov, D. V.; Samoylovich, M. I.; Kuznetsov, E. A.

2018-04-01

High-temperature heat treatment has valuable impact on the structure and physical properties of artificial crystals with 3d metal and palladium particles. Artificial crystals are obtained by means of introduction of particles into the interspherical voids of opal matrices. The magnetic properties are studied at the temperatures ranging from 2 to 300 K and in fields up to 350 kOe. Microwave properties are investigated in the millimeter frequency range. The complex dielectric permittivity of several nanocomposites is measured. The influence of heat treatment up to 960 °C on the structure of artificial crystals is clarified.

The different conformations and crystal structures of dihydroergocristine

NASA Astrophysics Data System (ADS)

Mönch, B.; Kraus, W.; Köppen, R.; Emmerling, F.

2016-02-01

The identification of different forms of dihydroergocristine (DHEC) was carried out by crystallization from different organic solvents. DHEC was identified as potential template for molecularly imprinted polymers (MIPs) for the epimeric specific analysis of ergot alkaloids (EAs) in food. DHEC was crystallized from different solvents in order to mimic the typical MIP synthesis conditions. Four new solvatomorphs of DHEC were obtained. All solvatomorphs contain a water molecule in the crystal structure, whereas three compounds contain an additional solvent molecule. Based on the conformation of DHEC a comparison with typical EA molecules was possible. The analysis showed that DHEC is a suitable template for MIPs for EAs.

In situ data collection and structure refinement from microcapillary protein crystallization

PubMed Central

Yadav, Maneesh K.; Gerdts, Cory J.; Sanishvili, Ruslan; Smith, Ward W.; Roach, L. Spencer; Ismagilov, Rustem F.; Kuhn, Peter; Stevens, Raymond C.

2007-01-01

In situ X-ray data collection has the potential to eliminate the challenging task of mounting and cryocooling often fragile protein crystals, reducing a major bottleneck in the structure determination process. An apparatus used to grow protein crystals in capillaries and to compare the background X-ray scattering of the components, including thin-walled glass capillaries against Teflon, and various fluorocarbon oils against each other, is described. Using thaumatin as a test case at 1.8 Å resolution, this study demonstrates that high-resolution electron density maps and refined models can be obtained from in situ diffraction of crystals grown in microcapillaries. PMID:17468785

Optimization of crystallization conditions for biological macromolecules.

PubMed

McPherson, Alexander; Cudney, Bob

2014-11-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success.

Optimization of crystallization conditions for biological macromolecules

PubMed Central

McPherson, Alexander; Cudney, Bob

2014-01-01

For the successful X-ray structure determination of macromolecules, it is first necessary to identify, usually by matrix screening, conditions that yield some sort of crystals. Initial crystals are frequently microcrystals or clusters, and often have unfavorable morphologies or yield poor diffraction intensities. It is therefore generally necessary to improve upon these initial conditions in order to obtain better crystals of sufficient quality for X-ray data collection. Even when the initial samples are suitable, often marginally, refinement of conditions is recommended in order to obtain the highest quality crystals that can be grown. The quality of an X-ray structure determination is directly correlated with the size and the perfection of the crystalline samples; thus, refinement of conditions should always be a primary component of crystal growth. The improvement process is referred to as optimization, and it entails sequential, incremental changes in the chemical parameters that influence crystallization, such as pH, ionic strength and precipitant concentration, as well as physical parameters such as temperature, sample volume and overall methodology. It also includes the application of some unique procedures and approaches, and the addition of novel components such as detergents, ligands or other small molecules that may enhance nucleation or crystal development. Here, an attempt is made to provide guidance on how optimization might best be applied to crystal-growth problems, and what parameters and factors might most profitably be explored to accelerate and achieve success. PMID:25372810

Vladimir V. Lunin | NREL

Science.gov Websites

Protein crystallization X-ray diffraction data collection Protein structure determination Obtaining structures of protein-ligand complexes Site-directed mutagenesis Structure-function relationship Enzymatic CelA," Science (2013) "Sequence, Structure, and Evolution of Cellulases in Glycoside

The Effect of Temperature and Solution pH on the Nucleation of Tetragonal Lysozyme Crystals

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Jacobs, Randolph S.; Frazier, Tyralynn; Snell, Edward H.; Pusey, Marc L.

1999-01-01

Part of the challenge of macromolecular crystal growth for structure determination is obtaining crystals with a volume suitable for x-ray analysis. In this respect an understanding of the effect of solution conditions on macromolecule nucleation rates is advantageous. This study investigated the effects of supersaturation, temperature, and pH on the nucleation rate of tetragonal lysozyme crystals. Batch crystallization plates were prepared at given solution concentrations and incubated at set temperatures over 1 week. The number of crystals per well with their size and axial ratios were recorded and correlated with solution conditions. Crystal numbers were found to increase with increasing supersaturation and temperature. The most significant variable, however, was pH; crystal numbers changed by two orders of magnitude over the pH range 4.0-5.2. Crystal size also varied with solution conditions, with the largest crystals obtained at pH 5.2. Having optimized the crystallization conditions, we prepared a batch of crystals under the same initial conditions, and 50 of these crystals were analyzed by x-ray diffraction techniques. The results indicate that even under the same crystallization conditions, a marked variation in crystal properties exists.

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function.

PubMed

Prill, Dragica; Juhás, Pavol; Billinge, Simon J L; Schmidt, Martin U

2016-01-01

A method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may be used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.

Magnetically-induced ferroelectricity in the (ND4)2[FeCl5(D2O)] molecular compound

PubMed Central

Alberto Rodríguez-Velamazán, José; Fabelo, Óscar; Millán, Ángel; Campo, Javier; Johnson, Roger D.; Chapon, Laurent

2015-01-01

The number of magnetoelectric multiferroic materials reported to date is scarce, as magnetic structures that break inversion symmetry and induce an improper ferroelectric polarization typically arise through subtle competition between different magnetic interactions. The (NH4)2[FeCl5(H2O)] compound is a rare case where such improper ferroelectricity has been observed in a molecular material. We have used single crystal and powder neutron diffraction to obtain detailed solutions for the crystal and magnetic structures of (NH4)2[FeCl5(H2O)], from which we determined the mechanism of multiferroicity. From the crystal structure analysis, we observed an order-disorder phase transition related to the ordering of the ammonium counterion. We have determined the magnetic structure below TN, at 2 K and zero magnetic field, which corresponds to a cycloidal spin arrangement with magnetic moments contained in the ac-plane, propagating parallel to the c-axis. The observed ferroelectricity can be explained, from the obtained magnetic structure, via the inverse Dzyaloshinskii-Moriya mechanism. PMID:26417890

Investigation of angular dependence on photonic bandgap for 1-D photonic crystal

NASA Astrophysics Data System (ADS)

Nigam, Anjali; Suthar, B.; Bhargava, A.; Vijay, Y. K.

2018-05-01

In the present communication, we study the one-dimensional photonic crystal structure. The photonic band structure has been obtained using Plane Wave Expansion Method (PWEM). The studied has been extended to investigate the angular dependence on photonic bandgap for 1-D photonic crystal. The photonic bandgap is same both for TE and TM mode for normal incidence, while both mode move separate with an incidence angle. The photonic bandgap is almost unaffected with angle for TE mode while the bandgap decreases with an incidence angle for TM mode.

Protein Crystal Malic Enzyme

NASA Technical Reports Server (NTRS)

1992-01-01

Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

Synthesis, crystal structure and magnetic properties of a novel tetranuclear oxo-bridged iron(III) butterfly

NASA Astrophysics Data System (ADS)

Arizaga, Livia; Gancheff, Jorge S.; Faccio, Ricardo; Cañón-Mancisidor, Walter; González, Ricardo; Kremer, Carlos; Chiozzone, Raúl

2014-01-01

A novel carboxylate/picolinate oxo-bridged iron(III) cluster, namely [Na2(H2O)8][Fe4(μ-O)2(O2CPh)7(pic)2]2·2H2O (1) where pic = picolinate, has been obtained by reacting "basic iron benzoate" [Fe3O(O2CPh)6(H2O)3](O2CPh) with sodium picolinate in acetonitrile. The compound has been characterized by elemental analysis and IR spectroscopy and its crystal structure has been determined by single-crystal X-ray diffraction.

Radiation-damage-assisted ferroelectric domain structuring in magnesium-doped lithium niobate

NASA Astrophysics Data System (ADS)

Jentjens, L.; Peithmann, K.; Maier, K.; Steigerwald, H.; Jungk, T.

2009-06-01

Irradiation of 5% magnesium-doped lithium niobate crystals (LiNbO3:Mg) with high-energy, low-mass 3He ions, which are transmitted through the crystal, changes the domain reversal properties of the material. This enables easier domain engineering compared to non-irradiated material and assists the formation of small-sized periodically poled domains in LiNbO3:Mg. Periodic domain structures exhibiting a width of ≈520 nm are obtained in radiation-damaged sections of the crystals. The ferroelectric poling behavior between irradiated and non-treated material is compared.

From Recombinant Expression to Crystals: A Step-by-Step Guide to GPCR Crystallography.

PubMed

Shukla, Arun K; Kumari, Punita; Ghosh, Eshan; Nidhi, Kumari

2015-01-01

G protein-coupled receptors (GPCRs) are the primary targets of drugs prescribed for many human pathophysiological conditions such as hypertension, allergies, schizophrenia, asthma, and various types of cancer. High-resolution structure determination of GPCRs has been a key focus area in GPCR biology to understand the basic mechanism of their activation and signaling and to materialize the long-standing dream of structure-based drug design on these versatile receptors. There has been tremendous effort at this front in the past two decades and it has culminated into crystal structures of 27 different receptors so far. The recent progress in crystallization and structure determination of GPCRs has been driven by innovation and cutting-edge developments at every step involved in the process of crystallization. Here, we present a step-by-step description of various steps involved in GPCR crystallization starting from recombinant expression to obtaining diffracting crystals. We also discuss the next frontiers in GPCR biology that are likely to be a primary focus for crystallography efforts in the next decade or so. © 2015 Elsevier Inc. All rights reserved.

The formation and optical properties of planar waveguide in laser crystal Nd:YGG by carbon ion implantation

NASA Astrophysics Data System (ADS)

Zhao, Jin-Hua; Qin, Xi-Feng; Wang, Feng-Xiang; Jiao, Yang; Guan, Jing; Fu, Gang

2017-10-01

As one kind of prominent laser crystal, Nd:Y3Ga5O12 (Nd:YGG) crystal has outstanding performance on laser excitation at multi-wavelength which have shown promising applications in optical communication field. In addition, Nd:YGG crystal has potential applications in medical field due to its ability of emit the laser at 1110 nm. Optical waveguide structure with high quality could improve the efficiency of laser emission. In this work, we fabricated the optical planar waveguide on Nd:YGG crystal by medium mass ion implantation which was convinced an effective method to realize a waveguide structure with superior optical properties. The sample is implanted by C ions at energy of 5.0 MeV with the fluence of 1 × 1015 ions/cm2. We researched the optical propagation properties in the Nd:YGG waveguide by end-face coupling and prism coupling method. The Nd ions fluorescent properties are obtained by a confocal micro-luminescence measurement. The fluorescent properties of Nd ions obtained good reservation after C ion implantation. Our work has reference value for the application of Nd:YGG crystal in the field of optical communication.

Melt Flow before Crystal Seeding in Cz Si Growth with Transversal MF

NASA Astrophysics Data System (ADS)

Iizuka, Masaya; Mukaiyama, Yuji; Demina, S. E.; Kalaev, V. V.

2017-06-01

Industrial Cz growth of Si crystal of 300 mm and higher diameter usually requires DC magnetic fields (MFs) to suppress turbulence in the melt. We present 3D unsteady analysis of melt turbulent convection in an industrial Cz system coupled with the effect of the transversal MF for different argon gas flow rates for the stage before crystal seeding. We have performed detailed 2D axisymmetric modeling of global heat transfer in the whole Cz furnace. Radiative heat fluxes obtained in 2D modeling have been used in detailed 3D steady and unsteady modeling of crystallization zone. LES method is applied as a predictive approach for modeling of turbulent flow of silicon melt. We have obtained flow structure and temperature distribution in the melt, which were different from previously reported data. We have observed a well-fixed dark spike which includes low temperature melt area on the melt free surface in MF cases. These results indicates that MF and argon flow rate conditions are important to achieve stable positioning of the dark spike on the melt free surface for optimized crystal seeding without uncontrollable meltdown and single crystal structure loss.

A comparative study on the crystal structure of bicycle analogues to the natural phytotoxin helminthosporins

NASA Astrophysics Data System (ADS)

Barbosa, Luiz Cláudio de Almeida; Teixeira, Robson Ricardo; Nogueira, Leonardo Brandão; Maltha, Celia Regina Alvares; Doriguetto, Antônio Carlos; Martins, Felipe Terra

2016-02-01

Herein we described structural insights of a series of analogues to helminthosporin phytotoxins. The key reaction used to prepare the compounds corresponded to the [3 + 4] cycloaddition between the oxyallyl cation generated from 2,4-dibromopentan-3-one and different furans. Their structures were confirmed upon IR, NMR and X-ray diffraction analyses. While bicycles 7, 8 and 9 crystallize in the centrosymmetric monoclinic space group P21/c, compound 10 was solved in the noncentrosymmetric orthorhombic space group P212121. The solid materials obtained were shown to be racemic crystals (7, 8, 9) or racemic conglomerate (10). In all compounds, there is formation of a bicycle featured by fused tetrahydropyranone and 2,5-dihydrofuran rings. They adopt chair and envelope conformations, respectively. Crystal packing of all compounds is stabilized through C-H•••O contacts. Conformational aspects as well as similarities and differences among the crystal structures of the synthesized analogues are discussed.

Sodium Chloride Crystal-Induced SERS Platform for Controlled Highly Sensitive Detection of Illicit Drugs.

PubMed

Yu, Borong; Li, Pan; Zhou, Binbin; Tang, Xianghu; Li, Shaofei; Yang, Liangbao

2018-04-03

A sodium chloride crystal-driven spontaneous 'hot spot' structure was demonstrated as a SERS-active platform, to get reproducible SERS signals, and eliminate the need for mapping large areas, in comparison with solution phase testing. During the process of solvent evaporation, the crystals produced induced silver aggregates to assemble around themselves. The micro-scale crystals can also act as a template to obtain an optical position, such that the assembled hot area is conveniently located during SERS measurements. More importantly, the chloride ions added in colloids can also replace the citrate and on the surface of the silver sol, and further decrease the background interference. High quality SERS spectra from heroin, methamphetamine (MAMP), and cocaine have been obtained on the crystal-driven hot spot structure with high sensitivity and credible reproducibility. This approach can not only bring the nanoparticles to form plasmonic hot spots in a controlled way, and thus provide high sensitivity, but also potentially be explored as an active substrate for label-free detection of other illicit drugs or additives. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Expression, purification and crystallization of a lyssavirus matrix (M) protein

PubMed Central

Assenberg, René; Delmas, Olivier; Graham, Stephen C.; Verma, Anil; Berrow, Nick; Stuart, David I.; Owens, Raymond J.; Bourhy, Hervé; Grimes, Jonathan M.

2008-01-01

The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number of factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6122 or P6522, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress. PMID:18391421

Crystallization and preliminary X-ray crystallographic analysis of two vascular apoptosis-inducing proteins (VAPs) from Crotalus atrox venom

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

Igarashi, Tomoko; Oishi, Yuko; Araki, Satohiko

Vascular apoptosis-inducing protein 1 (VAP1) and VAP2 from C. atrox venom were crystallized in variety of different crystal forms. Diffraction data sets were obtained to 2.5 and 2.15 Å resolution for VAP1 and VAP2, respectively. VAPs are haemorrhagic snake-venom toxins belonging to the reprolysin family of zinc metalloproteinases. In vitro, VAPs induce apoptosis specifically in cultured vascular endothelial cells. VAPs have a modular structure that bears structural homology to mammalian ADAMs (a disintegrin and metalloproteinases). VAP1 is a homodimer with a MW of 110 kDa in which the monomers are connected by a single disulfide bridge. VAP2 is homologous tomore » VAP1 and exists as a monomer with a MW of 55 kDa. In the current study, several crystal forms of VAP1 and VAP2 were obtained using the vapour-diffusion method and diffraction data sets were collected using SPring-8 beamlines. The best crystals of VAP1 and VAP2 generated data sets to 2.5 and 2.15 Å resolution, respectively.« less

The role of hydrogen bonds in the crystals of 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate and 4-hydroxybenzenesulfonate - X-ray and spectroscopic studies.

PubMed

Bryndal, I; Marchewka, M; Wandas, M; Sąsiadek, W; Lorenc, J; Lis, T; Dymińska, L; Kucharska, E; Hanuza, J

2014-04-05

Two new organic-organic salts, 2-amino-4-methyl-5-nitropyridinium trifluoroacetate monohydrate (AMNP-TFA), and 2-amino-4-methyl-5-nitropyridinium 4-hydroxybenzenesulfonate (AMNP-HBS), were obtained and characterized by means of FT-IR, FT-Raman and single crystal X-ray crystallography. In the former crystal, the cations, anions and water molecules are linked into layers by three types of hydrogen bonds, NPH⋯O, NAH⋯O and OH⋯O. These layers are connected by weaker CH⋯O hydrogen bonds. In the latter crystal, the cations and anions form one-dimensional structure through a number of hydrogen-bonding interactions involving the OH, NH(+) and NH2 groups as donors. In this case the NPH⋯O and NAH⋯O hydrogen bonds are formed. The combination of interactions between cations and anions results in the formation of columns. Additionally, there are π-π stacking interactions between the columns. The obtained X-ray structural data are related to the vibrational spectra of the studied crystals. Copyright © 2013 Elsevier B.V. All rights reserved.

LCP crystallization and X-ray diffraction analysis of VcmN, a MATE transporter from Vibrio cholerae

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

Kusakizako, Tsukasa; Tanaka, Yoshiki; Hipolito, Christopher J.

A V. cholerae MATE transporter was crystallized using the lipidic cubic phase (LCP) method. X-ray diffraction data sets were collected from single crystals obtained in a sandwich plate and a sitting-drop plate to resolutions of 2.5 and 2.2 Å, respectively. Multidrug and toxic compound extrusion (MATE) transporters, one of the multidrug exporter families, efflux xenobiotics towards the extracellular side of the membrane. Since MATE transporters expressed in bacterial pathogens contribute to multidrug resistance, they are important therapeutic targets. Here, a MATE-transporter homologue from Vibrio cholerae, VcmN, was overexpressed in Escherichia coli, purified and crystallized in lipidic cubic phase (LCP). X-raymore » diffraction data were collected to 2.5 Å resolution from a single crystal obtained in a sandwich plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 52.3, b = 93.7, c = 100.2 Å. As a result of further LCP crystallization trials, crystals of larger size were obtained using sitting-drop plates. X-ray diffraction data were collected to 2.2 Å resolution from a single crystal obtained in a sitting-drop plate. The crystal belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 61.9, b = 91.8, c = 100.9 Å. The present work provides valuable insights into the atomic resolution structure determination of membrane transporters.« less

An overview of heavy-atom derivatization of protein crystals

PubMed Central

Pike, Ashley C. W.; Garman, Elspeth F.; Krojer, Tobias; von Delft, Frank; Carpenter, Elisabeth P.

2016-01-01

Heavy-atom derivatization is one of the oldest techniques for obtaining phase information for protein crystals and, although it is no longer the first choice, it remains a useful technique for obtaining phases for unknown structures and for low-resolution data sets. It is also valuable for confirming the chain trace in low-resolution electron-density maps. This overview provides a summary of the technique and is aimed at first-time users of the method. It includes guidelines on when to use it, which heavy atoms are most likely to work, how to prepare heavy-atom solutions, how to derivatize crystals and how to determine whether a crystal is in fact a derivative. PMID:26960118

Structural colored gels for tunable soft photonic crystals.

PubMed

Harun-Ur-Rashid, Mohammad; Seki, Takahiro; Takeoka, Yukikazu

2009-01-01

A periodically ordered interconnecting porous structure can be embodied in chemical gels by using closest-packed colloidal crystals as templates. The interconnecting porosity not only provides a quick response but also endows the porous gels with structural color arising from coherent Bragg optical diffraction. The structural colors revealed by porous gels can be regulated by several techniques, and thus, it is feasible to obtain desirable, smart, soft materials. A well-known thermosensitive monomer, N-isopropylacrylamide (NIPA), and other minor monomers were used to fabricate various structural colored gels. The selection of minor monomers depended on the targeted properties. This review focuses on the synthesis of templates, structural colored porous gels, and the applications of structural colored gel as smart soft materials for tunable photonic crystals. (c) 2009 The Japan Chemical Journal Forum and Wiley Periodicals, Inc.

Solid state parameters, structure elucidation, High Resolution X-Ray Diffraction (HRXRD), phase matching, thermal and impedance analysis on L-Proline trichloroacetate (L-PTCA) NLO single crystals.

PubMed

Kalaiselvi, P; Raj, S Alfred Cecil; Jagannathan, K; Vijayan, N; Bhagavannarayana, G; Kalainathan, S

2014-11-11

Nonlinear optical single crystal of L-Proline trichloroacetate (L-PTCA) was successfully grown by Slow Evaporation Solution Technique (SEST). The grown crystals were subjected to single crystal X-ray diffraction analysis to confirm the structure. From the single crystal XRD data, solid state parameters were determined for the grown crystal. The crystalline perfection has been evaluated using high resolution X-ray diffractometer. The frequencies of various functional groups were identified from FTIR spectral analysis. The percentage of transmittance was obtained from UV Visible spectral analysis. TGA-DSC measurements indicate the thermal stability of the crystal. The dielectric constant, dielectric loss and ac conductivity were measured by the impedance analyzer. The DC conductivity was calculated by the cole-cole plot method. Copyright © 2014 Elsevier B.V. All rights reserved.

Crystallization and preliminary X-ray diffraction studies of polyketide synthase-1 (PKS-1) from Cannabis sativa

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

Taguchi, Chiho; Quantum Beam Science Directorate, Japan Atomic Energy Agency; Taura, Futoshi

Polyketide synthase-1 from C. sativa has been crystallized. The crystal diffracted to 1.55 Å resolution with sufficient quality for further structure determination. Polyketide synthase-1 (PKS-1) is a novel type III polyketide synthase that catalyzes the biosynthesis of hexanoyl triacetic acid lactone in Cannabis sativa (Mexican strain). PKS-1 was overproduced in Escherichia coli, purified and finally crystallized in two different space groups. The crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M calcium acetate and 20%(w/v) polyethylene glycol 3350 diffracted to 1.65 Å resolution and belonged to space group P1, with unit-cell parameters a = 54.3, b =more » 59.3, c = 62.6 Å, α = 69, β = 81, γ = 80°. Another crystal obtained in 0.1 M HEPES buffer pH 7.5 containing 0.2 M sodium chloride and 20%(w/v) polyethylene glycol 3350 diffracted to 1.55 Å resolution and belonged to space group P2{sub 1}2{sub 1}2{sub 1}, with unit-cell parameters a = 54.3, b = 110, c = 130 Å. These data will enable us to determine the crystal structure of PKS-1.« less

Photonic crystal fiber sensing characteristics research based on alcohol asymmetry filling

NASA Astrophysics Data System (ADS)

Shi, Fu-quan; Luo, Yan; Li, Hai-tao; Peng, Bao-jin

2018-02-01

A new type of Sagnac fiber temperature sensor based on alcohol asymmetric filling photonic crystal fiber is proposed. First, the corrosion of photonic crystal fiber and the treatment of air hole collapse are carried out. Then, the asymmetric structure of photonic crystal fiber is filled with alcohol, and then the structure is connected to the Sagnac interference ring. When the temperature changes, the thermal expansion effect of filling alcohol will lead to the change of birefringence of photonic crystal fiber, so that the interference spectrum of the sensor will drift along with the change of temperature. The experimental results show that the interference red shift will occur with the increase of temperature, and the temperature sensitivity is 0.1864nm/ °C. The sensor has high sensitivity to temperature. At the same time, the structure has the advantages of high stability, anti electromagnetic interference and easy to build. It provides a new method for obtaining birefringence in ordinary photonic crystal fibers.

A framework for multi-scale simulation of crystal growth in the presence of polymers.

PubMed

Mandal, Taraknath; Huang, Wenjun; Mecca, Jodi M; Getchell, Ashley; Porter, William W; Larson, Ronald G

2017-03-01

We present a multi-scale simulation method for modeling crystal growth in the presence of polymer excipients. The method includes a coarse-grained (CG) model for small molecules of known crystal structure whose force field is obtained using structural properties from atomistic simulations. This CG model is capable of stabilizing the molecular crystal structure and capturing the crystal growth from the melt for a wide range of small organic molecules, as demonstrated by application of our method to the molecules isoniazid, urea, sulfamethoxazole, prilocaine, oxcarbazepine, and phenytoin. This CG model can also be used to study the effect of additives, such as polymers, on the inhibition of crystal growth by polymers, as exemplified by our simulation of suppression of the rate of crystal growth of phenytoin, an active pharmaceutical ingredient (API), by a cellulose excipient, functionalized with acetate (Ac), hydroxy-propyl (Hp) and succinate (Su) groups. We show that the efficacy of the cellulosic polymers in slowing crystal growth of small molecules strongly depends on the functional group substitution on the cellulose backbone, with the acetate substituent group slowing crystal growth more than does the deprotonated succinate group, which we confirm by experimental drug supersaturation studies.

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.

Controlled In Meso Phase Crystallization – A Method for the Structural Investigation of Membrane Proteins

PubMed Central

Kubicek, Jan; Schlesinger, Ramona; Baeken, Christian; Büldt, Georg; Schäfer, Frank; Labahn, Jörg

2012-01-01

We investigated in meso crystallization of membrane proteins to develop a fast screening technology which combines features of the well established classical vapor diffusion experiment with the batch meso phase crystallization, but without premixing of protein and monoolein. It inherits the advantages of both methods, namely (i) the stabilization of membrane proteins in the meso phase, (ii) the control of hydration level and additive concentration by vapor diffusion. The new technology (iii) significantly simplifies in meso crystallization experiments and allows the use of standard liquid handling robots suitable for 96 well formats. CIMP crystallization furthermore allows (iv) direct monitoring of phase transformation and crystallization events. Bacteriorhodopsin (BR) crystals of high quality and diffraction up to 1.3 Å resolution have been obtained in this approach. CIMP and the developed consumables and protocols have been successfully applied to obtain crystals of sensory rhodopsin II (SRII) from Halobacterium salinarum for the first time. PMID:22536388

Electron paramagnetic resonance study of radiation-induced paramagnetic centers in succinic anhydride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz; Er, Emine

2017-09-01

Succinic anhydride single crystals were exposed to 60Co-gamma irradiation at room temperature. The irradiated single crystals were investigated at 125 K by Electron Paramagnetic Resonance (EPR) Spectroscopy. The investigation of EPR spectra of irradiated single crystals of succinic anhydride showed the presence of two succinic anhydride anion radicals. The anion radicals observed in gamma-irradiated succinic anhydride single crystal were created by the scission of the carbon-oxygen double bond. The structure of EPR spectra demonstrated that the hyperfine splittings arise from the same radical species. The reduction of succinic anhydride was identified which is formed by the addition of an electron to oxygen of the Csbnd O bond. The g values, the hyperfine structure constants and direction cosines of the radiation damage centers observed in succinic anhydride single crystal were obtained.

Improved performance of HgCdTe infrared detector focal plane arrays by modulating light field based on photonic crystal structure

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

Liang, Jian; Hu, Weida, E-mail: wdhu@mail.sitp.ac.cn; Ye, Zhenhua

2014-05-14

An HgCdTe long-wavelength infrared focal plane array photodetector is proposed by modulating light distributions based on the photonic crystal. It is shown that a promising prospect of improving performance is better light harvest and dark current limitation. To optimize the photon field distributions of the HgCdTe-based photonic crystal structure, a numerical method is built by combining the finite-element modeling and the finite-difference time-domain simulation. The optical and electrical characteristics of designed HgCdTe mid-wavelength and long-wavelength photon-trapping infrared detector focal plane arrays are obtained numerically. The results indicate that the photon crystal structure, which is entirely compatible with the large infraredmore » focal plane arrays, can significantly reduce the dark current without degrading the quantum efficiency compared to the regular mesa or planar structure.« less

Calculated photonic structures for infrared emittance control

NASA Astrophysics Data System (ADS)

Rung, Andreas; Ribbing, Carl G.

2002-06-01

Using an available program package based on the transfer-matrix method, we calculated the photonic band structure for two different structures: a quasi-three-dimensional crystal of square air rods in a high-index matrix and an opal structure of high-index spheres in a matrix of low index, epsilon = 1.5. The high index used is representative of gallium arsenide in the thermal infrared range. The geometric parameters of the rod dimension, sphere radius, and lattice constants were chosen to give total reflectance for normal incidence, i.e., minimum thermal emittance, in either one of the two infrared atmospheric windows. For these four photonic crystals, the bulk reflectance spectra and the wavelength-averaged thermal emittance as a function of crystal thickness were calculated. The results reveal that potentially useful thermal signature suppression is obtained for crystals as thin as 20-50 mum, i.e., comparable with that of a paint layer.

Low-Temperature Crystal Structures of the Hard Core Square Shoulder Model.

PubMed

Gabriëlse, Alexander; Löwen, Hartmut; Smallenburg, Frank

2017-11-07

In many cases, the stability of complex structures in colloidal systems is enhanced by a competition between different length scales. Inspired by recent experiments on nanoparticles coated with polymers, we use Monte Carlo simulations to explore the types of crystal structures that can form in a simple hard-core square shoulder model that explicitly incorporates two favored distances between the particles. To this end, we combine Monte Carlo-based crystal structure finding algorithms with free energies obtained using a mean-field cell theory approach, and draw phase diagrams for two different values of the square shoulder width as a function of the density and temperature. Moreover, we map out the zero-temperature phase diagram for a broad range of shoulder widths. Our results show the stability of a rich variety of crystal phases, such as body-centered orthogonal (BCO) lattices not previously considered for the square shoulder model.

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations

PubMed Central

Ahlstrom, Logan S.; Vorontsov, Ivan I.; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations. PMID:28107510

Effect of the Crystal Environment on Side-Chain Conformational Dynamics in Cyanovirin-N Investigated through Crystal and Solution Molecular Dynamics Simulations.

PubMed

Ahlstrom, Logan S; Vorontsov, Ivan I; Shi, Jun; Miyashita, Osamu

2017-01-01

Side chains in protein crystal structures are essential for understanding biochemical processes such as catalysis and molecular recognition. However, crystal packing could influence side-chain conformation and dynamics, thus complicating functional interpretations of available experimental structures. Here we investigate the effect of crystal packing on side-chain conformational dynamics with crystal and solution molecular dynamics simulations using Cyanovirin-N as a model system. Side-chain ensembles for solvent-exposed residues obtained from simulation largely reflect the conformations observed in the X-ray structure. This agreement is most striking for crystal-contacting residues during crystal simulation. Given the high level of correspondence between our simulations and the X-ray data, we compare side-chain ensembles in solution and crystal simulations. We observe large decreases in conformational entropy in the crystal for several long, polar and contacting residues on the protein surface. Such cases agree well with the average loss in conformational entropy per residue upon protein folding and are accompanied by a change in side-chain conformation. This finding supports the application of surface engineering to facilitate crystallization. Our simulation-based approach demonstrated here with Cyanovirin-N establishes a framework for quantitatively comparing side-chain ensembles in solution and in the crystal across a larger set of proteins to elucidate the effect of the crystal environment on protein conformations.

Crystal structure determination of new antimitotic agent bis(p-fluorobenzyl)trisulfide.

PubMed

An, Haoyun; Hu, Xiurong; Gu, Jianming; Chen, Linshen; Xu, Weiming; Mo, Xiaopeng; Xu, Wanhong; Wang, Xiaobo; Xu, Xiao

2008-01-01

The purpose of this research was to investigate the physical characteristics and crystalline structure of bis(p-fluorobenzyl)trisulfide, a new anti-tumor agent. Methods used included X-ray single crystal diffraction, X-ray powder diffraction (XRPD), Fourier-transform infrared (FT-IR) spectroscopy, differential scanning calorimetric (DSC) and thermogravimetric (TG) analyses. The findings obtained with X-ray single crystal diffraction showed that a monoclinic unit cell was a = 12.266(1) A, b = 4.7757(4) A, c = 25.510(1) A, beta = 104.25(1) degrees ; cell volume = 1,448.4(2) A(3), Z = 4, and space group C2/c. The XRPD studies of the four crystalline samples, obtained by recrystallization from four different solvents, indicated that they had the same diffraction patterns. The diffraction pattern stimulated from the crystal structure data is in excellent agreement with the experimental results. In addition, the identical FT-IR spectra of the four crystalline samples revealed absorption bands corresponding to S-S and C-S stretching as well as the characteristic aromatic substitution. Five percent weight loss at 163.3 degrees C was observed when TG was used to study the decomposition process in the temperature range of 20-200 degrees C. DSC also allowed for the determination of onset temperatures at 60.4(1)-60.7(3) degrees C and peak temperatures at 62.1(3)-62.4(3) degrees C for the four crystalline samples studied. The results verified that the single crystal structure shared the same crystal form with the four crystalline samples investigated.

Multilevel organization in hybrid thin films for optoelectronic applications.

PubMed

Vohra, Varun; Bolognesi, Alberto; Calzaferri, Gion; Botta, Chiara

2009-10-20

In this work we report two simple approaches to prepare hybrid thin films displaying a high concentration of zeolite crystals that could be used as active layers in optoelectronic devices. In the first approach, in order to organize nanodimensional zeolite crystals of 40 nm diameter in an electroactive environment, we chemically modify their external surface and play on the hydrophilic/hydrophobic forces. We obtain inorganic nanocrystals that self-organize in honeycomb electroluminescent polymer structures obtained by breath figure formation. The different functionalizations of the zeolite surface result in different organizations inside the cavities of the polymeric structure. The second approach involving soft-litography techniques allows one to arrange single dye-loaded zeolite L crystals of 800 nm of length by mechanical loading into the nanocavities of a conjugated polymer. Both techniques result in the formation of thin hybrid films displaying three levels of organization: organization of the dye molecules inside the zeolite nanochannels, organization of the zeolite crystals inside the polymer cavities, and micro- or nanostructuration of the polymer.

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

Han, Fei; Wan, Xiangang; Phelan, Daniel

ZrCuSi 2-type CePd 1-xBi 2 crystals were obtained from excess Bi flux. Magnetic susceptibility measurements reveal that CePd 1-xBi 2 is a highly anisotropic antiferromagnet with transition temperature at 6 K, and a magnetic-field-induced metamagnetic transition at 5 T. An enhanced Sommerfeld coefficient of γ of 0.199 J-mol-Ce -1K -2 obtained from specific heat measurements suggests a moderate Kondo effect in CePd 1-xBi 2. In addition to the antiferromagnetic peak the resistivity curve shows a shoulder-like behavior which could be attributed to the presence of Kondo effect and crystal-electric-field effects in this compound. Magnetoresistance and Hall effect measurements suggest anmore » interplay between Kondo and crystal-electric-field effects which reconstructs the Fermi surface topology of CePd 1-xBi 2 around 75 K. Electronic structure calculations reveal the Pd vacancies are important to the magnetic structure and enhance the crystal-electric-field effects which quench the orbital moment of Ce at low temperatures.« less

High-Resolution Protein Structure Determination by Serial Femtosecond Crystallography

PubMed Central

Boutet, Sébastien; Lomb, Lukas; Williams, Garth J.; Barends, Thomas R. M.; Aquila, Andrew; Doak, R. Bruce; Weierstall, Uwe; DePonte, Daniel P.; Steinbrener, Jan; Shoeman, Robert L.; Messerschmidt, Marc; Barty, Anton; White, Thomas A.; Kassemeyer, Stephan; Kirian, Richard A.; Seibert, M. Marvin; Montanez, Paul A.; Kenney, Chris; Herbst, Ryan; Hart, Philip; Pines, Jack; Haller, Gunther; Gruner, Sol M.; Philipp, Hugh T.; Tate, Mark W.; Hromalik, Marianne; Koerner, Lucas J.; van Bakel, Niels; Morse, John; Ghonsalves, Wilfred; Arnlund, David; Bogan, Michael J.; Caleman, Carl; Fromme, Raimund; Hampton, Christina Y.; Hunter, Mark S.; Johansson, Linda C.; Katona, Gergely; Kupitz, Christopher; Liang, Mengning; Martin, Andrew V.; Nass, Karol; Redecke, Lars; Stellato, Francesco; Timneanu, Nicusor; Wang, Dingjie; Zatsepin, Nadia A.; Schafer, Donald; Defever, James; Neutze, Richard; Fromme, Petra; Spence, John C. H.; Chapman, Henry N.; Schlichting, Ilme

2013-01-01

Structure determination of proteins and other macromolecules has historically required the growth of high-quality crystals sufficiently large to diffract x-rays efficiently while withstanding radiation damage. We applied serial femtosecond crystallography (SFX) using an x-ray free-electron laser (XFEL) to obtain high-resolution structural information from microcrystals (less than 1 micrometer by 1 micrometer by 3 micrometers) of the well-characterized model protein lysozyme. The agreement with synchrotron data demonstrates the immediate relevance of SFX for analyzing the structure of the large group of difficult-to-crystallize molecules. PMID:22653729

Crystal structure of new AsS{sub 2} compound

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

Bolotina, N. B., E-mail: bolotina@ns.crys.ras.ru; Brazhkin, V. V.; Dyuzheva, T. I.

2013-01-15

AsS{sub 2} single crystals have been obtained for the first time from an As{sub 2}S{sub 3} melt at pressures above 6 GPa and temperatures above 800 K in the As{sub 2}S{sub 3} {yields} AsS + AsS{sub 2} reaction. The monoclinic structure of the new high-pressure phase is solved by X-ray diffraction analysis and compared to the structure of high-pressure AsS phase, which was studied previously.

Synthesis and crystal structure of the solid solution Co3(SeO3)3-x(PO3OH)x(H2O) involving crystallographic split positions of Se4+ and P5+.

PubMed

Zimmermann, Iwan; Johnsson, Mats

2013-10-21

Three new cobalt selenite hydroxo-phosphates laying in the solid solution Co3(SeO3)3-x(PO3OH)x(H2O), with x = 0.8, x = 1.0, and x = 1.2 are reported. Single crystals were obtained by hydrothermal synthesis and the crystal structure was determined by single crystal X-ray diffraction. The structure can be described as a 3D framework having selenite and hydroxo-phosphate groups protruding into channels in the crystal structure. Se(4+) and P(5+) share a split position in the structure so that either SeO3 groups having a stereochemically active lone pair or tetrahedrally coordinated PO3OH groups are present. The OH-group is thus only present when the split position is occupied by P(5+). The crystal water is coordinated to a cobalt atom and TG and IR measurements show that the water and hydroxyl groups leave the structure at unusually high temperatures (>450 °C). Magnetic susceptibility measurements show antiferromagnetic coupling below 16 K and a magnetic moment of 4.02(3) μB per Co atom was observed.

Mutation of Surface Residues to Promote Crystallization of Activated Factor XI as a Complex with Benzamidine: an Essential Step for the Iterative Structure-Based Design of Factor XI Inhibitors

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

Jin,L.; Pandey, P.; Babine, R.

Activated factor XI (FXIa) is a key enzyme in the amplification phase of the blood-coagulation cascade. Thus, a selective FXIa inhibitor may have lesser bleeding liabilities and provide a safe alternative for antithrombosis therapy to available drugs on the market. In a previous report, the crystal structures of the catalytic domain of FXIa (rhFXI370-607) in complex with various ecotin mutants have been described [Jin et al. (2005), Journal of Biological Chemistry 280, 4704-4712]. However, ecotin forms a matrix-like interaction with rhFXI370-607 and is impossible to displace with small-molecule inhibitors; ecotin crystals are therefore not suitable for iterative structure-based ligand design.more » In addition, rhFXI370-607 did not crystallize in the presence of small-molecule ligands. In order to obtain the crystal structure of rhFXI370-607 with a weak small-molecule ligand, namely benzamidine, several rounds of surface-residue mutation were implemented to promote crystal formation of rhFXI370-607. A quadruple mutant of rhFXI370-607 (rhFXI370-607-S434A, T475A, C482S, K437A) readily crystallized in the presence of benzamidine. The benzamidine in the preformed crystals was easily exchanged with other FXIa small-molecule inhibitors. These crystals have facilitated the structure-based design of small-molecule FXIa inhibitors.« less

EPR study of free radical in gamma-irradiated bis(cyclopentadienyl)zirconium dichloride single crystal

NASA Astrophysics Data System (ADS)

Caliskan, Betul; Caliskan, Ali Cengiz

2017-06-01

Bis(cyclopentadienyl)zirconium dichloride (BCZD; zirconocene dichloride) single crystals were exposed to 60Co-γ irradiation at room temperature. The irradiated single crystals were investigated between 125 and 470 K by electron paramagnetic resonance spectroscopy. The spectra of the crystals were found to be temperature independent. The paramagnetic center was attributed to the cyclopentadienyl radical. The g values of the radiation damage center observed in BCZD single crystal and the hyperfine structure constants of the free electron with nearby protons were obtained.

Preparation and magnetic properties of nickel nanowires by reduction in ethylene glycol medium under the influence of magnetic field

NASA Astrophysics Data System (ADS)

Sun, Wanshuo; Cheng, Junsheng; Li, Lankai; Chen, Shunzhong; Chang, Kun

2017-01-01

Nickel nanowires have successfully been fabricated through a simple liquid reduction in ethylene glycol medium with a 0.3T magnetic field applied. The effect of uniform magnetic field and solvent on the morphology and the crystal structure of magnetic nickel were studied. Scanning electron microscope images and transmission electron scope images s how that the effect of the external magnetic field on the morphology of nickel nanowires. X-ray diffraction shows the crystal structure of as-prepared products. And a energy disperse spectroscopy and a vibrating sample magnetometer are used to analyze the composition and static magnetic properties. The results show that the straight wires with an average diameter of about 100 nm and a length of several microns were obtained and mainly composed by fcc structure in the solvent of ethylene glycol. Magnetic measurements show that the saturation magnetization of the as-obtained products in a 0.3 T external magnetic field is 36 emu/g, less than that of bulk nickel crystal, and the coercivity of them is 186 emu/g, larger than that of bulk crystal with the mole ratio of sodium borohydride to nickel sulfate is 1:1000. This kind of nanowires array has potential applications with the special one-dimensional structures.

Density functional theory determination of structural and electronic properties of struvite.

PubMed

Romanowski, Zbigniew; Kempisty, Paweł; Prywer, Jolanta; Krukowski, Stanisław; Torzewska, Agnieszka

2010-07-29

Crystallographic structure, total energy, electronic structure, and the most important elastic properties of struvite, NH(4)MgPO(4).6H(2)O, the main component of infectious urinary stones, are presented. The calculations were performed using ab initio full-electron calculations within the density functional theory-generalized gradient approximation (DFT-GGA) framework. The obtained crystallographic symmetry and the calculated lattice parameters and also the elastic constants are in good agreement with the experimental data. The elastic properties are essential for establishing an optimal response of urinary stones during shock-wave lithotripsy. The calculated electronic charge distribution confirms the layered structure of the struvite crystals. The polar character of the crystal, well-known from crystal growth experiments, was also confirmed by the magnitude of spontaneous polarization which was obtained from direct determination of the electrical dipole density. The calculated value of spontaneous polarization is equal to -8.8 microC cm(-2). This feature may play a key role in struvite crystallization, electrically binding the charged active impurities and other active species, and consequently determining urinary stone formation. We also present the results of our own experiment of the mineralization of struvite induced to growth by Proteus bacteria which are mainly isolated from infectious urinary stones.

TaRh2B2 and NbRh2B2: Superconductors with a chiral noncentrosymmetric crystal structure.

PubMed

Carnicom, Elizabeth M; Xie, Weiwei; Klimczuk, Tomasz; Lin, Jingjing; Górnicka, Karolina; Sobczak, Zuzanna; Ong, Nai Phuan; Cava, Robert J

2018-05-01

It is a fundamental truth in solid compounds that the physical properties follow the symmetry of the crystal structure. Nowhere is the effect of symmetry more pronounced than in the electronic and magnetic properties of materials-even the projection of the bulk crystal symmetry onto different crystal faces is known to have a substantial impact on the surface electronic states. The effect of bulk crystal symmetry on the properties of superconductors is widely appreciated, although its study presents substantial challenges. The effect of a lack of a center of symmetry in a crystal structure, for example, has long been understood to necessitate that the wave function of the collective electron state that gives rise to superconductivity has to be more complex than usual. However, few nonhypothetical materials, if any, have actually been proven to display exotic superconducting properties as a result. We introduce two new superconductors that in addition to having noncentrosymmetric crystal structures also have chiral crystal structures. Because the wave function of electrons in solids is particularly sensitive to the host material's symmetry, crystal structure chirality is expected to have a substantial effect on their superconducting wave functions. Our two experimentally obtained chiral noncentrosymmetric superconducting materials have transition temperatures to superconductivity that are easily experimentally accessible, and our basic property characterization suggests that their superconducting properties may be unusual. We propose that their study may allow for a more in-depth understanding of how chirality influences the properties of superconductors and devices that incorporate them.

Influence of computational domain size on the pattern formation of the phase field crystals

NASA Astrophysics Data System (ADS)

Starodumov, Ilya; Galenko, Peter; Alexandrov, Dmitri; Kropotin, Nikolai

2017-04-01

Modeling of crystallization process by the phase field crystal method (PFC) represents one of the important directions of modern computational materials science. This method makes it possible to research the formation of stable or metastable crystal structures. In this paper, we study the effect of computational domain size on the crystal pattern formation obtained as a result of computer simulation by the PFC method. In the current report, we show that if the size of a computational domain is changed, the result of modeling may be a structure in metastable phase instead of pure stable state. The authors present a possible theoretical justification for the observed effect and provide explanations on the possible modification of the PFC method to account for this phenomenon.

A novel ultra-broadband single polarization single mode photonic crystal fiber

NASA Astrophysics Data System (ADS)

Jiang, Linghong; Zheng, Yi; Hou, Lantian; Zheng, Kai; Peng, Jiying; Zhao, Xingtao

2017-08-01

The concept of employing a central hole infiltrated with nematic liquid crystal (NLC) and two additional air holes in the core region is exploited to obtain an ultra-broadband single polarization single mode photonic crystal fiber (SPSM-PCF). The effects of structural parameters on the SPSM operation are studied using the full-vectorial finite element method. Numerical results show that the proposed structure can attain the SPSM operation bandwidth of 1610 nm (from 1.51 to 3.12 μm) with confinement loss lower than 0.01 dB/km. The SPSM operation range can also be widely tuned to shorter wavelengths by adjusting the structure parameters. And meanwhile, a broad dispersion-flattened SPSM PCF is also obtained around the communication wavelength. Moreover, the dual-core SPSM PCF has also been investigated, enabling potential applications in the wavelength splitter of 1.31 and 1.55 μm bands at a short fiber length of 1.629 mm with SPSM operation.

Structure stability of HKUST-1 towards water and ethanol and their effect on its CO2 capture properties.

PubMed

Álvarez, J Raziel; Sánchez-González, Elí; Pérez, Eric; Schneider-Revueltas, Emilia; Martínez, Ana; Tejeda-Cruz, Adriana; Islas-Jácome, Alejandro; González-Zamora, Eduardo; Ibarra, Ilich A

2017-07-18

Water and ethanol stabilities of the crystal structure of the Cu-based metal-organic framework (MOF) HKUST-1 have been investigated. Vapour (water and ethanol) sorption isotherms and cyclability were measured by a dynamic strategy. The ethanol sorption capacity of HKUST-1 at 303 K remained unchanged contrasting water sorption (which decreased along with the sorption experiment time). Considering the binding energy of each sorbate with the open Cu(ii) sites, obtained by the use of diffusion coefficients, we showed the superior crystal stability of the HKUST-1 framework towards ethanol. Finally, a small quantity of ethanol (pre-adsorbed) slightly enhanced CO 2 capture without crystal structure degradation.

Band structures in a two-dimensional phononic crystal with rotational multiple scatterers

NASA Astrophysics Data System (ADS)

Song, Ailing; Wang, Xiaopeng; Chen, Tianning; Wan, Lele

2017-03-01

In this paper, the acoustic wave propagation in a two-dimensional phononic crystal composed of rotational multiple scatterers is investigated. The dispersion relationships, the transmission spectra and the acoustic modes are calculated by using finite element method. In contrast to the system composed of square tubes, there exist a low-frequency resonant bandgap and two wide Bragg bandgaps in the proposed structure, and the transmission spectra coincide with band structures. Specially, the first bandgap is based on locally resonant mechanism, and the simulation results agree well with the results of electrical circuit analogy. Additionally, increasing the rotation angle can remarkably influence the band structures due to the transfer of sound pressure between the internal and external cavities in low-order modes, and the redistribution of sound pressure in high-order modes. Wider bandgaps are obtained in arrays composed of finite unit cells with different rotation angles. The analysis results provide a good reference for tuning and obtaining wide bandgaps, and hence exploring the potential applications of the proposed phononic crystal in low-frequency noise insulation.

Structural and electron charge density studies of a nonlinear optical compound 4,4 di-methyl amino cyano biphenyl

NASA Astrophysics Data System (ADS)

Naima, Boubegra; Abdelkader, Chouaih; Mokhtaria, Drissi; Fodil, Hamzaoui

2014-01-01

The 4,4 dimethyl amino cyano biphenyl crystal (DMACB) is characterized by its nonlinear activity. The intra molecular charge transfer of this molecule results mainly from the electronic transmission of the electro-acceptor (cyano) and electro-donor (di-methyl-amino) groups. An accurate electron density distribution around the molecule has been calculated based on a high-resolution X-ray diffraction study. The data were collected at 123 K using graphite-monochromated Mo K α radiation to sin(β)/λ = 1.24 Å-1. The integrated intensities of 13796 reflections were measured and reduced to 6501 independent reflections with I >= 3σ(I). The crystal structure was refined using the experimental model of Hansen and Coppens (1978). The crystal structure has been validated and deposited at the Cambridge Crystallographic Data Centre with the deposition number CCDC 876507. In this article, we present the thermal motion and the structural analysis obtained from the least-square refinement based on F2 and the electron density distribution obtained from the multipolar model.

The Effect of Temperature and Solution pH on Tetragonal Lysozyme Nucleation Kinetics

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Jacobs, Randolph S.; Frazier, Tyralynn; Snell, Edward H.; Pusey, Marc L.

1998-01-01

Part of the challenge of macromolecular crystal growth for structure determination is obtaining an appropriate number of crystals with a crystal volume suitable for x-ray analysis. In this respect an understanding of the effect of solution conditions on macromolecule nucleation rates is advantageous. This study investigated the effects of supersaturation, temperature and pH on the nucleation rate of tetragonal lysozyme crystals. Batch crystallization plates were prepared at given solution concentrations and incubated at set temperatures over one week. The number of crystals per well with their size and axial ratios were recorded and correlated with solution conditions, Duplicate experiments indicate the reproducibility of the technique, Crystal numbers were found to increase with increasing supersaturation and temperature. The most significant variable however, was pH, where crystal numbers changed by two orders of magnitude over the pH range 4.0 to 5.2. Crystal size varied also with solution conditions, with the largest crystals being obtained at pH 5.2. Having optimized the crystallization conditions, a batch of crystals were prepared under exactly the same conditions and fifty of these crystals were analyzed by x-ray techniques. The results indicate that even under the same crystallization conditions, a marked variation in crystal properties exists.

Crystallization kinetics of Mg–Cu–Yb–Ca–Ag metallic glasses

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

Tsarkov, Andrey A., E-mail: tsarkov@misis.ru; WPI Advanced Institute for Materials Research, Tohoku University, Katahira 2-1-1, Aoba-Ku, Sendai 980-8577; Zanaeva, Erzhena N.

The paper presents research into a Mg–Cu–Yb system based metallic glassy alloys. Metallic glasses were prepared using induction melting and further injection on a spinning copper wheel. The effect of alloying by Ag and Ca on the glass forming ability and the kinetics of crystallization of Mg–Cu–Yb system based alloys were studied. The differential scanning calorimeter and X-ray diffractometer were used to investigate the kinetics of crystallization and the phase composition of the samples. An indicator of glass forming ability, effective activation energy of crystallization, and enthalpy of mixing were calculated. An increase of the Ca and Ag content hasmore » a positive effect on the glass forming ability, the effective activation energy of crystallization, and the enthalpy of mixing. The highest indicators of the glass forming ability and the thermal stability were found for alloys that contain both alloying elements. The Ag addition suppresses precipitation of the Mg{sub 2}Cu phase during crystallization. A dual-phase glassy-nanocrystalline Mg structure was obtained in Mg{sub 65}Cu{sub 25}Yb{sub 10} and Mg{sub 59.5}Cu{sub 22.9}Yb{sub 11}Ag{sub 6.6} alloys after annealing. Bulk samples with a composite glassy-crystalline structure were obtained in Mg{sub 59.5}Cu{sub 22.9}Yb{sub 11}Ag{sub 6.6} and Mg{sub 64}Cu{sub 21}Yb{sub 9.5}Ag{sub 5.5} alloys. A thermodynamic database for the Mg–Cu–Yb–Ca–Ag system was created to compare the process of crystallization of alloys with polythermal sections of the Mg–Cu–Yb–Ca–Ag phase diagram. - Highlights: • New alloy compositions based on Mg–Cu–Yb system were developed and investigated. • Increasing content of Ag and Ca leads to improving GFA. • Bulk samples with a composite glassy-crystalline structure were obtained. • Thermodynamic database for Mg–Cu–Yb–Ca–Ag system was created.« less

Center for Macromolecular Crystallography, University of Alabama in Birmingham

NASA Technical Reports Server (NTRS)

Navia, Manuel A.

1991-01-01

Porcine pancreatic elastase (PPE) crystals grown under microgravity conditions on mission STS-26 of the Space Shuttle Discovery were shown to diffract to considerably higher resolution than the best PPE crystals grown by us on the ground. We have now independently refined both the microgravity and ground-based data. Preliminary results of these refinements are summarized. These results show nearly a doubling of experimental diffraction data for this structure, exceeding 1.3 A resolution. Improved phase information derived from the refined structure of PPE based on this microgravity data has allowed us to interpret previously-uninterpretable electron density obtained from ground-based crystals of a complex of PPE with a chemically-reactive inhibitor. Intermediate stages in the enzyme-inhibitor reaction mechanism in the crystal can now be directly observed. Further refinement of PPE structures is in progress.

Structural Variation of LaMnO3+δ by Oxygen Nonstoichiometry

NASA Astrophysics Data System (ADS)

Niwa, Eiki; Maeda, Hiroki; Hashimoto, Takuya; Mizusaki, Junichiro

2013-07-01

The relationship between oxygen content and crystal structure of LaMnO3+δ, which is mother phase of cathode material for solid oxide fuel cells, has been investigated by X-ray diffraction, thermogravimetry and iodometric titration. It was confirmed that LaMnO3+δ with different oxygen content can be prepared by controlling sintering temperature in static air. Crystal system of LaMnO3.17±0.02 and LaMnO3.13±0.01 at room temperature was rhombohedral with space group of Rbar {3}c, whereas crystal structure of LaMnO3.08±0.01 was orthorhombic whose space group was proposed to be Pmna (No. 53). With increase of oxygen content in LaMnO3+δ, molar volume decreased and higher crystal symmetry was obtained.

Bi-directional evolutionary optimization for photonic band gap structures

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

Meng, Fei; School of Civil Engineering, Central South University, Changsha 410075; Huang, Xiaodong, E-mail: huang.xiaodong@rmit.edu.au

2015-12-01

Toward an efficient and easy-implement optimization for photonic band gap structures, this paper extends the bi-directional evolutionary structural optimization (BESO) method for maximizing photonic band gaps. Photonic crystals are assumed to be periodically composed of two dielectric materials with the different permittivity. Based on the finite element analysis and sensitivity analysis, BESO starts from a simple initial design without any band gap and gradually re-distributes dielectric materials within the unit cell so that the resulting photonic crystal possesses a maximum band gap between two specified adjacent bands. Numerical examples demonstrated the proposed optimization algorithm can successfully obtain the band gapsmore » from the first to the tenth band for both transverse magnetic and electric polarizations. Some optimized photonic crystals exhibit novel patterns markedly different from traditional designs of photonic crystals.« less

L-Nitroargininium picrate

NASA Astrophysics Data System (ADS)

Apreyan, R. A.; Fleck, M.; Atanesyan, A. K.; Sukiasyan, R. P.; Petrosyan, A. M.

2015-12-01

L-Nitroargininium picrate has been obtained from an aqueous solution containing equimolar quantities of L-nitroarginine and picric acid by slow evaporation. Single crystal was grown by evaporation method. Crystal structure was determined at room temperature. The salt crystallizes in monoclinic crystal system (space group P21). Vibrational spectra and thermal properties were studied. Second harmonic generation efficiency measured by powder method is found to be four times higher than in L-nitroarginine, which in turn is ten times more efficient than KDP (KH2PO4).

Towards solution and refinement of organic crystal structures by fitting to the atomic pair distribution function

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

Prill, Dragica; Juhas, Pavol; Billinge, Simon J. L.

2016-01-01

In this study, a method towards the solution and refinement of organic crystal structures by fitting to the atomic pair distribution function (PDF) is developed. Approximate lattice parameters and molecular geometry must be given as input. The molecule is generally treated as a rigid body. The positions and orientations of the molecules inside the unit cell are optimized starting from random values. The PDF is obtained from carefully measured X-ray powder diffraction data. The method resembles `real-space' methods for structure solution from powder data, but works with PDF data instead of the diffraction pattern itself. As such it may bemore » used in situations where the organic compounds are not long-range-ordered, are poorly crystalline, or nanocrystalline. The procedure was applied to solve and refine the crystal structures of quinacridone (β phase), naphthalene and allopurinol. In the case of allopurinol it was even possible to successfully solve and refine the structure in P1 with four independent molecules. As an example of a flexible molecule, the crystal structure of paracetamol was refined using restraints for bond lengths, bond angles and selected torsion angles. In all cases, the resulting structures are in excellent agreement with structures from single-crystal data.« less

The topological pressure-temperature phase diagram and crystal structures of the dimorphic system spiperone.

PubMed

Robert, B; Perrin, M-A; Coquerel, G; Céolin, R; Rietveld, I B

2016-03-01

The topological pressure-temperature phase diagram for the dimorphism of spiperone, a potent neuroleptic drug, has been constructed using literature data and improved crystal structures obtained with new crystallographic data from single-crystal X-ray diffraction at various temperatures. It is inferred that form II, which is the more dense form and exhibits the lower melting temperature, becomes the more stable phase under pressure. Under ambient conditions, form I is more stable. Copyright © 2015 Académie Nationale de Pharmacie. Published by Elsevier Masson SAS. All rights reserved.

Enhanced oxidation stability of quasi core-shell alloyed CdSeS quantum dots prepared through aqueous microwave synthesis technique.

PubMed

Zhan, Hong-Ju; Zhou, Pei-Jiang; Ma, Rong; Liu, Xi-Jing; He, Yu-Ning; Zhou, Chuan-Yun

2014-01-01

Quasi core shell alloyed CdSeS quantum dots (QDs) have been prepared through a facile aqueous-phase route employing microwave irradiation technique. The optical spectroscopy and structure characterization evidenced the quasi core shell alloyed structures of CdSeS QDs. The X-ray diffraction patterns of the obtained CdSeS QDs displayed peak positions very close to those of bulk cubic CdS crystal structures and the result of X-ray photoelectron spectroscopy data re-confirmed the thick CdS shell on the CdSe core. The TEM images and HRTEM images of the CdSeS QDs ascertained the well-defined spherical particles and a relatively narrow size distribution. On the basis, the stability of the obtained QDs in an oxidative environment was also discussed using etching reaction by H2O2. The experiments result showed the as-prepared QDs present high tolerance towards H2O2, obviously superior to the commonly used CdTe QDs and core-shell CdTe/CdS QDs, which was attributed to the unique quasi core-shell CdSeS crystal structure and the small lattice mismatch between CdSe and CdS semiconductor materials. This assay provided insight to obtain high stable crystal structured semiconductor nanocrystals in the design and synthesis process.

RNi2B2C (R = Ho, Dy, Tb and Pr) single crystals grown by the cold copper crucible method

NASA Astrophysics Data System (ADS)

Durán, A.; Munoz, E.; Bernès, S.; Escudero, R.

2000-08-01

Single crystals of RNi2B2C (R = Ho, Dy, Tb, Pr) have been grown on cold copper crucibles in a high-frequency induction furnace. As a result, shiny metallic and brittle platelike single crystals were obtained. They were examined by x-ray and scanning electron microscopy with WDX/EDX for local composition analysis and show a very good crystallographic structure and compositions. Resistivity and dc magnetic measurements were performed to study superconducting and magnetic properties. Besides known electronic properties of the RNi2B2C family, we report for the first time results for PrNi2B2C single crystals successfully obtained by this technique.

Prevention of trace and major element leaching from coal combustion products by hydrothermally-treated coal ash

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

Adnadjevic, B.; Popovic, A.; Mikasinovic, B.

2009-07-01

The most important structural components of coal ash obtained by coal combustion in 'Nikola Tesla A' power plant located near Belgrade (Serbia) are amorphous alumosilicate, alpha-quartz, and mullite. The phase composition of coal ash can be altered to obtain zeolite type NaA that crystallizes in a narrow crystallization field (SiO{sub 2}/Al{sub 2}O{sub 3}; Na{sub 2}O/SiO{sub 2}; H{sub 2}O/Na{sub 2}O ratios). Basic properties (crystallization degree, chemical composition, the energy of activation) of obtained zeolites were established. Coal ash extracts treated with obtained ion-exchange material showed that zeolites obtained from coal ash were able to reduce the amounts of iron, chromium, nickel,more » zinc, copper, lead, and manganese in ash extracts, thus proving its potential in preventing pollution from dump effluent waters.« less

Growth and characterization of LiInSe2 single crystals

NASA Astrophysics Data System (ADS)

Ma, Tianhui; Zhu, Chongqiang; Lei, Zuotao; Yang, Chunhui; Sun, Liang; Zhang, Hongchen

2015-04-01

Large and crack-free LiInSe2 single crystals were obtained by the vertical gradient freezing method with adding a temperature oscillation technology in a two-zone furnace. X-ray diffraction data showed that the pure LiInSe2 compound was synthesized. The grown crystals had different color depending on melt composition. The atomic ratios of elements of LiInSe2 crystals were obtained by an Inductively Coupled Plasma-Atomic Emission Spectrometry (ICP-AES), and the structural formula were calculated according to the relative contents of elements. The average absorption coefficients were estimated by using average reflection indices. The absorption coefficients of the thermal annealing samples are 0.6 cm-1 at 2-3 μm. The transparent range of our LiInSe2 crystals is from 0.6 μm to 13.5 μm.

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

Guo, Feng; Jin, Tengchuan; Howard, Andrew

The crystallization of the brazil nut allergen Ber e 2 is reported. Peanut and tree-nut allergies have attracted considerable attention because of their frequency and their lifelong persistence. Brazil-nut (Bertholletia excelsa) allergies have been well documented and the 11S legumin-like seed storage protein Ber e 2 (excelsin) is one of the two known brazil-nut allergens. In this study, Ber e 2 was extracted from brazil-nut kernels and purified to high purity by crystalline precipitation and gel-filtration chromatography. Well diffracting single crystals were obtained using the hanging-drop vapour-diffusion method. A molecular-replacement structural solution has been obtained. Refinement of the structure ismore » currently under way.« less

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3.

PubMed

Strutynska, Nataliia Yu; Bondarenko, Marina A; Ogorodnyk, Ivan V; Baumer, Vyacheslav N; Slobodyanik, Nikolay S

2015-03-01

Potassium rubidium cobalt(II)/titanium(IV) tris-(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/Ti(IV))O6 octa-hedra (point group symmetry .3.) and PO4 tetra-hedra. The K(+) and Rb(+) cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms.

Purification, crystallization and characterization of the Pseudomonas outer membrane protein FapF, a functional amyloid transporter.

PubMed

Rouse, Sarah L; Hawthorne, Wlliam J; Lambert, Sebastian; Morgan, Marc L; Hare, Stephen A; Matthews, Stephen

2016-12-01

Bacteria often produce extracellular amyloid fibres via a multi-component secretion system. Aggregation-prone, unstructured subunits cross the periplasm and are secreted through the outer membrane, after which they self-assemble. Here, significant progress is presented towards solving the high-resolution crystal structure of the novel amyloid transporter FapF from Pseudomonas, which facilitates the secretion of the amyloid-forming polypeptide FapC across the bacterial outer membrane. This represents the first step towards obtaining structural insight into the products of the Pseudomonas fap operon. Initial attempts at crystallizing full-length and N-terminally truncated constructs by refolding techniques were not successful; however, after preparing FapF 106-430 from the membrane fraction, reproducible crystals were obtained using the sitting-drop method of vapour diffusion. Diffraction data have been processed to 2.5 Å resolution. These crystals belonged to the monoclinic space group C121, with unit-cell parameters a = 143.4, b = 124.6, c = 80.4 Å, α = γ = 90, β = 96.32° and three monomers in the asymmetric unit. It was found that the switch to complete detergent exchange into C8E4 was crucial for forming well diffracting crystals, and it is suggested that this combined with limited proteolysis is a potentially useful protocol for membrane β-barrel protein crystallography. The three-dimensional structure of FapF will provide invaluable information on the mechanistic differences of biogenesis between the curli and Fap functional amyloid systems.

Metacridamide B methanol-d4 monosolvate

USDA-ARS?s Scientific Manuscript database

The title compound was extracted from conidia of the fungus Metarhizium acridum. Crystals were obtained as a methanol-d4 solvate. The tail part of the 4-methylhexan-2-yl group exhibits disorder over two positions, with an occupancy ratio of 0.682 (9):0.318 (9). The crystal structure confirms the abs...

The Crystal and Molecular Structure of Dianhydrogossypol

USDA-ARS?s Scientific Manuscript database

Dianhydrogossypol (4,4'-dihydroxy-5,5'-diisopropyl-7,7'-dimethyl-bis(3H-naphtho[1,8-bc]furan-3-one)) was made by refluxing gossypol in m-xylene. Proton NMR confirmed that complete conversion was achieved over several hours. Single crystals were obtained by slow evaporation of the product from dichl...

High-Pressure Single-Crystal Structures of 3D Lead-Halide Hybrid Perovskites and Pressure Effects on their Electronic and Optical Properties.

PubMed

Jaffe, Adam; Lin, Yu; Beavers, Christine M; Voss, Johannes; Mao, Wendy L; Karunadasa, Hemamala I

2016-04-27

We report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX3 (MA = CH3NH3 (+), X = Br(-) or I(-)) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites' precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaque black with compression. Indeed, electronic conductivity measurements of (MA)PbI3 obtained within a diamond-anvil cell show that the material's resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(Br x I1-x )3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors.

High-Pressure Single-Crystal Structures of 3D Lead-Halide Hybrid Perovskites and Pressure Effects on their Electronic and Optical Properties

PubMed Central

2016-01-01

We report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX3 (MA = CH3NH3+, X = Br– or I–) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites’ precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaque black with compression. Indeed, electronic conductivity measurements of (MA)PbI3 obtained within a diamond-anvil cell show that the material’s resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(BrxI1–x)3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors. PMID:27163050

High-pressure single-crystal structures of 3D lead-halide hybrid perovskites and pressure effects on their electronic and optical properties

DOE PAGES

Jaffe, Adam; Lin, Yu; Beavers, Christine M.; ...

2016-04-06

Here, we report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX 3 (MA = CH 3NH 3 +, X = Br – or I –) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites’ precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaquemore » black with compression. Indeed, electronic conductivity measurements of (MA)PbI 3 obtained within a diamond-anvil cell show that the material’s resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(Br xI 1–x) 3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors.« less

Low carrier semiconductor like behavior in Lu3Ir4Ge13 single crystal

NASA Astrophysics Data System (ADS)

Kumar, Anil; Matteppanavar, Shidaling; Thamizhavel, A.; Ramakrishnan, S.

2018-04-01

Single crystal of Lu3Ir4Ge13 crystallizing in the Yb3Rh4Sn13-type cubic crystal structure has been grown by Czochralski method in a tetra-arc furnace. In this paper we report on the crystal structure, magnetic and transport properties of Lu3Ir4Ge13. The analysis of the powder x-ray diffraction (XRD) studies revealed that Lu3Ir4Ge13 crystallizes in a cubic structure with the space group Pm-3n, no. 223. The lattice parameter was obtained from the Rietveld refinement of the room temperature XRD data which amounts to 8.904 (3) Å with low R factors. The temperature dependence of the resistivity exhibited semiconductor like behavior till 1.8 K, with a broad hump around 15 - 62 K. This hump was observed in both warming and cooling cycle with a very small hysteresis, it may be due to the existence of structural transition from high - low symmetry. The temperature dependent magnetization data shows the diamagnetic behavior with an anomaly around 70 K, which is well supported by the derivative of resistivity data.

A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software.

PubMed

Mylona, Anastasia; Carr, Stephen; Aller, Pierre; Moraes, Isabel; Treisman, Richard; Evans, Gwyndaf; Foadi, James

2017-08-04

The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences.

A Novel Approach to Data Collection for Difficult Structures: Data Management for Large Numbers of Crystals with the BLEND Software

PubMed Central

Mylona, Anastasia; Carr, Stephen; Aller, Pierre; Moraes, Isabel; Treisman, Richard; Evans, Gwyndaf; Foadi, James

2018-01-01

The present article describes how to use the computer program BLEND to help assemble complete datasets for the solution of macromolecular structures, starting from partial or complete datasets, derived from data collection from multiple crystals. The program is demonstrated on more than two hundred X-ray diffraction datasets obtained from 50 crystals of a complex formed between the SRF transcription factor, its cognate DNA, and a peptide from the SRF cofactor MRTF-A. This structure is currently in the process of being fully solved. While full details of the structure are not yet available, the repeated application of BLEND on data from this structure, as they have become available, has made it possible to produce electron density maps clear enough to visualise the potential location of MRTF sequences. PMID:29456874

Numerical study on characteristic of two-dimensional metal/dielectric photonic crystals

NASA Astrophysics Data System (ADS)

Zong, Yi-Xin; Xia, Jian-Bai; Wu, Hai-Bin

2017-04-01

An improved plan-wave expansion method is adopted to theoretically study the photonic band diagrams of two-dimensional (2D) metal/dielectric photonic crystals. Based on the photonic band structures, the dependence of flat bands and photonic bandgaps on two parameters (dielectric constant and filling factor) are investigated for two types of 2D metal/dielectric (M/D) photonic crystals, hole and cylinder photonic crystals. The simulation results show that band structures are affected greatly by these two parameters. Flat bands and bandgaps can be easily obtained by tuning these parameters and the bandgap width may reach to the maximum at certain parameters. It is worth noting that the hole-type photonic crystals show more bandgaps than the corresponding cylinder ones, and the frequency ranges of bandgaps also depend strongly on these parameters. Besides, the photonic crystals containing metallic medium can obtain more modulation of photonic bands, band gaps, and large effective refractive index, etc. than the dielectric/dielectric ones. According to the numerical results, the needs of optical devices for flat bands and bandgaps can be met by selecting the suitable geometry and material parameters. Project supported by the National Basic Research Program of China (Grant No. 2011CB922200) and the National Natural Science Foundation of China (Grant No. 605210010).

Purification, crystallization and preliminary X-ray study of the fungal laccase from Cerrena maxima

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

Lyashenko, Andrey V.; Zhukhlistova, Nadegda E.; Gabdoulkhakov, Azat G.

2006-10-01

The crystallization and preliminary X-ray structure at 1.9 Å resolution of the fungal laccase from C. maxima are presented. Laccases are members of the blue multi-copper oxidase family that oxidize substrate molecules by accepting electrons at a mononuclear copper centre and transferring them to a trinuclear centre. Dioxygen binds to the trinuclear centre and, following the transfer of four electrons, is reduced to two molecules of water. Crystals of the laccase from Cerrena maxima have been obtained and X-ray data were collected to 1.9 Å resolution using synchrotron radiation. A preliminary analysis shows that the enzyme has the typical laccasemore » structure and several carbohydrate sites have been identified. The carbohydrate chains appear to be involved in stabilization of the intermolecular contacts in the crystal structure, thus promoting the formation of well ordered crystals of the enzyme. Here, the results of an X-ray crystallographic study on the laccase from the fungus Cerrena maxima are reported. Crystals that diffract well to a resolution of at least 1.9 Å (R factor = 18.953%; R{sub free} = 23.835; r.m.s.d. bond lengths, 0.06 Å; r.m.s.d. bond angles, 1.07°) have been obtained despite the presence of glycan moieties. The overall spatial organization of C. maxima laccase and the structure of its copper-containing active centre have been determined by the molecular-replacement method using the laccase from Trametes versicolor (Piontek et al., 2002 ▶) as a structural template. In addition, four glycan-binding sites were identified and the 1.9 Å X-ray data were used to determine the previously unknown primary structure of this protein. The identity (calculated from sequence alignment) between the C. maxima laccase and the T. versicolor laccase is about 87%. Tyr196 and Tyr372 show significant extra density at the ortho positions and this has been interpreted in terms of NO{sub 2} substituents.« less

The collection of MicroED data for macromolecular crystallography.

PubMed

Shi, Dan; Nannenga, Brent L; de la Cruz, M Jason; Liu, Jinyang; Sawtelle, Steven; Calero, Guillermo; Reyes, Francis E; Hattne, Johan; Gonen, Tamir

2016-05-01

The formation of large, well-ordered crystals for crystallographic experiments remains a crucial bottleneck to the structural understanding of many important biological systems. To help alleviate this problem in crystallography, we have developed the MicroED method for the collection of electron diffraction data from 3D microcrystals and nanocrystals of radiation-sensitive biological material. In this approach, liquid solutions containing protein microcrystals are deposited on carbon-coated electron microscopy grids and are vitrified by plunging them into liquid ethane. MicroED data are collected for each selected crystal using cryo-electron microscopy, in which the crystal is diffracted using very few electrons as the stage is continuously rotated. This protocol gives advice on how to identify microcrystals by light microscopy or by negative-stain electron microscopy in samples obtained from standard protein crystallization experiments. The protocol also includes information about custom-designed equipment for controlling crystal rotation and software for recording experimental parameters in diffraction image metadata. Identifying microcrystals, preparing samples and setting up the microscope for diffraction data collection take approximately half an hour for each step. Screening microcrystals for quality diffraction takes roughly an hour, and the collection of a single data set is ∼10 min in duration. Complete data sets and resulting high-resolution structures can be obtained from a single crystal or by merging data from multiple crystals.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature.

PubMed

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-06

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

NASA Astrophysics Data System (ADS)

Tsujino, Soichiro; Tomizaki, Takashi

2016-05-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography.

Ultrasonic acoustic levitation for fast frame rate X-ray protein crystallography at room temperature

PubMed Central

Tsujino, Soichiro; Tomizaki, Takashi

2016-01-01

Increasing the data acquisition rate of X-ray diffraction images for macromolecular crystals at room temperature at synchrotrons has the potential to significantly accelerate both structural analysis of biomolecules and structure-based drug developments. Using lysozyme model crystals, we demonstrated the rapid acquisition of X-ray diffraction datasets by combining a high frame rate pixel array detector with ultrasonic acoustic levitation of protein crystals in liquid droplets. The rapid spinning of the crystal within a levitating droplet ensured an efficient sampling of the reciprocal space. The datasets were processed with a program suite developed for serial femtosecond crystallography (SFX). The structure, which was solved by molecular replacement, was found to be identical to the structure obtained by the conventional oscillation method for up to a 1.8-Å resolution limit. In particular, the absence of protein crystal damage resulting from the acoustic levitation was carefully established. These results represent a key step towards a fully automated sample handling and measurement pipeline, which has promising prospects for a high acquisition rate and high sample efficiency for room temperature X-ray crystallography. PMID:27150272

Preparation, structural characterization, and decomposition studies of two new γ-octamolybdates of 4-methylpyridine.

PubMed

Szymańska, Anna; Nitek, Wojciech; Rutkowska-Zbik, Dorota; Łasocha, Wiesław

We synthesized two new γ-octamolybdates, and determined their crystal structures from single-crystal X-ray diffraction data. Orange-yellow tetrakis(4-methylpyridinium) bis(4-methylpyridine)-γ-octamolybdate 1 crystallizes in space group P2 1 /c with a  = 11.586(2) Å, b  = 15.526(2) Å, c  = 16.247(2) Å, β  = 118.753(1)º, Z  = 2. White tetrakis(4-methylpyridinium) bis(4-methylpyridine)-γ-octamolybdate hydrate 2 crystallizes in space group C2/c with a  = 27.086(4) Å, b  = 11.917(2) Å, c  = 19.332(2) Å, β  = 124.427(1)º, Z  = 4. Results of crystal structure determinations are presented and discussed in this paper. Thermal stability and decomposition studies of the obtained two new γ-octamolybdates were performed using TG/DSC and XRPD methods. Both compounds decomposed with the formation of 4-methylpyridinium β-octamolybdate. The two compounds are pseudo-polymorphs, exhibiting both striking similarities as well as significant differences in their structures and properties.

Crystal structures of tiotropium bromide and its monohydrate in view of combined solid-state nuclear magnetic resonance and gauge-including projector-augmented wave studies.

PubMed

Pindelska, Edyta; Szeleszczuk, Lukasz; Pisklak, Dariusz Maciej; Majka, Zbigniew; Kolodziejski, Waclaw

2015-07-01

Tiotropium bromide is an anticholinergic bronchodilator used in the management of chronic obstructive pulmonary disease. The crystal structures of this compound and its monohydrate have been previously solved and published. However, in this paper, we showed that those structures contain some major errors. Our methodology based on combination of the solid-state nuclear magnetic resonance (NMR) spectroscopy and quantum mechanical gauge-including projector-augmented wave (GIPAW) calculations of NMR shielding constants enabled us to correct those errors and obtain reliable structures of the studied compounds. It has been proved that such approach can be used not only to perform the structural analysis of a drug substance and to identify its polymorphs, but also to verify and optimize already existing crystal structures. © 2015 Wiley Periodicals, Inc. and the American Pharmacists Association.

‘Pd20Sn13’ revisited: crystal structure of Pd6.69Sn4.31

PubMed Central

Klein, Wilhelm; Jin, Hanpeng; Hlukhyy, Viktor; Fässler, Thomas F.

2015-01-01

The crystal structure of the title compound was previously reported with composition ‘Pd20Sn13’ [Sarah et al. (1981 ▸). Z. Metallkd, 72, 517–520]. For the original structure model, as determined from powder X-ray data, atomic coordinates from the isostructural compound Ni13Ga3Ge6 were transferred. The present structure determination, resulting in a composition Pd6.69Sn4.31, is based on single crystal X-ray data and includes anisotropic displacement parameters for all atoms as well as standard uncertainties for the atomic coordinates, leading to higher precision and accuracy for the structure model. Single crystals of the title compound were obtained via a solid-state reaction route, starting from the elements. The crystal structure can be derived from the AlB2 type of structure after removing one eighth of the atoms at the boron positions and shifting adjacent atoms in the same layer in the direction of the voids. One atomic site is partially occupied by both elements with a Pd:Sn ratio of 0.38 (3):0.62 (3). One Sn and three Pd atoms are located on special positions with site symmetry 2. (Wyckoff letter 3a and 3b). PMID:26279872

Mapping the conformational space accessible to BACE2 using surface mutants and cocrystals with Fab fragments, Fynomers and Xaperones.

PubMed

Banner, David W; Gsell, Bernard; Benz, Jörg; Bertschinger, Julian; Burger, Dominique; Brack, Simon; Cuppuleri, Simon; Debulpaep, Maja; Gast, Alain; Grabulovski, Dragan; Hennig, Michael; Hilpert, Hans; Huber, Walter; Kuglstatter, Andreas; Kusznir, Eric; Laeremans, Toon; Matile, Hugues; Miscenic, Christian; Rufer, Arne C; Schlatter, Daniel; Steyaert, Jan; Stihle, Martine; Thoma, Ralf; Weber, Martin; Ruf, Armin

2013-06-01

The aspartic protease BACE2 is responsible for the shedding of the transmembrane protein Tmem27 from the surface of pancreatic β-cells, which leads to inactivation of the β-cell proliferating activity of Tmem27. This role of BACE2 in the control of β-cell maintenance suggests BACE2 as a drug target for diabetes. Inhibition of BACE2 has recently been shown to lead to improved control of glucose homeostasis and to increased insulin levels in insulin-resistant mice. BACE2 has 52% sequence identity to the well studied Alzheimer's disease target enzyme β-secretase (BACE1). High-resolution BACE2 structures would contribute significantly to the investigation of this enzyme as either a drug target or anti-target. Surface mutagenesis, BACE2-binding antibody Fab fragments, single-domain camelid antibody VHH fragments (Xaperones) and Fyn-kinase-derived SH3 domains (Fynomers) were used as crystallization helpers to obtain the first high-resolution structures of BACE2. Eight crystal structures in six different packing environments define an ensemble of low-energy conformations available to the enzyme. Here, the different strategies used for raising and selecting BACE2 binders for cocrystallization are described and the crystallization success, crystal quality and the time and resources needed to obtain suitable crystals are compared.

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

Assenberg, René; Delmas, Olivier; Graham, Stephen C.

The expression, purification and crystallization of the full-length matrix protein from three lyssaviruses is described. The matrix (M) proteins of lyssaviruses (family Rhabdoviridae) are crucial to viral morphogenesis as well as in modulating replication and transcription of the viral genome. To date, no high-resolution structural information has been obtained for full-length rhabdovirus M. Here, the cloning, expression and purification of the matrix proteins from three lyssaviruses, Lagos bat virus (LAG), Mokola virus and Thailand dog virus, are described. Crystals have been obtained for the full-length M protein from Lagos bat virus (LAG M). Successful crystallization depended on a number ofmore » factors, in particular the addition of an N-terminal SUMO fusion tag to increase protein solubility. Diffraction data have been recorded from crystals of native and selenomethionine-labelled LAG M to 2.75 and 3.0 Å resolution, respectively. Preliminary analysis indicates that these crystals belong to space group P6{sub 1}22 or P6{sub 5}22, with unit-cell parameters a = b = 56.9–57.2, c = 187.9–188.6 Å, consistent with the presence of one molecule per asymmetric unit, and structure determination is currently in progress.« less

Synthesis, growth, crystal structure, optical and third order nonlinear optical properties of quinolinium derivative single crystal: PNQI

NASA Astrophysics Data System (ADS)

Karthigha, S.; Krishnamoorthi, C.

2018-03-01

An organic quinolinium derivative nonlinear optical (NLO) crystal, 1-ethyl-2-[2-(4-nitro-phenyl)-vinyl]-quinolinium iodide (PNQI) was synthesized and successfully grown by slow evaporation solution growth technique. Formation of a crystalline compound was confirmed by single crystal X-ray diffraction. The quinolinium compound PNQI crystallizes in the triclinic crystal system with a centrosymmetric space group of P-1 symmetry. The molecular structure of PNQI was confirmed by 1H NMR and 13C NMR spectral studies. The thermal properties of the crystal have been investigated by thermogravimetric (TG) and differential scanning calorimetry (DSC) studies. The optical characteristics obtained from UV-Vis-NIR spectral data were described and the cut-off wavelength observed at 506 nm. The etching study was performed to analyse the growth features of PNQI single crystal. The third order NLO properties such as nonlinear refractive index (n2), nonlinear absorption coefficient (β) and nonlinear susceptibility (χ (3)) of the crystal were investigated using Z-scan technique at 632.8 nm of Hesbnd Ne laser.

Protein nanocrystallography: growth mechanism and atomic structure of crystals induced by nanotemplates.

PubMed

Pechkova, E; Vasile, F; Spera, R; Fiordoro, S; Nicolini, C

2005-11-01

Protein nanocrystallography, a new technology for crystal growth based on protein nanotemplates, has recently been shown to produce diffracting, stable and radiation-resistant lysozyme crystals. This article, by computing these lysozyme crystals' atomic structures, obtained by the diffraction patterns of microfocused synchrotron radiation, provides a possible mechanism for this increased stability, namely a significant decrease in water content accompanied by a minor but significant alpha-helix increase. These data are shown to be compatible with the circular dichroism and two-dimensional Fourier transform spectra of high-resolution H NMR of proteins dissolved from the same nanotemplate-based crystal versus those from a classical crystal. Finally, evidence for protein direct transfer from the nanotemplate to the drop and the participation of the template proteins in crystal nucleation and growth is provided by high-resolution NMR spectrometry and mass spectrometry. Furthermore, the lysozyme nanotemplate appears stable up to 523 K, as confirmed by a thermal denaturation study using spectropolarimetry. The overall data suggest that heat-proof lysozyme presence in the crystal provides a possible explanation of the crystal's resistance to synchrotron radiation.

Structure of CPV17 polyhedrin determined by the improved analysis of serial femtosecond crystallographic data

DOE PAGES

Ginn, Helen M.; Messerschmidt, Marc; Ji, Xiaoyun; ...

2015-03-09

The X-ray free-electron laser (XFEL) allows the analysis of small weakly diffracting protein crystals, but has required very many crystals to obtain good data. Here we use an XFEL to determine the room temperature atomic structure for the smallest cytoplasmic polyhedrosis virus polyhedra yet characterized, which we failed to solve at a synchrotron. These protein microcrystals, roughly a micron across, accrue within infected cells. We use a new physical model for XFEL diffraction, which better estimates the experimental signal, delivering a high-resolution XFEL structure (1.75 Å), using fewer crystals than previously required for this resolution. The crystal lattice and proteinmore » core are conserved compared with a polyhedrin with less than 10% sequence identity. We explain how the conserved biological phenotype, the crystal lattice, is maintained in the face of extreme environmental challenge and massive evolutionary divergence. Our improved methods should open up more challenging biological samples to XFEL analysis.« less

Purification, crystallization and preliminary crystallographic studies of the TLDc domain of oxidation resistance protein 2 from zebrafish

PubMed Central

Alsarraf, Husam M. A. B.; Laroche, Fabrice; Spaink, Herman; Thirup, Søren; Blaise, Mickael

2011-01-01

Cell metabolic processes are constantly producing reactive oxygen species (ROS), which have deleterious effects by triggering, for example, DNA damage. Numerous enzymes such as catalase, and small compounds such as vitamin C, provide protection against ROS. The TLDc domain of the human oxidation resistance protein has been shown to be able to protect DNA from oxidative stress; however, its mechanism of action is still not understood and no structural information is available on this domain. Structural information on the TLDc domain may therefore help in understanding exactly how it works. Here, the purification, crystallization and preliminary crystallographic studies of the TLDc domain from zebrafish are reported. Crystals belonging to the orthorhombic space group P21212 were obtained and diffracted to 0.97 Å resolution. Selenomethionine-substituted protein could also be crystallized; these crystals diffracted to 1.1 Å resolution and the structure could be solved by SAD/MAD methods. PMID:22102041

The Crystal and Molecular Structure of an Asymmetric Diacetylene Monomer, 6-(2-methyl-4-nitroanilino)-2,4-hexadiyne-1-ol

NASA Technical Reports Server (NTRS)

Vlasse, Marcus; Paley, Mark S.

1993-01-01

The crystal and molecular structure of an asymmetric diacetylene monomer has been determined from x-ray diffraction data. The crystals, obtained from an acetone/pentane solution, are orthorhombic, Fdd2 with Z = 16 in a unit cell having dimensions of a = 42.815(6) A, b = 22.224(5) A, c = 4.996(l) A. The structure was solved by direct methods and refined by least- squares techniques to an R(sub F) of 6.4% for 988 reflections and 171 variables. The diacetylene chains are disposed in the unit cell in a complex manner in order to satisfy the hydrogen- bonding, crystal packing, and symmetry requirements of the system. The solid state polymerization mechanism is discussed with respect to the geometric disposition of the diacetylene chains. These chains are far apart and incorrectly oriented with respect to each other to permit polymerization in the crystal by means of 1,4-addition, consistent with the Baughman mechanistic model.

Crystallization and preliminary crystallographic investigation of a low-pH native insulin monomer with flexible behaviour.

PubMed

Zhang, Youshang; Whittingham, Jean L; Turkenburg, Johan P; Dodson, Eleanor J; Brange, Jens; Dodson, G Guy

2002-01-01

Insulin naturally aggregates as dimers and hexamers, whose structures have been extensively analysed by X-ray crystallography. Structural determination of the physiologically relevant insulin monomer, however, is an unusual challenge owing to the difficulty in finding solution conditions in which the concentration of insulin is high enough for crystallization yet the molecule remains monomeric. By utilizing solution conditions known to inhibit insulin assembly, namely 20% acetic acid, crystals of insulin in the monomeric state have been obtained. The crystals are strongly diffracting and a data set extending to 1.6 A has recently been collected. The crystals nominally belong to the space group I422, with unit-cell parameters a = b = 57.80, c = 54.61 A, giving rise to one molecule in the asymmetric unit. Preliminary electron-density maps show that whilst most of the insulin monomer is well ordered and similar in conformation to other insulin structures, parts of the B-chain C-terminus main chain adopt more than one conformation.

Single crystal growth of spin-ladder compound La8Cu7O19 by the travelling-solvent floating zone method

NASA Astrophysics Data System (ADS)

Mohan, A.; Singh, S.; Partzsch, S.; Zwiebler, M.; Geck, J.; Wurmehl, S.; Büchner, B.; Hess, C.

2016-08-01

Large single crystals of La8Cu7O19 have been grown using the travelling-solvent floating zone method. A rather high oxygen pressure of 9 bar in the growth chamber and a slow growth speed of 0.5 mm/h were among the most important parameters in stabilizing the growth of this incongruently melting compound. Interestingly, a novel growth scenario has been witnessed. The crystal structure of the grown La8Cu7O19 crystal has been analyzed using single crystal diffractometry to extract important structural parameters of this compound. We find that La8Cu7O19 crystallizes in a monoclinic structure with space group C 2 / c and has the lattice parameters a ≈ 13.83 Å, b ≈ 3.75 Å, c ≈ 34.59 Å, and β ≈ 99.33 °, in good agreement with the data obtained on polycrystalline samples in the literature. The magnetization shows a highly anisotropic behavior, and an anomaly at T ≈103 K.

Vibrational and structural investigation of SOUL protein single crystals by using micro-Raman spectroscopy

NASA Astrophysics Data System (ADS)

Rossi, Barbara; Giarola, Marco; Mariotto, Gino; Ambrosi, Emmanuele; Monaco, Hugo L.

2010-05-01

Protein SOUL is a new member of the recently discovered putative heme-binding protein family called SOUL/HEBP and, to date, no structural information exists for this protein. Here, micro-Raman spectroscopy is used to study the vibrational properties of single crystals obtained from recombinant protein SOUL by means of two different optimization routes. This spectroscopic approach offers the valuable advantage of the in-situ collection of experimental data from protein crystals, placed onto a hanging-drop plate, under the same conditions used to grow the crystals. By focusing on the regions of amides I and III bands, some secondary structure characteristic features have been recognized. Moreover, some side-chain marker bands were observed in the Raman spectra of SOUL crystals and the unambiguous assignment of these peaks inferred by comparing the experimental Raman spectra of pure amino acids and their Raman intensities computed using quantum chemical calculations. Our comparative analysis allows to get a deeper understanding of the side-chain environments and of the interactions involving these specific amino acids in the two different SOUL crystals.

On beam shaping of the field radiated by a line source coupled to finite or infinite photonic crystals.

PubMed

Ceccuzzi, Silvio; Jandieri, Vakhtang; Baccarelli, Paolo; Ponti, Cristina; Schettini, Giuseppe

2016-04-01

Comparison of the beam-shaping effect of a field radiated by a line source, when an ideal infinite structure constituted by two photonic crystals and an actual finite one are considered, has been carried out by means of two different methods. The lattice sums technique combined with the generalized reflection matrix method is used to rigorously investigate the radiation from the infinite photonic crystals, whereas radiation from crystals composed of a finite number of rods along the layers is analyzed using the cylindrical-wave approach. A directive radiation is observed with the line source embedded in the structure. With an increased separation distance between the crystals, a significant edge diffraction appears that provides the main radiation mechanism in the finite layout. Suitable absorbers are implemented to reduce the above-mentioned diffraction and the reflections at the boundaries, thus obtaining good agreement between radiation patterns of a localized line source coupled to finite and infinite photonic crystals, when the number of periods of the finite structure is properly chosen.

A new crystal form of a hyperthermophilic endocellulase

PubMed Central

Kataoka, Misumi; Ishikawa, Kazuhiko

2014-01-01

The hyperthermophilic glycoside hydrolase family endocellulase 12 from the archaeon Pyrococcus furiosus (EGPf; Gene ID PF0854; EC 3.2.1.4) catalyzes the hydrolytic cleavage of the β-1,4-glucosidic linkage in β-glucan in lignocellulose biomass. A crystal of EGPf was previously prepared at pH 9.0 and its structure was determined at an atomic resolution of 1.07 Å. This article reports the crystallization of EGPf at the more physiologically relevant pH of 5.5. Structure determination showed that this new crystal form has the symmetry of space group C2. Two molecules of the enzyme are observed in the asymmetric unit. Crystal packing is weak at pH 5.5 owing to two flexible interfaces between symmetry-related molecules. Comparison of the EGPf structures obtained at pH 9.0 and pH 5.5 reveals a significant conformational difference at the active centre and in the surface loops. The interfaces in the vicinity of the flexible surface loops impact the quality of the EGPf crystal. PMID:25005081

Highly resistive C-doped hydride vapor phase epitaxy-GaN grown on ammonothermally crystallized GaN seeds

NASA Astrophysics Data System (ADS)

Iwinska, Malgorzata; Piotrzkowski, Ryszard; Litwin-Staszewska, Elzbieta; Sochacki, Tomasz; Amilusik, Mikolaj; Fijalkowski, Michal; Lucznik, Boleslaw; Bockowski, Michal

2017-01-01

GaN crystals were grown by hydride vapor phase epitaxy (HVPE) and doped with C. The seeds were high-structural-quality ammonothermally crystallized GaN. The grown crystals were highly resistive at 296 K and of high structural quality. High-temperature Hall effect measurements revealed p-type conductivity and a deep acceptor level in the material with an activation energy of 1 eV. This is in good agreement with density functional theory calculations based on hybrid functionals as presented by the Van de Walle group. They obtained an ionization energy of 0.9 eV when C was substituted for N in GaN and acted as a deep acceptor.

Luminescence spectra of a cholesteric photonic crystal

NASA Astrophysics Data System (ADS)

Dolganov, P. V.

2017-05-01

The transmission and luminescence spectra of a cholesteric photonic crystal doped with an organic dye are measured. The density of photon states is calculated using the material parameters obtained from the comparison of the experimental and theoretical spectra. The shape of the luminescence spectra is modified with respect to the density of photon states owing to the difference in the structure of the normal modes of the photonic crystal near the short-wavelength and long-wavelength edges of the photonic quasi-band gap upon the "pushing" of the photon states from the gap and to the nonvanishing orientation ordering of the luminescent molecules. The luminescence spectrum calculated taking into account the chiral structure of the photonic crystal agrees with the experimental spectrum.

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Astrophysics Data System (ADS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-11-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

Study of Fluid Flow Control in Protein Crystallization using Strong Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, Narayanan; Leslie, Fred; Ciszak, Ewa

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in "microgravity", researchers have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. Whether this limited convection in a magnetic field will provide the environment for the growth of high quality crystals is still a matter of conjecture that our research will address. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. Once the basic understanding is obtained, the study will focus on testing the hypothesis on proteins of pyruvate dehydrogenase complex (PDC), proteins E1 and E3. Obtaining high crystal quality of these proteins is of great importance to structural biologists since their structures need to be determined. Specific goals for the investigation are: 1. To develop an understanding of convection control in diamagnetic fluids with concentration gradients through experimentation and numerical modeling. Specifically solutal buoyancy driven convection due to crystal growth will be considered. 2. To develop predictive measures for successful crystallization in a magnetic field using analyses and numerical modeling for use in future protein crystal growth experiments. This will establish criteria that can be used to estimate the efficacy of magnetic field flow damping on crystallization of candidate proteins. 3. To demonstrate the understanding of convection damping by high magnetic fields to a class of proteins that is of interest and whose structure is as yet not determined. 4. To compare quantitatively, the quality of the grown crystals with and without a magnetic field. X-ray diffraction techniques will be used for the comparative studies. In a preliminary set of experiments, we studied crystal dissolution effects in a 5 Tesla magnet available at NASA Marshall Space Flight Center (MSFC). Using a Schlieren setup, a 1mm crystal of Alum (Aluminum-Potassium Sulfate) was introduced in a 75% saturated solution and the resulting dissolution plume was observed. The experiment was conducted both in the presence and absence of a magnetic field gradient. The magnet produces a gradient field of approx. 1 Tesla2/cm. Image analysis of the recorded images indicated an enhanced plume velocity that was of the order of the measurement limit. For this experiment, both the gradient and gravity fields are in the same direction resulting in an enhanced effective gravity that tends to accelerate the observed plume velocity. While the results are not conclusive, pending further tests, it clearly points out the inadequacy of the MSFC magnet for conducting protein crystallization experiments and the need for a stronger magnet. In spacebased experiments, however, where the gravitational effects are small, only a weak magnetic field will be required to control or mitigate the effects of convective contamination.

The Use of Atomic-Force Microscopy for Studying the Crystallization Process of Amorphous Alloys

NASA Astrophysics Data System (ADS)

Elmanov, G. N.; Ivanitskaya, E. A.; Dzhumaev, P. S.; Skrytniy, V. I.

The crystallization process of amorphous alloys is accompanied by the volume changes as a result of structural phase transitions. This leads to changes in the surface topography, which was studied by atomic force microscopy (AFM). The changes of the surface topography, structure and phase composition during multistage crystallization process of the metallic glasses with composition Ni71,5Cr6,8Fe2,7B11,9Si7,1 and Ni63,4Cr7,4Fe4,3Mn0,8B15,6Si8,5 (AWS BNi2) has been investigated. The obtained results on changing of the surface topography in crystallization process are in good agreement with the data of X-ray diffraction analysis (XRD). The nature of redistribution of some alloy components in the crystallization process has been suggested.

Features of the structural states of KNbO{sub 3} single crystals before and after fast-neutron irradiation

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

Stash, A. I., E-mail: astas@yandex.ru; Ivanov, S. A.; Stefanovich, S. Yu.

Neutron irradiation is a unique tool for forming new structural states of ferroelectrics, which cannot be obtained by conventional methods. The inf luence of the irradiation by two doses of fast neutrons (F = 1 × 10{sup 17} and 3 × 10{sup 17} cm{sup –2}) on the structure and properties of KNbO{sub 3} single crystals has been considered for the first time. The developed method for taking into account the experimental correction to the diffuse scattering has been used to analyze the structural changes occurring in KNbO{sub 3} samples at T = 295 K and their correlations with the behaviormore » of dielectric and nonlinear optical characteristics. The irradiation to the aforementioned doses retains the KNbO{sub 3} polar structure, shifting Т{sub Ð}¡ to lower temperatures and significantly affecting only the thermal parameters and microstructure of single crystals. Neutron irradiation with small atomic displacements provides a structure similar to the high-temperature modification of an unirradiated KNbO{sub 3} crystal.« less

High power tapered lasers with optimized photonic crystal structure for low divergence and high efficiency

NASA Astrophysics Data System (ADS)

Ma, Xiaolong; Qu, Hongwei; Qi, Aiyi; Zhou, Xuyan; Ma, Pijie; Liu, Anjin; Zheng, Wanhua

2018-04-01

High power tapered lasers are designed and fabricated. A one-dimensional photonic crystal structure in the vertical direction is adopted to narrow the far field divergence. The thickness of the defect layer and the photonic crystal layers are optimized by analyzing the optical field theoretically. For tapered lasers, the continuous-wave power is 7.3 W and the pulsed power is 17 W. A maximum wall-plug efficiency of 46% under continuous-wave operation and 49.3% in pulsed mode are obtained. The beam divergences are around 11° and 6° for the vertical and lateral directions, respectively. High beam qualities are also obtained with a vertical M2 value of 1.78 and a lateral M2 value of 1.62. As the current increases, the lateral M2 value increases gradually while the vertical M2 value remains around 2.

Variable two-crystal cascade for conical refraction.

PubMed

Peet, V

2015-05-15

The cascade conical refraction occurs when a collimated light beam is passed consequently along the optic axes of several biaxial crystals arranged in a series. For commonly used optical arrangements, the general structure of light emerging from such a cascade is rigorously determined by the used crystals, leaving few possibilities for the variations of the established light pattern. A simple modification of a two-crystal arrangement where one of the two crystals is placed beyond the imaging lens is reported. This modification adds an extreme versatility to the effect and allows one to tune continuously the actual cascade parameters. As a result, practically any pattern of two-crystal cascade conical refraction can be obtained for any pair of biaxial crystals.

In-situ nano-crystal-to-crystal transformation synthesis of energetic materials based on three 5,5′-azotetrazolate Cr(III) salts

PubMed Central

Miao, Yu; Qiu, Yanxuan; Cai, Jiawei; Wang, Zizhou; Yu, Xinwei; Dong, Wen

2016-01-01

The in-situ nano-crystal-to-crystal transformation (SCCT) synthesis provides a powerful approach for tailoring controllable feature shapes and sizes of nano crystals. In this work, three nitrogen-rich energetic nano-crystals based on 5,5′-azotetrazolate(AZT2−) Cr(III) salts were synthesized by means of SCCT methodology. SEM and TEM analyses show that the energetic nano-crystals feature a composition- and structure-dependent together with size-dependent thermal stability. Moreover, nano-scale decomposition products can be obtained above 500 °C, providing a new method for preparing metallic oxide nano materials. PMID:27869221

One-dimensional magnetophotonic crystals with magnetooptical double layers

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

Berzhansky, V. N., E-mail: v.n.berzhansky@gmail.com; Shaposhnikov, A. N.; Prokopov, A. R.

2016-11-15

One-dimensional magnetophotonic microcavity crystals with nongarnet dielectric mirrors are created and investigated. The defect layers in the magnetophotonic crystals are represented by two bismuth-substituted yttrium iron garnet Bi:YIG layers with various bismuth contents in order to achieve a high magnetooptical response of the crystals. The parameters of the magnetophotonic crystal layers are optimized by numerical solution of the Maxwell equations by the transfer matrix method to achieve high values of Faraday rotation angle Θ{sub F} and magnetooptical Q factor. The calculated and experimental data agree well with each other. The maximum values of Θ{sub F} =–20.6°, Q = 8.1° atmore » a gain t = 16 are obtained for magnetophotonic crystals with m = 7 pairs of layers in Bragg mirrors, and the parameters obtained for crystals with m = 4 and t = 8.5 are Θ{sub F} =–12.5° and Q = 14.3°. It is shown that, together with all-garnet and multimicrocavities magnetophotonic crystals, such structures have high magnetooptical characteristics.« less

Microgravity

NASA Image and Video Library

2000-05-01

The structure of the Satellite Tobacco Mosaic Viurus (STMV)--one of the smallest viruses known--has been successfully reduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystals grown on Earth, the crystals grown under microgravity conditions were visually perfect, with no striations or clumping of crystals. Furthermore, the x-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This stylized ribbon model shows the protein coat in white and the nucleic acid in yellow. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, University of California at Irvin.

Microgravity

NASA Image and Video Library

2000-05-01

The structure of the Satellite Tobacco Mosaic Virus (STMV)--one of the smallest viruses known--has been successfully deduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the same time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystal grown on Earth, the crystals grown under microgravity conditions were viusally perfect, with no striations or clumping of crystals. Furthermore, the X-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This computer model shows the external coating or capsid. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, Univeristy of California at Irvin.

Satellite Tobacco Mosaic Virus (STMV)

NASA Technical Reports Server (NTRS)

2000-01-01

The structure of the Satellite Tobacco Mosaic Virus (STMV)--one of the smallest viruses known--has been successfully deduced using STMV crystals grown aboard the Space Shuttle in 1992 and 1994. The STMV crystals were up to 30 times the volume of any seen in the laboratory. At the same time they gave the best resolution data ever obtained on any virus crystal. STMV is a small icosahedral plant virus, consisting of a protein shell made up of 60 identical protein subunits of molecular weight 17,500. Particularly noteworthy is the fact that, in contrast to the crystal grown on Earth, the crystals grown under microgravity conditions were viusally perfect, with no striations or clumping of crystals. Furthermore, the X-ray diffraction data obtained from the space-grown crystals was of a much higher quality than the best data available at that time from ground-based crystals. This computer model shows the external coating or capsid. STMV is used because it is a simple protein to work with; studies are unrelated to tobacco. Credit: Dr. Alex McPherson, Univeristy of California at Irvin.

Lab-on-a-Chip Based Protein Crystallization

NASA Technical Reports Server (NTRS)

vanderWoerd, Mark J.; Brasseur, Michael M.; Spearing, Scott F.; Whitaker, Ann F. (Technical Monitor)

2001-01-01

We are developing a novel technique with which we will grow protein crystals in very small volumes, utilizing chip-based, microfluidic ("LabChip") technology. This development, which is a collaborative effort between NASA's Marshall Space Flight Center and Caliper Technologies Corporation, promises a breakthrough in the field of protein crystal growth. Our initial results obtained from two model proteins, Lysozyme and Thaumatin, show that it is feasible to dispense and adequately mix protein and precipitant solutions on a nano-liter scale. The mixtures have shown crystal growth in volumes in the range of 10 nanoliters to 5 microliters. In addition, large diffraction quality crystals were obtained by this method. X-ray data from these crystals were shown to be of excellent quality. Our future efforts will include the further development of protein crystal growth with LabChip(trademark) technology for more complex systems. We will initially address the batch growth method, followed by the vapor diffusion method and the liquid-liquid diffusion method. The culmination of these chip developments is to lead to an on orbit protein crystallization facility on the International Space Station. Structural biologists will be invited to utilize the on orbit Iterative Biological Crystallization facility to grow high quality macromolecular crystals in microgravity.

Preparation and characterization of superfine ammonium perchlorate (AP) crystals through ceramic membrane anti-solvent crystallization

NASA Astrophysics Data System (ADS)

Ma, Zhenye; Li, Cheng; Wu, Rujun; Chen, Rizhi; Gu, Zhenggui

2009-10-01

In this paper, a novel ceramic membrane anti-solvent crystallization (CMASC) method was proposed for the safe and rapid preparation ammonium perchlorate (AP) crystals, in which the acetone and ethyl acetate were chosen as solvent and anti-solvent, respectively. Comparing with the conventional liquid anti-solvent crystallization (LASC), CMASC which successfully introduces ceramic membrane with regular pore structure to the LASC as feeding medium, is favorable to control the rate of feeding rate and, therefore, to obtain size and morphology controllable AP. Several kinds of micro-sized AP particles with different morphology were obtained including polyhedral-like, quadrate-like to rod-like. The effect of processing parameters on the crystal size and shape of AP crystals such as volume ratio of anti-solvent to solvent, feeding pressure and crystallization temperature were investigated. It is found that higher volume ratio of anti-solvent to solvent, higher feeding pressure and higher temperature result in smaller particle size. Scaning electron microscopy (SEM) and X-ray diffraction (XRD) were used to characterize the resulting AP crystals. The nucleation and growth kinetic of the resulting AP crystals were also discussed.

Supramolecular architectures constructed through self-assembly of a chalcone and substituted diazo-β-diketones

NASA Astrophysics Data System (ADS)

Prajapati, R.; Mishra, L.; Grabowski, S. J.; Govil, G.; Dubey, S. K.

2008-05-01

Organic compounds namely pyridyl chalcone viz. 3-[4-(3-oxo-3-pyridin-2-yl-propenyl)-phenyl]-1-pyridin-2-yl-propenone (L 1), p-cholorophenyldiazopentane-2,4-dione (L 2) and p-methyl phenyldiazopentane-2,4-dione (L 3) have been characterized by their single-crystal X-ray crystallographic studies. Several structural motifs resulting upon their self-association through probable non-covalent interactions have been discussed. The studies of related motifs found in Cambridge Structural Database are performed and the results are related to the structural data obtained for crystal structures reported here in.

Millimeter-Wave Spectroscopy, X-ray Crystal Structure, and Quantum Chemical Studies of Diketene: Resolving Ambiguities Concerning the Structure of the Ketene Dimer.

PubMed

Orr, Vanessa L; Esselman, Brian J; Dorman, P Matisha; Amberger, Brent K; Guzei, Ilia A; Woods, R Claude; McMahon, Robert J

2016-10-06

The pure rotational spectrum of diketene has been studied in the millimeter-wave region from ∼240 to 360 GHz. For the ground vibrational state and five vibrationally excited satellites (ν 24 , 2ν 24 , 3ν 24 , 4ν 24 , and ν 16 ), the observed spectrum allowed for the measurement, assignment, and least-squares fitting a total of more than 10 000 distinct rotational transitions. In each case, the transitions were fit to single-state, complete or near-complete sextic centrifugally distorted rotor models to near experimental error limits using Kisiel's ASFIT. Additionally, we obtained less satisfactory least-squares fits to single-state centrifugally distorted rotor models for three additional vibrational states: ν 24 + ν 16 , ν 23 , and 5ν 24 . The structure of diketene was optimized at the CCSD(T)/ANO1 level, and the vibration-rotation interaction (α i ) values for each normal mode were determined with a CCSD(T)/ANO1 VPT2 anharmonic frequency calculation. These α i values were helpful in identifying the previously unreported ν 16 and ν 23 fundamental states. We obtained a single-crystal X-ray structure of diketene at -173 °C. The bond distances are increased in precision by more than an order of magnitude compared to those in the 1958 X-ray crystal structure. The improved accuracy of the crystal structure geometry resolves the discrepancy between previous computational and experimental structures. The rotational transition frequencies provided herein should be useful for a millimeter-wave or terahertz search for diketene in the interstellar medium.

Single crystal Ce doped scintillator material with garnet structure sensitive to gamma ray and neutron radiation

NASA Astrophysics Data System (ADS)

Solodovnikov, D.; Weber, M. H.; Haven, D. T.; Lynn, K. G.

2012-08-01

A mixed garnet scintillator host material is obtained from the melt—Yttrium Gadolinium Gallium Aluminum Garnet (YGGAG). In addition to the high thermal and chemical stability and radiation hardness found in garnet crystals, it offers sensitivity to neutrons due to the presence of Gd atoms, has lower melting temperature than yttrium aluminum garnet, and similar crystallization behavior suitable for growth of large volume crystals. Crystals of YGGAG doped with Ce of 10×10×10 mm3 have already demonstrated energy resolution of 10% at 662 keV.

Characterization of a defective PbWO4 crystal cut along the a-c crystallographic plane: structural assessment and a novel photoelastic stress analysis

NASA Astrophysics Data System (ADS)

Montalto, L.; Natali, P. P.; Daví, F.; Mengucci., P.; Paone, N.; Rinaldi, D.

2017-12-01

Among scintillators, the PWO is one of the most widely used, for instance in CMS calorimeter at CERN and PANDA project. Crystallographic structure and chemical composition as well as residual stress condition, are indicators of homogeneity and good quality of the crystal. In this paper, structural characterization of a defective PbWO4 (PWO) crystal has been performed by X-ray Diffraction (XRD), Energy Dispersive Spectroscopy (EDS) and Photoelasticity in the unusual (a, c) crystallographic plane. XRD and EDS analysis have been used to investigate crystallographic orientation and chemical composition, while stress distribution, which indicates macroscopic inhomogeneities and defects, has been obtained by photoelastic approaches, in Conoscopic and Sphenoscopic configuration. Since the sample is cut along the (a, c) crystallographic plane, a new method is proposed for the interpretation of the fringe pattern. The structural analysis has detected odds from the nominal lattice dimension, which can be attributed to the strong presence of Pb and W. A strong inhomogeneity over the crystal sample has been revealed by the photoelastic inspection. The results give reliability to the proposed procedure which is exploitable in crystals with other structures.

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

PubMed

Eibl, O

1995-02-15

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

Continuous-wave mid-infrared photonic crystal light emitters at room temperature

NASA Astrophysics Data System (ADS)

Weng, Binbin; Qiu, Jijun; Shi, Zhisheng

2017-01-01

Mid-infrared photonic crystal enhanced lead-salt light emitters operating under continuous-wave mode at room temperature were investigated in this work. For the device, an active region consisting of 9 pairs of PbSe/Pb0.96Sr0.04Se quantum wells was grown by molecular beam epitaxy method on top of a Si(111) substrate which was initially dry-etched with a two-dimensional photonic crystal structure in a pattern of hexagonal holes. Because of the photonic crystal structure, an optical band gap between 3.49 and 3.58 µm was formed, which matched with the light emission spectrum of the quantum wells at room temperature. As a result, under optical pumping, using a near-infrared continuous-wave semiconductor laser, the device exhibited strong photonic crystal band-edge mode emissions and delivered over 26.5 times higher emission efficiency compared to the one without photonic crystal structure. The output power obtained was up to 7.68 mW (the corresponding power density was 363 mW/cm2), and a maximum quantum efficiency reached to 1.2%. Such photonic crystal emitters can be used as promising light sources for novel miniaturized gas-sensing systems.

Electron tomography and computer visualisation of a three-dimensional 'photonic' crystal in a butterfly wing-scale.

PubMed

Argyros, A; Manos, S; Large, M C J; McKenzie, D R; Cox, G C; Dwarte, D M

2002-01-01

A combination of transmission electron tomography and computer modelling has been used to determine the three-dimensional structure of the photonic crystals found in the wing-scales of the Kaiser-I-Hind butterfly (Teinopalpus imperialis). These scales presented challenges for electron microscopy because the periodicity of the structure was comparable to the thickness of a section and because of the complex connectivity of the object. The structure obtained has been confirmed by taking slices of the three-dimensional computer model constructed from the tomography and comparing these with transmission electron microscope (TEM) images of microtomed sections of the actual scale. The crystal was found to have chiral tetrahedral repeating units packed in a triclinic lattice.

Valence-band and core-level photoemission study of single-crystal Bi2CaSr2Cu2O8 superconductors

NASA Astrophysics Data System (ADS)

Shen, Z.-X.; Lindberg, P. A. P.; Wells, B. O.; Mitzi, D. B.; Lindau, I.; Spicer, W. E.; Kapitulnik, A.

1988-12-01

High-quality single crystals of Bi2CaSr2Cu2O8 superconductors have been prepared and cleaved in ultrahigh vacuum. Low-energy electron diffraction measurements show that the surface structure is consistent with the bulk crystal structure. Ultraviolet photoemission and x-ray photoemission experiments were performed on these well-characterized sample surfaces. The valence-band and the core-level spectra obtained from the single-crystal surfaces are in agreement with spectra recorded from polycrystalline samples, justifying earlier results from polycrystalline samples. Cu satellites are observed both in the valence band and Cu 2p core level, signaling the strong correlation among the Cu 3d electrons. The O 1s core-level data exhibit a sharp, single peak at 529-eV binding energy without any clear satellite structures.

Crystal-Packing Trends for a Series of 6,9,12,15,18-Pentaaryl-1-hydro[60]fullerenes

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

Kennedy, Robert D.; Halim, Merissa; Khan, Saeed I.

2012-06-11

The relationship between the size of the substituents of aryl groups in a series of fifteen 6,9,12,15,18-pentaaryl-1-hydro[60]fullerenes and the solid-state structures and packing motifs of these compounds has been analyzed. Pentaarylfullerenes have a characteristic “badminton shuttlecock” shape that causes several derivatives to crystallize into columnar stacks. However, many pentaarylfullerenes form non-stacked structures with, for example, dimeric, layered, diamondoid, or feather-in-cavity relationships between molecules. Computational modeling gave a qualitative estimate of the best shape match between the ball and socket surfaces of each pentaarylfullerene. The best match was for pentaarylfullerenes with large, spherically shaped para-substituents on the aryl groups. The seriesmore » of pentaarylfullerenes was characterized by single-crystal X-ray diffraction. A total of 34 crystal structures were obtained as various solvates and were categorized by their packing motifs.« less

Crystal structures of the ATP-binding and ADP-release dwells of the V1 rotary motor

PubMed Central

Suzuki, Kano; Mizutani, Kenji; Maruyama, Shintaro; Shimono, Kazumi; Imai, Fabiana L.; Muneyuki, Eiro; Kakinuma, Yoshimi; Ishizuka-Katsura, Yoshiko; Shirouzu, Mikako; Yokoyama, Shigeyuki; Yamato, Ichiro; Murata, Takeshi

2016-01-01

V1-ATPases are highly conserved ATP-driven rotary molecular motors found in various membrane systems. We recently reported the crystal structures for the Enterococcus hirae A3B3DF (V1) complex, corresponding to the catalytic dwell state waiting for ATP hydrolysis. Here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free V1 crystals in ADP. In the presence of 20 μM ADP, two ADP molecules bind to two of three binding sites and cooperatively induce conformational changes of the third site to an ATP-binding mode, corresponding to the ATP-binding dwell. In the presence of 2 mM ADP, all nucleotide-binding sites are occupied by ADP to induce conformational changes corresponding to the ADP-release dwell. Based on these and previous findings, we propose a V1-ATPase rotational mechanism model. PMID:27807367

Crystal structure, spectrum character and explosive property of a new cocrystal CL-20/DNT

NASA Astrophysics Data System (ADS)

Liu, Ke; Zhang, Gao; Luan, Jieyu; Chen, Zhiqun; Su, Pengfei; Shu, Yuanjie

2016-04-01

A new cocrystal explosive of 2,4,6,8,10,12-hexanitrohexaazaiso-wurtzitane(CL-20) and 2,5-dinitrotoluene(DNT) in a molar ratio of 1:2 has been prepared by slow solvent evaporation method. Crystal structure of the cocrystal characterized by single crystal X-ray diffraction (SXRD) reveals that the cocrystal is formed by intermolecular hydrogen bond interactions and belongs to the triclinic system with P-1 group. Moreover, the obivious differences of powder X-ray diffraction (PXRD) patterns, infrared spectroscopy and Raman spectroscopy confirm that the intermolecular interactions have great influence for the crystal structure and formation of cocrystal. The cocrystal exhibits a lower impact height of 44 cm, suggesting a substantial reduction of sensitivity in comparison with CL-20. And thermal test results showed cocrystal obtains a lower melting point than DNT, which means huge advantages in blasting engineering.

Au133(SPh-tBu)52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

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

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the “nanostructure problem”. Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Au 133 (SPh - t Bu) 52 Nanomolecules: X-ray Crystallography, Optical, Electrochemical, and Theoretical Analysis

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

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au-133(SPh-tBu)(52), was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than inmore » the slightly larger Au-144(SCH2CH2Ph)(60). Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.« less

Synthesis, crystal structures, spectral, thermal and antimicrobial properties of new Zn(II) 5-iodo- and 5-bromosalicylates

NASA Astrophysics Data System (ADS)

Košická, Petra; Győryová, Katarína; Smolko, Lukáš; Gyepes, Róbert; Hudecová, Daniela

2018-03-01

Two new analogous zinc(II) complexes containing 5-iodo- and 5-bromosalicylate ligands, respectively, were prepared in single-crystal form and characterized by IR spectroscopy, thermal analysis and elemental analysis. The solid-state structures of prepared complexes were determined by single crystal X-ray crystallography. Both complexes are isostructural and their crystal structures composed of neutral molecules [Zn(5-Xsal)2(H2O)2] (where X = Br, I, sal = salicylato). Central Zn(II) atom is in both complexes coordinated by six oxygen atoms, four of which are from two chelate bonded 5-halosalicylates and remaining two from coordinated water molecules. The found chelate binding mode is in line with the Δ values calculated from IR spectral data. Antimicrobial activity of prepared complexes was studied against selected bacteria, yeast and filamentous fungi. Obtained results indicate that 5-iodosalicylate complex is more antimicrobially active than its 5-bromo substituted analogue.

Au133(SPh-tBu)52 nanomolecules: X-ray crystallography, optical, electrochemical, and theoretical analysis.

PubMed

Dass, Amala; Theivendran, Shevanuja; Nimmala, Praneeth Reddy; Kumara, Chanaka; Jupally, Vijay Reddy; Fortunelli, Alessandro; Sementa, Luca; Barcaro, Giovanni; Zuo, Xiaobing; Noll, Bruce C

2015-04-15

Crystal structure determination has revolutionized modern science in biology, chemistry, and physics. However, the difficulty in obtaining periodic crystal lattices which are needed for X-ray crystal analysis has hindered the determination of atomic structure in nanomaterials, known as the "nanostructure problem". Here, by using rigid and bulky ligands, we have overcome this limitation and successfully solved the X-ray crystallographic structure of the largest reported thiolated gold nanomolecule, Au133S52. The total composition, Au133(SPh-tBu)52, was verified using high resolution electrospray ionization mass spectrometry (ESI-MS). The experimental and simulated optical spectra show an emergent surface plasmon resonance that is more pronounced than in the slightly larger Au144(SCH2CH2Ph)60. Theoretical analysis indicates that the presence of rigid and bulky ligands is the key to the successful crystal formation.

Structures of a bi-functional Kunitz-type STI family inhibitor of serine and aspartic proteases: Could the aspartic protease inhibition have evolved from a canonical serine protease-binding loop?

PubMed

Guerra, Yasel; Valiente, Pedro A; Pons, Tirso; Berry, Colin; Rudiño-Piñera, Enrique

2016-08-01

Bi-functional inhibitors from the Kunitz-type soybean trypsin inhibitor (STI) family are glycosylated proteins able to inhibit serine and aspartic proteases. Here we report six crystal structures of the wild-type and a non-glycosylated mutant of the bifunctional inhibitor E3Ad obtained at different pH values and space groups. The crystal structures show that E3Ad adopts the typical β-trefoil fold of the STI family exhibiting some conformational changes due to pH variations and crystal packing. Despite the high sequence identity with a recently reported potato cathepsin D inhibitor (PDI), three-dimensional structures obtained in this work show a significant conformational change in the protease-binding loop proposed for aspartic protease inhibition. The E3Ad binding loop for serine protease inhibition is also proposed, based on structural similarity with a novel non-canonical conformation described for the double-headed inhibitor API-A from the Kunitz-type STI family. In addition, structural and sequence analyses suggest that bifunctional inhibitors of serine and aspartic proteases from the Kunitz-type STI family are more similar to double-headed inhibitor API-A than other inhibitors with a canonical protease-binding loop. Copyright © 2016. Published by Elsevier Inc.

The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry.

PubMed

Johnstone, Timothy C

2014-01-08

The crystal structure of the anticancer drug oxaliplatin, [Pt( R,R- DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P2 1 , confirming the sole presence of the R , R enantiomer of the DACH ligand [M. A. Bruck et al. , Inorg. Chim. Acta , 92 (1984) 279-284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P2 1 /m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al. , Polyhedron , 22 (2003) 1529-1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt( R , R -DACH)I 2 , and a platinum(IV) derivative, trans -[Pt( R , R -DACH)(oxalate)(OH) 2 ], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R , R . A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P2 1 /m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained.

The Crystal Structure of Oxaliplatin: A Case of Overlooked Pseudo Symmetry

PubMed Central

Johnstone, Timothy C.

2013-01-01

The crystal structure of the anticancer drug oxaliplatin, [Pt(R,R-DACH)(oxalate)] (DACH = diaminocyclohexane), was first reported in the non-centrosymmetric space group P21, confirming the sole presence of the R,R enantiomer of the DACH ligand [M. A. Bruck et al., Inorg. Chim. Acta, 92 (1984) 279–284]. It was later proposed that the crystal structure is better described in the centrosymmetric space group P21/m, signifying the presence of the compound as a racemic mixture [A. S. Abu-Surrah et al., Polyhedron, 22 (2003) 1529–1534]. Herein is presented a reinvestigation of this crystal structure, which shows that the discrepancy between the two proposed space group assignments arises from overlooked pseudo symmetry. The crystal structures of the synthetic precursor to oxaliplatin, Pt(R,R-DACH)I2, and a platinum(IV) derivative, trans-[Pt(R,R-DACH)(oxalate)(OH)2], were also determined, and the absolute configuration of the DACH ligand in each was confirmed to be R,R. A spectroscopic investigation of the optical rotatory dispersion (ORD) of the oxaliplatin crystals was carried out to further confirm the lack of the true crystallographic mirror plane required for a P21/m solution. The ORD was theoretically simulated, in one instance, by applying the Kramers-Kronig transform to the computed circular dichroism spectrum and was found to corroborate the spectroscopic and crystallographic findings. Finally, a brief discussion is given of the importance of discussing the details of nuanced crystal structures and of providing evidence in addition to X-ray structure determination if chemically unexpected results are obtained. PMID:24415827

Determination of Other Related Carotenoids Substances in Astaxanthin Crystals Extracted from Adonis amurensis.

PubMed

Zhang, Li-hua; Peng, Yong-jian; Xu, Xin-de; Wang, Sheng-nan; Yu, Lei-ming; Hong, Yi-min; Ma, Jin-ping

2015-01-01

Astaxanthin is a kind of important carotenoids with powerful antioxidation capacity and other health functions. Extracting from Adonis amurensis is a promising way to obtain natural astaxanthin. However, how to ensure the high purity and to investigate related substances in astaxanthin crystals are necessary issues. In this study, to identify possible impurities, astaxanthin crystal was first extracted from Adonis amurensis, then purified by saponification and separation. The concentration of total carotenoids in purified astaxanthin crystals was as high as 97% by weight when analyzed by UV-visible absorption spectra. After identified with TLC, HPLC and MS, besides free astaxanthin as main ingredient in the crystals, there existed four other unknown related substances, which were further investigated by HPLC/ESI/MS with the positive ion mode combining with other auxiliary reference data obtained in stress tests, at last it was confirmed that four related carotenoids substances were three structural isomers of semi-astacene and adonirubin.

Increasing low frequency sound attenuation using compounded single layer of sonic crystal

NASA Astrophysics Data System (ADS)

Gulia, Preeti; Gupta, Arpan

2018-05-01

Sonic crystals (SC) are man-made periodic structures where sound hard scatterers are arranged in a crystalline manner. SC reduces noise in a particular range of frequencies called as band gap. Sonic crystals have a promising application in noise shielding; however, the application is limited due to the size of structure. Particularly for low frequencies, the structure becomes quite bulky, restricting its practical application. This paper presents a compounded model of SC, which has the same overall area and filling fraction but with increased low frequency sound attenuation. Two cases have been considered, a three layer SC and a compounded single layer SC. Both models have been analyzed using finite element simulation and plane wave expansion method. Band gaps for periodic structures have been obtained using both methods which are in good agreement. Further, sound transmission loss has been evaluated using finite element method. The results demonstrate the use of compounded model of Sonic Crystal for low frequency sound attenuation.

Protein crystal structure obtained at 2.9 Å resolution from injecting bacterial cells into an X-ray free-electron laser beam

PubMed Central

Sawaya, Michael R.; Cascio, Duilio; Gingery, Mari; Rodriguez, Jose; Goldschmidt, Lukasz; Colletier, Jacques-Philippe; Messerschmidt, Marc M.; Boutet, Sébastien; Koglin, Jason E.; Williams, Garth J.; Brewster, Aaron S.; Nass, Karol; Hattne, Johan; Botha, Sabine; Doak, R. Bruce; Shoeman, Robert L.; DePonte, Daniel P.; Park, Hyun-Woo; Federici, Brian A.; Sauter, Nicholas K.; Schlichting, Ilme; Eisenberg, David S.

2014-01-01

It has long been known that toxins produced by Bacillus thuringiensis (Bt) are stored in the bacterial cells in crystalline form. Here we describe the structure determination of the Cry3A toxin found naturally crystallized within Bt cells. When whole Bt cells were streamed into an X-ray free-electron laser beam we found that scattering from other cell components did not obscure diffraction from the crystals. The resolution limits of the best diffraction images collected from cells were the same as from isolated crystals. The integrity of the cells at the moment of diffraction is unclear; however, given the short time (∼5 µs) between exiting the injector to intersecting with the X-ray beam, our result is a 2.9-Å-resolution structure of a crystalline protein as it exists in a living cell. The study suggests that authentic in vivo diffraction studies can produce atomic-level structural information. PMID:25136092

Photonic crystal microprisms obtained by carving artificial opals

NASA Astrophysics Data System (ADS)

Fenollosa, R.; Ibisate, M.; Rubio, S.; López, C.; Meseguer, F.; Sánchez-Dehesa, J.

2003-01-01

A method for fabrication of photonic crystal prisms is demonstrated. The procedure is based on micromanipulation techniques, here applied to artificial opals. By means of a microgrinder an opal prism comprising a single crystal (several tens of microns in size) has been carved with three different faces: (111), (110), and (100). The faces were morphologically characterized by scanning electron microscopy and their optical reflectance spectra measured and compared with the theoretical band structure.

Terahertz Spectroscopy and Solid-State Density Functional Theory Calculations of Cyanobenzaldehyde Isomers.

PubMed

Dash, Jyotirmayee; Ray, Shaumik; Nallappan, Kathirvel; Kaware, Vaibhav; Basutkar, Nitin; Gonnade, Rajesh G; Ambade, Ashootosh V; Joshi, Kavita; Pesala, Bala

2015-07-23

Spectral signatures in the terahertz (THz) frequency region are mainly due to bulk vibrations of the molecules. These resonances are highly sensitive to the relative position of atoms in a molecule as well as the crystal packing arrangement. To understand the variation of THz resonances, THz spectra (2-10 THz) of three structural isomers: 2-, 3-, and 4-cyanobenzaldehyde have been studied. THz spectra obtained from Fourier transform infrared (FTIR) spectrometry of these isomers show that the resonances are distinctly different especially below 5 THz. For understanding the intermolecular interactions due to hydrogen bonds, four molecule cluster simulations of each of the isomers have been carried out using the B3LYP density functional with the 6-31G(d,p) basis set in Gaussian09 software and the compliance constants are obtained. However, to understand the exact reason behind the observed resonances, simulation of each isomer considering the full crystal structure is essential. The crystal structure of each isomer has been determined using X-ray diffraction (XRD) analysis for carrying out crystal structure simulations. Density functional theory (DFT) simulations using CRYSTAL14 software, utilizing the hybrid density functional B3LYP, have been carried out to understand the vibrational modes. The bond lengths and bond angles from the optimized structures are compared with the XRD results in terms of root-mean-square-deviation (RMSD) values. Very low RMSD values confirm the overall accuracy of the results. The simulations are able to predict most of the spectral features exhibited by the isomers. The results show that low frequency modes (<3 THz) are mediated through hydrogen bonds and are dominated by intermolecular vibrations.

Crystal structure and superconductivity in atomic hydrogen: Deformation between I41/amd and Fddd

NASA Astrophysics Data System (ADS)

Ishikawa, T.; Nagara, H.; Oda, T.; Suzuki, N.; Shimizu, K.

2017-10-01

We investigated crystal structures of solid metallic hydrogen using the potential energy surface trekking for structure search. We applied this technique to a tetragonal I41/amd structure at pressures of 500 and 600 GPa and obtained the transformation into multiple orthorhombic Fddd structures, which are formed by distortions in the ab plane of I41/amd. The potential barriers are easily surmounted by few trekking steps, which indicates that in solid metallic hydrogen crystal structure is softened with respect to the distortion and is easily fluctuated among the I41/amd and Fddd structures. Calculated superconducting critical temperatures show 269 K for I41/amd and 263 K for Fddd at 500 GPa. The structures are softened and the electron-phonon coupling are enhanced with pressurization to 600 GPa. As the results, the superconducting critical temperature is increased to 281 K for I41/amd, whereas it is decreased to 252 K for Fddd owing to its larger phonon softening than that of I41/amd.

High-resolution X-ray crystal structure of bovine H-protein using the high-pressure cryocooling method.

PubMed

Higashiura, Akifumi; Ohta, Kazunori; Masaki, Mika; Sato, Masaru; Inaka, Koji; Tanaka, Hiroaki; Nakagawa, Atsushi

2013-11-01

Recently, many technical improvements in macromolecular X-ray crystallography have increased the number of structures deposited in the Protein Data Bank and improved the resolution limit of protein structures. Almost all high-resolution structures have been determined using a synchrotron radiation source in conjunction with cryocooling techniques, which are required in order to minimize radiation damage. However, optimization of cryoprotectant conditions is a time-consuming and difficult step. To overcome this problem, the high-pressure cryocooling method was developed (Kim et al., 2005) and successfully applied to many protein-structure analyses. In this report, using the high-pressure cryocooling method, the X-ray crystal structure of bovine H-protein was determined at 0.86 Å resolution. Structural comparisons between high- and ambient-pressure cryocooled crystals at ultra-high resolution illustrate the versatility of this technique. This is the first ultra-high-resolution X-ray structure obtained using the high-pressure cryocooling method.

Controlling Chirality of Entropic Crystals

NASA Astrophysics Data System (ADS)

Damasceno, Pablo F.; Karas, Andrew S.; Schultz, Benjamin A.; Engel, Michael; Glotzer, Sharon C.

2015-10-01

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

Raman spectroscopic investigations on natural samples from the Integrated Ocean Drilling Program (IODP) Expedition 311: indications for heterogeneous compositions in hydrate crystals.

PubMed

Schicks, J M; Ziemann, M A; Lu, H; Ripmeester, J A

2010-12-01

Natural gas hydrates usually are found in the form of structure I, encasing predominantly methane in the hydrate lattices as guest molecules, sometimes also minor amount of higher hydrocarbons, CO2 or H2S. Raman spectroscopy is an approved tool to determine the composition of the hydrate phase. Thus, in this study Raman spectroscopic analyses have been applied to hydrate samples obtained from Integrated Ocean Drilling Program (IODP) Expedition 311 in two different approaches: studying the samples randomly taken from the hydrate core, and--as a new application--mapping small areas on the surface of clear hydrate crystals. The results obtained imply that the gas composition of hydrate, in terms of relative concentrations of CH4 and H2S, is not homogeneous over a core or even within a crystal. The mapping method yielded results with very high lateral resolution, indicating the coexistence of different phases with the same structure but different compositions within a hydrate crystal. Copyright © 2010 Elsevier B.V. All rights reserved.

Improving Processes of Mechanized Pulsed Arc Welding of Low-Frequency Range Variation of Mode Parameters

NASA Astrophysics Data System (ADS)

Saraev, Yu N.; Solodskiy, S. A.; Ulyanova, O. V.

2016-04-01

A new technology of low-frequency modulation of the arc current in MAG and MIG welding is presented. The technology provides control of thermal and crystallization processes, stabilizes the time of formation and crystallization of the weld pool. Conducting theoretical studies allowed formulating the basic criteria for obtaining strong permanent joints for high-duty structures, providing conditions for more equilibrium structure of the deposited metal and the smaller width of the HAZ. The stabilization of time of the formation and crystallization of the weld pool improves the formation of the weld and increases productivity in welding thin sheet metal.

Temperature-dependent dielectric functions and interband critical points of sulfur-rich TlIn(S1-xSex)2 layered solid solution crystals

NASA Astrophysics Data System (ADS)

Gomonnai, O. O.; Gordan, O.; Guranich, P. P.; Slivka, A. G.; Gomonnai, A. V.; Zahn, D. R. T.

2017-12-01

Real and imaginary parts of the dielectric function of TlIn(S1-xSex)2 (x = 0.05, 0.08, 0.25) single crystals were determined in the spectral range from 1 to 5 eV within a temperature interval 140-293 K from spectroscopic ellipsometry measurements. The energies of interband transitions (critical points) of the TlIn(S1-xSex)2 crystals were obtained from the second derivative of the real and imaginary parts of dielectric function. Structural phase transitions are behind the observed change of electronic band structure.

Crystal structure of an intermolecular 2:1 complex between adenine and thymine. Evidence for both Hoogsteen and 'quasi-Watson-Crick' interactions.

PubMed

Chandrasekhar, Sosale; Naik, Tangali R Ravikumar; Nayak, Susanta K; Row, Tayur N Guru

2010-06-15

The titled complex, obtained by co-crystallization (EtOH/25 degrees C), is apparently the only known complex of the free bases. Its crystal structure, as determined by X-ray diffraction at both 90 K and 313 K, showed that one A-T pair involves a Hoogsteen interaction, and the other a Watson-Crick interaction but only with respect to the adenine unit. The absence of a clear-cut Watson-Crick base pair raises intriguing questions about the basis of the DNA double helix. Copyright 2010 Elsevier Ltd. All rights reserved.

Using Strong Magnetic Fields to Control Solutal Convection

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2003-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity , we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagnetic salts and solutions in magnetic fields and compare them to analytical predictions.

Countering Solutal Buoyant Convection with High Magnetic Fields

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2002-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular crystals for diffraction analyses has been the central focus for biochemist, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitant, other possible phases of the protein, foreign particles, the walls of the container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and sedimentation, as is achieved in microgravity, we have been able to dramatically effect the movement and distribution of macromolecules in the fluid, and thus their transport, formation of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with concentration for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteracts terrestrial gravity. The general objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the current status of the investigation and discuss results from the experimental and modeling efforts.

Goniometer-based femtosecond crystallography with X-ray free electron lasers

DOE PAGES

Cohen, Aina E.; Soltis, S. Michael; González, Ana; ...

2014-10-31

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. With smaller crystals, high-density grids were usedmore » to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β 2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources.« less

Goniometer-based femtosecond crystallography with X-ray free electron lasers

PubMed Central

Cohen, Aina E.; Soltis, S. Michael; González, Ana; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Baxter, Elizabeth L.; Brehmer, Winnie; Brewster, Aaron S.; Brunger, Axel T.; Calero, Guillermo; Chang, Joseph F.; Chollet, Matthieu; Ehrensberger, Paul; Eriksson, Thomas L.; Feng, Yiping; Hattne, Johan; Hedman, Britt; Hollenbeck, Michael; Holton, James M.; Keable, Stephen; Kobilka, Brian K.; Kovaleva, Elena G.; Kruse, Andrew C.; Lemke, Henrik T.; Lin, Guowu; Lyubimov, Artem Y.; Manglik, Aashish; Mathews, Irimpan I.; McPhillips, Scott E.; Nelson, Silke; Peters, John W.; Sauter, Nicholas K.; Smith, Clyde A.; Song, Jinhu; Stevenson, Hilary P.; Tsai, Yingssu; Uervirojnangkoorn, Monarin; Vinetsky, Vladimir; Wakatsuki, Soichi; Weis, William I.; Zadvornyy, Oleg A.; Zeldin, Oliver B.; Zhu, Diling; Hodgson, Keith O.

2014-01-01

The emerging method of femtosecond crystallography (FX) may extend the diffraction resolution accessible from small radiation-sensitive crystals and provides a means to determine catalytically accurate structures of acutely radiation-sensitive metalloenzymes. Automated goniometer-based instrumentation developed for use at the Linac Coherent Light Source enabled efficient and flexible FX experiments to be performed on a variety of sample types. In the case of rod-shaped Cpl hydrogenase crystals, only five crystals and about 30 min of beam time were used to obtain the 125 still diffraction patterns used to produce a 1.6-Å resolution electron density map. For smaller crystals, high-density grids were used to increase sample throughput; 930 myoglobin crystals mounted at random orientation inside 32 grids were exposed, demonstrating the utility of this approach. Screening results from cryocooled crystals of β2-adrenoreceptor and an RNA polymerase II complex indicate the potential to extend the diffraction resolution obtainable from very radiation-sensitive samples beyond that possible with undulator-based synchrotron sources. PMID:25362050

Ultralow chirp photonic crystal fiber Mach-Zehnder interferometer.

PubMed

Carvalho, William O F; Spadoti, Danilo H; Silvestre, Enrique; Beltran-Mejia, Felipe

2018-05-20

A photonic crystal fiber Mach-Zehnder interferometer design was optimized to obtain high performance and ultralow chirp. Two long-period gratings were used to excite the cladding modes, and the rich structure of the cladding was tailored to obtain a slightly chirped free spectral range, as required by the Telecommunication Standardization Sector of the International Telecommunication Union (ITU-T) Norm G.694.1. Finally, a fabrication tolerance analysis was performed. The advantages of the proposed device are an ultralow chirp, high bandwidth, and fabrication robustness tolerance.

Freeze-Casting Produces a Graphene Oxide Aerogel with a Radial and Centrosymmetric Structure.

PubMed

Wang, Chunhui; Chen, Xiong; Wang, Bin; Huang, Ming; Wang, Bo; Jiang, Yi; Ruoff, Rodney S

2018-05-14

We report the assembly of graphene oxide (G-O) building blocks into a vertical and radially aligned structure by a bidirectional freeze-casting approach. The crystallization of water to ice assembles the G-O sheets into a structure, a G-O aerogel whose local structure mimics turbine blades. The centimeter-scale radiating structure in this aerogel has many channels whose width increases with distance from the center. This was achieved by controlling the formation of the ice crystals in the aqueous G-O dispersion that grew radially in the shape of lamellae during freezing. Because the shape and size of ice crystals is influenced by the G-O sheets, different additives (ethanol, cellulose nanofibers, and chitosan) that can form hydrogen bonds with H 2 O were tested and found to affect the interaction between the G-O and formation of ice crystals, producing ice crystals with different shapes. A G-O/chitosan aerogel with a spiral pattern was also obtained. After chemical reduction of G-O, our aerogel exhibited elasticity and absorption capacity superior to that of graphene aerogels with "traditional" pore structures made by conventional freeze-casting. This methodology can be expanded to many other configurations and should widen the use of G-O (and reduced G-O and "graphenic") aerogels.

Crystal structure of langbeinite-related Rb0.743K0.845Co0.293Ti1.707(PO4)3

PubMed Central

Strutynska, Nataliia Yu.; Bondarenko, Marina A.; Ogorodnyk, Ivan V.; Baumer, Vyacheslav N.; Slobodyanik, Nikolay S.

2015-01-01

Potassium rubidium cobalt(II)/titanium(IV) tris­(orthophosphate), Rb0.743K0.845Co0.293Ti1.707(PO4)3, has been obtained using a high-temperature crystallization method. The obtained compound has a langbeinite-type structure. The three-dimensional framework is built up from mixed-occupied (Co/TiIV)O6 octa­hedra (point group symmetry .3.) and PO4 tetra­hedra. The K+ and Rb+ cations are statistically distributed over two distinct sites (both with site symmetry .3.) in the large cavities of the framework. They are surrounded by 12 O atoms. PMID:25844179

Recent Advances in the Understanding of the Influence of Electric and Magnetic Fields on Protein Crystal Growth

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

Pareja-Rivera, Carina; Cuéllar-Cruz, Mayra; Esturau-Escofet, Nuria

Here, in this contribution we use nonconventional methods that help to increase the success rate of a protein crystal growth, and consequently of structural projects using X-ray diffraction techniques. In order to achieve this purpose, this contribution presents new approaches involving more sophisticated techniques of protein crystallization, not just for growing protein crystals of different sizes by using electric fields, but also for controlling crystal size and orientation. Also, this latter was possible through the use of magnetic fields that allow to obtain protein crystals suitable for both high-resolution X-ray and neutron diffraction crystallography where big crystals are required. Thismore » contribution discusses some pros, cons and realities of the role of electromagnetic fields in protein crystallization research, and their effect on protein crystal contacts. Additionally, we discuss the importance of room and low temperatures during data collection. Finally, we also discuss the effect of applying a rather strong magnetic field of 16.5 T, for shorts and long periods of time, on protein crystal growth, and on the 3D structure of two model proteins.« less

Recent Advances in the Understanding of the Influence of Electric and Magnetic Fields on Protein Crystal Growth

DOE PAGES

Pareja-Rivera, Carina; Cuéllar-Cruz, Mayra; Esturau-Escofet, Nuria; ...

2016-12-05

Here, in this contribution we use nonconventional methods that help to increase the success rate of a protein crystal growth, and consequently of structural projects using X-ray diffraction techniques. In order to achieve this purpose, this contribution presents new approaches involving more sophisticated techniques of protein crystallization, not just for growing protein crystals of different sizes by using electric fields, but also for controlling crystal size and orientation. Also, this latter was possible through the use of magnetic fields that allow to obtain protein crystals suitable for both high-resolution X-ray and neutron diffraction crystallography where big crystals are required. Thismore » contribution discusses some pros, cons and realities of the role of electromagnetic fields in protein crystallization research, and their effect on protein crystal contacts. Additionally, we discuss the importance of room and low temperatures during data collection. Finally, we also discuss the effect of applying a rather strong magnetic field of 16.5 T, for shorts and long periods of time, on protein crystal growth, and on the 3D structure of two model proteins.« less

Structure of a nanobody-stabilized active state of the β(2) adrenoceptor.

PubMed

Rasmussen, Søren G F; Choi, Hee-Jung; Fung, Juan Jose; Pardon, Els; Casarosa, Paola; Chae, Pil Seok; Devree, Brian T; Rosenbaum, Daniel M; Thian, Foon Sun; Kobilka, Tong Sun; Schnapp, Andreas; Konetzki, Ingo; Sunahara, Roger K; Gellman, Samuel H; Pautsch, Alexander; Steyaert, Jan; Weis, William I; Kobilka, Brian K

2011-01-13

G protein coupled receptors (GPCRs) exhibit a spectrum of functional behaviours in response to natural and synthetic ligands. Recent crystal structures provide insights into inactive states of several GPCRs. Efforts to obtain an agonist-bound active-state GPCR structure have proven difficult due to the inherent instability of this state in the absence of a G protein. We generated a camelid antibody fragment (nanobody) to the human β(2) adrenergic receptor (β(2)AR) that exhibits G protein-like behaviour, and obtained an agonist-bound, active-state crystal structure of the receptor-nanobody complex. Comparison with the inactive β(2)AR structure reveals subtle changes in the binding pocket; however, these small changes are associated with an 11 Å outward movement of the cytoplasmic end of transmembrane segment 6, and rearrangements of transmembrane segments 5 and 7 that are remarkably similar to those observed in opsin, an active form of rhodopsin. This structure provides insights into the process of agonist binding and activation.

Multi-Conformer Ensemble Docking to Difficult Protein Targets

DOE PAGES

Ellingson, Sally R.; Miao, Yinglong; Baudry, Jerome; ...

2014-09-08

We investigate large-scale ensemble docking using five proteins from the Directory of Useful Decoys (DUD, dud.docking.org) for which docking to crystal structures has proven difficult. Molecular dynamics trajectories are produced for each protein and an ensemble of representative conformational structures extracted from the trajectories. Docking calculations are performed on these selected simulation structures and ensemble-based enrichment factors compared with those obtained using docking in crystal structures of the same protein targets or random selection of compounds. We also found simulation-derived snapshots with improved enrichment factors that increased the chemical diversity of docking hits for four of the five selected proteins.more » A combination of all the docking results obtained from molecular dynamics simulation followed by selection of top-ranking compounds appears to be an effective strategy for increasing the number and diversity of hits when using docking to screen large libraries of chemicals against difficult protein targets.« less

Assembly of the most topologically regular two-dimensional micro and nanocrystals with spherical, conical, and tubular shapes

NASA Astrophysics Data System (ADS)

Roshal, D. S.; Konevtsova, O. V.; Myasnikova, A. E.; Rochal, S. B.

2016-11-01

We consider how to control the extension of curvature-induced defects in the hexagonal order covering different curved surfaces. In these frames we propose a physical mechanism for improving structures of two-dimensional spherical colloidal crystals (SCCs). For any SCC comprising of about 300 or less particles the mechanism transforms all extended topological defects (ETDs) in the hexagonal order into the point disclinations. Perfecting the structure is carried out by successive cycles of the particle implantation and subsequent relaxation of the crystal. The mechanism is potentially suitable for obtaining colloidosomes with better selective permeability. Our approach enables modeling the most topologically regular tubular and conical two-dimensional nanocrystals including various possible polymorphic forms of the HIV viral capsid. Different HIV-like shells with an arbitrary number of structural units (SUs) and desired geometrical parameters are easily formed. Faceting of the obtained structures is performed by minimizing the suggested elastic energy.

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate.

PubMed

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-09-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxyacetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a=72.39, b=127.71, c=157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site.

Molecular dynamics simulation of fast particle irradiation on the single crystal CeO2

NASA Astrophysics Data System (ADS)

Sasajima, Y.; Ajima, N.; Osada, T.; Ishikawa, N.; Iwase, A.

2013-11-01

We used a molecular dynamics method to simulate structural relaxation caused by the high-energy-ion irradiation of single crystal CeO2. As the initial condition, we assumed high thermal energy was supplied to the individual atoms within a cylindrical region of nanometer-order diameter located in the center of the single crystal. The potential proposed by Inaba et al. was utilized to calculate interactions between atoms [H. Inaba, R. Sagawa, H. Hayashi, K. Kawamura, Solid State Ionics 122 (1999) 95-103]. The supplied thermal energy was first spent to change the crystal structure into an amorphous one within a short period of about 0.3 ps, then it was dissipated in the crystal. We compared the obtained results with those of computer simulations for UO2 and found that CeO2 was more stable than UO2 when supplied with high thermal energy.

Extremely frequency-widened terahertz wave generation using Cherenkov-type radiation.

PubMed

Suizu, Koji; Koketsu, Kaoru; Shibuya, Takayuki; Tsutsui, Toshihiro; Akiba, Takuya; Kawase, Kodo

2009-04-13

Terahertz (THz) wave generation based on nonlinear frequency conversion is promising way for realizing a tunable monochromatic bright THz-wave source. Such a development of efficient and wide tunable THz-wave source depends on discovery of novel brilliant nonlinear crystal. Important factors of a nonlinear crystal for THz-wave generation are, 1. High nonlinearity and 2. Good transparency at THz frequency region. Unfortunately, many nonlinear crystals have strong absorption at THz frequency region. The fact limits efficient and wide tunable THz-wave generation. Here, we show that Cherenkov radiation with waveguide structure is an effective strategy for achieving efficient and extremely wide tunable THz-wave source. We fabricated MgO-doped lithium niobate slab waveguide with 3.8 microm of thickness and demonstrated difference frequency generation of THz-wave generation with Cherenkov phase matching. Extremely frequency-widened THz-wave generation, from 0.1 to 7.2 THz, without no structural dips successfully obtained. The tuning frequency range of waveguided Cherenkov radiation source was extremely widened compare to that of injection seeded-Terahertz Parametric Generator. The tuning range obtained in this work for THz-wave generation using lithium niobate crystal was the widest value in our knowledge. The highest THz-wave energy obtained was about 3.2 pJ, and the energy conversion efficiency was about 10(-5) %. The method can be easily applied for many conventional nonlinear crystals, results in realizing simple, reasonable, compact, high efficient and ultra broad band THz-wave sources.

Electronic structure and magnetic properties of the strong-rung spin-1 ladder compound Rb3Ni2(NO3)7

NASA Astrophysics Data System (ADS)

Pchelkina, Z. V.; Mazurenko, V. V.; Volkova, O. S.; Deeva, E. B.; Morozov, I. V.; Shutov, V. V.; Troyanov, S. I.; Werner, J.; Koo, C.; Klingeler, R.; Vasiliev, A. N.

2018-04-01

Rb3Ni2(NO3)7 was obtained by crystallization from anhydrous nitric acid solution of rubidium nitrate and nickel nitrate hexahydrate. The crystal structure determined on single crystals implies isolated spin-1 two-leg ladders of Ni2 + ions connected by (NO3)- groups as basic elements. Magnetic susceptibility, specific heat in magnetic fields up to 9 T, magnetization, and high-frequency electron spin resonance studies performed on powder samples show the absence of long-range magnetic order at T ≥2 K. Electronic structure calculations and the detailed analysis of the experimental data enable quantitative estimates of the relevant parameters of the S =1 ladders in Rb3Ni2(NO3)7 . The rung coupling J1=10.16 K, the leg coupling J2=1.5 K, and the Ising-type anisotropy |A |=8.6 K are obtained. The scenario of a valence-bond solidlike quantum ground state realized in the two-leg Ni2 + ladders is further corroborated by model simulations of the magnetic susceptibility.

Coarse-grained modeling of crystal growth and polymorphism of a model pharmaceutical molecule.

PubMed

Mandal, Taraknath; Marson, Ryan L; Larson, Ronald G

2016-10-04

We describe a systematic coarse-graining method to study crystallization and predict possible polymorphs of small organic molecules. In this method, a coarse-grained (CG) force field is obtained by inverse-Boltzmann iteration from the radial distribution function of atomistic simulations of the known crystal. With the force field obtained by this method, we show that CG simulations of the drug phenytoin predict growth of a crystalline slab from a melt of phenytoin, allowing determination of the fastest-growing surface, as well as giving the correct lattice parameters and crystal morphology. By applying meta-dynamics to the coarse-grained model, a new crystalline form of phenytoin (monoclinic, space group P2 1 ) was predicted which is different from the experimentally known crystal structure (orthorhombic, space group Pna2 1 ). Atomistic simulations and quantum calculations then showed the polymorph to be meta-stable at ambient temperature and pressure, and thermodynamically more stable than the conventional orthorhombic crystal at high pressure. The results suggest an efficient route to study crystal growth of small organic molecules that could also be useful for identification of possible polymorphs as well.

Solvent-induced controllable synthesis, single-crystal to single-crystal transformation and encapsulation of Alq3 for modulated luminescence in (4,8)-connected metal-organic frameworks.

PubMed

Lan, Ya-Qian; Jiang, Hai-Long; Li, Shun-Li; Xu, Qiang

2012-07-16

In this work, for the first time, we have systematically demonstrated that solvent plays crucial roles in both controllable synthesis of metal-organic frameworks (MOFs) and their structural transformation process. With solvent as the only variable, five new MOFs with different structures have been constructed, in which one MOF undergoes solvent-induced single-crystal to single-crystal (SCSC) transformation that involves not only solvent exchange but also the cleavage and formation of coordination bonds. Particularly, a significant crystallographic change has been realized through an unprecedented three-step SCSC transformation process. Furthermore, we have demonstrated that the obtained MOF could be an excellent host for chromophores such as Alq3 for modulated luminescent properties.

Fluorescence XAS using Ge PAD: Application to High-Temperature Superconducting Thin Film Single Crystals

NASA Astrophysics Data System (ADS)

Oyanagi, H.; Tsukada, A.; Naito, M.; Saini, N. L.; Zhang, C.

2007-02-01

A Ge pixel array detector (PAD) with 100 segments was used in fluorescence x-ray absorption spectroscopy (XAS) study, probing local structure of high temperature superconducting thin film single crystals. Independent monitoring of individual pixel outputs allows real-time inspection of interference of substrates which has long been a major source of systematic error. By optimizing grazing-incidence angle and azimuthal orientation, smooth extended x-ray absorption fine structure (EXAFS) oscillations were obtained, demonstrating that strain effects can be studied using high-quality data for thin film single crystals grown by molecular beam epitaxy (MBE). The results of (La,Sr)2CuO4 thin film single crystals under strain are related to the strain dependence of the critical temperature of superconductivity.

Single crystals of the 96 K superconductor (Hg,Cu)Ba2CuO4+δ: Growth, structure and magnetism

NASA Astrophysics Data System (ADS)

Pelloquin, D.; Hardy, V.; Maignan, A.; Raveau, B.

1997-02-01

Single crystals of the 1201 (n = 1) (Hg,Cu)Ba2CuO4+δ mercury based cuprate have been grown by using a simple process without dry box. The as-synthesized crystals exhibit constant Tc(onset) of 96 K with sharp superconducting transitions. The electron microscopy coupled with EDX analyses evidence a ``1201''-type structure while a mercury deficiency is observed balanced by an excess of copper. The structural refinements based on single-crystal X-ray diffraction data confirm the electron deficiency on the Hg site (0,0,0) and show a splitting of the latter along the c axis correlated to the partial substitution of Cu for Hg. This structural study leads to the following formula Hg0.84Cu0.16Ba2CuO4.19. The magnetic study of a large crystal (1.1 × 0.38 × 0.065 mm3) shows that the (Hg,Cu)-1201 crystals exhibit an irreversibility line higher than that of the 1201 Hg0.8Bi0.2Ba2CuO4+δ crystal (Tc = 75 K). From the reversible magnetization, a λab(0) = 2470 Å value can be extrapolated. Using a 3D-2D decoupling formula, we obtain γ = 29 for the electronic anisotropy of this phase.

New structure type in the mixed-valent compound YbCu4Ga8.

PubMed

Subbarao, Udumula; Gutmann, Matthias J; Peter, Sebastian C

2013-02-18

The new compound YbCu(4)Ga(8) was obtained as large single crystals in high yield from reactions run in liquid gallium. Preliminary investigations suggest that YbCu(4)Ga(8) crystallizes in the CeMn(4)Al(8) structure type, tetragonal space group I4/mmm, and lattice constants are a = b = 8.6529(4) Å and c = 5.3976(11) Å. However, a detailed single-crystal XRD revealed a tripling of the c axis and crystallizing in a new structure type with lattice constants of a = b = 8.6529(4) Å and c = 15.465(1) Å. The structural model was further confirmed by neutron diffraction measurements on high-quality single crystal. The crystal structure of YbCu(4)Ga(8) is composed of pseudo-Frank-Kasper cages occupying one ytterbium atom in each ring which are shared through the corner along the ab plane, resulting in a three-dimensional network. The magnetic susceptibility of YbCu(4)Ga(8) investigated in the temperature range 2-300 K showed Curie-Weiss law behavior above 100 K, and the experimentally measured magnetic moment indicates mixed-valent ytterbium. Electrical resistivity measurements show the metallic nature of the compound. At low temperatures, variation of ρ as a function of T indicates a possible Fermi-liquid state at low temperatures.

Fractional conductivity in 2D and 3D crystals

NASA Astrophysics Data System (ADS)

Sidharth, B. G.; Das, Abhishek; Valluri, S. R.

2018-04-01

In this work, we show that the phenomenon of fractional quantum Hall effect can be obtained for 2D and 3D crystal structures, using the noncommutative nature of spacetime and the Lambert W function. This fractional conductivity has been shown to be a consequence of the noncommutative geometry underlying the structure of graphene. Also, it has been shown, for graphene, that in the 3D case the conductivity is extremely small and depends on the self-energy that arises due to random fluctuations or zitterbewegung.

Microgravity

NASA Image and Video Library

1992-06-01

Malic Enzyme is a target protein for drug design because it is a key protein in the life cycle of intestinal parasites. After 2 years of effort on Earth, investigators were unable to produce any crystals that were of high enough quality and for this reason the structure of this important protein could not be determined. Crystals obtained from one STS-50 were of superior quality allowing the structure to be determined. This is just one example why access to space is so vital for these studies. Principal Investigator is Larry DeLucas.

Novel Crystal Structure C60 Nanowire

NASA Astrophysics Data System (ADS)

Mickelson, William; Aloni, Shaul; Han, Weiqiang; Cumings, John; Zettl, Alex

2003-03-01

We have created insulated C60 nanowire by packing C60 molecules into the interior of insulating boron nitride (BN) nanotubes. For small-diameter BN tubes, the wire consists of a linear chain of C60's. With increasing BN tube inner diameter, novel C60 stacking configurations are obtained (including helical, hollow core, and incommensurate) which are unknown for bulk or thin film forms of C60. C60 in BN nanotubes presents a model system for studying the properties of new dimensionally-constrained "silo" crystal structures.

Salt-induced aggregation of lysozyme: Implications for crystal growth

NASA Technical Reports Server (NTRS)

Wilson, Lori J.

1994-01-01

Crystallization of proteins is a prerequisite for structural analysis by x-ray crystallography. While improvements in protein crystals have been obtained in microgravity onboard the U.S. Space Shuttle, attempts to improve the crystal growth process both on the ground and in space have been limited by our lack of understanding of the mechanisms involved. Almost all proteins are crystallized with the aid of a precipitating agent. Many of the common precipitating agents are inorganic salts. An understanding of the role of salts on the aggregation of protein monomers is the key to the elucidation of the mechanisms involved in protein crystallization. In order for crystallization to occur individual molecules must self-associate into aggregates. Detection and characterization of aggregates in supersaturated protein solutions is the first step in understanding salt-induced crystallization.

An automated parallel crystallisation search for predicted crystal structures and packing motifs of carbamazepine.

PubMed

Florence, Alastair J; Johnston, Andrea; Price, Sarah L; Nowell, Harriott; Kennedy, Alan R; Shankland, Norman

2006-09-01

An automated parallel crystallisation search for physical forms of carbamazepine, covering 66 solvents and five crystallisation protocols, identified three anhydrous polymorphs (forms I-III), one hydrate and eight organic solvates, including the single-crystal structures of three previously unreported solvates (N,N-dimethylformamide (1:1); hemi-furfural; hemi-1,4-dioxane). Correlation of physical form outcome with the crystallisation conditions demonstrated that the solvent adopts a relatively nonspecific role in determining which polymorph is obtained, and that the previously reported effect of a polymer template facilitating the formation of form IV could not be reproduced by solvent crystallisation alone. In the accompanying computational search, approximately half of the energetically feasible predicted crystal structures exhibit the C=O...H--N R2(2)(8)dimer motif that is observed in the known polymorphs, with the most stable correctly corresponding to form III. Most of the other energetically feasible structures, including the global minimum, have a C=O...H--N C(4) chain hydrogen bond motif. No such chain structures were observed in this or any other previously published work, suggesting that kinetic, rather than thermodynamic, factors determine which of the energetically feasible crystal structures are observed experimentally, with the kinetics apparently favouring nucleation of crystal structures based on the CBZ-CBZ R2(2)(8) motif. (c) 2006 Wiley-Liss, Inc. and the American Pharmacists Association.

Crystal growth of HVPE-GaN doped with germanium

NASA Astrophysics Data System (ADS)

Iwinska, M.; Takekawa, N.; Ivanov, V. Yu.; Amilusik, M.; Kruszewski, P.; Piotrzkowski, R.; Litwin-Staszewska, E.; Lucznik, B.; Fijalkowski, M.; Sochacki, T.; Teisseyre, H.; Murakami, H.; Bockowski, M.

2017-12-01

Crystallization by hydride vapor phase epitaxy method of gallium nitride single crystals doped with germanium and properties of the obtained material are described in this paper. Growth was performed in hydrogen and nitrogen carrier gas. The results were studied and compared. Influence of different flows of germanium tetrachloride, precursor of germanium, on the grown crystals was investigated. Ammonothermal GaN substrates were used as seeds for crystallization. Structural, electrical, and optical properties of HVPE-GaN doped with germanium are presented and discussed in detail. They were compared to properties of HVPE-GaN doped with silicon and also grown on native seeds of high quality.

The Crystal Structures of Potentially Tautomeric Compounds

NASA Astrophysics Data System (ADS)

Furmanova, Nina G.

1981-08-01

Data on the structures of potentially proto-, metallo-, and carbono-tropic compounds, obtained mainly by X-ray diffraction, are surveyed. The results of neutron and electron diffraction studies have also been partly used. It is shown that a characteristic feature of all the systems considered is the formation of hydrogen or secondary bonds ensuring the contribution of both possible tautomeric forms to the structure. Systematic consideration of the experimental data leads to the conclusion that there is a close relation between the crystal structure and the dynamic behaviour of the molecules in solution and that secondary and hydrogen bonds play a significant role in the tautomeric transition. The bibliography includes 152 references.

The transmission spectrum of sound through a phononic crystal subjected to liquid flow

NASA Astrophysics Data System (ADS)

Declercq, Nico F.; Chehami, Lynda; Moiseyenko, Rayisa P.

2018-01-01

The influence of liquid-flow up to 7 mm/s is examined on transmission spectra of phononic crystals, revealing a potential use for slow liquid-flow measurement techniques. It is known that transmission of ultrasound through a phononic crystal is determined by its periodicity and depends on the material characteristics of the crystal's constituents. Here, the crystal consists of metal rods with the space in between filled with water. Previous studies have assumed still water in the crystal, and here, we consider flowing liquid. First, the crystal bandgaps are investigated in still water, and the results of transmission experiments are compared with theoretical band structures obtained with the finite element method. Then, changes in transmission spectra are investigated for different speeds of liquid flow. Two situations are investigated: a crystal is placed with a principal symmetry axis in the flow direction ( ΓX) and then at an angle ( ΓM). The good stability of the bandgap structure of the transmission spectrum for both directions is observed, which may be of importance for the application of phononic crystals as acoustic filters in an environment of flowing liquid. Minor transmission amplitude changes on the other hand reveal a possibility for slow liquid flow measurements.

Fluorescent Approaches to High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Forsythe, Elizabeth

2005-01-01

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, 51%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear hits. Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Fluorescent Approaches to High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Minamitani, Elizabeth Forsythe; Pusey, Marc L.

2004-01-01

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically cannot reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of a macromolecules purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals will show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "bits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Fluorescent Approaches to High Throughput Crystallography

NASA Technical Reports Server (NTRS)

Pusey, Marc L.; Forsythe, Elizabeth

2004-01-01

X-ray crystallography remains the primary method for determining the structure of macromolecules. The first requirement is to have crystals, and obtaining them is often the rate-limiting step. The numbers of crystallization trials that are set up for any one protein for structural genomics, and the rate at which they are being set up, now overwhelm the ability for strictly human analysis of the results. Automated analysis methods are now being implemented with varying degrees of success, but these typically can not reliably extract intermediate results. By covalently modifying a subpopulation, less than or = 1%, of a macromolecule solution with a fluorescent probe, the labeled material will add to a growing crystal as a microheterogeneous growth unit. Labeling procedures can be readily incorporated into the final stages of purification. The covalently attached probe will concentrate in the crystal relative to the solution, and under fluorescent illumination the crystals show up as bright objects against a dark background. As crystalline packing is more dense than amorphous precipitate, the fluorescence intensity can be used as a guide in distinguishing different types of precipitated phases, even in the absence of obvious crystalline features, widening the available potential lead conditions in the absence of clear "hits." Non-protein structures, such as salt crystals, will not incorporate the probe and will not show up under fluorescent illumination. Also, brightly fluorescent crystals are readily found against less fluorescent precipitated phases, which under white light illumination may serve to obscure the crystals. Automated image analysis to find crystals should be greatly facilitated, without having to first define crystallization drop boundaries and by having the protein or protein structures all that show up. The trace fluorescently labeled crystals will also emit with sufficient intensity to aid in the automation of crystal alignment using relatively low cost optics, further increasing throughput at synchrotrons. This presentation will focus on the methodology for fluorescent labeling, the crystallization results, and the effects of the trace labeling on the crystal quality.

Alkylaminopyridine-Modified Aluminum Aminoterephthalate Metal-Organic Frameworks as Components of Reactive Self-Detoxifying Materials

DTIC Science & Technology

2012-08-07

was obtained from the Cambridge Structural Database (ref code OCUNAC). Chromium was substituted with aluminum in the reference crystal structure and the...structure when starting from similar synthesis compositions;30 as a result, the MIL-53 structure is encountered with a broader variety of trivalent metals

Crystal engineering: co-crystals of cinnamic acid derivatives with a pyridyl derivative co-crystallizer.

PubMed

Lorenzo, Daniel A; Forrest, Sebastian J K; Sparkes, Hazel A

2016-02-01

A number of hydrogen-bonded co-crystals, consisting of a cinnamic acid derivative and a pyridyl co-crystallizer, have been synthesized and their properties investigated by X-ray diffraction. Samples were prepared by recrystallization or solvent drop grinding of trans-cinnamic acid (1), 4-methylcinnamic acid (2), 4-methoxy cinnamic acid (3) or 3,4-methoxy cinnamic acid (4), with 4,4-dipyridyl (A), iso-nicotinamide (B) or nicotinamide (C). The X-ray single-crystal structures of seven novel co-crystals, obtained through recrystallization, are examined and the hydrogen-bonding interactions discussed. Consistent hydrogen-bonding motifs were observed for samples prepared when using 4,4-dipyridyl (A) or iso-nicotinamide (B) as the co-crystallizing agent. Powder X-ray diffraction analysis of the samples prepared by solvent drop grinding suggests the formation of ten co-crystals.

Controlling Chirality of Entropic Crystals.

PubMed

Damasceno, Pablo F; Karas, Andrew S; Schultz, Benjamin A; Engel, Michael; Glotzer, Sharon C

2015-10-09

Colloidal crystal structures with complexity and diversity rivaling atomic and molecular crystals have been predicted and obtained for hard particles by entropy maximization. However, thus far homochiral colloidal crystals, which are candidates for photonic metamaterials, are absent. Using Monte Carlo simulations we show that chiral polyhedra exhibiting weak directional entropic forces self-assemble either an achiral crystal or a chiral crystal with limited control over the crystal handedness. Building blocks with stronger faceting exhibit higher selectivity and assemble a chiral crystal with handedness uniquely determined by the particle chirality. Tuning the strength of directional entropic forces by means of particle rounding or the use of depletants allows for reconfiguration between achiral and homochiral crystals. We rationalize our findings by quantifying the chirality strength of each particle, both from particle geometry and potential of mean force and torque diagrams.

Thermo-Physical Properties of B2O3-Containing Mold Flux for High Carbon Steels in Thin Slab Continuous Casters: Structure, Viscosity, Crystallization, and Wettability

NASA Astrophysics Data System (ADS)

Park, Jun-Yong; Kim, Gi Hyun; Kim, Jong Bae; Park, Sewoong; Sohn, Il

2016-08-01

The effect of B2O3 on the thermo-physical properties of commercial mold fluxes, including the viscosity, crystallization behavior, and wettability, was investigated. Viscosity was measured using the rotating spindle method, and CCT (continuous cooling transformation) diagrams were obtained to investigate the crystallization behavior at various cooling rates using CLSM (confocal laser scanning microscope). The wettability of the fluxes was determined by measuring the contact angles at 1573 K (1300 °C) using the digital images generated by the sessile drop method and were used to calculate the surface tension, interfacial tension, and work of adhesion for Flux A (existing flux) and B (modified flux). These thermo-physical properties were correlated with the structural analysis obtained using FT-IR (Fourier transform-infrared), Raman and MAS-NMR (magic angle spin-nuclear magnetic resonance) spectroscopy. In addition, DTA (differential thermal analysis) was performed on the samples to measure the liquidus temperatures. Higher B2O3 concentrations resulted in lower liquidus temperatures, consequently decreasing the viscosity, the break temperature, and the crystallization temperature. However, B2O3 addition accelerated crystal growth owing to the higher diffusion kinetics of the cations, which also reduced the size of the liquid/solid co-existing region.

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.

Mechanochromic response of the barbules in peacock tail feather

NASA Astrophysics Data System (ADS)

Jiang, Yonggang; Wang, Rui; Feng, Lin; Zhang, Deyuan

2018-01-01

Peacock tail feathers exhibit diverse striking brilliancy, as the cortex in different colored barbules of the feathers contains a 2-D photonic-crystal structure. The mechanochromic response of the 2-D photonic structure in peacock feather barbules is measured for the first time, by combining an in-situ stretching device and a reflectivity measurement system. The reflectance spectra of the barbule specimen blueshifts own to stretching along its longitudinal direction. A high strain sensitivity of 5.3 nm/% is obtained for green barbules. It could be of great help in bionic design of strain sensors using 2D photonic crystal structures.

Extended-Range Ultrarefractive 1D Photonic Crystal Prisms

NASA Technical Reports Server (NTRS)

Ting, David Z.

2007-01-01

A proposal has been made to exploit the special wavelength-dispersive characteristics of devices of the type described in One-Dimensional Photonic Crystal Superprisms (NPO-30232) NASA Tech Briefs, Vol. 29, No. 4 (April 2005), page 10a. A photonic crystal is an optical component that has a periodic structure comprising two dielectric materials with high dielectric contrast (e.g., a semiconductor and air), with geometrical feature sizes comparable to or smaller than light wavelengths of interest. Experimental superprisms have been realized as photonic crystals having three-dimensional (3D) structures comprising regions of amorphous Si alternating with regions of SiO2, fabricated in a complex process that included sputtering. A photonic crystal of the type to be exploited according to the present proposal is said to be one-dimensional (1D) because its contrasting dielectric materials would be stacked in parallel planar layers; in other words, there would be spatial periodicity in one dimension only. The processes of designing and fabricating 1D photonic crystal superprisms would be simpler and, hence, would cost less than do those for 3D photonic crystal superprisms. As in 3D structures, 1D photonic crystals may be used in applications such as wavelength-division multiplexing. In the extended-range configuration, it is also suitable for spectrometry applications. As an engineered structure or artificially engineered material, a photonic crystal can exhibit optical properties not commonly found in natural substances. Prior research had revealed several classes of photonic crystal structures for which the propagation of electromagnetic radiation is forbidden in certain frequency ranges, denoted photonic bandgaps. It had also been found that in narrow frequency bands just outside the photonic bandgaps, the angular wavelength dispersion of electromagnetic waves propagating in photonic crystal superprisms is much stronger than is the angular wavelength dispersion obtained by use of conventional prisms and diffraction gratings and is highly nonlinear.

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

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

An intercalation-locked parallel-stranded DNA tetraplex

DOE PAGES

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

2015-01-27

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

Recombinant production, crystallization and X-ray crystallographic structure determination of the peptidyl-tRNA hydrolase of Pseudomonas aeruginosa

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

Hughes, Ronny C.; McFeeters, Hana; Coates, Leighton

The peptidyl-tRNA hydrolase enzyme from the pathogenic bacterium Pseudomonas aeruginosa (Pth; EC 3.1.1.29) has been cloned, expressed in Escherichia coli and crystallized for X-ray structural analysis. Suitable crystals were grown using the sitting-drop vapour-diffusion method after one week of incubation against a reservoir solution consisting of 20% polyethylene glycol 4000, 100 mM Tris pH 7.5, 10%(v/v) isopropyl alcohol. The crystals were used to obtain the three-dimensional structure of the native protein at 1.77 Å resolution. The structure was determined by molecular replacement of the crystallographic data processed in space group P6122 with unit-cell parameters a = b = 63.62,c =more » 155.20 Å, α = β = 90, γ = 120°. The asymmetric unit of the crystallographic lattice was composed of a single copy of the enzyme molecule with a 43% solvent fraction, corresponding to a Matthews coefficient of 2.43 Å3 Da-1. The crystallographic structure reported here will serve as the foundation for future structure-guided efforts towards the development of novel small-molecule inhibitors specific to bacterial Pths.« less

Crystallization mechanisms of acicular crystals

NASA Astrophysics Data System (ADS)

Puel, François; Verdurand, Elodie; Taulelle, Pascal; Bebon, Christine; Colson, Didier; Klein, Jean-Paul; Veesler, Stéphane

2008-01-01

In this contribution, we present an experimental investigation of the growth of four different organic molecules produced at industrial scale with a view to understand the crystallization mechanism of acicular or needle-like crystals. For all organic crystals studied in this article, layer-by-layer growth of the lateral faces is very slow and clear, as soon as the supersaturation is high enough, there is competition between growth and surface-activated secondary nucleation. This gives rise to pseudo-twinned crystals composed of several needle individuals aligned along a crystallographic axis; this is explained by regular over- and inter-growths as in the case of twinning. And when supersaturation is even higher, nucleation is fast and random. In an industrial continuous crystallization, the rapid growth of needle-like crystals is to be avoided as it leads to fragile crystals or needles, which can be partly broken or totally detached from the parent crystals especially along structural anisotropic axis corresponding to weaker chemical bonds, thus leading to slower growing faces. When an activated mechanism is involved such as a secondary surface nucleation, it is no longer possible to obtain a steady state. Therefore, the crystal number, size and habit vary significantly with time, leading to troubles in the downstream processing operations and to modifications of the final solid-specific properties. These results provide valuable information on the unique crystallization mechanisms of acicular crystals, and show that it is important to know these threshold and critical values when running a crystallizer in order to obtain easy-to-handle crystals.

Orthorhombic YBaCo{sub 4}O{sub 8.4} crystals as a result of saturation of hexagonal YBaCo{sub 4}O{sub 7} crystals with oxygen

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

Podberezskaya, N. V., E-mail: podberez@niic.nsc.ru; Bolotina, N. B., E-mail: nb-bolotina@mail.ru; Komarov, V. Yu., E-mail: komarov-v-y@niic.nsc.ru

Hexagonal YBaCo{sub 4}O{sub 7} crystals (sp. gr. P6{sub 3}mc, a{sub h} = 6.3058(4) Å, c{sub h} = 10.2442(7) Å, Z = 2) are saturated with oxygen to the YBaCo{sub 4}O{sub 8.4} composition and studied by X-ray diffraction (XRD) analysis. The saturation is completed by a structural first-order phase transition to orthorhombic crystals (sp. gr. Pbc2{sub 1}, a{sub o} = 31.8419(2) Å, b{sub o} = 10.9239(5) Å, c{sub o} = 10.0960(5) Å, Z = 20). The connection of two lattices is expressed in terms of the action of matrix (500/120/001) on the hexagonal basis. Five structural fragments of the same typemore » but with different degrees of order alternate along the long axis of the oxygen-saturated orthorhombic structure. The XRD data on single crystals differ from the results obtained by other researchers on ceramic samples; possible causes of these differences are discussed.« less

Structure and magnetic properties of flux grown single crystals of Co3-xFexSn2S2 shandites

NASA Astrophysics Data System (ADS)

Kassem, Mohamed A.; Tabata, Yoshikazu; Waki, Takeshi; Nakamura, Hiroyuki

2016-01-01

We report a successful single crystal growth of the shandite-type half-metallic ferromagnet Co3Sn2S2, and its Fe-substituted compounds, Co3-xFexSn2S2, by employing the flux method. Although Fe3Sn2S2 is unstable phase, we found that using the self Sn flux enables us to obtain single phase crystals up to x=0.53. The chemical composition of the grown plate-shaped single crystals was examined using wavelength-dispersive X-ray spectroscopy. The shandite structure with R 3 ̅m symmetry was confirmed by powder X-ray diffraction and the crystal structure parameters were refined using the Rietveld method. Magnetization measurements show suppression of the ferromagnetic order upon Fe-substitution , as well as in other substituted systems such as In- and Ni-substituted Co3Sn2S2. The almost identical magnetic phase diagrams of the Fe- and In-substituted compounds indicate that the electron number is dominantly significant to the magnetism in the Co-based shandite.

Determination of the Molecular Structures of Ferric Enterobactin and Ferric Enantioenterobactin Using Racemic Crystallography.

PubMed

Johnstone, Timothy C; Nolan, Elizabeth M

2017-10-25

Enterobactin is a secondary metabolite produced by Enterobacteriaceae for acquiring iron, an essential metal nutrient. The biosynthesis and utilization of enterobactin permits many Gram-negative bacteria to thrive in environments where low soluble iron concentrations would otherwise preclude survival. Despite extensive work carried out on this celebrated molecule since its discovery over 40 years ago, the ferric enterobactin complex has eluded crystallographic structural characterization. We report the successful growth of single crystals containing ferric enterobactin using racemic crystallization, a method that involves cocrystallization of a chiral molecule with its mirror image. The structures of ferric enterobactin and ferric enantioenterobactin obtained in this work provide a definitive assignment of the stereochemistry at the metal center and reveal secondary coordination sphere interactions. The structures were employed in computational investigations of the interactions of these complexes with two enterobactin-binding proteins, which illuminate the influence of metal-centered chirality on these interactions. This work highlights the utility of small-molecule racemic crystallography for obtaining elusive structures of coordination complexes.

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

DOE PAGES

Edlund, Petra; Takala, Heikki; Claesson, Elin; ...

2016-10-19

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

The room temperature crystal structure of a bacterial phytochrome determined by serial femtosecond crystallography

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

Edlund, Petra; Takala, Heikki; Claesson, Elin

Phytochromes are a family of photoreceptors that control light responses of plants, fungi and bacteria. A sequence of structural changes, which is not yet fully understood, leads to activation of an output domain. Time-resolved serial femtosecond crystallography (SFX) can potentially shine light on these conformational changes. Here we report the room temperature crystal structure of the chromophore-binding domains of the Deinococcus radiodurans phytochrome at 2.1 Å resolution. The structure was obtained by serial femtosecond X-ray crystallography from microcrystals at an X-ray free electron laser. We find overall good agreement compared to a crystal structure at 1.35 Å resolution derived frommore » conventional crystallography at cryogenic temperatures, which we also report here. The thioether linkage between chromophore and protein is subject to positional ambiguity at the synchrotron, but is fully resolved with SFX. As a result, the study paves the way for time-resolved structural investigations of the phytochrome photocycle with time-resolved SFX.« less

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.

Growth and characterization of pure and Ca2+ doped MnHg(SCN)4 single crystals

NASA Astrophysics Data System (ADS)

Latha, C.; Mahadevan, C. K.; Guo, Li; Liu, Jinghe

2018-05-01

Manganese-mercury thiocyanate, MnHg(SCN)4, crystal is considered to be an important organometallic nonlinear optical (NLO) material exhibiting higher thermal stability and second harmonic generation (SHG) efficiency. In order to understand the effect of Ca2+ as an impurity on the physicochemical properties, we have grown pure and Ca2+ doped (with a concentration of 1 mol%) MnHg(SCN)4 single crystals by the free evaporation of solvent method and characterized structurally, chemically, optically and electrically by adopting the available standard methods. Results obtained indicate that Ca2+ doping increases significantly the optical transmittance, SHG efficiency, and DC electrical conductivity and decreases the dielectric loss factor (improves the crystal quality), and AC electrical conductivity without distorting the crystal structure. Also, the low dielectric constant (εr) values observed for both the pure and doped crystals considered at near ambient temperatures indicate the possibility of using these crystals not only as potential NLO materials (useful in the photonics industry) but also as promising low εr value dielectric materials (useful in the microelectronics industry).

The development and application of new crystallization method for tobacco mosaic virus coat protein.

PubMed

Li, Xiangyang; Song, Baoan; Hu, Deyu; Wang, Zhenchao; Zeng, Mengjiao; Yu, Dandan; Chen, Zhuo; Jin, Linhong; Yang, Song

2012-11-21

Although tobacco mosaic virus (TMV) coat protein (CP) has been isolated from virus particles and its crystals have grown in ammonium sulfate buffers for many years, to date, no one has reported on the crystallization of recombinant TMV-CP connecting peptides expressed in E. coli. In the present papers genetically engineered TMV-CP was expressed, into which hexahistidine (His) tags or glutathione-S-transferase (GST) tags were incorporated. Considering that GST-tags are long peptides and His-tags are short peptides, an attempt was made to grow crystals of TMV-CP cleaved GST-tags (WT-TMV-CP32) and TMV-CP incorporated His-tags (WT-His-TMV-CP12) simultaneously in ammonium sulfate buffers and commercial crystallization reagents. It was found that the 20S disk form of WT-TMV-CP32 and WT-His-TMV-CP12 did not form high resolution crystals by using various crystallization buffers and commercial crystallization reagents. Subsequently, a new experimental method was adopted in which a range of truncated TMV-CP was constructed by removing several amino acids from the N- or the C-terminal, and high resolution crystals were grown in ammonium sulfate buffers and commercial crystallization reagents. The new crystallization method was developed and 3.0 Å resolution macromolecular crystal was thereby obtained by removing four amino acids at the C-terminal of His-TMV-CP and connecting six His-tags at the N-terminal of His-TMV-CP (TR-His-TMV-CP19). The Four-layer aggregate disk structure of TR-His-TMV-CP19 was solved. This phenomenon showed that peptides at the C-terminus hindered the growth of high resolution crystals and the peptides interactions at the N-terminus were attributed to the quality of TMV-CP crystals. A 3.0 Å resolution macromolecular crystal of TR-His-TMV-CP19 was obtained and the corresponding structure was solved by removing four amino acids at the C-terminus of TMV-CP and connecting His-tags at the N-terminus of TMV-CP. It indicated that short peptides influenced the resolution of TMV-CP crystals.

A facile approach towards synthesis, characterization, single crystal structure, and DFT study of 5-bromosalicylalcohol

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

Rastogi, Rupali, E-mail: rastogirupali@ymail.com; Tarannum, Nazia; Butcher, R. J.

2016-03-15

5-Bromosalicylalcohol was prepared by the interaction of NaBH{sub 4} and 5-bromosalicylaldehyde. The use of sodium borohydride makes the reaction easy, facile, economic and does not require any toxic catalyst. The compound is characterized by FTIR, {sup 1}H NMR, {sup 13}C NMR, TEM and ESI-mass spectra. Crystal structure is determined by single crystal X-ray analysis. Quantum mechanical calculations of geometries, energies and thermodynamic parameters are carried out using density functional theory (DFT/B3LYP) method with 6-311G(d,p) basis set. The optimized geometrical parameters obtained by B3LYP method show good agreement with experimental data.

Magnetic Control of Convection during Protein Crystallization

NASA Technical Reports Server (NTRS)

Ramachandran, N.; Leslie, F. W.

2004-01-01

An important component in biotechnology, particularly in the area of protein engineering and rational drug design is the knowledge of the precise three-dimensional molecular structure of proteins. The quality of structural information obtained from X-ray diffraction methods is directly dependent on the degree of perfection of the protein crystals. As a consequence, the growth of high quality macromolecular Crystals for diffraction analyses has been the central focus for bio-chemists, biologists, and bioengineers. Macromolecular crystals are obtained from solutions that contain the crystallizing species in equilibrium with higher aggregates, ions, precipitants, other possible phases of the protein, foreign particles, the walls of container, and a likely host of other impurities. By changing transport modes in general, i.e., reduction of convection and Sedimentation as is achieved in "microgravity", we have been able to dramatically affect the movement and distribution of macromolecules in the fluid, and thus their transport, f o d o n of crystal nuclei, and adsorption to the crystal surface. While a limited number of high quality crystals from space flights have been obtained, as the recent National Research Council (NRC) review of the NASA microgravity crystallization program pointed out, the scientific approach and research in crystallization of proteins has been mainly empirical yielding inconclusive results. We postulate that we can reduce convection in ground-based experiments and we can understand the different aspects of convection control through the use of strong magnetic fields and field gradients. We postulate that limited convection in a magnetic field will provide the environment for the growth of high quality crystals. The approach exploits the variation of fluid magnetic susceptibility with counteracts on for this purpose and the convective damping is realized by appropriately positioning the crystal growth cell so that the magnetic susceptibility force counteract terrestrial gravity. The genera1 objective is to test the hypothesis of convective control using a strong magnetic field and magnetic field gradient and to understand the nature of the various forces that come into play. Specifically we aim to delineate causative factors and to quantify them through experiments, analysis and numerical modeling. The paper will report on the experimental results using paramagentic salts and solutions in magnetic fields and compare them to analyticalprctions.

Human 3α-hydroxysteroid dehydrogenase type 3: structural clues of 5α-DHT reverse binding and enzyme down-regulation decreasing MCF7 cell growth.

PubMed

Zhang, Bo; Hu, Xiao-Jian; Wang, Xiao-Qiang; Thériault, Jean-François; Zhu, Dao-Wei; Shang, Peng; Labrie, Fernand; Lin, Sheng-Xiang

2016-04-15

Human 3α-HSD3 (3α-hydroxysteroid dehydrogenase type 3) plays an essential role in the inactivation of the most potent androgen 5α-DHT (5α-dihydrotestosterone). The present study attempts to obtain the important structure of 3α-HSD3 in complex with 5α-DHT and to investigate the role of 3α-HSD3 in breast cancer cells. We report the crystal structure of human 3α-HSD3·NADP(+)·A-dione (5α-androstane-3,17-dione)/epi-ADT (epiandrosterone) complex, which was obtained by co-crystallization with 5α-DHT in the presence of NADP(+) Although 5α-DHT was introduced during the crystallization, oxidoreduction of 5α-DHT occurred. The locations of A-dione and epi-ADT were identified in the steroid-binding sites of two 3α-HSD3 molecules per crystal asymmetric unit. An overlay showed that A-dione and epi-ADT were oriented upside-down and flipped relative to each other, providing structural clues for 5α-DHT reverse binding in the enzyme with the generation of different products. Moreover, we report the crystal structure of the 3α-HSD3·NADP(+)·4-dione (4-androstene-3,17-dione) complex. When a specific siRNA (100 nM) was used to suppress 3α-HSD3 expression without interfering with 3α-HSD4, which shares a highly homologous active site, the 5α-DHT concentration increased, whereas MCF7 cell growth was suppressed. The present study provides structural clues for 5α-DHT reverse binding within 3α-HSD3, and demonstrates for the first time that down-regulation of 3α-HSD3 decreases MCF7 breast cancer cell growth. © 2016 The Author(s). Published by Portland Press Limited on behalf of the Biochemical Society.

Crystal growth of carbonate apatite using a CaCO3 flux.

PubMed

Suetsugu, Y; Tanaka, J

1999-09-01

Single crystals of carbonate apatite were grown using a CaCO3 flux under an Ar gas pressure of 55 MPa. The crystals obtained were observed by scanning electron microscopy, optical microscopy and X-ray diffraction. Electron probe microanalyses and thermal analyses were performed. CO3 ions in planar triangle form replaced both OH sites and PO4 tetrahedral sites in the apatite structure: in particular, the OH sites were perfectly substituted by CO3 ions using this method.

Changes in the IR Spectra of Aqueous Solutions of Alkali Metal Chlorides during Crystallization

NASA Astrophysics Data System (ADS)

Koroleva, A. V.; Matveev, V. K.; Koroleva, L. A.; Pentin, Yu. A.

2018-02-01

The IR spectra of aqueous solutions of sodium chloride and rubidium chloride with the same concentration of 0.1 M upon freezing are studied in the middle IR region. The changes that occur in the absorption bands of the bending ν2, compound ν2 + νL, and stretching (ν1, 2ν2, and ν3) vibrations of water molecules with gradual crystallization of the solutions are studied. The obtained spectra of crystallized solutions are compared to the IR spectrum of ice Ih. Analysis allows conclusions about the structure of the investigated frozen crystallized solutions.

Monitoring structural transformations in crystals. 7. 1-Chloroanthracene and its photodimer.

PubMed

Turowska-Tyrk, Ilona; Grześniak, Karolina

2004-02-01

Crystals of the 1-chloroanthracene photodimer, viz. trans-bi(1-chloro-9,10-dihydro-9,10-anthracenediyl), C(28)H(18)Cl(2), were obtained from the solid-state [4+4]-photodimerization of the monomer, C(14)H(9)Cl, followed by recrystallization. The symmetry of the product molecules is defined by the orientation of the reactant molecules in the crystal. The mutual orientation parameters calculated for adjacent monomers explain the reactivity of the compound. The molecules in the crystal of the monomer and the recrystallized photodimer pack differently and the photodimer has crystallographically imposed inversion symmetry.

Investigation of the nanodomain structure formation by piezoelectric force microscopy and Raman confocal microscopy in LiNbO3 and LiTaO3 crystals

NASA Astrophysics Data System (ADS)

Shur, V. Ya.; Zelenovskiy, P. S.; Nebogatikov, M. S.; Alikin, D. O.; Sarmanova, M. F.; Ievlev, A. V.; Mingaliev, E. A.; Kuznetsov, D. K.

2011-09-01

Piezoelectric force microscopy (PFM) and Raman confocal microscopy have been used for studying the nanodomain structures in congruent LiNbO3 and LiTaO3 crystals. The high-resolution nanodomain images at the surface were observed via PFM. Raman confocal microscopy has been used for the visualization of the nanodomain structures in the bulk via layer-by-layer scanning at various depths. It has been shown experimentally that the nanodomain images obtained at different depths correspond to domain images at the polar surface obtained at different moments: the deeper the nanodomain, the earlier the moment. Such a correlation was applied for the reconstruction of the evolution of the domain structures with charged domain walls. The studied domain structures were obtained in highly non-equilibrium switching conditions realized in LiNbO3 and LiTaO3 via pulse laser irradiation and the electric field poling of LiNbO3, with the surface layer modified by ion implantation. The revealed main stages of the domain structure evolution allow the authors to demonstrate that all geometrically different nanodomain structures observed in LiNbO3 and LiTaO3 appeared as a result of discrete switching.

The 1.1 Å resolution structure of a periplasmic phosphate-binding protein from Stenotrophomonas maltophilia: a crystallization contaminant identified by molecular replacement using the entire Protein Data Bank.

PubMed

Keegan, Ronan; Waterman, David G; Hopper, David J; Coates, Leighton; Taylor, Graham; Guo, Jingxu; Coker, Alun R; Erskine, Peter T; Wood, Steve P; Cooper, Jonathan B

2016-08-01

During efforts to crystallize the enzyme 2,4-dihydroxyacetophenone dioxygenase (DAD) from Alcaligenes sp. 4HAP, a small number of strongly diffracting protein crystals were obtained after two years of crystal growth in one condition. The crystals diffracted synchrotron radiation to almost 1.0 Å resolution and were, until recently, assumed to be formed by the DAD protein. However, when another crystal form of this enzyme was eventually solved at lower resolution, molecular replacement using this new structure as the search model did not give a convincing solution with the original atomic resolution data set. Hence, it was considered that these crystals might have arisen from a protein impurity, although molecular replacement using the structures of common crystallization contaminants as search models again failed. A script to perform molecular replacement using MOLREP in which the first chain of every structure in the PDB was used as a search model was run on a multi-core cluster. This identified a number of prokaryotic phosphate-binding proteins as scoring highly in the MOLREP peak lists. Calculation of an electron-density map at 1.1 Å resolution based on the solution obtained with PDB entry 2q9t allowed most of the amino acids to be identified visually and built into the model. A BLAST search then indicated that the molecule was most probably a phosphate-binding protein from Stenotrophomonas maltophilia (UniProt ID B4SL31; gene ID Smal_2208), and fitting of the corresponding sequence to the atomic resolution map fully corroborated this. Proteins in this family have been linked to the virulence of antibiotic-resistant strains of pathogenic bacteria and with biofilm formation. The structure of the S. maltophilia protein has been refined to an R factor of 10.15% and an Rfree of 12.46% at 1.1 Å resolution. The molecule adopts the type II periplasmic binding protein (PBP) fold with a number of extensively elaborated loop regions. A fully dehydrated phosphate anion is bound tightly between the two domains of the protein and interacts with conserved residues and a number of helix dipoles.

Purification, crystallization and preliminary crystallographic analysis of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli.

PubMed

Seo, Kyung Hye; Supangat; Kim, Hye Lim; Park, Young Shik; Jeon, Che Ok; Lee, Kon Ho

2008-02-01

6-Pyruvoyltetrahydropterin synthase from E. coli (ePTPS) has been crystallized using the hanging-drop vapour-diffusion method. Hexagonal- and rectangular-shaped crystals were obtained. Diffraction data were collected from the hexagonal and rectangular crystals to 3.0 and 2.3 A resolution, respectively. The hexagonal plate-shaped crystals belonged to space group P321, with unit-cell parameters a = b = 112.59, c = 68.82 A , and contained two molecules in the asymmetric unit. The rectangular crystals belonged to space group I222, with unit-cell parameters a = 112.76, b = 117.66, c = 153.57 A , and contained six molecules in the asymmetric unit. The structure of ePTPS in both crystal forms has been determined by molecular replacement.

Purification, crystallization and preliminary crystallographic analysis of a 6-pyruvoyltetrahydropterin synthase homologue from Esherichia coli

PubMed Central

Seo, Kyung Hye; Supangat; Kim, Hye Lim; Park, Young Shik; Jeon, Che Ok; Lee, Kon Ho

2008-01-01

6-Pyruvoyltetrahydropterin synthase from E. coli (ePTPS) has been crystallized using the hanging-drop vapour-diffusion method. Hexagonal- and rectangular-shaped crystals were obtained. Diffraction data were collected from the hexagonal and rectangular crystals to 3.0 and 2.3 Å resolution, respectively. The hexagonal plate-shaped crystals belonged to space group P321, with unit-cell parameters a = b = 112.59, c = 68.82 Å, and contained two molecules in the asymmetric unit. The rectangular crystals belonged to space group I222, with unit-cell parameters a = 112.76, b = 117.66, c = 153.57 Å, and contained six molecules in the asymmetric unit. The structure of ePTPS in both crystal forms has been determined by molecular replacement. PMID:18271114

Studying the properties of a predicted tetragonal silicon by first principles

NASA Astrophysics Data System (ADS)

Xue, Han-Yu; Zhang, Can; Pang, Dong-Dong; Huang, Xue-Qian; Lv, Zhen-Long; Duan, Man-Yi

2018-03-01

Silicon is a very important material in many technological fields. It also has a complicated phase diagram of scientific interest. Here we reported a new allotrope of silicon obtained from crystal structure prediction. We studied its electronic, vibrational, dielectric, elastic and hardness properties by first-principles calculations. The results indicate that it is an indirect narrow-band-gap semiconductor. It is dynamically stable with a doubly degenerate infrared-active mode at its Brillouin zone center. Born effective charges of the constituent element are very small, resulting in a negligible ionic dielectric contribution. Calculated elasticity-related quantities imply that it is mechanically stable but anisotropic. There exist slowly increasing stages in the stress-strain curves of this crystal, which make it difficult to estimate the hardness of the crystal by calculating its ideal strengths. Taking advantage of the hardness model proposed by Šimůnek, we obtained a value of 12.0 GPa as its hardness. This value is lower than that of the cubic diamond-structural Si by about 5.5%.

Ellipsometry study of optical parameters of AgIn5S8 crystals

NASA Astrophysics Data System (ADS)

Isik, Mehmet; Gasanly, Nizami

2015-12-01

AgIn5S8 crystals grown by Bridgman method were characterized for optical properties by ellipsometry measurements. Spectral dependence of optical parameters; real and imaginary parts of the pseudodielectric function, pseudorefractive index, pseudoextinction coefficient, reflectivity and absorption coefficient were obtained from ellipsometry experiments carried out in the 1.2-6.2 eV range. Direct band gap energy of 1.84 eV was found from the analysis of absorption coefficient vs. photon energy. The oscillator energy, dispersion energy and zero-frequency refractive index, high-frequency dielectric constant values were found from the analysis of the experimental data using Wemple-DiDomenico and Spitzer-Fan models. Crystal structure and atomic composition ratio of the constituent elements in the AgIn5S8 crystal were revealed from structural characterization techniques of X-ray diffraction and energy dispersive spectroscopy.

Gaia: automated quality assessment of protein structure models.

PubMed

Kota, Pradeep; Ding, Feng; Ramachandran, Srinivas; Dokholyan, Nikolay V

2011-08-15

Increasing use of structural modeling for understanding structure-function relationships in proteins has led to the need to ensure that the protein models being used are of acceptable quality. Quality of a given protein structure can be assessed by comparing various intrinsic structural properties of the protein to those observed in high-resolution protein structures. In this study, we present tools to compare a given structure to high-resolution crystal structures. We assess packing by calculating the total void volume, the percentage of unsatisfied hydrogen bonds, the number of steric clashes and the scaling of the accessible surface area. We assess covalent geometry by determining bond lengths, angles, dihedrals and rotamers. The statistical parameters for the above measures, obtained from high-resolution crystal structures enable us to provide a quality-score that points to specific areas where a given protein structural model needs improvement. We provide these tools that appraise protein structures in the form of a web server Gaia (http://chiron.dokhlab.org). Gaia evaluates the packing and covalent geometry of a given protein structure and provides quantitative comparison of the given structure to high-resolution crystal structures. dokh@unc.edu Supplementary data are available at Bioinformatics online.

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.

Fluorescence X-ray absorption spectroscopy using a Ge pixel array detector: application to high-temperature superconducting thin-film single crystals.

PubMed

Oyanagi, H; Tsukada, A; Naito, M; Saini, N L; Lampert, M O; Gutknecht, D; Dressler, P; Ogawa, S; Kasai, K; Mohamed, S; Fukano, A

2006-07-01

A Ge pixel array detector with 100 segments was applied to fluorescence X-ray absorption spectroscopy, probing the local structure of high-temperature superconducting thin-film single crystals (100 nm in thickness). Independent monitoring of pixel signals allows real-time inspection of artifacts owing to substrate diffractions. By optimizing the grazing-incidence angle theta and adjusting the azimuthal angle phi, smooth extended X-ray absorption fine structure (EXAFS) oscillations were obtained for strained (La,Sr)2CuO4 thin-film single crystals grown by molecular beam epitaxy. The results of EXAFS data analysis show that the local structure (CuO6 octahedron) in (La,Sr)2CuO4 thin films grown on LaSrAlO4 and SrTiO3 substrates is uniaxially distorted changing the tetragonality by approximately 5 x 10(-3) in accordance with the crystallographic lattice mismatch. It is demonstrated that the local structure of thin-film single crystals can be probed with high accuracy at low temperature without interference from substrates.

Crystal growth, electronic structure and optical properties of Sr2Mg(BO3)2

NASA Astrophysics Data System (ADS)

Lv, Xianshun; Wei, Lei; Wang, Xuping; Xu, Jianhua; Yu, Huajian; Hu, Yanyan; Zhang, Huadi; Zhang, Cong; Wang, Jiyang; Li, Qinggang

2018-02-01

Single crystals of Sr2Mg(BO3)2 (SMBO) were grown by Kyropoulos method. X-ray powder diffraction (XRD) analysis, transmission spectrum, thermal properties, band structure, density of states and charge distribution as well as Raman spectra of SMBO were described. The as-grown SMBO crystals show wide transparency range with UV cut-off below 180 nm. A direct band gap of 4.66 eV was obtained from the calculated electronic structure results. The calculated band structure and density of states results indicated the top valence band is determined by O 2p states whereas the low conduction band mainly consists of Sr 5s states. Twelve Raman peaks were observed in the experimental spectrum, fewer than the number predicted by the site group analysis. Raman peaks of SMBO were assigned combining first-principle calculation and site group analysis results. The strongest peak at 917 cm-1 in the experimental spectrum is assigned to symmetric stretching mode A1‧(ν1) of free BO3 units. SMBO is a potential Raman crystal which can be used in deep UV laser frequency conversion.

Effect of cationic substitution on the double-well hydrogen-bond potential in [K1-x(NH4)x]3H(SO4)2 proton conductors: a single-crystal neutron diffraction study.

PubMed

Choudhury, R R; Chitra, R; Selezneva, E V; Makarova, I P

2017-10-01

The structure of the mixed crystal [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 as obtained from single-crystal neutron diffraction is compared with the previously reported room-temperature neutron structure of crystalline K 3 H(SO 4 ) 2 . The two structures are very similar, as indicated by the high value of their isostructurality index (94.8%). It was found that the replacement of even a small amount (3%) of K + with NH 4 + has a significant influence on the short strong hydrogen bond connecting the two SO 4 2- ions. Earlier optical measurements had revealed that the kinetics of the superionic transition in the solid solution [K 1-x (NH 4 ) x ] 3 H(SO 4 ) 2 are much faster than in K 3 H(SO 4 ) 2 ; this reported difference in the kinetics of the superionic phase transition in this class of crystal is explained on the basis of the difference in strength of the hydrogen-bond interactions in the two structures.

Poly(acrylic acid) to induce competitive crystallization of a theophylline/oxalic acid cocrystal and a theophylline polymorph

NASA Astrophysics Data System (ADS)

Jang, Jisun; Kim, Il Won

2016-01-01

Polymeric additives to induce competitive crystallization of pharmaceutical compounds were explored. A cocrystal of theophylline and oxalic acid was used as a model system, and poly(acrylic acid), poly(caprolactone), and poly(ethylene glycol) were the additives. The cocrystal formation was selectively hindered with addition of poly(acrylic acid). First the size of the cocrystals were reduced, and eventually the cocrystallization was inhibited to generate neat theophylline crystals. The theophylline crystals were of a distinctively different crystal structure from known polymorphs, based on powder X-ray diffraction. They were also obtained in nanoscale size, when millimeter-scale crystals formed without poly(acrylic acid). Polymeric additives that could form specific interactions with crystallizing compounds seem to be useful tools for the phase and size control of pharmaceutical crystals.

Crystallization of human nicotinamide phosphoribosyltransferase

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

Takahashi, Ryo; Nakamura, Shota; Yoshida, Takuya

2007-05-01

Human nicotinamide phosphoribosyltransferase has been crystallized using microseeding methods and X-ray diffraction data have been collected at 2.0 Å resolution. In the NAD biosynthetic pathway, nicotinamide phosphoribosyltransferase (NMPRTase; EC 2.4.2.12) plays an important role in catalyzing the synthesis of nicotinamide mononucleotide from nicotinamide and 5′-phosphoribosyl-1′-pyrophosphate. Because the diffraction pattern of the initally obtained crystals was not suitable for structure analysis, the crystal quality was improved by successive use of the microseeding technique. The resultant crystals diffracted to 2.0 Å resolution. These crystals belonged to space group P21, with unit-cell parameters a = 60.56, b = 106.40, c = 82.78 Å.more » Here, the crystallization of human NMPRTase is reported in the free form; the crystals should be useful for inhibitor-soaking experiments on the enzyme.« less

Distribution function of random strains in an elastically anisotropic continuum and defect strengths of T m3 + impurity ions in crystals with zircon structure

NASA Astrophysics Data System (ADS)

Malkin, B. Z.; Abishev, N. M.; Baibekov, E. I.; Pytalev, D. S.; Boldyrev, K. N.; Popova, M. N.; Bettinelli, M.

2017-07-01

We construct a distribution function of the strain-tensor components induced by point defects in an elastically anisotropic continuum, which can be used to account quantitatively for many effects observed in different branches of condensed matter physics. Parameters of the derived six-dimensional generalized Lorentz distribution are expressed through the integrals computed over the array of strains. The distribution functions for the cubic diamond and elpasolite crystals and tetragonal crystals with the zircon and scheelite structures are presented. Our theoretical approach is supported by a successful modeling of specific line shapes of singlet-doublet transitions of the T m3 + ions doped into AB O4 (A =Y , Lu; B =P , V) crystals with zircon structure, observed in high-resolution optical spectra. The values of the defect strengths of impurity T m3 + ions in the oxygen surroundings, obtained as a result of this modeling, can be used in future studies of random strains in different rare-earth oxides.

Effect of severe plastic deformation on the structure and crystal-lattice distortions in the Ni3(Al, X) ( X = Ti, Nb) intermetallic compound

NASA Astrophysics Data System (ADS)

Kazantseva, N. V.; Pilyugin, V. P.; Danilov, S. E.; Kolosov, V. Yu.

2015-05-01

A systematic combined study of crystal lattice distortions caused by doping and by severe plastic deformation (SPD) of Ti- and Nb-doped Ni3Al intermetallic compound has been carried out using methods of X-ray diffraction, electron microscopy, and electrical-resistance measurements. The degree of imperfection of the alloys has been estimated based on the results obtained by all three methods. The degree of structural perfection of niobium-doped crystals was found to be higher than in the case of Ti doping. The character of stresses (tensile stresses after doping; and compressive stresses after SPD) in the crystal lattice has been established and their values have been calculated. A significant increase in the density of dislocations, point defects, and lattice curvature has been found after SPD. A nanocrystalline structure is formed in these alloys, but no complete disordering of the intermetallic phase is observed.

Synthesis, crystal structure and electrical properties of N,N-dimethylanilinium trichloridostannate (II): (C8H12N)SnCl3

NASA Astrophysics Data System (ADS)

Chouaib, H.; Kamoun, S.; Costa, L. C.; Graça, M. P. F.

2015-12-01

A new (C8H12N)SnCl3 crystal of the general formula AMX3 was grown by soft chemistry method. X-ray study shows that the crystal crystallized in a monoclinic system with the space group P21/a. The structure was solved by Patterson method and refined to a final value of R = 0.0304 for 1157 independent observed reflections. The cohesion and the stability of the atomic arrangement result from the N-H … Cl hydrogen bonds between (C8H12N)+ cations and isolated (SnCl3)- anions. At high temperature this compound exhibits a structural phase transition at 340 K. This transition has been characterized by differential scanning calorimetric and impedance spectroscopy. The impedance data were well fitted to an Rp//CPE equivalent electrical circuit model. The close values of activation energies, obtained from the thermal behavior of the conductivity and the relaxation time confirm the presence of a hopping transport mechanism.

Synthesis, crystal structure and magnetic properties of superconducting single crystals of HgBa2CuO4+δ

NASA Astrophysics Data System (ADS)

Bertinotti, A.; Viallet, V.; Colson, D.; Marucco, J.-F.; Hammann, J.; Forget, A.; Le Bras, G.

1996-02-01

Single crystals of HgBa2CuO4+δ of submillimetric sizes were grown with the same one step, low pressure, gold amalgamation technique used to obtain single crystals of HgBa2Ca2Cu3O8+δ. Remarkable superconducting properties are displayed by the samples which are optimally doped as grown. The sharpness of the transition profiles of the magnetic susceptibility, its anisotropy dependence and the volume fraction exhibiting the Meissner effect exceed the values obtained with the best crystal samples of Hg-1223. X-rays show that no substitutional defects have been found in the mercury plane, in particular no mixed occupancy of copper at the mercury site. The interstitial oxygen content at (1/2, 1/2, 0) δ = 0.066+/-0.008 is about one third that observed in optimally doped Hg-1223, resulting in an identical doping level per CuO2 plane in both compounds.

The role of disclinations on the organization and conductivity in liquid crystal nanocomposites

NASA Astrophysics Data System (ADS)

Martinez-Miranda, Luz J.; Romero-Hasler, P.; Meneses-Franco, A.; Soto-Bustamante, E. A.

The structure of TiO2 nanoparticles in a liquid crystal nanocomposite was found to be an oblique structure due to the alignment of the TiO2 with respect to the liquid crystals. This order is anisotropic due to the ordering of the liquid crystals. The particles are highly localized in the nanocomposite, which has consequences in the electrical percolation. We want to obtain an understanding of how the nanoparticles organize in this highly localized fashion. The nanoparticles and the liquid crystals phase separate, with the nanoparticles accumulating in the defects exhibited by the liquid crystal even after being sonicated initially. The liquid crystal is polymerized by the process of electropolymerization that takes place in the isotropic phase of the monomers. The nanoparticles are free to move away from the defects where they phase separate since the defects disappear in the isotropic. We believe the polymerization imposes a limitation in the movement of the nanoparticles. The combination of the accumulation in the disclinations, the polymerization in the isotropic and the formation of the liquid crystal unit side chains can affect the conductivity of the nanocomposite. NSF-OISE-1157589; Fondecyt Project 1130187; CONICYT scholarships 21130413 and 21090713.

Serial crystallography captures enzyme catalysis in copper nitrite reductase at atomic resolution from one crystal.

PubMed

Horrell, Sam; Antonyuk, Svetlana V; Eady, Robert R; Hasnain, S Samar; Hough, Michael A; Strange, Richard W

2016-07-01

Relating individual protein crystal structures to an enzyme mechanism remains a major and challenging goal for structural biology. Serial crystallography using multiple crystals has recently been reported in both synchrotron-radiation and X-ray free-electron laser experiments. In this work, serial crystallography was used to obtain multiple structures serially from one crystal (MSOX) to study in crystallo enzyme catalysis. Rapid, shutterless X-ray detector technology on a synchrotron MX beamline was exploited to perform low-dose serial crystallography on a single copper nitrite reductase crystal, which survived long enough for 45 consecutive 100 K X-ray structures to be collected at 1.07-1.62 Å resolution, all sampled from the same crystal volume. This serial crystallography approach revealed the gradual conversion of the substrate bound at the catalytic type 2 Cu centre from nitrite to nitric oxide, following reduction of the type 1 Cu electron-transfer centre by X-ray-generated solvated electrons. Significant, well defined structural rearrangements in the active site are evident in the series as the enzyme moves through its catalytic cycle, namely nitrite reduction, which is a vital step in the global denitrification process. It is proposed that such a serial crystallography approach is widely applicable for studying any redox or electron-driven enzyme reactions from a single protein crystal. It can provide a 'catalytic reaction movie' highlighting the structural changes that occur during enzyme catalysis. The anticipated developments in the automation of data analysis and modelling are likely to allow seamless and near-real-time analysis of such data on-site at some of the powerful synchrotron crystallographic beamlines.

Cloning, expression, purification and preliminary crystallographic analysis of the short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica

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

Harmer, Nicholas J., E-mail: nic@cryst.bioc.cam.ac.uk; King, Jerry D.; Department of Veterinary Medicine, Cambridge CB3 0ES

2007-08-01

The expression, purification, and crystallisation of the short-chain dehydrogenases WbmF, WbmG and WbmH from B. bronchiseptica are described. Native diffraction data to 1.5, 2.0, and 2.2 Å were obtained for the three proteins, together with complexes with nucleotides. The short-chain dehydrogenase enzymes WbmF, WbmG and WbmH from Bordetella bronchiseptica were cloned into Escherichia coli expression vectors, overexpressed and purified to homogeneity. Crystals of all three wild-type enzymes were obtained using vapour-diffusion crystallization with high-molecular-weight PEGs as a primary precipitant at alkaline pH. Some of the crystallization conditions permitted the soaking of crystals with cofactors and nucleotides or nucleotide sugars, whichmore » are possible substrate compounds, and further conditions provided co-complexes of two of the proteins with these compounds. The crystals diffracted to resolutions of between 1.50 and 2.40 Å at synchrotron X-ray sources. The synchrotron data obtained were sufficient to determine eight structures of the three enzymes in complex with a variety of cofactors and substrate molecules.« less

On the Relationship of the Fractal Dimension of Structure with the State of Drying Drops of Crystallizing Solutions (Thermodynamic and Experimental Modeling)

NASA Astrophysics Data System (ADS)

Golovanova, O. A.; Chikanova, E. S.; Fedoseev, V. B.

2018-05-01

The processes occurring in aqueous salt solutions have been investigated based on thermodynamic and experimental modeling. The self-organization in a drying drop of dehydrated liquids is analyzed using the fractal theory, due to which the quantitative characteristics of the crystallization processes in a small volume are obtained.

Synthesis, high-resolution NMR spectroscopic analysis, and single-crystal X-ray diffraction of isoxazoline tetracycles.

PubMed

Fascio, Mirta L; Alvarez-Larena, Angel; D'Accorso, Norma B

2002-11-29

Three isoxazoline tetracycles were obtained enantiomerically pure by intramolecular 1,3-dipolar cycloaddition. The characterization of the new compounds was performed by high-resolution 1H and 13C NMR spectroscopy. The relative configuration of the new chiral centers was determined by NOESY experiments and confirmed by single-crystal X-ray structural analysis.

Inorganic pyrophosphatase crystals from Thermococcus thioreducens for X-ray and neutron diffraction.

PubMed

Hughes, Ronny C; Coates, Leighton; Blakeley, Matthew P; Tomanicek, Steve J; Langan, Paul; Kovalevsky, Andrey Y; García-Ruiz, Juan M; Ng, Joseph D

2012-12-01

Inorganic pyrophosphatase (IPPase) from the archaeon Thermococcus thioreducens was cloned, overexpressed in Escherichia coli, purified and crystallized in restricted geometry, resulting in large crystal volumes exceeding 5 mm3. IPPase is thermally stable and is able to resist denaturation at temperatures above 348 K. Owing to the high temperature tolerance of the enzyme, the protein was amenable to room-temperature manipulation at the level of protein preparation, crystallization and X-ray and neutron diffraction analyses. A complete synchrotron X-ray diffraction data set to 1.85 Å resolution was collected at room temperature from a single crystal of IPPase (monoclinic space group C2, unit-cell parameters a=106.11, b=95.46, c=113.68 Å, α=γ=90.0, β=98.12°). As large-volume crystals of IPPase can be obtained, preliminary neutron diffraction tests were undertaken. Consequently, Laue diffraction images were obtained, with reflections observed to 2.1 Å resolution with I/σ(I) greater than 2.5. The preliminary crystallographic results reported here set in place future structure-function and mechanism studies of IPPase.

Antiferromagnetic Kondo lattice in the layered compound CePd 1 - x Bi 2 and comparison to the superconductor LaPd 1 - x Bi 2

DOE PAGES

Han, Fei; Wan, Xiangang; Phelan, Daniel; ...

2015-07-13

ZrCuSi 2-type CePd 1-xBi 2 crystals were obtained from excess Bi flux. Magnetic susceptibility measurements reveal that CePd 1-xBi 2 is a highly anisotropic antiferromagnet with transition temperature at 6 K, and a magnetic-field-induced metamagnetic transition at 5 T. An enhanced Sommerfeld coefficient of γ of 0.199 J-mol-Ce -1K -2 obtained from specific heat measurements suggests a moderate Kondo effect in CePd 1-xBi 2. In addition to the antiferromagnetic peak the resistivity curve shows a shoulder-like behavior which could be attributed to the presence of Kondo effect and crystal-electric-field effects in this compound. Magnetoresistance and Hall effect measurements suggest anmore » interplay between Kondo and crystal-electric-field effects which reconstructs the Fermi surface topology of CePd 1-xBi 2 around 75 K. Electronic structure calculations reveal the Pd vacancies are important to the magnetic structure and enhance the crystal-electric-field effects which quench the orbital moment of Ce at low temperatures.« less

Photonic guiding structures in lithium niobate crystals produced by energetic ion beams

NASA Astrophysics Data System (ADS)

Chen, Feng

2009-10-01

A range of ion beam techniques have been used to fabricate a variety of photonic guiding structures in the well-known lithium niobate (LiNbO3 or LN) crystals that are of great importance in integrated photonics/optics. This paper reviews the up-to-date research progress of ion-beam-processed LiNbO3 photonic structures and reports on their fabrication, characterization, and applications. Ion beams are being used with this material in a wide range of techniques, as exemplified by the following examples. Ion beam milling/etching can remove the selected surface regions of LiNbO3 crystals via the sputtering effects. Ion implantation and swift ion irradiation can form optical waveguide structures by modifying the surface refractive indices of the LiNbO3 wafers. Crystal ion slicing has been used to obtain bulk-quality LiNbO3 single-crystalline thin films or membranes by exfoliating the implanted layer from the original substrate. Focused ion beams can either generate small structures of micron or submicron dimensions, to realize photonic bandgap crystals in LiNbO3, or directly write surface waveguides or other guiding devices in the crystal. Ion beam-enhanced etching has been extensively applied for micro- or nanostructuring of LiNbO3 surfaces. Methods developed to fabricate a range of photonic guiding structures in LiNbO3 are introduced. Modifications of LiNbO3 through the use of various energetic ion beams, including changes in refractive index and properties related to the photonic guiding structures as well as to the materials (i.e., electro-optic, nonlinear optic, luminescent, and photorefractive features), are overviewed in detail. The application of these LiNbO3 photonic guiding structures in both micro- and nanophotonics are briefly summarized.

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

Structure of fructose bisphosphate aldolase from Bartonella henselae bound to fructose 1,6-bisphosphate

PubMed Central

Gardberg, Anna; Abendroth, Jan; Bhandari, Janhavi; Sankaran, Banumathi; Staker, Bart

2011-01-01

Fructose bisphosphate aldolase (FBPA) enzymes have been found in a broad range of eukaryotic and prokaryotic organisms. FBPA catalyses the cleavage of fructose 1,6-bisphosphate into glyceraldehyde 3-phosphate and dihydroxy­acetone phosphate. The SSGCID has reported several FBPA structures from pathogenic sources, including the bacterium Brucella melitensis and the protozoan Babesia bovis. Bioinformatic analysis of the Bartonella henselae genome revealed an FBPA homolog. The B. henselae FBPA enzyme was recombinantly expressed and purified for X-ray crystallographic studies. The purified enzyme crystallized in the apo form but failed to diffract; however, well diffracting crystals could be obtained by cocrystallization in the presence of the native substrate fructose 1,6-bisphosphate. A data set to 2.35 Å resolution was collected from a single crystal at 100 K. The crystal belonged to the orthorhombic space group P212121, with unit-cell parameters a = 72.39, b = 127.71, c = 157.63 Å. The structure was refined to a final free R factor of 22.2%. The structure shares the typical barrel tertiary structure and tetrameric quaternary structure reported for previous FBPA structures and exhibits the same Schiff base in the active site. PMID:21904049

Crystallization kinetics of the Cu{sub 50}Zr{sub 50} metallic glass under isothermal conditions

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

Gao, Qian; Jian, Zengyun, E-mail: jianzengyun@xatu.edu.cn; Xu, Junfeng

2016-12-15

Amorphous structure of the melt-spun Cu{sub 50}Zr{sub 50} amorphous alloy ribbons were confirmed by X-ray diffraction (XRD) and high-resolution transmission electron microscopy (HR-TEM). Isothermal crystallization kinetics of these alloy ribbons were investigated using differential scanning calorimetry (DSC). Besides, Arrhenius and Johnson-Mehl-Avrami (JMA) equations were utilized to obtain the isothermal crystallization kinetic parameters. As shown in the results, the local activation energy E{sub α} decreases by a large margin at the crystallized volume fraction α<0.1, which proves that crystallization process is increasingly easy. In addition, the local activation energy E{sub α} is basically constant at 0.1

Crystal structure of a new amine nitrate: 4-dimethylaminopyridinium nitrate (C{sub 7}H{sub 11}N{sub 2})NO{sub 3}

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

Benhassan, D., E-mail: houcine-naili@yahoo.com; Rekik, W.; Naïli, H.

2015-12-15

The title compound (C{sub 7}H{sub 11}N{sub 2})NO{sub 3} (I) was obtained by the slow evaporation method at room temperature. Its crystal structure consists of organic cations (C{sub 7}H{sub 11}N{sub 2}){sup +} and nitrate anions (NO{sub 3}){sup –} linked by two types of hydrogen bonds. Each monoprotonated nitrogen atom, called bifurcated, is engaged in two N–H···O hydrogen bonds with two symmetric oxygen atoms. In addition, the crystal structure stability is established by C–H···O hydrogen bonds that ensure the formation of infinite layers, parallel to (001) plane. These layers are related together through π···π interactions established between aromatic amines.

Charge-transport in tin-iodide perovskite CH3NH3SnI3: origin of high conductivity.

PubMed

Takahashi, Yukari; Obara, Rena; Lin, Zheng-Zhong; Takahashi, Yukihiro; Naito, Toshio; Inabe, Tamotsu; Ishibashi, Shoji; Terakura, Kiyoyuki

2011-05-28

The structural and electrical properties of a metal-halide cubic perovskite, CH(3)NH(3)SnI(3), have been examined. The band structure, obtained using first-principles calculation, reveals a well-defined band gap at the Fermi level. However, the temperature dependence of the single-crystal electrical conductivity shows metallic behavior down to low temperatures. The temperature dependence of the thermoelectric power is also metallic over the whole temperature range, and the large positive value indicates that charge transport occurs with a low concentration of hole carriers. The metallic properties of this as-grown crystal are thus suggested to result from spontaneous hole-doping in the crystallization process, rather than the semi-metal electronic structure. The present study shows that artificial hole doping indeed enhances the conductivity.

Crystal structures of different substrates of bacteriorhodopsin's M intermediate at various pH levels.

PubMed

Yamamoto, Masataka; Hayakawa, Naoki; Murakami, Midori; Kouyama, Tsutomu

2009-10-30

The hexagonal P622 crystal of bacteriorhodopsin, which is made up of stacked membranes, is stable provided that the precipitant concentration in the soaking solution is higher than a critical value (i.e., 1.5 M ammonium sulfate). Diffraction data showed that the crystal lattice shrank linearly with increasing precipitant concentration, due primarily to narrowing of intermembrane spaces. Although the crystal shrinkage did not affect the rate of formation of the photoreaction M intermediate, its lifetime increased exponentially with the precipitant concentration. It was suggested that the energetic barrier of the M-to-N transition becomes higher when the motional freedom of the EF loop is reduced by crystal lattice force. As a result of this property, the M state accumulated predominantly when the crystal that was soaked at a high precipitant concentration was illuminated at room temperature. Structural data obtained at various pH levels showed that the overall structure of M is not strongly dependent on pH, except that Glu194 and Glu204 in the proton release complex are more separated at pH 7 than at pH 4.4. This result suggests that light-induced disruption of the paired structure of Glu194 and Glu204 is incomplete when external pH is lower than the pK(a) value of the proton release group in the M state.

3D holographic polymer photonic crystal for superprism application

NASA Astrophysics Data System (ADS)

Chen, Jiaqi; Jiang, Wei; Chen, Xiaonan; Wang, Li; Zhang, Sasa; Chen, Ray T.

2007-02-01

Photonic crystal based superprism offers a new way to design new optical components for beam steering and DWDM application. 3D photonic crystals are especially attractive as they could offer more control of the light beam based on the needs. A polygonal prism based holographic fabrication method has been demonstrated for a three-dimensional face-centered-cubic (FCC)-type submicron polymer photonic crystal using SU8 as the photo-sensitive material. Therefore antivibration equipment and complicated optical alignment system are not needed and the requirement for the coherence of the laser source is relaxed compared with the traditional holographic setup. By changing the top-cut prism structure, the polarization of the laser beam, the exposure and development conditions we can achieve different kinds of triclinic or orthorhombic photonic crystals on demand. Special fabrication treatments have been introduced to ensure the survivability of the fabricated large area (cm2) nano-structures. Scanning electron microscopy and diffraction results proved the good uniformity of the fabricated structures. With the proper design of the refraction prism we have achieved a partial bandgap for S+C band (1460-1565nm) in the [111] direction. The transmission and reflection spectra obtained by Fourier transform infrared spectroscopy (FTIR) are in good agreement with simulated band structure. The superprism effects around 1550nm wavelength for the fabricated 3D polymer photonic crystal have been theoretically calculated and such effects can be used for beam steering purpose.

Fabrication, characterization and cell cultures on a novel composite chitosan-nano-hydroxyapatite scaffold.

PubMed

Palazzo, B; Gallo, A; Casillo, A; Nitti, P; Ambrosio, L; Piconi, C

2011-01-01

This paper deals with the characterizations made during the development of a nano-HAp loaded chitosan scaffold, obtained by the freeze-drying technique combined with a novel in situ crystal growth method. The nano-composites were characterized by a highly porous and interconnected structure. The XRD patterns and calculated domain sizes of the HAp nano-crystals nucleated on the chitosan scaffolds are very similar to the ones recorded for deproteinated bone apatite. Both osteoblasts (MG63) and mesenchimal cells (hMSC) were showing good proliferation and adhesion onto the scaffolds. The presence of extensive filopodia and excellent spreading in and around the interconnected porous structure, indicated a strong cellular adhesion and growth. Moreover a good hMSC osteogenic differentiation has been verified. The observations related to well-developed structure morphology, physicochemical properties and high cytocompatibility suggest that the obtained chitosan-nHA porous scaffolds are potential candidate materials for bone regeneration.

Formation of a new crystalline form of anhydrous β-maltose by ethanol-mediated crystal transformation.

PubMed

Verhoeven, Nicolas; Neoh, Tze Loon; Ohashi, Tetsuya; Furuta, Takeshi; Kurozumi, Sayaka; Yoshii, Hidefumi

2012-04-01

β-Maltose monohydrate was transformed into an anhydrous form by ethanol-mediated method under several temperatures with agitation. A new stable anhydrous form of β-maltose (Mβ(s)) was obtained, as substantiated by the X-ray diffraction patterns. Mβ(s) obtained by this method presented a fine porous structure, resulting in greater specific surface area compared to those of β-maltose monohydrate and anhydrous β-maltose obtained by vacuum drying (Mβ(h)). The crystal transformation presumably consisted of two steps: dehydration reaction from the hydrous to amorphous forms and crystal formation from the amorphous forms to the noble anhydrous form. The kinetics of these reactions were determined by thermal analysis using Jander's equation and Arrhenius plots. The overall activation energies of the dehydration reaction and the formation of anhydrous maltose were evaluated to be 100 and 90 kJ/mol, respectively. Copyright © 2012 Elsevier Ltd. All rights reserved.

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

NASA Astrophysics Data System (ADS)

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

2018-02-01

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

Synthesis, characterization, crystal structure and theoretical study of a compound with benzodiazole ring: antimicrobial activity and DNA binding.

PubMed

Latha, P; Kodisundaram, P; Sundararajan, M L; Jeyakumar, T

2014-08-14

2-(Thiophen-2-yl)-1-((thiophen-2-yl)methyl)-1H-1,3-benzodiazole (HL) is synthesized and characterized by elemental analysis, UV-Vis, FT-IR, (1)H, (13)C NMR, mass spectra, scanning electron microscope (SEM) and single crystal X-ray diffraction. The crystal structure is stabilized by intermolecular CH⋯N and CH⋯π interactions. The molecular structure is also optimized at the B3LYP/6-31G level using density functional theory (DFT). The structural parameters from the theory are nearer to those of crystal, the calculated total energy of coordination is -1522.814a.u. The energy of HOMO-LUMO and the energy gap are -0.20718, -0.04314, 0.16404a.u, respectively. All data obtained from the spectral studies support the structural properties of the compound HL. The benzimidazole ring is essentially planar. The in vitro biological screening effects of the synthesized compound is tested against four bacterial and four fungal strains by well diffusion method. Antioxidant property and DNA binding behaviour of the compound has been investigated using spectrophotometric method. Copyright © 2014 Elsevier B.V. All rights reserved.

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

Baig, M.; Brown, A.; Eswaramoorthy, S.

Klebsiella pneumoniae, a gram-negative enteric bacterium, is found in nosocomial infections which are acquired during hospital stays for about 10% of hospital patients in the United States. The crystal structure of a putative oxidoreductase from K. pneumoniae has been determined. The structural information of this K. pneumoniae protein was used to understand its function. Crystals of the putative oxidoreductase enzyme were obtained by the sitting drop vapor diffusion method using Polyethylene glycol (PEG) 3350, Bis-Tris buffer, pH 5.5 as precipitant. These crystals were used to collect X-ray data at beam line X12C of the National Synchrotron Light Source (NSLS) atmore » Brookhaven National Laboratory (BNL). The crystal structure was determined using the SHELX program and refi ned with CNS 1.1. This protein, which is involved in the catalysis of an oxidation-reduction (redox) reaction, has an alpha/beta structure. It utilizes nicotinamide adenine dinucleotide phosphate (NADP) or nicotine adenine dinucleotide (NAD) to perform its function. This structure could be used to determine the active and co-factor binding sites of the protein, information that could help pharmaceutical companies in drug design and in determining the protein’s relationship to disease treatment such as that for pneumonia and other related pathologies.« less

Effective pore size and radius of capture for K(+) ions in K-channels.

PubMed

Moldenhauer, Hans; Díaz-Franulic, Ignacio; González-Nilo, Fernando; Naranjo, David

2016-02-02

Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius (r(E)) in several K-channel crystal structures. r(E) was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent r(E) estimates for MthK and Kv1.2/2.1 structures, with r(E) = 5.3-5.9 Å and r(E) = 4.5-5.2 Å, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture (r(C)) for two electrophysiological counterparts, the large conductance calcium activated K-channel (r(C) = 2.2 Å) and the Shaker Kv-channel (r(C) = 0.8 Å), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between r(E) and r(C), produced consistent size radii of 3.1-3.7 Å and 3.6-4.4 Å for hydrated K(+) ions. These hydrated K(+) estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively.

Silicide surface phases on gold

NASA Technical Reports Server (NTRS)

Green, A. K.; Bauer, E.

1981-01-01

The crystalline silicide layers formed on (111) and (100) surfaces of Au films on various Si single-crystal substrates are studied by LEED and AES in conjunction with sputter-depth profiling as a function of annealing temperature. On the (111) surface, three basic silicide structures are obtained corresponding to layers of various thicknesses as obtained by different preparation conditions. The (100) surface shows only two different structures. None of the structures is compatible with the various bulk silicide structures deduced from X-ray diffraction. Using LEED as a criterion for the presence or absence of silicide on the surface, smaller layer thicknesses are obtained than reported previously on the basis of AES studies.

The effect of ultrasonic intensity on the crystal structure of palm oil.

PubMed

Patrick, Maria; Blindt, Renoo; Janssen, Jo

2004-05-01

It has been known for a long time that both the crystal structure and kinetics of crystallisation can be affected by ultrasound. In the past systems used have relied on high power ultrasonic probes to produce crystals. The majority of these probes produce cavitation in the system and it has been difficult to differentiate between effects caused by the ultrasound alone or by the cavitation produced by ultrasound on the crystal structure. Some materials, such as fats, are very susceptible to the production of free radicals that lead to "off-flavours" being obtained. These "off-flavours" are easily produced when the standard high power probes are used. This has meant that, although the crystal structure of the final product might be improved, the presence of 'off' flavours has prevented ultrasound being considered as a commercial technique for the crystallisation of edible fats. At Unilever R&D a system has been developed which can investigate the effect of ultrasound on the crystallisation of fats under controlled conditions covering a range of intensities and cooling rates. The intensity levels used were both below and above the cavitational threshold. By keeping the cooling regime constant it has been possible to show that the structure of the final product can vary from a material looking similar to cottage cheese through to a fine cream simply by varying the ultrasonic intensity. This paper describes the effect of ultrasound on both the crystal structure and kinetics of palm oil crystallisation at intensities below and above the cavitational threshold.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape

PubMed Central

Sripathi, Kamali N.; Tay, Wendy W.; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G.

2014-01-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2′-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. PMID:24854621

Tailor-made force fields for crystal-structure prediction.

PubMed

Neumann, Marcus A

2008-08-14

A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

Crystal structure of human tooth enamel studied by neutron diffraction

NASA Astrophysics Data System (ADS)

Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

2015-02-01

Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

Study of a splat cooled Cu-Zr-noncrystalline phase.

NASA Technical Reports Server (NTRS)

Revcolevschi, A.; Grant, N. J.

1972-01-01

By rapid quenching from the melt, using the splat forming gun technique, a noncrystalline phase has been obtained in a Cu-Zr alloy containing 60 at. % Cu. Upon heating, rapid crystallization of the samples takes place at 477 C with a heat release of about 700 cal per mol. The variation of the electrical resistivity of the samples with temperature confirms the transformation. Very high resolution electron microscopy studies of the structural changes of the samples upon heating are presented and show the gradual crystallization of the amorphous structure.

Multi-wavelength laser emission in dye-doped photonic liquid crystals.

PubMed

Wang, Chun-Ta; Lin, Tsung-Hsien

2008-10-27

Multi-wavelength lasing in a dye-doped cholesteric liquid crystal (CLC) cell is demonstrated. By adding oversaturated chiral dopant, the multi-photonic band CLC structure can be obtained with non-uniform chiral solubility. Under appropriate excitation, multi-wavelength lasing can be achieved with a multi-photonic band edge CLC structure. The number of lasing wavelengths can be controlled under various temperature processes. Nine wavelength CLC lasings were observed simultaneously. The wavelength range covers around 600-675nm. Furthermore, reversible tuning of multi-wavelength lasing was achieved by controlling CLC device temperature.

The structure of small, vapor-deposited particles. II - Experimental study of particles with hexagonal profile

NASA Technical Reports Server (NTRS)

Yacaman, M. J.; Heinemann, K.; Yang, C. Y.; Poppa, H.

1979-01-01

'Multiply-twinned' gold particles with hexagonal bright field TEM profile were determined to be icosahedra composed of 20 identical and twin-related tetrahedral building units that do not have an fcc structure. The crystal structure of these slightly deformed tetrahedra is rhombohedral. Experimental evidence supporting this particle model was obtained by selected-zone dark field and weak beam dark field electron microscopy. In conjunction with the results of part I, it has been concluded that multiply-twinned gold particles of pentagonal or hexagonal profile that are found during the early stages of the vapor deposition growth process on alkali halide surfaces do not have an fcc crystal structure, which is in obvious contrast to the structure of bulk gold.

Structural Studies of Bacterioferritin B (BfrB) from Pseudomonas aeruginosa Suggest a Gating Mechanism for Iron Uptake via the Ferroxidase Center¥

PubMed Central

Weeratunga, Saroja K.; Lovell, Scott; Yao, Huili; Battaile, Kevin P.; Fischer, Christopher J.; Gee, Casey E.; Rivera, Mario

2010-01-01

The structure of recombinant P. aeruginosa bacterioferritin B (Pa BfrB) has been solved from crystals grown from protein devoid of core mineral iron (as-isolated) and from protein mineralized with ~ 600 iron atoms (mineralized). Structures were also obtained from crystals grown from mineralized BfrB after soaking them in FeSO4 solution (Fe soak) and in separate experiments after soaking them in FeSO4 solution followed by soaking in crystallization solution (double soak). Although the structures consist of a typical bacterioferritin fold comprised of a nearly spherical 24-mer assembly that binds 12 heme molecules, comparison of microenvironments observed in the distinct structures provided interesting insights: The ferroxidase center in the as-isolated, mineralized and double soak structures is empty. The ferroxidase ligands (except His130) are poised to bind iron with minimal conformational changes. The His130 side chain, on the other hand, must rotate toward the ferroxidase center to coordinate iron. In comparison, the structure obtained from crystals soaked in an FeSO4 solution display a fully occupied ferroxidase center and iron bound to the internal, Fe(in), and external, Fe(out), surfaces of Pa BfrB. The conformation of His130 in this structure is rotated toward the ferroxidase center and coordinates an iron ion. The structures also revealed a pore on the surface of Pa BfrB that likely serves as an entry port for Fe2+ to the ferroxidase center. On its opposite end the pore is capped by the side chain of His130 when it adopts its “gate closed” conformation that enables coordination to a ferroxidase iron. A change to its “gate-open”, non-coordinative conformation, creates a path for the translocation of iron from the ferroxidase center to the interior cavity. These structural observations, together with findings obtained from iron incorporation measurements in solution suggest that the ferroxidase pore is the dominant entry route for the uptake of iron by Pa BfrB. These findings, which are clearly distinct from those made with E. coli Bfr (Crow, A. C., Lawson, T. L., Lewin, A., Moore, G. R., and Le Brun, N. E. (2009) J. Am. Chem. Soc. 131, 6808–6813) indicate that not all bacterioferritins operate in the same manner. PMID:20067302

A new route for the synthesis of titanium silicalite-1

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

Vasile, Aurelia, E-mail: aurelia_vasile@yahoo.com; Busuioc-Tomoiaga, Alina Maria; Catalysis Research Department, ChemPerformance SRL, Iasi 700337

2012-01-15

Graphical abstract: Well-prepared TS-1 was synthesized by an innovative procedure using inexpensive reagents such as fumed silica and TPABr as structure-directing agent. This is the first time when highly crystalline TS-1 is obtained in basic medium, using sodium hydroxide as HO{sup -} ion source required for the crystallization process. Hydrolysis of titanium source has been prevented by titanium complexation with acetylacetone before structuring gel. Highlights: Black-Right-Pointing-Pointer TS-1 was obtained using cheap reagents as fumed silica and tetrapropylammonium bromide. Black-Right-Pointing-Pointer First time NaOH was used as source of OH{sup -} ions required for crystallization process. Black-Right-Pointing-Pointer The hydrolysis Ti alkoxides wasmore » controlled by Ti complexation with 2,4-pentanedione. -- Abstract: A new and efficient route using inexpensive reagents such as fumed silica and tetrapropylammonium bromide is proposed for the synthesis of titanium silicalite-1. High crystalline titanium silicalite-1 was obtained in alkaline medium, using sodium hydroxide as HO{sup -} ion source required for the crystallization process. Hydrolysis of titanium source with formation of insoluble oxide species was prevented by titanium complexation with before structuring gel. The final solids were fully characterized by powder X-ray diffraction, scanning electron microscopy, Fourier transform infrared, ultraviolet-visible diffuse reflectance, Raman and atomic absorption spectroscopies, as well as nitrogen sorption analysis. It was found that a molar ratio Ti:Si of about 0.04 in the initial reaction mixture is the upper limit to which well formed titanium silicalite-1 with channels free of crystalline or amorphous material can be obtained. Above this value, solids with MFI type structure containing both Ti isomorphously substituted in the network and extralattice anatase nanoparticles inside of channels is formed.« less

The crystal structure of paramagnetic copper(II) oxalate (CuC₂O₄): formation and thermal decomposition of randomly stacked anisotropic nano-sized crystallites.

PubMed

Christensen, Axel Nørlund; Lebech, Bente; Andersen, Niels Hessel; Grivel, Jean-Claude

2014-11-28

Synthetic copper(II) oxalate, CuC2O4, was obtained in a precipitation reaction between a copper(II) solution and an aqueous solution of oxalic acid. The product was identified from its conventional X-ray powder patterns which match that of the copper mineral Moolooite reported to have the composition CuC2O4·0.44H2O. Time resolved in situ investigations of the thermal decomposition of copper(II) oxalate using synchrotron X-ray powder diffraction showed that in air the compound converts to Cu2O at 215 °C and oxidizes to CuO at 345 °C. Thermo gravimetric analysis performed in an inert Ar-gas reveals that the material contains no crystal water and reduces to pure Cu at 295 °C. Magnetic susceptibility measurements in the temperature range from 2 K to 300 K show intriguing paramagnetic behaviour with no sign of magnetic order down to 2 K. A crystal structure investigation is made based on powder diffraction data using one neutron diffraction pattern obtained at 5 K (λ = 1.5949(1) Å) combined with one conventional and two synchrotron X-ray diffraction patterns obtained at ambient temperature using λ = 1.54056, 1.0981 and λ = 0.50483(1) Å, respectively. Based on the X-ray synchrotron data the resulting crystal structure is described in the monoclinic space group P2₁/c (#14) in the P12₁/n1 setting with unit cell parameters a = 5.9598(1) Å, b = 5.6089(1) Å, c = 5.1138 (1) Å, β = 115.320(1)°. The composition is CuC2O4 with atomic coordinates determined by FullProf refinement of the neutron diffraction data. The crystal structure consists of a random stacking of CuC2O4 micro-crystallites where half the Cu-atoms are placed at (2a) and the other half at (2b) positions with the corresponding oxalate molecules centred around the corresponding (2b) and (2a) site positions, respectively. The diffraction patterns obtained for both kinds of radiation show considerable broadening of several Bragg peaks caused by highly anisotropic microstructural size and strain effects. In contrast to the water reported to be present in Moolooite, neither thermogravimetric nor the in situ thermal decomposition investigations and crystal structure analysis of the neutron diffraction data revealed any trace of water. An appendix contains details about the profile parameters for the diffractometers used at the European Synchrotron Radiation Facility and the Institute Max von Laue-Paul Langevin.

Learning about Biomolecular Solvation from Water in Protein Crystals.

PubMed

Altan, Irem; Fusco, Diana; Afonine, Pavel V; Charbonneau, Patrick

2018-03-08

Water occupies typically 50% of a protein crystal and thus significantly contributes to the diffraction signal in crystallography experiments. Separating its contribution from that of the protein is, however, challenging because most water molecules are not localized and are thus difficult to assign to specific density peaks. The intricateness of the protein-water interface compounds this difficulty. This information has, therefore, not often been used to study biomolecular solvation. Here, we develop a methodology to surmount in part this difficulty. More specifically, we compare the solvent structure obtained from diffraction data for which experimental phasing is available to that obtained from constrained molecular dynamics (MD) simulations. The resulting spatial density maps show that commonly used MD water models are only partially successful at reproducing the structural features of biomolecular solvation. The radial distribution of water is captured with only slightly higher accuracy than its angular distribution, and only a fraction of the water molecules assigned with high reliability to the crystal structure is recovered. These differences are likely due to shortcomings of both the water models and the protein force fields. Despite these limitations, we manage to infer protonation states of some of the side chains utilizing MD-derived densities.

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

Hou, Kun; Gao, Ziwei, E-mail: zwgao@snnu.edu.cn; Da, Min

Highlights: Black-Right-Pointing-Pointer Highly oriented and well-defined ZnO urchin-like crystals were successfully fabricated by a facile and effective hydrotherm method. Black-Right-Pointing-Pointer Polyvinylpyrrolidone- and hydrogen peroxide-assisted synthesis of ZnO could optimize its crystalline quality and the obtained ZnO have smooth surface, radial growth of morphology, obvious crystal edges and decreased defects. Black-Right-Pointing-Pointer The physicochemical properties of samples were studied by analysis of its structure, morphology, surface and optical properties. Black-Right-Pointing-Pointer This study represented a multistep mechanism based on [Zn(OH){sub 4}]{sup 2-} growth units about formation such urchin-like structure. -- Abstract: The urchin-like ZnO microcrystals with high crystallinity decomposed from [Zn(OH){sub 4}]{sup 2-}more » directly were obtained via a hydrothermal method. The morphology, particle size, crystalline structure and fluorescence of the as-prepared ZnO were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD) and photoluminescence (PL) analyses. The results demonstrated that the urchin-like ZnO crystals with wurtzite structure had a narrow distribution in size, which could be adjusted in the range of 30-80 {mu}m by varying reaction time. Broad visible light emission peak was also observed in the PL spectra of the synthesized ZnO products. A multistep growth process about how to form such a structure was proposed.« less

Exploration of N-arylpiperazine Binding Sites of D2 Dopaminergic Receptor.

PubMed

Soskic, Vukic; Sukalovic, Vladimir; Kostic-Rajacic, Sladjana

2015-01-01

The crystal structures of the D3 dopamine receptor and several other G-protein coupled receptors (GPCRs) were published in recent times. Those 3D structures are used by us and other scientists as a template for the homology modeling and ligand docking analysis of related GPCRs. Our main scientific interest lies in the field of pharmacologically active N-arylpiperazines that exhibit antipsychotic and/or antidepressant properties, and as such are dopaminergic and serotonergic receptor ligands. In this short review article we are presenting synthesis and biological data on the new N-arylpipereazine as well our results on molecular modeling of the interactions of those N-arylpiperazines with the model of D2 dopamine receptors. To obtain that model the crystal structure of the D3 dopamine receptor was used. Our results show that the N-arylpiperazines binding site consists of two pockets: one is the orthosteric binding site where the N-arylpiperazine part of the ligand is docked and the second is a non-canonical accessory binding site for N-arylpipereazine that is formed by a second extracellular loop (ecl2) of the receptor. Until now, the structure of this receptor region was unresolved in crystal structure analyses of the D3 dopamine receptor. To get a more complete picture of the ligand - receptor interaction, DFT quantum mechanical calculations on N-arylpiperazine were performed and the obtained models were used to examine those interactions.

Growth of InAs/InP core-shell nanowires with various pure crystal structures.

PubMed

Gorji Ghalamestani, Sepideh; Heurlin, Magnus; Wernersson, Lars-Erik; Lehmann, Sebastian; Dick, Kimberly A

2012-07-20

We have studied the epitaxial growth of an InP shell on various pure InAs core nanowire crystal structures by metal-organic vapor phase epitaxy. The InP shell is grown on wurtzite (WZ), zinc-blende (ZB), and {111}- and {110}-type faceted ZB twin-plane superlattice (TSL) structures by tuning the InP shell growth parameters and controlling the shell thickness. The growth results, particularly on the WZ nanowires, show that homogeneous InP shell growth is promoted at relatively high temperatures (∼500 °C), but that the InAs nanowires decompose under the applied conditions. In order to protect the InAs core nanowires from decomposition, a short protective InP segment is first grown axially at lower temperatures (420-460 °C), before commencing the radial growth at a higher temperature. Further studies revealed that the InP radial growth rate is significantly higher on the ZB and TSL nanowires compared to WZ counterparts, and shows a strong anisotropy in polar directions. As a result, thin shells were obtained during low temperature InP growth on ZB structures, while a higher temperature was used to obtain uniform thick shells. In addition, a schematic growth model is suggested to explain the basic processes occurring during the shell growth on the TSL crystal structures.

Improved purification, crystallization and primary structure of pyruvate:ferredoxin oxidoreductase from Halobacterium halobium.

PubMed

Plaga, W; Lottspeich, F; Oesterhelt, D

1992-04-01

An improved purification procedure, including nickel chelate affinity chromatography, is reported which resulted in a crystallizable pyruvate:ferredoxin oxidoreductase preparation from Halobacterium halobium. Crystals of the enzyme were obtained using potassium citrate as the precipitant. The genes coding for pyruvate:ferredoxin oxidoreductase were cloned and their nucleotide sequences determined. The genes of both subunits were adjacent to one another on the halobacterial genome. The derived amino acid sequences were confirmed by partial primary structure analysis of the purified protein. The structural motif of thiamin-diphosphate-binding enzymes was unequivocally located in the deduced amino acid sequence of the small subunit.

OsN2: Crystal structure and electronic properties

NASA Astrophysics Data System (ADS)

Montoya, Javier A.; Hernandez, Alexander D.; Sanloup, Chrystèle; Gregoryanz, Eugene; Scandolo, Sandro

2007-01-01

Osmium nitride belongs to a family of nitrides synthesized recently at high pressures from their parent elements. Here we show, based on first-principles calculations, that the crystal structure of osmium nitride is isostructural to marcasite. Excellent agreement is obtained between the authors' results and x-ray, Raman, and compressibility measurements. In the OsN2 marcasite structure single-bonded N2 units occupy the interstitial sites of the Os close-packed lattice, giving rise to a metallic compound. A comparison between the formation energies of OsN2 and PtN2 explains the similar thermodynamic conditions of formation reported experimentally for the two compounds.

RBAP, a rhodamine B-based derivative: synthesis, crystal structure analysis, molecular simulation, and its application as a selective fluorescent chemical sensor for Sn2+.

PubMed

Bao, Xiaofeng; Cao, Xiaowei; Nie, Xuemei; Jin, Yanyan; Zhou, Baojing

2014-06-11

A new fluorescent chemosensor based on a Rhodamine B and a benzyl 3-aminopropanoate conjugate (RBAP) was designed, synthesized, and structurally characterized. Its single crystal structure was obtained and analyzed by X-ray analysis. In a MeOH/H2O (2:3, v/v, pH 5.95) solution RBAP exhibits a high selectivity and excellent sensitivity for Sn2+ ions in the presence of many other metal cations. The binding analysis using the Job's plot suggested the RBAP formed a 1:1 complex with Sn2+.

Experiment and density functional theory analyses of GdTaO4 single crystal

NASA Astrophysics Data System (ADS)

Ding, Shoujun; Kinross, Ashlie; Wang, Xiaofei; Yang, Huajun; Zhang, Qingli; Liu, Wenpeng; Sun, Dunlu

2018-05-01

GdTaO4 is a type of excellent materials that can be used as scintillation, laser matrix as well as self-activated phosphor has generated significant interest. Whereas its band structure, electronic structure and optical properties are still need elucidation. To solve this intriguing problem, high-quality GdTaO4 single crystal (M-type) was grown successfully using Czochralski method. Its structure as well as optical properties was determined in experiment. Moreover, a systematic theoretical calculation based on the density function theory methods were performed on M-type and M‧-type GdTaO4 and their band structure, density of state as well as optical properties were obtained. Combine with the performed experiment results, the calculated results were proved with high reliability. Hence, the calculated results obtained in this work could provide a deep understanding of GdTaO4 material, which also useful for the further investigation on GdTaO4 material.

Using cryoEM Reconstruction and Phase Extension to Determine Crystal Structure of Bacteriophage $${\\Phi}$$6 Major Capsid Protein

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

Nemecek, Daniel; Plevka, Pavel; Boura, Evzen

2013-11-29

Bacteriophagemore » $${\\Phi}$$6 is a double-stranded RNA virus that has been extensively studied as a model organism. In this paper we describe structure determination of $${\\Phi}$$6 major capsid protein P1. The protein crystallized in base centered orthorhombic space group C2221. Matthews’s coefficient indicated that the crystals contain from four to seven P1 subunits in the crystallographic asymmetric unit. The self-rotation function had shown presence of fivefold axes of non-crystallographic symmetry in the crystals. Thus, electron density map corresponding to a P1 pentamer was excised from a previously determined cryoEM reconstruction of the $${\\Phi}$$6 procapsid at 7 Å resolution and used as a model for molecular replacement. The phases for reflections at higher than 7 Å resolution were obtained by phase extension employing the fivefold non-crystallographic symmetry present in the crystal. Lastly, the averaged 3.6 Å-resolution electron density map was of sufficient quality to allow model building.« less

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.

Fab Chaperone-Assisted RNA Crystallography (Fab CARC).

PubMed

Sherman, Eileen; Archer, Jennifer; Ye, Jing-Dong

2016-01-01

Recent discovery of structured RNAs such as ribozymes and riboswitches shows that there is still much to learn about the structure and function of RNAs. Knowledge learned can be employed in both biochemical research and clinical applications. X-ray crystallography gives unparalleled atomic-level structural detail from which functional inferences can be deduced. However, the difficulty in obtaining high-quality crystals and their phasing information make it a very challenging task. RNA crystallography is particularly arduous due to several factors such as RNA's paucity of surface chemical diversity, lability, repetitive anionic backbone, and flexibility, all of which are counterproductive to crystal packing. Here we describe Fab chaperone assisted RNA crystallography (CARC), a systematic technique to increase RNA crystallography success by facilitating crystal packing as well as expediting phase determination through molecular replacement of conserved Fab domains. Major steps described in this chapter include selection of a synthetic Fab library displayed on M13 phage against a structured RNA crystallization target, ELISA for initial choice of binding Fabs, Fab expression followed by protein A affinity then cation exchange chromatography purification, final choice of Fab by binding specificity and affinity as determined by a dot blot assay, and lastly gel filtration purification of a large quantity of chosen Fabs for crystallization.

Strong transmittance above the light line in mid-infrared two-dimensional photonic crystals

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

Kraeh, Christian, E-mail: christian.kraeh@tum.de; Walter Schottky Institut, Technische Universität München, Am Coulombwall 4, D-85748 Garching; Martinez-Hurtado, J. L.

2015-06-14

The mid-infrared region of the electromagnetic spectrum between 3 and 8 μm hosts absorption lines of gases relevant for chemical and biological sensing. 2D photonic crystal structures capable of guiding light in this region of the spectrum have been widely studied, and their implementation into miniaturized sensors has been proposed. However, light guiding in conventional 2D photonic crystals is usually restricted to a frequency range below the light line, which is the dispersion relation of light in the media surrounding the structures. These structures rely on total internal reflection for confinement of the light in z-direction normal to the lattice plane.more » In this work, 2D mid-infrared photonic crystals consisting of microtube arrays that mitigate these limitations have been developed. Due to their high aspect ratios of ∼1:30, they are perceived as semi-infinite in the z-direction. Light transmission experiments in the 5–8 μm range reveal attenuations as low as 0.27 dB/100 μm, surpassing the limitations for light guiding above the light line in conventional 2D photonic crystals. Fair agreement is obtained between these experiments, 2D band structure and transmission simulations.« less

Femtosecond X-ray protein nanocrystallography.

PubMed

Chapman, Henry N; Fromme, Petra; Barty, Anton; White, Thomas A; Kirian, Richard A; Aquila, Andrew; Hunter, Mark S; Schulz, Joachim; DePonte, Daniel P; Weierstall, Uwe; Doak, R Bruce; Maia, Filipe R N C; Martin, Andrew V; Schlichting, Ilme; Lomb, Lukas; Coppola, Nicola; Shoeman, Robert L; Epp, Sascha W; Hartmann, Robert; Rolles, Daniel; Rudenko, Artem; Foucar, Lutz; Kimmel, Nils; Weidenspointner, Georg; Holl, Peter; Liang, Mengning; Barthelmess, Miriam; Caleman, Carl; Boutet, Sébastien; Bogan, Michael J; Krzywinski, Jacek; Bostedt, Christoph; Bajt, Saša; Gumprecht, Lars; Rudek, Benedikt; Erk, Benjamin; Schmidt, Carlo; Hömke, André; Reich, Christian; Pietschner, Daniel; Strüder, Lothar; Hauser, Günter; Gorke, Hubert; Ullrich, Joachim; Herrmann, Sven; Schaller, Gerhard; Schopper, Florian; Soltau, Heike; Kühnel, Kai-Uwe; Messerschmidt, Marc; Bozek, John D; Hau-Riege, Stefan P; Frank, Matthias; Hampton, Christina Y; Sierra, Raymond G; Starodub, Dmitri; Williams, Garth J; Hajdu, Janos; Timneanu, Nicusor; Seibert, M Marvin; Andreasson, Jakob; Rocker, Andrea; Jönsson, Olof; Svenda, Martin; Stern, Stephan; Nass, Karol; Andritschke, Robert; Schröter, Claus-Dieter; Krasniqi, Faton; Bott, Mario; Schmidt, Kevin E; Wang, Xiaoyu; Grotjohann, Ingo; Holton, James M; Barends, Thomas R M; Neutze, Richard; Marchesini, Stefano; Fromme, Raimund; Schorb, Sebastian; Rupp, Daniela; Adolph, Marcus; Gorkhover, Tais; Andersson, Inger; Hirsemann, Helmut; Potdevin, Guillaume; Graafsma, Heinz; Nilsson, Björn; Spence, John C H

2011-02-03

X-ray crystallography provides the vast majority of macromolecular structures, but the success of the method relies on growing crystals of sufficient size. In conventional measurements, the necessary increase in X-ray dose to record data from crystals that are too small leads to extensive damage before a diffraction signal can be recorded. It is particularly challenging to obtain large, well-diffracting crystals of membrane proteins, for which fewer than 300 unique structures have been determined despite their importance in all living cells. Here we present a method for structure determination where single-crystal X-ray diffraction 'snapshots' are collected from a fully hydrated stream of nanocrystals using femtosecond pulses from a hard-X-ray free-electron laser, the Linac Coherent Light Source. We prove this concept with nanocrystals of photosystem I, one of the largest membrane protein complexes. More than 3,000,000 diffraction patterns were collected in this study, and a three-dimensional data set was assembled from individual photosystem I nanocrystals (∼200 nm to 2 μm in size). We mitigate the problem of radiation damage in crystallography by using pulses briefer than the timescale of most damage processes. This offers a new approach to structure determination of macromolecules that do not yield crystals of sufficient size for studies using conventional radiation sources or are particularly sensitive to radiation damage.

Micro- and nano-porous surface patterns prepared by surface-confined directional melt crystallization of solvent

NASA Astrophysics Data System (ADS)

Kim, Byoung Soo; Kim, Hyun Jin; An, Suyeong; Chi, Sangwon; Kim, Junseok; Lee, Jonghwi

2017-07-01

Recently, numerous attempts have been made to engineer micro- and nano-porous surface patterns or to develop convenient preparation methods for the practical applications of self-cleaning surfaces, water-repellent surfaces, novel textures, etc. Herein, we introduce a simple, cheap, and repeatable crystallization-based method to produce porous surface structures, on any surface of already fabricated polymeric materials. Contact of the solvent phase with cooled polymer surfaces enabled the limited dissolution of the surfaces and the subsequent extremely fast melt crystallization of the solvent. After removing the crystals, various micro- and nano-porous patterns were obtained, whose pore sizes ranged over three orders of magnitude. Pore depth was linearly dependent on the dissolution time. Crystal growth was mainly directed normal to the surfaces, but it was also controlled in-plane, resulting in cylindrical or lamellar structures. Superhydrophobic surfaces were successfully prepared on both polystyrene and polycarbonate. This process offers a novel surface engineering tool for a variety of polymer surfaces, whose topology can be conveniently controlled over a wide range by crystal engineering.

Crystallization and preliminary X-ray analysis of pyruvate kinase from Bacillus stearothermophilus

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

Suzuki, Kenichiro; Ito, Sohei; Shimizu-Ibuka, Akiko

2005-08-01

This report describes the crystallization and X-ray diffraction data collection of three types (wild-type, W416F/V435W and C9S/C268S) of B. stearothermophilus. Crystals of C9S/C268S belonged to space group P6{sub 2}22 and diffracted to a resolution of 2.4 Å. Pyruvate kinase (PK) from a moderate thermophile, Bacillus stearothermophilus (BstPK), is an allosteric enzyme activated by AMP and ribose 5-phosphate but not by fructose 1,6-bisphosphate (FBP). However, almost all other PKs are activated by FBP. The wild-type and W416F/V435W mutant BstPKs were crystallized by the hanging-drop vapour-diffusion method. However, they were unsuitable for structural analysis because their data sets exhibited low completeness. Amore » crystal suitable for structural analysis was obtained using C9S/C268S enzyme. The crystal belonged to space group P6{sub 2}22, with unit-cell parameters a = b = 145.97, c = 118.03 Å.« less

Point defect disorder in high-temperature solution grown Sr6Tb0.94Fe1.06(BO3)6 single crystals

NASA Astrophysics Data System (ADS)

Velázquez, M.; Péchev, S.; Duttine, M.; Wattiaux, A.; Labrugère, C.; Veber, Ph.; Buffière, S.; Denux, D.

2018-08-01

New Sr6Tb0.94Fe1.06(BO3)6 single crystals were obtained from lithium borate high-temperature solution growth under controlled atmosphere. Their average crystal structure was found to adopt the trigonal R-3 space group with lattice parameters a = 12.2164 Å and c = 9.1934 Å. A combined multiscale characterization approach, involving diffuse reflectance, X-ray photoelectron (XPS) and Mössbauer spectroscopies, was undertaken to establish the exact nature of the point defect disorder in this crystal structure. The FeTb× antisite disorder in the Sr6Tb0.94Fe1.06(BO3)6 single crystals is different from the kind of point defect disorder known to exist in the powder phase material counterpart. The absence of Tb4+ cations in the crystal lattice was established by XPS, and that of any phase transition down to 4 K was checked by specific heat measurements. The magnetic susceptibility curve was found to follow a Curie-Weiss behaviour in the 4-354 K temperature range.

Redetermination of the crystal structure of the 2D heterometallic framework prepared from [Ni(cyclam)]2+ and [Re(CN)7]3-

NASA Astrophysics Data System (ADS)

Sukhikh, Taisiya S.; Vostrikova, Kira E.

2018-02-01

A new XRD experiment and crystal structure refinement was performed for the earlier published compound in the paper "Heterobimetallic coordination polymers involving 3d metal complexes and heavier transition metals cyanometallates" by Peresypkina et al. (2015) [1]. A choice of a crystal cell taking in consideration the superstructural reflections allowed to obtain more reliable data about the symmetry and bond distances in the heterometallic 2D framework {[Ni(cyclam)]2[ReO(OH)0.5(MeOH)0.5(CN)4]}2.5+. Additionally, doubling of the parameter c permitted to get more details about interlayer space. As a result, disordered perchlorate anions and solvate molecules were located.

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin.

PubMed

Lee, BoRam; Zhang, Renhao; Du, Wen-Xian; Grauke, Larry J; McHugh, Tara H; Zhang, Yu-Zhu

2014-08-01

Tree nuts are responsible for many cases of severe food allergies. The 7S seed storage protein vicilin has been identified as a food allergen in many kinds of tree nuts. The vicilin protein consists of an N-terminal low-complexity region with antimicrobial activity and a C-terminal domain that forms a trimeric structure that belongs to the cupin superfamily. In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369-792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space group P212121.

Expression, purification and crystallization of pecan (Carya illinoinensis) vicilin

PubMed Central

Lee, BoRam; Zhang, Renhao; Du, Wen-Xian; Grauke, Larry J.; McHugh, Tara H.; Zhang, Yu-Zhu

2014-01-01

Tree nuts are responsible for many cases of severe food allergies. The 7S seed storage protein vicilin has been identified as a food allergen in many kinds of tree nuts. The vicilin protein consists of an N-terminal low-complexity region with antimicrobial activity and a C-terminal domain that forms a trimeric structure that belongs to the cupin superfamily. In this study, vicilin from pecan (Carya illinoinensis) was isolated and was expressed in bacteria for the first time. The cupin structural core of the protein, residues 369–792, was purified by metal-affinity and gel-filtration chromatography to high purity. Vicilin crystals were obtained and the best crystal diffracted to 2.65 Å resolution in space group P212121. PMID:25084379

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

Yakubovich, O. V., E-mail: yakubol@geol.msu.ru; Biralo, G. V.; Dimitrova, O. V.

The crystal structure of the (Al,V){sub 4}(P{sub 4}O{sub 12}){sub 3} solid solution, obtained in the single-crystal form by hydrothermal synthesis in the Al(OH){sub 3}-VO{sub 2}-NaCl-H{sub 3}PO{sub 4}-H{sub 2}O system, has been solved by X-ray diffraction analysis (Xcalibur-S-CCD diffractometer, R = 0.0257): a = 13.7477(2) Angstrom-Sign , sp. gr. I 4 bar 3d, Z = 4, and {rho}{sub calcd} = 2.736 g/cm{sup 3}. It is shown that the crystal structure of the parent cubic Al{sub 4}(P{sub 4}O{sub 12}){sub 3} modification can formally be considered an archetype for the formation of double isosymmetric tetraphosphates on its basis.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

NASA Astrophysics Data System (ADS)

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-01

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation.

PubMed

Takemura, Kazuhiro; Guo, Hao; Sakuraba, Shun; Matubayasi, Nobuyuki; Kitao, Akio

2012-12-07

We propose a method to evaluate binding free energy differences among distinct protein-protein complex model structures through all-atom molecular dynamics simulations in explicit water using the solution theory in the energy representation. Complex model structures are generated from a pair of monomeric structures using the rigid-body docking program ZDOCK. After structure refinement by side chain optimization and all-atom molecular dynamics simulations in explicit water, complex models are evaluated based on the sum of their conformational and solvation free energies, the latter calculated from the energy distribution functions obtained from relatively short molecular dynamics simulations of the complex in water and of pure water based on the solution theory in the energy representation. We examined protein-protein complex model structures of two protein-protein complex systems, bovine trypsin/CMTI-1 squash inhibitor (PDB ID: 1PPE) and RNase SA/barstar (PDB ID: 1AY7), for which both complex and monomer structures were determined experimentally. For each system, we calculated the energies for the crystal complex structure and twelve generated model structures including the model most similar to the crystal structure and very different from it. In both systems, the sum of the conformational and solvation free energies tended to be lower for the structure similar to the crystal. We concluded that our energy calculation method is useful for selecting low energy complex models similar to the crystal structure from among a set of generated models.

Three-dimensional reconstruction of the size and shape of protein microcrystals using Bragg coherent diffractive imaging

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

Coughlan, H. D.; Darmanin, C.; Kirkwood, H. J.

2016-03-14

Three-dimensional imaging of protein crystals during X-ray diffraction experiments opens up a range of possibilities for optimising crystal quality and gaining new insights into the fundamental processes that drive radiation damage. Obtaining this information at the appropriate lengthscales however is extremely challenging. One approach that has been recently demonstrated as a promising avenue for charactering the size and shape of protein crystals at nanometre lengthscales is Bragg Coherent Diffractive Imaging (BCDI). BCDI is a recently developed technique that is able to recover the phase of the continuous diffraction intensity signal around individual Bragg peaks. When data is collected at multiplemore » points on a rocking curve a Reciprocal Space Map (RSM) can be assembled and then inverted using BCDI to obtain a three-dimensional image of the crystal. The first demonstration of two-dimensional BCDI of protein crystals was reported by Boutet at al., recently this work was extended to the study of radiation damage of micron-sized crystals. Here we present the first three-dimensional reconstructions of a Lysozyme protein crystal using BDI. The results are validated against RSM and TEM data and have implications for both radiation damage studies and for developing new approaches to structure retrieval from micron-sized protein crystals.« less

Fast optical detecting media based on semiconductor nanostructures for recording images obtained using charges of free photocarriers

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

Kasherininov, P. G., E-mail: peter.kasherininov@mail.ioffe.ru; Tomasov, A. A.; Beregulin, E. V.

2011-01-15

Available published data on the properties of optical recording media based on semiconductor structures are reviewed. The principles of operation, structure, parameters, and the range of application for optical recording media based on MIS structures formed of photorefractive crystals with a thick layer of insulator and MIS structures with a liquid crystal as the insulator (the MIS LC modulators), as well as the effect of optical bistability in semiconductor structures (semiconductor MIS structures with nanodimensionally thin insulator (TI) layer, M(TI)S nanostructures). Special attention is paid to recording media based on the M(TI)S nanostructures promising for fast processing of highly informativemore » images and to fabrication of optoelectronic correlators of images for noncoherent light.« less

Co-crystallization of cholesterol and calcium phosphate as related to atherosclerosis

NASA Astrophysics Data System (ADS)

Hirsch, Danielle; Azoury, Reuven; Sarig, Sara

1990-09-01

Calcification of atherosclerotic plaques occurs very frequently and aggravates the disease. In biological systems, epitaxial relationships between crystal structures may be important in nucleating the deposit of a solid phase. The biologically preferred calcium phosphate species, apatite, and cholesterol crystal have structurally compatible crystallographic faces which allow epitaxial growth of one crystal upon another. The present study describes a new approach to explore, in vitro, the crystallization processes of calcium phosphate (CaP) with cholesterol (CS) and cholestanol (CN) which are related to atherosclerosis. Aqueous solutions containing calcium and phosphate ions or CaP crystals as hydroxyapatite were added into saturated ethanolic solutions of CS or CS and 10% CN. After precipitation, crystals were collected and analyzed by nuclear magnetic resonance (NMR), infra-red (IR), X-ray, scanning electron microscope (SEM-LINK), differential scanning calorimeter (DSC) and atomic absorption. The principal result is the well-formed crystals precipitation when an aqueous solution and CaP seed crystals were added to saturated solutions of CS and 10% CN. Cholesterol-cholestanol dihydrate (CC2W) crystals precipitated in the presence of CaP seeds were compared to the CC2W crystals obtained without the mineral compound. The results of this comparison indicate a special link between crystals of CaP and CC2W, and support the epitaxial relationship between the two kinds of crystals. The potential of CC2W crystals to be precipitated by CaP seed crystals prove likewise the possible significant role of the cholestanol metabolite in the process of cholesterol crystallization and calcification in the arteries.

Pin-Hole Free Perovskite Film for Solar Cells Application Prepared by Controlled Two-Step Spin-Coating Method

NASA Astrophysics Data System (ADS)

Bahtiar, A.; Rahmanita, S.; Inayatie, Y. D.

2017-05-01

Morphology of perovskite film is a key important for achieving high performance perovskite solar cells. Perovskite films are commonly prepared by two-step spin-coating method. However, pin-holes are frequently formed in perovskite films due to incomplete conversion of lead-iodide (PbI2) into perovskite CH3NH3PbI3. Pin-holes in perovskite film cause large hysteresis in current-voltage curve of solar cells due to large series resistance between perovskite layer-hole transport material. Moreover, crystal structure and grain size of perovskite crystal are also other important parameters for achieving high performance solar cells, which are significantly affected by preparation of perovskite film. We studied the effect of preparation of perovskite film using controlled spin-coating parameters on crystal structure and morphological properties of perovskite film. We used two-step spin-coating method for preparation of perovskite film with varied spinning speed, spinning time and temperature of spin-coating process to control growth of perovskite crystal aimed to produce high quality perovskite crystal with pin-hole free and large grain size. All experiment was performed in air with high humidity (larger than 80%). The best crystal structure, pin-hole free with large grain crystal size of perovskite film was obtained from film prepared at room temperature with spinning speed 1000 rpm for 20 seconds and annealed at 100°C for 300 seconds.

Bulk growth of <001> organic nonlinear optical (NLO) L-arginine 4-nitrophenolate 4-nitrophenol dihydrate (LAPP) single crystals by SR method

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

Pandian, Muthu Senthil, E-mail: senthilpandianm@ssn.edu.in; Sivasubramani, V.; Ramasamy, P.

2015-06-24

A transparent uniaxial L-arginine 4-nitrophenolate 4-nitrophenol dehydrate (LAPP) single crystal having dimension of 20 mm diameter and 45 mm length was grown by Sankaranarayanan-Ramasamy (SR) method with a growth rate of 1 mm per day. Using an identical solution the conventional crystal grown to a dimension of 8×5×5 mm{sup 3} was obtained over a period of 30 days. The crystal structure has been confirmed by single crystal X-ray diffraction measurement. The crystalline perfection of LAPP crystals grown by slow evaporation solution technique (SEST) and SR method were characterized using Vickers microhardness, UV-Vis NIR, chemical etching, dark and photo current measurements. The above study indicatesmore » that the crystal quality of the Sankaranarayanan-Ramasamy (SR) method grown LAPP is good compared to the conventional method grown crystal.« less

Systematic Improvement of Protein Crystals by Determining the Supersolubility Curves of Phase Diagrams

PubMed Central

Saridakis, Emmanuel; Chayen, Naomi E.

2003-01-01

A systematic approach for improving protein crystals by growing them in the metastable zone using the vapor diffusion technique is described. This is a simple technique for optimization of crystallization conditions. Screening around known conditions is performed to establish a working phase diagram for the crystallization of the protein. Dilutions of the crystallization drops across the supersolubility curve into the metastable zone are then carried out as follows: the coverslips holding the hanging drops are transferred, after being incubated for some time at conditions normally giving many small crystals, over reservoirs at concentrations which normally yield clear drops. Fewer, much larger crystals are obtained when the incubation times are optimized, compared with conventional crystallization at similar conditions. This systematic approach has led to the structure determination of the light-harvesting protein C-phycocyanin to the highest-ever resolution of 1.45 Å. PMID:12547801

Preliminary X-ray crystallographic analysis of SMU.573, a putative sugar kinase from Streptococcus mutans

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

Zhou, Yan-Feng; Li, Lan-Fen; Yang, Cheng

2008-01-01

SMU.573 from S. mutans was expressed in E. coli and crystallized. The crystals belong to space group I4 and 2.5 Å resolution diffraction data were collected at an in-house chromium radiation source. SMU.573 from Streptococcus mutans is a structurally and functionally uncharacterized protein that was selected for structural biology studies. Native and SeMet-labelled proteins were expressed with an N-His tag in Escherichia coli BL21 (DE3) and purified by Ni{sup 2+}-chelating and size-exclusion chromatography. Crystals of the SeMet-labelled protein were obtained by the hanging-drop vapour-diffusion method and a 2.5 Å resolution diffraction data set was collected using an in-house chromium radiationmore » source. The crystals belong to space group I4, with unit-cell parameters a = b = 96.53, c = 56.26 Å, α = β = γ = 90°.« less

Synthesis and structure identification of 2-amino-4, 6- dimethyl pyrimidine with gallic acid and pimelic acid

NASA Astrophysics Data System (ADS)

Mekala, R.; Jagdish, P.; Mathammal, R.

2018-07-01

Reaction of 2-amino-4, 6- dimethyl pyrimidine with carboxylic acid such as gallic acid and pimelic acid, yielded a salt and co-crystal, respectively. The new crystal forms were obtained from slow evaporation technique. The crystal structure and hydrogen bond interaction of the two crystals were determined by single X-ray diffraction analysis. Inter molecular interactions of the compounds were investigated using the 3D Hirshfeld surfaces and the associated 2D fingerprint plots. The functional groups were identified by the FTIR, FT-Raman spectral studies. The presence of carbon and hydrogen in the two samples were identified by the 1H and 13C NMR analysis. The excited energy was observed using UV-Visible spectral analysis. The fluorescence spectra revealed the emission state of the two samples. The thermal behaviour and stability of the two compounds were evaluated by the TGA-DSC analysis.

The Preparation and Characterization of Natrolite Synthetized by Purified Attapulgite

NASA Astrophysics Data System (ADS)

Li, H. J.; Zhou, X. D.; Zhang, J. M.; Wu, X. Y.; Gao, H. B.

2017-06-01

This paper mainly researched the hydrothermal synthesis of Natrolite, using amorphous silicon source from the purified attapulgite. The effects of silicon source, silicon aluminum ratio, crystallization time and crystallization temperature on the synthesis of natrolite were investigated. The results showed that the optimal synthesis condition of natrolite was: Hydrothermal activated ATP with NaOH was silicon source, silicon aluminum ratio was 10:1, crystallization time lasted to 72h and crystallization temperature was 150°C, the template was removed by calcining 8 hours at 550°C. The structural formula of obtained natrolite is Na2Al2Si3O10•2H2O.

A short review of theoretical and empirical models for characterization of optical materials doped with the transition metal and rare earth ions

NASA Astrophysics Data System (ADS)

Su, P.; Ma, C.-G.; Brik, M. G.; Srivastava, A. M.

2018-05-01

In this paper, a brief retrospective review of the main developments in crystal field theory is provided. We have examined how different crystal field models are applied to solve the problems that arise in the spectroscopy of optically active ions. Attention is focused on the joint application of crystal field and density functional theory (DFT) based models, which takes advantages of strong features of both individual approaches and allows for obtaining a complementary picture of the electronic properties of a doped crystal with impurity energy levels superimposed onto the host band structure.

Structure of Leishmania major Methionyl-tRNA Synthetase in Complex with Intermediate Products Methionyladenylate and Pyrophosphate

PubMed Central

Larson, Eric T.; Kim, Jessica E.; Zucker, Frank H.; Kelley, Angela; Mueller, Natascha; Napuli, Alberto J.; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G.J.

2011-01-01

Leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions people at risk. Due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from Leishmania major in hopes of creating a platform for the rational design of new therapeutics. Crystals of the catalytic core of methionyl-tRNA synthetase from L. major (LmMetRS) were obtained with the substrates MgATP and methionine present in the crystallization medium. These crystals yielded the 2.0 Å resolution structure of LmMetRS in complex with two products, methionyladenylate and pyrophosphate, along with a Mg2+ ion that bridges them. This is the first class I aminoacyl-tRNA synthetase (aaRS) structure with pyrophosphate bound. The residues of the class I aaRS signature sequence motifs, KISKS and HIGH, make numerous contacts with the pyrophosphate. Substantial differences between the LmMetRS structure and previously reported complexes of E. coli MetRS (EcMetRS) with analogs of the methionyladenylate intermediate product are observed, even though one of these analogs only differs by one atom from the intermediate. The source of these structural differences is attributed to the presence of the product pyrophosphate in LmMetRS. Analysis of the LmMetRS structure in light of the Aquifex aeolicus MetRS-tRNAMet complex shows that major rearrangements of multiple structural elements of enzyme and/or tRNA are required to allow the CCA acceptor triplet to reach the methionyladenylate intermediate in the active site. Comparison with sequences of human cytosolic and mitochondrial MetRS reveals interesting differences near the ATP- and methionine-binding regions of LmMetRS, suggesting that it should be possible to obtain compounds that selectively inhibit the parasite enzyme. PMID:21144880

Enzyme catalysis captured using multiple structures from one crystal at varying temperatures.

PubMed

Horrell, Sam; Kekilli, Demet; Sen, Kakali; Owen, Robin L; Dworkowski, Florian S N; Antonyuk, Svetlana V; Keal, Thomas W; Yong, Chin W; Eady, Robert R; Hasnain, S Samar; Strange, Richard W; Hough, Michael A

2018-05-01

High-resolution crystal structures of enzymes in relevant redox states have transformed our understanding of enzyme catalysis. Recent developments have demonstrated that X-rays can be used, via the generation of solvated electrons, to drive reactions in crystals at cryogenic temperatures (100 K) to generate 'structural movies' of enzyme reactions. However, a serious limitation at these temperatures is that protein conformational motion can be significantly supressed. Here, the recently developed MSOX (multiple serial structures from one crystal) approach has been applied to nitrite-bound copper nitrite reductase at room temperature and at 190 K, close to the glass transition. During both series of multiple structures, nitrite was initially observed in a 'top-hat' geometry, which was rapidly transformed to a 'side-on' configuration before conversion to side-on NO, followed by dissociation of NO and substitution by water to reform the resting state. Density functional theory calculations indicate that the top-hat orientation corresponds to the oxidized type 2 copper site, while the side-on orientation is consistent with the reduced state. It is demonstrated that substrate-to-product conversion within the crystal occurs at a lower radiation dose at 190 K, allowing more of the enzyme catalytic cycle to be captured at high resolution than in the previous 100 K experiment. At room temperature the reaction was very rapid, but it remained possible to generate and characterize several structural states. These experiments open up the possibility of obtaining MSOX structural movies at multiple temperatures (MSOX-VT), providing an unparallelled level of structural information during catalysis for redox enzymes.

Characterization of Structural Defects in Wide Band-Gap Compound Materials for Semiconductor and Opto-Electronic Applications

NASA Astrophysics Data System (ADS)

Goue, Ouloide Yannick

Single crystals of binary and ternary compounds are touted to replace silicon for specialized applications in the semiconductor industry. However, the relative high density of structural defects in those crystals has hampered the performance of devices built on them. In order to enhance the performance of those devices, structurally perfect single crystals must be grown. The aim of this thesis is to investigate the interplay between crystal growth process and crystal quality as well as structural defect types and transport property. To this end, the thesis is divided into two parts. The first part provides a general review of the theory of crystal growth (chapter I), an introduction to the materials being investigated (chapter II and III) and the characterization techniques being used (chapter IV). • In chapter I, a brief description of the theory of crystal growth is provided with an eye towards the driving force behind crystal nucleation and growth along with the kinetic factors affecting crystal growth. The case of crystal growth of silicon carbide (SiC) by physical vapor transport (PVT) and chemical vapor deposition (CVD) is discussed. The Bridgman, travelling heater method (THM) and physical transport growth of cadmium zinc telluride (CZT) is also treated. In chapters II and III, we introduce the compound materials being investigated in this study. While a description of their crystal structure and properties is provided, the issues associated with their growth are discussed. In chapter IV, a description of the characterization techniques used in these studies is presented. These techniques are synchrotron X-ray topography (SXRT), transmission electron microscopy, transmission infrared microscopy (TIM), micro-Raman spectroscopy (muRS) and light microscopy. Extensive treatment of SXRT technique is also provided. In the second part, the experimental results obtained in the course of these studies are presented and discussed. These results are divided into three subsections. • The development of a new technique for the production of large and high quality silicon carbide single crystal boule is proposed. This technique herein referred to as Large Tapered Crystal (LTC) growth consists of two steps: growth of long SiC rod crystal by solvent-laser heated floating zone (Solvent-LHFZ) and lateral expansion of a seed by hot wall chemical vapor deposition (HWCVD). Solvent-LHFZ was successful as SiC rod crystals, replicating the polytype structure of the starting seed, were achieved at a growth rate varying from 4 to 100mum/hr. However, SXRT revealed the presence of an inhomogeneous strain in the grown crystal rod. This was further confirmed by SEM images, which showed the platelet-like morphology of the growth front with pockets in which iron (Fe)-rich material from the Fe solvent is trapped. It was furthermore observed that at high Fe to Si ratio (˜1.9), no growth was achieved. HWCVD enlargement was also successful as SiC boules, replicating the polytype structure of the starting seed, were achieved at growth rate of about 180mum/hr. The boules had a faceted hexagonal morphology with a strain-free surface marked by steps. Combination of SXRT, TEM and muRS revealed the presence of stacking disorder in the seed (3C, 4H and 15R-SiC) that replicated in the homoepitaxial layer. The formation of the observed stacking disorder is attributed to the low energy difference between stacking configurations on the growth surface as proposed by Takahashi and Ohtani. • The influence of structural defect type and distribution on minority carrier lifetime in 4H-SiC epilayers was investigated. Structural defect type and distribution map was obtained using SXRT, whereas minority carrier lifetime map was obtained using muPCD. Decrease in carrier lifetime observed from muPCD map was associated with specific structural defects such as low angle grain boundaries (LAGBs), stacking faults (SFs), interfacial dislocations (IDs), half loop arrays (HLAs) as well as basal plane dislocations (BPDs) pinned at TSDs. While the effect of morphological defects was mitigated, combination of defects such as microcracks, overlapping triangular defects and BPD half loops were observed to reduce carrier lifetime. Furthermore, regions of high dislocation density were associated with low carrier lifetime. • Finally, the effect of cadmium (Cd) overpressure on the quality of cadmium zinc telluride crystal ingots was investigated for two set of samples (set 1 and 2). Overall, high resistivity single crystals were achieved. Evaluation of the crystal quality by SXRT revealed that under certain Cd overpressures and growth conditions, the quality of the grown boule improved. Similarly, transmission infrared (IR) microscopy showed a correlation between the size/density and distribution of Te inclusions/precipitates and Cd overpressure. The size of Te inclusions was observed to decrease as a function of Cd overpressure as predicted from partial pressure data for stoichiometric melt. The best improvement in crystalline quality were observed for samples from set 1at a Cd reservoir of 785 °C and for set 2 samples for a Cd reservoir at 825 °C. This difference in Cd reservoir temperature for stoichiometric growth between set 1 and set 2 was attributed to other factors such as rate of cooling of Cd reservoir, rate of cooling of the crystal along with control of the melt interface. The summary of these results and the implication of this growth approach for producing high quality CZT single crystals are discussed.

Dependence of Internal Crystal Structures of InAs Nanowires on Electrical Characteristics of Field Effect Transistors

NASA Astrophysics Data System (ADS)

Han, Sangmoon; Choi, Ilgyu; Lee, Kwanjae; Lee, Cheul-Ro; Lee, Seoung-Ki; Hwang, Jeongwoo; Chung, Dong Chul; Kim, Jin Soo

2018-02-01

We report on the dependence of internal crystal structures on the electrical properties of a catalyst-free and undoped InAs nanowire (NW) formed on a Si(111) substrate by metal-organic chemical vapor deposition. Cross-sectional transmission electron microscopy images, obtained from four different positions of a single InAs NW, indicated that the wurtzite (WZ) structure with stacking faults was observed mostly in the bottom region of the NW. Vertically along the InAs NW, the amount of stacking faults decreased and a zinc-blende (ZB) structure was observed. At the top of the NW, the ZB structure was prominently observed. The resistance and resistivity of the top region of the undoped InAs NW with the ZB structure were measured to be 121.5 kΩ and 0.19 Ω cm, respectively, which are smaller than those of the bottom region with the WZ structure, i.e., 251.8 kΩ and 0.39 Ω cm, respectively. The reduction in the resistance of the top region of the NW is attributed to the improvement in the crystal quality and the change in the ZB crystal structure. For a field effect transistor with an undoped InAs NW channel, the drain current versus drain-source voltage characteristic curves under various negative gate-source voltages were successfully observed at room temperature.

Liquid crystals of carbon nanotubes and graphene.

PubMed

Zakri, Cécile; Blanc, Christophe; Grelet, Eric; Zamora-Ledezma, Camilo; Puech, Nicolas; Anglaret, Eric; Poulin, Philippe

2013-04-13

Liquid crystal ordering is an opportunity to develop novel materials and applications with spontaneously aligned nanotubes or graphene particles. Nevertheless, achieving high orientational order parameter and large monodomains remains a challenge. In addition, our restricted knowledge of the structure of the currently available materials is a limitation for fundamental studies and future applications. This paper presents recent methodologies that have been developed to achieve large monodomains of nematic liquid crystals. These allow quantification and increase of their order parameters. Nematic ordering provides an efficient way to prepare conductive films that exhibit anisotropic properties. In particular, it is shown how the electrical conductivity anisotropy increases with the order parameter of the nematic liquid crystal. The order parameter can be tuned by controlling the length and entanglement of the nanotubes. In the second part of the paper, recent results on graphene liquid crystals are reported. The possibility to obtain water-based liquid crystals stabilized by surfactant molecules is demonstrated. Structural and thermodynamic characterizations provide indirect but statistical information on the dimensions of the graphene flakes. From a general point of view, this work presents experimental approaches to optimize the use of nanocarbons as liquid crystals and provides new methodologies for the still challenging characterization of such materials.

Automated preparation method for colloidal crystal arrays of monodisperse and binary colloid mixtures by contact printing with a pintool plotter.

PubMed

Burkert, Klaus; Neumann, Thomas; Wang, Jianjun; Jonas, Ulrich; Knoll, Wolfgang; Ottleben, Holger

2007-03-13

Photonic crystals and photonic band gap materials with periodic variation of the dielectric constant in the submicrometer range exhibit unique optical properties such as opalescence, optical stop bands, and photonic band gaps. As such, they represent attractive materials for the active elements in sensor arrays. Colloidal crystals, which are 3D gratings leading to Bragg diffraction, are one potential precursor of such optical materials. They have gained particular interest in many technological areas as a result of their specific properties and ease of fabrication. Although basic techniques for the preparation of regular patterns of colloidal crystals on structured substrates by self-assembly of mesoscopic particles are known, the efficient fabrication of colloidal crystal arrays by simple contact printing has not yet been reported. In this article, we present a spotting technique used to produce a microarray comprising up to 9600 single addressable sensor fields of colloidal crystal structures with dimensions down to 100 mum on a microfabricated substrate in different formats. Both monodisperse colloidal crystals and binary colloidal crystal systems were prepared by contact printing of polystyrene particles in aqueous suspension. The array morphology was characterized by optical light microscopy and scanning electron microscopy, which revealed regularly ordered crystalline structures for both systems. In the case of binary crystals, the influence of the concentration ratio of the large and small particles in the printing suspension on the obtained crystal structure was investigated. The optical properties of the colloidal crystal arrays were characterized by reflection spectroscopy. To examine the stop bands of the colloidal crystal arrays in a high-throughput fashion, an optical setup based on a CCD camera was realized that allowed the simultaneous readout of all of the reflection spectra of several thousand sensor fields per array in parallel. In agreement with Bragg's relation, the investigated arrays exhibited strong opalescence and stop bands in the expected wavelength range, confirming the successful formation of highly ordered colloidal crystals. Furthermore, a narrow distribution of wavelength-dependent stop bands across the sensor array was achieved, demonstrating the capability of producing highly reproducible crystal spots by the contact printing method with a pintool plotter.

Ultraviolet Laser Lithography of Titania Photonic Crystals for Terahertz-Wave Modulation.

PubMed

Kirihara, Soshu; Nonaka, Koki; Kisanuki, Shoichiro; Nozaki, Hirotoshi; Sakaguchi, Keito

2018-05-18

Three-dimensional (3D) microphotonic crystals with a diamond structure composed of titania microlattices were fabricated using ultraviolet laser lithography, and the bandgap properties in the terahertz (THz) electromagnetic-wave frequency region were investigated. An acrylic resin paste with titania fine particle dispersions was used as the raw material for additive manufacturing. By scanning a spread paste surface with an ultraviolet laser beam, two-dimensional solid patterns were dewaxed and sintered. Subsequently, 3D structures with a relative density of 97% were created via layer lamination and joining. A titania diamond lattice with a lattice constant density of 240 µm was obtained. The properties of the electromagnetic wave were measured using a THz time-domain spectrometer. In the transmission spectra for the Γ-X direction, a forbidden band was observed from 0.26 THz to 0.44 THz. The frequency range of the bandgap agreed well with calculated results obtained using the plane⁻wave expansion method. Additionally, results of a simulation via transmission-line modeling indicated that a localized mode can be obtained by introducing a plane defect between twinned diamond lattice structures.

The statistical kinematical theory of X-ray diffraction as applied to reciprocal-space mapping

PubMed

Nesterets; Punegov

2000-11-01

The statistical kinematical X-ray diffraction theory is developed to describe reciprocal-space maps (RSMs) from deformed crystals with defects of the structure. The general solutions for coherent and diffuse components of the scattered intensity in reciprocal space are derived. As an example, the explicit expressions for intensity distributions in the case of spherical defects and of a mosaic crystal were obtained. The theory takes into account the instrumental function of the triple-crystal diffractometer and can therefore be used for experimental data analysis.

Computational analysis of heat transfer, thermal stress and dislocation density during resistively Czochralski growth of germanium single crystal

NASA Astrophysics Data System (ADS)

Tavakoli, Mohammad Hossein; Renani, Elahe Kabiri; Honarmandnia, Mohtaram; Ezheiyan, Mahdi

2018-02-01

In this paper, a set of numerical simulations of fluid flow, temperature gradient, thermal stress and dislocation density for a Czochralski setup used to grow IR optical-grade Ge single crystal have been done for different stages of the growth process. A two-dimensional steady state finite element method has been applied for all calculations. The obtained numerical results reveal that the thermal field, thermal stress and dislocation structure are mainly dependent on the crystal height, heat radiation and gas flow in the growth system.

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

PubMed

Martí-Rujas, Javier; Kawano, Masaki

2013-02-19

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

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.

Biochemical and Structural Properties of a Thermostable Mercuric Ion Reductase from Metallosphaera sedula

PubMed Central

Artz, Jacob H.; White, Spencer N.; Zadvornyy, Oleg A.; Fugate, Corey J.; Hicks, Danny; Gauss, George H.; Posewitz, Matthew C.; Boyd, Eric S.; Peters, John W.

2015-01-01

Mercuric ion reductase (MerA), a mercury detoxification enzyme, has been tuned by evolution to have high specificity for mercuric ions (Hg2+) and to catalyze their reduction to a more volatile, less toxic elemental form. Here, we present a biochemical and structural characterization of MerA from the thermophilic crenarchaeon Metallosphaera sedula. MerA from M. sedula is a thermostable enzyme, and remains active after extended incubation at 97°C. At 37°C, the NADPH oxidation-linked Hg2+ reduction specific activity was found to be 1.9 μmol/min⋅mg, increasing to 3.1 μmol/min⋅mg at 70°C. M. sedula MerA crystals were obtained and the structure was solved to 1.6 Å, representing the first solved crystal structure of a thermophilic MerA. Comparison of both the crystal structure and amino acid sequence of MerA from M. sedula to mesophillic counterparts provides new insights into the structural determinants that underpin the thermal stability of the enzyme. PMID:26217660

Effect of scanning velocity on femtosecond laser-induced periodic surface structures on HgCdTe crystal

NASA Astrophysics Data System (ADS)

Gu, Hongan; Dai, Ye; Wang, Haodong; Yan, Xiaona; Ma, Guohong

2017-12-01

In this paper, a femtosecond laser line-scanning irradiation was used to induce the periodic surface microstructure on HgCdTe crystal. Low spatial frequency laser induced periodic surface structures of 650-770 nm and high spatial frequency laser induced periodic surface structures of 152-246 nm were respectively found with different scanning speeds. The evolution process from low spatial frequency laser induced periodic surface structures to high spatial frequency laser induced periodic surface structures is characterized by scanning electron microscope. Their spatial periods deduced by using a two-dimensional Fourier transformation partly agree with the predictions of the Sipe-Drude theory. Confocal micro-Raman spectral show that the atomic arrangement of induced low spatial frequency laser-induced structures are basically consistent with the crystal in the central area of laser-scanning line, however a new peak at 164 cm-1 for the CdTe-like mode becomes evident due to the Hg vaporization when strong laser ablation happens. The obtained surface periodic ripples may have applications in fabricating advanced infrared detector.

The prediction of crystal structure by merging knowledge methods with first principles quantum mechanics

NASA Astrophysics Data System (ADS)

Ceder, Gerbrand

2007-03-01

The prediction of structure is a key problem in computational materials science that forms the platform on which rational materials design can be performed. Finding structure by traditional optimization methods on quantum mechanical energy models is not possible due to the complexity and high dimensionality of the coordinate space. An unusual, but efficient solution to this problem can be obtained by merging ideas from heuristic and ab initio methods: In the same way that scientist build empirical rules by observation of experimental trends, we have developed machine learning approaches that extract knowledge from a large set of experimental information and a database of over 15,000 first principles computations, and used these to rapidly direct accurate quantum mechanical techniques to the lowest energy crystal structure of a material. Knowledge is captured in a Bayesian probability network that relates the probability to find a particular crystal structure at a given composition to structure and energy information at other compositions. We show that this approach is highly efficient in finding the ground states of binary metallic alloys and can be easily generalized to more complex systems.

The mold integration method for the calculation of the crystal-fluid interfacial free energy from simulations

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

Espinosa, J. R.; Vega, C.; Sanz, E.

2014-10-07

The interfacial free energy between a crystal and a fluid, γ{sub cf}, is a highly relevant parameter in phenomena such as wetting or crystal nucleation and growth. Due to the difficulty of measuring γ{sub cf} experimentally, computer simulations are often used to study the crystal-fluid interface. Here, we present a novel simulation methodology for the calculation of γ{sub cf}. The methodology consists in using a mold composed of potential energy wells to induce the formation of a crystal slab in the fluid at coexistence conditions. This induction is done along a reversible pathway along which the free energy difference betweenmore » the initial and the final states is obtained by means of thermodynamic integration. The structure of the mold is given by that of the crystal lattice planes, which allows to easily obtain the free energy for different crystal orientations. The method is validated by calculating γ{sub cf} for previously studied systems, namely, the hard spheres and the Lennard-Jones systems. Our results for the latter show that the method is accurate enough to deal with the anisotropy of γ{sub cf} with respect to the crystal orientation. We also calculate γ{sub cf} for a recently proposed continuous version of the hard sphere potential and obtain the same γ{sub cf} as for the pure hard sphere system. The method can be implemented both in Monte Carlo and Molecular Dynamics. In fact, we show that it can be easily used in combination with the popular Molecular Dynamics package GROMACS.« less

Novel fluorescence adjustable photonic crystal materials

NASA Astrophysics Data System (ADS)

Zhu, Cheng; Liu, Xiaoxia; Ni, Yaru; Fang, Jiaojiao; Fang, Liang; Lu, Chunhua; Xu, Zhongzi

2017-11-01

Novel photonic crystal materials (PCMs) with adjustable fluorescence were fabricated by distributing organic fluorescent powders of Yb0.2Er0.4Tm0.4(TTA)3Phen into the opal structures of self-assembled silica photonic crystals (PCs). Via removing the silica solution in a constant speed, PCs with controllable thicknesses and different periodic sizes were obtained on glass slides. Yb0.2Er0.4Tm0.4(TTA)3Phen powders were subsequently distributed into the opal structures. The structures and optical properties of the prepared PCMs were investigated. Finite-difference-time-domain (FDTD) calculation was used to further analyze the electric field distributions in PCs with different periodic sizes while the relation between periodic sizes and fluorescent spectra of PCMs was discussed. The results showed that the emission color of the PCMs under irradiation of 980 nm laser can be easily adjusted from green to blue by increasing the periodic size from 250 to 450 nm.

Synthesis and Crystal Structure of a New Ruthenium Silicophosphate: RuP 3SiO 11

NASA Astrophysics Data System (ADS)

Fukuoka, Hiroshi; Imoto, Hideo; Saito, Taro

1996-01-01

A new ruthenium silicophosphate RuP3SiO11was obtained and the structure was determined by single-crystal X-ray diffraction. It crystallizes in the trigonal space groupR3cwitha= 8.253(3)Å,c= 39.317(4)Å,V= 2319(2)Å3,Z= 12,R= 0.029, andRW= 0.026. The structure is composed of RuO6, Si2O7, and P2O7units. The Si2O7unit shares the six oxygen atoms with six P2O7units, while the P2O7unit shares the six oxygen atoms with two Si2O7units and four RuO6octahedra. The anionic part forms an infinite three-dimensional network of silicophosphate. RuP3SiO11is isotypic with MoP3SiO11.

Optical spectra and band structure of Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals: experiment and theory.

PubMed

Reshak, A H; Parasyuk, O V; Fedorchuk, A O; Kamarudin, H; Auluck, S; Chyský, J

2013-12-05

Theoretical and experimental studies of the Ag(x)Ga(x)Ge(1-x)Se2 (x = 0.333, 0.250, 0.200, 0.167) single crystals are performed. These crystals possess a lot of intrinsic defects which are responsible for their optoelectronic features. The theoretical investigations were performed by means of DFT calculations using different exchange-correlation potentials. The experimental studies were carried out using the modulated VUV ellipsometry for dielectric constants and birefringence studies. The comparison of the structure obtained from X-ray with the theoretically optimized structure is presented. The crucial role of the intrinsic defect states is manifested in the choice of the exchange correlation potential used. The data may be applicable for a large number of the ternary chalcogenides which are sensitive to the presence of the local disordered states near the band edges.

Crystallization and preliminary X-ray analysis of native and selenomethionyl vinorine synthase from Rauvolfia serpentina.

PubMed

Ma, Xueyan; Koepke, Juergen; Bayer, Anja; Fritzsch, Günter; Michel, Hartmut; Stöckigt, Joachim

2005-06-01

Vinorine synthase (VS) is a central enzyme of the biosynthesis of the antiarrhythmic drug ajmaline and is a member of the BAHD superfamily of acyltransferases. So far, no three-dimensional structure with significant sequence homology with VS is known. Crystals of VS and selenomethionyl-labelled VS from the medicinal plant Rauvolfia serpentina have been obtained by the hanging-drop technique at 305 K with ammonium sulfate and PEG 400 as precipitants. VS crystals diffract to 2.8 A and belong to space group P2(1)2(1)2(1), with unit-cell parameters a = 82.3, b = 89.6, c = 136.2 A. The selenomethionyl VS crystal was nearly isomorphous with the VS crystal.

Growth, structural, optical, thermal and mechanical properties of cytosinium hydrogen selenite: A novel nonlinear optical single crystal

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

Jaikumar, P.; Sathiskumar, S.; Balakrishnan, T., E-mail: balacrystalgrowth@gmail.com

Highlights: • Growth of bulk single crystals of cytosinium hydrogen selenite (CHS) is reported. • Dielectric constant of CHS is measured as a function of Frequency and temperature. • Lower cut off value of UV–vis-NIR spectrum of CHS crystal is observed at 210 nm. • Meyer’s index value of CHS crystal calculated identifies it as a soft material. • Powder SHG efficiency of CHS is about 1.5 times that of KDP crystal. - Abstract: A novel nonlinear optical single crystal of cytosinium hydrogen selenite was grown from aqueous solution of cytosinium hydrogen selenite by slow solvent evaporation method at roommore » temperature. The structural properties of grown crystal have been studied by single crystal and powder X-ray diffraction analysis. Presence of various functional groups was identified from Fourier transform infrared spectroscopy. The optical transmittance and absorbance spectra were recorded by UV–vis-NIR spectrometer and the grown crystal possesses good transparency in the entire visible region. The dielectric constant and dielectric loss of the crystal were calculated as a function of frequency at different temperatures. The mechanical strength of the cytosinium hydrogen selenite crystal was estimated using Vicker’s microhardness tester. Etch patterns of the cytosinium hydrogen selenite crystal were obtained using distilled water as etchant for different etching time. Second harmonic generation efficiency tested using Nd:YAG laser is about 1.5 times that of KDP.« less

Direct Observation of Protein Microcrystals in Crystallization Buffer by Atmospheric Scanning Electron Microscopy

PubMed Central

Maruyama, Yuusuke; Ebihara, Tatsuhiko; Nishiyama, Hidetoshi; Konyuba, Yuji; Senda, Miki; Numaga-Tomita, Takuro; Senda, Toshiya; Suga, Mitsuo; Sato, Chikara

2012-01-01

X-ray crystallography requires high quality crystals above a given size. This requirement not only limits the proteins to be analyzed, but also reduces the speed of the structure determination. Indeed, the tertiary structures of many physiologically important proteins remain elusive because of the so-called “crystallization bottleneck”. Once microcrystals have been obtained, crystallization conditions can be optimized to produce bigger and better crystals. However, the identification of microcrystals can be difficult due to the resolution limit of optical microscopy. Electron microscopy has sometimes been utilized instead, with the disadvantage that the microcrystals usually must be observed in vacuum, which precludes the usage for crystal screening. The atmospheric scanning electron microscope (ASEM) allows samples to be observed in solution. Here, we report the use of this instrument in combination with a special thin-membrane dish with a crystallization well. It was possible to observe protein crystals of lysozyme, lipase B and a histone chaperone TAF-Iβ in crystallization buffers, without the use of staining procedures. The smallest crystals observed with ASEM were a few μm in width, and ASEM can be used with non-transparent solutions. Furthermore, the growth of salt crystals could be monitored in the ASEM, and the difference in contrast between salt and protein crystals made it easy to distinguish between these two types of microcrystals. These results indicate that the ASEM could be an important new tool for the screening of protein microcrystals. PMID:22949879

Direct observation of protein microcrystals in crystallization buffer by atmospheric scanning electron microscopy.

PubMed

Maruyama, Yuusuke; Ebihara, Tatsuhiko; Nishiyama, Hidetoshi; Konyuba, Yuji; Senda, Miki; Numaga-Tomita, Takuro; Senda, Toshiya; Suga, Mitsuo; Sato, Chikara

2012-01-01

X-ray crystallography requires high quality crystals above a given size. This requirement not only limits the proteins to be analyzed, but also reduces the speed of the structure determination. Indeed, the tertiary structures of many physiologically important proteins remain elusive because of the so-called "crystallization bottleneck". Once microcrystals have been obtained, crystallization conditions can be optimized to produce bigger and better crystals. However, the identification of microcrystals can be difficult due to the resolution limit of optical microscopy. Electron microscopy has sometimes been utilized instead, with the disadvantage that the microcrystals usually must be observed in vacuum, which precludes the usage for crystal screening. The atmospheric scanning electron microscope (ASEM) allows samples to be observed in solution. Here, we report the use of this instrument in combination with a special thin-membrane dish with a crystallization well. It was possible to observe protein crystals of lysozyme, lipase B and a histone chaperone TAF-Iβ in crystallization buffers, without the use of staining procedures. The smallest crystals observed with ASEM were a few μm in width, and ASEM can be used with non-transparent solutions. Furthermore, the growth of salt crystals could be monitored in the ASEM, and the difference in contrast between salt and protein crystals made it easy to distinguish between these two types of microcrystals. These results indicate that the ASEM could be an important new tool for the screening of protein microcrystals.

New structural phase obtained by exerting high pressure on (Br2)n@AFI composite material

NASA Astrophysics Data System (ADS)

Yao, Zhen; Lv, Jia-Yin; Liu, Bo; Liu, Bing-Bing; Yang, Bai

2018-06-01

In this paper, we present a theoretical study on the high-pressure behaviors of a (Br2)n@AlPO4-5 (AFI) peapod structure. The influence of the encapsulated Br2 molecule on the structural deformation of AFI crystal is analyzed using the volume-pressure function. The bonding process of the linearly arrayed Br2 molecule transferring to the bromine atomic chain is analyzed by the electron density distribution. A new high-pressure phase with P2 point group symmetry is obtained as the pressure increases to 34 GPa. In addition, electron density difference calculations are used to study the systematic charge transformation. Further analysis indicates that the encapsulated Br2 molecules can significantly modify the electronic structure of the AFI crystal. The band gap of the (Br2)n@AFI decreases with pressure and closes at 9 GPa. Moreover, the calculated bulk modulus and electronic properties indicate that the new structural phase is metallic with a high hardness, providing a new strategy for exploring novel nanomaterials.

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

Antao, S.M.

The crystal structure of a biogenic aragonite from the nacre of an ammonite shell was obtained using synchrotron high-resolution powder X-ray diffraction (HRPXRD) data and Rietveld structure refinement. The well-preserved ammonite sample is from Alberta, Canada, and is from the Cretaceous period. The aragonite structure was refined in space group Pmcn, Z = 4, and the cell parameters obtained are a = 4.96265(2), b = 7.97016(4), c = 5.74474(3) {angstrom}, and V = 227.222(2) {angstrom}{sup 3}. The chemical analyses indicate a formula of [Ca{sub 0.995}Sr{sub 0.004}Ba{sub 0.001}]{Sigma} = 1.0(CO{sub 3}). The average and distances are 2.5281(3) and 1.2871(6)more » {angstrom}, respectively, and the average angle is 119.94(8){sup o}. The CO{sub 3} groups are non-planar. Based on crystal-structure data for biogenic and non-biogenic aragonite samples, aragonite from ammonite nacre has minimal structural distortions and is very similar to non-biogenic aragonite, in particular, a sample from Spain.« less

A Few Good Crystals Please

NASA Technical Reports Server (NTRS)

Judge, Russell A.; Snell, Edward H.

1999-01-01

Part of the challenge of macromolecular crystal growth for structure determination is obtaining an appropriate number of crystals with a crystal volume suitable for X-ray analysis. In this respect an understanding of the effect of solution conditions on macromolecule nucleation rates is advantageous. This study investigated the effects of solution conditions on the nucleation rate and final crystal size of two crystal systems; tetragonal lysozyme and glucose isomerase. Batch crystallization plates were prepared at given solution concentration and incubated at set temperatures over one week. The number of crystals per well with their size and axial ratios were recorded and correlated with solution conditions. Duplicate experiments indicate the reproducibility of the technique. Results for each system showing the effect of supersaturation, incubation temperature and solution pH on nucleation rates will be presented and discussed. In the case of lysozyme, having optimized solution conditions to produce an appropriate number of crystals of a suitable size, a batch of crystals were prepared under exactly the same conditions. Fifty of these crystals were analyzed by x-ray techniques. The results indicate that even under the same crystallization conditions, a marked variation in crystal properties exists.

Biochemical, spectroscopic and X-ray structural analysis of deuterated multicopper oxidase CueO prepared from a new expression construct for neutron crystallography.

PubMed

Akter, Mahfuza; Inoue, Chika; Komori, Hirofumi; Matsuda, Nana; Sakurai, Takeshi; Kataoka, Kunishige; Higuchi, Yoshiki; Shibata, Naoki

2016-10-01

Multicopper oxidases oxidize various phenolic and nonphenolic compounds by using molecular oxygen as an electron acceptor to produce water. A multicopper oxidase protein, CueO, from Escherichia coli is involved in copper homeostasis in the bacterial cell. Although X-ray crystallographic studies have been conducted, the reduction mechanism of oxygen and the proton-transfer pathway remain unclear owing to the difficulty in identifying H atoms from X-ray diffraction data alone. To elucidate the reaction mechanism using neutron crystallography, a preparation system for obtaining large, high-quality single crystals of deuterated CueO was developed. Tiny crystals were obtained from the deuterated CueO initially prepared from the original construct. The X-ray crystal structure of the deuterated CueO showed that the protein contained an incompletely truncated signal sequence at the N-terminus, which resulted in the heterogeneity of the protein sample for crystallization. Here, a new CueO expression system that had an HRV3C cleavage site just after the signal sequence was constructed. Deuterated CueO from the new construct was expressed in cells cultured in deuterated algae-extract medium and the signal sequence was completely eliminated by HRV3C protease. The deuteration level of the purified protein was estimated by MALDI-TOF mass spectrometry to be at least 83.2% compared with nondeuterated protein. Nondeuterated CueO crystallized in space group P2 1 , with unit-cell parameters a = 49.51, b = 88.79, c = 53.95 Å, β = 94.24°, and deuterated CueO crystallized in space group P2 1 2 1 2 1 , with unit-cell parameters a = 49.91, b = 106.92, c = 262.89 Å. The crystallographic parameters for the crystals of the new construct were different from those previously reported for nondeuterated crystals. The nondeuterated and deuterated CueO from the new construct had similar UV-Vis spectra, enzymatic activities and overall structure and geometry of the ligands of the Cu atoms in the active site to those of previously reported CueO structures. These results indicate that the CueO protein prepared using the new construct is suitable for further neutron diffraction studies.

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

Jaffe, Adam; Lin, Yu; Beavers, Christine M.

Here, we report the first high-pressure single-crystal structures of hybrid perovskites. The crystalline semiconductors (MA)PbX 3 (MA = CH 3NH 3 +, X = Br – or I –) afford us the rare opportunity of understanding how compression modulates their structures and thereby their optoelectronic properties. Using atomic coordinates obtained from high-pressure single-crystal X-ray diffraction we track the perovskites’ precise structural evolution upon compression. These structural changes correlate well with pressure-dependent single-crystal photoluminescence (PL) spectra and high-pressure bandgaps derived from density functional theory. We further observe dramatic piezochromism where the solids become lighter in color and then transition to opaquemore » black with compression. Indeed, electronic conductivity measurements of (MA)PbI 3 obtained within a diamond-anvil cell show that the material’s resistivity decreases by 3 orders of magnitude between 0 and 51 GPa. The activation energy for conduction at 51 GPa is only 13.2(3) meV, suggesting that the perovskite is approaching a metallic state. Furthermore, the pressure response of mixed-halide perovskites shows new luminescent states that emerge at elevated pressures. We recently reported that the perovskites (MA)Pb(Br xI 1–x) 3 (0.2 < x < 1) reversibly form light-induced trap states, which pin their PL to a low energy. This may explain the low voltages obtained from solar cells employing these absorbers. Our high-pressure PL data indicate that compression can mitigate this PL redshift and may afford higher steady-state voltages from these absorbers. These studies show that pressure can significantly alter the transport and thermodynamic properties of these technologically important semiconductors.« less

Investigation of the influence of vanadium, iron and nickel dopants on the morphology, and crystal structure and photocatalytic properties of titanium dioxide based nanopowders.

PubMed

Shao, Godlisten N; Jeon, Sun-Jeong; Haider, M Salman; Abbass, Nadir; Kim, Hee Taik

2016-07-15

Photoactive V, Fe and Ni doped TiO2 (M-TiO2) nanopowders were synthesized by a modified two-step sol-gel process in the absence of additives. Titanium oxychloride, which is a rarely-used TiO2 precursor was used to yield M-TiO2 photocatalysts with preferential photochemical performance in the presence of natural solar irradiation. The obtained samples were calcined at different calcination temperatures ranging from 450 to 800°C to evaluate the influence of the sintering on the physicochemical properties. The properties of the obtained samples were examined by XRF, XRD, Raman spectroscopy, UV-visible DRS, XPS, nitrogen gas physisorption studies, SEM-EDAX and HRTEM analyses. Structural characterization of the samples revealed the incorporation of these transition metal element into TiO2. It was also depicted that the morphology, crystal structure, optical and photochemical properties of the obtained samples were largely dependent on the calcination temperature and the type of dopant used during the preparation process. The photochemical performance of the samples was investigated in the photodegradation of methylene blue in the presence of natural sunlight. The experimental results indicated that the VT600 sample possessed the highest activity due to its superior properties. This study provides a systematic preparation and selection of the precursor, dopant and calcination temperature that are suitable for the formation of TiO2-based heterogeneous photocatalysts with appealing morphology, crystal structure, optical and photochemical properties for myriad of applications. Copyright © 2016 Elsevier Inc. All rights reserved.

Magnetic and magnetostrictive behavior of Dy 3+ doped CoFe 2O 4 single crystals grown by flux method

NASA Astrophysics Data System (ADS)

Kambale, Rahul C.; Song, K. M.; Won, C. J.; Lee, K. D.; Hur, N.

2012-02-01

We studied the effect of Dy 3+ content on the magnetic properties of cobalt ferrite single crystal. The single crystals of CoFe 1.9Dy 0.1O 4 were grown by the flux method using Na 2B 4O 7.10 H 2O (Borax) as a solvent (flux). The black and shiny single crystals were obtained as a product. The X-ray diffraction analysis at room temperature confirmed the spinel cubic structure with lattice constant a=8.42 Å of the single crystals. The compositional analysis endorses the presence of constituents Co, Fe and Dy elements after sintering at 1300 °C within the final structure. The magnetic hysteresis measurements at various temperatures viz. 10 K, 100 K, 200 K and 300 K reveal the soft ferrimagnetic nature of the single crystal than that of for pure CoFe 2O 4. The observed saturation magnetization ( Ms) and coercivity ( Hc) are found to be lower than that of pure CoFe 2O 4 single crystal. The magnetostriction ( λ) measurement was carried out along the [001] direction. The magnetic measurements lead to conclude that the present single crystals can be used for magneto-optic recording media.

Interatomic Potentials for Structure Simulation of Alkaline-Earth Cuprates

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

Eremin, N.N.; Leonyuk, L.I.; Urusov, V.S.

2001-05-01

A specific potential model of interionic interactions was derived in which the crystal structures of alkaline-earth cuprates were satisfactorily described and some of their physical properties were predicted. It was found that a harmonic three-particle O-Cu-O potential and some Morse-type contributions to the simple Buckingham-type Cu-O repulsive potential enable one to improve essentially the results of crystal structure modeling for cuprates. The obtained potential set seems to be well transferable for different cuprates, despite the variety in linkages of the CuO{sub 4} groups. In the present work this potential set model was applied in the crystal structure modeling for Ca{submore » 2}CuO{sub 3}, CaCuO{sub 2}, SrCuO{sub 3}, (Sr{sub 1.19}Ca{sub 0.73})Cu{sub 2}O{sub 4}, and BaCuO{sub 2}. Some elastic and energetic properties of the compounds under question were predicted.« less

Synthesis, spectral, structural prediction and computational studies of octylcarbazole ornamented 3-phenothiazinal

NASA Astrophysics Data System (ADS)

Karuppasamy, Ayyanar; Udhaya kumar, Chandran; Karthikeyan, Subramanian; Velayutham Pillai, Muthiah Pillai; Ramalingan, Chennan

2017-11-01

A novel conjugated octylcarbazole ornamented 3-phenothiazinal, 10-(9-octyl-9H-carbazol-3-yl)-10H-phenothiazine-3-carbaldehyde (OCPTC) was synthesized and fully characterized by 1H-NMR, 13C-NMR, elemental and single crystal XRD analyses. The optimized geometrical structure, vibrational frequencies and NMR have been computed with M06-2X method using 6-31+G(d,p) basis set. Total electronic energies and HOMO-LUMO energy gaps in gas phase are discussed. The geometrical parameters of the title compound obtained from single crystal XRD studies have been found in accord with the calculated (DFT) values. The experimental and theoretical FT-IR and NMR results of the title molecule have been investigated. The experimentally observed vibrational frequencies have been compared with the calculated ones, which are in good agreement with each other. Single crystal X-ray structural analysis of OCPTC, evidences the ''butterfly conformation'' of phenothiazine ring with nearly perpendicular orientation of the carbazole structural motif to the phenothiazine moiety.

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy.

PubMed

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

High-throughput search of ternary chalcogenides for p-type transparent electrodes

PubMed Central

Shi, Jingming; Cerqueira, Tiago F. T.; Cui, Wenwen; Nogueira, Fernando; Botti, Silvana; Marques, Miguel A. L.

2017-01-01

Delafossite crystals are fascinating ternary oxides that have demonstrated transparent conductivity and ambipolar doping. Here we use a high-throughput approach based on density functional theory to find delafossite and related layered phases of composition ABX2, where A and B are elements of the periodic table, and X is a chalcogen (O, S, Se, and Te). From the 15 624 compounds studied in the trigonal delafossite prototype structure, 285 are within 50 meV/atom from the convex hull of stability. These compounds are further investigated using global structural prediction methods to obtain their lowest-energy crystal structure. We find 79 systems not present in the materials project database that are thermodynamically stable and crystallize in the delafossite or in closely related structures. These novel phases are then characterized by calculating their band gaps and hole effective masses. This characterization unveils a large diversity of properties, ranging from normal metals, magnetic metals, and some candidate compounds for p-type transparent electrodes. PMID:28266587

Unravelling surface and interfacial structures of a metal-organic framework by transmission electron microscopy

NASA Astrophysics Data System (ADS)

Zhu, Yihan; Ciston, Jim; Zheng, Bin; Miao, Xiaohe; Czarnik, Cory; Pan, Yichang; Sougrat, Rachid; Lai, Zhiping; Hsiung, Chia-En; Yao, Kexin; Pinnau, Ingo; Pan, Ming; Han, Yu

2017-05-01

Metal-organic frameworks (MOFs) are crystalline porous materials with designable topology, porosity and functionality, having promising applications in gas storage and separation, ion conduction and catalysis. It is challenging to observe MOFs with transmission electron microscopy (TEM) due to the extreme instability of MOFs upon electron beam irradiation. Here, we use a direct-detection electron-counting camera to acquire TEM images of the MOF ZIF-8 with an ultralow dose of 4.1 electrons per square ångström to retain the structural integrity. The obtained image involves structural information transferred up to 2.1 Å, allowing the resolution of individual atomic columns of Zn and organic linkers in the framework. Furthermore, TEM reveals important local structural features of ZIF-8 crystals that cannot be identified by diffraction techniques, including armchair-type surface terminations and coherent interfaces between assembled crystals. These observations allow us to understand how ZIF-8 crystals self-assemble and the subsequent influence of interfacial cavities on mass transport of guest molecules.

Syntheses, crystal structures and properties of novel copper(II) complexes obtained by reactions of copper(II) sulfate pentahydrate with tripodal ligands.

PubMed

Zhao, Wei; Fan, Jian; Song, You; Kawaguchi, Hiroyuki; Okamura, Taka-aki; Sun, Wei-Yin; Ueyama, Norikazu

2005-04-21

Three novel metal-organic frameworks (MOFs), [Cu(1)SO4].H2O (4), [Cu2(2)2(SO4)2].4H2O (5) and [Cu(3)(H2O)]SO4.5.5H2O (6), were obtained by hydrothermal reactions of CuSO4.5H2O with the corresponding ligands, which have different flexibility. The structures of the synthesized complexes were determined by single-crystal X-ray diffraction analyses. Complex 4 has a 2D network structure with two types of metallacycles. Complex 5 also has a 2D network structure in which each independent 2D sheet contains two sub-layers bridged by oxygen atoms of the sulfate anions. Complex 6 has a 2D puckered structure in which the sulfate anions serve as counter anions, which are different from those in complexes 4 (terminators) and 5 (bridges). The different structures of complexes 4, 5 and 6 indicate that the nature of organic ligands affected the structures of the assemblies greatly. The magnetic behavior of complex 5 and anion-exchange properties of complex 6 were investigated.

Enrofloxacinium citrate monohydrate: Preparation, crystal structure, thermal stability and IR-characterization

NASA Astrophysics Data System (ADS)

Golovnev, Nicolay N.; Vasiliev, Alexander D.; Kirik, Sergei D.

2012-08-01

Enrofloxacinium citrate monohydrate (I), CHFNO3+·CHO7-·HO, [C19H22FN3O3 - enrofloxacin, EnrH] has been crystallized from the mutual solution of citric acid and enrofloxacin in ambient conditions. The colorless crystals have been investigated using X-ray single crystal and powder techniques, and characterized by differential scanning calorimetry, thermogravimetry and infrared spectroscopy. The obtained compound can be considered as a salt with enrofloxacinium in the role of a cation and citrate as an anion. The ions ratio equals to 1:1. The compound crystallizes in the triclinic lattice with a = 9.0489(8) Å, b = 9.6531(8) Å, c = 14.913(1) Å, α = 98.813(1)°, β = 92.029(1)°, γ = 91.013(1)°, Z = 2, V = 1286.1(2) Å3, S.G. P1¯. The crystal structure determination reveals the importance of inter- and intramolecular interactions in the crystal formation. The EnrH2+ and HCit molecular ions are packed in alternating layers with water molecules inserted into the citrate layers. A citrate ion in the layer is linked via H-bondings with two adjacent ones and three water molecules. Enrofloxacinium cations are packaged by means of a benched mode and every cation is linked by three intermolecular thymus type H-bondings with nitrogens of adjacent cations and by two links with the oxygen of the citrate ions. The infrared spectra gave the evidence of H-bonding formation in the obtained salt. The π-stacking interactions are observed between the aromatic cycles of the adjacent cations which are located in an antiparallel style in a layer.

Synthesis, Crystal Structure, and Magnetic Properties of the YbFeTi2O7 Compound

NASA Astrophysics Data System (ADS)

Drokina, T. V.; Petrakovskii, G. A.; Molokeev, M. S.; Velikanov, D. A.

2018-03-01

We report on the synthesis conductions and results of experimental investigations of the crystal structure and magnetic properties of a new magnetic compound YbFeTi2O7. According to the X-ray diffractometry data, the crystal structure of the investigated compound is described by the rhombic space group Pcnb with unit cell parameters of a = 9.8115(1) Å, b = 13.5106(2) Å, and c = 7.31302(9) Å and atomic disordering in the distribution of iron ions Fe3+ over five structural sites. The magnetic measurements in the lowtemperature region revealed a kink in the temperature dependence of the magnetic moment and its dependence on the sample magnetic prehistory. The experimental results obtained suggest that with a decrease in temperature the sample passes from the paramagnetic state to the spin-glass-like magnetic state characterized by a freezing temperature of T f = 4.5 K at the preferred antiferromagnetic exchange coupling in the sample spin system. The chemical pressure variation upon replacement of rare-earth ion R by Yb in the RFeTi2O7 system does not change the crystal lattice symmetry and magnetic state.

Structural characterization, AC conductivity, optical properties and biochemical study of a new hybrid phosphate: Scavenger of free radicals

NASA Astrophysics Data System (ADS)

Fezai, Ramzi; Hemissi, Hanene; Mezni, Ali; Rzaigui, Mohamed

2017-12-01

Single crystal of the hybrid compound [p-(F)C6H4NH3]6P6O18·2H2O has been grown with sizes up to 0.65 × 0.45 × 0.3 mm3 by the slow evaporation method. The crystal structure of this material was determined by single crystal X-ray diffraction. It crystallizes in the triclinic space group P 1 bar with the lattice parameters a = 10.16(3) Å, b = 15.87(3) Å, c = 16.36(4) Å, α = 80.93(2)°, β = 85.92(18)°, γ = 85.31(2)°, V = 2591.1(12) Å3 and Z = 2. Its crystal structure is a packing of alternated inorganic and organic layers parallel to (a, c) planes. The cohesion of the structure is essentially ensured by a hydrogen bonding network as well as electrostatic and Van Der Waals interactions and also F…F interactions so as to increase the stability of the 3D-network. The effect of the nature of the substituent in para-position with respect to amine group on obtained structures and on other studied properties was discussed. Crystal symmetry is confirmed by 31P MAS-NMR. Furthermore, IR characteristics and thermal analysis are given. The luminescent properties of this material have been carried out at room temperature based on UV absorption spectroscopy data. AC conductivity of this compound has been investigated by means of impedance spectroscopy measurements in the 303-383 K temperature range. The antioxidant study was determined, in vitro, using 1,1-diphenyl-2-picrylhydrazyl (DPPH), hydroxyl radical and reducing power and with ascorbic acid as a control. X-rays structural results are correlated with electrical and antioxidant findings.

Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.

PubMed

Sripathi, Kamali N; Tay, Wendy W; Banáš, Pavel; Otyepka, Michal; Šponer, Jiří; Walter, Nils G

2014-07-01

The hepatitis delta virus (HDV) ribozyme is a member of the class of small, self-cleaving catalytic RNAs found in a wide range of genomes from HDV to human. Both pre- and post-catalysis (precursor and product) crystal structures of the cis-acting genomic HDV ribozyme have been determined. These structures, together with extensive solution probing, have suggested that a significant conformational change accompanies catalysis. A recent crystal structure of a trans-acting precursor, obtained at low pH and by molecular replacement from the previous product conformation, conforms to the product, raising the possibility that it represents an activated conformer past the conformational change. Here, using fluorescence resonance energy transfer (FRET), we discovered that cleavage of this ribozyme at physiological pH is accompanied by a structural lengthening in magnitude comparable to previous trans-acting HDV ribozymes. Conformational heterogeneity observed by FRET in solution appears to have been removed upon crystallization. Analysis of a total of 1.8 µsec of molecular dynamics (MD) simulations showed that the crystallographically unresolved cleavage site conformation is likely correctly modeled after the hammerhead ribozyme, but that crystal contacts and the removal of several 2'-oxygens near the scissile phosphate compromise catalytic in-line fitness. A cis-acting version of the ribozyme exhibits a more dynamic active site, while a G-1 residue upstream of the scissile phosphate favors poor fitness, allowing us to rationalize corresponding changes in catalytic activity. Based on these data, we propose that the available crystal structures of the HDV ribozyme represent intermediates on an overall rugged RNA folding free-energy landscape. © 2014 Sripathi et al.; Published by Cold Spring Harbor Laboratory Press for the RNA Society.

Fine tuning of optical signals in nanoporous anodic alumina photonic crystals by apodized sinusoidal pulse anodisation.

PubMed

Santos, Abel; Law, Cheryl Suwen; Chin Lei, Dominique Wong; Pereira, Taj; Losic, Dusan

2016-11-03

In this study, we present an advanced nanofabrication approach to produce gradient-index photonic crystal structures based on nanoporous anodic alumina. An apodization strategy is for the first time applied to a sinusoidal pulse anodisation process in order to engineer the photonic stop band of nanoporous anodic alumina (NAA) in depth. Four apodization functions are explored, including linear positive, linear negative, logarithmic positive and logarithmic negative, with the aim of finely tuning the characteristic photonic stop band of these photonic crystal structures. We systematically analyse the effect of the amplitude difference (from 0.105 to 0.840 mA cm -2 ), the pore widening time (from 0 to 6 min), the anodisation period (from 650 to 950 s) and the anodisation time (from 15 to 30 h) on the quality and the position of the characteristic photonic stop band and the interferometric colour of these photonic crystal structures using the aforementioned apodization functions. Our results reveal that a logarithmic negative apodisation function is the most optimal approach to obtain unprecedented well-resolved and narrow photonic stop bands across the UV-visible-NIR spectrum of NAA-based gradient-index photonic crystals. Our study establishes a fully comprehensive rationale towards the development of unique NAA-based photonic crystal structures with finely engineered optical properties for advanced photonic devices such as ultra-sensitive optical sensors, selective optical filters and all-optical platforms for quantum computing.

A phase width for CaGaSn. Crystal structure of mixed intermetallic Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} and SmGa{sub x}Sn{sub 3−x}, stability, geometry and electronic structure

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

Tillard, Monique, E-mail: mtillard@univ-montp2.fr

X-ray single-crystal structure has been established for new compositions in intermetallic systems of tin and gallium. Crystals were successfully obtained in alloys prepared from elements. The structure of SmGaSn{sub 2} (cubic Pm3̄m, a=4.5778(8) Å, Z=1, R1=0.012) is described with atomic disorder at all Sn/Ga positions and the structure of Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} (hexagonal, P6{sub 3}/mmc, a=4.2233(9), c=17.601(7) Å, Z=1, R1=0.062) raises an interesting question about existence of a composition domain for CaGaSn. Finally, Ca{sub 4}Ga{sub 4.9}Sn{sub 3.1} should be considered as a particular composition of Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}, a compound assumed to exist in the range x ~more » 0−1. Partial atomic ordering characterizes the Sn/Ga puckered layers of hexagons whose geometries are analyzed and discussed comparatively with analogous arrangements in AlB{sub 2} related hexagonal compounds. The study is supported by rigid band model and DFT calculations performed for different experimental and hypothetic arrangements. - Graphical abstract: A phase width for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x} belonging to the hexagonal YPtAs structure-type. - Highlights: • Single crystals of mixed tin gallium ternary intermetallics were obtained. • Partial ordering at metal sites and phase width are evidenced for Ca{sub 4}Ga{sub 4+x}Sn{sub 4−x}. • Layer deviation to flatness is studied comparatively with related structures. • Geometry and stability analyses based on DFT calculations are provided.« less

Solid state structural investigations of the bis(chalcone) compound with single crystal X-ray crystallography, DFT, gamma-ray spectroscopy and chemical spectroscopy methods

NASA Astrophysics Data System (ADS)

Yakalı, Gül; Biçer, Abdullah; Eke, Canel; Cin, Günseli Turgut

2018-04-01

A bis(chalcone), (2E,6E)-2,6-bis((E)-3phenylallidene)cyclohexanone, was characterized by 1H NMR, 13C NMR, FTIR, UV-Vis spectroscopy, gamma-ray spectroscopy and single crystal X- ray structural analysis. The optimized molecular structure of the compound is calculated using DFT/B3LYP with 6-31G (d,p) level. The calculated geometrical parameters are in good agreement with the experimental data obtained from our reported X-ray structure. The powder and single crystal compounds were gama-irradiated using clinical electron linear accelerator and 60Co gamma-ray source, respectively. Spectral studies (1H NMR, 13C NMR, FTIR and UV-Vis) of powder chalcone compound were also investigated before and after irradiation. Depending on the irradiation notable changes were observed in spectral features powder sample. Single crystal X-ray diffraction investigation shows that both unirradiated and irradiated single crystal samples crystallizes in a orthorhombic crystal system in the centrosymmetric space group Pbcn and exhibits an C-H..O intramolecular and intermolecular hydrogen bonds. The crystal packing is stabilised by strong intermolecular bifurcate C-H..O hydrogen bonds and π…π stacking interactions. The asymmetric unit of the title compound contains one-half of a molecule. The other half of the molecule is generated with (1-x,y,-3/2-z) symmetry operator. The molecule is almost planar due to having π conjugated system of chalcones. However, irradiated single crystal compound showed significant changes lattice parameters, crystal volume and density. According to results of gamma-ray spectroscopy, radioactive elements of powder compound which are 123Sb(n,g),124Sb,57Fe(g,p),56Mn, 55Mn(g,n), and 54Mn were determined using photoactivation analysis. However, the most intensive gamma-ray energy signals are 124Sb.

Preparation and Optical Properties of Spherical Inverse Opals by Liquid Phase Deposition Using Spherical Colloidal Crystals

NASA Astrophysics Data System (ADS)

Aoi, Y.; Tominaga, T.

2013-03-01

Titanium dioxide (TiO2) inverse opals in spherical shape were prepared by liquid phase deposition (LPD) using spherical colloidal crystals as templates. Spherical colloidal crystals were produced by ink-jet drying technique. Aqueous emulsion droplets that contain polystyrene latex particles were ejected into air and dried. Closely packed colloidal crystals with spherical shape were obtained. The obtained spherical colloidal crystals were used as templates for the LPD. The templates were dispersed in the deposition solution of the LPD, i.e. a mixed solution of ammonium hexafluorotitanate and boric acid and reacted for 4 h at 30 °C. After the LPD process, the interstitial spaces of the spherical colloidal crystals were completely filled with titanium oxide. Subsequent heat treatment resulted in removal of templates and spherical titanium dioxide inverse opals. The spherical shape of the template was retained. SEM observations indicated that the periodic ordered voids were surrounded by titanium dioxide. The optical reflectance spectra indicated that the optical properties of the spherical titanium dioxide inverse opals were due to Bragg diffractions from the ordered structure. Filling in the voids of the inverse opals with different solvents caused remarkable changes in the reflectance peak.

Novel growth techniques of group-IV based semiconductors on insulator for next-generation electronics

NASA Astrophysics Data System (ADS)

Miyao, Masanobu; Sadoh, Taizoh

2017-05-01

Recent progress in the crystal growth of group-IV-based semiconductor-on-insulators is reviewed from physical and technological viewpoints. Liquid-phase growth based on SiGe-mixing-triggered rapid-melting growth enables formation of hybrid (100) (110) (111)-orientation Ge-on-insulator (GOI) structures, which show defect-free GOI with very high carrier mobility (˜1040 cm2 V-1 s-1). Additionally, SiGe mixed-crystals with laterally uniform composition were obtained by eliminating segregation phenomena during the melt-back process. Low-temperature solid-phase growth has been explored by combining this process with ion-beam irradiation, additional doping of group-IV elements, metal induced lateral crystallization with/without electric field, and metal-induced layer exchange crystallization. These efforts have enabled crystal growth on insulators below 400 °C, achieving high carrier mobility (160-320 cm2 V-1 s-1). Moreover, orientation-controlled SiGe and Ge films on insulators have been obtained below the softening temperatures of conventional plastic films (˜300 °C). Detailed characterization provides an understanding of physical phenomena behind these crystal growth techniques. Applying these methods when fabricating next-generation electronics is also discussed.

Cloning, purification, crystallization and preliminary X-ray crystallographic analysis of MCAT from Synechocystis sp. PCC 6803.

PubMed

Liu, Yinghui; Zhang, Yanming; Cao, Xupeng; Xue, Song

2013-11-01

Malonyl-coenzymeA:acyl-carrier protein transacylase (MCAT), which catalyzes the transfer of the malonyl group from malonyl-CoA to acyl-carrier protein (ACP), is an essential enzyme in type II fatty-acid synthesis. The enzyme MCAT from Synechocystis sp. PCC 6803 (spMCAT), the first MCAT counterpart from a cyanobacterium, was cloned, purified and crystallized in order to determine its three-dimensional crystal structure. A higher-quality crystal with better diffraction was obtained by crystallization optimization. The crystal diffracted to 1.8 Å resolution and belonged to the orthorhombic space group P2(1)2(1)2, with unit-cell parameters a = 43.22, b = 149.21, c = 40.59 Å. Matthews coefficient calculations indicated that the crystal contained one spMCAT molecule in the asymmetric unit with a Matthews coefficient of 2.18 Å(3) Da(-1) and a solvent content of 43.65%.

Crystal structure and vibrational spectra of melaminium arsenate

NASA Astrophysics Data System (ADS)

Anbalagan, G.; Marchewka, M. K.; Pawlus, K.; Kanagathara, N.

2015-01-01

The crystals of the new melaminium arsenate (MAS) [C3H7N6+ṡH2AsO4-] were obtained by the slow evaporation of an aqueous solution at room temperature. Single crystal X-ray diffraction analysis reveals that the crystal belongs to triclinic system with centro symmetric space group P-1. The crystals are built up from single protonated melaminium residues and single dissociated arsenate H2AsO4- anions. The protonated melaminium ring is almost planar. A combination of ionic and donor-acceptor hydrogen-bond interactions linking together the melaminium and arsenate residues forms a three-dimensional network. Vibrational spectroscopic analysis is reported on the basis of FT-IR and FT-Raman spectra recorded at room temperature. Hydrogen bonded network present in the crystal gives notable vibrational effect. DSC has also been performed for the crystal shows no phase transition in the studied temperature range (113-293 K).

Structures of NodZ α1,6-fucosyltransferase in complex with GDP and GDP-fucose

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

Brzezinski, Krzysztof; Polish Academy of Sciences, 61-704 Poznan; Dauter, Zbigniew

Crystal structures of the bacterial α1,6-fucosyltransferase NodZ in complex with GDP and GDP-fucose are presented. Rhizobial NodZ α1,6-fucosyltransferase (α1,6-FucT) catalyzes the transfer of the fucose (Fuc) moiety from guanosine 5′-diphosphate-β-l-fucose to the reducing end of the chitin oligosaccharide core during Nod-factor (NF) biosynthesis. NF is a key signalling molecule required for successful symbiosis with a legume host for atmospheric nitrogen fixation. To date, only two α1,6-FucT structures have been determined, both without any donor or acceptor molecule that could highlight the structural background of the catalytic mechanism. Here, the first crystal structures of α1,6-FucT in complex with its substrate GDP-Fucmore » and with GDP, which is a byproduct of the enzymatic reaction, are presented. The crystal of the complex with GDP-Fuc was obtained through soaking of native NodZ crystals with the ligand and its structure has been determined at 2.35 Å resolution. The fucose residue is exposed to solvent and is disordered. The enzyme–product complex crystal was obtained by cocrystallization with GDP and an acceptor molecule, penta-N-acetyl-l-glucosamine (penta-NAG). The structure has been determined at 1.98 Å resolution, showing that only the GDP molecule is present in the complex. In both structures the ligands are located in a cleft formed between the two domains of NodZ and extend towards the C-terminal domain, but their conformations differ significantly. The structures revealed that residues in three regions of the C-terminal domain, which are conserved among α1,2-, α1,6- and protein O-fucosyltransferases, are involved in interactions with the sugar-donor molecule. There is also an interaction with the side chain of Tyr45 in the N-terminal domain, which is very unusual for a GT-B-type glycosyltransferase. Only minor conformational changes of the protein backbone are observed upon ligand binding. The only exception is a movement of the loop located between strand βC2 and helix αC3. In addition, there is a shift of the αC3 helix itself upon GDP-Fuc binding.« less

Effective pore size and radius of capture for K+ ions in K-channels

PubMed Central

Moldenhauer, Hans; Díaz-Franulic, Ignacio; González-Nilo, Fernando; Naranjo, David

2016-01-01

Reconciling protein functional data with crystal structure is arduous because rare conformations or crystallization artifacts occur. Here we present a tool to validate the dimensions of open pore structures of potassium-selective ion channels. We used freely available algorithms to calculate the molecular contour of the pore to determine the effective internal pore radius (rE) in several K-channel crystal structures. rE was operationally defined as the radius of the biggest sphere able to enter the pore from the cytosolic side. We obtained consistent rE estimates for MthK and Kv1.2/2.1 structures, with rE = 5.3–5.9 Å and rE = 4.5–5.2 Å, respectively. We compared these structural estimates with functional assessments of the internal mouth radii of capture (rC) for two electrophysiological counterparts, the large conductance calcium activated K-channel (rC = 2.2 Å) and the Shaker Kv-channel (rC = 0.8 Å), for MthK and Kv1.2/2.1 structures, respectively. Calculating the difference between rE and rC, produced consistent size radii of 3.1–3.7 Å and 3.6–4.4 Å for hydrated K+ ions. These hydrated K+ estimates harmonize with others obtained with diverse experimental and theoretical methods. Thus, these findings validate MthK and the Kv1.2/2.1 structures as templates for open BK and Kv-channels, respectively. PMID:26831782

Preparation, characterization and crystal structures of three salts of the quaterpyridine ligand

NASA Astrophysics Data System (ADS)

Ciesielski, Artur; Stefankiewicz, Artur R.; Patroniak, Violetta; Kubicki, Maciej

2009-07-01

As a result of a reaction between 6,6'''-dimethyl-2,2':6',2'':6'',2'''-quaterpyridine C 22H 18N 4 and lanthanide(III) salts, compounds, [C 22H 20N 4] 2+·2(CF 3SO 3) - ( 1) and [C 22H 20N 4] 2+·2(ClO 4) - ( 2), have been obtained. They were characterized by spectroscopic techniques (ESI-MS, NMR, IR), elemental analysis, and their formulae were confirmed on the basis of X-ray crystallography. It turned out that the perchlorate crystallizes as two solvates: with acetonitrile and disordered water molecules. These are the first structural characterization of a 6,6'″-dimethyl-2,2':6',2″:6″,2'″-quaterpyridinium dication. Due to the intramolecular hydrogen bond it adopts the previously unobserved cis/trans/cis conformation. In all three crystals the dications have C i symmetry, they occupy the special positions in their respective space groups. In the crystal structures the π-π stacking and weak hydrogen bonds add directionality to the dominating electrostatic interactions between cations and anions.

Debranching and Crystallization of Waxy Maize Starch in Relation to Enzyme Digestibility

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

Cai, L.; Shi, Y; Rong, L

Molecular and crystal structures as well as morphology during debranching and crystallization of waxy maize starch at a high solid content (25%, w/w) were investigated, and the results were related to the digestibility of debranched products. The starch was cooked at 115-120 C for 10 min, cooled to 50 C and debranched by isoamylase. After 1 h of debranching, wormlike objects with 5-10 nm width and ca. 30 nm length were observed by transmission electron microscopy. Further release of linear chains and crystallization led to assembly of semi-crystalline structures in the form of nano-particles and subsequent growth of nano-particles intomore » large aggregates. After 24 h at 50 C, a debranched starch product with an A-type X-ray diffraction pattern, a high melting temperature (90-140 C), and high resistant starch content (71.4%) was obtained. Small-angle X-ray scattering results indicated that all debranched products were surface fractal in a dry state (4% moisture) but had a mass fractal structure when hydrated (e.g. 45% moisture).« less

Float zone growth and spectroscopic properties of Yb:CaYAlO4 single crystal for ultra-short pulse lasers

NASA Astrophysics Data System (ADS)

Narita, Moe; Higuchi, Mikio; Ogawa, Takayo; Wada, Satoshi; Miura, Akira; Tadanaga, Kiyoharu

2018-06-01

Yb:CaYAlO4 single crystals were grown by the floating zone method and their spectral properties were investigated. Void formation was effectively suppressed by using a feed rod of Y-rich composition with the aid of a double zone-pass technique. For the oxygen excess composition of Yb:Ca0.9925Y1.0075AlO4.00375, a void-free crystal was obtained by performing only the double zone-pass. On the other hand, for cation-deficient type of Yb:Ca0.9925Y1.005AlO4, void-free crystal could not be obtained by performing the double zone-pass. The void formation is attributable to the constitutional supercooling caused by segregation of main constituents of Y and Ca, and the congruent composition may exist in the Y-rich region with existence of interstitial excess oxide ions. The absorption cross section for σ-polarization was slightly larger than that for π-polarization, which is reasonable on the basis of the crystal structure of CaYAlO4.

Finite-Difference Time-Domain Analysis of Tapered Photonic Crystal Fiber

NASA Astrophysics Data System (ADS)

Ali, M. I. Md; Sanusidin, S. N.; Yusof, M. H. M.

2018-03-01

This paper brief about the simulation of tapered photonic crystal fiber (PCF) LMA-8 single-mode type based on correlation of scattering pattern at wavelength of 1.55 μm, analyzation of transmission spectrum at wavelength over the range of 1.0 until 2.5 μm and correlation of transmission spectrum with the refractive index change in photonic crystal holes with respect to taper size of 0.1 until 1.0 using Optiwave simulation software. The main objective is to simulate using Finite-Difference Time-Domain (FDTD) technique of tapered LMA-8 PCF and for sensing application by improving the capabilities of PCF without collapsing the crystal holes. The types of FDTD techniques used are scattering pattern and transverse transmission and principal component analysis (PCA) used as a mathematical tool to model the data obtained by MathCad software. The simulation results showed that there is no obvious correlation of scattering pattern at a wavelength of 1.55 μm, a correlation obtained between taper sizes with a transverse transmission and there is a parabolic relationship between the refractive index changes inside the crystal structure.

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

Ranieri, M.G.A., E-mail: gabi.ranieri@ig.com.br; Aguiar, E.C.; Cilense, M.

Highlights: • Bi{sub 4}Ti{sub 3}O{sub 12} thick films were obtained by SSR and PPM methods. • Both systems crystallize in an orthorhombic structure. • Textured characteristics were evidenced. • Grain morphology affects the P–E loops. - Abstract: Bismuth titanate powders (Bi{sub 4}Ti{sub 3}O{sub 12}-BIT) were fabricated by solid state reaction (SSR) and polymeric precursor method (PPM). From these powders, Bi{sub 4}Ti{sub 3}O{sub 12} pellets were obtained by tape-casting using plate-like templates particles prepared by a molten salt method. The BIT phase crystallizes in an orthorhombic structure type with space group Fmmm. Agglomeration of the particles, which affects the densification ofmore » the ceramic, electrical conduction and leakage current at high electric fields, was monitored by transmission electronic microscopy (TEM) analyses. FEG-SEM indicated that different shape of grains of BIT ceramics was influenced by the processing route. Both SSR and PPM methods lead to unsaturated P–E loops of BIT ceramics originating from the highly c-axis orientation and high conductivity which was affected by charge carriers flowing normally to the grain boundary of the crystal lattice.« less

Crystallization of FcpA from Leptospira, a novel flagellar protein that is essential for pathogenesis.

PubMed

San Martin, Fabiana; Mechaly, Ariel E; Larrieux, Nicole; Wunder, Elsio A; Ko, Albert I; Picardeau, Mathieu; Trajtenberg, Felipe; Buschiazzo, Alejandro

2017-03-01

The protein FcpA is a unique component of the flagellar filament of spirochete bacteria belonging to the genus Leptospira. Although it plays an essential role in translational motility and pathogenicity, no structures of FcpA homologues are currently available in the PDB. Its three-dimensional structure will unveil the novel motility mechanisms that render pathogenic Leptospira particularly efficient at invading and disseminating within their hosts, causing leptospirosis in humans and animals. FcpA from L. interrogans was purified and crystallized, but despite laborious attempts no useful X ray diffraction data could be obtained. This challenge was solved by expressing a close orthologue from the related saprophytic species L. biflexa. Three different crystal forms were obtained: a primitive and a centred monoclinic form, as well as a hexagonal variant. All forms diffracted X-rays to suitable resolutions for crystallographic analyses, with the hexagonal type typically reaching the highest limits of 2.0 Å and better. A variation of the quick-soaking procedure resulted in an iodide derivative that was instrumental for single-wavelength anomalous diffraction methods.

Crystal and molecular structure of N-(4-nitrophenyl)-β-alanine—Its vibrational spectra and theoretical calculations

NASA Astrophysics Data System (ADS)

Marchewka, M. K.; Drozd, M.; Janczak, J.

2011-08-01

The N-(4-nitrophenyl)-β-alanine in crystalline form directly by the addition of 4-nitroaniline to the acrylic acid in aqueous solution has been obtained. The title β-alanine derivative crystallizes in the P2 1/ c space group of monoclinic system with four molecules per unit cell. The X-ray geometry of β-alanine derivative molecule has been compared with those obtained by molecular orbital calculations corresponding to the gas phase. In the crystal the molecules related by an inversion center interact via symmetrically equivalent O-H⋯O hydrogen bonds with O⋯O distance of 2.656(2) Å forming a dimeric structure. The dimers of β-alanine derivative weakly interact via N-H⋯O hydrogen bonds between the H atom of β-amine groups and one of O atom of nitro groups. The room temperature powder vibrational (infrared and Raman) measurements are in accordance with the X-ray analysis. In aqueous solution of 4-nitroaniline and acrylic acid, the double C dbnd C bond of vinyl group of acrylic acid breaks as result of 4-nitroaniline addition.

L-Cysteine halogenides: A new family of salts with an L-cysteine⋯L-cysteinium dimeric cation

NASA Astrophysics Data System (ADS)

Ghazaryan, V. V.; Minkov, V. S.; Boldyreva, E. V.; Petrosyan, A. M.

2016-10-01

Two L-cysteinium-halogenides with (L-cysteine···L-cysteinium) dimeric cations have been obtained, (L-Cys⋯L-Cys+)·Cl-, and (L-Cys⋯L-Cys+)·Br-. Both salts crystallize in monoclinic space group P21. Although these salts have the same dimeric cations and isotypical halogen anions, crystal packing is different. The main difference between the two salts rests in the conformation of (L-Cys⋯L-Cys+) dimeric cation, which also differs from that of the dimeric cation in the previously reported compound L-Cys+(L-Cys⋯L-Cys+)·F-·(F-⋯HF). The dimeric cation is formed by a very short O-H⋯O hydrogen bond with d(O···O) of 2.449(2) Å and 2.435(11) Å in the chloride and bromide, respectively. In addition to crystal structure analysis, Infrared and Raman spectra have been registered and discussed with a particular focus on intermolecular interactions. The L-Cys+·Br-·H2O salt with a simple L-cysteinium cation was also obtained and the crystal structure solved. It resembles its chloride analogue, L-Cys+·Cl-·H2O.

Langmuir-Blodgett nanotemplates for protein crystallography.

PubMed

Pechkova, Eugenia; Nicolini, Claudio

2017-12-01

The new generation of synchrotrons and microfocused beamlines has enabled great progress in X-ray protein crystallography, resulting in new 3D atomic structures for proteins of high interest to the pharmaceutical industry and life sciences. It is, however, often still challenging to produce protein crystals of sufficient size and quality (order, intensity of diffraction, radiation stability). In this protocol, we provide instructions for performing the Langmuir-Blodgett (LB) nanotemplate method, a crystallization approach that can be used for any protein (including membrane proteins). We describe how to produce highly ordered 2D LB protein monolayers at the air-water interface and deposit them on glass slides. LB-film formation can be observed by surface-pressure measurements and Brewster angle microscopy (BAM), although its quality can be characterized by atomic force microscopy (AFM) and nanogravimetry. Such films are then used as a 2D template for triggering 3D protein crystal formation by hanging-drop vapor diffusion. The procedure for forming the 2D template takes a few minutes. Structural information about the protein reorganization in the LB film during the crystallization process on the nano level can be obtained using an in situ submicron GISAXS (grazing-incidence small-angle X-ray scattering) method. MicroGISAXS spectra, measured directly at the interface of the LB films and protein solution in real time, as described in this protocol, can be interpreted in terms of the buildup of layers, islands, or holes. In our experience, the obtained LB crystals take 1-10 d to prepare and they are more ordered and radiation stable as compared with those produced using other crystallization methods.

Room temperature aluminum antimonide radiation detector and methods thereof

DOEpatents

Lordi, Vincenzo; Wu, Kuang Jen J.; Aberg, Daniel; Erhart, Paul; Coombs, III, Arthur W; Sturm, Benjamin W

2015-03-03

In one embodiment, a method for producing a high-purity single crystal of aluminum antimonide (AlSb) includes providing a growing environment with which to grow a crystal, growing a single crystal of AlSb in the growing environment which comprises hydrogen (H.sub.2) gas to reduce oxide formation and subsequent incorporation of oxygen impurities in the crystal, and adding a controlled amount of at least one impurity to the growing environment to effectively incorporate at least one dopant into the crystal. In another embodiment, a high energy radiation detector includes a single high-purity crystal of AlSb, a supporting structure for the crystal, and logic for interpreting signals obtained from the crystal which is operable as a radiation detector at a temperature of about 25.degree. C. In one embodiment, a high-purity single crystal of AlSb includes AlSb and at least one dopant selected from a group consisting of selenium (Se), tellurium (Te), and tin (Sn).

Circularly polarized vacuum field in three-dimensional chiral photonic crystals probed by quantum dot emission

NASA Astrophysics Data System (ADS)

Takahashi, S.; Ota, Y.; Tajiri, T.; Tatebayashi, J.; Iwamoto, S.; Arakawa, Y.

2017-11-01

The modification of a circularly polarized vacuum field in three-dimensional chiral photonic crystals was measured by spontaneous emission from quantum dots in the structures. Due to the circularly polarized eigenmodes along the helical axis in the GaAs-based mirror-asymmetric structures we studied, we observed highly circularly polarized emission from the quantum dots. Both spectroscopic and time-resolved measurements confirmed that the obtained circularly polarized light was influenced by a large difference in the photonic density of states between the orthogonal components of the circular polarization in the vacuum field.

A New Method of Obtaining an n- p-Structure on the Basis of the Defective Semiconductor AgIn5S8

NASA Astrophysics Data System (ADS)

Guseinov, A. G.; Salmanov, V. M.; Mamedov, R. M.; Dzhabrailova, R.; Magomedov, A. Z.

2018-02-01

The type of electrical conductivity of A 1 B 3 5 C 6 8 semiconductor compounds with defective crystalline structure is modified by the influence of powerful laser radiation. It is shown that at certain power and wavelength of laser radiation acting on the single-crystal п-AgIn5S8, an area with the p-type of conductivity is formed in the irradiated region of the crystal. Current-voltage characteristics of homo-junctions created on the basis of n-AgIn5S8 are recorded.

Crystal structure of a new variety of lead dodecaborate Pb{sub 6}(Li{sub 0.65}Na{sub 0.19})[B{sub 12}O{sub 24}]I{sub 0.84} {center_dot} 0.168H{sub 2}O and its comparison with beryl and cordierite

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

Belokoneva, E. L., E-mail: elbel@geol.msu.ru; Derkach, I. K.; Dimitrova, O. V.

2013-05-15

Crystals of a new representative of ring-radical dodecaborates Pb{sub 6}(Li{sub 0.65}Na{sub 0.19})[B{sub 12}O{sub 24}]I{sub 0.84} {center_dot} 0.168H{sub 2}O, space group R3bar m , are obtained under hydrothermal conditions. The structure is determined with-out preliminary knowledge of the chemical formula. It is close to that of the Pb{sub 6}[B{sub 12}O{sub 24}] {center_dot} H{sub 2}O dodecaborate studied earlier, but unlike the latter structure it contains admixtures of iodide anion, lithium cation, and water molecule, which incompletely populate positions in channels. The formation of the second variety, which brings to light ion-exchange properties of the crystals, is due to mineralizing ions available inmore » the concen-trated solution in the course of crystallization. The new compound is compared with beryl and cordierite, which have close structures with channels capable of capturing various groups. Structures of synthetic Na and Ag dodecaborates with analogous but distorted ring dodecaborate radicals are discussed.« less

Crystal structure of Rb{sub 2}Mn{sub 3}(H{sub 2}O){sub 2}[P{sub 2}O{sub 7}]{sub 2}, a new representative of the family of hydrated diphosphates

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

Kiriukhina, G. V., E-mail: g-biralo@yandex.ru; Yakubovich, O. V.; Dimitrova, O. V.

2016-09-15

The crystal structure of Rb{sub 2}Mn{sub 3}(H{sub 2}O){sub 2}[P{sub 2}O{sub 7}]{sub 2}, a new phase obtained in the form of single crystals under hydrothermal conditions in the MnCl{sub 2}–Rb{sub 3}PO{sub 4}–H{sub 2}O system, is determined by X-ray diffraction (Xcalibur-S-CCD diffractometer, R = 0.0270): a = 9.374(2), b = 8.367(2), c = 9.437(2) Å, ß = 99.12(2)°, space group P2{sub 1}/c, Z = 2, D{sub x} = 3.27 g/cm{sup 3}. A correlation between the unit-cell parameters and the size of cations forming the crystal structures of isostructural A{sub 2}M{sub 3}(H{sub 2}O){sub 2}[P{sub 2}O{sub 7}]{sub 2} diphosphates (A = K, NH{sub 4},more » Rb, or Na; {sub M} = Mn, Fe, Co, or Ni) is revealed. It is shown that, due to the topological similarity, the structures of diphosphates and orthophosphates of the farringtonite structural type can undergo mutual transformations.« less

Crystal structure, detonation performance, and thermal stability of a new polynitro cage compound: 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptacyclo [5.5.1.1(3, 11).1 (5, 9)] pentadecane.

PubMed

Zhang, Jian-ying; Du, Hong-chen; Wang, Fang; Gong, Xue-dong; Ying, San-jiu

2012-06-01

A new polynitro cage compound 2, 4, 6, 8, 10, 12, 13, 14, 15-nonanitro-2, 4, 6, 8, 10, 12, 13, 14, 15-nonaazaheptcyclo [5.5.1.1(3,11).1(5,9)] pentadecane (NNNAHP) was designed in the present work. Its molecular structure was optimized at the B3LYP/6-31 G(d,p) level of density functional theory (DFT) and crystal structure was predicted using the Compass and Dreiding force fields and refined by DFT GGA-RPBE method. The obtained crystal structure of NNNAHP belongs to the P-1 space group and the lattice parameters are a = 9.99 Å, b = 10.78 Å, c = 9.99 Å, α = 90.01°, β = 120.01°, γ = 90.00°, and Z = 2, respectively. Based on the optimized crystal structure, the band gap, density of state, thermodynamic properties, infrared spectrum, strain energy, detonation characteristics, and thermal stability were predicted. Calculation results show that NNNAHP has detonation properties close to those of CL-20 and is a high energy density compound with moderate stability.

Synthesis, crystal structure, spectroscopic characterization, docking simulation and density functional studies of 1-(3,4-dimethoxyphenyl) -3-(4-flurophenyl)-propan-1-one

NASA Astrophysics Data System (ADS)

Khamees, Hussien Ahmed; Jyothi, Mahima; Khanum, Shaukath Ara; Madegowda, Mahendra

2018-06-01

The compound 1-(3,4-dimethoxyphenyl)-3-(4-flurophenyl)-propan-1-one (DFPO) was synthesized by Claisen-Schmidt condensation reaction and the single crystals were obtained by slow evaporation method. Three-dimensional structure was confirmed by single crystal X-ray diffraction method and exhibiting the triclinic crystal system with space group P-1. The crystal structure is stabilized by Csbnd H⋯O intermolecular and weak interactions. Computed molecular geometry has been obtained by density functional theory (DFT) and compared with experimental results. The spectra of both FT-IR in the range (4000-400 cm-1) and FT- Raman (3500-50 cm-1) of DFPO were recorded experimentally and computed by (DFT) using B3LYP/6-311G (d,p) as basis sets. Intramolecular charge transfer has been scanned using natural bond orbital (NBO) analysis and revealed the various contribution of bonding and lone pair to the stabilization of molecule. Nonlinear optical activity (NLO) of the title compound has been determined by second harmonic generation (SHG) and computed using DFT method. Hyperpolarizability, HOMO-LUMO energy gap, hardness, softness electronegativity and others Global reactivity descriptors of DFPO has been calculated and revealed complete picture of chemical reactivity of DFPO. Hirshfeld surface analyses were applied to investigate the intermolecular interactions and revealed that more than two-thirds of the inter contacts are associated with O⋯H, C⋯H and H⋯H interactions. Docking studies of DFPO showed inhibition of Vascular endothelial growth Factor human receptor (VEGFR-2) signalling pathway, which indicates DFPO as anti-angiogenesis, that play pivotal role in cancer, so we suggest it for clinical studies to evaluate its potential to treat human cancers.

Synthesis, crystal structure and high temperature phase transition in the new organic-inorganic hybrid [N(C4H9)4]3Zn2Cl7H2O crystals

NASA Astrophysics Data System (ADS)

Ben Gzaiel, Malika; Oueslati, Abderrazek; Lhoste, Jérôme; Gargouri, Mohamed; Bulou, Alain

2015-06-01

The present paper accounts for the synthesis, crystal structure, differential scanning calorimetry and vibrational spectroscopy of a new compound tri-tetrabutylammonium heptachloro-dizincate (I) grown at room temperature by slow evaporation of aqueous solution. From X-ray diffraction data collected at room temperature, it is concluded that it crystallizes in the monoclinic system (P21/n space group) containing ZnCl42- and ZnCl3H2O1- tetrahedra. The atomic arrangement can be described by an alternation of organic and organic-inorganic layers stacked along the c direction. Differential scanning calorimetry (DSC) in the range 250-450 K disclosed a reversible structural phase transition of order-disorder type at 358 K, prior to the melting at 395 K. The temperature dependence of the Raman spectra of [N(C4H9)4]3Zn2Cl7H2O single crystals was studied in the spectral range 100-3500 cm-1 and for temperatures between 300 and 386 K. The most important changes are observed for the line at 261 cm-1 issued from ν1(ZnCl4). The analysis of the wavenumber, intensity and the line width based on an order-disorder model allowed to obtain information relative to the activation energy and the correlation length. The decrease of the activation energy with increasing temperature has been interpreted in term of a change in the re-orientation motion of the anionic parts. The assumption of cluster fluctuations also allowed the critical exponents to be obtained for the transition δ = 0.011 and the correlation length ξ0 = 598 Å.