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Sample records for crystal structure prediction

  1. Crystal structure and prediction.

    PubMed

    Thakur, Tejender S; Dubey, Ritesh; Desiraju, Gautam R

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  2. Crystal Structure and Prediction

    NASA Astrophysics Data System (ADS)

    Thakur, Tejender S.; Dubey, Ritesh; Desiraju, Gautam R.

    2015-04-01

    The notion of structure is central to the subject of chemistry. This review traces the development of the idea of crystal structure since the time when a crystal structure could be determined from a three-dimensional diffraction pattern and assesses the feasibility of computationally predicting an unknown crystal structure of a given molecule. Crystal structure prediction is of considerable fundamental and applied importance, and its successful execution is by no means a solved problem. The ease of crystal structure determination today has resulted in the availability of large numbers of crystal structures of higher-energy polymorphs and pseudopolymorphs. These structural libraries lead to the concept of a crystal structure landscape. A crystal structure of a compound may accordingly be taken as a data point in such a landscape.

  3. Predicting crystal structures of organic compounds.

    PubMed

    Price, Sarah L

    2014-04-07

    Currently, organic crystal structure prediction (CSP) methods are based on searching for the most thermodynamically stable crystal structure, making various approximations in evaluating the crystal energy. The most stable (global minimum) structure provides a prediction of an experimental crystal structure. However, depending on the specific molecule, there may be other structures which are very close in energy. In this case, the other structures on the crystal energy landscape may be polymorphs, components of static or dynamic disorder in observed structures, or there may be no route to nucleating and growing these structures. A major reason for performing CSP studies is as a complement to solid form screening to see which alternative packings to the known polymorphs are thermodynamically feasible.

  4. Crystal structure prediction of rigid molecules.

    PubMed

    Elking, Dennis M; Fusti-Molnar, Laszlo; Nichols, Anthony

    2016-08-01

    A non-polarizable force field based on atomic multipoles fit to reproduce experimental crystal properties and ab initio gas-phase dimers is described. The Ewald method is used to calculate both long-range electrostatic and 1/r(6) dispersion energies of crystals. The dispersion energy of a crystal calculated by a cutoff method is shown to converge slowly to the exact Ewald result. A method for constraining space-group symmetry during unit-cell optimization is derived. Results for locally optimizing 4427 unit cells including volume, cell parameters, unit-cell r.m.s.d. and CPU timings are given for both flexible and rigid molecule optimization. An algorithm for randomly generating rigid molecule crystals is described. Using the correct experimentally determined space group, the average and maximum number of random crystals needed to find the correct experimental structure is given for 2440 rigid single component crystals. The force field energy rank of the correct experimental structure is presented for the same set of 2440 rigid single component crystals assuming the correct space group. A complete crystal prediction is performed for two rigid molecules by searching over the 32 most probable space groups.

  5. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang; Sharma, Vinit; Oganov, Artem R.; Ramprasad, Ramamurthy

    2014-10-01

    The recently developed evolutionary algorithm USPEX proved to be a tool that enables accurate and reliable prediction of structures. Here we extend this method to predict the crystal structure of polymers by constrained evolutionary search, where each monomeric unit is treated as a building block with fixed connectivity. This greatly reduces the search space and allows the initial structure generation with different sequences and packings of these blocks. The new constrained evolutionary algorithm is successfully tested and validated on a diverse range of experimentally known polymers, namely, polyethylene, polyacetylene, poly(glycolic acid), poly(vinyl chloride), poly(oxymethylene), poly(phenylene oxide), and poly (p-phenylene sulfide). By fixing the orientation of polymeric chains, this method can be further extended to predict the structures of complex linear polymers, such as all polymorphs of poly(vinylidene fluoride), nylon-6 and cellulose. The excellent agreement between predicted crystal structures and experimentally known structures assures a major role of this approach in the efficient design of the future polymeric materials.

  6. Crystal Structure Prediction for Cyclotrimethylene Trinitramine (RDX) from First Principles

    DTIC Science & Technology

    2009-04-01

    REPORT Crystal structure prediction for cyclotrimethylene trinitramine (RDX) from ?rst principles 14. ABSTRACT 16. SECURITY CLASSIFICATION OF: Crystal... structure prediction and molecular dynamics methods were applied to the cyclotrimethylene trinitramine (RDX) crystal to explore the stability rankings...500 high-density structures resulting from molecular packing were minimized and the 14 lowest-energy structures were subjected to isothermal

  7. Predicting crystal structure by merging data mining with quantum mechanics.

    PubMed

    Fischer, Christopher C; Tibbetts, Kevin J; Morgan, Dane; Ceder, Gerbrand

    2006-08-01

    Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

  8. High-speed prediction of crystal structures for organic molecules

    NASA Astrophysics Data System (ADS)

    Obata, Shigeaki; Goto, Hitoshi

    2015-02-01

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

  9. Crystal Structure Prediction from First Principles: The Crystal Structures of Glycine

    PubMed Central

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-01-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the Genetic Algorithms search implemented in Modified Genetic Algorithm for Crystals coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable. PMID:25843964

  10. Crystal structure prediction from first principles: The crystal structures of glycine

    NASA Astrophysics Data System (ADS)

    Lund, Albert M.; Pagola, Gabriel I.; Orendt, Anita M.; Ferraro, Marta B.; Facelli, Julio C.

    2015-04-01

    Here we present the results of our unbiased searches of glycine polymorphs obtained using the genetic algorithms search implemented in MGAC, modified genetic algorithm for crystals, coupled with the local optimization and energy evaluation provided by Quantum Espresso. We demonstrate that it is possible to predict the crystal structures of a biomedical molecule using solely first principles calculations. We were able to find all the ambient pressure stable glycine polymorphs, which are found in the same energetic ordering as observed experimentally and the agreement between the experimental and predicted structures is of such accuracy that the two are visually almost indistinguishable.

  11. Toward the Prediction of Organic Hydrate Crystal Structures.

    PubMed

    Hulme, Ashley T; Price, Sarah L

    2007-07-01

    Lattice energy minimization studies on four ordered crystal structures of ice and 22 hydrates of approximately rigid organic molecules (along with 11 corresponding anhydrate structures) were used to establish a model potential scheme, based on the use of a distributed multipole electrostatic model, that can reasonably reproduce the crystal structures. Transferring the empirical repulsion-dispersion potentials for organic oxygen and polar hydrogen atoms to water appears more successful for modeling ice phases than using common water potentials derived from liquid properties. Lattice energy differences are reasonable but quite sensitive to the exact conformation of water and the organic molecule used in the rigid molecule modeling. This potential scheme was used to test a new approach of predicting the crystal structure of 5-azauracil monohydrate (an isolated site hydrate) based on seeking dense crystal packings of 66 5-azauracil···water hydrogen-bonded clusters, derived from an analysis of hydrate hydrogen bond geometries involving the carbonyl- and aza-group acceptors in the Cambridge Structural Database. The known structure was found within 5 kJ mol(-1) of the global minimum in static lattice energy and as the third most stable structure, within 1 kJ mol(-1), when thermal effects at ambient temperature were considered. Thus, although the computational prediction of whether an organic molecule will crystallize in a hydrated form poses many challenges, the prediction of plausible structures for hydrogen-bonded monohydrates is now possible.

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

    PubMed

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

    2009-12-24

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

  13. Sixth blind test of organic crystal-structure prediction methods.

    PubMed

    Groom, Colin R; Reilly, Anthony M

    2014-08-01

    Over the past 15 years progress in predicting crystal structures of small organic molecules has been charted by a series of blind tests hosted by the Cambridge Crystallographic Data Centre. This letter announces a sixth blind test to take place between September 2014 and August 2015, giving details of the target systems and the revised procedure. We hope that as many methods as possible will be assessed and benchmarked in this new blind test.

  14. How evolutionary crystal structure prediction works--and why.

    PubMed

    Oganov, Artem R; Lyakhov, Andriy O; Valle, Mario

    2011-03-15

    Once the crystal structure of a chemical substance is known, many properties can be predicted reliably and routinely. Therefore if researchers could predict the crystal structure of a material before it is synthesized, they could significantly accelerate the discovery of new materials. In addition, the ability to predict crystal structures at arbitrary conditions of pressure and temperature is invaluable for the study of matter at extreme conditions, where experiments are difficult. Crystal structure prediction (CSP), the problem of finding the most stable arrangement of atoms given only the chemical composition, has long remained a major unsolved scientific problem. Two problems are entangled here: search, the efficient exploration of the multidimensional energy landscape, and ranking, the correct calculation of relative energies. For organic crystals, which contain a few molecules in the unit cell, search can be quite simple as long as a researcher does not need to include many possible isomers or conformations of the molecules; therefore ranking becomes the main challenge. For inorganic crystals, quantum mechanical methods often provide correct relative energies, making search the most critical problem. Recent developments provide useful practical methods for solving the search problem to a considerable extent. One can use simulated annealing, metadynamics, random sampling, basin hopping, minima hopping, and data mining. Genetic algorithms have been applied to crystals since 1995, but with limited success, which necessitated the development of a very different evolutionary algorithm. This Account reviews CSP using one of the major techniques, the hybrid evolutionary algorithm USPEX (Universal Structure Predictor: Evolutionary Xtallography). Using recent developments in the theory of energy landscapes, we unravel the reasons evolutionary techniques work for CSP and point out their limitations. We demonstrate that the energy landscapes of chemical systems have an

  15. Clathrate Structure Determination by Combining Crystal Structure Prediction with Computational and Experimental (129) Xe NMR Spectroscopy.

    PubMed

    Selent, Marcin; Nyman, Jonas; Roukala, Juho; Ilczyszyn, Marek; Oilunkaniemi, Raija; Bygrave, Peter J; Laitinen, Risto; Jokisaari, Jukka; Day, Graeme M; Lantto, Perttu

    2017-01-23

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

  16. EVO—Evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Bahmann, Silvia; Kortus, Jens

    2013-06-01

    We present EVO—an evolution strategy designed for crystal structure search and prediction. The concept and main features of biological evolution such as creation of diversity and survival of the fittest have been transferred to crystal structure prediction. EVO successfully demonstrates its applicability to find crystal structures of the elements of the 3rd main group with their different spacegroups. For this we used the number of atoms in the conventional cell and multiples of it. Running EVO with different numbers of carbon atoms per unit cell yields graphite as the lowest energy structure as well as a diamond-like structure, both in one run. Our implementation also supports the search for 2D structures and was able to find a boron sheet with structural features so far not considered in literature. Program summaryProgram title: EVO Catalogue identifier: AEOZ_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEOZ_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GNU General Public License version 3 No. of lines in distributed program, including test data, etc.: 23488 No. of bytes in distributed program, including test data, etc.: 1830122 Distribution format: tar.gz Programming language: Python. Computer: No limitations known. Operating system: Linux. RAM: Negligible compared to the requirements of the electronic structure programs used Classification: 7.8. External routines: Quantum ESPRESSO (http://www.quantum-espresso.org/), GULP (https://projects.ivec.org/gulp/) Nature of problem: Crystal structure search is a global optimisation problem in 3N+3 dimensions where N is the number of atoms in the unit cell. The high dimensional search space is accompanied by an unknown energy landscape. Solution method: Evolutionary algorithms transfer the main features of biological evolution to use them in global searches. The combination of the "survival of the fittest" (deterministic) and the

  17. On Predicting the Crystal Structure of Energetic Materials From Quantum Mechanics

    DTIC Science & Technology

    2008-12-01

    ON PREDICTING THE CRYSTAL STRUCTURE OF ENERGETIC MATERIALS FROM QUANTUM MECHANICS Betsy M. Rice* U. S. Army Research Laboratory, AMSRD-ARL-WM...cyclotrimethylenetrinitramine (RDX) is used to predict polymorphic structures of crystalline RDX. The potential was first used in crystal structure prediction...methods which generate polymorphs of RDX and provide a 0 K ordering in energy. The 13 low energy- structures generated by crystal structure prediction

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

    PubMed

    Price, Sarah Sally L

    2009-01-20

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

  19. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    NASA Astrophysics Data System (ADS)

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-07-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib.

  20. Prediction of new crystal structure phases in metal borides

    NASA Astrophysics Data System (ADS)

    Kolmogorov, Aleksey

    2006-03-01

    Identification of novel crystal structures is an important step for predicting new stable compounds in alloys, since most theoretical search algorithms are restricted to a given prototype library or a lattice type. Performing ab initio data mining [1] of intermetallic compounds we have discovered that even in such a well-studied class of systems as metal borides there are previously unknown phases comparable in energy to the existing ones [2]. We demonstrate that even though the new structures are relatively simple, their identification is not straightforward. We systematically investigate the stability and electronic properties of the new metal boride phases. Our calculations show that some phases exhibit electronic features similar to those in the famous MgB2 and could be good superconductors. The new phases are likely to have random stacking faults, so they might not be detected with standard x-ray methods. Our results could thus be used as an important guide in the search for new superconducting metal borides. [1] S. Curtarolo et al., Phys. Rev. Lett. 91, 135503 (2003). [2] A.N. Kolmogorov et al., submitted (2005).

  1. Combined crystal structure prediction and high-pressure crystallization in rational pharmaceutical polymorph screening

    PubMed Central

    Neumann, M. A.; van de Streek, J.; Fabbiani, F. P. A.; Hidber, P.; Grassmann, O.

    2015-01-01

    Organic molecules, such as pharmaceuticals, agro-chemicals and pigments, frequently form several crystal polymorphs with different physicochemical properties. Finding polymorphs has long been a purely experimental game of trial-and-error. Here we utilize in silico polymorph screening in combination with rationally planned crystallization experiments to study the polymorphism of the pharmaceutical compound Dalcetrapib, with 10 torsional degrees of freedom one of the most flexible molecules ever studied computationally. The experimental crystal polymorphs are found at the bottom of the calculated lattice energy landscape, and two predicted structures are identified as candidates for a missing, thermodynamically more stable polymorph. Pressure-dependent stability calculations suggested high pressure as a means to bring these polymorphs into existence. Subsequently, one of them could indeed be crystallized in the 0.02 to 0.50 GPa pressure range and was found to be metastable at ambient pressure, effectively derisking the appearance of a more stable polymorph during late-stage development of Dalcetrapib. PMID:26198974

  2. Prediction of crystal structures from crystal chemistry rules by simulated annealing

    NASA Astrophysics Data System (ADS)

    Pannetier, J.; Bassas-Alsina, J.; Rodriguez-Carvajal, J.; Caignaert, V.

    1990-07-01

    THE prediction of the structure of inorganic crystalline solids from the knowledge of their chemical composition is still a largely unresolved problem1-3. The usual approach to this problem is to minimize, for a selection of candidate models, the potential energy of the system with respect to the structural parameters of these models: the solution is the arrangement that comes out lowest in energy. Methods using this procedure may differ in the origin (ab initio or empirical) of the interatomic potentials used, but they usually restrict themselves to optimizing a structural arrangement within the constraints of given symmetry and bond topology. As a result, they do not truly address the problem of predicting the unknown structure of a real compound. The method we describe here is an attempt at solving the following problem: given the chemical composition of a crystalline compound and the values of its unit-cell parameters, find its structure (topology and bond distances) by optimizing the arrangement of ions, atoms or molecules in accordance with a set of prescribed rules. The procedure uses simple, empirical crystal chemistry arguments (Pauling's principles for ionic compounds4) and a powerful stochastic search procedure, known as simulated annealing5 to identify the best atomic model or models. We discuss the potential of the method for structure determination and refinement, using results obtained for several known inorganic structures, and by the determination of a previously unknown structure. Although the approach is limited to the case of inorganic compounds, it is nevertheless very general, and would apply to any crystalline structure provided that the principles governing the architecture of the solid can be properly described.

  3. Using crystal structure prediction to rationalize the hydration propensities of substituted adamantane hydrochloride salts.

    PubMed

    Mohamed, Sharmarke; Karothu, Durga Prasad; Naumov, Panče

    2016-08-01

    The crystal energy landscapes of the salts of two rigid pharmaceutically active molecules reveal that the experimental structure of amantadine hydrochloride is the most stable structure with the majority of low-energy structures adopting a chain hydrogen-bond motif and packings that do not have solvent accessible voids. By contrast, memantine hydrochloride which differs in the substitution of two methyl groups on the adamantane ring has a crystal energy landscape where all structures within 10 kJ mol(-1) of the global minimum have solvent-accessible voids ranging from 3 to 14% of the unit-cell volume including the lattice energy minimum that was calculated after removing water from the hydrated memantine hydrochloride salt structure. The success in using crystal structure prediction (CSP) to rationalize the different hydration propensities of these substituted adamantane hydrochloride salts allowed us to extend the model to predict under blind test conditions the experimental crystal structures of the previously uncharacterized 1-(methylamino)adamantane base and its corresponding hydrochloride salt. Although the crystal structure of 1-(methylamino)adamantane was correctly predicted as the second ranked structure on the static lattice energy landscape, the crystallization of a Z' = 3 structure of 1-(methylamino)adamantane hydrochloride reveals the limits of applying CSP when the contents of the crystallographic asymmetric unit are unknown.

  4. Predicted and experimental crystal structures of ethyl-tert-butyl ether.

    PubMed

    Hammer, Sonja M; Alig, Edith; Fink, Lothar; Schmidt, Martin U

    2011-04-01

    Possible crystal structures of ethyl-tert-butyl ether (ETBE) were predicted by global lattice-energy minimizations using the force-field approach. 33 structures were found within an energy range of 2 kJmol(-1) above the global minimum. Low-temperature crystallization experiments were carried out at 80-160 K. The crystal structure was determined from X-ray powder data. ETBE crystallizes in C2/m, Z = 4, with molecules on mirror planes. The ETBE molecule adopts a trans conformation with a (CH(3))(3)C-O-C-C torsion angle of 180°. The experimental structure corresponds with high accuracy to the predicted structure with energy rank 2, which has an energy of 0.54 kJmol(-1) above the global minimum and is the most dense low-energy structure. In some crystallization experiments a second polymorph was observed, but the quality of the powder data did not allow the determination of the crystal structure. Possibilities and limitations are discussed for solving crystal structures from powder diffraction data by real-space methods and lattice-energy minimizations.

  5. Experimental and predicted crystal structures of Pigment Red 168 and other dihalogenated anthanthrones.

    PubMed

    Schmidt, Martin U; Paulus, Erich F; Rademacher, Nadine; Day, Graeme M

    2010-10-01

    The crystal structures of 4,10-dibromo-anthanthrone (Pigment Red 168; 4,10-dibromo-dibenzo[def,mno]chrysene-6,12-dione), 4,10-dichloro- and 4,10-diiodo-anthanthrone have been determined by single-crystal X-ray analyses. The dibromo and diiodo derivatives crystallize in P2(1)/c, Z = 2, the dichloro derivative in P1, Z = 1. The molecular structures are almost identical and the unit-cell parameters show some similarities for all three compounds, but the crystal structures are neither isotypic to another nor to the unsubstituted anthanthrone, which crystallizes in P2(1)/c, Z = 8. In order to explain why the four anthanthrone derivatives have four different crystal structures, lattice-energy minimizations were performed using anisotropic atom-atom model potentials as well as using the semi-classical density sums (SCDS-Pixel) approach. The calculations showed the crystal structures of the dichloro and the diiodo derivatives to be the most stable ones for the corresponding compound; whereas for dibromo-anthanthrone the calculations suggest that the dichloro and diiodo structure types should be more stable than the experimentally observed structure. An experimental search for new polymorphs of dibromo-anthanthrone was carried out, but the experiments were hampered by the remarkable insolubility of the compound. A metastable nanocrystalline second polymorph of the dibromo derivative does exist, but it is not isostructural to the dichloro or diiodo compound. In order to determine the crystal structure of this phase, crystal structure predictions were performed in various space groups, using anisotropic atom-atom potentials. For all low-energy structures, X-ray powder patterns were calculated and compared with the experimental diagram, which consisted of a few broad lines only. It turned out that the crystallinity of this phase was not sufficient to determine which of the calculated structures corresponds to the actual structure of this nanocrystalline polymorph.

  6. Predictions of Crystal Structure Based on Radius Ratio: How Reliable Are They?

    ERIC Educational Resources Information Center

    Nathan, Lawrence C.

    1985-01-01

    Discussion of crystalline solids in undergraduate curricula often includes the use of radius ratio rules as a method for predicting which type of crystal structure is likely to be adopted by a given ionic compound. Examines this topic, establishing more definitive guidelines for the use and reliability of the rules. (JN)

  7. Data mining approaches to high-throughput crystal structure and compound prediction.

    PubMed

    Hautier, Geoffroy

    2014-01-01

    Predicting unknown inorganic compounds and their crystal structure is a critical step of high-throughput computational materials design and discovery. One way to achieve efficient compound prediction is to use data mining or machine learning methods. In this chapter we present a few algorithms for data mining compound prediction and their applications to different materials discovery problems. In particular, the patterns or correlations governing phase stability for experimental or computational inorganic compound databases are statistically learned and used to build probabilistic or regression models to identify novel compounds and their crystal structures. The stability of those compound candidates is then assessed using ab initio techniques. Finally, we report a few cases where data mining driven computational predictions were experimentally confirmed through inorganic synthesis.

  8. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction.

    PubMed

    Whittleton, Sarah R; Otero-de-la-Roza, A; Johnson, Erin R

    2017-02-14

    Accurate energy ranking is a key facet to the problem of first-principles crystal-structure prediction (CSP) of molecular crystals. This work presents a systematic assessment of B86bPBE-XDM, a semilocal density functional combined with the exchange-hole dipole moment (XDM) dispersion model, for energy ranking using 14 compounds from the first five CSP blind tests. Specifically, the set of crystals studied comprises 11 rigid, planar compounds and 3 co-crystals. The experimental structure was correctly identified as the lowest in lattice energy for 12 of the 14 total crystals. One of the exceptions is 4-hydroxythiophene-2-carbonitrile, for which the experimental structure was correctly identified once a quasi-harmonic estimate of the vibrational free-energy contribution was included, evidencing the occasional importance of thermal corrections for accurate energy ranking. The other exception is an organic salt, where charge-transfer error (also called delocalization error) is expected to cause the base density functional to be unreliable. Provided the choice of base density functional is appropriate and an estimate of temperature effects is used, XDM-corrected density-functional theory is highly reliable for the energetic ranking of competing crystal structures.

  9. Evolutionary crystal structure prediction: discovering new minerals in the deep Earth.

    NASA Astrophysics Data System (ADS)

    Oganov, A. R.; Glass, C. W.

    2006-12-01

    Experimental determination of crystal structures at high pressure is often extremely difficult; given this and the strengths of quantum-mechanical simulations, theory presents an attractive tool to investigate matter at extreme conditions. However, crystal structure prediction on the basis of just the chemical formula has long been considered a formidable or even insoluble problem. Solving it would enable structural studies of planetary materials at extreme conditions [1,2] and probe changing chemistry at high pressure, solve structures where experimental data are insufficient, and design new materials entirely on the computer (once the structure is known, it is relatively easy to predict many of its properties e.g., [3]). Recently, we addressed this problem and devised a new method based on an ab initio evolutionary algorithm, which we implemented in the USPEX code (Universal Structure Predictor: Evolutionary Xtallography, [4-6]). USPEX uses ab initio free energy as evaluation function and features local optimization and spatial heredity, as well as further operators such as mutation and permutation. At given P-T conditions, USPEX finds the stable structure and a set of robust metastable structures, using no experimental information except the chemical composition. This method has been widely tested and applied to solve a number of important problems. In this talk I will discuss some of the applications of this method to a number of interesting materials at high pressure (C, O, S, MgSiO3, CO2, CaCO3, MgCO3). 1. Oganov A.R. & Ono S. (2004). Theoretical and experimental evidence for a post-perovskite phase of MgSiO3 in Earth's D" layer. Nature 430, 445-448. 2. Oganov A.R., Ono S. (2005). The high pressure phase of alumina and implications for Earth's D" layer. Proc. Natl. Acad. Sci. 102, 10828-10831. 3. Oganov A.R., Brodholt J.P., Price G.D. (2001). The elastic constants of MgSiO3 perovskite at pressures and temperatures of the Earth's mantle. Nature 411, 934-937. 4

  10. Crystal structure prediction and isostructurality of three small organic halogen compounds.

    PubMed

    Asmadi, Aldi; Kendrick, John; Leusen, Frank J J

    2010-08-14

    A theoretical investigation of the packing stabilities of three small organic halogen compounds is presented based on a crystal structure prediction (CSP) study. Each compound has four identical halogen atoms (fluorine, chlorine, and bromine) and a four-membered ring consisting of carbon and sulfur atoms arranged alternately. Two halogen atoms are attached to each carbon and two oxygen atoms are attached to each sulfur forming SO(2) functional groups. The crystal structures of these compounds have been determined experimentally and show distinct packing arrangements. Utilising the computational approaches implemented in the GRACE software package, each compound is subjected to a full CSP study using a force field specific for each molecule (called the tailor-made force field or TMFF) and a dispersion corrected solid-state density functional method (or DFT(d) method). Energetically feasible crystal structures are generated in all 230 space groups restricted to a single molecule in the crystallographic asymmetric unit (Z' = 1) using the TMFF of each molecule. Next, a selection of structures with low TMFF lattice energies are further refined with the DFT(d) method. The CSP results show that the experimental crystal structures of the molecules containing fluorine and chlorine are well described energetically and geometrically by their TMFFs and the DFT(d) method. Both approaches locate their experimental lattices as the most stable structures. For the molecule containing bromine, a crystal structure corresponding to the force field optimised experimental structure is located as the second structure in the list of force field predicted structures, ranked by calculated lattice energy. Despite the structural similarity of the predicted and experimental structures, close examination of the DFT(d) optimisation results of the experimental structure reveals a slightly lower energy structure than that found by the CSP simulations. Furthermore, minimisation of the force field

  11. Convergence Properties of Crystal Structure Prediction by Quasi-Random Sampling

    PubMed Central

    2015-01-01

    Generating sets of trial structures that sample the configurational space of crystal packing possibilities is an essential step in the process of ab initio crystal structure prediction (CSP). One effective methodology for performing such a search relies on low-discrepancy, quasi-random sampling, and our implementation of such a search for molecular crystals is described in this paper. Herein we restrict ourselves to rigid organic molecules and, by considering their geometric properties, build trial crystal packings as starting points for local lattice energy minimization. We also describe a method to match instances of the same structure, which we use to measure the convergence of our packing search toward completeness. The use of these tools is demonstrated for a set of molecules with diverse molecular characteristics and as representative of areas of application where CSP has been applied. An important finding is that the lowest energy crystal structures are typically located early and frequently during a quasi-random search of phase space. It is usually the complete sampling of higher energy structures that requires extended sampling. We show how the procedure can first be refined, through targetting the volume of the generated crystal structures, and then extended across a range of space groups to make a full CSP search and locate experimentally observed and lists of hypothetical polymorphs. As the described method has also been created to lie at the base of more involved approaches to CSP, which are being developed within the Global Lattice Energy Explorer (Glee) software, a few of these extensions are briefly discussed. PMID:26716361

  12. XTALOPT version r9: An open-source evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Falls, Zackary; Lonie, David C.; Avery, Patrick; Shamp, Andrew; Zurek, Eva

    2016-02-01

    A new version of XTALOPT, an evolutionary algorithm for crystal structure prediction, is available for download from the CPC library or the XTALOPT website, http://xtalopt.github.io. XTALOPT is published under the Gnu Public License (GPL), which is an open source license that is recognized by the Open Source Initiative. The new version incorporates many bug-fixes and new features, as detailed below.

  13. Prediction and Design of Materials from Crystal Structures to Nanocrystal Morphology and Assembly

    NASA Astrophysics Data System (ADS)

    Hennig, Richard

    2012-02-01

    Predictions of structure formation by computational methods have the potential to accelerate materials discovery and design. Here we present two computational approaches for the prediction of crystal structures and the morphology of nanoparticles. Many materials properties are controlled by composition and crystal structure. We show that evolutionary algorithms coupled to ab-initio relaxations can accurately predict the crystal structure and composition of compounds without any prior information about the system. We will discuss results for various systems including the prediction of unexpected quasi-1D and 2D electronic structures in Li-Be compounds under pressure [1] and of the crystal structure of the superconducting high-pressure phase of Eu [2]. The self-assembly of nanocrystals into mesoscale superlattices provides a path to the design of materials with tunable electronic, physical and chemical properties for various applications. The self-assembly is controlled by the nanocrystal shape and by ligand-mediated interactions between them. To understand this, it is necessary to know the effect of the ligands on the surface energies (which tune the nanocrystal shape), as well as the relative coverage of the different facets (which control the interactions). Density functional calculations for the binding energy of oleic acid-based ligands on PbSe nanocrystals determine the surface energies as a function of ligand coverage. The Wulff construction predicts the thermodynamic equilibrium shape of the PbSe nanocrystals as a function of the ligand coverage. We show that the different ligand binding energies on the 100 and 111 facets results in different ligand coverages on the facets and predict a transition in the equilibrium shape from octahedral to cubic when increasing the ligand concentration during synthesis. Our results furthermore suggest that the experimentally observed transformation of the nanocrystal superlattice structure from fcc to bcc is caused by the

  14. Ab initio crystal structure prediction of magnesium (poly)sulfides and calculation of their NMR parameters.

    PubMed

    Mali, Gregor

    2017-03-01

    Ab initio prediction of sensible crystal structures can be regarded as a crucial task in the quickly-developing methodology of NMR crystallography. In this contribution, an evolutionary algorithm was used for the prediction of magnesium (poly)sulfide crystal structures with various compositions. The employed approach successfully identified all three experimentally detected forms of MgS, i.e. the stable rocksalt form and the metastable wurtzite and zincblende forms. Among magnesium polysulfides with a higher content of sulfur, the most probable structure with the lowest formation energy was found to be MgS2, exhibiting a modified rocksalt structure, in which S(2-) anions were replaced by S2(2-) dianions. Magnesium polysulfides with even larger fractions of sulfur were not predicted to be stable. For the lowest-energy structures, (25)Mg quadrupolar coupling constants and chemical shift parameters were calculated using the density functional theory approach. The calculated NMR parameters could be well rationalized by the symmetries of the local magnesium environments, by the coordination of magnesium cations and by the nature of the surrounding anions. In the future, these parameters could serve as a reference for the experimentally determined (25)Mg NMR parameters of magnesium sulfide species.

  15. Ab-initio crystal structure prediction. A case study: NaBH{sub 4}

    SciTech Connect

    Caputo, Riccarda; Tekin, Adem

    2011-07-15

    Crystal structure prediction from first principles is still one of the most challenging and interesting issue in condensed matter science. we explored the potential energy surface of NaBH{sub 4} by a combined ab-initio approach, based on global structure optimizations and quantum chemistry. In particular, we used simulated annealing (SA) and density functional theory (DFT) calculations. The methodology enabled the identification of several local minima, of which the global minimum corresponded to the tetragonal ground-state structure (P4{sub 2}/nmc), and the prediction of higher energy stable structures, among them a monoclinic (Pm) one was identified to be 22.75 kJ/mol above the ground-state at T=298 K. In between, orthorhombic and cubic structures were recovered, in particular those with Pnma and F4-bar 3m symmetries. - Graphical abstract: The total electron energy difference of the calculated stable structures. Here, the tetragonal (IT 137) and the monoclinic (IT 6) symmetry groups corresponded to the lowest and the highest energy structures, respectively. Highlights: > Potential energy surface of NaBH{sub 4} is investigated. > This is done a combination of global structure optimizations based on simulated annealing and density functional calculations. > We successfully reproduced experimentally found tetragonal and orthorhombic structures of NaBH{sub 4}. > Furthermore, we found a new stable high energy structure.

  16. Dispersion corrected hartree-fock and density functional theory for organic crystal structure prediction.

    PubMed

    Brandenburg, Jan Gerit; Grimme, Stefan

    2014-01-01

    We present and evaluate dispersion corrected Hartree-Fock (HF) and Density Functional Theory (DFT) based quantum chemical methods for organic crystal structure prediction. The necessity of correcting for missing long-range electron correlation, also known as van der Waals (vdW) interaction, is pointed out and some methodological issues such as inclusion of three-body dispersion terms are discussed. One of the most efficient and widely used methods is the semi-classical dispersion correction D3. Its applicability for the calculation of sublimation energies is investigated for the benchmark set X23 consisting of 23 small organic crystals. For PBE-D3 the mean absolute deviation (MAD) is below the estimated experimental uncertainty of 1.3 kcal/mol. For two larger π-systems, the equilibrium crystal geometry is investigated and very good agreement with experimental data is found. Since these calculations are carried out with huge plane-wave basis sets they are rather time consuming and routinely applicable only to systems with less than about 200 atoms in the unit cell. Aiming at crystal structure prediction, which involves screening of many structures, a pre-sorting with faster methods is mandatory. Small, atom-centered basis sets can speed up the computation significantly but they suffer greatly from basis set errors. We present the recently developed geometrical counterpoise correction gCP. It is a fast semi-empirical method which corrects for most of the inter- and intramolecular basis set superposition error. For HF calculations with nearly minimal basis sets, we additionally correct for short-range basis incompleteness. We combine all three terms in the HF-3c denoted scheme which performs very well for the X23 sublimation energies with an MAD of only 1.5 kcal/mol, which is close to the huge basis set DFT-D3 result.

  17. Report on the sixth blind test of organic crystal structure prediction methods

    PubMed Central

    Reilly, Anthony M.; Cooper, Richard I.; Adjiman, Claire S.; Bhattacharya, Saswata; Boese, A. Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J.; Bylsma, Rita; Campbell, Josh E.; Car, Roberto; Case, David H.; Chadha, Renu; Cole, Jason C.; Cosburn, Katherine; Cuppen, Herma M.; Curtis, Farren; Day, Graeme M.; DiStasio Jr, Robert A.; Dzyabchenko, Alexander; van Eijck, Bouke P.; Elking, Dennis M.; van den Ende, Joost A.; Facelli, Julio C.; Ferraro, Marta B.; Fusti-Molnar, Laszlo; Gatsiou, Christina-Anna; Gee, Thomas S.; de Gelder, René; Ghiringhelli, Luca M.; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W. M.; Hoja, Johannes; Hylton, Rebecca K.; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T.; Kendrick, John; de Klerk, Niek J. J.; Ko, Hsin-Yu; Kuleshova, Liudmila N.; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J. J.; Lund, Albert M.; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E.; McCabe, Patrick; McMahon, David P.; Meekes, Hugo; Metz, Michael P.; Misquitta, Alston J.; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J.; Neumann, Marcus A.; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R.; Orendt, Anita M.; Pagola, Gabriel I.; Pantelides, Constantinos C.; Pickard, Chris J.; Podeszwa, Rafal; Price, Louise S.; Price, Sarah L.; Pulido, Angeles; Read, Murray G.; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P.; Singh, Pawanpreet; Sugden, Isaac J.; Szalewicz, Krzysztof; Taylor, Christopher R.; Tkatchenko, Alexandre; Tuckerman, Mark E.; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E.; de Wijs, Gilles A.; Yang, Jack; Zhu, Qiang; Groom, Colin R.

    2016-01-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and ‘best practices’ for performing CSP calculations. All of the targets, apart from a single potentially disordered Z′ = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms. PMID:27484368

  18. Report on the sixth blind test of organic crystal structure prediction methods.

    PubMed

    Reilly, Anthony M; Cooper, Richard I; Adjiman, Claire S; Bhattacharya, Saswata; Boese, A Daniel; Brandenburg, Jan Gerit; Bygrave, Peter J; Bylsma, Rita; Campbell, Josh E; Car, Roberto; Case, David H; Chadha, Renu; Cole, Jason C; Cosburn, Katherine; Cuppen, Herma M; Curtis, Farren; Day, Graeme M; DiStasio, Robert A; Dzyabchenko, Alexander; van Eijck, Bouke P; Elking, Dennis M; van den Ende, Joost A; Facelli, Julio C; Ferraro, Marta B; Fusti-Molnar, Laszlo; Gatsiou, Christina Anna; Gee, Thomas S; de Gelder, René; Ghiringhelli, Luca M; Goto, Hitoshi; Grimme, Stefan; Guo, Rui; Hofmann, Detlef W M; Hoja, Johannes; Hylton, Rebecca K; Iuzzolino, Luca; Jankiewicz, Wojciech; de Jong, Daniël T; Kendrick, John; de Klerk, Niek J J; Ko, Hsin Yu; Kuleshova, Liudmila N; Li, Xiayue; Lohani, Sanjaya; Leusen, Frank J J; Lund, Albert M; Lv, Jian; Ma, Yanming; Marom, Noa; Masunov, Artëm E; McCabe, Patrick; McMahon, David P; Meekes, Hugo; Metz, Michael P; Misquitta, Alston J; Mohamed, Sharmarke; Monserrat, Bartomeu; Needs, Richard J; Neumann, Marcus A; Nyman, Jonas; Obata, Shigeaki; Oberhofer, Harald; Oganov, Artem R; Orendt, Anita M; Pagola, Gabriel I; Pantelides, Constantinos C; Pickard, Chris J; Podeszwa, Rafal; Price, Louise S; Price, Sarah L; Pulido, Angeles; Read, Murray G; Reuter, Karsten; Schneider, Elia; Schober, Christoph; Shields, Gregory P; Singh, Pawanpreet; Sugden, Isaac J; Szalewicz, Krzysztof; Taylor, Christopher R; Tkatchenko, Alexandre; Tuckerman, Mark E; Vacarro, Francesca; Vasileiadis, Manolis; Vazquez-Mayagoitia, Alvaro; Vogt, Leslie; Wang, Yanchao; Watson, Rona E; de Wijs, Gilles A; Yang, Jack; Zhu, Qiang; Groom, Colin R

    2016-08-01

    The sixth blind test of organic crystal structure prediction (CSP) methods has been held, with five target systems: a small nearly rigid molecule, a polymorphic former drug candidate, a chloride salt hydrate, a co-crystal and a bulky flexible molecule. This blind test has seen substantial growth in the number of participants, with the broad range of prediction methods giving a unique insight into the state of the art in the field. Significant progress has been seen in treating flexible molecules, usage of hierarchical approaches to ranking structures, the application of density-functional approximations, and the establishment of new workflows and `best practices' for performing CSP calculations. All of the targets, apart from a single potentially disordered Z' = 2 polymorph of the drug candidate, were predicted by at least one submission. Despite many remaining challenges, it is clear that CSP methods are becoming more applicable to a wider range of real systems, including salts, hydrates and larger flexible molecules. The results also highlight the potential for CSP calculations to complement and augment experimental studies of organic solid forms.

  19. How important is thermal expansion for predicting molecular crystal structures and thermochemistry at finite temperatures?

    PubMed

    Heit, Yonaton N; Beran, Gregory J O

    2016-08-01

    Molecular crystals expand appreciably upon heating due to both zero-point and thermal vibrational motion, yet this expansion is often neglected in molecular crystal modeling studies. Here, a quasi-harmonic approximation is coupled with fragment-based hybrid many-body interaction calculations to predict thermal expansion and finite-temperature thermochemical properties in crystalline carbon dioxide, ice Ih, acetic acid and imidazole. Fragment-based second-order Möller-Plesset perturbation theory (MP2) and coupled cluster theory with singles, doubles and perturbative triples [CCSD(T)] predict the thermal expansion and the temperature dependence of the enthalpies, entropies and Gibbs free energies of sublimation in good agreement with experiment. The errors introduced by neglecting thermal expansion in the enthalpy and entropy cancel somewhat in the Gibbs free energy. The resulting ∼ 1-2 kJ mol(-1) errors in the free energy near room temperature are comparable to or smaller than the errors expected from the electronic structure treatment, but they may be sufficiently large to affect free-energy rankings among energetically close polymorphs.

  20. Prediction of the crystal structure types of equiatomic ternary silicides and germanides

    NASA Astrophysics Data System (ADS)

    Kiselyova, N. N.; Stolyarenko, A. V.; Sen'ko, O. V.; Dokukin, A. A.

    2013-05-01

    New unsynthesized equiatomic ABX ( A and B are various metals; X = Si or Ge) compounds are predicted, and their types of crystal structure are forecasted under standard conditions. Only the data on the properties of the elements—components of compounds are used for their prediction. The calculations are performed using a special-purpose software package of computer analysis of information intended for searching for regularities in databases on the properties of inorganic compounds, and this package is based on the methods of precedent pattern recognition. Computer analysis of the data on the well-known compounds shows that the functions that are most important for the classification of systems in the sign of formation or absence of equiatomic compounds are M( A) × M( B) and I( A) × I( X), where M is the Mendeleev-Pettifor number of element A or B and I is the thermal conductivity of element A or X. The parameters that most strongly separate compounds for crystal chemical classification are functions T( A) + T( B) (where T is the melting temperature of element A or B), I( A), M( A) × M( B), and I( A) × I( X).

  1. Crystal Structure Prediction and its Application in Earth and Materials Sciences

    NASA Astrophysics Data System (ADS)

    Zhu, Qiang

    First of all, we describe how to predict crystal structure by evolutionary approach, and extend this method to study the packing of organic molecules, by our specially designed constrained evolutionary algorithm. The main feature of this new approach is that each unit or molecule is treated as a whole body, which drastically reduces the search space and improves the efficiency. The improved method is possibly to be applied in the fields of (1) high pressure phase of simple molecules (H2O, NH3, CH4, etc); (2) pharmaceutical molecules (glycine, aspirin, etc); (3) complex inorganic crystals containing cluster or molecular unit, (Mg(BH4)2, Ca(BH4)2, etc). One application of the constrained evolutionary algorithm is given by the study of (Mg(BH4)2, which is a promising materials for hydrogen storage. Our prediction does not only reproduce the previous work on Mg(BH4)2 at ambient condition, but also yields two new tetragonal structures at high pressure, with space groups P4 and I41/acd are predicted to be lower in enthalpy, by 15.4 kJ/mol and 21.2 kJ/mol, respectively, than the earlier proposed P42nm phase. We have simulated X-ray diffraction spectra, lattice dynamics, and equations of state of these phases. The density, volume contraction, bulk modulus, and the simulated XRD patterns of P4 and I41/acd structures are in excellent agreement with the experimental results. Two kinds of oxides (Xe-O and Mg-O) have been studied under megabar pressures. For XeO, we predict the existence of thermodynamically stable Xe-O compounds at high pressures (XeO, XeO2 and XeO3 become stable at pressures of 83, 102 and 114 GPa, respectively). For Mg-O, our calculations find that two extraordinary compounds MgO2 and Mg3O 2 become thermodynamically stable at 116 GPa and 500 GPa, respectively. Our calculations indicate large charge transfer in these oxides for both systems, suggesting that large electronegativity difference and pressure are the key factors favouring their formations. We also

  2. Materials for Alternative Energies: Computational Materials Discovery and Crystal Structure Prediction

    NASA Astrophysics Data System (ADS)

    Wolverton, Chris

    2013-03-01

    Many of the key technological problems associated with alternative energies may be traced back to the lack of suitable materials. The materials discovery process may be greatly aided by the use of computational methods, particular those atomistic methods based on density functional theory. In this talk, we present an overview of recent work on energy-related materials from density-functional based approaches. We have developed novel computational tools which enable accurate prediction of crystal structures for new materials (using both Monte Carlo and Genetic Algorithm based approaches), materials discovery via high-throughput, data mining techniques, and automated phase diagram calculations. We highlight applications in the area of Li battery materials and hydrogen storage materials.

  3. Predicting the Crystal Structure and Phase Transitions in High-Entropy Alloys

    NASA Astrophysics Data System (ADS)

    King, D. M.; Middleburgh, S. C.; Edwards, L.; Lumpkin, G. R.; Cortie, M.

    2015-06-01

    High-entropy alloys (HEAs) have advantageous properties compared with other systems as a result of their chemistry and crystal structure. The transition between a face-centered cubic (FCC) and body-centered cubic (BCC) structure in the Al x CoCrFeNi high-entropy alloy system has been investigated on the atomic scale in this work. The Al x CoCrFeNi system, as well as being a useful system itself, can also be considered a model HEA material. Ordering in the FCC structure was investigated, and an order-disorder transition was predicted at ~600 K. It was found that, at low temperatures, an ordered lattice is favored over a truly random lattice. The fully disordered BCC structure was found to be unstable. When partial ordering was imposed (lowering the symmetry), with Al and Ni limited specific sites of the BCC system, the BCC packing was stabilized. Decomposition of the ordered BCC single phase into a dual phase (Al-Ni rich and Fe-Cr rich) is also considered.

  4. hβ2R-Gαs complex: prediction versus crystal structure--how valuable are predictions based on molecular modeling studies?

    PubMed

    Straßer, Andrea; Wittmann, Hans-Joachim

    2012-07-01

    In 2010, we predicted two models for the hβ(2)R-Gα(s) complex by combining the technique of homology modeling with a potential energy surface scan, since a complete crystal structure of the hβ(2)R-Gα(s) complex was not available. The crystal structure of opsin co-crystallized with part of the C-terminus of Gα (3DQB) was used as a template to model the hβ(2)R, whereas the crystal structure of Gα (1AZT) was used as a template to model Gα(s). Utilizing a potential energy surface scan between hβ(2)R and Gα(s), a six-dimensional potential energy surface was obtained. Two significant minimum regions were located on this surface, and each was associated with a distinct hβ(2)R-Gα(s) complex, namely model I and model II [Straßer A, Wittmann H-J (2010) J Mol Model 16:1307-1318]. The crystal structure of the hβ(2)R-Gα(s)βγ complex has recently been published. Thus, the aim of the current study was, on the one hand, to compare our predicted structures with the true crystal structure, and on the other to discuss the question: how valuable are predictions based on molecular modeling studies?

  5. Position of helical kinks in membrane protein crystal structures and the accuracy of computational prediction.

    PubMed

    Hall, Spencer E; Roberts, Kyle; Vaidehi, Nagarajan

    2009-01-01

    The structural features of helical transmembrane (TM) proteins, such as helical kinks, tilts, and rotational orientations are important in modulation of their function and these structural features give rise to functional diversity in membrane proteins with similar topology. In particular, the helical kinks caused by breaking of the backbone hydrogen bonds lead to hinge bending flexibility in these helices. Therefore it is important to understand the nature of the helical kinks and to be able to reproduce these kinks in structural models of membrane proteins. We have analyzed the position and extent of helical kinks in the transmembrane helices of all the crystal structures of membrane proteins taken from the MPtopo database, which are about 405 individual helices of length between 19 and 35 residues. 44% of the crystal structures of TM helices showed a significant helical kink, and 35% of these kinks are caused by prolines. Many of the non-proline helical kinks are caused by other residues like Ser and Gly that are located at the center of helical kinks. The side chain of Ser makes a hydrogen bond with the main chain carbonyl of the i - 4th or i + 4th residue thus making a kink. We have also studied how well molecular dynamics (MD) simulations on isolated helices can reproduce the position of the helical kinks in TM helices. Such a method is useful for structure prediction of membrane proteins. We performed MD simulations, starting from a canonical helix for the 405 TM helices. 1 ns of MD simulation results show that we can reproduce about 79% of the proline kinks, only 59% of the vestigial proline kinks and 18% of the non-proline helical kinks. We found that similar results can be obtained from choosing the lowest potential energy structure from the MD simulation. 4-14% more of the vestigial prolines were reproduced by replacing them with prolines before performing MD simulations, and changing the amino acid back to proline after the MD simulations. From these

  6. XTALOPT: An open-source evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2011-02-01

    The implementation and testing of XTALOPT, an evolutionary algorithm for crystal structure prediction, is outlined. We present our new periodic displacement (ripple) operator which is ideally suited to extended systems. It is demonstrated that hybrid operators, which combine two pure operators, reduce the number of duplicate structures in the search. This allows for better exploration of the potential energy surface of the system in question, while simultaneously zooming in on the most promising regions. A continuous workflow, which makes better use of computational resources as compared to traditional generation based algorithms, is employed. Various parameters in XTALOPT are optimized using a novel benchmarking scheme. XTALOPT is available under the GNU Public License, has been interfaced with various codes commonly used to study extended systems, and has an easy to use, intuitive graphical interface. Program summaryProgram title:XTALOPT Catalogue identifier: AEGX_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEGX_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: GPL v2.1 or later [1] No. of lines in distributed program, including test data, etc.: 36 849 No. of bytes in distributed program, including test data, etc.: 1 149 399 Distribution format: tar.gz Programming language: C++ Computer: PCs, workstations, or clusters Operating system: Linux Classification: 7.7 External routines: QT [2], OpenBabel [3], AVOGADRO [4], SPGLIB [8] and one of: VASP [5], PWSCF [6], GULP [7]. Nature of problem: Predicting the crystal structure of a system from its stoichiometry alone remains a grand challenge in computational materials science, chemistry, and physics. Solution method: Evolutionary algorithms are stochastic search techniques which use concepts from biological evolution in order to locate the global minimum on their potential energy surface. Our evolutionary algorithm, XTALOPT, is freely

  7. First principles predictions of van der Waals bonded inorganic crystal structures: Test case, HgCl2

    SciTech Connect

    Cooper, Valentino R; Donald, Kelling J

    2015-01-01

    We study the crystals structure and stability of four possible polymorphs of HgCl2 using first principles density functional theory. Mercury (II) halides are a unique class of materials which, depending on the halide species, form in a wide range of crystal structures, ranging from densely packed solids to layered materials and molecular solids. Predicting the groundstate structure of any member of this group from first principles, therefore, requires a general purpose functional that treats van der Waals bonding and covalent/ionic bonding adequately. Here, we demonstrate that the non-local van der Waals density functional paired with the C09 exchange functional meets this bar for HgCl2. In particular, this functional is able to predict the correct groundstate among the structures tested as well as having extremely good agreement with the experimentally known crystal structure. These results highlight the maturity of this functional and open the door to using this method for truly first principles crystal structure predictions.

  8. First Principles Predictions of Van Der Waals Bonded Inorganic Crystal Structures: Test Case, HgCl2

    NASA Astrophysics Data System (ADS)

    Cooper, Valentino R.; Donald, Kelling J.

    We study the crystals structure and stability of four possible polymorphs of HgCl2 using first principles density functional theory. Mercury (II) halides are a unique class of materials which, depending on the halide species, form in a wide range of crystal structures, ranging from densely packed solids to layered materials and molecular solids. Predicting the groundstate structure of any member of this group from first principles, therefore, requires a general purpose functional that treats van der Waals bonding and covalent/ionic bonding adequately. Here, we demonstrate that the non-local van der Waals density functional paired with the C09 exchange functional meets this bar for HgCl2. In particular, this functional is able to predict the correct groundstate among the structures tested as well as having extremely good agreement with the experimentally known crystal structure. These results highlight the maturity of this functional and open the door to using this method for truly first principles crystal structure predictions.

  9. A Distributed Computing Method for Crystal Structure Prediction of Flexible Molecules:  An Application to N-(2-Dimethyl-4,5-dinitrophenyl) Acetamide.

    PubMed

    Bazterra, Victor E; Thorley, Matthew; Ferraro, Marta B; Facelli, Julio C

    2007-01-01

    In this paper, we describe a new distributed computing framework for crystal structure prediction that is capable of performing crystal structure searches for flexible molecules within any space group and with an arbitrary number of molecules in the asymmetric unit. The distributed computing framework includes a series of tightly integrated computer programs for generating the molecule's force field, sampling possible crystal structures using a distributed parallel genetic algorithm, locally minimizing these structures and classifying, sorting, and archiving the most relevant ones. As an example, we report the results of its application to the prediction of the crystal structure of the elusive N-(2-dimethyl-4,5-dinitrophenyl) acetamide, a molecule for which its crystal structure proved to be one of the most difficult cases in the last CSP2004 blind test for crystal structure prediction.

  10. Prediction method of basic domain structure in Fe3%Si(110) single crystal with grooved surface

    NASA Astrophysics Data System (ADS)

    Iwata, K.; Fujikura, M.; Arai, S.; Ishiyama, K.

    2014-05-01

    This paper proposes the method to accurately predict the 180° basic domain width (Dw) in demagnetized states of the grooved Fe3%Si(110) single crystal with the tilt angle of [001] out of the sheet surface (β). The evaluation of Dw enables the estimation of the anomalous eddy current losses. In this paper, Dw is optimized to minimize the magnetic Gibbs free energy represented by vector potentials using the finite element method and the conjugate gradient method. The μ*-method is adopted to approximate the magnetization relaxation. The stray field energy generated by the magnetic charges occurring on both grooves cross section and sheet surfaces is considered in our proposed method. The validity of the proposed method was confirmed by comparison with the observed Dw. As a result, we could reveal the β dependence of Dw against the groove depth. Moreover, the theoretical threshold of the domain refinement due to the grooves has been suggested.

  11. An Insight into Sodiation of Antimony from First-Principles Crystal Structure Prediction

    NASA Astrophysics Data System (ADS)

    Caputo, Riccarda

    2016-02-01

    Elemental antimony has recently become an attractive anode material for potential application in rechargeable sodium-ion batteries. I present a first-principles study of the structure-composition dependence of the Na-Sb system for both sodiation and desodiation processes. The enthalpy of reaction of x moles of sodium with the hexagonal structure of antimony reveals several stable crystal structures for 0 < x ≤ 3, with variable composition states for 1.25 < x < 2.75. The direct and reverse reactions pass through similar states in terms of enthalpy of formation and symmetry representation of the corresponding optimized structures, in particular for x = 1 and x = 3, confirming the two known phases, namely NaSb and Na3Sb. The calculations suggest that the optimal composition range for reversible sodiation of antimony is 1 < x ≤ 3, thus avoiding the global minimum at x = 1. This can help to rationalize the structure-composition dependence of the electrochemical performance of antimony in Na-ion batteries.

  12. PHOENIX: a scoring function for affinity prediction derived using high-resolution crystal structures and calorimetry measurements.

    PubMed

    Tang, Yat T; Marshall, Garland R

    2011-02-28

    Binding affinity prediction is one of the most critical components to computer-aided structure-based drug design. Despite advances in first-principle methods for predicting binding affinity, empirical scoring functions that are fast and only relatively accurate are still widely used in structure-based drug design. With the increasing availability of X-ray crystallographic structures in the Protein Data Bank and continuing application of biophysical methods such as isothermal titration calorimetry to measure thermodynamic parameters contributing to binding free energy, sufficient experimental data exists that scoring functions can now be derived by separating enthalpic (ΔH) and entropic (TΔS) contributions to binding free energy (ΔG). PHOENIX, a scoring function to predict binding affinities of protein-ligand complexes, utilizes the increasing availability of experimental data to improve binding affinity predictions by the following: model training and testing using high-resolution crystallographic data to minimize structural noise, independent models of enthalpic and entropic contributions fitted to thermodynamic parameters assumed to be thermodynamically biased to calculate binding free energy, use of shape and volume descriptors to better capture entropic contributions. A set of 42 descriptors and 112 protein-ligand complexes were used to derive functions using partial least-squares for change of enthalpy (ΔH) and change of entropy (TΔS) to calculate change of binding free energy (ΔG), resulting in a predictive r2 (r(pred)2) of 0.55 and a standard error (SE) of 1.34 kcal/mol. External validation using the 2009 version of the PDBbind "refined set" (n = 1612) resulted in a Pearson correlation coefficient (R(p)) of 0.575 and a mean error (ME) of 1.41 pK(d). Enthalpy and entropy predictions were of limited accuracy individually. However, their difference resulted in a relatively accurate binding free energy. While the development of an accurate and applicable

  13. In silico prediction and screening of modular crystal structures via a high-throughput genomic approach

    PubMed Central

    Li, Yi; Li, Xu; Liu, Jiancong; Duan, Fangzheng; Yu, Jihong

    2015-01-01

    High-throughput computational methods capable of predicting, evaluating and identifying promising synthetic candidates with desired properties are highly appealing to today's scientists. Despite some successes, in silico design of crystalline materials with complex three-dimensionally extended structures remains challenging. Here we demonstrate the application of a new genomic approach to ABC-6 zeolites, a family of industrially important catalysts whose structures are built from the stacking of modular six-ring layers. The sequences of layer stacking, which we deem the genes of this family, determine the structures and the properties of ABC-6 zeolites. By enumerating these gene-like stacking sequences, we have identified 1,127 most realizable new ABC-6 structures out of 78 groups of 84,292 theoretical ones, and experimentally realized 2 of them. Our genomic approach can extract crucial structural information directly from these gene-like stacking sequences, enabling high-throughput identification of synthetic targets with desired properties among a large number of candidate structures. PMID:26395233

  14. High-pressure polymorphs of ZnCO3: Evolutionary crystal structure prediction

    PubMed Central

    Bouibes, A.; Zaoui, A.

    2014-01-01

    The high-pressure behavior of zinc carbonate ZnCO3 has been investigated using universal structure prediction method together with the density functional theory. In order to explore all possible structures under pressure, separate calculations at high pressure are done here with increasing number of formula units in the unit cell. Two pressures induced phase transitions were considered. The first one occurs at 78 GPa and the second one at 121 GPa. The most stable ZnCO3 at ambient condition corresponds to the space group R-3c (phase I), which is in favorable agreement with experiment. The structure with C2/m space group (phase II) becomes stable between 78 GPa and 121 GPa. Finally, the structure with the space group P212121 (phase III) becomes the most stable when the pressure achieves 121 GPa. Some mechanical properties of R-3c structure were –additionally- calculated and compared with the experimental and previous theoretical data. The resulting behaviors support our findings and confirm the obtained phase transition. Besides, from the analysis of the electronic charge density it comes that at 78 GPa, new bond between oxygen and zinc is formed, what is likely the main cause behind the phase transition. PMID:24894072

  15. Prediction of different crystal structure phases in metal borides: A lithium monoboride analog to MgB2

    NASA Astrophysics Data System (ADS)

    Kolmogorov, Aleksey N.; Curtarolo, Stefano

    2006-05-01

    Modern compound prediction methods can efficiently screen large numbers of crystal structure phases and direct the experimental search for new materials. One of the most challenging problems in alloy theory is the identification of stable phases with a never seen prototype; such predictions do not always follow rational strategies. While performing ab initio data mining of intermetallic compounds we made an unexpected discovery: even in such a well-studied class of systems as metal borides there are previously unknown layered phases comparable in energy to the existing ones. With ab initio calculations we show that the new metal-sandwich (MS) lithium monoboride phases are marginally stable under ambient conditions but become favored over the known stoichiometric compounds under moderate pressures. The MS lithium monoboride exhibits electronic features similar to those in magnesium diboride and is expected to be a good superconductor.

  16. Transferable force field for crystal structure predictions, investigation of performance and exploration of different rescoring strategies using DFT-D methods.

    PubMed

    Broo, Anders; Nilsson Lill, Sten O

    2016-08-01

    A new force field, here called AZ-FF, aimed at being used for crystal structure predictions, has been developed. The force field is transferable to a new type of chemistry without additional training or modifications. This makes the force field very useful in the prediction of crystal structures of new drug molecules since the time-consuming step of developing a new force field for each new molecule is circumvented. The accuracy of the force field was tested on a set of 40 drug-like molecules and found to be very good where observed crystal structures are found at the top of the ranked list of tentative crystal structures. Re-ranking with dispersion-corrected density functional theory (DFT-D) methods further improves the scoring. After DFT-D geometry optimization the observed crystal structure is found at the leading top of the ranking list. DFT-D methods and force field methods have been evaluated for use in predicting properties such as phase transitions upon heating, mechanical properties or intrinsic crystalline solubility. The utility of using crystal structure predictions and the associated material properties in risk assessment in connection with form selection in the drug development process is discussed.

  17. Predicting crystal structures and properties of matter under extreme conditions via quantum mechanics: The pressure is on

    SciTech Connect

    Zurek, Eva; Grochala, Wojciech

    2014-11-27

    Experimental studies of compressed matter are now routinely conducted at pressures exceeding 1 mln atm (100 GPa) and occasionally they even surpass 10 mln atm (1 TPa). The structure and properties of solids that have been so significantly squeezed differ considerably from those know at ambient pressures (1 atm), often times leading to new and unexpected physics. Chemical reactivity is also substantially altered in the extreme pressure regime. In this feature paper we describe how synergy between theory and experiment can pave the road towards new experimental discoveries. Because chemical rules-of-thumb established at 1 atm often fail to predict the structures of solids under high pressure, automated crystal structure prediction (CSP) methods have been increasingly employed. After outlining the most important CSP techniques, we showcase a few examples from the recent literature that exemplify just how useful theory can be as an aid in the interpretation of experimental data, describe exciting theoretical predictions that are guiding experiment, and discuss when the computational methods that are currently routinely employed fail. Lastly, we forecast important problems that will be targeted by theory as theoretical methods undergo rapid development, along with the simultaneous increase of computational power.

  18. Predicting crystal structures and properties of matter under extreme conditions via quantum mechanics: The pressure is on

    DOE PAGES

    Zurek, Eva; Grochala, Wojciech

    2014-11-27

    Experimental studies of compressed matter are now routinely conducted at pressures exceeding 1 mln atm (100 GPa) and occasionally they even surpass 10 mln atm (1 TPa). The structure and properties of solids that have been so significantly squeezed differ considerably from those know at ambient pressures (1 atm), often times leading to new and unexpected physics. Chemical reactivity is also substantially altered in the extreme pressure regime. In this feature paper we describe how synergy between theory and experiment can pave the road towards new experimental discoveries. Because chemical rules-of-thumb established at 1 atm often fail to predict themore » structures of solids under high pressure, automated crystal structure prediction (CSP) methods have been increasingly employed. After outlining the most important CSP techniques, we showcase a few examples from the recent literature that exemplify just how useful theory can be as an aid in the interpretation of experimental data, describe exciting theoretical predictions that are guiding experiment, and discuss when the computational methods that are currently routinely employed fail. Lastly, we forecast important problems that will be targeted by theory as theoretical methods undergo rapid development, along with the simultaneous increase of computational power.« less

  19. A crystal structure prediction enigma solved: the gallic acid monohydrate system - surprises at 10 K.

    PubMed

    Hoser, A A; Sovago, I; Lanza, A; Madsen, A Ø

    2017-01-10

    The seemingly unpredictable structure of gallic acid monohydrate form IV has been investigated using accurate X-ray diffraction measurements at temperatures of 10 and 123 K. The measurements demonstrate that the structure is commensurately modulated at 10 K and disordered at higher temperatures. Aided by charge-density modeling and periodic DFT calculations we show that the disorder gives a substantial stabilization of the structure.

  20. Predicting crystals of Janus colloids

    NASA Astrophysics Data System (ADS)

    Vissers, Teun; Preisler, Zdeněk; Smallenburg, Frank; Dijkstra, Marjolein; Sciortino, Francesco

    2013-04-01

    We present a numerical study on the phase diagram for a simple model of Janus colloids, including ordered and disordered structures. Using a range of techniques, we generate a set of crystal structures and investigate their relative stability field in the pressure-temperature and temperature-density planes by means of free-energy calculations and thermodynamic integration schemes. We find that despite the Janus colloids' simple architecture, they form stable crystal structures with complicated bond-topologies on an underlying face-centered-cubic or hexagonal-close-packed lattice. In addition, we find a phase consisting of wrinkled bilayer sheets, competing with both the fluid and the crystal phases. We detect a metastable gas-liquid coexistence which displays a micellization-driven re-entrant behavior.

  1. Crystal-structure prediction via the Floppy-Box Monte Carlo algorithm: Method and application to hard (non)convex particles

    NASA Astrophysics Data System (ADS)

    de Graaf, Joost; Filion, Laura; Marechal, Matthieu; van Roij, René; Dijkstra, Marjolein

    2012-12-01

    In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009), 10.1103/PhysRevLett.103.188302] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The handling of hard-particle interactions in the FBMC algorithm is given special attention, as (soft) short-range and semi-long-range interactions can be treated in an analogous way. We also discuss two types of algorithms for checking for overlaps between polyhedra, the method of separating axes and a triangular-tessellation based technique. These can be combined with the FBMC method to enable crystal-structure prediction for systems composed of highly shape-anisotropic particles. Moreover, we present the results for the dense crystal structures predicted using the FBMC method for 159 (non)convex faceted particles, on which the findings in [J. de Graaf, R. van Roij, and M. Dijkstra, Phys. Rev. Lett. 107, 155501 (2011), 10.1103/PhysRevLett.107.155501] were based. Finally, we comment on the process of crystal-structure prediction itself and the choices that can be made in these simulations.

  2. Crystal-structure prediction via the floppy-box Monte Carlo algorithm: method and application to hard (non)convex particles.

    PubMed

    de Graaf, Joost; Filion, Laura; Marechal, Matthieu; van Roij, René; Dijkstra, Marjolein

    2012-12-07

    In this paper, we describe the way to set up the floppy-box Monte Carlo (FBMC) method [L. Filion, M. Marechal, B. van Oorschot, D. Pelt, F. Smallenburg, and M. Dijkstra, Phys. Rev. Lett. 103, 188302 (2009)] to predict crystal-structure candidates for colloidal particles. The algorithm is explained in detail to ensure that it can be straightforwardly implemented on the basis of this text. The handling of hard-particle interactions in the FBMC algorithm is given special attention, as (soft) short-range and semi-long-range interactions can be treated in an analogous way. We also discuss two types of algorithms for checking for overlaps between polyhedra, the method of separating axes and a triangular-tessellation based technique. These can be combined with the FBMC method to enable crystal-structure prediction for systems composed of highly shape-anisotropic particles. Moreover, we present the results for the dense crystal structures predicted using the FBMC method for 159 (non)convex faceted particles, on which the findings in [J. de Graaf, R. van Roij, and M. Dijkstra, Phys. Rev. Lett. 107, 155501 (2011)] were based. Finally, we comment on the process of crystal-structure prediction itself and the choices that can be made in these simulations.

  3. Physical Studies of P450–P450 Interactions: Predicting Quaternary Structures of P450 Complexes in Membranes from Their X-ray Crystal Structures

    PubMed Central

    Reed, James R.; Backes, Wayne L.

    2017-01-01

    Cytochrome P450 enzymes, which catalyze oxygenation reactions of both exogenous and endogenous chemicals, are membrane bound proteins that require interaction with their redox partners in order to function. Those responsible for drug and foreign compound metabolism are localized primarily in the endoplasmic reticulum of liver, lung, intestine, and other tissues. More recently, the potential for P450 enzymes to exist as supramolecular complexes has been shown by the demonstration of both homomeric and heteromeric complexes. The P450 units in these complexes are heterogeneous with respect to their distribution and function, and the interaction of different P450s can influence P450-specific metabolism. The goal of this review is to examine the evidence supporting the existence of physical complexes among P450 enzymes. Additionally, the review examines the crystal lattices of different P450 enzymes derived from X-ray diffraction data to make assumptions regarding possible quaternary structures in membranes and in turn, to predict how the quaternary structures could influence metabolism and explain the functional effects of specific P450–P450 interactions. PMID:28194112

  4. Frustrated polymer crystal structures

    NASA Astrophysics Data System (ADS)

    Lotz, B.; Strasbourg, 67083

    1997-03-01

    Several crystal structures or polymorphs of chiral or achiral polymers and biopolymers with three fold conformation of the helix have been found to conform to a common and -with one exception(Puterman, M. et al, J. Pol. Sci., Pol. Phys. Ed., 15, 805 (1977))- hitherto unsuspected packing scheme. The trigonal unit-cell contains three isochiral helices; the azimuthal setting of one helix differs significantly from that of the other two, leading to a so-called frustrated packing scheme, in which the environment of conformationally identical helices differs. Two variants of the frustrated scheme are analyzed. Similarities with frustrated two dimensional magnetic systems are underlined. Various examples of frustration in polymer crystallography are illustrated via the elucidation or reinterpretation of crystal phases or polymorphs of polyolefins, polyesters, cellulose derivatives and polypeptides. Structural manifestations (including AFM evidence) and morphological consequences of frustration are presented, which help diagnose the existence of this original packing of polymers.(Work done with L. Cartier, D. Dorset, S. Kopp, T. Okihara, M. Schumacher, W. Stocker.)

  5. Inorganic Crystal Structure Database (ICSD)

    National Institute of Standards and Technology Data Gateway

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

  6. Characterization of some amino acid derivatives of benzoyl isothiocyanate: Crystal structures and theoretical prediction of their reactivity

    NASA Astrophysics Data System (ADS)

    Odame, Felix; Hosten, Eric C.; Betz, Richard; Lobb, Kevin; Tshentu, Zenixole R.

    2015-11-01

    The reaction of benzoyl isothiocyanate with L-serine, L-proline, D-methionine and L-alanine gave 2-[(benzoylcarbamothioyl)amino]-3-hydroxypropanoic acid (I), 1-(benzoylcarbamothioyl)pyrrolidine-2-carboxylic acid (II), 2-[(benzoylcarbamothioyl)amino]-4-(methylsulfanyl)butanoic acid (III) and 2-[(benzoylcarbamothioyl)amino]propanoic acid (IV), respectively. The compounds have been characterized by IR, NMR, microanalyses and mass spectrometry. The crystal structures of all the compounds have also been discussed. Compound II showed rotamers in solution. DFT calculations of the frontier orbitals of the compounds have been carried out to ascertain the groups that contribute to the HOMO and LUMO, and to study their contribution to the reactivity of these compounds. The calculations indicated that the carboxylic acid group in these compounds is unreactive hence making the conversion to benzimidazoles via cyclization on the carboxylic acids impractical. This has been further confirmed by the reaction of compounds I-IV, respectively, with o-phenylene diamine which was unsuccessful but gave compound V.

  7. Structures beyond crystals

    NASA Astrophysics Data System (ADS)

    Hargittai, István

    2010-07-01

    Dan Shechtman made a seminal observation of the appearance on "non-crystallographic" symmetry in an alloy at the US National Bureau of Standards on April 8, 1982. This day has become known as the date of the discovery of quasicrystals. It was not easy to gain recognition for this discovery and the first printed report about it appeared two and a half years after the observation, which then was followed by an avalanche of publications. This was as if theoreticians and other experimentalists had only been waiting for a pioneer to come out with this revolutionary experiment. The discovery of quasicrystals just as the discovery of the structure of biological macromolecules was part of the development in which the framework of classical crystallography was crumbling and generalized crystallography—the science of structures—has emerged that had long been advanced by J. Desmond Bernal and his pupils. The discovery of quasicrystals offers some lessons about the nature of scientific discovery. This contribution presents selected aspects of the recognition of the importance of structures beyond crystals and is by far not a complete history of the areas involved.

  8. THE CRYSTAL STRUCTURE OF DIPHENYLTELLURIUM DIBROMIDE,

    DTIC Science & Technology

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), X RAY DIFFRACTION, FOURIER ANALYSIS, LEAST SQUARES METHOD, MOLECULAR STRUCTURE, CHEMICAL BONDS.

  9. REFINEMENT OF THE CRYSTAL STRUCTURE OF GUANIDINIUM ALUMINUM SULFATE HEXAHYDRATE.

    DTIC Science & Technology

    FERROELECTRIC CRYSTALS, * CRYSTAL STRUCTURE ), (*GUANIDINES, CRYSTAL STRUCTURE ), (*ALUMINUM COMPOUNDS, CRYSTAL STRUCTURE ), SULFATES, HYDRATES, X RAY DIFFRACTION, CHROMIUM COMPOUNDS, CRYSTAL LATTICES, CHEMICAL BONDS

  10. Demonstration of Crystal Structure.

    ERIC Educational Resources Information Center

    Neville, Joseph P.

    1985-01-01

    Describes an experiment where equal parts of copper and aluminum are heated then cooled to show extremely large crystals. Suggestions are given for changing the orientation of crystals by varying cooling rates. Students are more receptive to concepts of microstructure after seeing this experiment. (DH)

  11. Generation of crystal structures using known crystal structures as analogues

    PubMed Central

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

    2016-01-01

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

  12. Crystal Structure of UGe 2

    NASA Astrophysics Data System (ADS)

    Oikawa, Kennichi; Kamiyama, Takashi; Asano, Hajime; Ōnuki, Yoshichika; Kohgi, Masahumi

    1996-10-01

    The crystal structure of UGe2 has been determined by the X-ray precession method and Rietveld analysis of neutron powder diffraction data. The crystal system is orthorhombic (space group Cmmm) with lattice parameters a=0.40089(1), b=1.50889(3) and c=0.40950(1) nm. The structure is isomorphic with one of the polymorphs of ThGe2.

  13. Model predictive control of MSMPR crystallizers

    NASA Astrophysics Data System (ADS)

    Moldoványi, Nóra; Lakatos, Béla G.; Szeifert, Ferenc

    2005-02-01

    A multi-input-multi-output (MIMO) control problem of isothermal continuous crystallizers is addressed in order to create an adequate model-based control system. The moment equation model of mixed suspension, mixed product removal (MSMPR) crystallizers that forms a dynamical system is used, the state of which is represented by the vector of six variables: the first four leading moments of the crystal size, solute concentration and solvent concentration. Hence, the time evolution of the system occurs in a bounded region of the six-dimensional phase space. The controlled variables are the mean size of the grain; the crystal size-distribution and the manipulated variables are the input concentration of the solute and the flow rate. The controllability and observability as well as the coupling between the inputs and the outputs was analyzed by simulation using the linearized model. It is shown that the crystallizer is a nonlinear MIMO system with strong coupling between the state variables. Considering the possibilities of the model reduction, a third-order model was found quite adequate for the model estimation in model predictive control (MPC). The mean crystal size and the variance of the size distribution can be nearly separately controlled by the residence time and the inlet solute concentration, respectively. By seeding, the controllability of the crystallizer increases significantly, and the overshoots and the oscillations become smaller. The results of the controlling study have shown that the linear MPC is an adaptable and feasible controller of continuous crystallizers.

  14. Crystal structure of triclopyr.

    PubMed

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-09-01

    In the title compound {systematic name: 2-[(3,5,6-tri-chloro-pyridin-2-yl)-oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol-ecules in which the dihedral angles between the mean plane of the carb-oxy-lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter-molecular O-H⋯O hydrogen bonds form dimers through an R 2 (2)(8) ring motif and are extended into chains along [100] by weak π-π inter-actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter-molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4).

  15. Crystal structure of triclopyr

    PubMed Central

    Cho, Seonghwa; Kim, Jineun; Jeon, Youngeun; Kim, Tae Ho

    2014-01-01

    In the title compound {systematic name: 2-[(3,5,6-tri­chloro­pyridin-2-yl)­oxy]acetic acid}, the herbicide triclopyr, C7H4Cl3NO3, the asymmetric unit comprises two independent mol­ecules in which the dihedral angles between the mean plane of the carb­oxy­lic acid group and the pyridyl ring plane are 79.3 (6) and 83.8 (5)°. In the crystal, pairs of inter­molecular O—H⋯O hydrogen bonds form dimers through an R 2 2(8) ring motif and are extended into chains along [100] by weak π–π inter­actions [ring centroid separations = 3.799 (4) and 3.810 (4) Å]. In addition, short inter­molecular Cl⋯Cl contacts [3.458 (2) Å] connect the chains, yielding a two-dimensional architecture extending parallel to (020). The crystal studied was found to be non-merohedrally twinned with the minor component being 0.175 (4). PMID:25309266

  16. Crystal structure of fluroxypyr

    PubMed Central

    Park, Hyunjin; Choi, Myong Yong; Kwon, Eunjin; Kim, Tae Ho

    2016-01-01

    In the title pyridine herbicide {systematic name: 2-[(4-amino-3,5-di­chloro-6-fluoro­pyridin-2-yl)­oxy]acetic acid}, C7H5Cl2FN2O3, the mean plane of the carb­oxy­lic acid substituent and the pyridyl ring plane subtend a dihedral angle of 77.5 (1)°. In the crystal, pairs of O—H⋯O hydrogen bonds form inversion dimers with R 2 2(8) ring motifs. These are extended into chains along [011] by N—H⋯F hydrogen bonds. In addition, inter­molecular N—H⋯O hydrogen bonds and weak π–π inter­actions [ring centroid separation = 3.4602 (9) Å] connect these chains into a three-dimensional network. PMID:27980844

  17. Crystal structure of mandipropamid.

    PubMed

    Park, Hyunjin; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-10-01

    In the title compound, C23H22ClNO4 (systematic name: (RS)-2-(4-chloro-phen-yl)-N-{2-[3-meth-oxy-4-(prop-2-yn-1-yl-oxy)phen-yl]eth-yl}-2-(prop-2-yn-yloxy)acetamide), an amide fungicide, the dihedral angle between the chloro-benzene and benzene rings is 65.36 (6)°. In the crystal, N-H⋯O hydrogen bonds lead to zigzag supra-molecular chains along the c axis (glide symmetry). These are connected into layers by C-H⋯O and C-H⋯π inter-actions; the layers stack along the a axis with no specific inter-molecular inter-actions between them.

  18. Crystal structure of flumioxazin

    PubMed Central

    Park, Hyunjin; Kim, Jineun; Kwon, Eunjin; Kim, Tae Ho

    2015-01-01

    The title compound {systematic name: 2-[7-fluoro-3,4-di­hydro-3-oxo-4-(prop-2-yn-1-yl)-2H-1,4-benzoxazin-6-yl]-4,5,6,7-tetra­hydro-1H-iso­indole-1,3(2H)-dione}, C19H15FN2O4, is a dicarboximide herbicide. The dihedral angle between the male­imide and benzene ring planes is 66.13 (5)°. In the crystal, C—H⋯O and C—H⋯F hydrogen bonds and weak C—H⋯π inter­actions [3.5601 (19) Å] link adjacent mol­ecules, forming two-dimensional networks extending parallel to the (110) plane. PMID:26594468

  19. Extracting Crystal Chemistry from Amorphous Carbon Structures.

    PubMed

    Deringer, Volker L; Csányi, Gábor; Proserpio, Davide M

    2017-03-08

    Carbon allotropes have been explored intensively by ab initio crystal structure prediction, but such methods are limited by the large computational cost of the underlying density functional theory (DFT). Here we show that a novel class of machine-learning-based interatomic potentials can be used for random structure searching and readily predicts several hitherto unknown carbon allotropes. Remarkably, our model draws structural information from liquid and amorphous carbon exclusively, and so does not have any prior knowledge of crystalline phases: it therefore demonstrates true transferability, which is a crucial prerequisite for applications in chemistry. The method is orders of magnitude faster than DFT and can, in principle, be coupled with any algorithm for structure prediction. Machine-learning models therefore seem promising to enable large-scale structure searches in the future.

  20. Crystal structure determination of Efavirenz

    SciTech Connect

    Popeneciu, Horea Dumitru, Ristoiu; Tripon, Carmen Borodi, Gheorghe Pop, Mihaela Maria

    2015-12-23

    Needle-shaped single crystals of the title compound, C{sub 14}H{sub 9}ClF{sub 3}NO{sub 2}, were obtained from a co-crystallization experiment of Efavirenz with maleic acid in a (1:1) ratio, using methanol as solvent. Crystal structure determination at room temperature revealed a significant anisotropy of the lattice expansion compared to the previously reported low-temperature structure. In both low- and room temperature structures the cyclopropylethynyl fragment in one of the asymmetric unit molecules is disordered. While at low-temperature only one C atom exhibits positional disorder, at room temperature the disorder is present for two C atoms of the cyclopropane ring.

  1. Crystal structure refinement with SHELXL.

    PubMed

    Sheldrick, George M

    2015-01-01

    The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as `a CIF') containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  2. Crystal structure refinement with SHELXL

    SciTech Connect

    Sheldrick, George M.

    2015-01-01

    New features added to the refinement program SHELXL since 2008 are described and explained. The improvements in the crystal structure refinement program SHELXL have been closely coupled with the development and increasing importance of the CIF (Crystallographic Information Framework) format for validating and archiving crystal structures. An important simplification is that now only one file in CIF format (for convenience, referred to simply as ‘a CIF’) containing embedded reflection data and SHELXL instructions is needed for a complete structure archive; the program SHREDCIF can be used to extract the .hkl and .ins files required for further refinement with SHELXL. Recent developments in SHELXL facilitate refinement against neutron diffraction data, the treatment of H atoms, the determination of absolute structure, the input of partial structure factors and the refinement of twinned and disordered structures. SHELXL is available free to academics for the Windows, Linux and Mac OS X operating systems, and is particularly suitable for multiple-core processors.

  3. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

    We study the nucleation of crystalline cluster phases in the generalized exponential model with exponent n = 4. Due to the finite value of this pair potential for zero separation, at high densities the system forms cluster crystals with multiply occupied lattice sites. Here, we investigate the microscopic mechanisms that lead to the formation of cluster crystals from a supercooled liquid in the low-temperature region of the phase diagram. Using molecular dynamics and umbrella sampling, we calculate the free energy as a function of the size of the largest crystalline nucleus in the system, and compare our results with predictions from classical nucleation theory. Employing bond-order parameters based on a Voronoi tessellation to distinguish different crystal structures, we analyze the average composition of crystalline nuclei. We find that even for conditions where a multiply occupied fcc crystal is the thermodynamically stable phase, the nucleation into bcc cluster crystals is strongly preferred. Furthermore, we study the particle mobility in the supercooled liquid and in the cluster crystal. In the cluster crystal, the motion of individual particles is captured by a simple reaction-diffusion model introduced previously to model the kinetics of hydrogen bonds.

  4. Predicting complex mineral structures using genetic algorithms.

    PubMed

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  5. Crystal structure of guggulsterone Z

    SciTech Connect

    Gupta, V. K. Bandhoria, P.; Gupta, B. D.; Gupta, K. K.

    2006-03-15

    The crystal structure of the title compound (4,17(20)-trans-pregnadiene-3,16-dione, C{sub 21}H{sub 28}O{sub 2}) has been determined by direct methods using single-crystal X-ray diffraction data. The compound crystallizes into the orthorhombic space group P2{sub 1}2{sub 1}2{sub 1} with the unit cell parameters a = 7.908(2) A, b = 13.611(3) A, c = 16.309(4) A, and Z = 4. The structure has been refined to R = 0.058 for 3667 observed reflections. The bond distances and angles are in good agreement with guggulsterone E and other related steroid molecules. Ring A exists in the distorted sofa conformation, while rings B and C adopt the distorted chair conformation. Five-membered ring D is intermediate between the half-chair and envelope conformations. The A/B ring junction is quasi-trans, while ring systems B/C and C/D are trans fused about the C(8)-C(9) and C(13)-C(14) bonds, respectively. The steroid nucleus has a small twist, as shown by the C(19)-C(10)...C(13)-C(18) pseudo-torsion angle of 7.2{sup o}. The crystal structure is stabilized by intra-and intermolecular C-H...O hydrogen bonds.

  6. THE CRYSTAL STRUCTURE OF ANTIMONY (III) SULFOBROMIDE, SBSBR,

    DTIC Science & Technology

    ANTIMONY COMPOUNDS, *SULFUR COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , BROMIDES, SYMMETRY(CRYSTALLOGRAPHY), FOURIER ANALYSIS, MOLECULAR STRUCTURE, CRYSTAL LATTICES, CHEMICAL BONDS, X RAY DIFFRACTION.

  7. Construction of crystal structure prototype database: methods and applications

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  8. Construction of crystal structure prototype database: methods and applications.

    PubMed

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

    2017-04-26

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

  9. Crystal Engineering: from Structure to Function

    NASA Astrophysics Data System (ADS)

    Hollingsworth, Mark D.

    2002-03-01

    Modern crystal engineering has emerged as a rich discipline whose success requires an iterative process of synthesis, crystallography, crystal structure analysis, and computational methods. By focusing on the molecular recognition events during nucleation and growth, chemists have uncovered new ways of controlling the internal structure and symmetry of crystals and of producing materials with useful chemical and physical properties.

  10. Microfluidic Approaches for Protein Crystal Structure Analysis.

    PubMed

    Maeki, Masatoshi; Yamaguchi, Hiroshi; Tokeshi, Manabu; Miyazaki, Masaya

    2016-01-01

    This review summarizes two microfluidic-based protein crystallization methods, protein crystallization behavior in the microfluidic devices, and their applications for X-ray crystal structure analysis. Microfluidic devices provide many advantages for protein crystallography; they require small sample volumes, provide high-throughput screening, and allow control of the protein crystallization. A droplet-based protein crystallization method is a useful technique for high-throughput screening and the formation of a single crystal without any complicated device fabrication process. Well-based microfluidic platforms also enable effective protein crystallization. This review also summarizes the protein crystal growth behavior in microfluidic devices as, is known from viewpoints of theoretical and experimental approaches. Finally, we introduce applications of microfluidic devices for on-chip crystal structure analysis.

  11. Predicting crystal growth via a unified kinetic three-dimensional partition model.

    PubMed

    Anderson, Michael W; Gebbie-Rayet, James T; Hill, Adam R; Farida, Nani; Attfield, Martin P; Cubillas, Pablo; Blatov, Vladislav A; Proserpio, Davide M; Akporiaye, Duncan; Arstad, Bjørnar; Gale, Julian D

    2017-04-03

    Understanding and predicting crystal growth is fundamental to the control of functionality in modern materials. Despite investigations for more than one hundred years, it is only recently that the molecular intricacies of these processes have been revealed by scanning probe microscopy. To organize and understand this large amount of new information, new rules for crystal growth need to be developed and tested. However, because of the complexity and variety of different crystal systems, attempts to understand crystal growth in detail have so far relied on developing models that are usually applicable to only one system. Such models cannot be used to achieve the wide scope of understanding that is required to create a unified model across crystal types and crystal structures. Here we describe a general approach to understanding and, in theory, predicting the growth of a wide range of crystal types, including the incorporation of defect structures, by simultaneous molecular-scale simulation of crystal habit and surface topology using a unified kinetic three-dimensional partition model. This entails dividing the structure into 'natural tiles' or Voronoi polyhedra that are metastable and, consequently, temporally persistent. As such, these units are then suitable for re-construction of the crystal via a Monte Carlo algorithm. We demonstrate our approach by predicting the crystal growth of a diverse set of crystal types, including zeolites, metal-organic frameworks, calcite, urea and l-cystine.

  12. Uranocircite: luminescence and crystal structure

    SciTech Connect

    Matkovskiy, A.O.; Sidorenko, G.A.; Tarashchan, A.N.

    1981-01-01

    A study on the determination of the complex structure of the electron-vibration spectra and the elucidation of their relation to crystallochemical factors in uranocircite is presented. The work was performed on samples from zones of a single crystal of the same natural meta-uranocircite, differing in color, and also on other specimens from various Soviet and foreign deposits. Of the 15 meta-uranocircite specimens investigated, in 14 cases the luminescence spectra were homoypic and were a series of equidistant groups of lines of the fine structure; the spectral position of which was practically constant for all the specimens. The degree of hydration was found to have practically no influence on the luminescence of the meta-uranocircite. The investigation supports the supposition that there are marked differences in the structures of minerals of the uran-mica group, although in the authors' opinion, the mechanism itself of multi-center radiation is universal and manifested for all secondary uranium minerals. (JMT)

  13. Millimeter-wave Bragg diffraction of microfabricated crystal structures

    NASA Astrophysics Data System (ADS)

    Yuan, C. P.; Lin, S. Y.; Chang, T. H.; Shew, B. Y.

    2011-06-01

    A compact diffraction apparatus is developed with millimeter-wave propagation between two parallel plates. Two types of microfabricated model crystals are individually mounted on a rotatable structure. In contrast to previous work, the experimental results agree well with Bragg's predictions because multiple scattering is minimized in this configuration. Factors that affect the resolution and signal strength, such as the number of scatterers, cylinder radius, and the distance between the detector and the model crystal, are analyzed. The apparatus offers a visually accessible way to teach students about crystal structure as well as scattering and diffraction.

  14. Crystal fingerprint space--a novel paradigm for studying crystal-structure sets.

    PubMed

    Valle, Mario; Oganov, Artem R

    2010-09-01

    The initial aim of the crystal fingerprint project was to solve a very specific problem: to classify and remove duplicate crystal structures from the results generated by the evolutionary crystal-structure predictor USPEX. These duplications decrease the genetic diversity of the population used by the evolutionary algorithm, potentially leading to stagnation and, after a certain time, reducing the likelihood of predicting essentially new structures. After solving the initial problem, the approach led to unexpected discoveries: unforeseen correlations, useful derived quantities and insight into the structure of the overall set of results. All of these were facilitated by the project's underlying idea: to transform the structure sets from the physical configuration space to an abstract, high-dimensional space called the fingerprint space. Here every structure is represented as a point whose coordinates (fingerprint) are computed from the crystal structure. Then the space's distance measure, interpreted as structure 'closeness', enables grouping of structures into similarity classes. This model provides much flexibility and facilitates access to knowledge and algorithms from fields outside crystallography, e.g. pattern recognition and data mining. The current usage of the fingerprint-space model is revealing interesting properties that relate to chemical and crystallographic attributes of a structure set. For this reason, the mapping of structure sets to fingerprint space could become a new paradigm for studying crystal-structure ensembles and global chemical features of the energy landscape.

  15. Synthesis, characterization, crystal structure and predicting the second-order optical nonlinearity of a new dicobalt(III) complex with Schiff base ligand

    NASA Astrophysics Data System (ADS)

    Zarei, Seyed Amir; Piltan, Mohammad; Hassanzadeh, Keyumars; Akhtari, Keivan; Cinčić, Dominik

    2015-03-01

    The synthesis and characterization of dicobalt(III) complex [Co2L2(OMe)2] of the tetradentate Schiff base ligand N,N‧-bis(2-hydroxybenzylidene)-2,2-dimethyl-1,3-propanediamine (H2L) is reported. The crystal structure of the complex has been determined that exhibited the pseudo-octahedral geometry around both cobalt(III) ions. In the complexation process, H2L acts as two negatively charged tetradentate ligand, L2-, and methoxy group plays as bridging ligand. The geometry structure of the complex is optimized by density functional theory (DFT) using B3LYP/6-311G(d,p). The calculated geometric parameters are in good agreement with the corresponding experimental data. Second-Order Nonlinear Optical (NLO) property of the complex is evaluated by DFT/B3LYP/6-311G(d,p) on the base of the optimized structure that shows the enhancement relative to the calculated value of H2L. The calculated NLO value of the complex is much greater than the corresponding value of urea.

  16. Crystal structure analysis of intermetallic compounds

    NASA Technical Reports Server (NTRS)

    Conner, R. A., Jr.; Downey, J. W.; Dwight, A. E.

    1968-01-01

    Study concerns crystal structures and lattice parameters for a number of new intermetallic compounds. Crystal structure data have been collected on equiatomic compounds, formed between an element of the Sc, Ti, V, or Cr group and an element of the Co or Ni group. The data, obtained by conventional methods, are presented in an easily usable tabular form.

  17. THE CRYSTAL STRUCTURE OF ALPHA-DIMETHYLTELLURIUM DICHLORIDE,

    DTIC Science & Technology

    TELLURIUM COMPOUNDS, *ORGANOMETALLIC COMPOUNDS, CRYSTAL STRUCTURE , CRYSTAL STRUCTURE , CHLORIDES, SYMMETRY(CRYSTALLOGRAPHY), MOLECULAR STRUCTURE, CHEMICAL BONDS, X RAY DIFFRACTION, ANISOTROPY, FOURIER ANALYSIS.

  18. Preparation and Characterization of [pi]-Stacking Quinodimethane Oligothiophenes. Predicting Semiconductor Behavior and Bandwidths from Crystal Structures and Molecular Orbital Calculations

    SciTech Connect

    Janzen, Daron E.; Burand, Michael W.; Ewbank, Paul C.; Pappenfus, Ted M.; Higuchi, Hiroyuki; da Silva, Demetrio A.; Young, Victor G.; Bredas, Jean-Luc; Mann, Kent R.

    2010-11-16

    A series of new quinodimethane-substituted terthiophene and quaterthiophene oligomers has been investigated for comparison with a previously studied quinoid oligothiophene that has demonstrated high mobilities and ambipolar transport behavior in thin-film transistor devices. Each new quinoidal thiophene derivative shows a reversible one-electron oxidation between 0.85 and 1.32 V, a quasi-reversible one-electron second oxidation between 1.37 and 1.96 V, and a reversible two-electron reduction between -0.05 and -0.23 V. The solution UV-vis-NIR spectrum of each compound is dominated by an intense epsilon congruent with 100,000 M{sup -1} cm{sup -1} low energy pi-pi transition that has a lambda(max) ranging between 648 and 790 nm. All X-ray crystal structures exhibit very planar quinoidal backbones and short intermolecular pi-stacking distances (3.335-3.492 A). Structures exhibit a single pi-stacking distance with parallel cofacial stacking (sulfur atoms of equivalent rings pointed in the same direction) or with alternating distances and antiparallel cofacial stacking (sulfur atoms of equivalent rings pointed in the opposite direction). Examples of the layered and herringbone-packing motifs are observed for both the parallel and the antiparallel cofacial stacking. Analysis of the X-ray structures and molecular orbital calculations indicates that all of these compounds have one-dimensional electronic band structures as a result of the pi-stacking. For structures with a unique pi-stacking distance, a simple geometric overlap parameter calculated from the shape of the molecule and the slip from perfect registry in the pi-stack correlates well with the transfer integrals (t) calculated using molecular orbital theory. The calculated valence (633 meV) and conduction (834 meV) bandwidths for a quinoid quaterthiophene structure are similar to those calculated for the benchmark pentacene and indicate that both hole and electron mobilities could be significant.

  19. Crystal structures of the human adiponectin receptors

    PubMed Central

    Tanabe, Hiroaki; Fujii, Yoshifumi; Hosaka, Toshiaki; Motoyama, Kanna; Ikeda, Mariko; Wakiyama, Motoaki; Terada, Takaho; Ohsawa, Noboru; Hato, Masakatsu; Ogasawara, Satoshi; Hino, Tomoya; Murata, Takeshi; Iwata, So; Hirata, Kunio; Kawano, Yoshiaki; Yamamoto, Masaki; Kimura-Someya, Tomomi; Shirouzu, Mikako; Yamauchi, Toshimasa; Kadowaki, Takashi; Yokoyama, Shigeyuki

    2015-01-01

    Adiponectin stimulation of its receptors, AdipoR1 and AdipoR2, increases AMPK and PPAR activities, respectively, thereby contributing to healthy longevity as key anti-diabetic molecules. AdipoR1 and AdipoR2 were predicted to contain seven transmembrane helices with the opposite topology to G protein-coupled receptor (GPCR)s. Here we report the crystal structures of human AdipoR1 and AdipoR2 at 2.9- and 2.4-Å resolution, respectively, which represent a novel class of receptor structure. The seven-transmembrane helices, conformationally distinct from those of GPCRs, enclose a large cavity where three conserved histidine residues coordinate a zinc ion. The zinc-binding structure may play a role in the adiponectin-stimulated AMPK phosphorylation and UCP2 upregulation. Adiponectin may broadly interact with the extracellular face, rather than the C-terminal flexible tail, of the receptors. The present information will facilitate the understanding of novel structure-function relationships and the development and optimization of AdipoR agonists for the treatment of obesity-related diseases, such as type 2 diabetes. PMID:25855295

  20. Structure-Based Predictions of Activity Cliffs

    PubMed Central

    Husby, Jarmila; Bottegoni, Giovanni; Kufareva, Irina; Abagyan, Ruben; Cavalli, Andrea

    2015-01-01

    In drug discovery, it is generally accepted that neighboring molecules in a given descriptors' space display similar activities. However, even in regions that provide strong predictability, structurally similar molecules can occasionally display large differences in potency. In QSAR jargon, these discontinuities in the activity landscape are known as ‘activity cliffs’. In this study, we assessed the reliability of ligand docking and virtual ligand screening schemes in predicting activity cliffs. We performed our calculations on a diverse, independently collected database of cliff-forming co-crystals. Starting from ideal situations, which allowed us to establish our baseline, we progressively moved toward simulating more realistic scenarios. Ensemble- and template-docking achieved a significant level of accuracy, suggesting that, despite the well-known limitations of empirical scoring schemes, activity cliffs can be accurately predicted by advanced structure-based methods. PMID:25918827

  1. Predicting patchy particle crystals: Variable box shape simulations and evolutionary algorithms

    NASA Astrophysics Data System (ADS)

    Bianchi, Emanuela; Doppelbauer, Günther; Filion, Laura; Dijkstra, Marjolein; Kahl, Gerhard

    2012-06-01

    We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an approach based on Monte Carlo simulations in the isobaric-isothermal ensemble and (ii) an optimization technique based on ideas of evolutionary algorithms. We show that the two methods are equally successful and provide consistent results on crystalline phases of patchy particle systems.

  2. Crystal structure of meteoritic schreibersites: determination of absolute structure

    NASA Astrophysics Data System (ADS)

    Skála, Roman; Císařová, Ivana

    Minerals of the schreibersite nickelphosphide series (Fe,Ni)3P crystallize in the non-centrosymmetric space group Ibar 4. As a consequence, they can possess two different spatial arrangements of the constituting atoms within the unit cell, related by the inversion symmetry operation. Here, we present the crystal structure refinements from single crystal X-ray diffraction data for schreibersite grains from iron meteorites Acuña, Carlton, Hex River Mts. (three different crystals), Odessa (two different crystals), Sikhote Alin, and Toluca aiming for the determination of the absolute structure of the examined crystals. The crystals studied cover the composition range from 58 mol% to 80 mol% Fe3P end-member. Unit-cell parameter a and volume of the unit cell V, as well as certain topological structural parameters tightly correlate with Fe3P content. Unit-cell parameter c, on the other hand, does not show such strong correlation. Eight of the nine crystal structure refinements allowed unambiguous absolute structure assignment. The single crystal extracted from Toluca is, however, of poor quality and consequently the structure refinement did not provide as good results as the rest of the materials. Also, this crystal has only weak inversion distinguishing power to provide unequivocal absolute structure determination. Six of the eight unambiguous absolute structure determinations indicated inverted atomic arrangement compared to that reported in earlier structure refinements (here called standard). Only two grains, one taken from Odessa iron and the other from the Hex River Mts. meteorite, reveal the dominance of standard crystal structure setting.

  3. Structures of cyano-biphenyl liquid crystals

    NASA Technical Reports Server (NTRS)

    Chu, Yuan-Chao; Tsang, Tung; Rahimzadeh, E.; Yin, L.

    1989-01-01

    The structures of p-alkyl- p'-cyano- bicyclohexanes, C(n)H(2n+1) (C6H10)(C6H10) CN (n-CCH), and p-alkyl- p'-cyano- biphenyls, C(n)H(2n+1) (C6H4)(C6H4) CN (n-CBP), were studied. It is convenient to use an x ray image intensification device to search for symmetric x ray diffraction patterns. Despite the similarities in molecular structures of these compounds, very different crystal structures were found. For the smectic phase of 2CCH, the structure is close to rhombohedral with threefold symmetry. In contrast, the structure is close to hexagonal close-packed with two molecules per unit cell for 4CCH. Since intermolecular forces may be quite weak for these liquid crystals systems, it appears that crystal structures change considerably when the alkyl chain length is slightly altered. Different structures were also found in the crystalline phase of n-CBP for n = 6 to 9. For n = 7 to 9, the structures are close to monclinic. The structures are reminiscent of the smectic-A liquid crystal structures with the linear molecules slightly tilted away from the c-axis. In contrast, the structure is quite different for n = 6 with the molecules nearly perpendicular to the c-axis.

  4. Crystal structure of riboflavin synthase

    SciTech Connect

    Liao, D.-I.; Wawrzak, Z.; Calabrese, J.C.; Viitanen, P.V.; Jordan, D.B.

    2010-03-05

    Riboflavin synthase catalyzes the dismutation of two molecules of 6,7-dimethyl-8-(1'-D-ribityl)-lumazine to yield riboflavin and 4-ribitylamino-5-amino-2,6-dihydroxypyrimidine. The homotrimer of 23 kDa subunits has no cofactor requirements for catalysis. The enzyme is nonexistent in humans and is an attractive target for antimicrobial agents of organisms whose pathogenicity depends on their ability to biosynthesize riboflavin. The first three-dimensional structure of the enzyme was determined at 2.0 {angstrom} resolution using the multiwavelength anomalous diffraction (MAD) method on the Escherichia coli protein containing selenomethionine residues. The homotrimer consists of an asymmetric assembly of monomers, each of which comprises two similar {beta} barrels and a C-terminal {alpha} helix. The similar {beta} barrels within the monomer confirm a prediction of pseudo two-fold symmetry that is inferred from the sequence similarity between the two halves of the protein. The {beta} barrels closely resemble folds found in phthalate dioxygenase reductase and other flavoproteins. The three active sites of the trimer are proposed to lie between pairs of monomers in which residues conserved among species reside, including two Asp-His-Ser triads and dyads of Cys-Ser and His-Thr. The proposed active sites are located where FMN (an analog of riboflavin) is modeled from an overlay of the {beta} barrels of phthalate dioxygenase reductase and riboflavin synthase. In the trimer, one active site is formed, and the other two active sites are wide open and exposed to solvent. The nature of the trimer configuration suggests that only one active site can be formed and be catalytically competent at a time.

  5. Datamining protein structure databanks for crystallization patterns of proteins.

    PubMed

    Valafar, Homayoun; Prestegard, James H; Valafar, Faramarz

    2002-12-01

    A study of 345 protein structures selected among 1,500 structures determined by nuclear magnetic resonance (NMR) methods, revealed useful correlations between crystallization properties and several parameters for the studied proteins. NMR methods of structure determination do not require the growth of protein crystals, and hence allow comparison of properties of proteins that have or have not been the subject of crystallographic approaches. One- and two-dimensional statistical analyses of the data confirmed a hypothesized relation between the size of the molecule and its crystallization potential. Furthermore, two-dimensional Bayesian analysis revealed a significant relationship between relative ratio of different secondary structures and the likelihood of success for crystallization trials. The most immediate result is an apparent correlation of crystallization potential with protein size. Further analysis of the data revealed a relationship between the unstructured fraction of proteins and the success of its crystallization. Utilization of Bayesian analysis on the latter correlation resulted in a prediction performance of about 64%, whereas a two-dimensional Bayesian analysis succeeded with a performance of about 75%.

  6. Crystal structure of a Trypanosoma brucei metacaspase.

    PubMed

    McLuskey, Karen; Rudolf, Jana; Proto, William R; Isaacs, Neil W; Coombs, Graham H; Moss, Catherine X; Mottram, Jeremy C

    2012-05-08

    Metacaspases are distantly related caspase-family cysteine peptidases implicated in programmed cell death in plants and lower eukaryotes. They differ significantly from caspases because they are calcium-activated, arginine-specific peptidases that do not require processing or dimerization for activity. To elucidate the basis of these differences and to determine the impact they might have on the control of cell death pathways in lower eukaryotes, the previously undescribed crystal structure of a metacaspase, an inactive mutant of metacaspase 2 (MCA2) from Trypanosoma brucei, has been determined to a resolution of 1.4 Å. The structure comprises a core caspase fold, but with an unusual eight-stranded β-sheet that stabilizes the protein as a monomer. Essential aspartic acid residues, in the predicted S1 binding pocket, delineate the arginine-specific substrate specificity. In addition, MCA2 possesses an unusual N terminus, which encircles the protein and traverses the catalytic dyad, with Y31 acting as a gatekeeper residue. The calcium-binding site is defined by samarium coordinated by four aspartic acid residues, whereas calcium binding itself induces an allosteric conformational change that could stabilize the active site in a fashion analogous to subunit processing in caspases. Collectively, these data give insights into the mechanistic basis of substrate specificity and mode of activation of MCA2 and provide a detailed framework for understanding the role of metacaspases in cell death pathways of lower eukaryotes.

  7. Crystal structure of enolase from Drosophila melanogaster.

    PubMed

    Sun, Congcong; Xu, Baokui; Liu, Xueyan; Zhang, Zhen; Su, Zhongliang

    2017-04-01

    Enolase is an important enzyme in glycolysis and various biological processes. Its dysfunction is closely associated with diseases. Here, the enolase from Drosophila melanogaster (DmENO) was purified and crystallized. A crystal of DmENO diffracted to 2.0 Å resolution and belonged to space group R32. The structure was solved by molecular replacement. Like most enolases, DmENO forms a homodimer with conserved residues in the dimer interface. DmENO possesses an open conformation in this structure and contains conserved elements for catalytic activity. This work provides a structural basis for further functional and evolutionary studies of enolase.

  8. Natural photonic crystals: formation, structure, function

    NASA Astrophysics Data System (ADS)

    Bartl, Michael H.; Dahlby, Michael R.; Barrows, Frank P.; Richens, Zachary J.; Terooatea, Tommy; Jorgensen, Matthew R.

    2012-03-01

    The structure and properties of natural photonic crystals are discussed using the colored scales of the beetle Lamprocyphus augustus as an example. While the exact mechanism behind the formation of these biopolymeric photonic structures has yet to be fully explored, similarities of these structures to intracellular cubic membrane architectures are introduced. Some crucial parameters behind the formation of cubic membranes are discussed. Using these insights, intracellular cubic membrane structures are transformed into an extracellular environment.

  9. Optical extinction due to intrinsic structural variations of photonic crystals

    NASA Astrophysics Data System (ADS)

    Koenderink, A. Femius; Lagendijk, Ad; Vos, Willem L.

    2005-10-01

    Unavoidable variations in size and position of the building blocks of photonic crystals cause light scattering and extinction of coherent beams. We present a model for both two- and three-dimensional photonic crystals that relates the extinction length to the magnitude of the variations. The predicted lengths agree well with our experiments on high-quality opals and inverse opals, and with literature data analyzed by us. As a result, control over photons is limited to distances up to 50 lattice parameters (˜15 μm) in state-of-the-art structures, thereby impeding applications that require large photonic crystals, such as proposed optical integrated circuits. Conversely, scattering in photonic crystals may lead to different physics such as Anderson localization and nonclassical diffusion.

  10. The crystal structure and crystal chemistry of fernandinite and corvusite

    USGS Publications Warehouse

    Evans, H.T.; Post, J.E.; Ross, D.R.; Nelen, J.A.

    1994-01-01

    Using type material of fernandinite from Minasragra, Peru, and corvusite from the Jack Claim, La Sal Mountains, Utah, the properties and crystal chemistry of these minerals have been determined by Rietveld analysis of the powder X-ray-diffraction patterns. The crystal structure of both species is isotypic with the V2O5 -type layer first found for ??-Ag0.68V2O5; it consists of chains of VO6 octahedra linked by opposite corners (parallel to b) condensed by edge-sharing to form the layer. The vanadium has average valence 4.8, and the resulting layer-charge is balanced by varying amounts of Ca, Na, and K in the interlayer region accompanied by labile water. This study has confirmed the validity of fernandinite as a unique mineral species. It is closely related to corvusite, from which it is distinguished on the basis of the dominant interlayer cation: Ca for fernandinite, Na for curvusite. -Authors

  11. Crystal Structures of Sialyltransferase from Photobacterium damselae

    PubMed Central

    Huynh, Nhung; Li, Yanhong; Yu, Hai; Huang, Shengshu; Lau, Kam; Chen, Xi; Fisher, Andrew J.

    2014-01-01

    Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2–6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2–6-linked sialosides. Here we report three crystal structures of this enzyme. Two structures with and without a donor substrate analogue CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks the Ig-domain. Comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold. PMID:25451227

  12. Crystal structure and chirality of natural floridoside.

    PubMed

    Simon-Colin, Christelle; Michaud, François; Léger, Jean-Michel; Deslandes, Eric

    2003-10-31

    The crystal structure and absolute configuration of natural floridoside (2-O-alpha-D-galactopyranosylglycerol) were determined by single-crystal X-ray diffraction analysis. The space group is orthorhombic P2(1)2(1)2(1) with Z=4, a=4.885(1), b=9.734(1), c=23.886(2) A at 296 +/- 2 K. The structure was solved by a direct method and refined to R=0.0351 from 1914 reflections of Cu Kalpha radiation.

  13. Predicting equilibrium uranium isotope fractionation in crystals and solution

    NASA Astrophysics Data System (ADS)

    Schauble, E. A.

    2015-12-01

    Despite the rapidly growing interest in using 238U/235U measurements as a proxy for changes in oxygen abundance in surface and near-surface environments, the present theoretical understanding of uranium isotope fractionation is limited to a few simple gas-phase molecules and analogues of dissolved species (e.g., 1,2,3). Understanding uranium isotope fractionation behavior in more complicated species, such as crystals and adsorption complexes, will help in the design and interpretation of experiments and field studies, and may suggest other uses for 38U/235U measurements. In this study, a recently developed first-principles method for estimating the nuclear volume component of field shift fractionation in crystals and complex molecular species (4) is combined with mass-dependent fractionation theory to predict equilibrium 38U/235U fractionations in aqueous and crystalline uranium compounds, including uraninite (UO2). The nuclear field shift effect, caused by the interaction of electrons with the finite volume of the positive charge distribution in uranium nuclei, is estimated using Density Functional Theory and the Projector Augmented Wave method (DFT-PAW). Tests against relativistic electronic structure calculations and Mössbauer isomer shift data indicate that the DFT-PAW method is reasonably accurate, while being much better suited to models of complex and crystalline species. Initial results confirm previous predictions that the nuclear volume effect overwhelms mass depdendent fractionation in U(VI)-U(IV) exchange reactions, leading to higher 238U/235U in U(IV) species (i.e., for UO2 xtal vs. UO22+aq, ln αNV ≈ +1.8‰ , ln αMD ≈ -0.8‰, ln αTotal ≈ +1.0‰ at 25ºC). UO2 and U(H2O)94+, are within ~0.4‰ of each other, while U(VI) species appear to be more variable. This suggests that speciation is likely to significantly affect natural uranium isotope fractionations, in addition to oxidation state. Tentatively, it appears that uranyl-type (UO22

  14. Crystal structure of canagliflozin hemihydrate.

    PubMed

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-05-01

    There are two canagliflozin mol-ecules (A and B) and one water mol-ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro-phen-yl)thio-phen-2-yl]meth-yl}-4-methylphen-yl)-6-(hy-droxy-meth-yl)-3,4,5,6-tetra-hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl-benzene and thio-phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro-benzene and thio-phene rings are 24.2 (6) and 20.5 (9)° in mol-ecules A and B, respectively. The hydro-pyran ring exhibits a chair conformation in both canagliflozin mol-ecules. In the crystal, the canagliflozin mol-ecules and lattice water mol-ecules are connected via O-H⋯O hydrogen bonds into a three-dimensional supra-molecular architecture.

  15. Crystal structure of canagliflozin hemihydrate

    PubMed Central

    Liu, Kai-Hang; Gu, Jian-Ming; Hu, Xiu-Rong; Tang, Gu-Ping

    2016-01-01

    There are two canagliflozin mol­ecules (A and B) and one water mol­ecule in the asymmetric unit of the title compound, C24H25FO5S·0.5H2O [systematic name: (2S,3R,4R,5S,6R)-2-(3-{[5-(4-fluoro­phen­yl)thio­phen-2-yl]meth­yl}-4-methylphen­yl)-6-(hy­droxy­meth­yl)-3,4,5,6-tetra­hydro-2H-pyran-3,4,5-triol hemihydrate]. The dihedral angles between the methyl­benzene and thio­phene rings are 115.7 (4) and 111.7 (4)°, while the dihedral angles between the fluoro­benzene and thio­phene rings are 24.2 (6) and 20.5 (9)° in mol­ecules A and B, respectively. The hydro­pyran ring exhibits a chair conformation in both canagliflozin mol­ecules. In the crystal, the canagliflozin mol­ecules and lattice water mol­ecules are connected via O—H⋯O hydrogen bonds into a three-dimensional supra­molecular architecture. PMID:27308030

  16. Crystal structure of Arabidopsis thaliana cytokinin dehydrogenase

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Bitto, Eduard; Aceti, David J.; Phillips, Jr., George N.

    2008-08-13

    Since first discovered in Zea mays, cytokinin dehydrogenase (CKX) genes have been identified in many plants including rice and Arabidopsis thaliana, which possesses CKX homologues (AtCKX1-AtCKX7). So far, the three-dimensional structure of only Z. mays CKX (ZmCKX1) has been determined. The crystal structures of ZmCKX1 have been solved in the native state and in complex with reaction products and a slowly reacting substrate. The structures revealed four glycosylated asparagine residues and a histidine residue covalently linked to FAD. Combined with the structural information, recent biochemical analyses of ZmCKX1 concluded that the final products of the reaction, adenine and a side chain aldehyde, are formed by nonenzymatic hydrolytic cleavage of cytokinin imine products resulting directly from CKX catalysis. Here, we report the crystal structure of AtCKX7 (gene locus At5g21482.1, UniProt code Q9FUJ1).

  17. Requirements for structure determination of aperiodic crystals

    SciTech Connect

    Li, X.; Stern, E.A.; Ma, Y. )

    1991-01-15

    Using computer simulation, we compared the Patterson functions of one-dimensional (1D) randomly packed and quasiperiodic Fibonacci lattices with or without disorder, and a 2D Penrose lattice and random packing of pentagons (icosahedral glass model). Based on these comparisons, we derived some empirical guidelines for distinguishing ideal quasicrystals from aperiodic crystals with disorder using diffraction data. In contrast to periodic crystals, it is essential to include the background to obtain correct Patterson functions of the average structure since the background contains unresolved peaks. In particular, a Bragg peak scattering measurement {ital cannot}, in general, determine the structure of aperiodic crystals. Instead, a diffuse scattering measurement is required, which determines the absolute value of the diffraction background, in addition to the Bragg peaks. We further estimate that, dependent upon the disorder present, it is necessary to include up to 75% of the total diffracted intensity in any analysis.

  18. Analysis of Shannon entropy for protein crystallization and prediction of crystallization pH and precipitants

    NASA Astrophysics Data System (ADS)

    Pérez-Priede, Mónica; García-Granda, Santiago

    2017-02-01

    This is a new attempt at analysing crystallization data from Protein Data Bank. In line with the idea that crystallization conditions are intimately related with amino acid sequences, we have computed the Shannon entropy of polypeptides and polynucleotides and we have discovered a relationship between Shannon entropy and molecular weight, and also between the entropy of polypeptides, and the precipitants used in crystallization experiments. In fact, the Shannon entropy and the molecular weight of proteins are good precipitant predictors. On the other hand, we have proposed the hypothesis that homologous proteins may have similar crystallization conditions, and we have tried to find evidence that supports it, predicting the crystallization pH of a large amount of polypeptide sequences by means of a nearest neighbour approach combined with local sequence alignment.

  19. Shear induced structures in crystallizing cocoa butter

    NASA Astrophysics Data System (ADS)

    Mazzanti, Gianfranco; Guthrie, Sarah E.; Sirota, Eric B.; Marangoni, Alejandro G.; Idziak, Stefan H. J.

    2004-03-01

    Cocoa butter is the main structural component of chocolate and many cosmetics. It crystallizes in several polymorphs, called phases I to VI. We used Synchrotron X-ray diffraction to study the effect of shear on its crystallization. A previously unreported phase (phase X) was found and a crystallization path through phase IV under shear was observed. Samples were crystallized under shear from the melt in temperature controlled Couette cells, at final crystallization temperatures of 17.5^oC, 20^oC and 22.5^oC in Beamline X10A of NSLS. The formation of phase X was observed at low shear rates (90 s-1) and low crystallization temperature (17.5^oC), but was absent at high shear (720 s-1) and high temperature (20^oC). The d-spacing and melting point suggest that this new phase is a mixture rich on two of the three major components of cocoa butter. We also found that, contrary to previous reports, the transition from phase II to phase V can happen through the intermediate phase IV, at high shear rates and temperature.

  20. Crystal structure of monobasic sodium tartrate monohydrate

    SciTech Connect

    Titaeva, E. K. Somov, N. V.; Portnov, V. N.; Titaev, D. N.

    2015-01-15

    Crystals of a new polymorphic modification of monobasic sodium tartrate monohydrate NaHC{sub 4}H{sub 4}O{sub 6} · H{sub 2}O have been grown in a metasilicate gel. Their atomic structure is solved by X-ray diffraction.

  1. Structure analysis on synthetic emerald crystals

    NASA Astrophysics Data System (ADS)

    Lee, Pei-Lun; Lee, Jiann-Shing; Huang, Eugene; Liao, Ju-Hsiou

    2013-05-01

    Single crystals of emerald synthesized by means of the flux method were adopted for crystallographic analyses. Emerald crystals with a wide range of Cr3+-doping content up to 3.16 wt% Cr2O3 were examined by X-ray single crystal diffraction refinement method. The crystal structures of the emerald crystals were refined to R 1 (all data) of 0.019-0.024 and w R 2 (all data) of 0.061-0.073. When Cr3+ substitutes for Al3+, the main adjustment takes place in the Al-octahedron and Be-tetrahedron. The effect of substitution of Cr3+ for Al3+ in the beryl structure results in progressively lengthening of the Al-O distance, while the length of the other bonds remains nearly unchanged. The substitution of Cr3+ for Al3+ may have caused the expansion of a axis, while keeping the c axis unchanged in the emerald lattice. As a consequence, the Al-O-Si and Al-O-Be bonding angles are found to decrease, while the angle of Si-O-Be increases as the Al-O distance increases during the Cr replacement.

  2. Ostwald-Meyers Metastable Region in LiBr Crystallization-Comparison of Measurements with Predictions.

    PubMed

    Duvall, Kristin N.; Dirksen, James A.; Ring, Terry A.

    2001-07-15

    Experiments have been performed to measure the Ostwald-Meyers metastable region during crystallization from concentrated LiBr solutions. Solution thermodynamics shows that several hydrated LiBr salts and ice can crystallize depending upon the concentration of LiBr in aqueous solution. The available solubility data were interpreted to give solubility products of several hydrated LiBr salts using the formulation of Helgeson, which accounts for the activity of water. The crystallization temperature was measured by monitoring to +/-0.01 degrees C the temperature of solutions inside test tubes placed in a cooling bath programmed at a cooling rate of 20 degrees C/h. A release of the heat of crystallization identifies the temperature of crystallization. The equilibrium solubility was verified by crystallization with seed crystals present. The crystallization temperature without seeds present was 10 to 20 degrees C less than the equilibrium solubility temperature corresponding to the Ostwald-Meyers metastable region. This crystallization temperature measured at 20 degrees C/h was shown to correspond to nucleation on the surface of the test tube with an interface energy of 40+/-1.2 erg/cm(2). Homogeneous nucleation from solution data shows the crystallization temperature to be from 40 to 50 degrees C below the equilibrium solubility curve and to be accurately predicted by homogeneous nucleation with an interface energy of 26 erg/cm(2), the literature value of the ice/water interface. Since the hydrated LiBr salts have surfaces that expose structured water molecules to the solution, this value is believed to be an appropriate value of the interface energy of the hydrated LiBr crystals. Crystallization temperature measurements were performed at different cooling rates, showing that slower cooling rates gave a narrower Ostwald-Myers metastable zone as is expected. Induction time measurements showed that the time to spontaneous crystallization increases as the supersaturation

  3. Crystal structure of a plectonemic RNA supercoil

    SciTech Connect

    Stagno, Jason R.; Ma, Buyong; Li, Jess; Altieri, Amanda S.; Byrd, R. Andrew; Ji, Xinhua

    2012-12-14

    Genome packaging is an essential housekeeping process in virtually all organisms for proper storage and maintenance of genetic information. Although the extent and mechanisms of packaging vary, the process involves the formation of nucleic-acid superstructures. Crystal structures of DNA coiled coils indicate that their geometries can vary according to sequence and/or the presence of stabilizers such as proteins or small molecules. However, such superstructures have not been revealed for RNA. Here we report the crystal structure of an RNA supercoil, which displays one level higher molecular organization than previously reported structures of DNA coiled coils. In the presence of an RNA-binding protein, two interlocking RNA coiled coils of double-stranded RNA, a 'coil of coiled coils', form a plectonemic supercoil. Molecular dynamics simulations suggest that protein-RNA interaction is required for the stability of the supercoiled RNA. This study provides structural insight into higher order packaging mechanisms of nucleic acids.

  4. 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.

  5. Crystal Structure of Human Enterovirus 71

    SciTech Connect

    Plevka, Pavel; Perera, Rushika; Cardosa, Jane; Kuhn, Richard J.; Rossmann, Michael G.

    2013-04-08

    Enterovirus 71 is a picornavirus associated with fatal neurological illness in infants and young children. Here, we report the crystal structure of enterovirus 71 and show that, unlike in other enteroviruses, the 'pocket factor,' a small molecule that stabilizes the virus, is partly exposed on the floor of the 'canyon.' Thus, the structure of antiviral compounds may require a hydrophilic head group designed to interact with residues at the entrance of the pocket.

  6. Are the Crystal Structures of Enantiopure and Racemic Mandelic Acids Determined by Kinetics or Thermodynamics?

    PubMed

    Hylton, Rebecca K; Tizzard, Graham J; Threlfall, Terence L; Ellis, Amy L; Coles, Simon J; Seaton, Colin C; Schulze, Eric; Lorenz, Heike; Seidel-Morgenstern, Andreas; Stein, Matthias; Price, Sarah L

    2015-09-02

    Mandelic acids are prototypic chiral molecules where the sensitivity of crystallized forms (enantiopure/racemic compound/polymorphs) to both conditions and substituents provides a new insight into the factors that may allow chiral separation by crystallization. The determination of a significant number of single crystal structures allows the analysis of 13 enantiopure and 30 racemic crystal structures of 21 (F/Cl/Br/CH3/CH3O) substituted mandelic acid derivatives. There are some common phenyl packing motifs between some groups of racemic and enantiopure structures, although they show very different hydrogen-bonding motifs. The computed crystal energy landscape of 3-chloromandelic acid, which has at least two enantiopure and three racemic crystal polymorphs, reveals that there are many more possible structures, some of which are predicted to be thermodynamically more favorable as well as slightly denser than the known forms. Simulations of mandelic acid dimers in isolation, water, and toluene do not differentiate between racemic and enantiopure dimers and also suggest that the phenyl ring interactions play a major role in the crystallization mechanism. The observed crystallization behavior of mandelic acids does not correspond to any simple "crystal engineering rules" as there is a range of thermodynamically feasible structures with no distinction between the enantiopure and racemic forms. Nucleation and crystallization appear to be determined by the kinetics of crystal growth with a statistical bias, but the diversity of the mandelic acid crystallization behavior demonstrates that the factors that influence the kinetics of crystal nucleation and growth are not yet adequately understood.

  7. Structures and Crystal Chemistry of Layered Materials

    NASA Astrophysics Data System (ADS)

    Partin, Daniel Edward

    The crystal chemistry of several layered materials has been explored using a variety of methods, with an emphasis on their structural aspects. In the second part of this work, the structure of several copper oxides that are of significance to the study of superconductors are described. The crystal structures of MgCl_2 and CdCl_2 have been refined using powder X-ray diffraction data. They have the space group Roverline{3}m. For magnesium chloride the unit cell constants are a = 3.6363(1) A, c = 17.6663(5) A. For cadmium chloride they are a = 3.8459(1) A, c = 17.4931(4) A. The structures and their relationship to that of fluorite are discussed within the framework of a Born-Mayer model. The crystal structure of Mg(OD)_2 has been refined from time-of flight (TOF) neutron diffraction data and found to be trigonal, Poverline {3}m1, a = 3.1455(1) A, c = 4.7646(3) A. The data were collected at 305 K. The O-D bond length is 0.937 (1) A (corrected for "riding" motion 0.948 A). An infrared/Raman study of Mg(OH)_2 was conducted in a diamond anvil cell in the pressure range from room pressure up to 7 Gpa. For layered crystals, it was found that as the internally fixed layers are moved apart the Madelung energy of the system becomes constant after a very short distance, although not necessarily that of the given crystal's energy at ambient conditions. The crystal structure of Sr(OD)_2 has been refined from time-of-flight neutron diffraction data and the deuterium positions found. Strontium deuteroxide crystallizes in the space group Pnma, with the unit cell constants of a = 9.8269(5) A, b = 3.9051(2) A, and c = 6.0733(3) A. The crystal structures of SrCuO_2 and Sr_2CuO_3 have been refined by time-of-flight neutron diffraction. For SrCuO_2 the space group is Cmcm, a = 3.57002(2), b = 16.32268(8), c = 3.91100(2); for Sr _2CuO_3 the space group is Immm, a = 3.49900(5), b = 12.7009(2), c = 3.91120(5). In both structures the strontium atoms are coordinated by seven oxygen atoms

  8. THE CRYSTAL STRUCTURE OF 2,7-DIACETOXYTRANS-15,16-DIMETHYL-15,16-DIHYDROPYRENE,

    DTIC Science & Technology

    AROMATIC COMPOUNDS, CRYSTAL STRUCTURE ), (*POLYCYCLIC COMPOUNDS, CRYSTAL STRUCTURE ), (* CRYSTAL STRUCTURE , POLYCYCLIC COMPOUNDS), ESTERS, MOLECULAR STRUCTURE, CHEMICAL BONDS, X RAY DIFFRACTION, SCINTILLATION COUNTERS, CANADA

  9. Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M.

    2007-08-22

    Laser-driven acceleration holds great promise for significantly improving accelerating gradient. However, scaling the conventional process of structure-based acceleration in vacuum down to optical wavelengths requires a substantially different kind of structure. We require an optical waveguide that (1) is constructed out of dielectric materials, (2) has transverse size on the order of a wavelength, and (3) supports a mode with speed-of-light phase velocity in vacuum. Photonic crystals---structures whose electromagnetic properties are spatially periodic---can meet these requirements. We discuss simulated photonic crystal accelerator structures and describe their properties. We begin with a class of two-dimensional structures which serves to illustrate the design considerations and trade-offs involved. We then present a three-dimensional structure, and describe its performance in terms of accelerating gradient and efficiency. We discuss particle beam dynamics in this structure, demonstrating a method for keeping a beam confined to the waveguide. We also discuss material and fabrication considerations. Since accelerating gradient is limited by optical damage to the structure, the damage threshold of the dielectric is a critical parameter. We experimentally measure the damage threshold of silicon for picosecond pulses in the infrared, and determine that our structure is capable of sustaining an accelerating gradient of 300 MV/m at 1550 nm. Finally, we discuss possibilities for manufacturing these structures using common microfabrication techniques.

  10. The Surface Structure of Ground Metal Crystals

    NASA Technical Reports Server (NTRS)

    Boas, W.; Schmid, E.

    1944-01-01

    The changes produced on metallic surfaces as a result of grinding and polishing are not as yet fully understood. Undoubtedly there is some more or less marked change in the crystal structure, at least, in the top layer. Hereby a diffusion of separated crystal particles may be involved, or, on plastic material, the formation of a layer in greatly deformed state, with possible recrystallization in certain conditions. Czochralski verified the existence of such a layer on tin micro-sections by successive observations of the texture after repeated etching; while Thomassen established, roentgenographically by means of the Debye-Scherrer method, the existence of diffused crystal fractions on the surface of ground and polished tin bars, which he had already observed after turning (on the lathe). (Thickness of this layer - 0.07 mm). Whether this layer borders direct on the undamaged base material or whether deformed intermediate layers form the transition, nothing is known. One observation ty Sachs and Shoji simply states that after the turning of an alpha-brass crystal the disturbance starting from the surface, penetrates fairly deep (approx. 1 mm) into the crystal (proof by recrystallization at 750 C).

  11. Structure prediction of magnetosome-associated proteins

    PubMed Central

    Nudelman, Hila; Zarivach, Raz

    2014-01-01

    Magnetotactic bacteria (MTB) are Gram-negative bacteria that can navigate along geomagnetic fields. This ability is a result of a unique intracellular organelle, the magnetosome. These organelles are composed of membrane-enclosed magnetite (Fe3O4) or greigite (Fe3S4) crystals ordered into chains along the cell. Magnetosome formation, assembly, and magnetic nano-crystal biomineralization are controlled by magnetosome-associated proteins (MAPs). Most MAP-encoding genes are located in a conserved genomic region – the magnetosome island (MAI). The MAI appears to be conserved in all MTB that were analyzed so far, although the MAI size and organization differs between species. It was shown that MAI deletion leads to a non-magnetic phenotype, further highlighting its important role in magnetosome formation. Today, about 28 proteins are known to be involved in magnetosome formation, but the structures and functions of most MAPs are unknown. To reveal the structure–function relationship of MAPs we used bioinformatics tools in order to build homology models as a way to understand their possible role in magnetosome formation. Here we present a predicted 3D structural models’ overview for all known Magnetospirillum gryphiswaldense strain MSR-1 MAPs. PMID:24523717

  12. Crystal structure representations for machine learning models of formation energies

    SciTech Connect

    Faber, Felix; Lindmaa, Alexander; von Lilienfeld, O. Anatole; Armiento, Rickard

    2015-04-20

    We introduce and evaluate a set of feature vector representations of crystal structures for machine learning (ML) models of formation energies of solids. ML models of atomization energies of organic molecules have been successful using a Coulomb matrix representation of the molecule. We consider three ways to generalize such representations to periodic systems: (i) a matrix where each element is related to the Ewald sum of the electrostatic interaction between two different atoms in the unit cell repeated over the lattice; (ii) an extended Coulomb-like matrix that takes into account a number of neighboring unit cells; and (iii) an ansatz that mimics the periodicity and the basic features of the elements in the Ewald sum matrix using a sine function of the crystal coordinates of the atoms. The representations are compared for a Laplacian kernel with Manhattan norm, trained to reproduce formation energies using a dataset of 3938 crystal structures obtained from the Materials Project. For training sets consisting of 3000 crystals, the generalization error in predicting formation energies of new structures corresponds to (i) 0.49, (ii) 0.64, and (iii) 0.37eV/atom for the respective representations.

  13. Gas hydrate single-crystal structure analyses.

    PubMed

    Kirchner, Michael T; Boese, Roland; Billups, W Edward; Norman, Lewis R

    2004-08-04

    The first single-crystal diffraction studies on methane, propane, methane/propane, and adamantane gas hydrates SI, SII, and SH have been performed. To circumvent the problem of very slow crystal growth, a novel technique of in situ cocrystallization of gases and liquids resulting in oligocrystalline material in a capillary has been developed. With special data treatment, termed oligo diffractometry, structural data of the gas hydrates of methane, acetylene, propane, a propane/ethanol/methane-mixture and an adamantane/methane-mixture were obtained. Cell parameters are in accord with reported values. Host network and guest are subject to extensive disorder, reducing the reliability of structural information. It was found that most cages are fully occupied by a guest molecule with the exception of the dodecahedral cage in the acetylene hydrate which is only filled to 60%. For adamantane in the icosahedral cage a disordered model is proposed.

  14. Structural phase transitions in layered perovskitelike crystals

    SciTech Connect

    Aleksandrov, K.S.

    1995-03-01

    Possible symmetry changes due to small tilts of octahedra are considered for layered perovskite-like crystals containing slabs of several ({ell}) layers of comer-sharing octahedra. In the crystals with {ell} > 1, four types of distortions are possible; as a rule, these distortions correspond to the librational modes of the parent lattice. Condensation of these soft modes is the reason for structural phase transitions or sequences of phase transitions. The results obtained are compared with the known experimental data for a number of layered ferroelectric and ferroelastic perovskite-like compounds. An application of the results to the initial stage of determining unknown structures is discussed with particular attention paid to high-temperature superconductors. 76 refs., 9 figs., 7 tabs.

  15. Crystal Structure and Properties of Tetrathiafulvalenium Triiodide.

    DTIC Science & Technology

    1979-12-03

    CK? Task No. NR 05- ;TECHNICAL RE 10.9 -, -rysta-i-Strictreand Prop-eities of/ -4V ’ t-Tetrathiafulvalenium Triiodide - K1oe by obert C./Teitelbaum...CRYSTAL STRUCTURE AND PROPERTIES OF TETRATHAFULVALENIUM TRIIODIDE la, b, *la 2 Idby Robert C. Teitelbaum, Tobin J. Marks a and Carroll K. Johnson...contains disordered chains of triiodide ions and disordered TTF stacks ((TTF + o7)(I )o.7). 4g, 6, reliminary X-ray crystallographic investigations sug

  16. Crystal Structures of New Ammonium 5-Aminotetrazolates

    PubMed Central

    Lampl, Martin; Salchner, Robert; Laus, Gerhard; Braun, Doris E.; Kahlenberg, Volker; Wurst, Klaus; Fuhrmann, Gerda; Schottenberger, Herwig; Huppertz, Hubert

    2015-01-01

    The crystal structures of three salts of anionic 5-aminotetrazole are described. The tetramethylammonium salt (P1‒) forms hydrogen-bonded ribbons of anions which accept weak C–H⋯N contacts from the cations. The cystamine salt (C2/c) shows wave-shaped ribbons of anions linked by hydrogen bonds to screw-shaped dications. The tetramethylguanidine salt (P21/c) exhibits layers of anions hydrogen-bonded to the cations. PMID:26753100

  17. Unified approach for determining tetragonal tungsten bronze crystal structures.

    PubMed

    Smirnov, M; Saint-Grégoire, P

    2014-05-01

    Tetragonal tungsten bronze (TTB) oxides are one of the most important classes of ferroelectrics. Many of these framework structures undergo ferroelastic transformations related to octahedron tilting deformations. Such tilting deformations are closely related to the rigid unit modes (RUMs). This paper discusses the whole set of RUMs in an ideal TTB lattice and possible crystal structures which can emerge owing to the condensation of some of them. Analysis of available experimental data for the TTB-like niobates lends credence to the obtained theoretical predictions.

  18. Surface-induced structures in nematic liquid crystal colloids

    NASA Astrophysics Data System (ADS)

    Chernyshuk, S. B.; Tovkach, O. M.; Lev, B. I.

    2014-08-01

    We predict theoretically the existence of a class of colloidal structures in nematic liquid crystal (NLC) cells, which are induced by surface patterns on the plates of the cell (like cells with UV-irradiated polyamide surfaces using micron sized masks in front of the cell). These bulk structures arise from nonuniform boundary conditions for the director distortions at the confining surfaces. In particular, we demonstrate that quadrupole spherical particles (like spheres with boojums or Saturn-ring director configurations) form a square lattice inside a planar NLC cell, which has checkerboard patterns on both its plates.

  19. Life Prediction of Turbine Blade Nickel Base Superalloy Single Crystals.

    DTIC Science & Technology

    1986-08-01

    different types of coatings . They are the conventional aluminide coating and the overlay coating with improved temperature capability.5 These coatings ...0.6% with a 2 min. hold in compression. Transverse cracks behaved differently in the aluminide (Codep) coated Ren6 N4+, and an example is given in...PREDICTION OF TURBINE BLADE NICKEL BASE SUPERALLOY SINGLE CRYSTALS N Dr. V. Srinivasan 0 Universal Energy Systems, Inc. 4401 Dayton-Xenia Road Dayton, Ohio

  20. Crystal structures of sialyltransferase from Photobacterium damselae

    DOE PAGES

    Huynh, Nhung; Li, Yanhong; Yu, Hai; ...

    2014-11-15

    Sialyltransferase structures fall into either GT-A or GT-B glycosyltransferase fold. Some sialyltransferases from the Photobacterium genus have been shown to contain an additional N-terminal immunoglobulin (Ig)-like domain. Photobacterium damselae α2–6-sialyltransferase has been used efficiently in enzymatic and chemoenzymatic synthesis of α2–6-linked sialosides. In this paper, we report three crystal structures of this enzyme. Two structures with and without a donor substrate analog CMP-3F(a)Neu5Ac contain an immunoglobulin (Ig)-like domain and adopt the GT-B sialyltransferase fold. The binary structure reveals a non-productive pre-Michaelis complex, which are caused by crystal lattice contacts that prevent the large conformational changes. The third structure lacks themore » Ig-domain. Finally, comparison of the three structures reveals small inherent flexibility between the two Rossmann-like domains of the GT-B fold.« less

  1. Lessons from crystal structures of kainate receptors.

    PubMed

    Møllerud, Stine; Frydenvang, Karla; Pickering, Darryl S; Kastrup, Jette Sandholm

    2017-01-01

    Kainate receptors belong to the family of ionotropic glutamate receptors. These receptors assemble from five subunits (GluK1-5) into tetrameric ion channels. Kainate receptors are located at both pre- and postsynaptic membranes in the central nervous system where they contribute to excitatory synaptic transmission and modulate network excitability by regulating neurotransmitter release. Dysfunction of kainate receptors has been implicated in several neurological disorders such as epilepsy, schizophrenia and depression. Here we provide a review on the current understanding of kainate receptor structure and how they bind agonists, antagonists and ions. The first structure of the ligand-binding domain of the GluK1 subunit was reported in 2005, seven years after publication of the crystal structure of a soluble construct of the ligand-binding domain of the AMPA-type subunit GluA2. Today, a full-length structure has been determined of GluK2 by cryo electron microscopy to 7.6 Å resolution as well as 84 high-resolution crystal structures of N-terminal domains and ligand-binding domains, including agonist and antagonist bound structures, modulatory ions and mutations. However, there are still many unanswered questions and challenges in front of us. This article is part of the Special Issue entitled 'Ionotropic glutamate receptors'.

  2. A DIRECT DETERMINATION OF THE CRYSTAL STRUCTURE OF 2,3,4,6-TETRANITROANILINE,

    DTIC Science & Technology

    ORGANIC NITROGEN COMPOUNDS, CRYSTAL STRUCTURE ), (* CRYSTAL STRUCTURE , EXPLOSIVES), (*EXPLOSIVES, CRYSTAL STRUCTURE ), AROMATIC COMPOUNDS, AMINES, NITRATES, LEAST SQUARES METHOD, FOURIER ANALYSIS, CHEMICAL BONDS.

  3. Predicting out-of-Equilibrium Phase Behavior in the Dynamic Self-Assembly of Colloidal Crystals

    NASA Astrophysics Data System (ADS)

    Swan, James; Sherman, Zachary

    Crystals self-assembled from colloidal particles are useful in an array of well demonstrated applications. During fabrication however, gelation and glassification often leave these materials arrested in defective or disordered metastable states. We show how time-dependent, pulsed interparticle interactions can avoid kinetic barriers and yield well-ordered crystalline domains for a suspension of hard, spherical colloidal particles interacting through short-range attractions. This dynamic self-assembly process is analogous to the flashing Brownian rachet. Although this is an inherently unsteady, out-of-equilibrium process, we can predict its outcome using appropriate time averages of equilibrium equations of state. The predicted phase behavior is tested and validated by examining the fluid/crystal coexistence of such dynamically self-assembling dispersions in Brownian dynamics simulations of sedimentation equilibrium and homogeneous nucleation. We also show that our dynamic self-assembly scheme offers control and tunability over the crystal growth kinetics and can even stabilize nonequilibrium structures.

  4. Fourier Analysis and Structure Determination--Part III: X-ray Crystal Structure Analysis.

    ERIC Educational Resources Information Center

    Chesick, John P.

    1989-01-01

    Discussed is single crystal X-ray crystal structure analysis. A common link between the NMR imaging and the traditional X-ray crystal structure analysis is reported. Claims that comparisons aid in the understanding of both techniques. (MVL)

  5. THE CRYSTAL STRUCTURE OF 2-(4’-AMINO-5’AMINO PYRIMIDY) -2-PENTENE-4-ONE.

    DTIC Science & Technology

    NITROGEN HETEROCYCLIC COMPOUNDS, CRYSTAL STRUCTURE ), (*AMINES, CRYSTAL STRUCTURE ), (*KETONES, CRYSTAL STRUCTURE ), CRYSTAL LATTICES, FOURIER ANALYSIS, LEAST SQUARES METHOD, MOLECULAR STRUCTURE, PYRIMIDINES, CHEMICAL BONDS

  6. Predictions of Crystal Structures from First Principles

    DTIC Science & Technology

    2007-06-01

    coefficients 2. Computational Details modeling the long-range dispersion and induction interactions were obtained from separate fits of these...Potential Energy Surface induction energy components are much less important, in particular for the second lowest minimum. Moreover, a large part of the...minima on the PES. from second -order Moller-Plesset (MP2) level The energies of the minima range between -12.5 and calculations used in the SRT

  7. Determining crystal structures through crowdsourcing and coursework

    PubMed Central

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Roque, Paulo Sergio Silveira Belo Nascimento; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-01-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality. PMID:27633552

  8. Determining crystal structures through crowdsourcing and coursework

    NASA Astrophysics Data System (ADS)

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A.; Cooper, Seth; Flatten, Jeff; Rogawski, David S.; Koropatkin, Nicole M.; Hailu, Tsinatkeab T.; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S.; Chapman, Matthew R.; Sikkema, Andrew P.; Skiba, Meredith A.; Maloney, Finn P.; Beinlich, Felix R. M.; Caglar, Ahmet; Coral, Alan; Jensen, Alice Elizabeth; Lubow, Allen; Boitano, Amanda; Lisle, Amy Elizabeth; Maxwell, Andrew T.; Failer, Barb; Kaszubowski, Bartosz; Hrytsiv, Bohdan; Vincenzo, Brancaccio; de Melo Cruz, Breno Renan; McManus, Brian Joseph; Kestemont, Bruno; Vardeman, Carl; Comisky, Casey; Neilson, Catherine; Landers, Catherine R.; Ince, Christopher; Buske, Daniel Jon; Totonjian, Daniel; Copeland, David Marshall; Murray, David; Jagieła, Dawid; Janz, Dietmar; Wheeler, Douglas C.; Cali, Elie; Croze, Emmanuel; Rezae, Farah; Martin, Floyd Orville; Beecher, Gil; de Jong, Guido Alexander; Ykman, Guy; Feldmann, Harald; Chan, Hugo Paul Perez; Kovanecz, Istvan; Vasilchenko, Ivan; Connellan, James C.; Borman, Jami Lynne; Norrgard, Jane; Kanfer, Jebbie; Canfield, Jeffrey M.; Slone, Jesse David; Oh, Jimmy; Mitchell, Joanne; Bishop, John; Kroeger, John Douglas; Schinkler, Jonas; McLaughlin, Joseph; Brownlee, June M.; Bell, Justin; Fellbaum, Karl Willem; Harper, Kathleen; Abbey, Kirk J.; Isaksson, Lennart E.; Wei, Linda; Cummins, Lisa N.; Miller, Lori Anne; Bain, Lyn; Carpenter, Lynn; Desnouck, Maarten; Sharma, Manasa G.; Belcastro, Marcus; Szew, Martin; Szew, Martin; Britton, Matthew; Gaebel, Matthias; Power, Max; Cassidy, Michael; Pfützenreuter, Michael; Minett, Michele; Wesselingh, Michiel; Yi, Minjune; Cameron, Neil Haydn Tormey; Bolibruch, Nicholas I.; Benevides, Noah; Kathleen Kerr, Norah; Barlow, Nova; Crevits, Nykole Krystyne; Dunn, Paul; Silveira Belo Nascimento Roque, Paulo Sergio; Riber, Peter; Pikkanen, Petri; Shehzad, Raafay; Viosca, Randy; James Fraser, Robert; Leduc, Robert; Madala, Roman; Shnider, Scott; de Boisblanc, Sharon; Butkovich, Slava; Bliven, Spencer; Hettler, Stephen; Telehany, Stephen; Schwegmann, Steven A.; Parkes, Steven; Kleinfelter, Susan C.; Michael Holst, Sven; van der Laan, T. J. A.; Bausewein, Thomas; Simon, Vera; Pulley, Warwick; Hull, William; Kim, Annes Yukyung; Lawton, Alexis; Ruesch, Amanda; Sundar, Anjali; Lawrence, Anna-Lisa; Afrin, Antara; Maheshwer, Bhargavi; Turfe, Bilal; Huebner, Christian; Killeen, Courtney Elizabeth; Antebi-Lerrman, Dalia; Luan, Danny; Wolfe, Derek; Pham, Duc; Michewicz, Elaina; Hull, Elizabeth; Pardington, Emily; Galal, Galal Osama; Sun, Grace; Chen, Grace; Anderson, Halie E.; Chang, Jane; Hewlett, Jeffrey Thomas; Sterbenz, Jennifer; Lim, Jiho; Morof, Joshua; Lee, Junho; Inn, Juyoung Samuel; Hahm, Kaitlin; Roth, Kaitlin; Nair, Karun; Markin, Katherine; Schramm, Katie; Toni Eid, Kevin; Gam, Kristina; Murphy, Lisha; Yuan, Lucy; Kana, Lulia; Daboul, Lynn; Shammas, Mario Karam; Chason, Max; Sinan, Moaz; Andrew Tooley, Nicholas; Korakavi, Nisha; Comer, Patrick; Magur, Pragya; Savliwala, Quresh; Davison, Reid Michael; Sankaran, Roshun Rajiv; Lewe, Sam; Tamkus, Saule; Chen, Shirley; Harvey, Sho; Hwang, Sin Ye; Vatsia, Sohrab; Withrow, Stefan; Luther, Tahra K.; Manett, Taylor; Johnson, Thomas James; Ryan Brash, Timothy; Kuhlman, Wyatt; Park, Yeonjung; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C. A.

    2016-09-01

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  9. Determining crystal structures through crowdsourcing and coursework.

    PubMed

    Horowitz, Scott; Koepnick, Brian; Martin, Raoul; Tymieniecki, Agnes; Winburn, Amanda A; Cooper, Seth; Flatten, Jeff; Rogawski, David S; Koropatkin, Nicole M; Hailu, Tsinatkeab T; Jain, Neha; Koldewey, Philipp; Ahlstrom, Logan S; Chapman, Matthew R; Sikkema, Andrew P; Skiba, Meredith A; Maloney, Finn P; Beinlich, Felix R M; Popović, Zoran; Baker, David; Khatib, Firas; Bardwell, James C A

    2016-09-16

    We show here that computer game players can build high-quality crystal structures. Introduction of a new feature into the computer game Foldit allows players to build and real-space refine structures into electron density maps. To assess the usefulness of this feature, we held a crystallographic model-building competition between trained crystallographers, undergraduate students, Foldit players and automatic model-building algorithms. After removal of disordered residues, a team of Foldit players achieved the most accurate structure. Analysing the target protein of the competition, YPL067C, uncovered a new family of histidine triad proteins apparently involved in the prevention of amyloid toxicity. From this study, we conclude that crystallographers can utilize crowdsourcing to interpret electron density information and to produce structure solutions of the highest quality.

  10. Crystal structure optimisation using an auxiliary equation of state.

    PubMed

    Jackson, Adam J; Skelton, Jonathan M; Hendon, Christopher H; Butler, Keith T; Walsh, Aron

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy-volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other "beyond" density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu2ZnSnS4 and the magnetic metal-organic framework HKUST-1.

  11. Crystal structure optimisation using an auxiliary equation of state

    SciTech Connect

    Jackson, Adam J.; Skelton, Jonathan M.; Hendon, Christopher H.; Butler, Keith T.; Walsh, Aron

    2015-11-14

    Standard procedures for local crystal-structure optimisation involve numerous energy and force calculations. It is common to calculate an energy–volume curve, fitting an equation of state around the equilibrium cell volume. This is a computationally intensive process, in particular, for low-symmetry crystal structures where each isochoric optimisation involves energy minimisation over many degrees of freedom. Such procedures can be prohibitive for non-local exchange-correlation functionals or other “beyond” density functional theory electronic structure techniques, particularly where analytical gradients are not available. We present a simple approach for efficient optimisation of crystal structures based on a known equation of state. The equilibrium volume can be predicted from one single-point calculation and refined with successive calculations if required. The approach is validated for PbS, PbTe, ZnS, and ZnTe using nine density functionals and applied to the quaternary semiconductor Cu{sub 2}ZnSnS{sub 4} and the magnetic metal-organic framework HKUST-1.

  12. Synthesis and structural characterization of a single-crystal to single-crystal transformable coordination polymer.

    PubMed

    Tian, Yuyang; Allan, Phoebe K; Renouf, Catherine L; He, Xiang; McCormick, Laura J; Morris, Russell E

    2014-01-28

    A single-crystal to single-crystal transformable coordination polymer compound was hydrothermally synthesized. The structural rearrangement is induced by selecting a ligand that contains both strong and weaker coordinating groups. Both hydrated and dehydrated structures were determined by single crystal X-ray analysis.

  13. The First Mammalian Aldehyde Oxidase Crystal Structure

    PubMed Central

    Coelho, Catarina; Mahro, Martin; Trincão, José; Carvalho, Alexandra T. P.; Ramos, Maria João; Terao, Mineko; Garattini, Enrico; Leimkühler, Silke; Romão, Maria João

    2012-01-01

    Aldehyde oxidases (AOXs) are homodimeric proteins belonging to the xanthine oxidase family of molybdenum-containing enzymes. Each 150-kDa monomer contains a FAD redox cofactor, two spectroscopically distinct [2Fe-2S] clusters, and a molybdenum cofactor located within the protein active site. AOXs are characterized by broad range substrate specificity, oxidizing different aldehydes and aromatic N-heterocycles. Despite increasing recognition of its role in the metabolism of drugs and xenobiotics, the physiological function of the protein is still largely unknown. We have crystallized and solved the crystal structure of mouse liver aldehyde oxidase 3 to 2.9 Å. This is the first mammalian AOX whose structure has been solved. The structure provides important insights into the protein active center and further evidence on the catalytic differences characterizing AOX and xanthine oxidoreductase. The mouse liver aldehyde oxidase 3 three-dimensional structure combined with kinetic, mutagenesis data, molecular docking, and molecular dynamics studies make a decisive contribution to understand the molecular basis of its rather broad substrate specificity. PMID:23019336

  14. Crystal Structure of the Human Primase*

    PubMed Central

    Baranovskiy, Andrey G.; Zhang, Yinbo; Suwa, Yoshiaki; Babayeva, Nigar D.; Gu, Jianyou; Pavlov, Youri I.; Tahirov, Tahir H.

    2015-01-01

    DNA replication in bacteria and eukaryotes requires the activity of DNA primase, a DNA-dependent RNA polymerase that lays short RNA primers for DNA polymerases. Eukaryotic and archaeal primases are heterodimers consisting of small catalytic and large accessory subunits, both of which are necessary for RNA primer synthesis. Understanding of RNA synthesis priming in eukaryotes is currently limited due to the lack of crystal structures of the full-length primase and its complexes with substrates in initiation and elongation states. Here we report the crystal structure of the full-length human primase, revealing the precise overall organization of the enzyme, the relative positions of its functional domains, and the mode of its interaction with modeled DNA and RNA. The structure indicates that the dramatic conformational changes in primase are necessary to accomplish the initiation and then elongation of RNA synthesis. The presence of a long linker between the N- and C-terminal domains of p58 provides the structural basis for the bulk of enzyme's conformational flexibility. Deletion of most of this linker affected the initiation and elongation steps of the primer synthesis. PMID:25550159

  15. Crystal Structure of the 30S Ribosomal Subunit from Thermus Thermophilus. Purification, Crystallization and Structure Determination

    SciTech Connect

    Clemons, William M.; Brodersen, Ditlev E.; McCutcheonn, John P.; May, Joanna L.C.; Carter, Andrew P.; Morgan-Warren, Robert J.; Wimberly, Brian T.; Ramakrishnan, Venki

    2009-10-07

    We describe the crystallization and structure determination of the 30 S ribosomal subunit from Thermus thermophilus. Previous reports of crystals that diffracted to 10 {angstrom} resolution were used as a starting point to improve the quality of the diffraction. Eventually, ideas such as the addition of substrates or factors to eliminate conformational heterogeneity proved less important than attention to detail in yielding crystals that diffracted beyond 3 {angstrom} resolution. Despite improvements in technology and methodology in the last decade, the structure determination of the 30 S subunit presented some very challenging technical problems because of the size of the asymmetric unit, crystal variability and sensitivity to radiation damage. Some steps that were useful for determination of the atomic structure were: the use of anomalous scattering from the LIII edges of osmium and lutetium to obtain the necessary phasing signal; the use of tunable, third-generation synchrotron sources to obtain data of reasonable quality at high resolution; collection of derivative data precisely about a mirror plane to preserve small anomalous differences between Bijvoet mates despite extensive radiation damage and multi-crystal scaling; the pre-screening of crystals to ensure quality, isomorphism and the efficient use of scarce third-generation synchrotron time; pre-incubation of crystals in cobalt hexaammine to ensure isomorphism with other derivatives; and finally, the placement of proteins whose structures had been previously solved in isolation, in conjunction with biochemical data on protein-RNA interactions, to map out the architecture of the 30 S subunit prior to the construction of a detailed atomic-resolution model.

  16. The Crystal Structure of Monovalent Streptavidin

    PubMed Central

    Zhang, Min; Biswas, Sangita; Deng, Wenbin; Yu, Hongjun

    2016-01-01

    The strong interaction between streptavidin (SA) and biotin is widely utilized in biotechnological applications. A SA variant, monovalent SA, was developed with a single and high affinity biotin-binding site within the intact tetramer. However, its structural characterization remains undetermined. Here, we seek to determine the crystal structure of monovalent SA at 1.7-Å resolution. We show that, in contrast to its ‘close-state’ in the only wild-type subunit, the L3,4 loops of three Dead SA subunits are free from crystal packing and remain in an ‘open state’, stabilized by a consistent H-bonding network involving S52. This H-bonding network also applies to the previously reported open state of the wild-type apo-SA. These results suggest that specific substitutions (N23A/S27D/S45A) at biotin-binding sites stabilize the open state of SA L3,4 loop, thereby further reducing biotin-binding affinity. The general features of the ‘open state’ SA among different SA variants may facilitate its rational design. The structural information of monovalent SA will be valuable for its applications across a wide range of biotechnological areas. PMID:28000673

  17. Crystal structure of a DNA catalyst.

    PubMed

    Ponce-Salvatierra, Almudena; Wawrzyniak-Turek, Katarzyna; Steuerwald, Ulrich; Höbartner, Claudia; Pena, Vladimir

    2016-01-14

    Catalysis in biology is restricted to RNA (ribozymes) and protein enzymes, but synthetic biomolecular catalysts can also be made of DNA (deoxyribozymes) or synthetic genetic polymers. In vitro selection from synthetic random DNA libraries identified DNA catalysts for various chemical reactions beyond RNA backbone cleavage. DNA-catalysed reactions include RNA and DNA ligation in various topologies, hydrolytic cleavage and photorepair of DNA, as well as reactions of peptides and small molecules. In spite of comprehensive biochemical studies of DNA catalysts for two decades, fundamental mechanistic understanding of their function is lacking in the absence of three-dimensional models at atomic resolution. Early attempts to solve the crystal structure of an RNA-cleaving deoxyribozyme resulted in a catalytically irrelevant nucleic acid fold. Here we report the crystal structure of the RNA-ligating deoxyribozyme 9DB1 (ref. 14) at 2.8 Å resolution. The structure captures the ligation reaction in the post-catalytic state, revealing a compact folding unit stabilized by numerous tertiary interactions, and an unanticipated organization of the catalytic centre. Structure-guided mutagenesis provided insights into the basis for regioselectivity of the ligation reaction and allowed remarkable manipulation of substrate recognition and reaction rate. Moreover, the structure highlights how the specific properties of deoxyribose are reflected in the backbone conformation of the DNA catalyst, in support of its intricate three-dimensional organization. The structural principles underlying the catalytic ability of DNA elucidate differences and similarities in DNA versus RNA catalysts, which is relevant for comprehending the privileged position of folded RNA in the prebiotic world and in current organisms.

  18. Crystal structure of Marburg virus VP24.

    PubMed

    Zhang, Adrianna P P; Bornholdt, Zachary A; Abelson, Dafna M; Saphire, Erica Ollmann

    2014-05-01

    The VP24 protein plays an essential, albeit poorly understood role in the filovirus life cycle. VP24 is only 30% identical between Marburg virus and the ebolaviruses. Furthermore, VP24 from the ebolaviruses is immunosuppressive, while that of Marburg virus is not. The crystal structure of Marburg virus VP24, presented here, reveals that although the core is similar between the viral genera, Marburg VP24 is distinguished by a projecting β-shelf and an alternate conformation of the N-terminal polypeptide.

  19. Elasticity of some mantle crystal structures. II.

    NASA Technical Reports Server (NTRS)

    Wang, H.; Simmons, G.

    1973-01-01

    The single-crystal elastic constants are determined as a function of pressure and temperature for rutile structure germanium dioxide (GeO2). The data are qualitatively similar to those of rutile TiO2 measured by Manghnani (1969). The compressibility in the c direction is less than one-half that in the a direction, the pressure derivative of the shear constant is negative, and the pressure derivative of the bulk modulus has a relatively high value of about 6.2. According to an elastic strain energy theory, the negative shear modulus derivative implies that the kinetic barrier to diffusion decreases with increasing pressure.

  20. Temperature dependent spin structures in Hexaferrite crystal

    NASA Astrophysics Data System (ADS)

    Chao, Y. C.; Lin, J. G.; Chun, S. H.; Kim, K. H.

    2016-01-01

    In this work, the Hexaferrite Ba0.5Sr1.5Zn2Fe12O22 (BSZFO) is studied due to its interesting characteristics of long-wavelength spin structure. Ferromagnetic resonance (FMR) is used to probe the magnetic states of BSZFO single crystal and its temperature dependence behavior is analyzed by decomposing the multiple lines of FMR spectra into various phases. Distinguished phase transition is observed at 110 K for one line, which is assigned to the ferro(ferri)-magnetic transition from non-collinear to collinear spin state.

  1. Ionic colloidal crystals: Ordered, multicomponent structures via controlled heterocoagulation.

    PubMed

    Maskaly, Garry R; García, R Edwin; Carter, W Craig; Chiang, Yet-Ming

    2006-01-01

    We propose a new type of ordered colloid, the "ionic colloidal crystal" (ICC), which is stabilized by attractive electrostatic interactions analogous to those in atomic ionic materials. The rapid self-organization of colloids via this method should result in a diversity of orderings that are analogous to ionic compounds. Most of these complex structures would be difficult to produce by other methods. We use a Madelung summation approach to evaluate the conditions where ICC's are thermodynamically stable. Using this model, we compare the relative electrostatic energies of various structures showing that the regions of ICC stability are determined by two dimensionless parameters representing charge balance and the spatial extent of the electrostatic interactions. Parallels and distinctions between ICC's and classical ionic crystals are discussed. Monte Carlo simulations are utilized to examine the glass transition and melting temperatures, between which crystallization can occur, of a model system having the rocksalt structure. These tools allow us to make a first-order prediction of the experimentally accessible regions of surface charge, particle size, ionic strength, and temperature where ICC formation is probable.

  2. Crystallization of RNA polymerase I subcomplex A14/A43 by iterative prediction, probing and removal of flexible regions

    PubMed Central

    Geiger, Sebastian R.; Kuhn, Claus.-D.; Leidig, Christoph; Renkawitz, Jörg; Cramer, Patrick

    2008-01-01

    The removal of flexible protein regions is generally used to promote crystallization, but advanced strategies to quickly remove multiple flexible regions from proteins or protein complexes are lacking. Here, it is shown how a protein heterodimer with multiple flexibilities, the RNA polymerase I subcomplex A14/A43, could be crystallized with the use of an iterative procedure of predicting flexible regions, experimentally testing and improving these predictions and combining deletions of flexible regions in a stepwise manner. This strategy should enable the crystallization of other proteins and subcomplexes with multiple flexibilities, as required for hybrid structure solution of large macromolecular assemblies. PMID:18453714

  3. Crystal structure of yeast Sco1

    SciTech Connect

    Abajian, Carnie; Rosenzweig, Amy C.

    2010-03-05

    The Sco family of proteins are involved in the assembly of the dinuclear CuA site in cytochrome c oxidase (COX), the terminal enzyme in aerobic respiration. These proteins, which are found in both eukaryotes and prokaryotes, are characterized by a conserved CXXXC sequence motif that binds copper ions and that has also been proposed to perform a thiol:disulfide oxidoreductase function. The crystal structures of Saccharomyces cerevisiae apo Sco1 (apo-ySco1) and Sco1 in the presence of copper ions (Cu-ySco1) were determined to 1.8- and 2.3-{angstrom} resolutions, respectively. Yeast Sco1 exhibits a thioredoxin-like fold, similar to that observed for human Sco1 and a homolog from Bacillus subtilis. The Cu-ySco1 structure, obtained by soaking apo-ySco1 crystals in copper ions, reveals an unexpected copper-binding site involving Cys181 and Cys216, cysteine residues present in ySco1 but not in other homologs. The conserved CXXXC cysteines, Cys148 and Cys152, can undergo redox chemistry in the crystal. An essential histidine residue, His239, is located on a highly flexible loop, denoted the Sco loop, and can adopt positions proximal to both pairs of cysteines. Interactions between ySco1 and its partner proteins yeast Cox17 and yeast COX2 are likely to occur via complementary electrostatic surfaces. This high-resolution model of a eukaryotic Sco protein provides new insight into Sco copper binding and function.

  4. Crystal structure of human nicotinamide riboside kinase.

    PubMed

    Khan, Javed A; Xiang, Song; Tong, Liang

    2007-08-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD(+) as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 A resolution and in a ternary complex with ADP and tiazofurin at 2.7 A resolution. The active site is located in a groove between the central parallel beta sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  5. Crystal structure of mammalian acid sphingomyelinase

    PubMed Central

    Gorelik, Alexei; Illes, Katalin; Heinz, Leonhard X.; Superti-Furga, Giulio; Nagar, Bhushan

    2016-01-01

    Acid sphingomyelinase (ASMase, ASM, SMPD1) converts sphingomyelin into ceramide, modulating membrane properties and signal transduction. Inactivating mutations in ASMase cause Niemann–Pick disease, and its inhibition is also beneficial in models of depression and cancer. To gain a better understanding of this critical therapeutic target, we determined crystal structures of mammalian ASMase in various conformations. The catalytic domain adopts a calcineurin-like fold with two zinc ions and a hydrophobic track leading to the active site. Strikingly, the membrane interacting saposin domain assumes either a closed globular conformation independent from the catalytic domain, or an open conformation, which establishes an interface with the catalytic domain essential for activity. Structural mapping of Niemann–Pick mutations reveals that most of them likely destabilize the protein's fold. This study sheds light on the molecular mechanism of ASMase function, and provides a platform for the rational development of ASMase inhibitors and therapeutic use of recombinant ASMase. PMID:27435900

  6. Structure, thermodynamics, and crystallization of amorphous hafnia

    SciTech Connect

    Luo, Xuhui; Demkov, Alexander A.

    2015-09-28

    We investigate theoretically amorphous hafnia using the first principles melt and quench method. We identify two types of amorphous structures of hafnia. Type I and type II are related to tetragonal and monoclinic hafnia, respectively. We find type II structure to show stronger disorder than type I. Using the phonon density of states, we calculate the specific heat capacity for type II amorphous hafnia. Using the nudged elastic band method, we show that the averaged transition barrier between the type II amorphous hafnia and monoclinic phase is approximately 0.09 eV/HfO{sub 2}. The crystallization temperature is estimated to be 421 K. The calculations suggest an explanation for the low thermal stability of amorphous hafnia.

  7. Crystal Structure of Human Nicotinamide Riboside Kinase

    SciTech Connect

    Khan,J.; Xiang, S.; Tong, L.

    2007-01-01

    Nicotinamide riboside kinase (NRK) has an important role in the biosynthesis of NAD{sup +} as well as the activation of tiazofurin and other NR analogs for anticancer therapy. NRK belongs to the deoxynucleoside kinase and nucleoside monophosphate (NMP) kinase superfamily, although the degree of sequence conservation is very low. We report here the crystal structures of human NRK1 in a binary complex with the reaction product nicotinamide mononucleotide (NMN) at 1.5 {angstrom} resolution and in a ternary complex with ADP and tiazofurin at 2.7 {angstrom} resolution. The active site is located in a groove between the central parallel {beta} sheet core and the LID and NMP-binding domains. The hydroxyl groups on the ribose of NR are recognized by Asp56 and Arg129, and Asp36 is the general base of the enzyme. Mutation of residues in the active site can abolish the catalytic activity of the enzyme, confirming the structural observations.

  8. The Crystal Structure of Human Argonaute2

    SciTech Connect

    Schirle, Nicole T.; MacRae, Ian J.

    2012-07-18

    Argonaute proteins form the functional core of the RNA-induced silencing complexes that mediate RNA silencing in eukaryotes. The 2.3 angstrom resolution crystal structure of human Argonaute2 (Ago2) reveals a bilobed molecule with a central cleft for binding guide and target RNAs. Nucleotides 2 to 6 of a heterogeneous mixture of guide RNAs are positioned in an A-form conformation for base pairing with target messenger RNAs. Between nucleotides 6 and 7, there is a kink that may function in microRNA target recognition or release of sliced RNA products. Tandem tryptophan-binding pockets in the PIWI domain define a likely interaction surface for recruitment of glycine-tryptophan-182 (GW182) or other tryptophan-rich cofactors. These results will enable structure-based approaches for harnessing the untapped therapeutic potential of RNA silencing in humans.

  9. Use of moments of momentum to predict the crystal habit in potassium hydrogen phthalate

    NASA Technical Reports Server (NTRS)

    Barber, Patrick G.; Petty, John T.

    1990-01-01

    A relatively simple calculation of the moments of momentum predicts the morphological order of crystal faces for potassium hydrogen phthalate. The effects on the habit caused by the addition of monomeric, dimeric, and larger aggregates during crystal growth are considered. The first six of the seven observed crystal faces are predicted with this method.

  10. Crystal structures of five 6-mercaptopurine derivatives.

    PubMed

    Gomes, Lígia R; Low, John Nicolson; Magalhães E Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-03-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(3-meth-oxy-phen-yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-meth-oxy-phen-yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-chloro-phen-yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan-yl]-1-(4-bromo-phen-yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth-oxy-phen-yl)-2-[(9H-purin-6-yl)sulfan-yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol-ecular and supra-molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol-ecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all mol-ecules are linked by weak C-H⋯O hydrogen bonds in their crystals. There is π-π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanyl-ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles.

  11. Practical lessons from protein structure prediction

    PubMed Central

    Ginalski, Krzysztof; Grishin, Nick V.; Godzik, Adam; Rychlewski, Leszek

    2005-01-01

    Despite recent efforts to develop automated protein structure determination protocols, structural genomics projects are slow in generating fold assignments for complete proteomes, and spatial structures remain unknown for many protein families. Alternative cheap and fast methods to assign folds using prediction algorithms continue to provide valuable structural information for many proteins. The development of high-quality prediction methods has been boosted in the last years by objective community-wide assessment experiments. This paper gives an overview of the currently available practical approaches to protein structure prediction capable of generating accurate fold assignment. Recent advances in assessment of the prediction quality are also discussed. PMID:15805122

  12. Predicting photoisomerization profile of the highly polymerized nematic azobenzene liquid crystal network: First principle calculation

    NASA Astrophysics Data System (ADS)

    Yun, J.; Li, C.; Chung, H.; Choi, J.; Cho, M.

    2015-05-01

    The cis profile of azobenzene is a key factor in predicting the photodeformation of the nematic azobenzene liquid crystal network (LCN). An ab initio based method for predicting the photoisomerization profile of azobenzene is developed by coupling the stimulated Raman adiabatic passage (STIRAP) method with non-linear Beers law, and compared with experimental data. Using this combined method, we calculate the photoisomerization profile of azobenzene with various light input conditions. We identify the cis profile of the nematic LCN structure evolves into a step-like decaying shape when the direction of polarized light is parallel to the nematic direction.

  13. Crystal structure of natural phaeosphaeride A

    PubMed Central

    Abzianidze, Victoria V.; Poluektova, Ekaterina V.; Bolshakova, Ksenia P.; Panikorovskii, Taras L.; Bogachenkov, Alexander S.; Berestetskiy, Alexander O.

    2015-01-01

    The asymmetric unit of the title compound, C15H23NO5, contains two independent mol­ecules. Phaeosphaeride A contains two primary sections, an alkyl chain consisting of five C atoms and a cyclic system consisting of fused five- and six-membered rings with attached substituents. In the crystal, the mol­ecules form layered structures. Nearly planar sheets, parallel to the (001) plane, form bilayers of two-dimensional hydrogen-bonded networks with the hy­droxy groups located on the inter­ior of the bilayer sheets. The network is constructed primarily of four O—H⋯O hydrogen bonds, which form a zigzag pattern in the (001) plane. The butyl chains inter­digitate with the butyl chains on adjacent sheets. The crystal was twinned by a twofold rotation about the c axis, with refined major–minor occupancy fractions of 0.718 (6):0.282 (6). PMID:26396831

  14. Crystal Structures of Respiratory Pathogen Neuraminidases

    SciTech Connect

    Hsiao, Y.; Parker, D; Ratner, A; Prince, A; Tong, L

    2009-01-01

    Currently there is pressing need to develop novel therapeutic agents for the treatment of infections by the human respiratory pathogens Pseudomonas aeruginosa and Streptococcus pneumoniae. The neuraminidases of these pathogens are important for host colonization in animal models of infection and are attractive targets for drug discovery. To aid in the development of inhibitors against these neuraminidases, we have determined the crystal structures of the P. aeruginosa enzyme NanPs and S. pneumoniae enzyme NanA at 1.6 and 1.7 {angstrom} resolution, respectively. In situ proteolysis with trypsin was essential for the crystallization of our recombinant NanA. The active site regions of the two enzymes are strikingly different. NanA contains a deep pocket that is similar to that in canonical neuraminidases, while the NanPs active site is much more open. The comparative studies suggest that NanPs may not be a classical neuraminidase, and may have distinct natural substrates and physiological functions. This work represents an important step in the development of drugs to prevent respiratory tract colonization by these two pathogens.

  15. Crystal structure of Junin virus nucleoprotein.

    PubMed

    Zhang, Yinjie; Li, Le; Liu, Xiang; Dong, Shishang; Wang, Wenming; Huo, Tong; Guo, Yu; Rao, Zihe; Yang, Cheng

    2013-10-01

    Junin virus (JUNV) has been identified as the aetiological agent of Argentine haemorrhagic fever (AHF), which is a serious public health problem with approximately 5 million people at risk. It is treated as a potential bioterrorism agent because of its rapid transmission by aerosols. JUNV is a negative-sense ssRNA virus that belongs to the genus Arenavirus within the family Arenaviridae, and its genomic RNA contains two segments encoding four proteins. Among these, the nucleoprotein (NP) has essential roles in viral RNA synthesis and immune suppression, but the molecular mechanisms of its actions are only partially understood. Here, we determined a 2.2 Å crystal structure of the C-terminal domain of JUNV NP. This structure showed high similarity to the Lassa fever virus (LASV) NP C-terminal domain. However, both the structure and function of JUNV NP showed differences compared with LASV NP. This study extends our structural insight into the negative-sense ssRNA virus NPs.

  16. Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering.

    PubMed

    Tothadi, Srinu; Desiraju, Gautam R

    2012-06-28

    The idea of a structural landscape is based on the fact that a large number of crystal structures can be associated with a particular organic molecule. Taken together, all these structures constitute the landscape. The landscape includes polymorphs, pseudopolymorphs and solvates. Under certain circumstances, it may also include multi-component crystals (or co-crystals) that contain the reference molecule as one of the components. Under still other circumstances, the landscape may include the crystal structures of molecules that are closely related to the reference molecule. The idea of a landscape is to facilitate the understanding of the process of crystallization. It includes all minima that can, in principle, be accessed by the molecule in question as it traverses the path from solution to the crystal. Isonicotinamide is a molecule that is known to form many co-crystals. We report here a 2:1 co-crystal of this amide with 3,5-dinitrobenzoic acid, wherein an unusual N-H···N hydrogen-bonded pattern is observed. This crystal structure offers some hints about the recognition processes between molecules that might be implicated during crystallization. Also included is a review of other recent results that illustrate the concept of the structural landscape.

  17. Predicting Molecular Crystal Properties from First Principles: Finite-Temperature Thermochemistry to NMR Crystallography.

    PubMed

    Beran, Gregory J O; Hartman, Joshua D; Heit, Yonaton N

    2016-11-15

    Molecular crystals occur widely in pharmaceuticals, foods, explosives, organic semiconductors, and many other applications. Thanks to substantial progress in electronic structure modeling of molecular crystals, attention is now shifting from basic crystal structure prediction and lattice energy modeling toward the accurate prediction of experimentally observable properties at finite temperatures and pressures. This Account discusses how fragment-based electronic structure methods can be used to model a variety of experimentally relevant molecular crystal properties. First, it describes the coupling of fragment electronic structure models with quasi-harmonic techniques for modeling the thermal expansion of molecular crystals, and what effects this expansion has on thermochemical and mechanical properties. Excellent agreement with experiment is demonstrated for the molar volume, sublimation enthalpy, entropy, and free energy, and the bulk modulus of phase I carbon dioxide when large basis second-order Møller-Plesset perturbation theory (MP2) or coupled cluster theories (CCSD(T)) are used. In addition, physical insight is offered into how neglect of thermal expansion affects these properties. Zero-point vibrational motion leads to an appreciable expansion in the molar volume; in carbon dioxide, it accounts for around 30% of the overall volume expansion between the electronic structure energy minimum and the molar volume at the sublimation point. In addition, because thermal expansion typically weakens the intermolecular interactions, neglecting thermal expansion artificially stabilizes the solid and causes the sublimation enthalpy to be too large at higher temperatures. Thermal expansion also frequently weakens the lower-frequency lattice phonon modes; neglecting thermal expansion causes the entropy of sublimation to be overestimated. Interestingly, the sublimation free energy is less significantly affected by neglecting thermal expansion because the systematic

  18. Exploring structural phase transitions of ion crystals

    PubMed Central

    Yan, L. L.; Wan, W.; Chen, L.; Zhou, F.; Gong, S. J.; Tong, X.; Feng, M.

    2016-01-01

    Phase transitions have been a research focus in many-body physics over past decades. Cold ions, under strong Coulomb repulsion, provide a repealing paradigm of exploring phase transitions in stable confinement by electromagnetic field. We demonstrate various conformations of up to sixteen laser-cooled 40Ca+ ion crystals in a home-built surface-electrode trap, where besides the usually mentioned structural phase transition from the linear to the zigzag, two additional phase transitions to more complicated two-dimensional configurations are identified. The experimental observation agrees well with the numerical simulation. Heating due to micromotion of the ions is analysed by comparison of the numerical simulation with the experimental observation. Our investigation implies very rich and complicated many-body behaviour in the trapped-ion systems and provides effective mechanism for further exploring quantum phase transitions and quantum information processing with ultracold trapped ions. PMID:26865229

  19. Crystal Structure of the VS ribozyme

    PubMed Central

    Suslov, Nikolai B.; DasGupta, Saurja; Huang, Hao; Fuller, James R.; Lilley, David M.J.; Rice, Phoebe A.; Piccirilli, Joseph A.

    2015-01-01

    Varkud Satellite (VS) ribozyme mediates rolling circle replication of a plasmid found in the Neurospora mitochondria. We report crystal structures of this ribozyme at 3.1Å resolution, revealing an intertwined dimer formed by an exchange of substrate helices. Within each protomer, an arrangement of three-way helical junctions organizes seven helices into a global fold that creates a docking site for the substrate helix of the other protomer, resulting in the formation of two active sites in trans. This mode of RNA-RNA association resembles the process of domain swapping in proteins and has implications for RNA regulation and evolution. Within each active site, adenine and guanine nucleobases abut the scissile phosphate, poised to serve direct roles in catalysis. Similarities to the active sites of the hairpin and hammerhead ribozymes highlight the functional significance of active site features, underscore the ability of RNA to access functional architectures from distant regions of sequence space, and suggest convergent evolution. PMID:26414446

  20. Crystal structure of a snake venom cardiotoxin

    SciTech Connect

    Rees, B.; Samama, J.P.; Thierry, J.C.; Gilibert, M.; Fischer, J.; Schweitz, H.; Lazdunski, M.; Moras, D.

    1987-05-01

    Cardiotoxin V/sup II/4 from Naja mossambica crystallizes in space group P6/sub 1/ (a = b = 73.9 A; c = 59.0 A) with two molecules of toxin (molecular mass = 6715 Da) in the asymmetric unit. The structure was solved by using a combination of multiple isomorphous replacement and density modification methods. Model building and least-squares refinement led to an agreement factor of 27% for a data set to 3-A resolution prior to any inclusion of solvent molecules. The topology of the molecule is similar to that found in short and long snake neurotoxins, which block the nicotinic acetylcholine receptor. Major differences occur in the conformation of the central loop, resulting in a change in the concavity of the molecule. Hydrophobic residues are clustered in two distinct areas. The existence of stable dimeric entities in the crystalline state, with the formation of a six-stranded antiparallel ..beta.. sheet, may be functionally relevant.

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

    ERIC Educational Resources Information Center

    Hong, Y. S.; And Others

    1980-01-01

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

  2. Crystal structure of human nicotinic acid phosphoribosyltransferase.

    PubMed

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss-Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent.

  3. Crystal structure of human nicotinic acid phosphoribosyltransferase

    PubMed Central

    Marletta, Ada Serena; Massarotti, Alberto; Orsomando, Giuseppe; Magni, Giulio; Rizzi, Menico; Garavaglia, Silvia

    2015-01-01

    Nicotinic acid phosphoribosyltransferase (EC 2.4.2.11) (NaPRTase) is the rate-limiting enzyme in the three-step Preiss–Handler pathway for the biosynthesis of NAD. The enzyme catalyzes the conversion of nicotinic acid (Na) and 5-phosphoribosyl-1-pyrophosphate (PRPP) to nicotinic acid mononucleotide (NaMN) and pyrophosphate (PPi). Several studies have underlined the importance of NaPRTase for NAD homeostasis in mammals, but no crystallographic data are available for this enzyme from higher eukaryotes. Here, we report the crystal structure of human NaPRTase that was solved by molecular replacement at a resolution of 2.9 Å in its ligand-free form. Our structural data allow the assignment of human NaPRTase to the type II phosphoribosyltransferase subfamily and reveal that the enzyme consists of two domains and functions as a dimer with the active site located at the interface of the monomers. The substrate-binding mode was analyzed by molecular docking simulation and provides hints into the catalytic mechanism. Moreover, structural comparison of human NaPRTase with the other two human type II phosphoribosyltransferases involved in NAD biosynthesis, quinolinate phosphoribosyltransferase and nicotinamide phosphoribosyltransferase, reveals that while the three enzymes share a conserved overall structure, a few distinctive structural traits can be identified. In particular, we show that NaPRTase lacks a tunnel that, in nicotinamide phosphoribosiltransferase, represents the binding site of its potent and selective inhibitor FK866, currently used in clinical trials as an antitumoral agent. PMID:26042198

  4. Crystal structure of Homo sapiens kynureninase.

    PubMed

    Lima, Santiago; Khristoforov, Roman; Momany, Cory; Phillips, Robert S

    2007-03-13

    Kynureninase is a member of a large family of catalytically diverse but structurally homologous pyridoxal 5'-phosphate (PLP) dependent enzymes known as the aspartate aminotransferase superfamily or alpha-family. The Homo sapiens and other eukaryotic constitutive kynureninases preferentially catalyze the hydrolytic cleavage of 3-hydroxy-l-kynurenine to produce 3-hydroxyanthranilate and l-alanine, while l-kynurenine is the substrate of many prokaryotic inducible kynureninases. The human enzyme was cloned with an N-terminal hexahistidine tag, expressed, and purified from a bacterial expression system using Ni metal ion affinity chromatography. Kinetic characterization of the recombinant enzyme reveals classic Michaelis-Menten behavior, with a Km of 28.3 +/- 1.9 microM and a specific activity of 1.75 micromol min-1 mg-1 for 3-hydroxy-dl-kynurenine. Crystals of recombinant kynureninase that diffracted to 2.0 A were obtained, and the atomic structure of the PLP-bound holoenzyme was determined by molecular replacement using the Pseudomonas fluorescens kynureninase structure (PDB entry 1qz9) as the phasing model. A structural superposition with the P. fluorescens kynureninase revealed that these two structures resemble the "open" and "closed" conformations of aspartate aminotransferase. The comparison illustrates the dynamic nature of these proteins' small domains and reveals a role for Arg-434 similar to its role in other AAT alpha-family members. Docking of 3-hydroxy-l-kynurenine into the human kynureninase active site suggests that Asn-333 and His-102 are involved in substrate binding and molecular discrimination between inducible and constitutive kynureninase substrates.

  5. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain.

    PubMed

    Bruhn, Jessica F; Kirchdoerfer, Robert N; Urata, Sarah M; Li, Sheng; Tickle, Ian J; Bricogne, Gérard; Saphire, Erica Ollmann

    2017-01-15

    Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (genera Marburgvirus and Ebolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

  6. Crystal structure of the superconducting phase of sulfur hydride

    NASA Astrophysics Data System (ADS)

    Einaga, Mari; Sakata, Masafumi; Ishikawa, Takahiro; Shimizu, Katsuya; Eremets, Mikhail I.; Drozdov, Alexander P.; Troyan, Ivan A.; Hirao, Naohisa; Ohishi, Yasuo

    2016-09-01

    A superconducting critical temperature above 200 K has recently been discovered in H2S (or D2S) under high hydrostatic pressure. These measurements were interpreted in terms of a decomposition of these materials into elemental sulfur and a hydrogen-rich hydride that is responsible for the superconductivity, although direct experimental evidence for this mechanism has so far been lacking. Here we report the crystal structure of the superconducting phase of hydrogen sulfide (and deuterium sulfide) in the normal and superconducting states obtained by means of synchrotron X-ray diffraction measurements, combined with electrical resistance measurements at both room and low temperatures. We find that the superconducting phase is mostly in good agreement with the theoretically predicted body-centred cubic (bcc) structure for H3S. The presence of elemental sulfur is also manifest in the X-ray diffraction patterns, thus proving the decomposition mechanism of H2S to H3S + S under pressure.

  7. Models of protein-ligand crystal structures: trust, but verify

    NASA Astrophysics Data System (ADS)

    Deller, Marc C.; Rupp, Bernhard

    2015-09-01

    X-ray crystallography provides the most accurate models of protein-ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein-ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein-ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein-ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein-ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein-ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein-ligand models for their computational and biological studies, and we provide an overview of how this can be achieved.

  8. Structure dependent hydrogen induced etching features of graphene crystals

    NASA Astrophysics Data System (ADS)

    Thangaraja, Amutha; Shinde, Sachin M.; Kalita, Golap; Papon, Remi; Sharma, Subash; Vishwakarma, Riteshkumar; Sharma, Kamal P.; Tanemura, Masaki

    2015-06-01

    H2 induced etching of graphene is of significant interest to understand graphene growth process as well as to fabricate nanoribbons and various other structures. Here, we demonstrate the structure dependent H2 induced etching behavior of graphene crystals. We synthesized graphene crystals on electro-polished Cu foil by an atmospheric pressure chemical vapor deposition process, where some of the crystals showed hexagonal shaped snowflake-dendritic morphology. Significant differences in H2 induced etching behavior were observed for the snowflake-dendritic and regular graphene crystals by annealing in a gas mixture of H2 and Ar. The regular graphene crystals were etched anisotropically creating hexagonal holes with pronounced edges, while etching of all the dendritic crystals occurred from the branches of lobs creating symmetrical fractal structures. The etching behavior provides important clue of graphene nucleation and growth as well as their selective etching to fabricate well-defined structures for nanoelectronics.

  9. Crystallization and Characterization of Galdieria sulphuraria RUBISCO in Two Crystal Forms: Structural Phase Transition Observed in P21 Crystal Form

    PubMed Central

    Baranowski, Michael; Stec, Boguslaw

    2007-01-01

    We have isolated ribulose-1,5-bisphosphate-carboxylase/oxygenase (RUBISCO) from the red algae Galdieria Sulphuraria. The protein crystallized in two different crystal forms, the I422 crystal form being obtained from high salt and the P21 crystal form being obtained from lower concentration of salt and PEG. We report here the crystallization, preliminary stages of structure determination and the detection of the structural phase transition in the P21 crystal form of G. sulphuraria RUBISCO. This red algae enzyme belongs to the hexadecameric class (L8S8) with an approximate molecular weight 0.6MDa. The phase transition in G. sulphuraria RUBISCO leads from two hexadecamers to a single hexadecamer per asymmetric unit. The preservation of diffraction power in a phase transition for such a large macromolecule is rare.

  10. Crystal structures of five 6-mercaptopurine derivatives

    PubMed Central

    Gomes, Lígia R.; Low, John Nicolson; Magalhães e Silva, Diogo; Cagide, Fernando; Borges, Fernanda

    2016-01-01

    The crystal structures of five 6-mercaptopurine derivatives, viz. 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(3-meth­oxy­phen­yl)ethan-1-one (1), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-meth­oxy­phen­yl)ethan-1-one (2), C16H14N4O3S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-chloro­phen­yl)ethan-1-one (3), C15H11ClN4O2S, 2-[(9-acetyl-9H-purin-6-yl)sulfan­yl]-1-(4-bromo­phen­yl)ethan-1-one (4), C15H11BrN4O2S, and 1-(3-meth­oxy­phen­yl)-2-[(9H-purin-6-yl)sulfan­yl]ethan-1-one (5), C14H12N4O2S. Compounds (2), (3) and (4) are isomorphous and accordingly their mol­ecular and supra­molecular structures are similar. An analysis of the dihedral angles between the purine and exocyclic phenyl rings show that the mol­ecules of (1) and (5) are essentially planar but that in the case of the three isomorphous compounds (2), (3) and (4), these rings are twisted by a dihedral angle of approximately 38°. With the exception of (1) all mol­ecules are linked by weak C—H⋯O hydrogen bonds in their crystals. There is π–π stacking in all compounds. A Cambridge Structural Database search revealed the existence of 11 deposited compounds containing the 1-phenyl-2-sulfanyl­ethanone scaffold; of these, only eight have a cyclic ring as substituent, the majority of these being heterocycles. PMID:27006794

  11. Crystal Structure of Human Kynurenine Aminotransferase ll*

    SciTech Connect

    Han,Q.; Robinson, H.; Li, J.

    2008-01-01

    Human kynurenine aminotransferase II (hKAT-II) efficiently catalyzes the transamination of knunrenine to kynurenic acid (KYNA). KYNA is the only known endogenous antagonist of N-methyl-d-aspartate (NMDA) receptors and is also an antagonist of 7-nicotinic acetylcholine receptors. Abnormal concentrations of brain KYNA have been implicated in the pathogenesis and development of several neurological and psychiatric diseases in humans. Consequently, enzymes involved in the production of brain KYNA have been considered potential regulatory targets. In this article, we report a 2.16 Angstroms crystal structure of hKAT-II and a 1.95 Angstroms structure of its complex with kynurenine. The protein architecture of hKAT-II reveals that it belongs to the fold-type I pyridoxal 5-phosphate (PLP)-dependent enzymes. In comparison with all subclasses of fold-type I-PLP-dependent enzymes, we propose that hKAT-II represents a novel subclass in the fold-type I enzymes because of the unique folding of its first 65 N-terminal residues. This study provides a molecular basis for future effort in maintaining physiological concentrations of KYNA through molecular and biochemical regulation of hKAT-II.

  12. Manipulating Heat Flow through 3 Dimensional Nanoscale Phononic Crystal Structure

    DTIC Science & Technology

    2014-06-02

    Nanoscale Phononic Crystal Structure 5a. CONTRACT NUMBER FA23861214047 5b. GRANT NUMBER 5c. PROGRAM ELEMENT NUMBER 6. AUTHOR(S) Baowen Li 5d...through computer simulation, how the three dimensional (3D) phononic crystal structures can confine phonon and thus reduce thermal conductivity...phononic crystal (PnC) with spherical pores, which can reduce thermal conductivity of bulk Si by a factor up to 10,000 times at room temperature. The

  13. Anomalous variations of crystal habits and solution properties in the context of the crystallization medium structure

    NASA Astrophysics Data System (ADS)

    Kiryanova, E. V.; Ugolkov, V. L.; Pyankova, L. A.; Filatov, S. K.

    2009-12-01

    The effect of the real structure of solutions on crystallization is one of the basic issues of crystallogenesis, which is also important for resolving problems of genetic mineralogy. The study of the NaNO3-H2O and KNO3-H2O model systems yielded new data on anomalous characteristics of crystal-forming systems, including morphological and kinetic properties of crystals, crystal-solution equilibrium, and physical properties of solutions (light scattering, thermal properties, IR parameters, pH), providing information on the structure of solutions. The internally consistent data confirm the previously suggested variations in structural heterogeneity of solutions related to minor (2-4%) variations in their composition, which result in numerous disturbances of monotonicity (thermal-concentration oscillations) in the liquidus curves of salts. It is shown that these variations can be caused by variable size and composition of crystal hydrate clusters. The experimental data indicate that the effect of the real solution structure on crystal morphology and crystal-solution equilibrium is enhanced in multicomponent systems, including natural crystal-forming systems. Anomalous faceting and habit, zoning, a sectorial structure of crystals, and nonuniform entrapment of admixtures cannot be ruled out in these systems.

  14. Undergraduates Improve upon Published Crystal Structure in Class Assignment

    ERIC Educational Resources Information Center

    Horowitz, Scott; Koldewey, Philipp; Bardwell, James C.

    2014-01-01

    Recently, 57 undergraduate students at the University of Michigan were assigned the task of solving a crystal structure, given only the electron density map of a 1.3 Å crystal structure from the electron density server, and the position of the N-terminal amino acid. To test their knowledge of amino acid chemistry, the students were not given the…

  15. Predicting Protein Structure Using Parallel Genetic Algorithms.

    DTIC Science & Technology

    1994-12-01

    By " Predicting rotein Structure D istribticfiar.. ................ Using Parallel Genetic Algorithms ,Avaiu " ’ •"... Dist THESIS I IGeorge H...iiLite-d Approved for public release; distribution unlimited AFIT/ GCS /ENG/94D-03 Predicting Protein Structure Using Parallel Genetic Algorithms ...1-1 1.2 Genetic Algorithms ......... ............................ 1-3 1.3 The Protein Folding Problem

  16. Growth and crystal structure of the BeAl 6O 10 single crystals

    NASA Astrophysics Data System (ADS)

    Alimpiev, A. I.; Merkulov, A. A.; Solntsev, V. P.; Tsvetkov, E. G.; Matrosov, V. N.; Pestryakov, E. V.

    2002-04-01

    Unlike earlier published works we have established incongruent melting for the compound BeAl 6O 10 (BHA). The conditions of growing crystals from their own melt with a superstoichiometric excess of BeO, using the Czochralski method, have been determined. The nature of inclusions in grown BHA crystals is described. On the basis of X-ray crystal structure analysis and data of spectroscopic studies the symmetry and space group of BHA crystal structure have been refined, as well as uncertainties arising in their interpretation are discussed.

  17. Collective prediction based on community structure

    NASA Astrophysics Data System (ADS)

    Jiang, Yasong; Li, Taisong; Zhang, Yan; Yan, Yonghong

    2017-01-01

    Collective prediction algorithms have been used to improve performances when network structures are involved in prediction tasks. The training dataset of such tasks often contain information of content, links and labels, while the testing dataset have only content and link information. Conventional collective prediction algorithms conduct predictions based on the content of a node and the information of its direct neighbors with a base classifier. However, the information of some direct neighbor nodes may be not consistent with the target one. In addition, the information of indirect neighbors can be helpful when that of direct neighbors is scant. In this paper, instead of using information of direct neighbors, we propose to apply community structures in networks to prediction tasks. A community detection method is aggregated into the collective prediction process to improve prediction performance. Experimental results show that the proposed algorithm outperforms a number of standard prediction algorithms specially under conditions that labeled training dataset are limited.

  18. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

    SciTech Connect

    Biedermannová, Lada Schneider, Bohdan

    2015-10-27

    The hydration of protein crystal structures was studied at the level of individual amino acids. The dependence of the number of water molecules and their preferred spatial localization on various parameters, such as solvent accessibility, secondary structure and side-chain conformation, was determined. Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

  19. Use of Pom Pons to Illustrate Cubic Crystal Structures.

    ERIC Educational Resources Information Center

    Cady, Susan G.

    1997-01-01

    Describes a method that uses olefin pom pons to illustrate cubic crystal structure. Facilitates hands-on examination of different packing arrangements such as hexagonal close-packed and cubic close-packed structures. (JRH)

  20. Crystal structure of Clostridium difficile toxin A

    PubMed Central

    Chumbler, Nicole M.; Rutherford, Stacey A.; Zhang, Zhifen; Farrow, Melissa A.; Lisher, John P.; Farquhar, Erik; Giedroc, David P.; Spiller, Benjamin W.; Melnyk, Roman A.; Lacy, D. Borden

    2016-01-01

    Clostridium difficile infection is the leading cause of hospital-acquired diarrhoea and pseudomembranous colitis. Disease is mediated by the actions of two toxins, TcdA and TcdB, which cause the diarrhoea, as well as inflammation and necrosis within the colon1,2. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host3,4. The multidomain toxins enter cells by receptor-mediated endocytosis and, upon exposure to the low pH of the endosome, insert into and deliver two enzymatic domains across the membrane. Eukaryotic inositol-hexakisphosphate (InsP6) binds an autoprocessing domain to activate a proteolysis event that releases the N-terminal glucosyltransferase domain into the cytosol. Here, we report the crystal structure of a 1,832-amino-acid fragment of TcdA (TcdA1832), which reveals a requirement for zinc in the mechanism of toxin autoprocessing and an extended delivery domain that serves as a scaffold for the hydrophobic α-helices involved in pH-dependent pore formation. A surface loop of the delivery domain whose sequence is strictly conserved among all large clostridial toxins is shown to be functionally important, and is highlighted for future efforts in the development of vaccines and novel therapeutics. PMID:27571750

  1. Crystal structure of oxam­yl

    PubMed Central

    Kwon, Eunjin; Park, Ki-Min; Park, Hyunjin; Kim, Tae Ho

    2016-01-01

    The title compound, C7H13N3O3S [systematic name: (Z)-methyl 2-di­methyl­amino-N-(methyl­carbamo­yloxy)-2-oxoethanimido­thio­ate], is an oxime carbamate acaride, insecticide and nematicide. The asymmetric unit comprises two independent mol­ecules, A and B. The dihedral angles between the mean planes [r.m.s. deviations = 0.0017 (A) and 0.0016 Å (B)] of the acetamide and oxyimino groups are 88.80 (8)° for A and 87.05 (8)° for B. In the crystal, N/C—H⋯O hydrogen bonds link adjacent mol­ecules, forming chains along the a axis. The chains are further linked by C—H⋯O hydrogen bonds, resulting in a three-dimensional network with alternating rows of A and B mol­ecules in the bc plane stacked along the a-axis direction. The structure was refined as an inversion twin with a final BASF parameter of 0.16 (9). PMID:27980838

  2. Microstructure and Crystal Structure in TAGS Compositions

    SciTech Connect

    Thompson, A. J.; Sharp, J; Rawn, Claudia J

    2009-01-01

    GeTe, a small bandgap semiconductor that has native p-type defects due to Ge vacancies, is an important constituent in the thermoelectric material known as TAGS. TAGS is an acronym for alloys of GeTe with AgSbTe{sub 2}, and compositions are normally designated as TAGS-x, where x is the fraction of GeTe. TAGS-85 is the most important with regard to applications, and there is also commercial interest in TAGS-80. The crystal structure of GeTe{sub 1+{delta}} has a composition-dependent phase transformation at a temperature ranging from 430 C ({delta} = 0) to {approx}400 C ({delta} = 0.02). The high-temperature form is cubic. The low-temperature form is rhombohedral for {delta} < 0.01, as is the case for good thermoelectric performance. Addition of AgSbTe{sub 2} shifts the phase transformation to lower temperatures, and one of the goals of this work is a systematic study of the dependence of transformation temperature on the parameter x. We present results on phase transformations and associated instabilities in TAGS compositions in the range of 70 at.% to 85 at.% GeTe.

  3. Preparation of iridescent colloidal crystal coatings with variable structural colors.

    PubMed

    Cong, Hailin; Yu, Bing; Wang, Shaopeng; Qi, Limin; Wang, Jilei; Ma, Yurong

    2013-07-29

    Iridescent colloidal crystal coatings with variable structural colors were fabricated by incorporating carbon black nanoparticles (CB-NPs) into the voids of polystyrene (PS) colloidal crystals. The structural color of the colloid crystal coatings was not only greatly enhanced after the composition but also varied with observation angles. By changing the diameter of monodisperse PS colloids in the composites, colloidal crystal coatings with three primary colors for additive or subtractive combination were obtained. After incorporation of the PS/CB-NPs hybrid coatings into polydimethylsiloxane (PDMS) matrix, manmade opal jewelry with variable iridescent colors was made facilely.

  4. Protein Structure Prediction with Visuospatial Analogy

    NASA Astrophysics Data System (ADS)

    Davies, Jim; Glasgow, Janice; Kuo, Tony

    We show that visuospatial representations and reasoning techniques can be used as a similarity metric for analogical protein structure prediction. Our system retrieves pairs of α-helices based on contact map similarity, then transfers and adapts the structure information to an unknown helix pair, showing that similar protein contact maps predict similar 3D protein structure. The success of this method provides support for the notion that changing representations can enable similarity metrics in analogy.

  5. Crystal structures of dihydroxyacetone and its derivatives.

    PubMed

    Slepokura, Katarzyna; Lis, Tadeusz

    2004-08-02

    The crystal and molecular structures of three crystalline forms of the dihydroxyacetone dimer, C6H12O6, DHA-dimer: alpha (1a), beta (1b), and gamma (1c), the hydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3)(2) x H2O, CaCl2(DHA)2 x H2O (2a), the tetrahydrated calcium chloride complex of dihydroxyacetone monomer, CaCl2(C3H6O3) x 4H2O, CaCl2(DHA) x 4H2O (2b), the dihydroxyacetone monomer, C3H6O3, DHA (2c), and dihydroxyacetone dimethyl acetal, C5H12O4, (MeO)2DHA (3) are described. Compounds 1a and 2b crystallize in the triclinic system, and 1b,c, 2a,c, and 3 are monoclinic. Molecules of all forms of dihydroxyacetone dimer 1a,b, and 1c are the trans isomers, with the 1,4-dioxane ring in the chair conformation and the hydroxyl and hydroxymethyl groups in axial and equatorial dispositions, respectively. The Ca2+ ions in 2a and 2b are bridged by the carbonyl O atoms from two symmetry-related DHA molecules to form centrosymmetric dimers with Ca...Ca distance of 4.307(2)A in 2a and 4.330(2) and 4.305(2)A in two crystallographically independent dimers in 2b. DHA molecules coordinate to the Ca2+ ions by hydroxyl and carbonyl oxygen atoms. The eight-coordinate polyhedra of Ca2+ are completed by water molecule and Cl- ion in 2a and by four water molecules in 2b. The dihydroxyacetone molecules in 2a,b, and 2c are in an extended conformation, with both hydroxyl groups being synperiplanar (sp) to the carbonyl O atom. All hydroxyl groups in 2c (along with water molecules in 2a and 2b) are involved as donors in medium strong and weak intermolecular O-H...O hydrogen bonding. Some of them, as well as carbonyl O atoms or Cl- ions in 2a and 2b, act as acceptors in C-H...O (and C-H...Cl) hydrogen interactions.

  6. Computational Prediction of RNA Tertiary Structure

    NASA Astrophysics Data System (ADS)

    Zhao, Yunjie; Gong, Zhou; Chen, Changjun; Xiao, Yi

    2012-02-01

    RNAs have been found to be involved in the biological processes. The large RNA usually consists of two basic elements: RNA hairpins and duplex. Due to the experimental determination difficulties, the few RNA tertiary structures limit our understanding of the specific regulation mechanisms and functions. Therefore, RNA tertiary structure prediction is very important for understanding RNA biological functions. Since RNA often folds hierarchically, one of the possible RNA structure prediction approaches is through the hierarchical steps. Here, we focus on the prediction method of RNA tertiary hairpin and duplex structures in which assembles the small tertiary structure fragments from well-defined RNA structural motifs. In a benchmark test with known experiment structures, more than half of the cases agree with the experimental structure better than 3 å RMSD over all the heavy atoms. The prediction results also reproduce the native like complementary base pairs of the secondary structures. Most importantly, the method performs the atomic accuracy of tertiary structures by about several minutes. We expect that the method will be a useful resource for RNA tertiary structure prediction and helpful to the biological research community.

  7. Structural Color Patterns by Electrohydrodynamic Jet Printed Photonic Crystals.

    PubMed

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

    2017-02-09

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

  8. Origin and structure of polar domains in doped molecular crystals

    PubMed Central

    Meirzadeh, E.; Azuri, I.; Qi, Y.; Ehre, D.; Rappe, A. M.; Lahav, M.; Kronik, L.; Lubomirsky, I.

    2016-01-01

    Doping is a primary tool for the modification of the properties of materials. Occlusion of guest molecules in crystals generally reduces their symmetry by the creation of polar domains, which engender polarization and pyroelectricity in the doped crystals. Here we describe a molecular-level determination of the structure of such polar domains, as created by low dopant concentrations (<0.5%). The approach comprises crystal engineering and pyroelectric measurements, together with dispersion-corrected density functional theory and classical molecular dynamics calculations of the doped crystals, using neutron diffraction data of the host at different temperatures. This approach is illustrated using centrosymmetric α-glycine crystals doped with minute amounts of different L-amino acids. The experimentally determined pyroelectric coefficients are explained by the structure and polarization calculations, thus providing strong support for the local and global understanding of how different dopants influence the properties of molecular crystals. PMID:27824050

  9. Ab initio solution of macromolecular crystal structures without direct methods.

    PubMed

    McCoy, Airlie J; Oeffner, Robert D; Wrobel, Antoni G; Ojala, Juha R M; Tryggvason, Karl; Lohkamp, Bernhard; Read, Randy J

    2017-04-04

    The majority of macromolecular crystal structures are determined using the method of molecular replacement, in which known related structures are rotated and translated to provide an initial atomic model for the new structure. A theoretical understanding of the signal-to-noise ratio in likelihood-based molecular replacement searches has been developed to account for the influence of model quality and completeness, as well as the resolution of the diffraction data. Here we show that, contrary to current belief, molecular replacement need not be restricted to the use of models comprising a substantial fraction of the unknown structure. Instead, likelihood-based methods allow a continuum of applications depending predictably on the quality of the model and the resolution of the data. Unexpectedly, our understanding of the signal-to-noise ratio in molecular replacement leads to the finding that, with data to sufficiently high resolution, fragments as small as single atoms of elements usually found in proteins can yield ab initio solutions of macromolecular structures, including some that elude traditional direct methods.

  10. Crystal structure of human nuclear pore complex component NUP43.

    PubMed

    Xu, Chao; Li, Zhihong; He, Hao; Wernimont, Amy; Li, Yanjun; Loppnau, Peter; Min, Jinrong

    2015-10-24

    Nuclear pore complexes (NPC) form nuclear pores that cross the nuclear envelope and allow molecules to transport between the nucleus and the cytoplasm. We solved the crystal structure of human Nup43 (hNUP43), an important component in the Nup107 subcomplex of NPC. hNup43 adopts a seven-bladed β-propeller fold. We confirmed by ITC that neither human Nup37 (hNup37) nor human Nup133 (hNup133) interacts with hNup43. We demonstrated by analytical gel filtration that the human Nup85-Seh1L binary complex recruits hNup43 to form a ternary complex. Based on amino acid sequence analysis, we predicted the hNup85-hSeh1L binding surface of hNup43.

  11. Energy-directed RNA structure prediction.

    PubMed

    Hofacker, Ivo L

    2014-01-01

    In this chapter we present the classic dynamic programming algorithms for RNA structure prediction by energy minimization, as well as variations of this approach that allow to compute suboptimal foldings, or even the partition function over all possible secondary structures. The latter are essential in order to deal with the inaccuracy of minimum free energy (MFE) structure prediction, and can be used, for example, to derive reliability measures that assign a confidence value to all or part of a predicted structure. In addition, we discuss recently proposed alternatives to the MFE criterion such as the use of maximum expected accuracy (MEA) or centroid structures. The dynamic programming algorithms implicitly assume that the RNA molecule is in thermodynamic equilibrium. However, especially for long RNAs, this need not be the case. In the last section we therefore discuss approaches for predicting RNA folding kinetics and co-transcriptional folding.

  12. Predicting pseudoknotted structures across two RNA sequences

    PubMed Central

    Sperschneider, Jana; Datta, Amitava; Wise, Michael J.

    2012-01-01

    Motivation: Laboratory RNA structure determination is demanding and costly and thus, computational structure prediction is an important task. Single sequence methods for RNA secondary structure prediction are limited by the accuracy of the underlying folding model, if a structure is supported by a family of evolutionarily related sequences, one can be more confident that the prediction is accurate. RNA pseudoknots are functional elements, which have highly conserved structures. However, few comparative structure prediction methods can handle pseudoknots due to the computational complexity. Results: A comparative pseudoknot prediction method called DotKnot-PW is introduced based on structural comparison of secondary structure elements and H-type pseudoknot candidates. DotKnot-PW outperforms other methods from the literature on a hand-curated test set of RNA structures with experimental support. Availability: DotKnot-PW and the RNA structure test set are available at the web site http://dotknot.csse.uwa.edu.au/pw. Contact: janaspe@csse.uwa.edu.au Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23044552

  13. A Dominant Factor for Structural Classification of Protein Crystals.

    PubMed

    Qi, Fei; Fudo, Satoshi; Neya, Saburo; Hoshino, Tyuji

    2015-08-24

    With the increasing number of solved protein crystal structures, much information on protein shape and atom geometry has become available. It is of great interest to know the structural diversity for a single kind of protein. Our preliminary study suggested that multiple crystal structures of a single kind of protein can be classified into several groups from the viewpoint of structural similarity. In order to broadly examine this finding, cluster analysis was applied to the crystal structures of hemoglobin (Hb), myoglobin (Mb), human serum albumin (HSA), hen egg-white lysozyme (HEWL), and human immunodeficiency virus type 1 protease (HIV-1 PR), downloaded from the Protein Data Bank (PDB). As a result of classification by cluster analysis, 146 crystal structures of Hb were separated into five groups. The crystal structures of Mb (n = 284), HEWL (n = 336), HSA (n = 63), and HIV-1 PR (n = 488) were separated into six, five, three, and six groups, respectively. It was found that a major factor causing these structural separations is the space group of crystals and that crystallizing agents have an influence on the crystal structures. Amino acid mutation is a minor factor for the separation because no obvious point mutation making a specific cluster group was observed for the five kinds of proteins. In the classification of Hb and Mb, the species of protein source such as humans, rabbits, and mice is another significant factor. When the difference in amino sequence is large among species, the species of protein source is the primary factor causing cluster separation in the classification of crystal structures.

  14. On the Crystal Structure of Ln

    SciTech Connect

    Olafsen, Anja; Larsson, Ann-Kristin; Fjellvaag, Helmer; Hauback, Bjoern C.

    2001-04-01

    The crystal structures of La{sub 2}O{sub 2}CO{sub 3} II and Nd{sub 2}O{sub 2}CO{sub 3} II have been shown by means of high-resolution powder neutron (PND) and synchrotron X-ray diffraction (SXRD) combined with selected area electron diffraction (SAED) studies to be far more complex than earlier anticipated, owing to ordering of carbonate groups between (Ln{sub 2}O{sub 2}{sup +2}){sub n} layers. In contrast to earlier descriptions, the carbonate groups appear to be rather regular. Relative to an average model, the SAED patterns show additional scattering in the form of closely distributed, but essentially discrete, spots along < 1/3, 1/3, 1 >. Most of the observed scattering, H, can be described as H=G{+-}m q{sub 1}+n q{sub 2}, where G is the Bragg reflections of the underlying average P6{sub 3}/mmc lattice, q1=[1/3, 1/3, {+-}1/2]*, q2=[1/3, 1/3, {+-}2/3]*, and m and n are integers. The additional scattering reflects ordering of the carbonate groups into trigonal layers between the (Ln{sub 2}O{sub 2}{sup +2}){sub n} layers, but it remains open whether q{sub 1} and q{sub 2} represent two separate structures with different stacking sequences of such layers or whether they correspond to an even more complex stacking sequence. In any case, some disorder and rotational domain twinning are present. Two structure models, one for each modulation wave vector, were constructed. Rietveld-type refinements of PND data of La{sub 2}O{sub 2}CO{sub 3} II were performed, approximating the complex, and at least partly disordered, stacking sequence as a two-phase mixture of the two modulated phases. Satisfactory convergence was achieved with R{sub p}=6.4%, R{sub wp}=8.3%, and {chi}{sup 2}=3.32. The isothermal expansivities, {alpha}{sub p}, for La{sub 2}O{sub 2}CO{sub 3} II and Nd{sub 2}O{sub 2}CO{sub 3} II between 298 and 893 K were determined as 2.92x10{sup {minus}5} and 2.70x10{sup {minus}5} K{sup {minus}1}, respectively.

  15. Structural and Thermoelectric Properties of Tungsten Diselenide Crystals

    NASA Astrophysics Data System (ADS)

    Patel, K. K.; Patel, K. D.; Patel, Mayur; Patel, C. A.; Pathak, V. M.; Srivastava, R.

    2011-12-01

    Crystals of Tungsten diselenide (WSe2) have been grown by direct vapour transport (DVT) technique using micro processor controlled dual zone horizontal furnace. The chemical composition and structure of grown crystals were confirmed using energy dispersive analysis of X-ray (EDAX) and X-ray diffraction (XRD). In the present investigation thermoelectric power measurements (TEP) have been carried out on the grown crystals. Different electrical transport parameters of semiconductors have been determined and discussed in the paper.

  16. Photonic Crystal Structures with Tunable Structure Color as Colorimetric Sensors

    PubMed Central

    Wang, Hui; Zhang, Ke-Qin

    2013-01-01

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors. PMID:23539027

  17. Photonic crystal structures with tunable structure color as colorimetric sensors.

    PubMed

    Wang, Hui; Zhang, Ke-Qin

    2013-03-28

    Colorimetric sensing, which transduces environmental changes into visible color changes, provides a simple yet powerful detection mechanism that is well-suited to the development of low-cost and low-power sensors. A new approach in colorimetric sensing exploits the structural color of photonic crystals (PCs) to create environmentally-influenced color-changeable materials. PCs are composed of periodic dielectrics or metallo-dielectric nanostructures that affect the propagation of electromagnetic waves (EM) by defining the allowed and forbidden photonic bands. Simultaneously, an amazing variety of naturally occurring biological systems exhibit iridescent color due to the presence of PC structures throughout multi-dimensional space. In particular, some kinds of the structural colors in living organisms can be reversibly changed in reaction to external stimuli. Based on the lessons learned from natural photonic structures, some specific examples of PCs-based colorimetric sensors are presented in detail to demonstrate their unprecedented potential in practical applications, such as the detections of temperature, pH, ionic species, solvents, vapor, humidity, pressure and biomolecules. The combination of the nanofabrication technique, useful design methodologies inspired by biological systems and colorimetric sensing will lead to substantial developments in low-cost, miniaturized and widely deployable optical sensors.

  18. Crystal structures of three bicyclic carbohydrate derivatives

    PubMed Central

    Schilde, Uwe; Kelling, Alexandra; Umbreen, Sumaira; Linker, Torsten

    2016-01-01

    The title compounds, [(1R,3R,4R,5R,6S)-4,5-bis­(acet­yloxy)-7-oxo-2-oxabi­cyclo[4.2.0]octan-3-yl]methyl acetate, C14H18O8, (I), [(1S,4R,5S,6R)-5-acet­yloxy-7-hy­droxy­imino-2-oxobi­cyclo­[4.2.0]octan-4-yl acetate, C11H15NO6, (II), and [(3aR,5R,6R,7R,7aS)-6,7-bis­(acet­yloxy)-2-oxo­octa­hydro­pyrano[3,2-b]pyrrol-5-yl]methyl acetate, C14H19NO8, (III), are stable bicyclic carbohydrate derivatives. They can easily be synthesized in a few steps from commercially available glycals. As a result of the ring strain from the four-membered rings in (I) and (II), the conformations of the carbohydrates deviate strongly from the ideal chair form. Compound (II) occurs in the boat form. In the five-membered lactam (III), on the other hand, the carbohydrate adopts an almost ideal chair conformation. As a result of the distortion of the sugar rings, the configurations of the three bicyclic carbohydrate derivatives could not be determined from their NMR coupling constants. From our three crystal structure determinations, we were able to establish for the first time the absolute configurations of all new stereocenters of the carbohydrate rings. PMID:27980845

  19. SCRATCH: a protein structure and structural feature prediction server

    PubMed Central

    Cheng, J.; Randall, A. Z.; Sweredoski, M. J.; Baldi, P.

    2005-01-01

    SCRATCH is a server for predicting protein tertiary structure and structural features. The SCRATCH software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. The user simply provides an amino acid sequence and selects the desired predictions, then submits to the server. Results are emailed to the user. The server is available at . PMID:15980571

  20. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    SciTech Connect

    Bruhn, Jessica F.; Kirchdoerfer, Robert N.; Urata, Sarah M.; Li, Sheng; Tickle, Ian J.; Bricogne, Gérard; Saphire, Erica Ollmann; Sundquist, W. I.

    2016-11-09

    ABSTRACT

    Marburg virus (MARV) is a highly pathogenic filovirus that is classified in a genus distinct from that of Ebola virus (EBOV) (generaMarburgvirusandEbolavirus, respectively). Both viruses produce a multifunctional protein termed VP35, which acts as a polymerase cofactor, a viral protein chaperone, and an antagonist of the innate immune response. VP35 contains a central oligomerization domain with a predicted coiled-coil motif. This domain has been shown to be essential for RNA polymerase function. Here we present crystal structures of the MARV VP35 oligomerization domain. These structures and accompanying biophysical characterization suggest that MARV VP35 is a trimer. In contrast, EBOV VP35 is likely a tetramer in solution. Differences in the oligomeric state of this protein may explain mechanistic differences in replication and immune evasion observed for MARV and EBOV.

    IMPORTANCEMarburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing

  1. Structure prediction and targeted synthesis: a new Na(n)N2 diazenide crystalline structure.

    PubMed

    Zhang, Xiuwen; Zunger, Alex; Trimarchi, Giancarlo

    2010-11-21

    Significant progress in theoretical and computational techniques for predicting stable crystal structures has recently begun to stimulate targeted synthesis of such predicted structures. Using a global space-group optimization (GSGO) approach that locates ground-state structures and stable stoichiometries from first-principles energy functionals by objectively starting from randomly selected lattice vectors and random atomic positions, we predict the first alkali diazenide compound Na(n)N(2), manifesting homopolar N-N bonds. The previously predicted Na(3)N structure manifests only heteropolar Na-N bonds and has positive formation enthalpy. It was calculated based on local Hartree-Fock relaxation of a fixed-structure type (Li(3)P-type) found by searching an electrostatic point-ion model. Synthesis attempts of this positive ΔH compound using activated nitrogen yielded another structure (anti-ReO(3)-type). The currently predicted (negative formation enthalpy) diazenide Na(2)N(2) completes the series of previously known BaN(2) and SrN(2) diazenides where the metal sublattice transfers charge into the empty N(2) Π(g) orbital. This points to a new class of alkali nitrides with fundamentally different bonding, i.e., homopolar rather than heteropolar bonds and, at the same time, illustrates some of the crucial subtleties and pitfalls involved in structure predictions versus planned synthesis. Attempts at synthesis of the stable Na(2)N(2) predicted here will be interesting.

  2. Isomorph invariance of the structure and dynamics of classical crystals

    NASA Astrophysics Data System (ADS)

    Albrechtsen, Dan E.; Olsen, Andreas E.; Pedersen, Ulf R.; Schrøder, Thomas B.; Dyre, Jeppe C.

    2014-09-01

    This paper shows by computer simulations that some crystalline systems have curves in their thermodynamic phase diagrams, so-called isomorphs, along which structure and dynamics in reduced units are invariant to a good approximation. The crystals are studied in a classical-mechanical framework, which is generally a good description except significantly below melting. The existence of isomorphs for crystals is validated by simulations of particles interacting via the Lennard-Jones pair potential arranged into a face-centered cubic (fcc) crystalline structure; the slow vacancy-jump dynamics of a defective fcc crystal is also shown to be isomorph invariant. In contrast, a NaCl crystal model does not exhibit isomorph invariances. Other systems simulated, though in less detail, are the Wahnström binary Lennard-Jones crystal with the MgZn2 Laves crystal structure, monatomic fcc crystals of particles interacting via the Buckingham pair potential and via a purely repulsive pair potential diverging at a finite separation, an ortho-terphenyl molecular model crystal, and SPC/E hexagonal ice. Except for NaCl and ice, the crystals simulated all have isomorphs. Based on previous simulations of liquid models, we conjecture that crystalline solids with isomorphs include most or all formed by atoms or molecules interacting via metallic or van der Waals forces, whereas covalently bonded or hydrogen-bonded crystals are not expected to have isomorphs; crystals of ions or dipolar molecules constitute a limiting case for which isomorphs are only expected when the Coulomb interactions are relatively weak. We briefly discuss the consequences of the findings for theories of melting and crystallization.

  3. Missing strings of residues in protein crystal structures.

    PubMed

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

    A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.

  4. Missing strings of residues in protein crystal structures

    PubMed Central

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

    A large fraction of the protein crystal structures deposited in the Protein Data Bank are incomplete, since the position of one or more residues is not reported, despite these residues are part of the material that was analyzed. This may bias the use of the protein crystal structures by molecular biologists. Here we observe that in the large majority of the protein crystal structures strings of residues are missing. Polar residues incline to occur in missing strings together with glycine, while apolar and aromatic residues tend to avoid them. Particularly flexible residues, as shown by their extremely high B-factors, by their exposure to the solvent and by their secondary structures, flank the missing strings. These data should be a helpful guideline for crystallographers that encounter regions of flat and uninterpretable electron density as well as end-users of crystal structures.

  5. Low-voltage tunable photonics devices: grove on thin porous structures containing liquid crystals

    NASA Astrophysics Data System (ADS)

    Criante, Luigino; Moretti, Luca; Scotognella, Francesco

    2013-09-01

    In this study we demonstrate the fabrication of one-dimensional porous multilayer photonic crystals made by metal oxide nanoparticles. We show the infiltration of these porous structures with a liquid crystal via a very simple method, resulting in a red shift of the photonic band gap due to increase of the effective refractive index of the medium. Taking advantage of structure thickness of only few micrometers, we have observed a blue shift of the photonic band gap owing the non-linear response of the liquid crystals by applying a very low external electric voltage, i.e. 8 V. The experimental observation of electric voltage tuning on the transmission spectrum has been corroborated by transfer matrix method simulations, by taking into account the non-linear optical properties of the liquid crystal. In this framework, we propose how the optical properties of these structure can be accurately predicted by our simulation software in terms of diffraction efficiency, of photonic band gap position when the porous photonic crystals is doped with a liquid crystal, of modulation of the photonic band gap position (electro-optic tuning) in the presence of applied voltage. According with results carried out by the custom simulation software it is possible to control the optical proprieties of the photonics crystal in very thin structures. Furthermore, the presented device could be very interesting for applications where high sensitivity sensor and selective color tunability is needed with the use of cheap and low voltage power supplies.

  6. Predicting RNA structure: advances and limitations.

    PubMed

    Hofacker, Ivo L; Lorenz, Ronny

    2014-01-01

    RNA secondary structures can be predicted using efficient algorithms. A widely used software package implementing a large number of computational methods is the ViennaRNA Package. This chapter describes how to use programs from the ViennaRNA Package to perform common tasks such as prediction of minimum free-energy structures, suboptimal structures, or base pairing probabilities, and generating secondary structure plots with reliability annotation. Moreover, we present recent methods to assess the folding kinetics of an RNA via 2D projections of the energy landscape, identification of local minima and energy barriers, or simulation of RNA folding as a Markov process.

  7. Enhanced multi-view prediction structure

    NASA Astrophysics Data System (ADS)

    Liu, Da; Li, Yi; Xiong, Yazhou; Wang, Li; Li, Chunyan; Yin, Fang

    2016-11-01

    In this paper, firstly an extended DFMC Structure is proposed, then HQF jump period in extended DFMC is presented. Considering temporal-view and interview prediction structure, HQF location is determined. From the HQF, an enhance LQF is proposed. Then considering the HQF and enhance LQF, improved interview prediction is proposed. Finally bit allocation in the proposed multi-view is proposed. Experimental results show that the proposed method can achieve better performance than the previous schemes.

  8. Structural and mechanical studies of cadmium manganese thiocyanate crystal

    NASA Astrophysics Data System (ADS)

    Manikandan, M. R.; Vijayaprasath, G.; babu, G. Anandha; Bhagavannarayan, G.; Vijayan, N.; Ravi, G.

    2012-06-01

    Single crystals of cadmium manganese thiocyanate (CMTC) have been synthesized successfully and grown by slow evaporation method. The structural perfection of the grown crystals has been analyzed by High resolution X-ray diffraction (HRXRD), which shows the crystalline perfection of the grown crystal is quite good. Optical behavior was assessed by UV-Vis analysis and found that no absorption in the UV visible region and it may be useful for second harmonic applications. The mechanical hardness of the grown crystals was studied and Vicker's microhardness, Stiffness constant was calculated.

  9. Hydroflux synthesis and crystal structure of new lanthanide tungstate oxyhydroxides

    NASA Astrophysics Data System (ADS)

    Latshaw, Allison M.; Smith, Mark D.; Chance, W. Michael; zur Loye, Hans-Conrad

    2015-04-01

    Single crystals of Na5Ln(OH)6WO4 where Ln = Er, Tm, and Yb were grown out of a NaOH hydroflux. The crystals were characterized by single crystal X-ray diffraction and were found to crystallize in the monoclinic space group I2/a. The lattice parameter ranges for the three structures are a = 11.2024(7) Å-11.2412(6) Å, b = 16.1850(10) Å-16.2220(10) Å, and c = 11.9913(7) Å-12.0323(7) Å while the β angle range is 101.999(2)°-102.025(2)°.

  10. Models of protein–ligand crystal structures: trust, but verify

    PubMed Central

    Deller, Marc C.

    2015-01-01

    X-ray crystallography provides the most accurate models of protein–ligand structures. These models serve as the foundation of many computational methods including structure prediction, molecular modelling, and structure-based drug design. The success of these computational methods ultimately depends on the quality of the underlying protein–ligand models. X-ray crystallography offers the unparalleled advantage of a clear mathematical formalism relating the experimental data to the protein–ligand model. In the case of X-ray crystallography, the primary experimental evidence is the electron density of the molecules forming the crystal. The first step in the generation of an accurate and precise crystallographic model is the interpretation of the electron density of the crystal, typically carried out by construction of an atomic model. The atomic model must then be validated for fit to the experimental electron density and also for agreement with prior expectations of stereochemistry. Stringent validation of protein–ligand models has become possible as a result of the mandatory deposition of primary diffraction data, and many computational tools are now available to aid in the validation process. Validation of protein–ligand complexes has revealed some instances of overenthusiastic interpretation of ligand density. Fundamental concepts and metrics of protein–ligand quality validation are discussed and we highlight software tools to assist in this process. It is essential that end users select high quality protein–ligand models for their computational and biological studies, and we provide an overview of how this can be achieved. PMID:25665575

  11. Growth, characterization and crystal structure analysis of rifapentine

    NASA Astrophysics Data System (ADS)

    Zhou, K.; Li, J.; Zheng, D. S.

    2010-11-01

    Single crystals of rifapentine have been grown by cooling technique. The crystal structure analysis and the molecular arrangement of these crystals have been determined using X-ray diffraction (XRD) method. From single-crystal XRD studies, it is found that the compound crystallizes in the monoclinic system with a space group P2 1, and the corresponding lattice parameters were calculated ( a = 12.278(3) Å, b = 19.768(4) Å, c = 12.473(3) Å, Z = 2, beta = 112.35(3)°). FT-IR spectra are recorded to identify the various functional groups present in the compound. The UV-Vis spectrum of rifapentine takes place at a wavelength of 236, 255, 334 and 474 nm, respectively. The thermal stability of the crystal is determined from TG/DTA curves.

  12. Comparison of hexagonal crystal structures between fluorapatite and polytetrafluoroethylene.

    PubMed

    Okazaki, Masayuki

    2017-01-01

    The crystallographic properties of fluorapatite (FAp) and polytetrafluoroethylene (PTFE) as biomedical materials were compared. Both materials contain fluorine and casually belong to the hexagonal crystal system. It is interesting that FAp is an inorganic ionic crystal, while PTFE is an organic covalent-bond crystal. Generally, fluorine contributes to the physicochemical stability and in some cases to the biocompatibility. The crystal structure of FAp was initially analyzed in 1930 by Náray-Szabó, although the analysis of hydroxyapatite (HAp) was markedly delayed until 1964. The computer graphics display demonstrated that fluoride ions serve to stabilize the hydroxyapatite crystals and prevent dental caries. On the other hand, PTFE crystal analysis was reported in 1954 by Bunn and Howells. The PTFE temperature-pressure phase diagram accepted for over 60 years is very complicated and insufficient. PTFE delicately changes its phase near room temperature, although at a glance it appears to have a simple form compared with DNA.

  13. Modelling organic crystal structures using distributed multipole and polarizability-based model intermolecular potentials.

    PubMed

    Price, Sarah L; Leslie, Maurice; Welch, Gareth W A; Habgood, Matthew; Price, Louise S; Karamertzanis, Panagiotis G; Day, Graeme M

    2010-08-14

    Crystal structure prediction for organic molecules requires both the fast assessment of thousands to millions of crystal structures and the greatest possible accuracy in their relative energies. We describe a crystal lattice simulation program, DMACRYS, emphasizing the features that make it suitable for use in crystal structure prediction for pharmaceutical molecules using accurate anisotropic atom-atom model intermolecular potentials based on the theory of intermolecular forces. DMACRYS can optimize the lattice energy of a crystal, calculate the second derivative properties, and reduce the symmetry of the spacegroup to move away from a transition state. The calculated terahertz frequency k = 0 rigid-body lattice modes and elastic tensor can be used to estimate free energies. The program uses a distributed multipole electrostatic model (Q, t = 00,...,44s) for the electrostatic fields, and can use anisotropic atom-atom repulsion models, damped isotropic dispersion up to R(-10), as well as a range of empirically fitted isotropic exp-6 atom-atom models with different definitions of atomic types. A new feature is that an accurate model for the induction energy contribution to the lattice energy has been implemented that uses atomic anisotropic dipole polarizability models (alpha, t = (10,10)...(11c,11s)) to evaluate the changes in the molecular charge density induced by the electrostatic field within the crystal. It is demonstrated, using the four polymorphs of the pharmaceutical carbamazepine C(15)H(12)N(2)O, that whilst reproducing crystal structures is relatively easy, calculating the polymorphic energy differences to the accuracy of a few kJ mol(-1) required for applications is very demanding of assumptions made in the modelling. Thus DMACRYS enables the comparison of both known and hypothetical crystal structures as an aid to the development of pharmaceuticals and other speciality organic materials, and provides a tool to develop the modelling of the

  14. DNA variability in five crystal structures of d(CGCAATTGCG).

    PubMed

    Valls, Núria; Wright, Glenford; Steiner, Roberto A; Murshudov, Garib N; Subirana, Juan A

    2004-04-01

    The deoxyoligonucleotide d(CGCAATTGCG) has previously been crystallized in four different space groups. The crystals diffract to moderate resolution (2.3-2.9 A). Here, a fifth crystal form that diffracts to higher resolution (1.6 A) is presented which was obtained thanks to the use of Co2+ and cryogenic temperatures. The availability of five different crystal structures allows a thorough analysis of the conformational variability of this DNA sequence. It is concluded that the central hexamer sequence CAATTG has a practically constant conformation under all conditions, whilst the terminal base pairs at both ends vary considerably as a result of differing interactions in the crystals. The new crystal structure presented here is stabilized by guanine-Co2+-guanine interactions and the formation of C1+ -G8.C3 triplexes between neighbouring duplexes. As a result of the higher resolution of the crystal structure, a more regular structure was obtained and a clear definition of the spine of hydration was observed which was not visible in the four previous structures.

  15. Room Temperature Crystallization of Hydroxyapatite in Porous Silicon Structures.

    PubMed

    Santana, M; Estevez, J O; Agarwal, V; Herrera-Becerra, R

    2016-12-01

    Porous silicon (PS) substrates, with different pore sizes and morphology, have been used to crystallize hydroxyapatite (HA) nano-fibers by an easy and economical procedure using a co-precipitation method at room temperature. In situ formation of HA nanoparticles, within the meso- and macroporous silicon structure, resulted in the formation of nanometer-sized hydroxyapatite crystals on/within the porous structure. The X-ray diffraction technique was used to determine the tetragonal structure of the crystals. Analysis/characterization demonstrates that under certain synthesis conditions, growth and crystallization of hydroxyapatite layer on/inside PS can be achieved at room temperature. Such composite structures expand the possibility of designing a new bio-composite material based on the hydroxyapatite and silicon synthesized at room temperature.

  16. Precise Identification of Graphene's Crystal Structures by Removable Nanowire Epitaxy.

    PubMed

    Kim, Jonghyeok; Lim, Kitaek; Lee, Yangjin; Kim, Jongin; Kim, Kihwan; Park, Jungwon; Kim, Kwanpyo; Lee, Won Chul

    2017-03-16

    Monitoring crystallographic orientations of graphene is important for the reliable generation of graphene-based nanostructures such as van der Waals heterostructures and graphene nanoribbons because their physical properties are dependent on crystal structures. However, facile and precise identification of graphene's crystallographic orientations is still challenging because the majority of current tools rely on complex atomic-scale imaging. Here, we present an identification method for the crystal orientations and grain boundaries of graphene using the directional alignment between epitaxially grown AuCN nanowires and the underlying graphene. Because the nanowires are visible in scanning electron microscopy, crystal orientations of graphene can be inspected with simple procedures. Kernel density estimation that we used in analyzing the nanowire directions enables precise measurement of graphene's crystal orientations. We also confirm that the imaged nanowires can be simply removed without degrading graphene's quality, thus showing that the present method can be practically used for measuring graphene's crystal structures.

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

    SciTech Connect

    Lau, Kah; Qiu, Dantong; Luo, Xiangyi; Greeley, Jeffrey; Curtiss, Larry; Lu, Jun; Amine, Khalil

    2015-01-14

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

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

    DOE PAGES

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

    2015-01-14

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

  19. Characteristics and Prediction of RNA Structure

    PubMed Central

    Zhu, Daming; Zhang, Caiming; Han, Huijian; Crandall, Keith A.

    2014-01-01

    RNA secondary structures with pseudoknots are often predicted by minimizing free energy, which is NP-hard. Most RNAs fold during transcription from DNA into RNA through a hierarchical pathway wherein secondary structures form prior to tertiary structures. Real RNA secondary structures often have local instead of global optimization because of kinetic reasons. The performance of RNA structure prediction may be improved by considering dynamic and hierarchical folding mechanisms. This study is a novel report on RNA folding that accords with the golden mean characteristic based on the statistical analysis of the real RNA secondary structures of all 480 sequences from RNA STRAND, which are validated by NMR or X-ray. The length ratios of domains in these sequences are approximately 0.382L, 0.5L, 0.618L, and L, where L is the sequence length. These points are just the important golden sections of sequence. With this characteristic, an algorithm is designed to predict RNA hierarchical structures and simulate RNA folding by dynamically folding RNA structures according to the above golden section points. The sensitivity and number of predicted pseudoknots of our algorithm are better than those of the Mfold, HotKnots, McQfold, ProbKnot, and Lhw-Zhu algorithms. Experimental results reflect the folding rules of RNA from a new angle that is close to natural folding. PMID:25110687

  20. Crystal structure of inhibitor of ;#954;B kinase [beta

    SciTech Connect

    Xu, Guozhou; Lo, Yu-Chih; Li, Qiubai; Napolitano, Gennaro; Wu, Xuefeng; Jiang, Xuliang; Dreano, Michel; Karin, Michael; Wu, Hao

    2011-07-26

    Inhibitor of {kappa}B (I{kappa}B) kinase (IKK) phosphorylates I{kappa}B proteins, leading to their degradation and the liberation of nuclear factor {kappa}B for gene transcription. Here we report the crystal structure of IKK{beta} in complex with an inhibitor, at a resolution of 3.6 {angstrom}. The structure reveals a trimodular architecture comprising the kinase domain, a ubiquitin-like domain (ULD) and an elongated, {alpha}-helical scaffold/dimerization domain (SDD). Unexpectedly, the predicted leucine zipper and helix-loop-helix motifs do not form these structures but are part of the SDD. The ULD and SDD mediate a critical interaction with I{kappa}B{alpha} that restricts substrate specificity, and the ULD is also required for catalytic activity. The SDD mediates IKK{beta} dimerization, but dimerization per se is not important for maintaining IKK{beta} activity and instead is required for IKK{beta} activation. Other IKK family members, IKK{alpha}, TBK1 and IKK-i, may have a similar trimodular architecture and function.

  1. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  2. Allophycocyanin and phycocyanin crystal structures reveal facets of phycobilisome assembly.

    PubMed

    Marx, Ailie; Adir, Noam

    2013-03-01

    X-ray crystal structures of the isolated phycobiliprotein components of the phycobilisome have provided high resolution details to the description of this light harvesting complex at different levels of complexity and detail. The linker-independent assembly of trimers into hexamers in crystal lattices of previously determined structures has been observed in almost all of the phycocyanin (PC) and allophycocyanin (APC) structures available in the Protein Data Bank. In this paper we describe the X-ray crystal structures of PC and APC from Synechococcus elongatus sp. PCC 7942, PC from Synechocystis sp. PCC 6803 and PC from Thermosynechococcus vulcanus crystallized in the presence of urea. All five structures are highly similar to other PC and APC structures on the levels of subunits, monomers and trimers. The Synechococcus APC forms a unique loose hexamer that may show the structural requirements for core assembly and rod attachment. While the Synechococcus PC assembles into the canonical hexamer, it does not further assemble into rods. Unlike most PC structures, the Synechocystis PC fails to form hexamers. Addition of low concentrations of urea to T. vulcanus PC inhibits this proteins propensity to form hexamers, resulting in a crystal lattice composed of trimers. The molecular source of these differences in assembly and their relevance to the phycobilisome structure is discussed.

  3. Stability of orientationally disordered crystal structures of colloidal hard dumbbells.

    PubMed

    Marechal, Matthieu; Dijkstra, Marjolein

    2008-06-01

    We study the stability of orientationally disordered crystal phases in a suspension of colloidal hard dumbbells using Monte Carlo simulations. For dumbbell bond length L/sigma<0.4 with L the separation of the two spheres of the dumbbell and sigma the diameter of the spheres, we determine the difference in Helmholtz free energy of a plastic crystal with a hexagonal-close-packed (hcp) and a face-centered-cubic (fcc) structure using thermodynamic integration and the lattice-switch Monte Carlo method. We find that the plastic crystal with the hcp structure is more stable than the one with the fcc structure for a large part of the stable plastic crystal regime. In addition, we study the stability of an orientationally disordered aperiodic crystal structure in which the spheres of the dumbbells are on a random-hexagonal-close-packed lattice, and the dumbbells are formed by taking random pairs of neighboring spheres. Using free-energy calculations, we determine the fluid-aperiodic crystal and periodic-aperiodic crystal coexistence regions for L/sigma>0.88 .

  4. Prediction of photonic crystal fiber characteristics by Neuro-Fuzzy system

    NASA Astrophysics Data System (ADS)

    Pourmahyabadi, M.; Mohammad Nejad, S.

    2009-10-01

    The most common methods applied in the analysis of photonic crystal fibers (PCFs) are finite difference time/frequency domain (FDTD/FDFD) method and finite element method (FEM). These methods are very general and reliable (well tested). They describe arbitrary structure but are numerically intensive and require detailed treatment of boundaries and complex definition of calculation mesh. So these conventional models that simulate the photonic response of PCFs are computationally expensive and time consuming. Therefore, a practical design process with trial and error cannot be done in a reasonable amount of time. In this article, an artificial intelligence method such as Neuro-Fuzzy system is used to establish a model that can predict the properties of PCFs. Simulation results show that this model is remarkably effective in predicting the properties of PCF such as dispersion, dispersion slope and loss over the C communication band.

  5. Predicting structure in nonsymmetric sparse matrix factorizations

    SciTech Connect

    Gilbert, J.R. ); Ng, E.G. )

    1992-10-01

    Many computations on sparse matrices have a phase that predicts the nonzero structure of the output, followed by a phase that actually performs the numerical computation. We study structure prediction for computations that involve nonsymmetric row and column permutations and nonsymmetric or non-square matrices. Our tools are bipartite graphs, matchings, and alternating paths. Our main new result concerns LU factorization with partial pivoting. We show that if a square matrix A has the strong Hall property (i.e., is fully indecomposable) then an upper bound due to George and Ng on the nonzero structure of L + U is as tight as possible. To show this, we prove a crucial result about alternating paths in strong Hall graphs. The alternating-paths theorem seems to be of independent interest: it can also be used to prove related results about structure prediction for QR factorization that are due to Coleman, Edenbrandt, Gilbert, Hare, Johnson, Olesky, Pothen, and van den Driessche.

  6. X-ray crystal structures of a severely desiccated protein.

    PubMed Central

    Bell, J. A.

    1999-01-01

    Unlike most protein crystals, form IX of bovine pancreatic ribonuclease A diffracts well when severely dehydrated. Crystal structures have been solved after 2.5 and 4 days of desiccation with CaSO4, at 1.9 and 2.0 A resolution, respectively. The two desiccated structures are very similar. An RMS displacement of 1.6 A is observed for main-chain atoms in each structure when compared to the hydrated crystal structure with some large rearrangements observed in loop regions. The structural changes are the result of intermolecular contacts formed by strong electrostatic interactions in the absence of a high dielectric medium. The electron density is very diffuse for some surface loops, consistent with a very disordered structure. This disorder is related to the conformational changes. These results help explain conformational changes during the lyophilization of protein and the associated phenomena of denaturation and molecular memory. PMID:10548049

  7. Crystal Structure of Human Plasma Platelet-Activating Factor Acetylhydrolase

    SciTech Connect

    Samanta, U.; Bahnson, B

    2008-01-01

    Human plasma platelet-activating factor (PAF) acetylhydrolase functions by reducing PAF levels as a general anti-inflammatory scavenger and is linked to anaphylactic shock, asthma, and allergic reactions. The enzyme has also been implicated in hydrolytic activities of other pro-inflammatory agents, such as sn-2 oxidatively fragmented phospholipids. This plasma enzyme is tightly bound to low and high density lipoprotein particles and is also referred to as lipoprotein-associated phospholipase A{sub 2}. The crystal structure of this enzyme has been solved from x-ray diffraction data collected to a resolution of 1.5{angstrom}. It has a classic lipase {alpha}/{beta}-hydrolase fold, and it contains a catalytic triad of Ser{sup 273}, His{sup 351}, and Asp{sup 296}. Two clusters of hydrophobic residues define the probable interface-binding region, and a prediction is given of how the enzyme is bound to lipoproteins. Additionally, an acidic patch of 10 carboxylate residues and a neighboring basic patch of three residues are suggested to play a role in high density lipoprotein/low density lipoprotein partitioning. A crystal structure is also presented of PAF acetylhydrolase reacted with the organophosphate compound paraoxon via its active site Ser{sup 273}. The resulting diethyl phosphoryl complex was used to model the tetrahedral intermediate of the substrate PAF to the active site. The model of interface binding begins to explain the known specificity of lipoprotein-bound substrates and how the active site can be both close to the hydrophobic-hydrophilic interface and at the same time be accessible to the aqueous phase.

  8. Improved Predictions of Secondary Structures for RNA

    NASA Astrophysics Data System (ADS)

    Jaeger, John A.; Turner, Douglas H.; Zuker, Michael

    1989-10-01

    The accuracy of computer predictions of RNA secondary structure from sequence data and free energy parameters has been increased to roughly 70%. Performance is judged by comparison with structures known from phylogenetic analysis. The algorithm also generates suboptimal structures. On average, the best structure within 10% of the lowest free energy contains roughly 90% of phylogenetically known helixes. The algorithm does not include tertiary interactions or pseudoknots and employs a crude model for single-stranded regions. The only favorable interactions are base pairing and stacking of terminal unpaired nucleotides at the ends of helixes. The excellent performance is consistent with these interactions being the primary interactions determining RNA secondary structure.

  9. Particle-swarm structure prediction on clusters

    NASA Astrophysics Data System (ADS)

    Lv, Jian; Wang, Yanchao; Zhu, Li; Ma, Yanming

    2012-08-01

    We have developed an efficient method for cluster structure prediction based on the generalization of particle swarm optimization (PSO). A local version of PSO algorithm was implemented to utilize a fine exploration of potential energy surface for a given non-periodic system. We have specifically devised a technique of so-called bond characterization matrix (BCM) to allow the proper measure on the structural similarity. The BCM technique was then employed to eliminate similar structures and define the desirable local search spaces. We find that the introduction of point group symmetries into generation of cluster structures enables structural diversity and apparently avoids the generation of liquid-like (or disordered) clusters for large systems, thus considerably improving the structural search efficiency. We have incorporated Metropolis criterion into our method to further enhance the structural evolution towards low-energy regimes of potential energy surfaces. Our method has been extensively benchmarked on Lennard-Jones clusters with different sizes up to 150 atoms and applied into prediction of new structures of medium-sized Lin (n = 20, 40, 58) clusters. High search efficiency was achieved, demonstrating the reliability of the current methodology and its promise as a major method on cluster structure prediction.

  10. Homodiselenacalix[4]arenes: Molecules with Unique Channelled Crystal Structures.

    PubMed

    Thomas, Joice; Dobrzańska, Liliana; Van Meervelt, Luc; Quevedo, Mario Alfredo; Woźniak, Krzysztof; Stachowicz, Marcin; Smet, Mario; Maes, Wouter; Dehaen, Wim

    2016-01-18

    A synthetic route towards homodiselenacalix[4]arene macrocycles is presented, based on the dynamic covalent chemistry of diselenides. The calixarene inner rim is decorated with either alkoxy or tert-butyl ester groups. Single-crystal X-ray analysis of two THF solvates with methoxy and ethoxy substituents reveals the high similarity of their molecular structures and alterations on the supramolecular level. In both crystal structures, solvent channels are present and differ in both shape and capacity. Furthermore, the methoxy-substituted macrocycle undergoes a single-crystal-to-single-crystal transformation during which the molecular structure changes its conformation from 1,3-alternate (loaded with THF/water) to 1,2-alternate (apohost form). Molecular modelling techniques were applied to explore the conformational and energetic behaviour of the macrocycles.

  11. Synthesis and crystal structure analysis of uranyl triple acetates

    NASA Astrophysics Data System (ADS)

    Klepov, Vladislav V.; Serezhkina, Larisa B.; Serezhkin, Victor N.; Alekseev, Evgeny V.

    2016-12-01

    Single crystals of triple acetates NaR[UO2(CH3COO)3]3·6H2O (R=Mg, Co, Ni, Zn), well-known for their use as reagents for sodium determination, were grown from aqueous solutions and their structural and spectroscopic properties were studied. Crystal structures of the mentioned phases are based upon {Na[UO2(CH3COO)3]3}2- clusters and [R(H2O)6]2+ aqua-complexes. The cooling of a single crystal of NaMg[UO2(CH3COO)3]3·6H2O from 300 to 100 K leads to a phase transition from trigonal to monoclinic crystal system. Intermolecular interactions between the structural units and their mutual packing were studied and compared from the point of view of the stereoatomic model of crystal structures based on Voronoi-Dirichlet tessellation. Using this method we compared the crystal structures of the triple acetates with Na[UO2(CH3COO)3] and [R(H2O)6][UO2(CH3COO)3]2 and proposed reasons of triple acetates stability. Infrared and Raman spectra were collected and their bands were assigned.

  12. SHAPE-Directed RNA Secondary Structure Prediction

    PubMed Central

    Low, Justin T.; Weeks, Kevin M.

    2010-01-01

    The diverse functional roles of RNA are determined by its underlying structure. Accurate and comprehensive knowledge of RNA structure would inform a broader understanding of RNA biology and facilitate exploiting RNA as a biotechnological tool and therapeutic target. Determining the pattern of base pairing, or secondary structure, of RNA is a first step in these endeavors. Advances in experimental, computational, and comparative analysis approaches for analyzing secondary structure have yielded accurate structures for many small RNAs, but only a few large (>500 nts) RNAs. In addition, most current methods for determining a secondary structure require considerable effort, analytical expertise, and technical ingenuity. In this review, we outline an efficient strategy for developing accurate secondary structure models for RNAs of arbitrary length. This approach melds structural information obtained using SHAPE chemistry with structure prediction using nearest-neighbor rules and the dynamic programming algorithm implemented in the RNAstructure program. Prediction accuracies reach ≥95% for RNAs on the kilobase scale. This approach facilitates both development of new models and refinement of existing RNA structure models, which we illustrate using the Gag-Pol frameshift element in an HIV-1 M-group genome. Most promisingly, integrated experimental and computational refinement brings closer the ultimate goal of efficiently and accurately establishing the secondary structure for any RNA sequence. PMID:20554050

  13. High-Pressure Crystal Structure, Lattice Vibrations, and Band Structure of BiSbO4.

    PubMed

    Errandonea, Daniel; Muñoz, Alfonso; Rodríguez-Hernández, Placida; Gomis, Oscar; Achary, S Nagabhusan; Popescu, Catalin; Patwe, Sadeque J; Tyagi, Avesh K

    2016-05-16

    The high-pressure crystal structure, lattice-vibrations, and electronic band structure of BiSbO4 were studied by ab initio simulations. We also performed Raman spectroscopy, infrared spectroscopy, and diffuse-reflectance measurements, as well as synchrotron powder X-ray diffraction. High-pressure X-ray diffraction measurements show that the crystal structure of BiSbO4 remains stable up to at least 70 GPa, unlike other known MTO4-type ternary oxides. These experiments also give information on the pressure dependence of the unit-cell parameters. Calculations properly describe the crystal structure of BiSbO4 and the changes induced by pressure on it. They also predict a possible high-pressure phase. A room-temperature pressure-volume equation of state is determined, and the effect of pressure on the coordination polyhedron of Bi and Sb is discussed. Raman- and infrared-active phonons were measured and calculated. In particular, calculations provide assignments for all the vibrational modes as well as their pressure dependence. In addition, the band structure and electronic density of states under pressure were also calculated. The calculations combined with the optical measurements allow us to conclude that BiSbO4 is an indirect-gap semiconductor, with an electronic band gap of 2.9(1) eV. Finally, the isothermal compressibility tensor for BiSbO4 is given at 1.8 GPa. The experimental (theoretical) data revealed that the direction of maximum compressibility is in the (0 1 0) plane at ∼33° (38°) to the c-axis and 47° (42°) to the a-axis. The reliability of the reported results is supported by the consistency between experiments and calculations.

  14. Structure of initial crystals formed during human amelogenesis

    NASA Astrophysics Data System (ADS)

    Cuisinier, F. J. G.; Voegel, J. C.; Yacaman, J.; Frank, R. M.

    1992-02-01

    X-ray diffraction analysis revealed only the existence of carbonated hydroxyapatite (c.HA) during amelogenesis, whereas conventional transmission electron microscopy investigations showed that developing enamel crystals have a ribbon-like habit. The described compositional changes could be an indication for the presence of minerals different from c.HA. However, the absence of identification of such a mineral shows the need of studies by high resolution electron microscopy (HREM) of initial formed human enamel crystals. We demonstrate the existence of two crystal families involved in the early stages of biomineralization: (a) nanometer-size particles which appeared as a precursor phase; (b) ribbon-like crystals, with a structure closely related to c.HA, which by a progressive thickening process tend to attain the mature enamel crystal habit.

  15. Evolution of molecular crystal optical phonons near structural phase transitions

    NASA Astrophysics Data System (ADS)

    Michki, Nigel; Niessen, Katherine; Xu, Mengyang; Markelz, Andrea

    Molecular crystals are increasingly important photonic and electronic materials. For example organic semiconductors are lightweight compared to inorganic semiconductors and have inexpensive scale up processing with roll to roll printing. However their implementation is limited by their environmental sensitivity, in part arising from the weak intermolecular interactions of the crystal. These weak interactions result in optical phonons in the terahertz frequency range. We examine the evolution of intermolecular interactions near structural phase transitions by measuring the optical phonons as a function of temperature and crystal orientation using terahertz time-domain spectroscopy. The measured orientation dependence of the resonances provides an additional constraint for comparison of the observed spectra with the density functional calculations, enabling us to follow specific phonon modes. We observe crystal reorganization near 350 K for oxalic acid as it transforms from dihydrate to anhydrous form. We also report the first THz spectra for the molecular crystal fructose through its melting point.

  16. Effect of structural imperfections on lasing characteristics of diode-pumped YVO{sub 4}, GdVO{sub 4} and mixed rare-earth vanadate crystals

    SciTech Connect

    Orlova, G Yu; Vlasov, V I; Zavartsev, Yu D; Zagumennyi, A I; Kalashnikova, I I; Kutovoi, S A; Naumov, V S; Sirotkin, A A

    2012-03-31

    The efficiency of diode-pumped lasers with gain elements made from yttrium, gadolinium, yttrium - gadolinium and yttrium - scandium orthovanadate crystals has been shown for the first time to be influenced by structural imperfections (quality) of the crystals. This allows one to predict lasing parameters of such crystals in a preliminary step, without fabricating gain elements.

  17. Crystal Structure of an LSD-Bound Human Serotonin Receptor

    SciTech Connect

    Wacker, Daniel; Wang, Sheng; McCorvy, John D.; Betz, Robin M.; Venkatakrishnan, A. J.; Levit, Anat; Lansu, Katherine; Schools, Zachary L.; Che, Tao; Nichols, David E.; Shoichet, Brian K.; Dror, Ron O.; Roth, Bryan L.

    2017-01-01

    The prototypical hallucinogen LSD acts via serotonin receptors, and here we describe the crystal structure of LSD in complex with the human serotonin receptor 5-HT2B. The complex reveals conformational rearrangements to accommodate LSD, providing a structural explanation for the conformational selectivity of LSD’s key diethylamide moiety. LSD dissociates exceptionally slow from both 5-HT2BR and 5-HT2AR—a major target for its psychoactivity. Molecular dynamics (MD) simulations suggest that LSD’s slow binding kinetics may be due to a “lid” formed by extracellular loop 2 (EL2) at the entrance to the binding pocket. A mutation predicted to increase the mobility of this lid greatly accelerates LSD’s binding kinetics and selectively dampens LSD-mediated β-arrestin2 recruitment. This study thus reveals an unexpected binding mode of LSD; illuminates key features of its kinetics, stereochemistry, and signaling; and provides a molecular explanation for LSD’s actions at human serotonin receptors.

  18. Measuring and predicting the diffraction properties of cylindrically bent potassium acid phthalate, KAP(001), crystals

    NASA Astrophysics Data System (ADS)

    Haugh, M. J.; Jacoby, K. D.

    2017-02-01

    This report presents the results from measuring the X-ray diffraction properties of a curved potassium acid phthalate (KAP(001)) spectrometer crystal using two measurement methods. One method used a diode type X-ray source and a dual goniometer analysis system, utilizing a flat, perfect KAP(001) crystal as the monochromator. The second method used a synchrotron source and dual crystal Si(111) monochromator. Bent crystals are used in X-ray spectrometers as dispersion elements. These crystals are bent into a circular cylinder section, and this bending can alter the rocking curve properties. The crystal rocking curves were measured for spectral energies ranging from 1250 to 4500 eV. A multi-lamellar model was compared to the measurements and showed good quantitative agreement. This provides a valuable tool for predicting the changes to the KAP (001) for any radius of curvature when the crystal is bent into a cylindrical section.

  19. Mg intercalation in layered and spinel host crystal structures for Mg batteries.

    PubMed

    Emly, Alexandra; Van der Ven, Anton

    2015-05-04

    We investigate electrochemical properties of Mg in layered and spinel intercalation compounds from first-principles using TiS2 as a model system. Our calculations predict that Mg(x)TiS2 in both the layered and spinel crystal structures exhibits sloping voltage profiles with steps at stoichiometric compositions due to Mg-vacancy ordering. Mg ions are predicted to occupy the octahedral sites in both layered and spinel TiS2 with diffusion mediated by hops between octahedral sites that pass through adjacent tetrahedral sites. Predicted migration barriers are substantially higher than typical Li-migration barriers in intercalation compounds. The migration barriers are shown to be very sensitive to lattice parameters of the host crystal structure. We also discuss the possible role of rehybridization between the transition metal and the anion in affecting migration barriers.

  20. Single-crystal structure of a covalent organic framework.

    PubMed

    Zhang, Yue-Biao; Su, Jie; Furukawa, Hiroyasu; Yun, Yifeng; Gándara, Felipe; Duong, Adam; Zou, Xiaodong; Yaghi, Omar M

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 °C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 °C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  1. Single-Crystal Structure of a Covalent Organic Framework

    SciTech Connect

    Zhang, YB; Su, J; Furukawa, H; Yun, YF; Gandara, F; Duong, A; Zou, XD; Yaghi, OM

    2013-11-06

    The crystal structure of a new covalent organic framework, termed COF-320, is determined by single-crystal 3D electron diffraction using the rotation electron diffraction (RED) method for data collection. The COF crystals are prepared by an imine condensation of tetra-(4-anilyl)methane and 4,4'-biphenyldialdehyde in 1,4-dioxane at 120 degrees C to produce a highly porous 9-fold interwoven diamond net. COF-320 exhibits permanent porosity with a Langmuir surface area of 2400 m(2)/g and a methane total uptake of 15.0 wt % (176 cm(3)/cm(3)) at 25 degrees C and 80 bar. The successful determination of the structure of COF-320 directly from single-crystal samples is an important advance in the development of COF chemistry.

  2. Crystal structure of TiBi2

    PubMed Central

    Watanabe, Kei; Yamane, Hisanori

    2016-01-01

    Black granular single crystals of monotitanium dibismuth, TiBi2, were synthesized by slow cooling of a mixture of Bi and Ti from 693 K. The title compound is isostructural with CuMg2 (ortho­rhom­bic Fddd symmetry). Ti atoms are located in square anti­prisms of Bi atoms. The network of one type of Bi atom spirals along the a-axis direction while honeycomb layers of the other type of Bi atom spreading in the ab plane inter­lace one another. PMID:27920910

  3. 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.

  4. Protein structure prediction provides comparable performance to crystallographic structures in docking-based virtual screening.

    PubMed

    Du, Hongying; Brender, Jeffrey R; Zhang, Jian; Zhang, Yang

    2015-01-01

    Structure based virtual screening has largely been limited to protein targets for which either an experimental structure is available or a strongly homologous template exists so that a high-resolution model can be constructed. The performance of state of the art protein structure predictions in virtual screening in systems where only weakly homologous templates are available is largely untested. Using the challenging DUD database of structural decoys, we show here that even using templates with only weak sequence homology (<30% sequence identity) structural models can be constructed by I-TASSER which achieve comparable enrichment rates to using the experimental bound crystal structure in the majority of the cases studied. For 65% of the targets, the I-TASSER models, which are constructed essentially in the apo conformations, reached 70% of the virtual screening performance of using the holo-crystal structures. A correlation was observed between the success of I-TASSER in modeling the global fold and local structures in the binding pockets of the proteins versus the relative success in virtual screening. The virtual screening performance can be further improved by the recognition of chemical features of the ligand compounds. These results suggest that the combination of structure-based docking and advanced protein structure modeling methods should be a valuable approach to the large-scale drug screening and discovery studies, especially for the proteins lacking crystallographic structures.

  5. Reduced ceria nanofilms from structure prediction.

    PubMed

    Kozlov, Sergey M; Demiroglu, Ilker; Neyman, Konstantin M; Bromley, Stefan T

    2015-03-14

    Experimentally, Ce2O3 films are used to study cerium oxide in its fully or partially reduced state, as present in many applications. We have explored the space of low energy Ce2O3 nanofilms using structure prediction and density functional calculations, yielding more than 30 distinct nanofilm structures. First, our results help to rationalize the roles of thermodynamics and kinetics in the preparation of reduced ceria nanofilms with different bulk crystalline structures (e.g. A-type or bixbyite) depending on the support used. Second, we predict a novel, as yet experimentally unresolved, nanofilm which has a structure that does not correspond to any previously reported bulk A2B3 phase and which has an energetic stability between that of A-type and bixbyite. To assist identification and fabrication of this new Ce2O3 nanofilm we calculate some observable properties and propose supports for its epitaxial growth.

  6. Boron-oxygen polyanion in the crystal structure of tunellite

    USGS Publications Warehouse

    Clark, J.R.

    1963-01-01

    The crystal structure of tunellite, SrO??3B2O 3??4H2O, with infinite sheets of composition n[B6O9(OH)2]2-, has cations and water molecules in the spaces within the sheets. Adjacent sheets are held together by hydrogen bonding through the water molecules. The boron-oxygen polyanions provide the first example in hydrated borate crystals of one oxygen linked to three borons.

  7. Atomic- Resolution Crystal Structure of the Antiviral Lectin Scytovirin

    SciTech Connect

    Moulaei,T.; Botos, I.; Ziolkowska, N.; Bokesch, H.; Krumpe, L.; McKee, T.; O'Keefe, B.; Dauter, Z.; Wlodawer, A.

    2007-01-01

    The crystal structures of the natural and recombinant antiviral lectin scytovirin (SVN) were solved by single-wavelength anomalous scattering and refined with data extending to 1.3 Angstroms and 1.0 Angstroms resolution, respectively. A molecule of SVN consists of a single chain 95 amino acids long, with an almost perfect sequence repeat that creates two very similar domains (RMS deviation 0.25 Angstroms for 40 pairs of Ca atoms). The crystal structure differs significantly from a previously published NMR structure of the same protein, with the RMS deviations calculated separately for the N- and C-terminal domains of 5.3 Angstroms and 3.7 Angstroms, respectively, and a very different relationship between the two domains. In addition, the disulfide bonding pattern of the crystal structures differs from that described in the previously published mass spectrometry and NMR studies.

  8. Band structures and localization properties of aperiodic layered phononic crystals

    NASA Astrophysics Data System (ADS)

    Yan, Zhi-Zhong; Zhang, Chuanzeng

    2012-03-01

    The band structures and localization properties of in-plane elastic waves with coupling of longitudinal and transverse modes oblique propagating in aperiodic phononic crystals based on Thue-Morse and Rudin-Shapiro sequences are studied. Using transfer matrix method, the concept of the localization factor is introduced and the correctness is testified through the Rytov dispersion relation. For comparison, the perfect periodic structure and the quasi-periodic Fibonacci system are also considered. In addition, the influences of the random disorder, local resonance, translational and/or mirror symmetries on the band structures of the aperiodic phononic crystals are analyzed in this paper.

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

    NASA Astrophysics Data System (ADS)

    Ankudinov, V. E.; Galenko, P. K.; Kropotin, N. V.; Krivilyov, M. D.

    2016-02-01

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

  10. Structure of ice crystallized from supercooled water.

    PubMed

    Malkin, Tamsin L; Murray, Benjamin J; Brukhno, Andrey V; Anwar, Jamshed; Salzmann, Christoph G

    2012-01-24

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples.

  11. Structure of ice crystallized from supercooled water

    PubMed Central

    Malkin, Tamsin L.; Murray, Benjamin J.; Brukhno, Andrey V.; Anwar, Jamshed; Salzmann, Christoph G.

    2012-01-01

    The freezing of water to ice is fundamentally important to fields as diverse as cloud formation to cryopreservation. At ambient conditions, ice is considered to exist in two crystalline forms: stable hexagonal ice and metastable cubic ice. Using X-ray diffraction data and Monte Carlo simulations, we show that ice that crystallizes homogeneously from supercooled water is neither of these phases. The resulting ice is disordered in one dimension and therefore possesses neither cubic nor hexagonal symmetry and is instead composed of randomly stacked layers of cubic and hexagonal sequences. We refer to this ice as stacking-disordered ice I. Stacking disorder and stacking faults have been reported earlier for metastable ice I, but only for ice crystallizing in mesopores and in samples recrystallized from high-pressure ice phases rather than in water droplets. Review of the literature reveals that almost all ice that has been identified as cubic ice in previous diffraction studies and generated in a variety of ways was most likely stacking-disordered ice I with varying degrees of stacking disorder. These findings highlight the need to reevaluate the physical and thermodynamic properties of this metastable ice as a function of the nature and extent of stacking disorder using well-characterized samples. PMID:22232652

  12. Ko Displacement Theory for Structural Shape Predictions

    NASA Technical Reports Server (NTRS)

    Ko, William L.

    2010-01-01

    The development of the Ko displacement theory for predictions of structure deformed shapes was motivated in 2003 by the Helios flying wing, which had a 247-ft (75-m) wing span with wingtip deflections reaching 40 ft (12 m). The Helios flying wing failed in midair in June 2003, creating the need to develop new technology to predict in-flight deformed shapes of unmanned aircraft wings for visual display before the ground-based pilots. Any types of strain sensors installed on a structure can only sense the surface strains, but are incapable to sense the overall deformed shapes of structures. After the invention of the Ko displacement theory, predictions of structure deformed shapes could be achieved by feeding the measured surface strains into the Ko displacement transfer functions for the calculations of out-of-plane deflections and cross sectional rotations at multiple locations for mapping out overall deformed shapes of the structures. The new Ko displacement theory combined with a strain-sensing system thus created a revolutionary new structure- shape-sensing technology.

  13. Crystal structure and texture changes during thermal cycling of TATB

    SciTech Connect

    Vogel, Sven C.; Yeager, John David

    2015-02-20

    Goals: Understand crystal structure and micro-structure changes during thermal cycling, understand reasons for ratcheting of TATB during thermal cycling, and Support of B61 LEP. Deliverables achieved: Completed in situ thermal cycling of loose powder and pressed pellet TATB on HIPPO, Quantified preferred orientation of pressed pellet, and quantified relative change of each of the six lattic parameters.

  14. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds.

    PubMed

    Jungblut, Swetlana; Dellago, Christoph

    2016-09-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure.

  15. Heterogeneous Crystallization on Pairs of Pre-Structured Seeds

    PubMed Central

    2016-01-01

    Studying the effects of small pre-structured seeds on the crystallization transition in an undercooled monodisperse Lennard-Jones fluid with transition interface path sampling combined with molecular dynamics simulations, we analyze the impact of the simultaneous presence of two seeds with various structures. In the presence of seeds with face- and body-centered cubic structures, we find that decreasing the seed-to-seed distance enhances the probability of the crystalline clusters formed on one of the seeds to grow beyond the critical size, thus, increasing the crystal nucleation rates. In contrast, when seeds have an icosahedral structure, the crystalline clusters form mostly in the bulk. The crystal nucleation rate, however, is also determined by the distance between the seeds with regular structure in which the lattice spacing is equal to the bulk lattice constant, pointing to a heterogeneous crystal nucleation that occurs away from the icosahedrally structured seeds. For slightly squeezed seeds, the effects of the presence of seeds with face- and body-centered cubic structures are reduced in comparison to the regular seeds, and we do not see any effect of the presence of the second seed for seeds with squeezed icosahedral structure. PMID:27479875

  16. Cascaded multiple classifiers for secondary structure prediction.

    PubMed Central

    Ouali, M.; King, R. D.

    2000-01-01

    We describe a new classifier for protein secondary structure prediction that is formed by cascading together different types of classifiers using neural networks and linear discrimination. The new classifier achieves an accuracy of 76.7% (assessed by a rigorous full Jack-knife procedure) on a new nonredundant dataset of 496 nonhomologous sequences (obtained from G.J. Barton and J.A. Cuff). This database was especially designed to train and test protein secondary structure prediction methods, and it uses a more stringent definition of homologous sequence than in previous studies. We show that it is possible to design classifiers that can highly discriminate the three classes (H, E, C) with an accuracy of up to 78% for beta-strands, using only a local window and resampling techniques. This indicates that the importance of long-range interactions for the prediction of beta-strands has been probably previously overestimated. PMID:10892809

  17. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, Stephen A.; Kway, Wayne L.; DeLoach, Laura D.; Krupke, William F.; Chai, Bruce H. T.

    1994-01-01

    Yb.sup.3+ and Nd.sup.3+ doped Sr.sub.5 (VO.sub.4).sub.3 F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr.sub.5 (VO.sub.4).sub.3 F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr.sub.5 (VO.sub.4).sub.3 F, where the Sr.sup.2+ and F.sup.- ions are replaced by related chemical species, have similar properties.

  18. Ytterbium- and neodymium-doped vanadate laser hose crystals having the apatite crystal structure

    DOEpatents

    Payne, S.A.; Kway, W.L.; DeLoach, L.D.; Krupke, W.F.; Chai, B.H.T.

    1994-08-23

    Yb[sup 3+] and Nd[sup 3+] doped Sr[sub 5](VO[sub 4])[sub 3]F crystals serve as useful infrared laser media that exhibit low thresholds of oscillation and high slope efficiencies, and can be grown with high optical quality. These laser media possess unusually high absorption and emission cross sections, which provide the crystals with the ability to generate greater gain for a given amount of pump power. Many related crystals such as Sr[sub 5](VO[sub 4])[sub 3]F crystals doped with other rare earths, transition metals, or actinides, as well as the many structural analogs of Sr[sub 5](VO[sub 4])[sub 3]F, where the Sr[sup 2+] and F[sup [minus

  19. Predicting continuous local structure and the effect of its substitution for secondary structure in fragment-free protein structure prediction.

    PubMed

    Faraggi, Eshel; Yang, Yuedong; Zhang, Shesheng; Zhou, Yaoqi

    2009-11-11

    Local structures predicted from protein sequences are used extensively in every aspect of modeling and prediction of protein structure and function. For more than 50 years, they have been predicted at a low-resolution coarse-grained level (e.g., three-state secondary structure). Here, we combine a two-state classifier with real-value predictor to predict local structure in continuous representation by backbone torsion angles. The accuracy of the angles predicted by this approach is close to that derived from NMR chemical shifts. Their substitution for predicted secondary structure as restraints for ab initio structure prediction doubles the success rate. This result demonstrates the potential of predicted local structure for fragment-free tertiary-structure prediction. It further implies potentially significant benefits from using predicted real-valued torsion angles as a replacement for or supplement to the secondary-structure prediction tools used almost exclusively in many computational methods ranging from sequence alignment to function prediction.

  20. Crystal structure of rubidium peroxide ammonia disolvate.

    PubMed

    Grassl, Tobias; Korber, Nikolaus

    2017-02-01

    The title compound, Rb2O2·2NH3, has been obtained as a reaction product of rubidium metal dissolved in liquid ammonia and glucuronic acid. As a result of the low-temperature crystallization, a disolvate was formed. To our knowledge, only one other solvate of an alkali metal peroxide is known: Na2O2·8H2O has been reported by Grehl et al. [Acta Cryst. (1995), C51, 1038-1040]. We determined the peroxide bond length to be 1.530 (11) Å, which is in accordance with the length reported by Bremm & Jansen [Z. Anorg. Allg. Chem. (1992), 610, 64-66]. One of the ammonia solvate molecules is disordered relative to a mirror plane, with 0.5 occupancy for the corresponding nitrogen atom.

  1. Crystal structure of rubidium peroxide ammonia disolvate

    PubMed Central

    Grassl, Tobias; Korber, Nikolaus

    2017-01-01

    The title compound, Rb2O2·2NH3, has been obtained as a reaction product of rubidium metal dissolved in liquid ammonia and glucuronic acid. As a result of the low-temperature crystallization, a disolvate was formed. To our knowledge, only one other solvate of an alkali metal peroxide is known: Na2O2·8H2O has been reported by Grehl et al. [Acta Cryst. (1995), C51, 1038–1040]. We determined the peroxide bond length to be 1.530 (11) Å, which is in accordance with the length reported by Bremm & Jansen [Z. Anorg. Allg. Chem. (1992), 610, 64–66]. One of the ammonia solvate molecules is disordered relative to a mirror plane, with 0.5 occupancy for the corresponding nitrogen atom. PMID:28217342

  2. Gene structure prediction by linguistic methods

    SciTech Connect

    Dong, S.; Searls, D.B.

    1994-10-01

    The higher-order structure of genes and other features of biological sequences can be described by means of formal grammars. These grammars can then be used by general-purpose parsers to detect and to assemble such structures by means of syntactic pattern recognition. We describe a grammar and parser for eukaryotic protein-encoding genes, which by some measures is as effective as current connectionist and combinatorial algorithms in predicting gene structures for sequence database entries. Parameters of the grammar rules are optimized for several different species, and mixing experiments are performed to determine the degree of species specificity and the relative importance of compositional, signal-based, and syntactic components in gene prediction. 24 refs., 5 figs., 3 tabs.

  3. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures.

    PubMed

    Biedermannová, Lada; Schneider, Bohdan

    2015-11-01

    Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon-donor hydrogen bonds, OH-π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations.

  4. Structure of the ordered hydration of amino acids in proteins: analysis of crystal structures

    PubMed Central

    Biedermannová, Lada; Schneider, Bohdan

    2015-01-01

    Crystallography provides unique information about the arrangement of water molecules near protein surfaces. Using a nonredundant set of 2818 protein crystal structures with a resolution of better than 1.8 Å, the extent and structure of the hydration shell of all 20 standard amino-acid residues were analyzed as function of the residue conformation, secondary structure and solvent accessibility. The results show how hydration depends on the amino-acid conformation and the environment in which it occurs. After conformational clustering of individual residues, the density distribution of water molecules was compiled and the preferred hydration sites were determined as maxima in the pseudo-electron-density representation of water distributions. Many hydration sites interact with both main-chain and side-chain amino-acid atoms, and several occurrences of hydration sites with less canonical contacts, such as carbon–donor hydrogen bonds, OH–π interactions and off-plane interactions with aromatic heteroatoms, are also reported. Information about the location and relative importance of the empirically determined preferred hydration sites in proteins has applications in improving the current methods of hydration-site prediction in molecular replacement, ab initio protein structure prediction and the set-up of molecular-dynamics simulations. PMID:26527137

  5. Synthesis, crystal structure and computational studies of 4-nitrobenzylphosphonic acid

    NASA Astrophysics Data System (ADS)

    Wilk, Magdalena; Jarzembska, Katarzyna N.; Janczak, Jan; Hoffmann, Józef; Videnova-Adrabinska, Veneta

    2014-09-01

    4-Nitrobenzylphosphonic acid (1a) has been synthesized and structurally characterized by vibrational spectroscopy (IR and Raman) and single-crystal X-ray diffraction. Additionally, Hirshfeld surface analysis and computational methods have been used to compare the intermolecular interactions in the crystal structures of 1a and its carboxylic analogue, 4-nitrobenzylcarboxylic acid (4-NBCA). The crystal structure analysis of 1a has revealed that the acid molecules are extended into helical chains along the b axis using one of the hydrogen bonds established between phosphonic groups. The second (P)Osbnd H⋯O(P) hydrogen bond cross-links the inversion-related chains to form a thick monolayer with phosphonic groups arranged inwards and aromatic rings outwards. The nitro groups serve to link the neighbouring monolayers by weak Csbnd H⋯O(N) hydrogen bonds. Computations have confirmed the great contribution of electrostatic interactions for the crystal lattice stability. The cohesive energy, computed for the crystal structure of 1a exceeds 200 kJ mol-1 in magnitude and is nearly twice as large as that of 4-NBCA. The calculated cohesive energy values have been further related to the results of thermal analyses.

  6. RNA Structure: Advances and Assessment of 3D Structure Prediction.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2017-03-30

    Biological functions of RNA molecules are dependent upon sustained specific three-dimensional (3D) structures of RNA, with or without the help of proteins. Understanding of RNA structure is frequently based on 2D structures, which describe only the Watson-Crick (WC) base pairs. Here, we hierarchically review the structural elements of RNA and how they contribute to RNA 3D structure. We focus our analysis on the non-WC base pairs and on RNA modules. Several computer programs have now been designed to predict RNA modules. We describe the RNA-Puzzles initiative, which is a community-wide, blind assessment of RNA 3D structure prediction programs to determine the capabilities and bottlenecks of current predictions. The assessment metrics used in RNA-Puzzles are briefly described. The detection of RNA 3D modules from sequence data and their automatic implementation belong to the current challenges in RNA 3D structure prediction. Expected final online publication date for the Annual Review of Biophysics Volume 46 is May 20, 2017. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

  7. Free-Standing Photonic Crystal Films with Gradient Structural Colors.

    PubMed

    Ding, Haibo; Liu, Cihui; Ye, Baofen; Fu, Fanfan; Wang, Huan; Zhao, Yuanjin; Gu, Zhongze

    2016-03-23

    Hydrogel colloidal crystal composite materials have a demonstrated value in responsive photonic crystals (PhCs) via controllable stimuli. Although they have been successfully exploited to generate a gradient of color distribution, the soft hydrogels have limitations in terms of stability and storage caused by dependence on environment. Here, we present a practical strategy to fabricate free-standing PhC films with a stable gradient of structural colors using binary polymer networks. A colloidal crystal hydrogel film was prepared for this purpose, with continuously varying photonic band gaps corresponding to the gradient of the press. Then, a second polymer network was used to lock the inside non-close-packed PhC structures and color distribution of the hydrogel film. It was demonstrated that our strategy could bring about a solution to the angle-dependent structural colors of the PhC films by coating the surface with special microstructures.

  8. Compact Couplers for Photonic Crystal Laser-Driven Accelerator Structures

    SciTech Connect

    Cowan, Benjamin; Lin, M.C.; Schwartz, Brian; Byer, Robert; McGuinness, Christopher; Colby, Eric; England, Robert; Noble, Robert; Spencer, James; /SLAC

    2012-07-02

    Photonic crystal waveguides are promising candidates for laser-driven accelerator structures because of their ability to confine a speed-of-light mode in an all-dielectric structure. Because of the difference between the group velocity of the waveguide mode and the particle bunch velocity, fields must be coupled into the accelerating waveguide at frequent intervals. Therefore efficient, compact couplers are critical to overall accelerator efficiency. We present designs and simulations of high-efficiency coupling to the accelerating mode in a three-dimensional photonic crystal waveguide from a waveguide adjoining it at 90{sup o}. We discuss details of the computation and the resulting transmission. We include some background on the accelerator structure and photonic crystal-based optical acceleration in general.

  9. Anisotropy of bond projections in simple crystal structures

    NASA Astrophysics Data System (ADS)

    Šimůnek, Antonín

    2011-10-01

    The nearest-neighbor bond distances represented by the stick-and-ball model of a crystal are projected into planes in order to find the directions from where the projections have maximum or minimum values. The projection directions and their corresponding values of the maxima and minima are presented for simple cubic, body-centered-cubic, face-centered-cubic, sodium chloride, zinc sulfide, diamond, fluorite, cesium chloride, hexagonal close-packed, tungsten carbide, wurtzite, graphite, graphene, and aluminum boride structures. The purely geometrical considerations quantitatively reflect an anisotropy of the bond projections and provide data for a large amount of materials crystallizing in these structures. The presented results can be applied to the description, analysis, and understanding of anisotropic effects related to bond projection in 14 crystal structures. The application of hardness anisotropy for BN, SiC, and TiC is shown.

  10. Predicting structured metadata from unstructured metadata

    PubMed Central

    Posch, Lisa; Panahiazar, Maryam; Dumontier, Michel; Gevaert, Olivier

    2016-01-01

    Enormous amounts of biomedical data have been and are being produced by investigators all over the world. However, one crucial and limiting factor in data reuse is accurate, structured and complete description of the data or data about the data—defined as metadata. We propose a framework to predict structured metadata terms from unstructured metadata for improving quality and quantity of metadata, using the Gene Expression Omnibus (GEO) microarray database. Our framework consists of classifiers trained using term frequency-inverse document frequency (TF-IDF) features and a second approach based on topics modeled using a Latent Dirichlet Allocation model (LDA) to reduce the dimensionality of the unstructured data. Our results on the GEO database show that structured metadata terms can be the most accurately predicted using the TF-IDF approach followed by LDA both outperforming the majority vote baseline. While some accuracy is lost by the dimensionality reduction of LDA, the difference is small for elements with few possible values, and there is a large improvement over the majority classifier baseline. Overall this is a promising approach for metadata prediction that is likely to be applicable to other datasets and has implications for researchers interested in biomedical metadata curation and metadata prediction. Database URL: http://www.yeastgenome.org/

  11. The Crystal Structure of GXGD Membrane Protease FlaK

    SciTech Connect

    J Hu; Y Xue; S Lee; Y Ha

    2011-12-31

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  12. The crystal structure of GXGD membrane protease FlaK

    SciTech Connect

    Hu, Jian; Xue, Yi; Lee, Sangwon; Ha, Ya

    2011-09-20

    The GXGD proteases are polytopic membrane proteins with catalytic activities against membrane-spanning substrates that require a pair of aspartyl residues. Representative members of the family include preflagellin peptidase, type 4 prepilin peptidase, presenilin and signal peptide peptidase. Many GXGD proteases are important in medicine. For example, type 4 prepilin peptidase may contribute to bacterial pathogenesis, and mutations in presenilin are associated with Alzheimer's disease. As yet, there is no atomic-resolution structure in this protease family. Here we report the crystal structure of FlaK, a preflagellin peptidase from Methanococcus maripaludis, solved at 3.6 {angstrom} resolution. The structure contains six transmembrane helices. The GXGD motif and a short transmembrane helix, helix 4, are positioned at the centre, surrounded by other transmembrane helices. The crystal structure indicates that the protease must undergo conformational changes to bring the GXGD motif and a second essential aspartyl residue from transmembrane helix 1 into close proximity for catalysis. A comparison of the crystal structure with models of presenilin derived from biochemical analysis reveals three common transmembrane segments that are similarly arranged around the active site. This observation reinforces the idea that the prokaryotic and human proteases are evolutionarily related. The crystal structure presented here provides a framework for understanding the mechanism of the GXGD proteases, and may facilitate the rational design of inhibitors that target specific members of the family.

  13. Crystal chemistry and structure refinement of five hydrated calcium borates

    USGS Publications Warehouse

    Clark, J.R.; Appleman, D.E.; Christ, C.L.

    1964-01-01

    The crystal structures of the five known members of the series Ca2B6O11??xH2O (x = 1, 5, 5, 7, 9, and 13) have been refined by full-matrix least-squares techniques, yielding bond distances and angles with standard errors of less than 0??01 A?? and 0??5??, respectively. The results illustrate the crystal chemical principles that govern the structures of hydrated borate compounds. The importance of hydrogen bonding in the ferroelectric transition of colemanite is confirmed by more accurate proton assignments. ?? 1964.

  14. Photonic crystals, light manipulation, and imaging in complex nematic structures

    NASA Astrophysics Data System (ADS)

    Ravnik, Miha; Å timulak, Mitja; Mur, Urban; Čančula, Miha; Čopar, Simon; Žumer, Slobodan

    2016-03-01

    Three selected approaches for manipulation of light by complex nematic colloidal and non-colloidal structures are presented using different own custom developed theoretical and modelling approaches. Photonic crystals bands of distorted cholesteric liquid crystal helix and of nematic colloidal opals are presented, also revealing distinct photonic modes and density of states. Light propagation along half-integer nematic disclinations is shown with changes in the light polarization of various winding numbers. As third, simulated light transmission polarization micrographs of nematic torons are shown, offering a new insight into the complex structure characterization. Finally, this work is a contribution towards using complex soft matter in optics and photonics for advanced light manipulation.

  15. An anisotropic micromechanics model for predicting the rafting direction in Ni-based single crystal superalloys

    NASA Astrophysics Data System (ADS)

    Li, Shuang-Yu; Wu, Wen-Ping; Chen, Ming-Xiang

    2016-02-01

    An anisotropic micromechanics model based on the equivalent inclusion method is developed to investigate the rafting direction of Ni-based single crystal superalloys. The micromechanical model considers actual cubic structure and orthogonal anisotropy properties. The von Mises stress, elastic strain energy density, and hydrostatic pressure in different inclusions of micromechanical model are calculated when applying a tensile or compressive loading along the [001] direction. The calculated results can successfully predict the rafting direction for alloys exhibiting a positive or a negative mismatch, which are in agreement with pervious experimental and theoretical studies. Moreover, the elastic constant differences and mismatch degree of the matrix and precipitate phases and their influences on the rafting direction are carefully discussed.

  16. AFM Studies of Salt Concentration Effects on the (110) Surface Structure of Tetragonal Lysozyme Crystals

    NASA Technical Reports Server (NTRS)

    Pusey, Marc Lee; Gorti, Sridhar; Forsythe, Elizabeth; Konnert, John

    2002-01-01

    Previous high resolution AFM studies of the (110) surface of tetragonal chicken egg white lysozyme crystals had shown that only one of two possible molecular surfaces is present, those constituting the completed 43 helices. These suggested that the crystal growth process was by the solution-phase assembly of the growth units, which then attach to the surface. However, the best fit for the imaged surfaces, vs. those predicted based upon the bulk crystallographic coordinates, were obtained when the packing about the 43 helices was "tightened up", while maintaining the underlying crystallographic unit cell spacing. This results in a widening of the gap between adjacent helices, and the top- most layer(s) may no longer be in contact. We postulated that the tightened packing about the helices is a result of the high salt concentrations in the bulk solution, used to crystallize the protein, driving hydrophobic interactions. Once the crystal surface is sufficiently buried by subsequent growth layers the ratio of salt to protein molecules decreases and the helices relax to their bulk crystallographic coordinates. The crystal surface helix structure is thus a reflection of the solution structure, and the tightness of the packing about the 43 helices would be a function of the bulk salt concentration. AFM images of the (110) surface of tetragonal lysozyme crystals grown under low (2%) and high (5%) NaCl concentrations reveal differences in the packing about the 43 helices consistent with the above proposal.

  17. Utilization of Protein Crystal Structures in Industry

    NASA Astrophysics Data System (ADS)

    Ishikawa, Kohki

    In industry, protein crystallography is used in mainly two technologies. One is structure-based drug design, and the other is structure-based enzyme engineering. Some successful cases together with recent advances are presented in this article. The cases include the development of an anti-influenza drug, and the introduction of engineered acid phosphatase to the manufacturing process of nucleotides used as umami seasoning.

  18. Synthesis, crystal structure, crystal growth and physical properties of N,N-diethyl anilinium picrate

    NASA Astrophysics Data System (ADS)

    Subramaniyan @ Raja, R.; Anandha Babu, G.; Ramasamy, P.

    2011-11-01

    Crystalline substance of N,N-diethyl anilinium picrate (NNDEAP) has been synthesized and single crystals of NNDEAP were successfully grown for the first time by the slow evaporation solution growth technique at room temperature with dimensions 14×10×10 mm3. The formation of the new crystal has been confirmed by single crystal X-ray diffraction studies. The structural perfection of the grown crystal was analyzed by high resolution X-ray diffraction (HRXRD) measurements. The functional groups of NNDEAP have been identified by Fourier transform infrared spectral studies. Thermogravimetric analysis (TGA) and differential thermal analysis (DTA) have also been carried out and the thermal behavior of NNDEAP has been studied. The UV-vis-NIR studies have been carried out to identify the optical transmittance and the cut off wavelength of NNDEAP is identified. The dielectric loss and the dielectric constant as a function of frequency and temperature were measured for the grown crystal and the nature of variation of dielectric constant εr and dielectric losses (tan δ) were studied. Vicker's hardness test has been carried out on NNDEAP to measure the load dependent hardness. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser.

  19. Solvent inclusion in the crystal structure of bis-[(adamantan-1-yl)methanaminium chloride] 1,4-dioxane hemisolvate monohydrate explained using the computed crystal energy landscape.

    PubMed

    Mohamed, Sharmarke

    2016-09-01

    Repeated attempts to crystallize 1-adamantane-methyl-amine hydro-chloride as an anhydrate failed but the salt was successfully crystallized as a solvate (2C11H20N(+)·2Cl(-)·0.5C4H8O2·H2O), with water and 1,4-dioxane playing a structural role in the crystal and engaging in hydrogen-bonding inter-actions with the cation and anion. Computational crystal-structure prediction was used to rationalize the solvent-inclusion behaviour of this salt by computing the solvent-accessible voids in the predicted low-energy structures for the anhydrate: the global lattice-energy minimum structure, which has the same packing of the ions as the solvate, has solvent-accessible voids that account for 3.71% of the total unit-cell volume and is 6 kJ mol(-1) more stable than the next most stable predicted structure.

  20. The crystal structure of URu3B2

    NASA Astrophysics Data System (ADS)

    Rogl, Peter

    1980-09-01

    The crystal structure of URu3B2 has been determined by single crystal X-ray analysis. URu3B2 crystallizes in the trigonal space group P3bar (C131) with hexagonal lattice a = 1.09531(14), c = 0.59353 (8) nm, Z = 8. Intensity measurements were obtained from a fourcircle diffractometer. The structure was solved by Patterson methods and refined by full matrix least squares calculation. The final R-value, R = ∑ |ΔF|/∑ F0, is 0.052 for an asymetric set of 962 independent reflections (l-F0l > 2 σ (F0)). The crystal structure is a twofold superstructure (distortion-derivative) of the CeCo3B2-type cell (a = 2a', c = 2c' and thus closely related to the CaCu5 type structure. The coordination numbers of U are 2 U + 12 Ru + (6 B) and those of Ru atoms 4 U + 6 Ru + 4 B. The isolated boron atoms have tetrakaidekahedral metal coordination 6 Ru + 3 U; no boron-boron contacts occur. The structural chemistry of (Th, U, RE)Ru3B2 phases is discussed.

  1. CRYSTAL STRUCTURE ANALYSIS OF A PUTATIVE OXIDOREDUCTASE FROM KLEBSIELLA PNEUMONIAE

    SciTech Connect

    Baig, M.; Brown, A.; Eswaramoorthy, S.; Swaminathan, S.

    2009-01-01

    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) at 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.

  2. Enhancing the Sensitivity of NDIR Spectroscopy Using Plasmonic Crystal Structures

    NASA Astrophysics Data System (ADS)

    Ahmed, Amr Elsayed Shebl Mahmoud

    Monitoring the concentration of methane is of crucial importance for health, safety, and maintenance. NDIR spectroscopy is a widely used commercially available method of monitoring the concentration of Gases. Enhancing the sensitivity of the IR detector enhances the limit of detection of NDIR sensors. Plasmonic crystal structures have been shown to enhance the absorption of EM radiation at certain wavelengths depending on their dimensions. In this thesis, a 13 fold enhancement in the LOD of a methane NDIR gas sensor was achieved by designing a plasmonic crystal structure. The structure is a layer of gold with a two dimensional array of micro sized holes. The dimensions of the structure were optimized by COMSOL(TM) simulations to get maximum absorption at lambda = 7:7 mum. The structure was fabricated and the NDIR sensor was developed to experimentally show the enhancement. The experimental results showed good agreement with the simulations and achieved the expected enhancement.

  3. Computational Study and Analysis of Structural Imperfections in 1D and 2D Photonic Crystals

    SciTech Connect

    Maskaly, Karlene Rosera

    2005-06-01

    increasing RMS roughness. Again, the homogenization approximation is able to predict these results. The problem of surface scratches on 1D photonic crystals is also addressed. Although the reflectivity decreases are lower in this study, up to a 15% change in reflectivity is observed in certain scratched photonic crystal structures. However, this reflectivity change can be significantly decreased by adding a low index protective coating to the surface of the photonic crystal. Again, application of homogenization theory to these structures confirms its predictive power for this type of imperfection as well. Additionally, the problem of a circular pores in 2D photonic crystals is investigated, showing that almost a 50% change in reflectivity can occur for some structures. Furthermore, this study reveals trends that are consistent with the 1D simulations: parameter changes that increase the absolute reflectivity of the photonic crystal will also increase its tolerance to structural imperfections. Finally, experimental reflectance spectra from roughened 1D photonic crystals are compared to the results predicted computationally in this thesis. Both the computed and experimental spectra correlate favorably, validating the findings presented herein.

  4. Reduced ceria nanofilms from structure prediction

    NASA Astrophysics Data System (ADS)

    Kozlov, Sergey M.; Demiroglu, Ilker; Neyman, Konstantin M.; Bromley, Stefan T.

    2015-02-01

    Experimentally, Ce2O3 films are used to study cerium oxide in its fully or partially reduced state, as present in many applications. We have explored the space of low energy Ce2O3 nanofilms using structure prediction and density functional calculations, yielding more than 30 distinct nanofilm structures. First, our results help to rationalize the roles of thermodynamics and kinetics in the preparation of reduced ceria nanofilms with different bulk crystalline structures (e.g. A-type or bixbyite) depending on the support used. Second, we predict a novel, as yet experimentally unresolved, nanofilm which has a structure that does not correspond to any previously reported bulk A2B3 phase and which has an energetic stability between that of A-type and bixbyite. To assist identification and fabrication of this new Ce2O3 nanofilm we calculate some observable properties and propose supports for its epitaxial growth.Experimentally, Ce2O3 films are used to study cerium oxide in its fully or partially reduced state, as present in many applications. We have explored the space of low energy Ce2O3 nanofilms using structure prediction and density functional calculations, yielding more than 30 distinct nanofilm structures. First, our results help to rationalize the roles of thermodynamics and kinetics in the preparation of reduced ceria nanofilms with different bulk crystalline structures (e.g. A-type or bixbyite) depending on the support used. Second, we predict a novel, as yet experimentally unresolved, nanofilm which has a structure that does not correspond to any previously reported bulk A2B3 phase and which has an energetic stability between that of A-type and bixbyite. To assist identification and fabrication of this new Ce2O3 nanofilm we calculate some observable properties and propose supports for its epitaxial growth. Electronic supplementary information (ESI) available: Graph of IP versus DFT relative energies for nanofilms, GGA + U calculated lattice parameters and

  5. Preparation, structural, and calorimetric characterization of bicomponent metallic photonic crystals

    NASA Astrophysics Data System (ADS)

    Kozlov, M. E.; Murthy, N. S.; Udod, I.; Khayrullin, I. I.; Baughman, R. H.; Zakhidov, A. A.

    2007-03-01

    We report preparation and characterization of novel bicomponent metal-based photonic crystals having submicron three-dimensional (3D) periodicity. Fabricated photonic crystals include SiO2 sphere lattices infiltrated interstitially with metals, carbon inverse lattices filled with metal or metal alloy spheres, Sb inverse lattices, and Sb inverse lattices filled with Bi spheres. Starting from a face centered SiO2 lattice template, these materials were obtained by sequences of either templating and template extraction or templating, template extraction, and retemplating. Surprising high fidelity was obtained for all templating and template extraction steps. Scanning electron microscopy (SEM), small angle X-ray scattering (SAXS) and differential scanning calorimetry (DSC) were used to characterize the structure and the effects of the structure on calorimetric properties. To the best of our knowledge, SAXS data on metallic photonic crystals were collected for first time.

  6. Direct band gap silicon crystals predicted by an inverse design method

    NASA Astrophysics Data System (ADS)

    Oh, Young Jun; Lee, In-Ho; Lee, Jooyoung; Kim, Sunghyun; Chang, Kee Joo

    2015-03-01

    Cubic diamond silicon has an indirect band gap and does not absorb or emit light as efficiently as other semiconductors with direct band gaps. Thus, searching for Si crystals with direct band gaps around 1.3 eV is important to realize efficient thin-film solar cells. In this work, we report various crystalline silicon allotropes with direct and quasi-direct band gaps, which are predicted by the inverse design method which combines a conformation space annealing algorithm for global optimization and first-principles density functional calculations. The predicted allotropes exhibit energies less than 0.3 eV per atom and good lattice matches, compared with the diamond structure. The structural stability is examined by performing finite-temperature ab initio molecular dynamics simulations and calculating the phonon spectra. The absorption spectra are obtained by solving the Bethe-Salpeter equation together with the quasiparticle G0W0 approximation. For several allotropes with the band gaps around 1 eV, photovoltaic efficiencies are comparable to those of best-known photovoltaic absorbers such as CuInSe2. This work is supported by the National Research Foundation of Korea (2005-0093845 and 2008-0061987), Samsung Science and Technology Foundation (SSTF-BA1401-08), KIAS Center for Advanced Computation, and KISTI (KSC-2013-C2-040).

  7. The crystal structure of a novel SAM-dependent methyltransferase PH1915 from Pyrococcus horikoshii.

    SciTech Connect

    Sun, W.; Xu, X.; Pavlova, M.; Edwards, A.; Joachimiak, A.; Savchenko, A.; Christendat, D.; Biosciences Division; Univ. of Toronto; Univ. Health Network

    2005-01-01

    The S-adenosyl-L-methionine (SAM)-dependent methyltransferases represent a diverse and biologically important class of enzymes. These enzymes utilize the ubiquitous methyl donor SAM as a cofactor to methylate proteins, small molecules, lipids, and nucleic acids. Here we present the crystal structure of PH1915 from Pyrococcus horikoshii OT3, a predicted SAM-dependent methyltransferase. This protein belongs to the Cluster of Orthologous Group 1092, and the presented crystal structure is the first representative structure of this protein family. Based on sequence and 3D structure analysis, we have made valuable functional insights that will facilitate further studies for characterizing this group of proteins. Specifically, we propose that PH1915 and its orthologs are rRNA- or tRNA-specific methyltransferases.

  8. Prediction of Fretting Crack Location and Orientation in a Single Crystal Nickel Alloy

    NASA Technical Reports Server (NTRS)

    Matlik, J. F.; Farris, T. N.; Haynes, J.; Swanson, G. R.; Ham-Battista, G.

    2005-01-01

    Fretting is a structural damage mechanism arising between two nominally clamped surfaces subjected to an oscillatory loading. A critical location for fretting induced damage has been identified at the blade/disk and blade/damper interfaces of gas turbine engine turbomachinery and space propulsion components. The high- temperature, high-frequency loading environment seen by these components lead to severe stress gradients at the edge-of-contact that could potentially foster crack growth leading to component failure. These contact stresses drive crack nucleation in fretting and are very sensitive to the geometry of the contacting bodies, the contact loads, materials, temperature, and contact surface tribology (friction). Recently, a high-frequency, high-temperature load frame has been designed for experimentally investigating fretting damage of single crystal nickel materials employed in aircraft and spacecraft turbomachinery. A modeling method for characterizing the fretting stresses of the spherical fretting contact stress behavior in this experiment is developed and described. The calculated fretting stresses for a series of experiments are then correlated to the observed fretting damage. Results show that knowledge of the normal stresses and resolved shear stresses on each crystal plane can aid in predicting crack locations and orientations.

  9. The clouded crystal ball: Comments on geophysical prediction

    NASA Technical Reports Server (NTRS)

    Silverman, S. M.

    1979-01-01

    The concepts of prediction in the geophysical domain are considered with emphasis on the areas of difficulties and the nature of these difficulties. Differences in defining and determining the validity and significance of hypotheses and observational correlations are covered.

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

    SciTech Connect

    Sankari, R. Siva; Perumal, Rajesh Narayana

    2014-04-24

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

  11. Unusual Features of Crystal Structures of Some Simple Copper Compounds

    ERIC Educational Resources Information Center

    Douglas, Bodie

    2009-01-01

    Some simple copper compounds have unusual crystal structures. Cu[subscript 3]N is cubic with N atoms at centers of octahedra formed by 6 Cu atoms. Cu[subscript 2]O (cuprite) is also cubic; O atoms are in tetrahedra formed by 4 Cu atoms. These tetrahedra are linked by sharing vertices forming two independent networks without linkages between them.…

  12. Crystal structures and morphologies of fractionated milk fat in nanoemulsions.

    PubMed

    Truong, Tuyen; Morgan, Garry P; Bansal, Nidhi; Palmer, Martin; Bhandari, Bhesh

    2015-03-15

    The triacylglycerol (TAG) crystal structures and morphologies of fractionated milk lipids in nanoemulsions were investigated at 4°C. Droplet size (0.17 versus 1.20 μm), lipid composition (stearin versus olein) and cooling rate (1 versus 10°C min(-1)) had an influence on the structural properties. Five crystal polymorphs (α, β'1, β'2, β1, and β2) were formed with either triple and/or double chain length structures in the solid phases of the emulsified systems. X-ray scattering peak intensities were reduced with the nanoemulsion particles. The internal structure of TAG exhibited stacking of individual lamellar layers (3.8-4.2 nm). Various anisometric shapes of fat nanoparticles were formed due to a highly sharp curvature of the nano-size droplets. The shape of olein nanoparticles was more polyhedral compared to the stearin. TAG crystals arranged in a planar-layered organisation at the slower cooling rate. These differences imply that the nanometric confinement of oil droplets modifies the fat crystal habit.

  13. Crystal structure and packing energy calculations of (+)-6-aminopenicillanic acid.

    PubMed

    Saouane, Sofiane; Buth, Gernot; Fabbiani, Francesca P A

    2013-11-01

    The X-ray single-crystal structure of (2S,5R,6R)-6-amino-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid, commonly known as (+)-6-aminopenicillanic acid (C8H12N2O3S) and a precursor of a variety of semi-synthetic penicillins, has been determined from synchrotron data at 150 K. The structure represents an ordered zwitterion and the crystals are nonmerohedrally twinned. The crystal structure is composed of a three-dimensional network built by three charge-assisted hydrogen bonds between the ammonium and carboxylate groups. The complementary analysis of the crystal packing by the PIXEL method brings to light the nature and ranking of the energetically most stabilizing intermolecular interaction energies. In accordance with the zwitterionic nature of the structure, PIXEL lattice energy calculations confirm the predominance of the Coulombic term (-379.1 kJ mol(-1)) ahead of the polarization (-141.4 kJ mol(-1)), dispersion (-133.7 kJ mol(-1)) and repulsion (266.3 kJ mol(-1)) contributions.

  14. Materials research at Stanford University. [composite materials, crystal structure, acoustics

    NASA Technical Reports Server (NTRS)

    1975-01-01

    Research activity related to the science of materials is described. The following areas are included: elastic and thermal properties of composite materials, acoustic waves and devices, amorphous materials, crystal structure, synthesis of metal-metal bonds, interactions of solids with solutions, electrochemistry, fatigue damage, superconductivity and molecular physics and phase transition kinetics.

  15. Crystal growth, spectral, structural and optical studies of π-conjugated stilbazolium crystal: 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate.

    PubMed

    Krishna Kumar, M; Sudhahar, S; Bhagavannarayana, G; Mohan Kumar, R

    2014-05-05

    Nonlinear optical (NLO) organic compound, 4-bromobenzaldehyde-4'-N'-methylstilbazolium tosylate was synthesized by reflux method. The formation of molecular complex was confirmed from (1)H NMR, FT-IR and FT-Raman spectral analyses. The single crystals were grown by slow evaporation solution growth method and the crystal structure and atomic packing of grown crystal was identified. The morphology and growth axis of grown crystal were determined. The crystal perfection was analyzed using high resolution X-ray diffraction study on (001) plane. Thermal stability, decomposition stages and melting point of the grown crystal were analyzed. The optical absorption coefficient (α) and energy band gap (E(g)) of the crystal were determined using UV-visible absorption studies. Second harmonic generation efficiency of the grown crystal was examined by Kurtz powder method with different particle size using 1064 nm laser. Laser induced damage threshold study was carried out for the grown crystal using Nd:YAG laser.

  16. Crystal structure and stereochemistry study of 2-substituted benzoxazole derivatives.

    PubMed

    Mabied, Ahmed F; Shalaby, Elsayed M; Zayed, Hamdia A; El-Kholy, Esmat; Farag, Ibrahim S A; Ahmed, Naima A

    2014-01-01

    The structure of 2-[(4-chlorophenylazo) cyanomethyl] benzoxazole, C15H9ClN4O (I), has triclinic ([Formula: see text]) symmetry. The structure displays N-H ⋯ N hydrogen bonding. The structure of 2-[(arylidene) cyanomethyl] benzoxazoles, C17H10N2O3 (II), has triclinic ([Formula: see text]) symmetry. The structure displays C-H ⋯ N, C-H ⋯ C hydrogen bonding. In (I), the chlorophenyl and benzoxazole groups adopt a trans configuration with respect to the central cyanomethyle hydrazone moiety. Compound (II) crystallized with two molecules in the asymmetric unit shows cisoid conformation between cyano group and benzoxazole nitrogen, contrary to (I). In (II) the benzodioxole has an envelope conformation (the C17 atom is the flap atom). The molecular geometry obtained using molecular mechanics (MM) calculations has been discussed along with the results of single crystal analysis.

  17. Crystal Structure of the Bacillus subtilis Superoxide Dismutase

    SciTech Connect

    Liu, Ping; Ewis, H.E.; Huang, Y.-J; Lu, C.-D.; Tai, P.C.; Weber, Irene T.

    2008-06-01

    The sodA gene of Bacillus subtilis was expressed in Escherichia coli, purified and crystallized. The crystal structure of MnSOD was solved by molecular replacement with four dimers per asymmetric unit and refined to an R factor of 21.1% at 1.8 {angstrom} resolution. The dimer structure is very similar to that of the related enzyme from B. anthracis. Larger structural differences were observed with the human MnSOD, which has one less helix in the helical domain and a longer loop between two -strands and also showed differences in three amino acids at the intersubunit interface in the dimer compared with the two bacterial MnSODs. These structural differences can be exploited in the design of drugs that selectively target the Bacillus enzymes.

  18. Effect of local structures on structural evolution during crystallization in undercooled metallic glass-forming liquids.

    PubMed

    Wu, Z W; Li, M Z; Wang, W H; Song, W J; Liu, K X

    2013-02-21

    The effect of local structures on structural evolution during the crystallization of undercooled ZrCu metallic glass-forming liquid was studied via molecular dynamics simulations. It is found that body-centered-cubic (bcc)-like clusters play a key role in structural evolution during crystallization. In contrast to previous speculations, the number of bcc-like crystal nuclei does not change much before the onset of crystallization. Instead, the development of a bcc-like critical nucleus during annealing leads to a strong spatial correlation with other nuclei in its surroundings, forming a crystalline structure template. It is also found that the size distribution of bcc-like nuclei follows a power-law form with an exponential cutoff in the early stage of annealing, but changes to a pure power-law behavior just before the onset of crystallization. This implies that the crystalline structure template has fractal feature and the undercooled liquids evolve to a self-organized critical state before the onset of crystallization, which might trigger the subsequent rapid crystallization. According to the graph theory analysis, it is also found that the observed large scatter of the onset time of crystallization in different liquid samples results from the connectivity of the bcc-like clusters.

  19. Single crystal growth, crystal structure characterization and magnetic properties of UCo0.5Sb2

    SciTech Connect

    Bukowski, Z. . E-mail: bukowski@int.pan.wroc.pl; Tran, V.H.; Stepien-Damm, J.; Troc, R.

    2004-11-01

    Single crystals of uranium intermetallic compound UCo0.5Sb2 were grown by means of the antimony-flux technique. The characterization of the samples has been carried out utilizing single crystal X-ray diffraction and magnetization measurements. UCo0.5Sb2 is found to crystallize in the tetragonal HfCuSi2-type structure, space group P4/nmm with Z=2 formula units per cell, and the lattice parameters a=0.4300(1) and c=0.8958(2)nm. The refinement of the occupancy parameters and the energy dispersive X-ray analysis have indicated a distinct deficiency on the cobalt sites. The results of magnetization measurements showed that UCo0.5Sb2 orders ferromagnetically below 65K with a huge magnetocrystalline anisotropy with the c direction being the easy magnetization axis.

  20. Crystallization studies of lunar igneous rocks: crystal structure of synthetic armalcolite.

    PubMed

    Lind, M D; Housley, R M

    1972-02-04

    Crystals of armalcolite, Mg(0.5)Fe(0.5)Ti(2)O(5), up to several millimeters in length have been grown from a glass initially having the composition of lunar rock 10017. A single-crystal x-ray study has confirmed that the crystals are isomorphous with pseudobrookite and has shown that the cations are strongly ordered, with the Ti(4+) ions occupying the 8f sites and the Fe(2+) and Mg(2+) ions randomly distributed over the 4c sites. An examination of karrooite, MgTi(2)O(5), has revealed a similar distribution of Mg(2+) and Ti(4+) ions. A reexamination of earlier x-ray and Mössbauer data for pseudobrookite, Fe(2)TiO(5), has shown that it is more consistent with this type of ordering than with the inverse structure that has been generally assumed.

  1. Crystal structures at high pressures and temperatures

    NASA Astrophysics Data System (ADS)

    Caldwell, Wendel Alexander

    2000-10-01

    The diamond anvil cell (DAC) is a unique instrument that can generate pressures equivalent to those inside planetary interiors (pressures on the order of 1 million atmospheres) under sustained conditions. When combined with a bright source of collimated x-rays, the DAC can be used to probe the structure of materials in-situ at ultra-high pressures. An understanding of the high-pressure structure of materials is important in determining what types of processes may take place in the Earth at great depths. Motivated by previous studies showing that xenon becomes metallic at pressures above ˜1 megabar (100 GPa), we examined the stable structures and reactivity of xenon at pressures approaching that of the core-mantle boundary in the Earth. Our findings indicate the transformation of xenon from face-centered cubic (fcc) to hexagonal close-packed (hcp) structures is kinetically hindered at room temperature, with the equilibrium fcc--hcp phase boundary at 21 (+/-3) gigapascals, a pressure lower than was previously thought. Additionally, we find no tendency on the part of xenon to form a metal alloy with iron or platinum to at least 100 to 150 gigapascals, making it unlikely that the Earth's core serves as a reservoir for primordial xenon. Measurements of the compressibility of natural (Mg.75,Fe .25)2SiO4 gamma-spinel at pressures of the Earth's transition zone yield a pressure derivative of the bulk modulus K0 ' = 6.3 (+/-0.3). As gamma-spinel is considered to be a dominant mineral phase of the transition-zone of the Earth's mantle (400--670 km depth), the relatively high value of K0' for gamma-spinel may help explain the rapid increase with depth of seismic velocities through the transition zone. The thermodynamics, mechanisms and kinetics of pressure-induced amorphization are not well understood. We report here new studies indicating little or no entropy difference between the crystalline and glassy states of Ca(OH) 2 (portlandite). Additional work on the pressure

  2. Predictive crystallization of ribonuclease A via rapid screening of osmotic second virial coefficients.

    PubMed

    Tessier, Peter M; Johnson, Harvey R; Pazhianur, Rajesh; Berger, Bryan W; Prentice, Jessica L; Bahnson, Brian J; Sandler, Stanley I; Lenhoff, Abraham M

    2003-02-01

    Important progress has been made in recent years toward developing a molecular-level understanding of protein phase behavior in terms of the osmotic second virial coefficient, a thermodynamic parameter that characterizes pairwise protein interactions. Yet there has been little practical application of this knowledge to the field of protein crystallization, largely because of the difficult and time-consuming nature of traditional techniques for characterizing protein interactions. Self-interaction chromatography has recently been proposed as a highly efficient method for measuring the osmotic second virial coefficient. The utility of the technique is examined in this work by characterizing virial coefficients for ribonuclease A under 59 solution conditions using several crystallization additives, including PEG, sodium chloride, ammonium sulfate, and propanol. The virial coefficient measurements show some counterintuitive trends and shed light on the previous difficulties in crystallizing ribonuclease A. Crystallization experiments at the corresponding solution conditions were conducted by using ultracentrifugal crystallization. Using this methodology, ribonuclease A crystals were obtained under conditions for which the virial coefficients fell within the "crystallization slot." Crystallographic characterization showed that the crystals diffract to high resolution. Metastable crystals were also obtained for conditions outside, but near, the "crystallization slot," and they could also be frozen and used to collect structural information.

  3. Crystal structure of new AsS2 compound

    NASA Astrophysics Data System (ADS)

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    2013-01-01

    AsS2 single crystals have been obtained for the first time from an As2S3 melt at pressures above 6 GPa and temperatures above 800 K in the As2S3 → AsS + AsS2 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.

  4. Single Crystal Structure Determination of Alumina to 1 Mbar

    NASA Astrophysics Data System (ADS)

    Dong, H.; Zhang, L.; Prakapenka, V.; Mao, H.

    2014-12-01

    Aluminum oxide (Al2O3) is an important ceramic material and a major oxide in the earth. Additionally, alumina is a widely used pressure standard in static high-pressure experiments (Cr3+-bearing corundum, ruby). The changes of its crystal structure with pressure (P) and temperature (T) are important for its applications and understanding its physical properties in the deep Earth. There have been numerous reports on the high P-T polymorphs of alumina. Previous theoretical calculations and experiments suggest that the crystal structure of Al2O3 evolves greatly at high P-T. In this study, we used the newly developed multigrain crystallography method combined with single-crystal x-ray diffraction analysis technique for the structure determination of alumina at high P-T to provide single-crystal structure refinement for high-pressure phases of Al2O3. Alumina powder was mixed with ~10% Pt and Ne was used as both pressure transmitting media and thermal insulating layers during laser-heating. Coarse-grained aggregates of Al2O3 were synthesized in a laser-heated diamond anvil cell. The structure change of Al2O3 was monitored by in situ x-ray diffraction at ~1 Mbar and 2700 K. The results allow us to distinguish the structural differences between the Rh2O3 (II) structure (space group Pbcn) and perovskite structure (space group Pbnm) for the first high-pressure phase of Al2O3. More detailed results will be discussed in the later work.

  5. Structural evolution in the crystallization of rapid cooling silver melt

    SciTech Connect

    Tian, Z.A.; Dong, K.J.; Yu, A.B.

    2015-03-15

    The structural evolution in a rapid cooling process of silver melt has been investigated at different scales by adopting several analysis methods. The results testify Ostwald’s rule of stages and Frank conjecture upon icosahedron with many specific details. In particular, the cluster-scale analysis by a recent developed method called LSCA (the Largest Standard Cluster Analysis) clarified the complex structural evolution occurred in crystallization: different kinds of local clusters (such as ico-like (ico is the abbreviation of icosahedron), ico-bcc like (bcc, body-centred cubic), bcc, bcc-like structures) in turn have their maximal numbers as temperature decreases. And in a rather wide temperature range the icosahedral short-range order (ISRO) demonstrates a saturated stage (where the amount of ico-like structures keeps stable) that breeds metastable bcc clusters. As the precursor of crystallization, after reaching the maximal number bcc clusters finally decrease, resulting in the final solid being a mixture mainly composed of fcc/hcp (face-centred cubic and hexagonal-closed packed) clusters and to a less degree, bcc clusters. This detailed geometric picture for crystallization of liquid metal is believed to be useful to improve the fundamental understanding of liquid–solid phase transition. - Highlights: • A comprehensive structural analysis is conducted focusing on crystallization. • The involved atoms in our analysis are more than 90% for all samples concerned. • A series of distinct intermediate states are found in crystallization of silver melt. • A novelty icosahedron-saturated state breeds the metastable bcc state.

  6. Multithreaded parsing for predicting RNA secondary structures.

    PubMed

    Al-Mulhem, Muhammed S

    2010-01-01

    Many computational approaches have been developed for modelling and analysing the RNA secondary structure. These approaches are based on diverse methods such as grammars, dynamic programming, matching and evolutionary algorithms. This paper proposes a new parsing algorithm for the prediction of RNA secondary structures. The proposed algorithm is based on the shift-reduce LR parsing algorithm for programming languages. It has two main contributions: it extends the LR parsing algorithm by using a Stochastic Context-Free Grammar (SCFG) instead of Context-Free Grammar (CFG) for parsing RNA secondary structures; it extends the LR parsing algorithm by using a multithreaded approach to handle the LR parsing conflicts resulting from the use of ambiguous grammars.

  7. Inhibitors of the kinase IspE: structure-activity relationships and co-crystal structure analysis.

    PubMed

    Hirsch, Anna K H; Alphey, Magnus S; Lauw, Susan; Seet, Michael; Barandun, Luzi; Eisenreich, Wolfgang; Rohdich, Felix; Hunter, William N; Bacher, Adelbert; Diederich, François

    2008-08-07

    Enzymes of the non-mevalonate pathway for isoprenoid biosynthesis are therapeutic targets for the treatment of important infectious diseases. Whereas this pathway is absent in humans, it is used by plants, many eubacteria and apicomplexan protozoa, including major human pathogens such as Plasmodium falciparum and Mycobacterium tuberculosis. Herein, we report on the design, preparation and biological evaluation of a new series of ligands for IspE protein, a kinase from this pathway. These inhibitors were developed for the inhibition of IspE from Escherichia coli, using structure-based design approaches. Structure-activity relationships (SARs) and a co-crystal structure of Aquifex aeolicus IspE bound to a representative inhibitor validate the proposed binding mode. The crystal structure shows that the ligand binds in the substrate-rather than the adenosine 5'-triphosphate (ATP)-binding pocket. As predicted, a cyclopropyl substituent occupies a small cavity not used by the substrate. The optimal volume occupancy of this cavity is explored in detail. In the co-crystal structure, a diphosphate anion binds to the Gly-rich loop, which normally accepts the triphosphate moiety of ATP. This structure provides useful insights for future structure-based developments of inhibitors for the parasite enzymes.

  8. Crystal structure of alpha poly-p-xylylene.

    NASA Technical Reports Server (NTRS)

    Kubo, S.; Wunderlich, B.

    1971-01-01

    A crystal structure of alpha poly-p-xylylene is proposed with the help of data of oriented crystals grown during polymerization. The unit cell is monoclinic with the parameters a = 8.57 A, b = 10.62 A, c = 6.54 A (chain axis), and beta = 101.3 deg. Four repeating units per cell lead to a calculated density of 1.185 g/cu cm and a packing density of 0.71. The probable space group is P2 sub 1/m.

  9. Structural, magnetic and optical properties of two concomitant molecular crystals

    NASA Astrophysics Data System (ADS)

    Silva, Manuela Ramos; Milne, Bruce; Coutinho, Joana T.; Pereira, Laura C. J.; Martín-Ramos, Pablo; Pereira da Silva, Pedro S.; Martín-Gil, Jesús

    2016-03-01

    A new 1D complex has been prepared and characterized. X-ray single crystal structure confirms that the Cu(II) ions assemble in alternating chains with Cu … Cu distances of 2.5685(4) and 3.1760(4) Å. The temperature dependence of the magnetic susceptibility reveals an antiferromagnetic interaction between the paddle-wheel copper centers with an exchange of -300 cm-1. The exchange integral was also determined by quantum chemical ab-initio calculations, using polarised and unpolarised basis sets reproducing well the experimental value. The second harmonic generation efficiency of a concomitantly crystallized material was evaluated and was found to be comparable to urea.

  10. Crystal structure of tin(IV) chloride octa-hydrate.

    PubMed

    Hennings, Erik; Schmidt, Horst; Voigt, Wolfgang

    2014-12-01

    The title compound, [SnCl4(H2O)2]·6H2O, was crystallized according to the solid-liquid phase diagram at lower temperatures. It is built-up of SnCl4(H2O)2 octa-hedral units (point group symmetry 2) and lattice water mol-ecules. An intricate three-dimensional network of O-H⋯O and O-H⋯Cl hydrogen bonds between the complex molecules and the lattice water molecules is formed in the crystal structure.

  11. Modeling liquid crystal bilayer structures with minimal surfaces.

    PubMed

    Enlow, J D; Enlow, R L; McGrath, K M; Tate, M W

    2004-01-22

    This paper describes a new convenient and accurate method of calculating x-ray diffraction integrated intensities from detailed cubic bilayer structures. The method is employed to investigate the structure of a particular surfactant system (didodecyldimethylammonium bromide in a solution of oil and heavy water), for which single-crystal experimental data have recently been collected. The diffracted peak intensities correlate well with theoretical structures based on mathematical minimal surfaces. Optimized electron density profiles of the bilayer are presented, providing new insight into key features of the bilayer structure.

  12. Crystallographic Structure, Intermolecular Packing Energetics, Crystal Morphology and Surface Chemistry of Salmeterol Xinafoate (Form I).

    PubMed

    Moldovan, Alexandru A; Rosbottom, Ian; Ramachandran, Vasuki; Pask, Christopher M; Olomukhoro, Oboroghene; Roberts, Kevin J

    2017-03-01

    Single crystals of salmeterol xinafoate (form I), prepared from slow cooled supersaturated propan-2-ol solutions, crystallize in a triclinic P1¯ symmetry with 2 closely related independent salt pairs within the asymmetric unit, with an approximately double-unit cell volume compared with the previously published crystal structure. Synthonic analysis of the bulk intermolecular packing confirms the similarity in packing energetics between the 2 salt pairs. The strongest synthons, as expected, are dominated by coulombic interactions. Morphologic prediction reveals a plate-like morphology, dominated by the {001}, {010}, and {100} surfaces, consistent with experimentally grown crystals. Although surface chemistry of the slow-growing {001} face comprises large sterically hindering phenyl groups, although weaker coulombic interactions still prevail from the alcohol group present on the phenyl and hydroxymethyl groups. The surface chemistry of the faster growing {010} and {100} faces are dominated by the significantly stronger cation/anion interactions occurring between the carboxylate and protonated secondary ammonium ion groups. The importance of understanding the cohesive and adhesive nature of the crystal surfaces of an active pharmaceutical ingredient, with respect to their interaction with other active pharmaceutical ingredient crystals and how that may affect formulation design, is highlighted.

  13. Crystal structure of 4-carbamoylpyridinium chloride

    PubMed Central

    Fellows, Simon M.; Prior, Timothy J.

    2016-01-01

    The hydro­chloride salt of isonicotinamide, C6H7N2O+·Cl−, has been synthesized from a dilute solution of hydro­chloric acid in aceto­nitrile. The compound displays monoclinic symmetry (space group C2/c) at 150 K, similar to the related hydro­chloride salt of nicotinamide. The asymmetric unit contains one protonated isonicotinamide mol­ecule and a chloride anion. An array of hydrogen-bonding inter­actions, including a peculiar bifurcated pyridinium–chloride inter­action, results in linear chains running almost perpendicularly in the [150] and [1-50] directions within the structure. A description of the hydrogen-bonding network and comparison with similar compounds are presented. PMID:27375858

  14. Crystal density predictions for nitramines based on quantum chemistry.

    PubMed

    Qiu, Ling; Xiao, Heming; Gong, Xuedong; Ju, Xuehai; Zhu, Weihua

    2007-03-06

    An efficient and convenient method for predicting the crystalline densities of energetic materials was established based on the quantum chemical computations. Density functional theory (DFT) with four different basis sets (6-31G(**), 6-311G(**), 6-31+G(**), and 6-311++G(**)) and various semiempirical molecular orbital (MO) methods have been employed to predict the molecular volumes and densities of a series of energetic nitramines including acyclic, monocyclic, and polycyclic/cage molecules. The relationships between the calculated values and experimental data were discussed in detail, and linear correlations were suggested and compared at different levels. The calculation shows that if the selected basis set is larger, it will expend more CPU (central processing unit) time, larger molecular volume and smaller density will be obtained. And the densities predicted by the semiempirical MO methods are all systematically larger than the experimental data. In comparison with other methods, B3LYP/6-31G(**) is most accurate and economical to predict the solid-state densities of energetic nitramines. This may be instructive to the molecular designing and screening novel HEDMs.

  15. Thermodynamic stability and structural properties of cluster crystals formed by amphiphilic dendrimers

    NASA Astrophysics Data System (ADS)

    Lenz, Dominic A.; Mladek, Bianca M.; Likos, Christos N.; Blaak, Ronald

    2016-05-01

    We pursue the goal of finding real-world examples of macromolecular aggregates that form cluster crystals, which have been predicted on the basis of coarse-grained, ultrasoft pair potentials belonging to a particular mathematical class [B. M. Mladek et al., Phys. Rev. Lett. 46, 045701 (2006)]. For this purpose, we examine in detail the phase behavior and structural properties of model amphiphilic dendrimers of the second generation by means of monomer-resolved computer simulations. On augmenting the density of these systems, a fluid comprised of clusters that contain several overlapping and penetrating macromolecules is spontaneously formed. Upon further compression of the system, a transition to multi-occupancy crystals takes place, the thermodynamic stability of which is demonstrated by means of free-energy calculations, and where the FCC is preferred over the BCC-phase. Contrary to predictions for coarse-grained theoretical models in which the particles interact exclusively by effective pair potentials, the internal degrees of freedom of these molecules cause the lattice constant to be density-dependent. Furthermore, the mechanical stability of monodisperse BCC and FCC cluster crystals is restricted to a bounded region in the plane of cluster occupation number versus density. The structural properties of the dendrimers in the dense crystals, including their overall sizes and the distribution of monomers are also thoroughly analyzed.

  16. Crystal structure and density of helium to 232 kbar

    NASA Technical Reports Server (NTRS)

    Mao, H. K.; Wu, Y.; Jephcoat, A. P.; Hemley, R. J.; Bell, P. M.; Bassett, W. A.

    1988-01-01

    The properties of helium and hydrogen at high pressure are topics of great interest to the understanding of planetary interiors. These materials constitute 95 percent of the entire solar system. A technique was presented for the measurement of X-ray diffraction from single-crystals of low-Z condenses gases in a diamond-anvil cell at high pressure. The first such single-crystal X-ray diffraction measurements on solid hydrogen to 26.5 GPa were presented. The application of this technique to the problem of the crystal structure, equation of state, and phase diagram of solid helium is reported. Crucial for X-ray diffraction studies of these materials is the use of a synchrotron radiation source which provides high brillance, narrow collimation of the incident and diffracted X-ray beams to reduce the background noise, and energy-dispersive diffraction techniques with polychromatic (white) radiation, which provides high detection efficiency.

  17. Growth and crystal structure of LiCuO 2

    NASA Astrophysics Data System (ADS)

    Imai, Katsuhiro; Koike, Masayoshi; Sawa, Hiroshi; Takei, Humihiko

    1993-03-01

    A new crystal LiCuO2 is synthesized from Li2CuO2 using a topotactic reaction by Li extraction. X-ray measurements reveal that the crystal system of the LiCuO2 is orthorhombic, the space group is Cmmm, and the lattice parameters are a = 5.7078(6) Å, b = 9.639(2) Å, and c = 2.7172(3) Å. The crystal structure determined by Rietveld analysis is closely related to that of Li2CuO2 and of NaCuO2. Magnetic measurement of LiCuO2 shows temperature-independent paramagnetism similar to that of NaCuO2.

  18. Octupolar versus dipolar crystalline structures for nonlinear optics: A dual crystal and propagative engineering approach

    NASA Astrophysics Data System (ADS)

    Zyss, J.; Brasselet, S.; Thalladi, V. R.; Desiraju, G. R.

    1998-07-01

    A new type of crystalline structure for nonlinear optics whereby octupolar symmetry features are displayed at both molecular and crystalline levels is exemplified by the prototype 2,4,6-triaryloxy-1,3,5-triazine (TPOT) crystal and analyzed in terms of both individual molecular responses and crystal packing features. Polarized harmonic light scattering permits the full determination of the molecular β hyperpolarizability tensor and confirms the octupolar trigonal symmetry of the TPOT molecule. An oriented gas model is used to infer therefrom an estimate of the crystalline nonlinear d tensor which is predicted to be of the same order as that of the reference dipolar N-4-nitrophenyl-(L)-prolinol crystal. The concept of optimal packing toward quadratic nonlinear optics, which had been initially introduced in the realm of quasi-one-dimensional structures, is revisited and enlarged to encompass more isotropic uniaxial structures potentially amenable, in the case of octupoles, to larger optimal values than in the one-dimensional case. Moreover, considerations pertaining to phase matching which had been left aside in the earlier one-dimensional optimization framework are now considered and the various type I and type II configurations compared for both one-dimensional and octupolar uniaxial structures. Application perspectives of octupolar structures toward short pulse nonlinear optics are discussed: their structurally built-in polarization independence is outlined as a major asset in contrast with the more traditional one-dimensional structures.

  19. Ligand Discovery from a Dopamine D3 Receptor Homology Model and Crystal Structure

    PubMed Central

    Carlsson, Jens; Coleman, Ryan G.; Setola, Vincent; Irwin, John J.; Fan, Hao; Schlessinger, Avner; Sali, Andrej

    2011-01-01

    G-Protein coupled receptors (GPCRs) are intensely studied as drug targets and for their role in signaling. With the determination of the first crystal structures, interest in structure-based ligand discovery has increased. Unfortunately, most GPCRs lack experimental structures. The determination of the D3 receptor structure, and a community challenge to predict it, enabled a fully prospective comparison of ligand discovery from a modeled structure versus that of the subsequently released crystal structure. Over 3.3 million molecules were docked against a homology model, and 26 of the highest ranking were tested for binding. Six had affinities from 0.2 to 3.1μM. Subsequently, the crystal structure was released and the docking screen repeated. Of the 25 compounds selected, five had affinities from 0.3 to 3.0μM. One of the novel ligands from the homology model screen was optimized for affinity to 81nM. The feasibility of docking screens against modeled GPCRs more generally is considered. PMID:21926995

  20. Myelin structures formed by thermotropic smectic liquid crystals.

    PubMed

    Peddireddy, Karthik; Kumar, Pramoda; Thutupalli, Shashi; Herminghaus, Stephan; Bahr, Christian

    2013-12-17

    We report on transient structures, formed by thermotropic smectic-A liquid crystals, resembling the myelin figures of lyotropic lamellar liquid crystals. The thermotropic myelin structures form during the solubilization of a smectic-A droplet in an aqueous phase containing a cationic surfactant at concentrations above the critical micelle concentration. Similar to the lyotropic myelin figures, the thermotropic myelins appear in an optical microscope as flexible tubelike structures growing at the smectic/aqueous interface. Polarizing microscopy and confocal fluorescence microscopy show that the smectic layers are parallel to the tube surface and form a cylindrically bent arrangement around a central line defect in the tube. We study the growth behavior of this new type of myelins and discuss similarities to and differences from the classical lyotropic myelin figures.

  1. Gas and crystal structures of CCl2FSCN

    NASA Astrophysics Data System (ADS)

    Martínez, Yanina Berrueta; Rodríguez Pirani, Lucas S.; Erben, Mauricio F.; Boese, Roland; Reuter, Christian G.; Vishnevskiy, Yury V.; Mitzel, Norbert W.; Della Védova, Carlos O.

    2017-03-01

    Dichlorofluoromethyl thiocyanate, CCl2FSCN, was structurally studied in the solid and in the gas phase by means of single-crystal X-ray (XRD) and gas electron diffraction (GED), respectively. In the gas phase the title molecule adopts two stable conformers, described by the FC-SC dihedral angle. The gauche-conformer (FC bond with respect to the SC bond) is more stable than the anti-conformer. In this work we present the first experimental evidence for the existence of the anti-CF2ClSCN form. In the solid state only the most stable gauche-conformer was found. Intermolecular interactions were detected in the crystal structure and analyzed. A structural comparison of the results with those of related species as CCl2FSCN, CCl3SCN and CH2ClSCN is presented.

  2. GPCR crystal structures: Medicinal chemistry in the pocket.

    PubMed

    Shonberg, Jeremy; Kling, Ralf C; Gmeiner, Peter; Löber, Stefan

    2015-07-15

    Recent breakthroughs in GPCR structural biology have significantly increased our understanding of drug action at these therapeutically relevant receptors, and this will undoubtedly lead to the design of better therapeutics. In recent years, crystal structures of GPCRs from classes A, B, C and F have been solved, unveiling a precise snapshot of ligand-receptor interactions. Furthermore, some receptors have been crystallized in different functional states in complex with antagonists, partial agonists, full agonists, biased agonists and allosteric modulators, providing further insight into the mechanisms of ligand-induced GPCR activation. It is now obvious that there is enormous diversity in the size, shape and position of the ligand binding pockets in GPCRs. In this review, we summarise the current state of solved GPCR structures, with a particular focus on ligand-receptor interactions in the binding pocket, and how this can contribute to the design of GPCR ligands with better affinity, subtype selectivity or efficacy.

  3. High-throughput study of crystal structures and stability of strengthening precipitates in Mg alloys

    NASA Astrophysics Data System (ADS)

    Wang, Dongshu; Amsler, Maxmilian; Hegde, Vinay; Saal, James; Issa, Ahmed; Zeng, Xiaoqin; Wolverton, Christopher

    Age hardening, in which precipitates form and impede the movement of dislocations, can be applied to magnesium alloys in order to increase their limited strengthening behavior. To help clarify the energetics of precipitation hardening of Mg alloys, we employed first principles density functional theory calculations to elucidate both crystal structures and energetics of a very large set of precipitates in Mg alloys. We find the enthalpy changes of (stable and metastable) observed precipitates during the age hardening process are consistent with the experimental sequence of formation for many Mg binary alloys (Mg- {Nd, Gd, Y, Sn, Al, Zn}). For cases where the metastable precipitate crystal structure is unavailable, we search over several prototypes and predict structures/stoichiometries for several ternary precipitates. In addition, high-throughput calculations are performed to construct hcp-based based convex hulls, which assist the identification of coherent GP zones and new metastable phases in age-hardened hcp systems.

  4. Crystal structure of a symbiosis-related lectin from octocoral.

    PubMed

    Kita, Akiko; Jimbo, Mitsuru; Sakai, Ryuichi; Morimoto, Yukio; Miki, Kunio

    2015-09-01

    D-Galactose-binding lectin from the octocoral, Sinularia lochmodes (SLL-2), distributes densely on the cell surface of microalgae, Symbiodinium sp., an endosymbiotic dinoflagellate of the coral, and is also shown to be a chemical cue that transforms dinoflagellate into a non-motile (coccoid) symbiotic state. SLL-2 binds with high affinity to the Forssman antigen (N-acetylgalactosamine(GalNAc)α1-3GalNAcβ1-3Galα1-4Galβ1-4Glc-ceramide), and the presence of Forssman antigen-like sugar on the surface of Symbiodinium CS-156 cells was previously confirmed. Here we report the crystal structures of SLL-2 and its GalNAc complex as the first crystal structures of a lectin involved in the symbiosis between coral and dinoflagellate. N-Linked sugar chains and a galactose derivative binding site common to H-type lectins were observed in each monomer of the hexameric SLL-2 crystal structure. In addition, unique sugar-binding site-like regions were identified at the top and bottom of the hexameric SLL-2 structure. These structural features suggest a possible binding mode between SLL-2 and Forssman antigen-like pentasaccharide.

  5. Prediction of crystal densities of organic explosives by group additivity

    SciTech Connect

    Stine, J R

    1981-08-01

    The molar volume of crystalline organic compound is assumed to be a linear combination of its constituent volumes. Compounds consisting only of the elements hydrogen, carbon, nitrogen, oxygen, and fluorine are considered. The constituent volumes are taken to be the volumes of atoms in particular bonding environments and are evaluated from a large set of crystallographic data. The predicted density has an expected error of about 3%. These results are applied to a large number of explosives compounds.

  6. Random hcp and fcc structures in thermoresponsive microgel crystals.

    PubMed

    Brijitta, J; Tata, B V R; Joshi, R G; Kaliyappan, T

    2009-08-21

    Monodisperse thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) microgel particles having a diameter of 520 nm were synthesized by free-radical precipitation polymerization and centrifuged to obtain a concentrated suspension. The centrifuged mother suspension was made to self-order into a crystalline state by repeated annealing beyond the volume phase transition (VPT) of the particles. We report here the three-dimensional (3D) real space structure, determined using a confocal laser scanning microscope, of PNIPAM microgel crystal samples prepared by two different recrystallized routes: (1) solidifying a shear melted colloidal liquid (referred as as-prepared sample) and (2) slow cooling of a colloidal liquid (referred as recrystallized sample). We have recorded images of several regions of the crystal with each region containing 15 horizontal crystal planes for determining the in-plane [two-dimensional (2D)] and 3D pair-correlation functions. The 2D pair-correlation function g(r) revealed hexagonal long-range order of particles in the layers with a lattice constant of 620 nm. The analysis of stacking sequence of layers recorded on as-prepared sample has revealed the existence of stacking disorder with an average stacking probability alpha approximately 0.42. This value of alpha together with the analysis of 3D pair-correlation function determined from particle positions revealed the structure of microgel crystals in the as-prepared sample to be random hexagonal close packing. We report the first observation of a split second peak in the 3D g(r) of the microgel crystals obtained from a shear melted liquid. Upon melting the sample above VPT and recrystallizing it the split second peak disappeared and the crystals are found to have a face centered cubic (fcc) structure with alpha approximately 0.95. From simulations, the split second peak is shown to arise from the displacement of some of the B-planes from the ideal hcp positions. The present results are discussed in

  7. Toward structure prediction of cyclic peptides.

    PubMed

    Yu, Hongtao; Lin, Yu-Shan

    2015-02-14

    Cyclic peptides are a promising class of molecules that can be used to target specific protein-protein interactions. A computational method to accurately predict their structures would substantially advance the development of cyclic peptides as modulators of protein-protein interactions. Here, we develop a computational method that integrates bias-exchange metadynamics simulations, a Boltzmann reweighting scheme, dihedral principal component analysis and a modified density peak-based cluster analysis to provide a converged structural description for cyclic peptides. Using this method, we evaluate the performance of a number of popular protein force fields on a model cyclic peptide. All the tested force fields seem to over-stabilize the α-helix and PPII/β regions in the Ramachandran plot, commonly populated by linear peptides and proteins. Our findings suggest that re-parameterization of a force field that well describes the full Ramachandran plot is necessary to accurately model cyclic peptides.

  8. Predicting road accidents: Structural time series approach

    NASA Astrophysics Data System (ADS)

    Junus, Noor Wahida Md; Ismail, Mohd Tahir

    2014-07-01

    In this paper, the model for occurrence of road accidents in Malaysia between the years of 1970 to 2010 was developed and throughout this model the number of road accidents have been predicted by using the structural time series approach. The models are developed by using stepwise method and the residual of each step has been analyzed. The accuracy of the model is analyzed by using the mean absolute percentage error (MAPE) and the best model is chosen based on the smallest Akaike information criterion (AIC) value. A structural time series approach found that local linear trend model is the best model to represent the road accidents. This model allows level and slope component to be varied over time. In addition, this approach also provides useful information on improving the conventional time series method.

  9. Structural engineering of three-dimensional phononic crystals

    NASA Astrophysics Data System (ADS)

    Delpero, Tommaso; Schoenwald, Stefan; Zemp, Armin; Bergamini, Andrea

    2016-02-01

    Artificially-structured materials are attracting the research interest of a growing community of scientists for the possibility to develop novel materials with advantageous properties that arise from the ability to tailor the propagation of elastic waves, and thus energy, through them. In this work, we propose a three-dimensional phononic crystal whose unit cell has been engineered to obtain a strong wave-attenuation band in the middle of the acoustic frequency range. The combination of its acoustic properties with the dimensions of the unit cell and its static mechanical properties makes it an interesting material for possibly several applications in civil and mechanical engineering, for instance as the core of an acoustically insulating sandwich panel. A sample of this crystal has been manufactured and experimentally tested with respect to its acoustic transmissibility. The performance of the phononic crystal core is remarkable both in terms of amplitude reduction in the transmissibility and width of the attenuation band. A parametric study has been finally conducted on selected geometrical parameters of the unit cell and on their effect on the macroscopic properties of the crystal. This work represents an application-oriented example of how the macroscopic properties of an artificially-structured material can be designed, according to specific needs, by a conventional engineering of its unit cell.

  10. Synthetic antibodies for specific recognition and crystallization of structured RNA

    PubMed Central

    Ye, Jing-Dong; Tereshko, Valentina; Frederiksen, John K.; Koide, Akiko; Fellouse, Frederic A.; Sidhu, Sachdev S.; Koide, Shohei; Kossiakoff, Anthony A.; Piccirilli, Joseph A.

    2008-01-01

    Antibodies that bind protein antigens are indispensable in biochemical research and modern medicine. However, knowledge of RNA-binding antibodies and their application in the ever-growing RNA field is lacking. Here we have developed a robust approach using a synthetic phage-display library to select specific antigen-binding fragments (Fabs) targeting a large functional RNA. We have solved the crystal structure of the first Fab–RNA complex at 1.95 Å. Capability in phasing and crystal contact formation suggests that the Fab provides a potentially valuable crystal chaperone for RNA. The crystal structure reveals that the Fab achieves specific RNA binding on a shallow surface with complementarity-determining region (CDR) sequence diversity, length variability, and main-chain conformational plasticity. The Fab–RNA interface also differs significantly from Fab–protein interfaces in amino acid composition and light-chain participation. These findings yield valuable insights for engineering of Fabs as RNA-binding modules and facilitate further development of Fabs as possible therapeutic drugs and biochemical tools to explore RNA biology. PMID:18162543

  11. One dimensional coordination polymers: Synthesis, crystal structures and spectroscopic properties

    NASA Astrophysics Data System (ADS)

    Karaağaç, Dursun; Kürkçüoğlu, Güneş Süheyla; Şenyel, Mustafa; Şahin, Onur

    2016-11-01

    Two new one dimensional (1D) cyanide complexes, namely [M(4-aepy)2(H2O)2][Pt(CN)4], (4-aepy = 4-(2-aminoethyl)pyridine M = Cu(II) (1) or Zn(II) (2)), have been synthesized and characterized by vibrational (FT-IR and Raman) spectroscopy, single crystal X-ray diffraction, thermal and elemental analyses techniques. The crystallographic analyses reveal that 1 and 2 are isomorphous and isostructural, and crystallize in the monoclinic system and C2 space group. The Pt(II) ions are coordinated by four cyanide-carbon atoms in the square-planar geometry and the [Pt(CN)4]2- ions act as a counter ion. The M(II) ions display an N4O2 coordination sphere with a distorted octahedral geometry, the nitrogen donors belonging to four molecules of the organic 4-aepy that act as unidentate ligands and two oxygen atoms from aqua ligands. The crystal structures of 1 and 2 are similar each other and linked via intermolecular hydrogen bonding, Pt⋯π interactions to form 3D supramolecular network. Vibration assignments of all the observed bands are given and the spectral features also supported to the crystal structures of the complexes.

  12. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-06-28

    Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 {angstrom} resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  13. Crystal structure of four-stranded Oxytricha telomeric DNA

    NASA Technical Reports Server (NTRS)

    Kang, C.; Zhang, X.; Ratliff, R.; Moyzis, R.; Rich, A.

    1992-01-01

    The sequence d(GGGGTTTTGGGG) from the 3' overhang of the Oxytricha telomere has been crystallized and its three-dimensional structure solved to 2.5 A resolution. The oligonucleotide forms hairpins, two of which join to make a four-stranded helical structure with the loops containing four thymine residues at either end. The guanine residues are held together by cyclic hydrogen bonding and an ion is located in the centre. The four guanine residues in each segment have a glycosyl conformation that alternates between anti and syn. There are two four-stranded molecules in the asymmetric unit showing that the structure has some intrinsic flexibility.

  14. Crystal structure and microstructure of cholesteryl oleyl carbonate.

    PubMed

    Das, Pradip; De, Joyes

    2011-01-01

    The crystal structure as well as the microstructure, i.e., size and strain, of crystallites of cholesteryl oleyl carbonate was determined from X-ray powder diffraction data. The X-ray line broadening was analyzed through the refinement of TCH-pseudo-Voigt function parameters (isotropic effects) and the refinement of multipolar functions, i.e., symmetrized cubic harmonics (anisotropic effects). The crystal structure turns out to be primitive monoclinic, space group Pc, type I monolayer having two molecules per unit cell with parameters: a=18.921±0.006Å, b=12.952±0.003Å, c=9.276±0.002Å and β=91.32±0.03°. The average size of a well ground specimen of crystallites was 60nm. The average micro-strain, e.g., 45×10(-4) has been tentatively attributed to fatty chain conformational disorder. The unit cell parameters, including the lamellar thickness, of COC crystal is very closely similar to those of another, structurally similar cholesterol ester, e.g., cholesteryl oleate (CO) crystal, space group P2(1), type II monolayer. Type I monolayer structure has been established for COC on the basis of the intensity calculations of the XRD profiles of both CO and COC. The dipolar and structural disorder in a 4:1 molar, binary mixture of CO and COC can be accommodated in an induced smectic phase with a lamellar thickness, which is nearly equal to that of pure CO or pure COC.

  15. Two crystal structures of the leupeptin-trypsin complex.

    PubMed Central

    Kurinov, I. V.; Harrison, R. W.

    1996-01-01

    Three-dimensional structures of trypsin with the reversible inhibitor leupeptin have been determined in two different crystal forms. The first structure was determined at 1.7 A resolution with R-factor = 17.7% in the trigonal crystal space group P3(1)21, with unit cell dimensions of a = b = 55.62 A, c = 110.51 A. The second structure was determined at a resolution of 1.8 A with R-factor = 17.5% in the orthorhombic space group P2(1)2(1)2(1), with unit cell dimensions of a = 63.69 A, b = 69.37 A, c = 63.01 A. The overall protein structure is very similar in both crystal forms, with RMS difference for main-chain atoms of 0.27 A. The leupeptin backbone forms four hydrogen bonds with trypsin and a fifth hydrogen bond interaction is mediated by a water molecule. The aldehyde carbonyl of leupeptin forms a covalent bond of 1.42 A length with side-chain oxygen of Ser-195 in the active site. The reaction of trypsin with leupeptin proceeds through the formation of stable tetrahedral complex in which the hemiacetal oxygen atom is pointing out of the oxyanion hole and forming a hydrogen bond with His-57. PMID:8845765

  16. Revisiting the crystal structure of rhombohedral lead metaniobate.

    PubMed

    Olsen, Gerhard Henning; Sørby, Magnus Helgerud; Hauback, Bjørn Christian; Selbach, Sverre Magnus; Grande, Tor

    2014-09-15

    Lead metaniobate (PbNb2O6) can exist both as a stable rhombohedral and a metastable orthorhombic tungsten-bronze-type polymorph. Although the orthorhombic is a well-known ferroelectric material, the rhombohedral polymorph has been far less studied. The crystal structure and energetic stability of the stable rhombohedral polymorph of lead metaniobate is re-examined by powder X-ray diffraction and powder neutron diffraction in combination with ab initio calculations. We show that this structure is described by the polar space group R3, in contradiction to the previously reported space group R3m. The crystal structure is unusual, consisting of edge-sharing dimers of NbO(6/2) octahedra forming layers with 6- and 3-fold rings of octahedra and lead ions in channels formed by these rings. The layers are connected by corner-sharing between octahedra. Finally, the crystal structure is discussed in relation to other AB2O6 compounds with B = Nb, Ta.

  17. Structural network efficiency predicts conversion to dementia

    PubMed Central

    Tuladhar, Anil M.; van Uden, Ingeborg W.M.; Rutten-Jacobs, Loes C.A.; Lawrence, Andrew; van der Holst, Helena; van Norden, Anouk; de Laat, Karlijn; van Dijk, Ewoud; Claassen, Jurgen A.H.R.; Kessels, Roy P.C.; Markus, Hugh S.; Norris, David G.

    2016-01-01

    Objective: To examine whether structural network connectivity at baseline predicts incident all-cause dementia in a prospective hospital-based cohort of elderly participants with MRI evidence of small vessel disease (SVD). Methods: A total of 436 participants from the Radboud University Nijmegen Diffusion Tensor and Magnetic Resonance Cohort (RUN DMC), a prospective hospital-based cohort of elderly without dementia with cerebral SVD, were included in 2006. During follow-up (2011–2012), dementia was diagnosed. The structural network was constructed from baseline diffusion tensor imaging followed by deterministic tractography and measures of efficiency using graph theory were calculated. Cox proportional regression analyses were conducted. Results: During 5 years of follow-up, 32 patients developed dementia. MRI markers for SVD were strongly associated with network measures. Patients with dementia showed lower total network strength and global and local efficiency at baseline as compared with the group without dementia. Lower global network efficiency was independently associated with increased risk of incident all-cause dementia (hazard ratio 0.63, 95% confidence interval 0.42–0.96, p = 0.032); in contrast, individual SVD markers including lacunes, white matter hyperintensities volume, and atrophy were not independently associated. Conclusions: These results support a role of network disruption playing a pivotal role in the genesis of dementia in SVD, and suggest network analysis of the connectivity of white matter has potential as a predictive marker in the disease. PMID:26888983

  18. Crystal structure search and electronic properties of alkali-doped phenanthrene and picene

    NASA Astrophysics Data System (ADS)

    Naghavi, S. Shahab; Tosatti, Erio

    2014-08-01

    Alkali-doped aromatic compounds have shown evidence of metallic and superconducting phases whose precise nature is still mysterious. In potassium and rubidium-doped phenanthrene, superconducting temperatures around 5 K have been detected, but such basic elements as the stoichiometry, crystal structure, and electronic bands are still speculative. We seek to predict the crystal structure of M3-phenanthrene (M = K, Rb) using ab initio evolutionary simulation in conjunction with density functional theory (DFT), and find metal but also insulator phases with distinct structures. The original P21 herringbone structure of the pristine molecular crystal is generally abandoned in favor of different packing and chemical motifs. The metallic phases are frankly ionic with three electrons acquired by each molecule. In the nonmagnetic insulating phases the alkalis coalesce reducing the donated charge from three to two per phenanthrene molecule. A similar search for K3-picene yields an old and a new structure, with unlike potassium positions and different electronic bands, but both metallic retaining the face-to-edge herringbone structure and the P21 symmetry of pristine picene. Both the new K3-picene and the best metallic M3-phenanthrene are further found to undergo a spontaneous transition from metal to antiferromagnetic insulator when spin polarization is allowed, a transition which is not necessarily real, but which underlines the necessity to include correlations beyond DFT. Features of the metallic phases that may be relevant to phonon-driven superconductivity are underlined.

  19. Structural phase transitions and topological defects in ion Coulomb crystals

    SciTech Connect

    Partner, Heather L.; Nigmatullin, Ramil; Burgermeister, Tobias; Keller, Jonas; Pyka, Karsten; Plenio, Martin B.; Retzker, Alex; Zurek, Wojciech Hubert; del Campo, Adolfo; Mehlstaubler, Tanja E.

    2014-11-19

    We use laser-cooled ion Coulomb crystals in the well-controlled environment of a harmonic radiofrequency ion trap to investigate phase transitions and defect formation. Topological defects in ion Coulomb crystals (kinks) have been recently proposed for studies of nonlinear physics with solitons and as carriers of quantum information. Defects form when a symmetry breaking phase transition is crossed non-adiabatically. For a second order phase transition, the Kibble-Zurek mechanism predicts that the formation of these defects follows a power law scaling in the rate of the transition. We demonstrate a scaling of defect density and describe kink dynamics and stability. We further discuss the implementation of mass defects and electric fields as first steps toward controlled kink preparation and manipulation.

  20. Electronic structures of doped BaFe2As2 materials: virtual crystal approximation versus super-cell approach

    NASA Astrophysics Data System (ADS)

    Sen, Smritijit; Ghosh, Haranath

    2016-12-01

    Using virtual crystal approximation and super-cell methods for doping, a detailed comparative study of electronic structures of various doped BaFe2As2 materials by first principles simulations is presented. Electronic structures remain unaltered for both the methods in case of passive site doping but in case of active site doping, the electronic structure for virtual crystal approximation method differ from that of the super-cell method specially in the higher doping concentrations. For example, both of these methods give rise to a similar density of states and band structures in case of hole doping (replacing K in place of Ba) and isovalent P doping on As site. But in case of electron doped (Co in place of Fe) systems with higher doping concentration, electronic structures calculated using virtual crystal approximation approach deviates from that of the super-cell method. On the other hand, in case of low isovalent Ru doping at the Fe site implemented by virtual crystal approximation, one acquires an extra shift in the chemical potential in comparison to that for the super-cell method. This shift may be utilized to predict the correct electronic structure as well as the calculated Fermi surfaces within virtual crystal approximation. But for higher Ru (that has different electronic configuration than Fe) doping concentration, simple shifting of chemical potential fails, the calculated electronic structure via virtual crystal approximation approach is very different from that by the super-cell formalism.

  1. Crystal structure of BIS(Betaine) hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Chen, Xiao-Ming; Mak, Thomas C. W.

    1990-11-01

    Bis(betaine) hydrochloride monohydrate, 2Me 3NCH 2COO·HCI·H 2O, crystallizes in space group Pnma (No. 62), with a=11.904(1), b=22.454(5), c=5.624(1) Å, and Z=4. The structure has been refined to RinF=0.046 for 863 observed (| Fo||>6σ| Fo|) Mo Kα data. the carboxylate groups of a pair of betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.454(4) Å. The crystal structure comprises a packing of such [(Me 3NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -·H 2O) ∞ zigzag chains running parallel to the c axis.

  2. Crystal structure of bis(pyridine betaine) hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

    Xiao-Ming, Chen; Mak, Thomas C. W.

    1990-04-01

    Bis(pyridine betaine) hydrochloride monohydrate, 2C 5H 5NCH 2COO·HCl·H 2O, crystallizes in space group Pnna (No. 52), with a=15.623(3), b=19.707(3), c=5.069(1) Å, and Z=4. The structure has been refined to RF=0.067 for 1207 observed (| F0|>6σ| F0|) Mo Kα data. The carboxylate groups of a pair of pyridine betaine molecules are bridged by a proton to form a centrosymmetric dimer featuring a very strong hydrogen bond of length 2.436(6) Å. The crystal structure comprises a packing of such [(C 5H 5NCH 2COO) 2H] + moieties and hydrogen-bonded (Cl -{dH 2O} ∞) zigzag chains running parallel to the c axis.

  3. Crystal structure of N'-hy-droxy-pyrimidine-2-carboximidamide.

    PubMed

    Jasmine, Nithianantham Jeeva; Muthiah, Packianathan Thomas; Stanley, Nithianantham

    2014-10-01

    The title compound, C5H6N4O, is approximately planar, with an angle of 11.04 (15)° between the planes of the pyrimidine ring and the non-H atoms of the carboximidamide unit. The mol-ecule adopts an E configuration about the C=N double bond. In the crystal, adjacent mol-ecules are linked by pairs of N-H⋯O hydrogen bonds, forming inversion dimers with an R 2 (2)(10) ring motif. The dimers are further linked via N-H⋯N and O-H⋯N hydrogen bonds into a sheet structure parallel to the ac plane. The crystal structure also features N-H⋯O and weak C-H⋯O hydrogen bonds and offset π-π stacking inter-actions between adjacent pyrimidine rings [centroid-centroid distance = 3.622 (1) Å].

  4. The crystal structure of ice under mesospheric conditions

    NASA Astrophysics Data System (ADS)

    Murray, Benjamin J.; Malkin, Tamsin L.; Salzmann, Christoph G.

    2015-05-01

    Ice clouds form in the summer high latitude mesopause region, which is the coldest part of the Earth's atmosphere. At these very low temperatures (<150 K) ice can exist in metastable forms, but the nature of these ices remains poorly understood. In this paper we show that ice which is grown at mesospherically relevant temperatures does not have a structure corresponding to the well-known hexagonal form or the metastable cubic form. Instead, the ice which forms under mesospheric conditions is a material in which cubic and hexagonal sequences of ice are randomly arranged to produce stacking disordered ice (ice Isd). The structure of this ice is in the trigonal crystal system, rather than the cubic or hexagonal systems, and is expected to produce crystals with aspect ratios consistent with lidar observations.

  5. Crystal structure of laser-induced subsurface modifications in Si

    SciTech Connect

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; Haberl, B.; Bradby, J. E.; Williams, J. S.; Huis in ’t Veld, A. J.

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystal structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.

  6. Crystal structure of tris-(hydroxyl-ammonium) orthophosphate.

    PubMed

    Leinemann, Malte; Jess, Inke; Boeckmann, Jan; Näther, Christian

    2015-11-01

    The crystal structure of the title salt, ([H3NOH](+))3·[PO4](3-), consists of discrete hydroxyl-ammonium cations and ortho-phos-phate anions. The atoms of the cation occupy general positions, whereas the anion is located on a threefold rotation axis that runs through the phospho-rus atom and one of the phosphate O atoms. In the crystal structure, cations and anions are linked by inter-molecular O-H⋯O and N-H⋯O hydrogen bonds into a three-dimensional network. Altogether, one very strong O-H⋯O, two N-H⋯O hydrogen bonds of medium strength and two weaker bifurcated N-H⋯O inter-actions are observed.

  7. Electronic structure of polymeric KC 60 - a crystal orbital analysis

    NASA Astrophysics Data System (ADS)

    Schulte, Joachim; Böhm, Michael C.

    1996-04-01

    The band structure of orthorhombic KC 60 is investigated by a crystal approach based on an intermediate neglect of differential orbital Hamiltonian. The title compound crystallizes in the space group Pnnm with covalent intermolecular carboncarbon bonds. Polymeric KC 60 is a metal with a low electronic density of states (DOS) at the Fermi energy ɛF. This metallic behaviour differs from the electronic ground state calculated for isotropic fcc KC 60 with potassium occupying the octahedral intersitial site. The reduced width of the conduction band in the fcc structure favours an insulating Mott state relative to the metallic configuration. The dimensionality of the title compound is discussed on the basis of intercell energies, the DOS profile and dispersion curves. The theoretical results are compared with experimental observations. Wiberg bond-indices are employed to describe the chemical bonding within the distorted C 60 soccerball.

  8. Structure development in silicon sheet by shaped crystallization

    NASA Technical Reports Server (NTRS)

    Leipold, M. H.; De Angelis, R. J.

    1978-01-01

    Models are presented for the development of a parallel twinned structure of the 110 plane type and the 112 line type in silicon ribbons. The models are believed to be mutually compatible and operable. The first model relates the requirements for super-cooling during crystallization. The existence of reentrant angles associated with the twin structure is proposed to provide a rough interface to reduce super-cooling. The spacing of the twins is proposed to be limited by the geometrical relationship between the thermal gradient in the liquid and the dimensions of the twinned crystallization front. The second model relates the thermal stress configuration to detail dislocation reactions which would be expected to develop twins. While a specific dislocation mechanism cannot yet be defined, a number of alternatives are presented. All of these various dislocation mechanisms would result in the observed crystalline configuration and the choice among them is not critical.

  9. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

    Kania, Iwona; Stadnicka, Katarzyna; Oleksyn, Barbara J

    2004-03-01

    X-ray crystal structure analysis was performed on single crystals of two diastereomeric enantiopure quinuclidines, (3R,8R)-3-vinyl-8-hydroxymethyl-quinuclidine (quincoridine, QCD) and (3R,8S)-3-vinyl-8-hydroxymethyl-quinuclidine (quincorine, QCI) as their salts with tartaric and p-toluenesulphonate anions, respectively. The molecules of these quinuclidine derivatives are considered here as fragments of the Cinchona alkaloids, quinidine and quinine. A comparison of the conformational features of QCD, QCI, and Cinchona alkaloids in the crystalline state shows that the molecular geometry of the title compounds is similar to that of threo-alkaloids (e.g., R,R isomer of epicinchonine) rather than to quinidine and quinine. The packing of the molecules in both structures is dominated by intermolecular hydrogen bonds.

  10. Engineering crystals by the strategy of molecular tectonics.

    PubMed

    Wuest, James D

    2005-12-21

    Detailed structures of molecular crystals cannot yet be predicted with consistent accuracy, but the strategy of molecular tectonics offers crystal engineers a powerful tool for designing molecules that are predisposed to form crystals with particular structural features and properties.

  11. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

    DOE PAGES

    Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; ...

    2016-04-12

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin filmmore » experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of the metastable material. In addition to reporting on the discovery of the simple binary SnN compound, this study illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.« less

  12. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures.

    PubMed

    Caskey, Christopher M; Holder, Aaron; Shulda, Sarah; Christensen, Steven T; Diercks, David; Schwartz, Craig P; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S; Tumas, William; Perkins, John D; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M; Zakutayev, Andriy

    2016-04-14

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  13. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

    SciTech Connect

    Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

    2016-04-12

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed II/IV valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of the metastable material. In addition to reporting on the discovery of the simple binary SnN compound, this study illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  14. Synthesis of a mixed-valent tin nitride and considerations of its possible crystal structures

    NASA Astrophysics Data System (ADS)

    Caskey, Christopher M.; Holder, Aaron; Shulda, Sarah; Christensen, Steven T.; Diercks, David; Schwartz, Craig P.; Biagioni, David; Nordlund, Dennis; Kukliansky, Alon; Natan, Amir; Prendergast, David; Orvananos, Bernardo; Sun, Wenhao; Zhang, Xiuwen; Ceder, Gerbrand; Ginley, David S.; Tumas, William; Perkins, John D.; Stevanovic, Vladan; Pylypenko, Svitlana; Lany, Stephan; Richards, Ryan M.; Zakutayev, Andriy

    2016-04-01

    Recent advances in theoretical structure prediction methods and high-throughput computational techniques are revolutionizing experimental discovery of the thermodynamically stable inorganic materials. Metastable materials represent a new frontier for these studies, since even simple binary non-ground state compounds of common elements may be awaiting discovery. However, there are significant research challenges related to non-equilibrium thin film synthesis and crystal structure predictions, such as small strained crystals in the experimental samples and energy minimization based theoretical algorithms. Here, we report on experimental synthesis and characterization, as well as theoretical first-principles calculations of a previously unreported mixed-valent binary tin nitride. Thin film experiments indicate that this novel material is N-deficient SnN with tin in the mixed ii/iv valence state and a small low-symmetry unit cell. Theoretical calculations suggest that the most likely crystal structure has the space group 2 (SG2) related to the distorted delafossite (SG166), which is nearly 0.1 eV/atom above the ground state SnN polymorph. This observation is rationalized by the structural similarity of the SnN distorted delafossite to the chemically related Sn3N4 spinel compound, which provides a fresh scientific insight into the reasons for growth of polymorphs of metastable materials. In addition to reporting on the discovery of the simple binary SnN compound, this paper illustrates a possible way of combining a wide range of advanced characterization techniques with the first-principle property calculation methods, to elucidate the most likely crystal structure of the previously unreported metastable materials.

  15. Crystal Structures of Cisplatin Bound to a Human Copper Chaperone

    SciTech Connect

    Boal, Amie K.; Rosenzweig, Amy C.

    2010-08-16

    Copper trafficking proteins, including the chaperone Atox1 and the P{sub 1B}-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.

  16. Woodpulp Crystal Structure and Its Effect on Nitrocellulose Physical Properties

    DTIC Science & Technology

    1980-09-01

    25963. 10 3. A.M. Hindelah and D.J. Johnson, "Crystallinity and Crystallite Size Treatment in Cellulose I Fibres : 1. Ramie and Fortisan," Polymer , Vol...nitrocellulose from N-7 and N-5 is attributed to the presence of Cellulose 11 crystal structure in the fibre . It does not appear to affect the...13, 1972, pp 42330. 4. V.W. Tripp, "Measurement of Crystallinity," High Polymers : Cellulose and Cellulose Derivatives Part IV, Vol V, 1971, Wiley

  17. Phytases: crystal structures, protein engineering and potential biotechnological applications.

    PubMed

    Yao, M-Z; Zhang, Y-H; Lu, W-L; Hu, M-Q; Wang, W; Liang, A-H

    2012-01-01

    Phytases are a group of enzymes capable of releasing phosphates from phytates, one of the major forms of phosphorus (P) in animal feeds of plant origin. These enzymes have been widely used in animal feed to improve phosphorus nutrition and to reduce phosphorus pollution in animal waste. This review covers the basic nomenclature and crystal structures of phytases and emphasizes both the protein engineering strategies used for the development of new, effective phytases with improved properties and the potential biotechnological applications of phytases.

  18. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    SciTech Connect

    Han,Q.; Robinson, H.; Gao, Y.; Vogelaar, N.; Wilson, S.; Rizzi, M.; Li, J.

    2006-01-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  19. Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.

    PubMed

    Han, Qian; Robinson, Howard; Gao, Yi Gui; Vogelaar, Nancy; Wilson, Scott R; Rizzi, Menico; Li, Jianyong

    2006-12-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75A high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1A resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  20. Predicted and experimental structures of integrins and beta-propellers.

    PubMed

    Springer, Timothy A

    2002-12-01

    Integrins and other cell surface receptors have been fertile grounds for structure prediction experiments. Recently determined structures show remarkable successes, especially with beta-propeller domain predictions, and also reveal how ligand binding by integrins is conformationally regulated.

  1. Crystal structure of lead(II) tartrate: a redetermination.

    PubMed

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.

  2. Nanoconfinement-induced structures in chiral liquid crystals.

    PubMed

    Melle, Michael; Theile, Madlona; Hall, Carol K; Schoen, Martin

    2013-08-28

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase.

  3. Pressure effects on crystal and electronic structure of bismuth tellurohalides

    NASA Astrophysics Data System (ADS)

    Rusinov, I. P.; Menshchikova, T. V.; Sklyadneva, I. Yu; Heid, R.; Bohnen, K.-P.; Chulkov, E. V.

    2016-11-01

    We study the possibility of pressure-induced transitions from a normal semiconductor to a topological insulator (TI) in bismuth tellurohalides using density functional theory and tight-binding method. In BiTeI this transition is realized through the formation of an intermediate phase, a Weyl semimetal, that leads to modification of surface state dispersions. In the topologically trivial phase, the surface states exhibit a Bychkov-Rashba type dispersion. The Weyl semimetal phase exists in a narrow pressure interval of 0.2 GPa. After the Weyl semimetal-TI transition occurs, the surface electronic structure is characterized by gapless states with linear dispersion. The peculiarities of the surface states modification under pressure depend on the band-bending effect. We have also calculated the frequencies of Raman active modes for BiTeI in the proposed high-pressure crystal phases in order to compare them with available experimental data. Unlike BiTeI, in BiTeBr and BiTeCl the topological phase transition does not occur. In BiTeBr, the crystal structure changes with pressure but the phase remains a trivial one. However, the transition appears to be possible if the low-pressure crystal structure is retained. In BiTeCl under pressure, the topological phase does not appear up to 18 GPa due to a relatively large band gap width in this compound.

  4. Crystal structure of lead(II) tartrate: a redetermination

    PubMed Central

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ6 O 1,O 3:O 1′:O 2,O 4:O 4′-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▸). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions. PMID:25705458

  5. The crystal structure of aluminum doped {beta}-rhombohedral boron

    SciTech Connect

    Bykova, Elena; Parakhonskiy, Gleb; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-15

    A crystal structure of aluminum doped {beta}-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B{sub 12} icosahedra with voids occupied by the B{sub 28}-B-B{sub 28} units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) A lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the {beta}-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB{sub 44.8(5)} and AlB{sub 37.8(5)}, which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB{sub 44.8(5)} is described in detail. - Graphical abstract: The atomic distribution near the B(15) atom (non-labeled atom in the center of the picture) shown along the c axis. Anisotropic displacement ellipses for Al(2) (D-site) and B(15) are shown with 50 % probability level. The mirror plane with Miller indices (1 1 0) and related to it (-1 2 0) and (-2 1 0) generated by the 3-fold rotation-inversion axis parallel to the c axis splits the position of B(16) over two sites. Highlights: Black-Right-Pointing-Pointer The crystal structure of the AlB{sub 44.8(5)} has been refined. Black-Right-Pointing-Pointer Aluminum atoms partially fill certain types of voids (the A1- and D-sites). Black-Right-Pointing-Pointer We have got two possible models of atomic distribution near the D-site.

  6. Evaluation, analysis and prediction of geologic structures

    NASA Astrophysics Data System (ADS)

    Woodward, Nicholas B.

    2012-08-01

    Balanced cross-sections claim to be better because they apply a rigorous set of rules to develop the conceptual model of the structures present in an area. Balanced cross-sections can be further improved and become more useful to understanding real physical problems by collection of additional data such as seismic reflection surveys, collection of additional stratigraphic data, or collection of rock fabric information. The additional information validates the initial model and provides details on deformation conditions and on local rock responses to the deformation. Although individual cross-sections are two dimensional, the objective of evaluation and analysis of deformed regions should be three dimensional whenever possible to recognize the challenges of the real world. Subsurface system analysis derived from the hydrologic community emphasizes conceptual model development through model verification, validation, uncertainty quantification, benchmarking and meta-analysis. Their approach includes many steps informally used by the structural geology community but in a much more explicit way. Newer geological applications of structural geology would benefit from this more rigorous approach for designing and doing performance predictions as technological needs become more socially sensitive such as for carbon storage sites, new areas of energy exploration in higher population density areas, or for nuclear waste storage facilities.

  7. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

  8. The first crystal structure of an archaeal helical repeat protein

    SciTech Connect

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-07-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The structure of ST1625p consists of a unique superhelix with a low-level structure resemblance to doamins from other proteins with known three-dimensional structures. The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.

  9. Ab initio Study of Structure and Hydrogen Bonding of Cellulose Crystals and Surfaces

    NASA Astrophysics Data System (ADS)

    Davenport, James; Li, Yan

    2011-03-01

    We have studied the equilibrium structure and hydrogen bonding of cellulose crystals and surfaces using semi-empirical dispersion corrections to density functional theory (DFT+D), which has been shown to be an efficient alternative to more advanced methods for weakly bound aromatic assemblies. The predicted crystal structures for both Iα and Iβ phases agree well with experiments. The cohesive energy was decomposed into interchain and intersheet interactions and analyzed in terms of hydrogen bonding and van der Waals dispersion forces. Both interactions were found to be responsible for holding cellulose sheets together. In particular, the dispersion corrections to DFT proved to be indispensable in reproducing the equilibrium intersheet distance and binding strength. Adsorption energy and configuration of water molecules on cellulose surfaces were found to depend sensitively on the surface orientation, adsorption site and contribution from vdW interactions. This work was funded by US Department of Energy under Contract No. DE-AC02-98CH10886.

  10. Crystal structure of inactive form of Rab3B

    SciTech Connect

    Zhang, Wei; Shen, Yang; Jiao, Ronghong; Liu, Yanli; Deng, Lingfu; Qi, Chao

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer This is the first structural information of human Rab3B. Black-Right-Pointing-Pointer To provides a structural basis for the GDP/GTP switch in controlling the activity of Rab3. Black-Right-Pointing-Pointer The charge distribution of Rab3B indicates its unique roles in vesicular trafficking. -- Abstract: Rab proteins are the largest family of ras-related GTPases in eukaryotic cells. They act as directional molecular switches at membrane trafficking, including vesicle budding, cargo sorting, transport, tethering, and fusion. Here, we generated and crystallized the Rab3B:GDP complex. The structure of the complex was solved to 1.9 A resolution and the structural base comparison with other Rab3 members provides a structural basis for the GDP/GTP switch in controlling the activity of small GTPase. The comparison of charge distribution among the members of Rab3 also indicates their different roles in vesicular trafficking.

  11. Gyroid cuticular structures in butterfly wing scales: biological photonic crystals.

    PubMed

    Michielsen, K; Stavenga, D G

    2008-01-06

    We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling fractions and lattice parameters. We give a brief discussion of the formation of cubic gyroid membranes from the smooth endoplasmic reticulum in the scale's cell, which dry and harden to leave the cuticular structure behind when the cell dies. The scales of C. rubi are a potentially attractive biotemplate for producing three-dimensional optical photonic crystals since for these scales the cuticle-filling fraction is nearly optimal for obtaining the largest photonic band gap in a gyroid structure.

  12. Blind protein structure prediction using accelerated free-energy simulations

    PubMed Central

    Perez, Alberto; Morrone, Joseph A.; Brini, Emiliano; MacCallum, Justin L.; Dill, Ken A.

    2016-01-01

    We report a key proof of principle of a new acceleration method [Modeling Employing Limited Data (MELD)] for predicting protein structures by molecular dynamics simulation. It shows that such Boltzmann-satisfying techniques are now sufficiently fast and accurate to predict native protein structures in a limited test within the Critical Assessment of Structure Prediction (CASP) community-wide blind competition. PMID:27847872

  13. Optimizing nondecomposable loss functions in structured prediction.

    PubMed

    Ranjbar, Mani; Lan, Tian; Wang, Yang; Robinovitch, Steven N; Li, Ze-Nian; Mori, Greg

    2013-04-01

    We develop an algorithm for structured prediction with nondecomposable performance measures. The algorithm learns parameters of Markov Random Fields (MRFs) and can be applied to multivariate performance measures. Examples include performance measures such as Fβ score (natural language processing), intersection over union (object category segmentation), Precision/Recall at k (search engines), and ROC area (binary classifiers). We attack this optimization problem by approximating the loss function with a piecewise linear function. The loss augmented inference forms a Quadratic Program (QP), which we solve using LP relaxation. We apply this approach to two tasks: object class-specific segmentation and human action retrieval from videos. We show significant improvement over baseline approaches that either use simple loss functions or simple scoring functions on the PASCAL VOC and H3D Segmentation datasets, and a nursing home action recognition dataset.

  14. Predicting missing links via structural similarity

    NASA Astrophysics Data System (ADS)

    Lyu, Guo-Dong; Fan, Chang-Jun; Yu, Lian-Fei; Xiu, Bao-Xin; Zhang, Wei-Ming

    2015-04-01

    Predicting missing links in networks plays a significant role in modern science. On the basis of structural similarity, our paper proposes a new node-similarity-based measure called biased resource allocation (BRA), which is motivated by the resource allocation (RA) measure. Comparisons between BRA and nine well-known node-similarity-based measures on five real networks indicate that BRA performs no worse than RA, which was the best node-similarity-based index in previous researches. Afterwards, based on localPath (LP) and Katz measure, we propose another two improved measures, named Im-LocalPath and Im-Katz respectively. Numerical results show that the prediction accuracy of both Im-LP and Im-Katz measure improve compared with the original LP and Katz measure. Finally, a new path-similarity-based measure and its improved measure, called LYU and Im-LYU measure, are proposed and especially, Im-LYU measure is shown to perform more remarkably than other mentioned measures.

  15. Fusion proteins as alternate crystallization paths to difficult structure problems

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  16. Anisotropy and Crystal Structure of the Cocos Plate,

    DTIC Science & Technology

    1973-08-08

    A0785 066 SCRIPPS INSTITUTION OF OCEANOGRAPHY LA JOLLA CA MAR-’ETC F/B 8/10 ANISOTROPY AND CRYSTAL STRUCTURE OF THE COCOS PLATE. (U) U NL AUG 73 6 6...514R. R W RAITT, M HENRYWiCLASSIFIED IGL-U39/73 N -EtohEEE END cIc - .,MPL-U-39/73 ISOTOPYAND CRUSTAL STRUCTURE OFTHE COCOS PLATE* George G. Shor, Jr...of Geophysics, 2525 Correa Road, Honolulu, Hawaii 96822. D P3 -e C7Bl 5 p. 71 R6 P.~- ABSTRACT ~,e~/ L Seismic studies in two locations on the Cocos

  17. Band structures in the nematic elastomers phononic crystals

    NASA Astrophysics Data System (ADS)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-02-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  18. Crystal structure of new AsS{sub 2} compound

    SciTech Connect

    Bolotina, N. B.; Brazhkin, V. V.; Dyuzheva, T. I.; Lityagina, L. M.; Kulikova, L. F.; Nikolaev, N. A.; Verin, I. A.

    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.

  19. Ice crystallization in ultrafine water-salt aerosols: nucleation, ice-solution equilibrium, and internal structure.

    PubMed

    Hudait, Arpa; Molinero, Valeria

    2014-06-04

    Atmospheric aerosols have a strong influence on Earth's climate. Elucidating the physical state and internal structure of atmospheric aqueous aerosols is essential to predict their gas and water uptake, and the locus and rate of atmospherically important heterogeneous reactions. Ultrafine aerosols with sizes between 3 and 15 nm have been detected in large numbers in the troposphere and tropopause. Nanoscopic aerosols arising from bubble bursting of natural and artificial seawater have been identified in laboratory and field experiments. The internal structure and phase state of these aerosols, however, cannot yet be determined in experiments. Here we use molecular simulations to investigate the phase behavior and internal structure of liquid, vitrified, and crystallized water-salt ultrafine aerosols with radii from 2.5 to 9.5 nm and with up to 10% moles of ions. We find that both ice crystallization and vitrification of the nanodroplets lead to demixing of pure water from the solutions. Vitrification of aqueous nanodroplets yields nanodomains of pure low-density amorphous ice in coexistence with vitrified solute rich aqueous glass. The melting temperature of ice in the aerosols decreases monotonically with an increase of solute fraction and decrease of radius. The simulations reveal that nucleation of ice occurs homogeneously at the subsurface of the water-salt nanoparticles. Subsequent ice growth yields phase-segregated, internally mixed, aerosols with two phases in equilibrium: a concentrated water-salt amorphous mixture and a spherical cap-like ice nanophase. The surface of the crystallized aerosols is heterogeneous, with ice and solution exposed to the vapor. Free energy calculations indicate that as the concentration of salt in the particles, the advance of the crystallization, or the size of the particles increase, the stability of the spherical cap structure increases with respect to the alternative structure in which a core of ice is fully surrounded by

  20. Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

    USGS Publications Warehouse

    Konnert, J.A.; Evans, H.T.

    1987-01-01

    The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

  1. Manganese oxide minerals: Crystal structures and economic and environmental significance

    PubMed Central

    Post, Jeffrey E.

    1999-01-01

    Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry. PMID:10097056

  2. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

  3. Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

    PubMed

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  4. Antibody structure determination using a combination of homology modeling, energy-based refinement, and loop prediction.

    PubMed

    Zhu, Kai; Day, Tyler; Warshaviak, Dora; Murrett, Colleen; Friesner, Richard; Pearlman, David

    2014-08-01

    We present the blinded prediction results in the Second Antibody Modeling Assessment (AMA-II) using a fully automatic antibody structure prediction method implemented in the programs BioLuminate and Prime. We have developed a novel knowledge based approach to model the CDR loops, using a combination of sequence similarity, geometry matching, and the clustering of database structures. The homology models are further optimized with a physics-based energy function (VSGB2.0), which improves the model quality significantly. H3 loop modeling remains the most challenging task. Our ab initio loop prediction performs well for the H3 loop in the crystal structure context, and allows improved results when refining the H3 loops in the context of homology models. For the 10 human and mouse derived antibodies in this assessment, the average RMSDs for the homology model Fv and framework regions are 1.19 Å and 0.74 Å, respectively. The average RMSDs for five non-H3 CDR loops range from 0.61 Å to 1.05 Å, and the H3 loop average RMSD is 2.91 Å using our knowledge-based loop prediction approach. The ab initio H3 loop predictions yield an average RMSD of 1.28 Å when performed in the context of the crystal structure and 2.67 Å in the context of the homology modeled structure. Notably, our method for predicting the H3 loop in the crystal structure environment ranked first among the seven participating groups in AMA-II, and our method made the best prediction among all participants for seven of the ten targets.

  5. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction†

    PubMed Central

    Héroux, Annie; Bozinovski, Dragana M.; Valley, Michael P.; Fitzpatrick, Paul F.; Orville, Allen M.

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 Å resolution or better are described of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct. The D402N enzyme has no detectable activity with neutral nitroalkanes (Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 23, 8738–8739). The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2’-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062–2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2’-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle. PMID:19265437

  6. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  7. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes.

    PubMed

    Goldenberg, Barbara L; Young, Victor G; Barany, George

    2015-10-01

    The present paper reports crystallographic studies on three related compounds that were of inter-est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro-gen-protecting groups: (N-methyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (3). Their mol-ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol-ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [110], which are linked by short Cl⋯Cl and S⋯O contacts forming sheets parallel to (001). In the crystal of (2), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O⋯Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking.

  8. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain

  9. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    NASA Astrophysics Data System (ADS)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

  10. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  11. Crystal structure of 1-methylimidazole 3-oxide monohydrate

    PubMed Central

    Frampton, Christopher S.; Murray, James I.; Spivey, Alan C.

    2017-01-01

    1-Methylimidazole 3-N-oxide (NMI-O) crystallizes as a monohydrate, C4H6N2O·H2O, in the monoclinic space group P21 with Z′ = 2 (mol­ecules A and B). The imidazole rings display a planar geometry (r.m.s. deviations = 0.0008 and 0.0002 Å) and are linked in the crystal structure into infinite zigzag strands of ⋯NMI-O(A)⋯OH2⋯NMI-O(B)⋯OH2⋯ units by O—H⋯O hydrogen bonds. These chains propagate along the b-axis direction of the unit cell. PMID:28316812

  12. Crystal structure and magnetism of UOsAl

    NASA Astrophysics Data System (ADS)

    Andreev, A. V.; Daniš, S.; Šebek, J.; Henriques, M. S.; Vejpravová, J.; Gorbunov, D. I.; Havela, L.

    2017-04-01

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn2 type, space group P63/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10-8 m3 mol-1 (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol-1 K-2.

  13. Faceting and commensurability in crystal structures of colloidal thin films.

    PubMed

    Ramiro-Manzano, F; Meseguer, F; Bonet, E; Rodriguez, I

    2006-07-14

    This Letter investigates the influence of finite size effects on the particle arrangement of thin film colloidal crystals. A rich variety of crystallographic faceting with large single domain microcrystallites is shown. Optical reflectance experiments together with scanning electron microscopy permit the identification of the crystal symmetry and the facet orientation, as well as the exact number of monolayers. When the cell thickness is not commensurable with a high symmetry layering, particles arrange themselves in a periodic distribution of (111)- and (100)-orientated face centered cubic (fcc) microcrystallites separated by planar defects. These structures can be described as a fcc ordering orientated along a vicinal surface, modified by a periodic distribution of fcc (111) stacking faults.

  14. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    PubMed

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

  15. Protein dynamics derived from clusters of crystal structures.

    PubMed Central

    van Aalten, D M; Conn, D A; de Groot, B L; Berendsen, H J; Findlay, J B; Amadei, A

    1997-01-01

    A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins. Images FIGURE 1 PMID:9414203

  16. The crystal structure of Sr(OD) 2

    NASA Astrophysics Data System (ADS)

    Partin, D. E.; O'Keeffe, M.

    1995-10-01

    The crystal structure of Sr(OD) 2 has been determined from a Reitveld refinement of time-of-flight neutron diffraction data, and the deuterium atom positions have been determined for the first time. The structure is orthorhombic: Pnma, a = 9.8269(5) Å, b = 3.9051(2) Å, c = 6.0733(3) Å, V = 233.06 Å 3, D x = 3.466 g cm -3, Rwp = 3.93%, Rp = 2.95%, reduced X2 = 4.774 for 81 variables. Although the data were collected at 12 K, the H atoms have large thermal parameters suggesting the possibility of some disorder. Relationships of the structure to the structures of YOOH, SrBr 2, SrI 2, and SrBr 2 · H 2O are discussed.

  17. Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii

    SciTech Connect

    Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J

    2010-01-01

    Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

  18. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    NASA Astrophysics Data System (ADS)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

  19. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    SciTech Connect

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H.

    2012-03-13

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

  20. Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate

    SciTech Connect

    Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso

    2010-03-05

    Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

  1. The crystal structure of superoxide dismutase from Plasmodium falciparum

    PubMed Central

    Boucher, Ian W; Brzozowski, Andrzej M; Brannigan, James A; Schnick, Claudia; Smith, Derek J; Kyes, Sue A; Wilkinson, Anthony J

    2006-01-01

    Background Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. Results The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 Å resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. Conclusion The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors. PMID:17020617

  2. Diterbium hepta­nickel: a crystal structure redetermination

    PubMed Central

    Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

    2014-01-01

    The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280–1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419–428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962 (4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an inter­growth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper icosa­hedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871

  3. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    SciTech Connect

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  4. Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis

    PubMed Central

    Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu

    2014-01-01

    Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964

  5. Lithium-cation conductivity and crystal structure of lithium diphosphate

    SciTech Connect

    Voronin, V.I.; Sherstobitova, E.A.; Blatov, V.A.; Shekhtman, G.Sh.

    2014-03-15

    The electrical conductivity of lithium diphosphate Li{sub 4}P{sub 2}O{sub 7} has been measured and jump-like increasing of ionic conductivity at 913 K has been found. The crystal structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction at 300–1050 K. At 913 K low temperature triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one, space group P2{sub 1}/n, a=8.8261(4) Å, b=5.2028(4) Å, c=13.3119(2) Å, β=104.372(6)°. The migration maps of Li{sup +} cations based on experimental data implemented into program package TOPOS have been explored. It was found that lithium cations in both low- and high temperature forms of Li{sub 4}P{sub 2}O{sub 7} migrate in three dimensions. Cross sections of the migrations channels extend as the temperature rises, but at the phase transition point have a sharp growth showing a strong “crystal structure – ion conductivity” correlation. -- Graphical abstract: Crystal structure of Li{sub 4}P{sub 2}O{sub 7} at 950 K. Red balls represent oxygen atoms; black lines show Li{sup +} ion migration channels in the layers perpendicular to [001] direction. Highlights: • Structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction. • At 913 K triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one. • The migration maps of Li{sup +} implemented into program package TOPOS have been explored. • Cross sections of the migrations channels at the phase transition have a sharp growth.

  6. Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52.

    PubMed

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

    The recently elucidated crystal structure of the technologically important amalgam Na11Hg52 is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice-sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general.

  7. Crystallization, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    DTIC Science & Technology

    1998-07-01

    COOPERATIVE AGREEMENT NUMBER DAMD17-95-2-5007 TITLE: Crystallization, X-ray Structure Determination and Structure-Based Drug Design for...approach for the develpment of anti-malarial agent using structure-based drug design . This technique will enable us to identify active site inhibitors...based drug design project high resolution three domensional structure of the enzyme - inhibitor complex provides the basis for further modifications

  8. Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2000-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enable the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable condensed phase fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new liquid crystal physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and

  9. Ab initio structure prediction of the antibody hypervariable H3 loop.

    PubMed

    Zhu, Kai; Day, Tyler

    2013-06-01

    Antibodies have the capability of binding a wide range of antigens due to the diversity of the six loops constituting the complementarity determining region (CDR). Among the six loops, the H3 loop is the most diverse in structure, length, and sequence identity. Prediction of the three-dimensional structures of antibodies, especially the CDR loops, is an important step in the computational design and engineering of novel antibodies for improved affinity and specificity. Although it has been demonstrated that the conformation of the five non-H3 loops can be accurately predicted by comparing their sequences against databases of canonical loop conformations, no such connection has been established for H3 loops. In this work, we present the results for ab initio structure prediction of the H3 loop using conformational sampling and energy calculations with the program Prime on a dataset of 53 loops ranging in length from 4 to 22 residues. When the prediction is performed in the crystal environment and including symmetry mates, the median backbone root mean square deviation (RMSD) is 0.5 Å to the crystal structure, with 91% of cases having an RMSD of less than 2.0 Å. When the prediction is performed in a noncrystallographic environment, where the scaffold is constructed by swapping the H3 loops between homologous antibodies, 70% of cases have an RMSD below 2.0 Å. These results show promise for ab initio loop predictions applied to modeling of antibodies.

  10. Unusual formation of single-crystal manganese sulfide microboxes co-mediated by the cubic crystal structure and shape.

    PubMed

    Zhang, Lei; Zhou, Liang; Wu, Hao Bin; Xu, Rong; Lou, Xiong Wen David

    2012-07-16

    Kept cubic: MnS microboxes, which act as an anode material for lithium ion batteries, are synthesized by a simple H(2)S gas sulfidation approach (TEM images show porous and hollow microcubes and a microbox). The formation of the single crystals is aided by the intrinsic cubic crystal structure and the nearly cubic shape of the MnCO(3) precursor.

  11. Crystal Structure of the Human Ephrin-A5 Ectodomain

    SciTech Connect

    Nikolov,D.; Li, C.; Lackmann, M.; Jeffrey, P.; Himanen, J.

    2007-01-01

    The Eph receptors, the largest subfamily of receptor tyrosine kinases, and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, pathfinding, and mobility in the nervous and cardiovascular systems. Recent structural studies have revealed unique molecular features that explain many of the biochemical and signaling properties of Ephs and ephrins. Nevertheless, open questions remain, including understanding the precise molecular mechanism underlining their binding-partner preferences and subclass specificity. In this study, we have determined and present the crystal structure of the extracellular domain of ephrin-A5--the first structure of an unbound A-class ephrin. The structure, determined at 2.1 Angstroms resolution, is a variation of the Greek key {beta}-barrel folding topology, containing eight {beta}-strands, and stabilized by two disulphide bonds. Overall, ephrin-A5 is structurally very similar to ephrin-B1 and ephrin-B2 but, unlike ephrin-B2, it does not show dimerization either in solution or in the crystals. Comparing free ephrin-A5 to the previously published structure of EphB2-bound ephrin-A5 reveals that significant conformational changes occur only around the G-H ephrin loop that upon binding bends toward the receptor. Interestingly, the G-H loop undergoes a very similar conformational rearrangement in ephrin-B2 upon receptor binding. The results of this study further emphasize the importance of the G-H loop for receptor recognition and selectivity, and could serve as a starting point for the development of structure-based Eph antagonists.

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

    ERIC Educational Resources Information Center

    Bindel, Thomas H.

    2008-01-01

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

  13. Supressed Water Crystallization in Nano-Structured Physical Hydrogel

    NASA Astrophysics Data System (ADS)

    Wiener, Clinton; Vogt, Bryan; Weiss, Robert

    2015-03-01

    Suppressed water crystallization occurs in some organisms, such as the common wood frog, which allows it to hibernate in a frozen state without damage to its cells. Knowledge of the behavior of supercooled water and alternate ice forms may have many implications to many fields of science. Supercooling of water by several degrees below the normal freezing point is often observed in hydrogels that have attractive interactions with water, e.g., hydrogen bonding. Repulsive confinement, such as in hydrophobic porous carbon, can have even more significant effects on the supercooling of the entrapped water. This talk describes the freezing behavior in nano-structured, hydrophobically modified poly(dimethyl acrylamide) hydrogels that possess attractive and repulsive interactions with water and are physically crosslinked by hydrophobic nanodomains. Three distinct water freezing regimes were observed in the hydrogel swollen to about 50% water by weight. Differential scanning calorimetry detected three crystallization exotherms at 254K, 244K, and 227K. Quasi-elastic neutron scattering experiments have shown that although the water mobility was suppressed at room temperature, the water remained significantly mobile below the normal freezing point of water. The talk will discuss how tuning the concentration of the hydrophobic composition of the hydrogel affects the porous length scales in the hydrogel, which may alter the state of water and the crystal form produced by supercooling.

  14. Crystal structure and vibrational spectra of betaine hydrogen selenate monohydrate

    NASA Astrophysics Data System (ADS)

    Baran, J.; Drozd, M.; Lis, T.; Śledź, M.; Barnes, A. J.; Ratajczak, H.

    1995-11-01

    The crystal structure of betaine hydrogen selenate monohydrate, (C 5H 12NO 2) +·(HSeO 4) -·(H 2O), BHSeH 2O, has been determined by X-ray diffraction as monoclinic, space group {P2 1}/{c} with a = 6.674(6), b = 11.912(9), c = 14.156(14) A, β = 100.61(4)° and Z = 4. It comprises protonated betaine moieties (betainium cations), hydrogen selenate anions and water molecules which are held together by a number of hydrogen bonds and form infinite chains. Two types of four-membered centrosymmetric rings are distinguished in the chain. The two rings share a common side. Powder FT-IR and FT-Raman spectra were measured for the title crystal, the dehydrated crystal (betaine hydrogen selenate, BHSe) and their deuterated analogues. Assignments of the observed bands to vibrations of the hydrogen bonds and internal vibrations of the hydrogen selenate anions and the betainium cations are proposed. DSC data are also presented.

  15. Natural pseudowollastonite: Crystal structure, associated minerals, and geological context

    NASA Astrophysics Data System (ADS)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.

    2012-03-01

    Pseudowollastonite, an extremely rare constituent of ultrahigh-temperature combustion metamorphic and igneous rocks, has been found as a rock-forming mineral in Ca-rich paralava veins of Nabi Musa fossil mud volcano (Dead Sea area). Pseudowollastonite-bearing paralavas are the products of combustion metamorphism associated with spontaneous burning of methane. The melt began to crystallize at 1480-1500 °C about the ambient pressure. Pseudowollastonite enters two mineral assemblages: (1) rankinite, larnite, nagelschmidtite, wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, cuspidine, and fluorapatite; (2) parawollastonite (2M), wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, fluorellestadite. In this study we present the first single-crystal structure determination of natural pseudowollastonite. Pseudowollastonite from Nabi Musa dome is stoichiometric CaSiO3 and belongs to the most widespread four-layer polytype: a = 6.83556(10) Å, b = 11.86962(18) Å, c = 19.6255(3) Å, β = 90.6805(13)°, V = 1592.21(4) Å3, space group C2/c. We argue that pseudowollastonite is so scarce in nature because its formation requires joint action of several uncommon factors: availability of hot melts of T > 1200 °C that bear free calcium but are poor in Mg and Fe (mostly as Fe3 +) and their crystallization in the shallow crust followed by quenching.

  16. Phase-field-crystal methodology for modeling of structural transformations.

    PubMed

    Greenwood, Michael; Rottler, Jörg; Provatas, Nikolas

    2011-03-01

    We introduce and characterize free-energy functionals for modeling of solids with different crystallographic symmetries within the phase-field-crystal methodology. The excess free energy responsible for the emergence of periodic phases is inspired by classical density-functional theory, but uses only a minimal description for the modes of the direct correlation function to preserve computational efficiency. We provide a detailed prescription for controlling the crystal structure and introduce parameters for changing temperature and surface energies, so that phase transformations between body-centered-cubic (bcc), face-centered-cubic (fcc), hexagonal-close-packed (hcp), and simple-cubic (sc) lattices can be studied. To illustrate the versatility of our free-energy functional, we compute the phase diagram for fcc-bcc-liquid coexistence in the temperature-density plane. We also demonstrate that our model can be extended to include hcp symmetry by dynamically simulating hcp-liquid coexistence from a seeded crystal nucleus. We further quantify the dependence of the elastic constants on the model control parameters in two and three dimensions, showing how the degree of elastic anisotropy can be tuned from the shape of the direct correlation functions.

  17. Crystal structure and spectroscopic investigations of an organic monophosphate

    SciTech Connect

    Dhaouadi, H.; Marouani, H. Rzaigui, M.; Madani, A.

    2008-12-01

    Single crystals of (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} are synthesized in water by interaction of H{sub 3}PO{sub 4} and (p-ClC{sub 6}H{sub 4}NH{sub 2}). This compound crystallizes in the orthorhombic system with the Pbca space group. Its unit-cell parameters are a = 9.724(3), b = 7.861(1), c = 25.078(6) A, V = 1917.1(6) A{sup 3} and Z = 8. The crystal structure has been solved and refined to R = 0.039, using 4298 independent reflections. The atomic arrangement can be described by inorganic layers parallel to ab plane, between which the organic cations are located. This compound exhibits a reversible phase transition at 403 K. The electrical conductivity measurements show that the (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} has a conductivity value which goes from {sigma} = 0.88 x 10{sup -6} {omega}{sup -1} cm{sup -1} at room temperature (293 K) to 3.31 x 10{sup -4} {omega}{sup -1} cm{sup -1} at 433 K. Its characterisation by TA, NMR and IR is reported too.

  18. Germanium FCC structure from a colloidal crystal template

    SciTech Connect

    Miguez, H.; Meseguer, F.; Lopez, C.; Holgado, M.; Andreasen, G.; Mifsud, A.; Fornes, V.

    2000-05-16

    Here, the authors show a method to fabricate a macroporous structure in which the pores, essentially identical, arrange regularly in a face-centered cubic (FCC) lattice. The result is a network of air spheres in a germanium medium. This structure presents the highest dielectric contrast ({epsilon}{sub Ge}/{epsilon}{sub air} = 16) ever achieved in the optical regime in such periodic structures, which could result in important applications in photonics. The authors employ solid silica colloidal crystals (opals) as templates within which a cyclic germanium growth process is carried out. Thus, the three-dimensional periodicity of the host is inherited by the guest. Afterward, the silica is removed and a germanium opal replica is obtained.

  19. Syntheses, spectroscopy and crystal structures of new group 4 metallasiloxanes

    NASA Astrophysics Data System (ADS)

    Voigt, Andreas; Murugavel, Ramaswamy; Roesky, Herbert W.; Schmidt, Hans-Georg

    1997-12-01

    The reactions of the organic-soluble (trimethylsilyl)arylaminosilanetriol RSi(OH) 3 (R = (2,6- i-Pr 2C 6H 3)NSiMe 3) (1) with titanocene dichloride and zirconocene dichloride in dimethoxyethane as the solvent leads to the formation of acyclic and cyclic siloxanes [RSi(OH) 2(OTiCp 2Cl)] (2) and [RSi(OH)(OZrCp 2)O] 2 (3), respectively. The molecular structures of the new products 2 and 3 have been established by means of their analytical and spectral data. Further, in each case the solid-state structure of the compounds has been determined by single crystal X-ray diffraction studies. The EI mass spectral data reveal the presence of higher molecular weight compounds in the gas phase corresponding to the bicyclic or cubic structures of 2 and 3, respectively.

  20. Crystal structure solution from experimentally determined atomic pair distribution functions

    SciTech Connect

    Juhas, P.; Granlund, L.; Gujarathi, S.R.; Duxbury, P.M.; Billinge, S.J.L.

    2010-05-25

    An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

  1. Crystal Structure of a Lipid G Protein-Coupled Receptor

    SciTech Connect

    Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C

    2012-03-01

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P1-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P1, resulting in the modulation of immune and stromal cell responses.

  2. The crystal structure and superconducting properties of monatomic bromine.

    PubMed

    Duan, Defang; Meng, Xing; Tian, Fubo; Chen, Changbo; Wang, Liancheng; Ma, Yanming; Cui, Tian; Liu, Bingbing; He, Zhi; Zou, Guangtian

    2010-01-13

    The crystal structure and superconducting properties of monatomic bromine under high pressure have been studied by first-principles calculations. We have found the following phase transition sequence with increasing pressure: from body-centered orthorhombic (bco, phase II) to body-centered tetragonal structure (bct, phase III) at 126 GPa, then to face-centered cubic structure (fcc, phase IV) at 157 GPa, which is stable at least up to 300 GPa. The calculated superconducting critical temperature T(c) = 1.46 K at 100 GPa is consistent with the experimental value of 1.5 K. In addition, our results of T(c) decrease with increasing pressure in all the monatomic phases of bromine, similar to monatomic iodine. Further calculations show that the decrease of λ with pressure in phase IV is mainly attributed to the weakening of the 'soft' vibrational mode caused by pressure.

  3. Crystal structure of the superantigen staphylococcal enterotoxin type A.

    PubMed Central

    Schad, E M; Zaitseva, I; Zaitsev, V N; Dohlsten, M; Kalland, T; Schlievert, P M; Ohlendorf, D H; Svensson, L A

    1995-01-01

    Staphylococcal enterotoxins are prototype superantigens characterized by their ability to bind to major histocompatibility complex (MHC) class II molecules and subsequently activate a large fraction of T-lymphocytes. The crystal structure of staphylococcal enterotoxin type A (SEA), a 27 kDa monomeric protein, was determined to 1.9 A resolution with an R-factor of 19.9% by multiple isomorphous replacement. SEA is a two domain protein composed of a beta-barrel and a beta-grasp motif demonstrating the same general structure as staphylococcal enterotoxins SEB and TSST-1. Unique for SEA, however, is a Zn2+ coordination site involved in MHC class II binding. Four amino acids including Ser1, His187, His225 and Asp227 were found to be involved in direct coordination of the metal ion. SEA is the first Zn2+ binding enterotoxin that has been structurally determined. Images PMID:7628431

  4. Crystal Structure of a Self-Spliced Group ll Intron

    SciTech Connect

    Toor,N.; Keating, K.; Taylor, S.; Pyle, A.

    2008-01-01

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  5. Crystal structure of Homo sapiens protein LOC79017

    SciTech Connect

    Bae, Euiyoung; Bingman, Craig A.; Aceti, David J.; Phillips, Jr., George N.

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  6. Crystal Structure of a Self-Spliced Group II Intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie

    2008-04-10

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  7. Structure and Chemical Durability of Lead Crystal Glass.

    PubMed

    Angeli, Frédéric; Jollivet, Patrick; Charpentier, Thibault; Fournier, Maxime; Gin, Stéphane

    2016-11-01

    Silicate glasses containing lead, also called lead crystal glasses, are commonly used as food product containers, in particular for alcoholic beverages. Lead's health hazards require major attention, which can first be investigated through the understanding of Pb release mechanisms in solution. The behavior of a commercial crystal glass containing 10.6 mol % of PbO (28.3 wt %) was studied in a reference solution of 4% acetic acid at 22, 40, and 70 °C at early and advanced stages of reaction. High-resolution solid-state (17)O and (29)Si NMR was used to probe the local structure of the pristine and, for the first time, of the altered lead crystal glass. Inserted into the vitreous structure between the network formers as Si-O-Pb bonds, Pb does not form Pb-O-Pb clusters which are expected to be more easily leached. A part of K is located near Pb, forming mixed Si-O-(Pb,K) near the nonbridging oxygens. Pb is always released into the solution following a diffusion-controlled dissolution over various periods of time, at a rate between 1 and 2 orders of magnitude lower than the alkalis (K and Na). The preferential release of alkalis is followed by an in situ repolymerization of the silicate network. Pb is only depleted in the outermost part of the alteration layer. In the remaining part, it stays mainly surrounded by Si in a stable structural configuration similar to that of the pristine glass. A simple model is proposed to estimate the Pb concentration as a function of glass surface, solution volume, temperature, and contact time.

  8. [Crystallography of drug polymorphism: emergence of new resolution methods and prediction of crystalline structures].

    PubMed

    Perrin, M A

    2002-05-01

    For the pharmaceutical and agrochemical industries, reducing development time is currently a primary objective to accelerate the marketing of new products. In-depth solid-state characterization is an essential element in achieving this performance. For this purpose, it is now recognized that, in a department of solid-state physical characterization, theoretical approaches have to be integrated with experimental tools. Benefiting from the constant improvement in computer hardware and software in terms of computing powers and algorithm development, these approaches appear to be a complementary method that can help explain and rationalize experimental data. In recent years, with the help of both molecular modeling tools and crystallographic databases, original methods have been developed and successfully applied to systems of variable complexity. The X-ray diffraction crystal structure determination makes it possible to calibrate the force field and to adapt it more precisely to the compound studied, thereby reducing one of the sources of uncertainty. Although crystal structures are preferentially determined from single crystal data, it has been recently shown that powder diffraction data can also be used when single crystals are missing. Therefore, the different benefits of such an approach are the following: ab initio predictive study of crystalline polymorphism, molecular packing analysis and detection of cleavage planes, prediction of morphology in vacuum. In conjunction with crystallite preferred orientation observed in powder patterns, grinding effects on the crystal habit and solvent effects in modifying growth can be clearly understood. Selected industrial cases exemplify the operational application of this methodology.

  9. Banded Structure and Domain Arrangements in PbTiO3 Single Crystals

    NASA Astrophysics Data System (ADS)

    Chou, Chen-Chia; Chen, Cheng-Sao

    1998-09-01

    In the present work we report the ferroelectric domain arrangements and characteristics of banded structures observed in flux-grown PbTiO3 single crystals. Investigations of etched crystals indicate that most of the specimens show banded structures which may correspond to surface relief characteristics of as-grown crystals. Banded structures, which are different from domain structures, possess structural characteristics similar to those of martensite variants in various alloys and ceramics. The stresses produced during transformation were relieved by the formation of the banded structures and the 90° domain structures, suggesting that the band structures and 90° domains are the products of self-accommodation in as-grown PbTiO3 crystals during the cubic/tetragonal (C/T) transformation. Image characteristics imply that banded-structure-induced domain intersections may store high strain energy in lead titanate crystals and therefore hinder polarization switching of the crystals.

  10. Crystal structure of rofecoxib bound to human cyclooxygenase-2.

    PubMed

    Orlando, Benjamin J; Malkowski, Michael G

    2016-10-01

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7 Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  11. Refinement of the crystal structure of lithium-bearing uvite

    SciTech Connect

    Rozhdestvenskaya, I. V. Frank-Kamenetskaya, O. V.; Kuznetsova, L. G.; Bannova, I. I.; Bronzova, Yu. M.

    2007-03-15

    The crystal structure of a natural calcium tourmaline, i.e., uvite with a high lithium content (0.51 au per formula (aupf) at the Y site, is refined to R = 0.019, R{sub w} = 0.020, and S = 1.11. It is shown that, in nature, there exist uvites in which the charge balance in the case where the Z site is occupied by trivalent cations is provided by the replacement of part of the divalent magnesium cations at the Y site by univalent cations, divalent calcium cations at the X site by sodium cations, and univalent anions at the W site by oxygen anions. The W site is found to be split into two sites, namely, the W1 and W11 sites (the W1-W11 distance is 0.14 A), which are partially occupied by the fluorine and oxygen anions, respectively. An analysis of the results obtained in this study and the data available in the literature on the crystal structure of uvites allows the conclusion that uvite can be considered a superspecies and that the nomenclature of this mineral group needs refinement with the use of structural data.

  12. Crystal structure of the yeast metacaspase Yca1.

    PubMed

    Wong, Ada Hang-Heng; Yan, Chuangye; Shi, Yigong

    2012-08-24

    Yca1, the only metacaspase in Saccharomyces cerevisiae, is thought to be a clan CD cysteine protease that includes the caspase subfamily. Although yeast is a single cell eukaryote, it can undergo a cell death process reminiscent of apoptosis. Yca1 has been reported to play an important role in the regulation of such apoptotic process. However, the structure and functional mechanism of Yca1 remain largely enigmatic. In this study, we report the crystal structure of the Yca1 metacaspase at 1.7 Å resolution, confirming a caspase-like fold. In sharp contrast to canonical caspases, however, Yca1 exists as a monomer both in solution and in the crystals. Canonical caspase contains six β-strands, with strand β6 pairing up with β6 of another caspase molecule to form a homodimerization interface. In Yca1, an extra pair of antiparallel β-strands forms a continuous β-sheet with the six caspase-common β-strands, blocking potential dimerization. Yca1 was reported to undergo autocatalytic processing in yeast; overexpression in bacteria also led to autoprocessing of Yca1 into two fragments. Unexpectedly, we found that both the autocatalytic processing and the proteolytic activity of Yca1 are greatly facilitated by the presence of calcium (Ca(2+)), but not other divalent cations. Our structural and biochemical characterization identifies Yca1 as a Ca(2+)-activated cysteine protease that may cleave specific substrates during stress response in yeast.

  13. Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.

    PubMed

    Clausen, Johannes D; Bublitz, Maike; Arnou, Bertrand; Olesen, Claus; Andersen, Jens Peter; Møller, Jesper Vuust; Nissen, Poul

    2016-04-05

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.

  14. Potassium and magnesium succinatouranilates - Synthesis and crystal structure

    NASA Astrophysics Data System (ADS)

    Novikov, S. A.; Grigoriev, M. S.; Serezhkina, L. B.; Serezhkin, V. N.

    2017-04-01

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K2[(UO2)2(C4H4O4)3] (1) and [Mg(H2O)6] [(UO2)2(C4H4O4)3]·2H2O (2), where C4H4O42- is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO2)2(C4H4O4)3]2- with the same A2Q023 crystallochemical formula (A=UO22+, Q02=C4O4H42-), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ions is one of the factors, which affects the structure of [(UO2)2(C4H4O4)3]2- anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A2Q023 crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality.

  15. Crystal structure of rofecoxib bound to human cyclooxygenase-2

    SciTech Connect

    Orlando, Benjamin J.; Malkowski, Michael G.

    2016-10-26

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7- Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  16. Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.

    SciTech Connect

    Zhang, R.; Evans, G.; Rotella, F. J.; Westbrook, E. M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F. R.

    1999-01-01

    IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.

  17. 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.

  18. Crystal structure of tris-(piperidinium) hydrogen sulfate sulfate.

    PubMed

    Lukianova, Tamara J; Kinzhybalo, Vasyl; Pietraszko, Adam

    2015-12-01

    In the title molecular salt, 3C5H12N(+)·HSO4 (-)·SO4 (2-), each cation adopts a chair conformation. In the crystal, the hydrogen sulfate ion is connected to the sulfate ion by a strong O-H⋯O hydrogen bond. The packing also features a number of N-H⋯O hydrogen bonds, which lead to a three-dimensional network structure. The hydrogen sulfate anion accepts four hydrogen bonds from two cations, whereas the sulfate ion, as an acceptor, binds to five separate piperidinium cations, forming seven hydrogen bonds.

  19. Study of the crystal structure of silicon nanoislands on sapphire

    SciTech Connect

    Krivulin, N. O. Pirogov, A. V.; Pavlov, D. A.; Bobrov, A. I.

    2015-02-15

    The results of studies of the crystal structure of silicon nanoislands on sapphire are reported. It is shown that the principal defects in silicon nanoislands on sapphire are twinning defects. As a result of the formation of such defects, different crystallographic orientations are formed in silicon nanoislands on sapphire. In the initial stages of the molecular-beam epitaxy of silicon on sapphire, there are two basic orientations: the (001) orientation parallel to the surface and the (001) orientation at an angle of 70° to the surface.

  20. 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.

  1. Photonic crystal digital alloys and their band structure properties.

    PubMed

    Lee, Jeongkug; Kim, Dong-Uk; Jeon, Heonsu

    2011-09-26

    We investigated semi-disordered photonic crystals (PCs), digital alloys, and made thorough comparisons with their counterparts, random alloys. A set of diamond lattice PC digital alloys operating in a microwave regime were prepared by alternately stacking two kinds of sub-PC systems composed of alumina and silica spheres of the same size. Measured transmission spectra as well as calculated band structures revealed that when the digital alloy period is short, band-gaps of the digital alloys are practically the same as those of the random alloys. This study indicates that the concept of digital alloys holds for photons in PCs as well.

  2. Structure and Dynamics of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2004-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase

  3. Crystal networks in silk fibrous materials: from hierarchical structure to ultra performance.

    PubMed

    Nguyen, Anh Tuan; Huang, Qiao-Ling; Yang, Zhen; Lin, Naibo; Xu, Gangqin; Liu, Xiang Yang

    2015-03-01

    This review provides a comprehensive survey of the structural characteristics of crystal networks of silk soft fibrous materials in correlation with the macroscopic properties/performance and the network formation mechanisms. The correlation between the hierarchical mesoscopic structures and the mechanical properties of silk soft fibrous materials including silk fibroin hydrogels and naturally spun silk fibers are addressed based on the hierarchical crystal network models. Namely, two types of hierarchical networks are identified: the weak nanofibril-nanofibril interaction case (i.e., silk fibroin hydrogels), and the strong nanofibril-nanofibril interaction case (i.e., silk fibers). The macroscopic properties, i.e., the rheological/mechanical properties, can be controlled in terms of tuning different levels of hierarchical network structures by ultrasonication-induced gelation, introducing the initial nucleation centers, etc. Such controls take effect by different mesoscale assembly pathways, which are found to occur via different routes of the nucleation and growth processes. Furthermore, the hierarchical network model of soft fibrous materials can be applied to explain the superior mechanical properties and the unique strain-hardening behaviors of spider silk fibers within the framework of hierarchical breaking mechanism. Obviously, a knowledge of crystal networks will allow the prediction of the performance and engineering strategy of silk fibrous materials in generals.

  4. Crystal structure of the human NKX2.5 homeodomain in complex with DNA target.

    PubMed

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O; Kasahara, Hideko; Nam, Hyun-Joo

    2012-08-14

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 Å resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  5. Crystal Structure of the Human NKX2.5 Homeodomain in Complex with DNA Target

    SciTech Connect

    Pradhan, Lagnajeet; Genis, Caroli; Scone, Peyton; Weinberg, Ellen O.; Kasahara, Hideko; Nam, Hyun-Joo

    2012-10-16

    NKX2.5 is a homeodomain containing transcription factor regulating cardiac formation and function, and its mutations are linked to congenital heart disease. Here we provide the first report of the crystal structure of the NKX2.5 homeodomain in complex with double-stranded DNA of its endogenous target, locating within the proximal promoter -242 site of the atrial natriuretic factor gene. The crystal structure, determined at 1.8 {angstrom} resolution, demonstrates that NKX2.5 homeodomains occupy both DNA binding sites separated by five nucleotides without physical interaction between themselves. The two homeodomains show identical conformation despite the differences in the DNA sequences they bind, and no significant bending of the DNA was observed. Tyr54, absolutely conserved in NK2 family proteins, mediates sequence-specific interaction with the TAAG motif. This high resolution crystal structure of NKX2.5 protein provides a detailed picture of protein and DNA interactions, which allows us to predict DNA binding of mutants identified in human patients.

  6. Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

    NASA Astrophysics Data System (ADS)

    Koley, Biplab; Chatterjee, S.; Jana, Partha P.

    2017-02-01

    A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

  7. Crystal structure of graphite under room-temperature compression and decompression

    SciTech Connect

    Wang, Yuejian; Panzik, Joseph E.; Kiefer, Boris; Lee, Kanani K.M.

    2012-10-23

    Recently, sophisticated theoretical computational studies have proposed several new crystal structures of carbon (e.g., bct-C{sub 4}, H-, M-, R-, S-, W-, and Z-carbon). However, until now, there lacked experimental evidence to verify the predicted high-pressure structures for cold-compressed elemental carbon at least up to 50 GPa. Here we present direct experimental evidence that this enigmatic high-pressure structure is currently only consistent with M-carbon, one of the proposed carbon structures. Furthermore, we show that this phase transition is extremely sluggish, which led to the observed broad x-ray diffraction peaks in previous studies and hindered the proper identification of the post-graphite phase in cold-compressed carbon.

  8. Crystal Structure of a Truncated Urease Accessory Protein UreF From Helicobacter pylori

    PubMed Central

    Lam, Robert; Romanov, Vladimir; Johns, Kathy; Battaile, Kevin P.; Wu-Brown, Jean; Guthrie, Jennifer L.; Hausinger, Robert P.; Pai, Emil F.; Chirgadze, Nickolay Y.

    2010-01-01

    Urease plays a central role in the pathogenesis of Helicobacter pylori in humans. Maturation of this nickel metalloenzyme in bacteria requires the participation of the accessory proteins UreD (termed UreH in H. pylori), UreF, and UreG which form sequential complexes with the urease apoprotein as well as UreE, a metallochaperone. Here, we describe the crystal structure of C-terminal truncated UreF from H. pylori (residues 1-233), the first UreF structure to be determined, at 1.55 Å resolution using SAD methods. UreF forms a dimer in vitro and adopts an all-helical fold congruent with secondary structure prediction. On the basis of evolutionary conservation analysis, the structure reveals a probable binding surface for interaction with other urease components as well as key conserved residues of potential functional relevance. PMID:20635345

  9. Three-dimensional modeling of nematic liquid crystal micro-optics structures with complex patterned electrodes

    NASA Astrophysics Data System (ADS)

    Rong, Xing; Kang, Shengwu; Zhang, Xinyu; Ji, An; Xie, Changsheng; Zhang, Tianxu

    2012-11-01

    In this paper, a three-dimensional (3-D) relaxation method is used to model the dynamic response behavior of liquid crystal (LC) directors in LC micro-optics structures with complex patterned electrodes. The method is based on Frank- Oseen continuum elastic theory by using a vectorial representation. This method can deal with liquid crystal structures with arbitrary patterned electrodes, and it is quite computational stability. Different numerical results obtained according the method are as follows: (1) the nematic LC structures with complex patterned electrodes applied by a constant voltage signal, and (2) the nematic LC structures with different thickness of LC layer, and (3) the nematic LC structures with different signal voltage. The typical results include the distribution of LC directors in LC layers, the distribution of electric potential in LC layers, and the distribution of phase retardation. The results show that the method can be used to effectively predict the formation of disclination lines, which has a strong impact on the performance of LC micro-optics structures.

  10. Quantum size effect in Pb(100) films: Critical role of crystal band structure

    NASA Astrophysics Data System (ADS)

    Wei, C. M.; Chou, M. Y.

    2007-05-01

    We report first-principles calculations of Pb(100) films up to 22 monolayers to study variations in the surface energy and work function as a function of film thickness. An even-odd oscillation is found in these two quantities, while a jelliumlike model for this s-p metal predicts a periodicity of about three monolayers. This unexpected result is explained by considering a coherent superposition of contributions from quantum-well states centered at both the Γ¯ and Mmacr points in the two-dimensional Brillouin zone, demonstrating the importance of crystal band structure in studying the quantum size effect in metal thin films.

  11. Diamond Opal-Replica Photonic Crystals and Graphitic Metallic Photonic Band Gap Structures: Fabrication and Properties

    NASA Astrophysics Data System (ADS)

    Zakhidov, A. A.; Baughman, R. H.; Iqbal, Z.; Khayrullin, I. I.; Ralchenko, V. G.

    1998-03-01

    We demonstrate a new method for the formation of photonic bandgap crystals that operate at optical wavelengths. This method involves the templating of a self-assempled SiO2 lattice with diamond, graphite, or amorphous forms of carbon, followed by the removal of the original SiO2 lattice matrix by chemical means. Such carbon opal replicas are the "air type" of photonic crystal (where air replaces silica spheres) that are most favourable for photonic bandgap formation. Surprisingly, the structure of the original opal lattice having a typical cubic lattice dimension of 250 nm) is reliably replicated down to the nanometer scale using either a diamond, graphite, or amorphous carbon templated material. The optical properties of these photonic bandgap crystals are reported and compared with both theory and experimental results on other types of opal-derived lattices that we have investigated. The graphitic reverse opal is the first example of a network type metallic photonic crystal for the optical domain, for which a large photonic bandgap have been predicted.

  12. Theoretical studies of the crystal structure of rare earths and actinides at zero temperature

    SciTech Connect

    Wills, J.M.; Eriksson, O.

    1993-07-01

    Accurate total energy electronic structure calculations have recently been carried out over a range of volumes for selected rare-earth and actinide elements in crystal structures, experimentally observed in these elements. Correct zero temperature crystal structures are obtained, and calculated equilibrium properties are in reasonable agreement with experiment. Results of these calculations indicate that the interactions underlying crystal structure stability are similar in itinerant f-electron metals and transition metals. The stable crystal structure at a particular volume is determined by a balance between one-electron bandwidths and band fillings and the electrostatic energy of the crystal lattice. Broad bands favor high-symmetry, close-packed structures while narrow bands favor low-symmetry, open structures; allowing for expansion as well as contraction, both transition and actinide elements can be stabilized in both low- and high-symmetry crystal structures.

  13. Theoretical studies of the crystal structure of rare earths and actinides at zero temperature

    SciTech Connect

    Wills, J.M. ); Eriksson, O. . Dept. of Physics)

    1993-01-01

    Accurate total energy electronic structure calculations have recently been carried out over a range of volumes for selected rare-earth and actinide elements in crystal structures, experimentally observed in these elements. Correct zero temperature crystal structures are obtained, and calculated equilibrium properties are in reasonable agreement with experiment. Results of these calculations indicate that the interactions underlying crystal structure stability are similar in itinerant f-electron metals and transition metals. The stable crystal structure at a particular volume is determined by a balance between one-electron bandwidths and band fillings and the electrostatic energy of the crystal lattice. Broad bands favor high-symmetry, close-packed structures while narrow bands favor low-symmetry, open structures; allowing for expansion as well as contraction, both transition and actinide elements can be stabilized in both low- and high-symmetry crystal structures.

  14. Single crystal structures of thallium (I) thorium fluorides and crystal chemistry of monovalent tetravalent cation pentafluorides

    NASA Astrophysics Data System (ADS)

    Oudahmane, Abdelghani; El-Ghozzi, Malika; Jouffret, Laurent; Avignant, Daniel

    2015-12-01

    Two thallium (I) thorium (IV) fluorides, TlTh3F13 and TlThF5 were obtained by solid state synthesis and their crystal structures determined from single crystal X-ray diffraction data recorded at room temperature with an APEX-II CCD diffractometer. TlTh3F13 is orthorhombic, space group Pmc21, with a=8.1801(2) Å, b=7.4479(2) Å, c=8.6375(2) Å, V=526.24(2) Å3, Z=2 and TlThF5 is monoclinic, space group P21/n, with a=8.1128(5) Å, b=7.2250(4) Å, c=8.8493(6) Å, β=116.683(3)°, V=463.46(5) Å3, Z=4. The structure of TlTh3F13 comprises layers of corner and edge-sharing ThF9 polyhedra further linked by chains of trans connected tricapped trigonal prisms ThF9 through corners and edges. The three dimensional thorium frameworks delimits channels parallel to [0 0 1] where the 11-coordinated Tl+ ions are arranged into double columns located in mirror planes of the structure. TlTh3F13 is isotypic with RbTh3F13, RbU3F13 and with one of the two polymorphs of CsTh3F13. The structure of TlThF5 may be regarded as a layer structure built up from the regular succession of 2∞[ M ‧F5 ] - corrugated layers further held by the Tl+ ions along the [1 0 1 ̅] direction. The layers are built up from edge and corner-sharing thorium polyhedra where each (ThF9)5- monocapped square antiprism is connected to five others by sharing three edges and two corners. TlThF5 is isostructural with β-NH4UF5 and with one of the polymorphs of CsThF5. A comparison of the different structural types of MM‧F5 pentafluorides is presented and a diagram of repartition of their structures is given. From the comparison of the Tl structures with their Rb or Cs homologs, where very similar monovalent cation environments are observed it should be concluded to a stereochemically inactivity of the 6s2 lone pair of Tl(I) in both TlTh3F13 and TlThF5, contrary to what is observed in richer Tl(I) content Tl3ThF7 fluorothorate.

  15. Photochemical manipulation of colloidal structures in liquid-crystal colloids

    NASA Astrophysics Data System (ADS)

    Yamamoto, T.; Tabe, Y.; Yokoyama, H.

    2007-05-01

    We investigated photochemical manipulation of physical properties and colloidal structures in liquid-crystal (LC) colloids containing azobenzene compounds. In a LC suspension where polymeric particles were dispersed in a host LC, we achieved photochemical control of light-scattering properties of the suspension. In a nematic phase, when the suspension was sandwiched with two glass plates, the film became opaque. This would be attributable to an appearance of both multidomain structures of LC alignment and mismatches of refractive indices between the materials. The opaque state turned into a transparent one when a nematic-to-isotropic phase transition was induced by the trans-to-cis photoisomerization of the azo-dye. This will result from a disappearance of both the multidomain structures and the refractive-index mismatches in the isotropic phase. The transparent film went back into the initial opaque film when the nematic phase was obtained by the cis-to-trans photoisomerization. In a LC emulsion in which glycerol or water droplets were dispersed in liquid crystals, we examined photochemical change of defect structures and inter-droplet distances by the photochemical manner. At the initial state, Saturn ring and hedgehog defects were formed around the droplets. For the glycerol droplets, we observed structural transformations between Saturn ring and boojums on irradiation with ultra-violet and visible light. For the water droplets, the inter-droplet distances varied by changing defect size on the irradiation. These phenomena would result from modulation of anchoring conditions of the droplets by the photoisomerization of the azo-dyes.

  16. Analysis of zinc binding sites in protein crystal structures.

    PubMed Central

    Alberts, I. L.; Nadassy, K.; Wodak, S. J.

    1998-01-01

    The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations. PMID:10082367

  17. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    PubMed Central

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith

    2008-01-01

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity. PMID:18799746

  18. Statistical energy analysis response prediction methods for structural systems

    NASA Technical Reports Server (NTRS)

    Davis, R. F.

    1979-01-01

    The results of an effort to document methods for accomplishing response predictions for commonly encountered aerospace structural configurations is presented. Application of these methods to specified aerospace structure to provide sample analyses is included. An applications manual, with the structural analyses appended as example problems is given. Comparisons of the response predictions with measured data are provided for three of the example problems.

  19. RNA-SSPT: RNA Secondary Structure Prediction Tools

    PubMed Central

    Ahmad, Freed; Mahboob, Shahid; Gulzar, Tahsin; din, Salah U; Hanif, Tanzeela; Ahmad, Hifza; Afzal, Muhammad

    2013-01-01

    The prediction of RNA structure is useful for understanding evolution for both in silico and in vitro studies. Physical methods like NMR studies to predict RNA secondary structure are expensive and difficult. Computational RNA secondary structure prediction is easier. Comparative sequence analysis provides the best solution. But secondary structure prediction of a single RNA sequence is challenging. RNA-SSPT is a tool that computationally predicts secondary structure of a single RNA sequence. Most of the RNA secondary structure prediction tools do not allow pseudoknots in the structure or are unable to locate them. Nussinov dynamic programming algorithm has been implemented in RNA-SSPT. The current studies shows only energetically most favorable secondary structure is required and the algorithm modification is also available that produces base pairs to lower the total free energy of the secondary structure. For visualization of RNA secondary structure, NAVIEW in C language is used and modified in C# for tool requirement. RNA-SSPT is built in C# using Dot Net 2.0 in Microsoft Visual Studio 2005 Professional edition. The accuracy of RNA-SSPT is tested in terms of Sensitivity and Positive Predicted Value. It is a tool which serves both secondary structure prediction and secondary structure visualization purposes. PMID:24250115

  20. Crystal structure of the petal death protein from carnation flower.

    PubMed

    Teplyakov, Alexey; Liu, Sijiu; Lu, Zhibing; Howard, Andrew; Dunaway-Mariano, Debra; Herzberg, Osnat

    2005-12-20

    Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.

  1. Crystal structures of vortioxetine and its methanol monosolvate

    PubMed Central

    Zhou, Xin-Bo; Gu, Jian-Ming; Sun, Meng-ying; Hu, Xiu-Rong; Wu, Su-Xiang

    2015-01-01

    Vortioxetine, C18H22N2S, (1), systematic name 1-{2-[(2,4-di­methyl­phen­yl)sulfan­yl]phen­yl}piperazine, a new drug used to treat patients with major depressive disorder, has been crystallized as the free base and its methanol monosolvate, C18H22N2S·CH3OH, (2). In both structures, the vortioxetine mol­ecules have similar conformations: in (1), the dihedral angle between the aromatic rings is 80.04 (16)° and in (2) it is 84.94 (13)°. The C—S—C bond angle in (1) is 102.76 (14)° and the corresponding angle in (2) is 103.41 (11)°. The piperazine ring adopts a chair conformation with the exocyclic N—C bond in a pseudo-equatorial orientation in both structures. No directional inter­actions beyond normal van der Waals contacts could be identified in the crystal of (1), whereas in (2), the vortioxetine and methanol mol­ecules are linked by N—H⋯O and O—H⋯N hydrogen bonds, generating [001] chains. PMID:26396746

  2. Structure of carboxymyoglobin in crystals and in solution.

    PubMed Central

    Makinen, M W; Houtchens, R A; Caughey, W S

    1979-01-01

    The configuration of the heme-carbonyl group upon binding of carbon monoxide to sperm whale myoglobin (Mb) in crystals is evaluated on the basis of infrared spectroscopic methods. Multiplets of the totally symmetric C-O stretching mode are observed for the heme-bound ligand near 1933, 1944, and 1967 cm-1, corresponding to three different heme-carbonyl conformers. Variations in the relative proportions of these conformers can be induced by incorporation of small fractions of metMb or deoxyMb into MbCO crystals. The configuration of the iron-carbonyl with respect to the immediate coordination environment of the heme iron is assigned for each v(CO) stretching frequency on the basis of a detailed comparison of the three-dimensional structures of the heme environments of MbCO, metMb, and deoxyMb defined by crystallographic methods. The structures of the three heme-carbonyl conformers account for the v(CO) infrared absorption bands that can be observed for MbCO in solution. PMID:293700

  3. Crystal structure of pyruvate decarboxylase from Zymobacter palmae

    PubMed Central

    Buddrus, Lisa; Andrews, Emma S. V.; Leak, David J.; Danson, Michael J.; Arcus, Vickery L.; Crennell, Susan J.

    2016-01-01

    Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg2+ ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and R r.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were R work = 0.186 (0.271 in the highest resolution bin) and R free = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions. PMID:27599861

  4. Crystal Structure of 3S-hydroxy-7 Melleine

    NASA Astrophysics Data System (ADS)

    Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

    2006-10-01

    A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, β=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, μ=0.112 mm-1, the final R=0.0498, ωR=0.101 for 2407 observed reflections (I>2σ(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 μg/disk in the preliminary test.

  5. Crystal structure of K[Hg(SCN)3] - a redetermination.

    PubMed

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ▶). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ∞[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926 (2) and 3.051 (3) Å.

  6. Evaluation of Predictability of Quartz-Crystal Oscillators and other Devices.

    DTIC Science & Technology

    1981-01-15

    AD-A096 3A0 NAVAL OBSERVATORY WAS14MNTON DC TIME SERVICE DIV F/6 9/5 EVALUATION OF PREDICTABILITY OF QUARTZ-CRYSTAL OSCILLATORS AND -4ETC(U) JAN 81 L...concluded that very simple prediction methods can suffice in maintaining a timing system. DO I2I 1473 EDITION OF’ I NOV065 IS 08SOLIETE NLSSFE S/N 0 102. LF...Discussion of Measurements.. .. .................. 2 Conclusions ....... .... .. ............................... 3 Appendix A.1 Disciplined Time Frequency

  7. Structure of cleaved (001) USb2 single crystal

    SciTech Connect

    Chen, Shao-ping; Hawley, Marilyn; Bauer, Eric D; Stockum, Phil B; Manoharan, Hari C

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features observed in the STM will be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites) and the presence of contaminants

  8. The crystal structure of {pi}-ErBO{sub 3}: New single-crystal data for an old problem

    SciTech Connect

    Pitscheider, Almut; Kaindl, Reinhard; Oeckler, Oliver; Huppertz, Hubert

    2011-01-15

    Single crystals of the orthoborate {pi}-ErBO{sub 3} were synthesized from Er{sub 2}O{sub 3} and B{sub 2}O{sub 3} under high-pressure/high-temperature conditions of 2 GPa and 800 {sup o}C in a Walker-type multianvil apparatus. The crystal structure was determined on the basis of single-crystal X-ray diffraction data, collected at room temperature. The title compound crystallizes in the monoclinic pseudowollastonite-type structure, space group C2/c, with the lattice parameters a=1128.4(2) pm, b=652.6(2) pm, c=954.0(2) pm, and {beta}=112.8(1){sup o} (R{sub 1}=0.0124 and wR{sub 2}=0.0404 for all data). -- graphical abstract: The first satisfying single-crystal structure determination of {pi}-ErBO{sub 3} sheds light on the extensively discussed structure of {pi}-orthoborates. The application of light pressure during the solid state synthesis yielded in high-quality crystals, due to pressure-induced crystallization. Research highlights: {yields} High-quality single crystals of {pi}-ErBO{sub 3} were prepared via high-pressure-induced crystallization. {yields} At least five different space groups for the rare-earth {pi}-orthoborates are reported. {yields} {pi}-ErBO{sub 3} is isotypic to the pseudowollastonite-type CaSiO{sub 3}. {yields} Remaining ambiguities regarding the structure of the rare-earth {pi}-orthoborates are resolved.

  9. Crystal structure of laser-induced subsurface modifications in Si

    DOE PAGES

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; ...

    2015-06-04

    Laser-induced subsurface modification of dielectric materials is a well-known technology. Applications include the production of optical components and selective etching. In addition to dielectric materials, the subsurface modification technology can be applied to silicon, by employing near to mid-infrared radiation. An application of subsurface modifications in silicon is laser-induced subsurface separation, which is a method to separate wafers into individual dies. Other applications for which proofs of concept exist are the formation of waveguides and resistivity tuning. However, limited knowledge is available about the crystal structure of subsurface modifications in silicon. In this paper, we investigate the geometry and crystalmore » structure of laser-induced subsurface modifications in monocrystalline silicon wafers. Finally, in addition to the generation of lattice defects, we found that transformations to amorphous silicon and Si-iii/Si-xii occur as a result of the laser irradiation.« less

  10. Structural noise tolerance of photonic crystal optical properties

    NASA Astrophysics Data System (ADS)

    Odontsengel, Nyam-Erdene; Cai, DongSheng; Cole, James B.

    2016-12-01

    Using nonstandard (NS) finite difference time domain (FDTD) scheme to perform 2D electromagnetic (EM) simulations, we investigate how the optical properties of 2D photonic crystals (PCs) are affected by various different kinds of structural noises in the PC lattice. While the transmission spectrum is strongly affected by noises, the position and the depth of the band gap in the transmission spectrum are remarkably robust. It is shown that rather coarse numerical grids can be used to evaluate various PC structures in NS-FDTD EM simulations. The combination of noises affects transmission spectrum in the same way as the most influential individual noise. It is shown that reducing the most influential individual noise is a very efficient method to make PC more accurate.

  11. Crystal structure of Hg2SO4 – a redetermination

    PubMed Central

    Weil, Matthias

    2014-01-01

    The crystal structure of mercury(I) sulfate (or mercurous sulfate), Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969 ▶). Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031 (7) compared to 2.500 (3)Å]. The structure consists of alternating rows along [001] of Hg2 2+ dumbbells (generated by inversion symmetry) and SO4 2− tetra­hedra (symmetry 2). The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetra­hedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework. PMID:25309168

  12. Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

    PubMed

    Yorinaga, Yutaka; Kumasaka, Takashi; Yamamoto, Masaki; Hamada, Kensaku; Kawamukai, Makoto

    2017-02-01

    Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the β-proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate-binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.

  13. Crystal structure of PvdO from Pseudomonas aeruginosa.

    PubMed

    Yuan, Zenglin; Gao, Fei; Bai, Guohui; Xia, Hengchuan; Gu, Lichuan; Xu, Sujuan

    2017-02-26

    Pyoverdine I (PVDI) is a water-soluble fluorescein siderophore with strong iron chelating ability from the gram-negative pathogen Pseudomonas aeruginosa PAO1. Compared to common siderophores, PVDI is a relatively large compound whose synthesis requires a group of enzymes with different catalytic activities. In addition to four nonribosomal peptide synthetases (NRPS) which are responsible for the production of the peptide backbone of PVDI, several additional enzymes are associated with the modification of the side chains. PvdO is one of these enzymes and participates in PVDI precursor maturation in the periplasm. We determined the crystal structure of PvdO at 1.24 Å resolution. The PvdO structure shares a common fold with some FGly-generating enzymes (FGE) and is stabilized by Ca(2+). However, the catalytic residues in FGE are not observed in PvdO, indicating PvdO adopts a unique catalytic mechanism.

  14. The first crystal structure of an archaeal helical repeat protein

    PubMed Central

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-01-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-­helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

  15. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    SciTech Connect

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  16. Crystal structure of a catalytic intermediate of the maltose transporter

    SciTech Connect

    Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A.; Davidson, Amy L.; Chen, Jue

    2008-08-20

    The maltose uptake system of Escherichia coli is a well-characterized member of the ATP-binding cassette transporter superfamily. Here we present the 2.8-{angstrom} crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP. This structure, stabilized by a mutation that prevents ATP hydrolysis, captures the ATP-binding cassette dimer in a closed, ATP-bound conformation. Maltose is occluded within a solvent-filled cavity at the interface of the two transmembrane subunits, about halfway into the lipid bilayer. The binding protein docks onto the entrance of the cavity in an open conformation and serves as a cap to ensure unidirectional translocation of the sugar molecule. These results provide direct evidence for a concerted mechanism of transport in which solute is transferred from the binding protein to the transmembrane subunits when the cassette dimer closes to hydrolyse ATP.

  17. The crystal structure of loparite: a new acentric variety

    NASA Astrophysics Data System (ADS)

    Popova, Elena A.; Lushnikov, Sergey G.; Yakovenchuk, Victor N.; Krivovichev, Sergey V.

    2017-02-01

    The crystal structure of a new structural variety of loparite (Na0.56Ce0.21La0.14Ca0.06Sr0.03Nd0.02Pr0.01)Σ=1.03(Ti0.83Nb0.15)Σ=0.98O3 from the Khibiny alkaline massif, Kola peninsula, Russia, was solved by direct methods and refined to R 1 = 0.029 for 492 unique observed reflections with I > 2σ(I). The mineral is orthorhombic, Ima2, a = 5.5129(2), b = 5.5129(2) and c = 7.7874(5) Å. Similarly to other perovskite-group minerals with the general formula ABO3, the crystal structure of loparite is based upon a three-dimensional framework of distorted corner-sharing BO6. The A cations are coordinated by 12 oxygen atoms and are situated in distorted cuboctahedral cavities. In contrast to the ideal perovskite-type structure ( Pmoverset{-}{3} m ), the unit cell is doubled along the c axis and the a and b axes are rotated in the ab plane at 45o. The BO6 octahedron displays distortion characteristic for the d 0 transition metal cations with the out-of-center shift of the B site. The symmetry reduction is also attributable to the distortion of the BO6 octahedra which are tilted and rotated with respect to the c axis. The occurrence of a new acentric variety of loparite can be explained by the pecularities of its chemical composition characterized by the increased content of Ti compared to the previously studied samples.

  18. Crystal Structure and Inhibition Studies of Transglutaminase from Streptomyces mobaraense*

    PubMed Central

    Yang, Ming-Te; Chang, Cheng-Hsiang; Wang, Jiou Ming; Wu, Tung Kung; Wang, Yu-Kuo; Chang, Chin-Yuan; Li, TienHsiung Thomas

    2011-01-01

    The crystal structure of the microbial transglutaminase (MTGase) zymogen from Streptomyces mobaraense has been determined at 1.9-Å resolution using the molecular replacement method based on the crystal structure of the mature MTGase. The overall structure of this zymogen is similar to that of the mature form, consisting of a single disk-like domain with a deep active cleft at the edge of the molecule. A major portion of the prosequence (45 additional amino acid residues at the N terminus of the mature transglutaminase) folds into an L-shaped structure, consisting of an extended N-terminal segment linked with a one-turn short helix and a long α-helix. Two key residues in the short helix of the prosequence, Tyr-12 and Tyr-16, are located on top of the catalytic triad (Cys-110, Asp-301, and His-320) to block access of the substrate acyl donors and acceptors. Biochemical characterization of the mature MTGase, using N-α-benzyloxycarbonyl-l-glutaminylglycine as a substrate, revealed apparent Km and kcat/Km values of 52.66 mm and 40.42 mm−1 min−1, respectively. Inhibition studies using the partial prosequence SYAETYR and homologous sequence SQAETYR showed a noncompetitive inhibition mechanism with IC50 values of 0.75 and 0.65 mm, respectively, but no cross-linking product formation. Nevertheless, the prosequence homologous oligopeptide SQAETQR, with Tyr-12 and Tyr-16 each replaced with Gln, exhibited inhibitory activity with the formation of the SQAETQR-monodansylcadaverine fluorophore cross-linking product (SQAETQR-C-DNS). MALDI-TOF tandem MS analysis of SQAETQR-C-DNS revealed molecular masses corresponding to those of NSQAETQC-C-DNS and C-DNS-NQRC sequences, suggesting the incorporation of C-DNS onto the C-terminal Gln residue of the prosequence homologous oligopeptide. These results support the putative functional roles of both Tyr residues in substrate binding and inhibition. PMID:21193394

  19. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    PubMed

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  20. New Ground-State Crystal Structure of Elemental Boron

    NASA Astrophysics Data System (ADS)

    An, Qi; Reddy, K. Madhav; Xie, Kelvin Y.; Hemker, Kevin J.; Goddard, William A.

    2016-08-01

    Elemental boron exhibits many polymorphs in nature based mostly on an icosahedral shell motif, involving stabilization of 13 strong multicenter intraicosahedral bonds. It is commonly accepted that the most thermodynamic stable structure of elemental boron at atmospheric pressure is the β rhombohedral boron (β -B ). Surprisingly, using high-resolution transmission electron microscopy, we found that pure boron powder contains grains of two different types, the previously identified β -B containing a number of randomly spaced twins and what appears to be a fully transformed twinlike structure. This fully transformed structure, denoted here as τ -B , is based on the C m c m orthorhombic space group. Quantum mechanics predicts that the newly identified τ -B structure is 13.8 meV /B more stable than β -B . The τ -B structure allows 6% more charge transfer from B57 units to nearby B12 units, making the net charge 6% closer to the ideal expected from Wade's rules. Thus, we predict the τ -B structure to be the ground state structure for elemental boron at atmospheric pressure.