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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.

    PubMed

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

    2014-10-21

    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. Tetrahedron-tiling method for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Hong, Qi-Jun; Yasi, Joseph; van de Walle, Axel

    2017-07-01

    Reliable and robust methods of predicting the crystal structure of a compound, based only on its chemical composition, is crucial to the study of materials and their applications. Despite considerable ongoing research efforts, crystal structure prediction remains a challenging problem that demands large computational resources. Here we propose an efficient approach for first-principles crystal structure prediction. The new method explores and finds crystal structures by tiling together elementary tetrahedra that are energetically favorable and geometrically matching each other. This approach has three distinguishing features: a favorable building unit, an efficient calculation of local energy, and a stochastic Monte Carlo simulation of crystal growth. By applying the method to the crystal structure prediction of various materials, we demonstrate its validity and potential as a promising alternative to current methods.

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

    DTIC Science & Technology

    2009-04-01

    of molecular parameters from corresponding values in an ideal RDX crystal; experimental and predicted orienta- tional parameters of symmetry equivalent...small molecules. Thus, this DFT+D method includes a significant degree of empiricism , in contrast to our SAPT(DFT)-based approach which is completely...in the tables denote only the starting configu- rations . In order to identify duplicate crystal structures pro- duced during the WMIN lattice energy

  13. 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.

  14. 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.

  15. Tailor-made force fields for crystal-structure prediction.

    PubMed

    Neumann, Marcus A

    2008-08-14

    A general procedure is presented to derive a complete set of force-field parameters for flexible molecules in the crystalline state on a case-by-case basis. The force-field parameters are fitted to the electrostatic potential as well as to accurate energies and forces generated by means of a hybrid method that combines solid-state density functional theory (DFT) calculations with an empirical van der Waals correction. All DFT calculations are carried out with the VASP program. The mathematical structure of the force field, the generation of reference data, the choice of the figure of merit, the optimization algorithm, and the parameter-refinement strategy are discussed in detail. The approach is applied to cyclohexane-1,4-dione, a small flexible ring. The tailor-made force field obtained for cyclohexane-1,4-dione is used to search for low-energy crystal packings in all 230 space groups with one molecule per asymmetric unit, and the most stable crystal structures are reoptimized in a second step with the hybrid method. The experimental crystal structure is found as the most stable predicted crystal structure both with the tailor-made force field and the hybrid method. The same methodology has also been applied successfully to the four compounds of the fourth CCDC blind test on crystal-structure prediction. For the five aforementioned compounds, the root-mean-square deviations between lattice energies calculated with the tailor-made force fields and the hybrid method range from 0.024 to 0.053 kcal/mol per atom around an average value of 0.034 kcal/mol per atom.

  16. 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

  17. 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.

  18. 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

  19. 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

  20. 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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2017-06-01

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

  3. 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).

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

    PubMed

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

    2017-10-10

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

  5. 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

  6. Polymorph identification and crystal structure determination by a combined crystal structure prediction and transmission electron microscopy approach.

    PubMed

    Eddleston, Mark D; Hejczyk, Katarzyna E; Bithell, Erica G; Day, Graeme M; Jones, William

    2013-06-10

    Electron diffraction offers advantages over X-ray based methods for crystal structure determination because it can be applied to sub-micron sized crystallites, and picogram quantities of material. For molecular organic species, however, crystal structure determination with electron diffraction is hindered by rapid crystal deterioration in the electron beam, limiting the amount of diffraction data that can be collected, and by the effect of dynamical scattering on reflection intensities. Automated electron diffraction tomography provides one possible solution. We demonstrate here, however, an alternative approach in which a set of putative crystal structures of the compound of interest is generated by crystal structure prediction methods and electron diffraction is used to determine which of these putative structures is experimentally observed. This approach enables the advantages of electron diffraction to be exploited, while avoiding the need to obtain large amounts of diffraction data or accurate reflection intensities. We demonstrate the application of the methodology to the pharmaceutical compounds paracetamol, scyllo-inositol and theophylline. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  7. An Efficient Scheme for Crystal Structure Prediction Based on Structural Motifs

    DOE PAGES

    Zhu, Zizhong; Wu, Ping; Wu, Shunqing; ...

    2017-05-15

    An efficient scheme based on structural motifs is proposed for the crystal structure prediction of materials. The key advantage of the present method comes in two fold: first, the degrees of freedom of the system are greatly reduced, since each structural motif, regardless of its size, can always be described by a set of parameters (R, θ, φ) with five degrees of freedom; second, the motifs could always appear in the predicted structures when the energies of the structures are relatively low. Both features make the present scheme a very efficient method for predicting desired materials. The method has beenmore » applied to the case of LiFePO4, an important cathode material for lithium-ion batteries. Numerous new structures of LiFePO4 have been found, compared to those currently available, available, demonstrating the reliability of the present methodology and illustrating the promise of the concept of structural motifs.« less

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. An adaptive genetic algorithm for crystal structure prediction

    SciTech Connect

    Wu, Shunqing; Ji, Min; Wang, Cai-Zhuang; Nguyen, Manh Cuong; Zhao, Xin; Umemoto, K.; Wentzcovitch, R. M.; Ho, Kai-Ming

    2013-12-18

    We present a genetic algorithm (GA) for structural search that combines the speed of structure exploration by classical potentials with the accuracy of density functional theory (DFT) calculations in an adaptive and iterative way. This strategy increases the efficiency of the DFT-based GA by several orders of magnitude. This gain allows a considerable increase in the size and complexity of systems that can be studied by first principles. The performance of the method is illustrated by successful structure identifications of complex binary and ternary intermetallic compounds with 36 and 54 atoms per cell, respectively. The discovery of a multi-TPa Mg-silicate phase with unit cell containing up to 56 atoms is also reported. Such a phase is likely to be an essential component of terrestrial exoplanetary mantles.

  13. 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)

  14. 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)

  15. 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.

  16. 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.

  17. 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

  18. Towards crystal structure prediction of complex organic compounds – a report on the fifth blind test

    PubMed Central

    Bardwell, David A.; Adjiman, Claire S.; Arnautova, Yelena A.; Bartashevich, Ekaterina; Boerrigter, Stephan X. M.; Braun, Doris E.; Cruz-Cabeza, Aurora J.; Day, Graeme M.; Della Valle, Raffaele G.; Desiraju, Gautam R.; van Eijck, Bouke P.; Facelli, Julio C.; Ferraro, Marta B.; Grillo, Damian; Habgood, Matthew; Hofmann, Detlef W. M.; Hofmann, Fridolin; Jose, K. V. Jovan; Karamertzanis, Panagiotis G.; Kazantsev, Andrei V.; Kendrick, John; Kuleshova, Liudmila N.; Leusen, Frank J. J.; Maleev, Andrey V.; Misquitta, Alston J.; Mohamed, Sharmarke; Needs, Richard J.; Neumann, Marcus A.; Nikylov, Denis; Orendt, Anita M.; Pal, Rumpa; Pantelides, Constantinos C.; Pickard, Chris J.; Price, Louise S.; Price, Sarah L.; Scheraga, Harold A.; van de Streek, Jacco; Thakur, Tejender S.; Tiwari, Siddharth; Venuti, Elisabetta; Zhitkov, Ilia K.

    2011-01-01

    Following on from the success of the previous crystal structure prediction blind tests (CSP1999, CSP2001, CSP2004 and CSP2007), a fifth such collaborative project (CSP2010) was organized at the Cambridge Crystallographic Data Centre. A range of methodologies was used by the participating groups in order to evaluate the ability of the current computational methods to predict the crystal structures of the six organic molecules chosen as targets for this blind test. The first four targets, two rigid molecules, one semi-flexible molecule and a 1:1 salt, matched the criteria for the targets from CSP2007, while the last two targets belonged to two new challenging categories – a larger, much more flexible molecule and a hydrate with more than one polymorph. Each group submitted three predictions for each target it attempted. There was at least one successful prediction for each target, and two groups were able to successfully predict the structure of the large flexible molecule as their first place submission. The results show that while not as many groups successfully predicted the structures of the three smallest molecules as in CSP2007, there is now evidence that methodologies such as dispersion-corrected density functional theory (DFT-D) are able to reliably do so. The results also highlight the many challenges posed by more complex systems and show that there are still issues to be overcome. PMID:22101543

  19. 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

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

    PubMed

    Case, David H; Campbell, Josh E; Bygrave, Peter J; Day, Graeme M

    2016-02-09

    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.

  1. 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

  2. XTALOPT Version r10: An open-source evolutionary algorithm for crystal structure prediction

    NASA Astrophysics Data System (ADS)

    Avery, Patrick; Falls, Zackary; Zurek, Eva

    2017-08-01

    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.

  3. 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.

  4. 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

  5. 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.

  6. 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.

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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).

  12. 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

  13. 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.

  14. Ground-state characterizations of systems predicted to exhibit L11 or L13 crystal structures

    NASA Astrophysics Data System (ADS)

    Nelson, Lance J.; Hart, Gus L. W.; Curtarolo, Stefano

    2012-02-01

    Despite their geometric simplicity, the crystal structures L11 (CuPt) and L13 (CdPt3) do not appear as ground states experimentally, except in Cu-Pt. We investigate the possibility that these phases are ground states in other binary intermetallic systems, but overlooked experimentally. Via the synergy between high-throughput and cluster-expansion computational methods, we conduct a thorough search for systems that may exhibit these phases and calculate order-disorder transition temperatures when they are predicted. High-throughput calculations predict L11 ground states in the systems Ag-Pd, Ag-Pt, Cu-Pt, Pd-Pt, Li-Pd, Li-Pt, and L13 ground states in the systems Cd-Pt, Cu-Pt, Pd-Pt, Li-Pd, Li-Pt. Cluster expansions confirm the appearance of these ground states in some cases. In the other cases, cluster expansion predicts unsuspected derivative superstructures as ground states. The order-disorder transition temperatures for all L11/L13 ground states were found to be sufficiently high that their physical manifestation may be possible.

  15. 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.

  16. XtalOpt  version r9: An open-source evolutionary algorithm for crystal structure prediction

    SciTech Connect

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

    2015-10-23

    This is a new version of XtalOpt, an evolutionary algorithm for crystal structure prediction 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. We have detailed the new version incorporates many bug-fixes and new features here and predict the crystal structure of a system from its stoichiometry alone, using evolutionary algorithms.

  17. 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

  18. 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?

  19. Exchange-Hole Dipole Dispersion Model for Accurate Energy Ranking in Molecular Crystal Structure Prediction II: Nonplanar Molecules.

    PubMed

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

    2017-10-03

    The crystal structure prediction (CSP) of a given compound from its molecular diagram is a fundamental challenge in computational chemistry with implications in relevant technological fields. A key component of CSP is the method to calculate the lattice energy of a crystal, which allows the ranking of candidate structures. This work is the second part of our investigation to assess the potential of the exchange-hole dipole moment (XDM) dispersion model for crystal structure prediction. In this article, we study the relatively large, nonplanar, mostly flexible molecules in the first five blind tests held by the Cambridge Crystallographic Data Centre. Four of the seven experimental structures are predicted as the energy minimum, and thermal effects are demonstrated to have a large impact on the ranking of at least another compound. As in the first part of this series, delocalization error affects the results for a single crystal (compound X), in this case by detrimentally overstabilizing the π-conjugated conformation of the monomer. Overall, B86bPBE-XDM correctly predicts 16 of the 21 compounds in the five blind tests, a result similar to the one obtained using the best CSP method available to date (dispersion-corrected PW91 by Neumann et al.). Perhaps more importantly, the systems for which B86bPBE-XDM fails to predict the experimental structure as the energy minimum are mostly the same as with Neumann's method, which suggests that similar difficulties (absence of vibrational free energy corrections, delocalization error,...) are not limited to B86bPBE-XDM but affect GGA-based DFT-methods in general. Our work confirms B86bPBE-XDM as an excellent option for crystal energy ranking in CSP and offers a guide to identify crystals (organic salts, conjugated flexible systems) where difficulties may appear.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Verifying predictions of the L13 crystal structure in Cd-Pt and Pd-Pt by exhaustive enumeration

    NASA Astrophysics Data System (ADS)

    Hart, Gus L. W.

    2009-07-01

    In 2001, S. Müller and A. Zunger [Phys. Rev. Lett. 87, 165502 (2001)] predicted a never-before-observed crystal structure in Ag-Pd. Recently, Curtarolo predicted the same structure to be stable in Pt-Cd and Pt-Pd [S. Curtarolo , CALPHAD: Comput. Coupling Phase Diagrams Thermochem. 29, 163 (2005)]. The predicted structure is unique in several ways. Though never seen in any other face-centered-cubic-based intermetallic binary compound or ordered alloy, it is relatively simple—it contains only four atoms per unit cell. Furthermore, the structure is the only one of this small size, except the L12 structure, that cannot be characterized as a simple stacking of layers where each layer contains only one kind of atom. We construct a first-principles-based Hamiltonian and search it for the thermodynamically stable (lowest energy) structures. Using a (practically) exhaustive enumeration of about three million of the most likely candidate structures, we find that this new structure, designated L13 , is indeed a ground state in both Cd-Pt and Pd-Pt. Experimental efforts to validate the predictions are underway.

  5. 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.

  6. 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.

  7. Ground-State Crystal Structure of Strontium Peroxide Predicted from First Principles.

    PubMed

    Wang, Yanchao; Wang, Sheng; Zhang, Yunwei; Lv, Jian; Chen, Yue; Zheng, Weitao; Ma, Yanming

    2017-07-03

    It has been widely believed that SrO2, a typical alkaline earth metal peroxide, should adopt the tetrahedral CaC2-type structure (space group I4/mmm) at ambient pressure. Here we report a monoclinic structure (space group C2c), as predicted from first-principles swarm structure searching simulations, is energetically more favorable than the CaC2-type structure at ambient pressure and low temperature, while the I4/mmm structure is only stable at high pressure (>20 GPa) or elevated temperature conditions. A key difference between these structures is the distinct orientation of peroxide ions. Especially, frozen-phonon calculations indicate that the C2c structure can be derived by a softening mode phonon from I4/mmm structure. Furthermore, a high-pressure phase of SrO2 with P21/c symmetries containing two layers of peroxide ions with different orientations is uncovered at pressures higher than 36 GPa. Our electronic band calculations indicate that all the stable structures of SrO2 are wide band gap semiconductors. Our results represent a step forward toward a more complete understanding of the structures and properties of alkaline earth metal peroxides.

  8. 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

  9. PHOENIX: A Scoring Function for Affinity Prediction Derived Using High-Resolution Crystal Structures and Calorimetry Measurements

    PubMed Central

    Tang, Yat T.; Marshall, Garland R.

    2011-01-01

    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 (r2pred) 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 (Rp) of 0.575 and a mean error (ME) of 1.41 pKd. 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

  10. 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

  11. 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

  12. First-principles prediction of a ground state crystal structure of magnesium borohydride.

    PubMed

    Ozolins, V; Majzoub, E H; Wolverton, C

    2008-04-04

    Mg(BH(4))(2) contains a large amount of hydrogen by weight and by volume, but its promise as a candidate for hydrogen storage is dependent on the currently unknown thermodynamics of H2 release. Using first-principles density-functional theory calculations and a newly developed prototype electrostatic ground state search strategy, we predict a new T=0 K ground state of Mg(BH(4))(2) with I4[over ]m2 symmetry, which is 5 kJ/mol lower in energy than the recently proposed P6(1) structure. The calculated thermodynamics of H(2) release are within the range required for reversible storage.

  13. 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.

  14. 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.

  15. 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

  16. 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.

  17. Genetic algorithm prediction of crystal structure of metastable Si-IX phase

    SciTech Connect

    Nguyen, Manh Cuong; Zhao, Xin; Wang, Yangang; Wang, Cai-Zhuang; Ho, Kai-Ming

    2013-12-14

    We performed genetic algorithm search for the atomic structure of the long Lime unsolved Si-IX phase. We found two new structures with space groups of P4(2)/m and P-4, respectively, which have lattice parameters in excellent agreement with the experimental data. The phonon calculations showed that the P4(2)/m structure exhibits a soft phonon mode, while the P-4 structure is dynamically stable. Our calculation also showed that the P-4 structure is a meta-stable structure in a pressure range from 0 to 40 GPa, The Si-IX phase could be a mixed phase consisting of the P4(2)/m and the P-4 structures. Published by Elsevier Ltd.

  18. 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.

  19. Synthetic Studies of Antimony Sulfur Iodide and Predictions/Synthesis of New Nitrogen Containing Crystal Structures.

    DTIC Science & Technology

    1983-02-01

    8 2 Cuspidine, Ca4S12O7F2 .......................................... 13 3 Cuspidine- Yttrium Aluminate...oxide, i.e., a 4known mineral, can we predict that an isotypic mixed oxyfluoride , oxynitride, oxyfluoronitride might probably exist. This would be...where N-containing species have been found.37 For the oxyfluorides , which are well-known, it appears that F goes to the 0(1) or apical site in *octahedral

  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. Prediction of molecular crystal structures by a crystallographic QM/MM model with full space-group symmetry.

    PubMed

    Mörschel, Philipp; Schmidt, Martin U

    2015-01-01

    A crystallographic quantum-mechanical/molecular-mechanical model (c-QM/MM model) with full space-group symmetry has been developed for molecular crystals. The lattice energy was calculated by quantum-mechanical methods for short-range interactions and force-field methods for long-range interactions. The quantum-mechanical calculations covered the interactions within the molecule and the interactions of a reference molecule with each of the surrounding 12-15 molecules. The interactions with all other molecules were treated by force-field methods. In each optimization step the energies in the QM and MM shells were calculated separately as single-point energies; after adding both energy contributions, the crystal structure (including the lattice parameters) was optimized accordingly. The space-group symmetry was maintained throughout. Crystal structures with more than one molecule per asymmetric unit, e.g. structures with Z' = 2, hydrates and solvates, have been optimized as well. Test calculations with different quantum-mechanical methods on nine small organic molecules revealed that the density functional theory methods with dispersion correction using the B97-D functional with 6-31G* basis set in combination with the DREIDING force field reproduced the experimental crystal structures with good accuracy. Subsequently the c-QM/MM method was applied to nine compounds from the CCDC blind tests resulting in good energy rankings and excellent geometric accuracies.

  4. Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs.

    PubMed

    Buch, V; Martonák, R; Parrinello, M

    2006-05-28

    Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.

  5. 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

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

    PubMed

    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.

  7. 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.)

  8. 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.

  9. Functional significance of protein assemblies predicted by the crystal structure of the restriction endonuclease BsaWI.

    PubMed

    Tamulaitis, Gintautas; Rutkauskas, Marius; Zaremba, Mindaugas; Grazulis, Saulius; Tamulaitiene, Giedre; Siksnys, Virginijus

    2015-09-18

    Type II restriction endonuclease BsaWI recognizes a degenerated sequence 5'-W/CCGGW-3' (W stands for A or T, '/' denotes the cleavage site). It belongs to a large family of restriction enzymes that contain a conserved CCGG tetranucleotide in their target sites. These enzymes are arranged as dimers or tetramers, and require binding of one, two or three DNA targets for their optimal catalytic activity. Here, we present a crystal structure and biochemical characterization of the restriction endonuclease BsaWI. BsaWI is arranged as an 'open' configuration dimer and binds a single DNA copy through a minor groove contacts. In the crystal primary BsaWI dimers form an indefinite linear chain via the C-terminal domain contacts implying possible higher order aggregates. We show that in solution BsaWI protein exists in a dimer-tetramer-oligomer equilibrium, but in the presence of specific DNA forms a tetramer bound to two target sites. Site-directed mutagenesis and kinetic experiments show that BsaWI is active as a tetramer and requires two target sites for optimal activity. We propose BsaWI mechanism that shares common features both with dimeric Ecl18kI/SgrAI and bona fide tetrameric NgoMIV/SfiI enzymes. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

  10. Photonic Crystal Laser Accelerator Structures

    SciTech Connect

    Cowan, Benjamin M

    2003-05-21

    Photonic crystals have great potential for use as laser-driven accelerator structures. A photonic crystal is a dielectric structure arranged in a periodic geometry. Like a crystalline solid with its electronic band structure, the modes of a photonic crystal lie in a set of allowed photonic bands. Similarly, it is possible for a photonic crystal to exhibit one or more photonic band gaps, with frequencies in the gap unable to propagate in the crystal. Thus photonic crystals can confine an optical mode in an all-dielectric structure, eliminating the need for metals and their characteristic losses at optical frequencies. We discuss several geometries of photonic crystal accelerator structures. Photonic crystal fibers (PCFs) are optical fibers which can confine a speed-of-light optical mode in vacuum. Planar structures, both two- and three-dimensional, can also confine such a mode, and have the additional advantage that they can be manufactured using common microfabrication techniques such as those used for integrated circuits. This allows for a variety of possible materials, so that dielectrics with desirable optical and radiation-hardness properties can be chosen. We discuss examples of simulated photonic crystal structures to demonstrate the scaling laws and trade-offs involved, and touch on potential fabrication processes.

  11. 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.

  12. 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.

  13. 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

  14. 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)

  15. Predictive control of crystal size distribution in protein crystallization.

    PubMed

    Shi, Dan; Mhaskar, Prashant; El-Farra, Nael H; Christofides, Panagiotis D

    2005-07-01

    This work focuses on the modelling, simulation and control of a batch protein crystallization process that is used to produce the crystals of tetragonal hen egg-white (HEW) lysozyme. First, a model is presented that describes the formation of protein crystals via nucleation and growth. Existing experimental data are used to develop empirical models of the nucleation and growth mechanisms of the tetragonal HEW lysozyme crystal. The developed growth and nucleation rate expressions are used within a population balance model to simulate the batch crystallization process. Then, model reduction techniques are used to derive a reduced-order moments model for the purpose of controller design. Online measurements of the solute concentration and reactor temperature are assumed to be available, and a Luenberger-type observer is used to estimate the moments of the crystal size distribution based on the available measurements. A predictive controller, which uses the available state estimates, is designed to achieve the objective of maximizing the volume-averaged crystal size while respecting constraints on the manipulated input variables (which reflect physical limitations of control actuators) and on the process state variables (which reflect performance considerations). Simulation results demonstrate that the proposed predictive controller is able to increase the volume-averaged crystal size by 30% and 8.5% compared to constant temperature control (CTC) and constant supersaturation control (CSC) strategies, respectively, while reducing the number of fine crystals produced. Furthermore, a comparison of the crystal size distributions (CSDs) indicates that the product achieved by the proposed predictive control strategy has larger total volume and lower polydispersity compared to the CTC and CSC strategies. Finally, the robustness of the proposed method (achieved due to the presence of feedback) with respect to plant-model mismatch is demonstrated. The proposed method is

  16. 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.

  17. 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

  18. PREDICTION OF PROTEIN CRYSTALLIZATION OUTCOME USING A HYBRID METHOD

    PubMed Central

    Zucker, Frank H.; Stewart, Christine; Rosa, Jaclyn dela; Kim, Jessica; Zhang, Li; Xiao, Liren; Ross, Jenni; Napuli, Alberto J.; Mueller, Natascha; Castaneda, Lisa J.; Nakazawa Hewitt, Stephen R.; Arakaki, Tracy L.; Larson, Eric T.; Subramanian, Easwara; Verlinde, Christophe L.M.J.; Fan, Erkang; Buckner, Frederick S.; Van Voorhis, Wesley C.; Merritt, Ethan A.; Hol, Wim G. J.

    2010-01-01

    The great power of protein crystallography to reveal biological structure is often limited by the tremendous effort required to produce suitable crystals. A hybrid crystal growth predictive model is presented that combines both experimental and sequence-derived data from target proteins, including novel variables derived from physico-chemical characterization such as R30, the ratio between a protein‘s DSF intensity at 30 °C and at Tm. This hybrid model is shown to be more powerful than sequence-based prediction alone – and more likely to be useful for prioritizing and directing the efforts of structural genomics and individual structural biology laboratories. PMID:20347992

  19. 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.

  20. 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).

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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

  6. Developing a Gel-Based Sensor Using Crystal Morphology Prediction.

    PubMed

    Veits, Gesine K; Carter, Kelsey K; Cox, Sarah J; McNeil, Anne J

    2016-09-21

    The stimuli-responsive nature of molecular gels makes them appealing platforms for sensing. The biggest challenge is in identifying an appropriate gelator for each specific chemical or biological target. Due to the similarities between crystallization and gel formation, we hypothesized that the tools used to predict crystal morphologies could be useful for identifying gelators. Herein, we demonstrate that new gelators can be discovered by focusing on scaffolds with predicted high aspect ratio crystals. Using this morphology prediction method, we identified two promising molecular scaffolds containing lead atoms. Because solvent is largely ignored in morphology prediction but can play a major role in gelation, each scaffold needed to be structurally modified before six new Pb-containing gelators were discovered. One of these new gelators was developed into a robust sensor capable of detecting lead at the U.S. Environmental Protection Agency limit for paint (5000 ppm).

  7. 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.

  8. Crystal structure refinement with SHELXL

    PubMed Central

    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. PMID:25567568

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Crystal structure of pymetrozine

    PubMed Central

    Jeon, Youngeun; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-01-01

    The title compound, C10H11N5O {systematic name: 6-methyl-4-[(E)-(pyridin-3-yl­methyl­idene)amino]-4,5-di­hydro-1,2,4-triazin-3(2H)-one}, C10H11N5O, is used as an anti­feedant in pest control. The asymmetric unit comprises two independent mol­ecules, A and B, in which the dihedral angles between the pyridinyl and triazinyl ring planes [r.m.s. deviations = 0.0132 and 0.0255 ] are 11.60 (6) and 18.06 (4)°, respectively. In the crystal, N—H⋯O, N—H⋯N, C—H⋯N and C—H⋯O hydrogen bonds, together with weak π–π inter­actions [ring-centroid separations = 3.5456 (9) and 3.9142 (9) Å], link the pyridinyl and triazinyl rings of A mol­ecules, generating a three-dimensional network. PMID:26279908

  14. Crystal structure of pymetrozine.

    PubMed

    Jeon, Youngeun; Kim, Jineun; Kang, Gihaeng; Kim, Tae Ho

    2015-07-01

    The title compound, C10H11N5O {systematic name: 6-methyl-4-[(E)-(pyridin-3-yl-methyl-idene)amino]-4,5-di-hydro-1,2,4-triazin-3(2H)-one}, C10H11N5O, is used as an anti-feedant in pest control. The asymmetric unit comprises two independent mol-ecules, A and B, in which the dihedral angles between the pyridinyl and triazinyl ring planes [r.m.s. deviations = 0.0132 and 0.0255 ] are 11.60 (6) and 18.06 (4)°, respectively. In the crystal, N-H⋯O, N-H⋯N, C-H⋯N and C-H⋯O hydrogen bonds, together with weak π-π inter-actions [ring-centroid separations = 3.5456 (9) and 3.9142 (9) Å], link the pyridinyl and triazinyl rings of A mol-ecules, generating a three-dimensional network.

  15. Synthesis, crystal structure analysis, molecular docking studies and density functional theory predictions of the local reactive properties and degradation properties of a novel halochalcone

    NASA Astrophysics Data System (ADS)

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

    2017-09-01

    In the present study, single crystals of E)-3-(3,5-dichlorophenyl)-1-(4-fluorophenyl)prop-2-en-1-one, were prepared and structurally characterized by single crystal X-ray diffraction analysis. The molecular structure crystallized in monoclinic crystal system with P21/c space group. Sensitivity of the title molecule towards electrophilic attacks has been examined by calculations of average localized ionization energies (ALIE) and their mapping to electron density surface. Further determination of atoms that could be important reactive centres has been performed by calculations of Fukui functions. Sensitivity of title molecule towards autoxidation and hydrolysis mechanisms has been assessed by calculations of bond dissociation energies and radial distribution functions (RDF), respectively. Also, in order to explore possible binding mode of the title compound towards Dihydrofolate reductase enzyme, we have utilized in silico molecular docking to explore possible binding modes of the title compound with the DHFR enzyme.

  16. Crystal Structure of Bi

    SciTech Connect

    Borg, Stefan; Svensson, Goeran

    2001-02-15

    The room temperature structures of the two-layer Aurivillius phases Bi{sub 2.5}Me{sub 0.5}Nb{sub 2}O{sub 9} (Me=Na, K) have been refined with the Rietveld method from powder neutron diffraction data ({lambda}=1.470 {angstrom}). They consist of (Bi{sub 2}O{sub 2}){sup 2+} layers interleaved with perovskite (Bi{sub 0.5}Me{sub 0.5}Nb{sub 2}O{sub 7}){sup 2-} (Me=Na, K) slabs. The structures were refined in the orthorhombic space group A2{sub 1}am, Z=4, and the unit cell parameters of the two oxides are a= 5.4937(3), b=5.4571(4), c=24.9169(14) {angstrom} and a=5.5005(8), b=5.4958(8), c=25.2524(16) {angstrom}, respectively. The orthorhombic distortion increases with decreasing Me+ cation size in the perovskite layer (Bi/Me){sup 2+} site and the lone pair electrons from the Bi{sup 3+} cation are influencing the site distortion. This is in agreement with other two-layer Aurivillius phases and originates from bonding requirements depending on size and electronic environment.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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)

  5. Optimization of photonic crystal structures.

    PubMed

    Smajic, Jasmin; Hafner, Christian; Erni, Daniel

    2004-11-01

    We report on the numerical structural optimization of two-dimensional photonic crystal (PhC) power dividers by using two different classes of optimization algorithms, namely, a modified truncated Newton (TN) gradient search as deterministic local optimization scheme and an evolutionary optimization representing the probabilistic global search strategies. Because of the severe accuracy requirements during optimization, the proper PhC device has been simulated by using the multiple-multipole program that is contained in the MaX-1 software package. With both optimizer classes, we found reliable and promising solutions that provide vanishing power reflection and perfect power balance at any specified frequency within the photonic bandgap. This outcome is astonishing in light of the discrete nature inherent in the underlying PhC structure, especially when the optimizer is allowed to intervene only within a very small volume of the device. Even under such limiting constraints structural optimization is not only feasible but has proven to be highly successful.

  6. 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.

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

    NASA Astrophysics Data System (ADS)

    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.

    2017-04-01

    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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. Optically switchable liquid crystal photonic structures.

    PubMed

    Urbas, Augustine; Tondiglia, Vincent; Natarajan, Lalgudi; Sutherland, Richard; Yu, Haiping; Li, J-H; Bunning, Timothy

    2004-10-27

    Photo-optic materials offer the possibility of light controlled photonic devices, intelligent and environmentally adaptive optical materials. One strategy for creating these materials is the combination of structure formation through holographic photopolymerization and the variable optical properties of liquid crystals. Holographically patterned, polymer stabilized liquid crystals (HPSLCs) have proven to be useful optical materials. By incorporating photo-optic, azobenzene-derived liquid crystal blends into such material systems, we have generated practical photoresponsive optical materials.

  13. Structural Transitions in Cholesteric Liquid Crystal Droplets

    SciTech Connect

    Zhou, Ye; Bukusoglu, Emre; Martínez-González, José A.; Rahimi, Mohammad; Roberts, Tyler F.; Zhang, Rui; Wang, Xiaoguang; Abbott, Nicholas L.; de Pablo, Juan J.

    2016-07-26

    Confinement of cholesteric liquid crystals (ChLC) into droplets leads to a delicate interplay between elasticity, chirality, and surface energy. In this work, we rely on a combination of theory and experiments to understand the rich morphological behavior that arises from that balance. More specifically, a systematic study of micrometer-sized ChLC droplets is presented as a function of chirality and surface energy (or anchoring). With increasing chirality, a continuous transition is observed from a twisted bipolar structure to a radial spherical structure, all within a narrow range of chirality. During such a transition, a bent structure is predicted by simulations and confirmed by experimental observations. Simulations are also able to capture the dynamics of the quenching process observed in experiments. Consistent with published work, it is found that nanoparticles are attracted to defect regions on the surface of the droplets. For weak anchoring conditions at the nanoparticle surface, ChLC droplets adopt a morphology similar to that of the equilibrium helical phase observed for ChLCs in the bulk. As the anchoring strength increases, a planar bipolar structure arises, followed by a morphological transition to a bent structure. The influence of chirality and surface interactions are discussed in the context of the potential use of ChLC droplets as stimuli-responsive materials for reporting molecular adsorbates.

  14. 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.

  15. The crystal structure Escherichia coli Spy

    PubMed Central

    Kwon, Eunju; Kim, Dong Young; Gross, Carol A; Gross, John D; Kim, Kyeong Kyu

    2010-01-01

    Escherichia coli spheroplast protein y (EcSpy) is a small periplasmic protein that is homologous with CpxP, an inhibitor of the extracytoplasmic stress reponse. Stress conditions such as spheroplast formation induce the expression of Spy via the Cpx or the Bae two-component systems in E. coli, though the function of Spy is unknown. Here, we report the crystal structure of EcSpy, which reveals a long kinked hairpin-like structure of four α-helices that form an antiparallel dimer. The dimer contains a curved oval shape with a highly positively charged concave surface that may function as a ligand binding site. Sequence analysis reveals that Spy is highly conserved over the Enterobacteriaceae family. Notably, three conserved regions that contain identical residues and two LTxxQ motifs are placed at the horizontal end of the dimer structure, stablizing the overall fold. CpxP also contains the conserved sequence motifs and has a predicted secondary structure similar to Spy, suggesting that Spy and CpxP likely share the same fold. PMID:20799348

  16. The crystal structure Escherichia coli Spy.

    PubMed

    Kwon, Eunju; Kim, Dong Young; Gross, Carol A; Gross, John D; Kim, Kyeong Kyu

    2010-11-01

    Escherichia coli spheroplast protein y (EcSpy) is a small periplasmic protein that is homologous with CpxP, an inhibitor of the extracytoplasmic stress response. Stress conditions such as spheroplast formation induce the expression of Spy via the Cpx or the Bae two-component systems in E. coli, though the function of Spy is unknown. Here, we report the crystal structure of EcSpy, which reveals a long kinked hairpin-like structure of four α-helices that form an antiparallel dimer. The dimer contains a curved oval shape with a highly positively charged concave surface that may function as a ligand binding site. Sequence analysis reveals that Spy is highly conserved over the Enterobacteriaceae family. Notably, three conserved regions that contain identical residues and two LTxxQ motifs are placed at the horizontal end of the dimer structure, stabilizing the overall fold. CpxP also contains the conserved sequence motifs and has a predicted secondary structure similar to Spy, suggesting that Spy and CpxP likely share the same fold.

  17. 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

  18. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

    Determining the crystal structure parameters of a material is an important issue in crystallography and material science. Knowing the crystal structure parameters helps in understanding the physical behavior of material. It can be difficult to obtain crystal parameters for complex structures, particularly those materials that show local symmetry as well as global symmetry. This work provides a tool that extracts crystal parameters such as primitive vectors, basis vectors and space groups from the atomic coordinates of crystal structures. A visualization tool for examining crystals is also provided. Accordingly, this work could help crystallographers, chemists and material scientists to analyze crystal structures efficiently. Program summaryTitle of program: BilKristal Catalogue identifier: ADYU_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/ADYU_v1_0 Program obtainable from: CPC Program Library, Queen's University of Belfast, N. Ireland Licensing provisions: None Programming language used: C, C++, Microsoft .NET Framework 1.1 and OpenGL Libraries Computer: Personal Computers with Windows operating system Operating system: Windows XP Professional RAM: 20-60 MB No. of lines in distributed program, including test data, etc.:899 779 No. of bytes in distributed program, including test date, etc.:9 271 521 Distribution format:tar.gz External routines/libraries: Microsoft .NET Framework 1.1. For visualization tool, graphics card driver should also support OpenGL Nature of problem: Determining crystal structure parameters of a material is a quite important issue in crystallography. Knowing the crystal structure parameters helps to understand physical behavior of material. For complex structures, particularly, for materials which also contain local symmetry as well as global symmetry, obtaining crystal parameters can be quite hard. Solution method: The tool extracts crystal parameters such as primitive vectors, basis vectors and identify the space group from

  19. 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.

  20. 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.

  1. Liquid crystal light valve structures

    NASA Technical Reports Server (NTRS)

    Koda, N. J. (Inventor)

    1985-01-01

    An improved photosensor film and liquid crystal light valves embodying said film is provided. The photosensor film and liquid crystal light valve is characterized by a significant lower image retention time while maintaining acceptable photosensitivity. The photosensor film is produced by sputter depositing CdS onto an ITO substrate in an atmosphere of argon/H2S gas while maintaining the substrate at a temperature in the range of about 130 C to about 200 C and while introducing nitrogen gas into the system to the extent of not more than about 1% of plasma mixture. Following sputter deposition of the CdS, the film is annealed in an inert gas at temperatures ranging from about 300 C to about 425 C.

  2. 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.

  3. 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.

  4. 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%.

  5. 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.

  6. Crystal structure of neotame anhydrate polymorph G.

    PubMed

    Dong, Zedong; Young, Victor G; Sheth, Agam; Munson, Eric J; Schroeder, Steve A; Prakash, Indra; Grant, David J W

    2002-10-01

    To determine the crystal structure of the neotame anhydrate polymorph G and to evaluate X-ray powder diffractometry (XRPD) with molecular modeling as an alternative method for determining the crystal structure of this conformationally flexible dipeptide. The crystal structure of polymorph G was determined by single crystal X-ray crystallography (SCXRD) and also from the X-ray powder diffraction (XRPD) pattern using molecular modeling (Cerius2, Powder Solve module). From SCXRD, polymorph G crystals are orthorhombic with space group of P2(1)2(1)2(1) with Z = 4, unit cell constants: a = 5.5999(4), b = 11.8921(8), c = 30.917(2) A, and one neotame molecule per asymmetric unit. The XRPD pattern of polymorph G, analyzed by Cerius2 software, led to the same P2(1)2(1)2(1) space group and almost identical unit cell dimensions. However, with 13 rigid bodies defined, Cerius2 gives a conformation of the neotame molecule, which is different from that determined by SCXRD. For neotame anhydrate polymorph G, the unit cell dimensions calculated from XRPD were almost identical to those determined by SCXRD. However, the crystal structure determined by XRPD closely resembled that determined by SCXRD, only when the correct conformation of the neotame molecule had been chosen before detailed analysis of the XRPD pattern.

  7. 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.

  8. 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.

  9. 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.

  10. Structure and stability prediction of compounds with evolutionary algorithms.

    PubMed

    Revard, Benjamin C; Tipton, William W; Hennig, Richard G

    2014-01-01

    Crystal structure prediction is a long-standing challenge in the physical sciences. In recent years, much practical success has been had by framing it as a global optimization problem, leveraging the existence of increasingly robust and accurate free energy calculations. This optimization problem has often been solved using evolutionary algorithms (EAs). However, many choices are possible when designing an EA for structure prediction, and innovation in the field is ongoing. We review the current state of evolutionary algorithms for crystal structure and composition prediction and discuss the details of methodological and algorithmic choices. Finally, we review the application of these algorithms to many systems of practical and fundamental scientific interest.

  11. 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.

  12. 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

  13. 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

  14. 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

  15. Machine learning for autonomous crystal structure identification.

    PubMed

    Reinhart, Wesley F; Long, Andrew W; Howard, Michael P; Ferguson, Andrew L; Panagiotopoulos, Athanassios Z

    2017-07-21

    We present a machine learning technique to discover and distinguish relevant ordered structures from molecular simulation snapshots or particle tracking data. Unlike other popular methods for structural identification, our technique requires no a priori description of the target structures. Instead, we use nonlinear manifold learning to infer structural relationships between particles according to the topology of their local environment. This graph-based approach yields unbiased structural information which allows us to quantify the crystalline character of particles near defects, grain boundaries, and interfaces. We demonstrate the method by classifying particles in a simulation of colloidal crystallization, and show that our method identifies structural features that are missed by standard techniques.

  16. 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.

  17. 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.

  18. 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

  19. 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).

  20. Crystal structure of the eukaryotic ribosome.

    PubMed

    Ben-Shem, Adam; Jenner, Lasse; Yusupova, Gulnara; Yusupov, Marat

    2010-11-26

    Crystal structures of prokaryotic ribosomes have described in detail the universally conserved core of the translation mechanism. However, many facets of the translation process in eukaryotes are not shared with prokaryotes. The crystal structure of the yeast 80S ribosome determined at 4.15 angstrom resolution reveals the higher complexity of eukaryotic ribosomes, which are 40% larger than their bacterial counterparts. Our model shows how eukaryote-specific elements considerably expand the network of interactions within the ribosome and provides insights into eukaryote-specific features of protein synthesis. Our crystals capture the ribosome in the ratcheted state, which is essential for translocation of mRNA and transfer RNA (tRNA), and in which the small ribosomal subunit has rotated with respect to the large subunit. We describe the conformational changes in both ribosomal subunits that are involved in ratcheting and their implications in coordination between the two associated subunits and in mRNA and tRNA translocation.

  1. 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.

  2. 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.

  3. Crystal structure of KPC-2

    PubMed Central

    Ke, Wei; Bethel, Christopher R.; Thomson, Jodi M.; Bonomo, Robert A.; van den Akker, Focco

    2008-01-01

    β-lactamases inactivate β-lactam antibiotics and are a major cause of antibiotic resistance. The recent outbreaks of Klebsiella pneumoniae carbapenem-resistant (KPC) infections mediated by KPC type β-lactamases are creating a serious threat to our “last resort” antibiotics, the carbapenems. KPC β-lactamases are thus carbapenemases and are a subclass of Class A β-lactamases that have evolved to efficiently hydrolyze carbapenems and cephamycins which contain substitutions at the α position proximal to the carbonyl group that normally render these β-lactams resistant to hydrolysis. To investigate the molecular basis of this carbapenemase activity, we have determined the structure of KPC-2 at 1.85Å resolution. The active site of KPC-2 reveals the presence of a bicine buffer molecule which interacts via its carboxyl group with conserved active site residues S130, K234, T235, and T237; this likely resembles the interactions the β-lactam carboxyl moiety makes in the Michaelis-Menten complex. Comparison of the KPC-2 structure with non-carbapenemases and previously determined NMC-A and SME-1 carbapenemase structures shows several active site alterations that are unique among carbapenemases. An outward shift of the catalytic S70 residue renders the active sites of the carbapenemases more shallow likely allowing easier access of the bulkier substrates. Further space for the α-substituents is likely provided by shifts in N132 and N170 in addition to concerted movements in the postulated carboxyl binding pocket that might allow the substrates to bind in a slightly different angle to accommodate these α-substituents. The structure of KPC-2 thus provides key insights into the carbapenemase activity of emerging Class A β-lactamases. PMID:17441734

  4. 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.

  5. 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.

  6. 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.

  7. Troublesome Crystal Structures: Prevention, Detection, and Resolution

    PubMed Central

    Harlow, Richard L.

    1996-01-01

    A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures. PMID:27805169

  8. Troublesome Crystal Structures: Prevention, Detection, and Resolution.

    PubMed

    Harlow, Richard L

    1996-01-01

    A large number of incorrect crystal structures is being published today. These structures are proving to be a particular problem to those of us who are interested in comparing structural moieties found in the databases in order to develop structure-property relationships. Problems can reside in the input data, e.g., wrong unit cell or low quality intensity data, or in the structural model, e.g., wrong space group or atom types. Many of the common mistakes are, however, relatively easy to detect and thus should be preventable; at the very least, suspicious structures can be flagged, if not by the authors then by the referees and, ultimately, the crystallographic databases. This article describes some of the more common mistakes and their effects on the resulting structures, lists a series of tests that can be used to detect incorrect structures, and makes a strong plea for the publication of higher quality structures.

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

    PubMed

    Allen, Frank H; Motherwell, W D Samuel

    2002-06-01

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

  10. 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.

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. 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.

  16. 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

  17. 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).

  18. Nonlinear coherent structures in granular crystals

    NASA Astrophysics Data System (ADS)

    Chong, C.; Porter, Mason A.; Kevrekidis, P. G.; Daraio, C.

    2017-10-01

    The study of granular crystals, which are nonlinear metamaterials that consist of closely packed arrays of particles that interact elastically, is a vibrant area of research that combines ideas from disciplines such as materials science, nonlinear dynamics, and condensed-matter physics. Granular crystals exploit geometrical nonlinearities in their constitutive microstructure to produce properties (such as tunability and energy localization) that are not conventional to engineering materials and linear devices. In this topical review, we focus on recent experimental, computational, and theoretical results on nonlinear coherent structures in granular crystals. Such structures—which include traveling solitary waves, dispersive shock waves, and discrete breathers—have fascinating dynamics, including a diversity of both transient features and robust, long-lived patterns that emerge from broad classes of initial data. In our review, we primarily discuss phenomena in one-dimensional crystals, as most research to date has focused on such scenarios, but we also present some extensions to two-dimensional settings. Throughout the review, we highlight open problems and discuss a variety of potential engineering applications that arise from the rich dynamic response of granular crystals.

  19. A unified picture of the crystal structures of metals

    NASA Astrophysics Data System (ADS)

    Söderlind, Per; Eriksson, Olle; Johansson, Börje; Wills, J. M.; Boring, A. M.

    1995-04-01

    THE crystal structures of the light actinides have intrigued physicists and chemists for several decades1. Simple metals and transition metals have close-packed, high-symmetry structures, such as body-centred cubic, face-centred cubic and hexagonal close packing. In contrast, the structures of the light actinides are very loosely packed and of low symmetry-tetragonal, orthorhombic and monoclinic. To understand these differences, we have performed total-energy calculations, as a function of volume, for both high-and low-symmetry structures of a simple metal (aluminium), a non-magnetic transition metal (niobium), a ferromagnetic transition metal (iron) and a light actinide (uranium). We find that the crystal structure of all of these metals is determined by the balance between electrostatic (Madelung) interactions, which favour high symmetry, and a Peierls distortion of the crystal lattice, which favours low symmetry. We show that simple metals and transition metals can adopt low-symmetry structures on expansion of the lattice; and we predict that, conversely, the light actinides will undergo transitions to structures of higher symmetry on compression.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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.

  5. 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

  6. Observations on the crystal structures of lueshite

    NASA Astrophysics Data System (ADS)

    Mitchell, Roger H.; Burns, Peter C.; Knight, Kevin S.; Howard, Christopher J.; Chakhmouradian, Anton R.

    2014-06-01

    Laboratory powder XRD patterns of the perovskite-group mineral lueshite from the type locality (Lueshe, Kivu, DRC) and pure NaNbO3 demonstrate that lueshite does not adopt the same space group ( Pbma; #57) as the synthetic compound. The crystal structures of lueshite (2 samples) from Lueshe, Mont Saint-Hilaire (Quebec, Canada) and Sallanlatvi (Kola, Russia) have been determined by single-crystal CCD X-ray diffraction. These room temperature X-ray data for all single-crystal samples can be satisfactorily refined in the orthorhombic space group Pbnm (#62). Cell dimensions, atomic coordinates of the atoms, bond lengths and octahedron tilt angles are given for four crystals. Conventional neutron diffraction patterns for Lueshe lueshite recorded over the temperature range 11-1,000 K confirm that lueshite does not adopt space group Pbma within these temperatures. Neutron diffraction indicates no phase changes on cooling from room temperature to 11 K. None of these neutron diffraction data give satisfactorily refinements but suggest that this is the space group Pbnm. Time-of-flight neutron diffraction patterns for Lueshe lueshite recorded from room temperature to 700 °C demonstrate phase transitions above 550 °C from Cmcm through P4 /mbm to above 650 °C. Cell dimensions and atomic coordinates of the atoms are given for the three high-temperature phases. The room temperature to 400 °C structures cannot be satisfactorily resolved, and it is suggested that the lueshite at room temperature consists of domains of pinned metastable phases with orthorhombic and/or monoclinic structures. However, the sequence of high-temperature phase transitions observed is similar to those determined for synthetic NaTaO3, suggesting that the equilibrated room temperature structure of lueshite is orthorhombic Pbnm.

  7. 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

  8. 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'.

  9. Experimental investigation and prediction of oiling out during crystallization process

    NASA Astrophysics Data System (ADS)

    Kiesow, Kai; Tumakaka, Feelly; Sadowski, Gabriele

    2008-08-01

    Oiling out is an unwanted effect during the cooling crystallization of complex molecules from solution: upon cooling, crystallization is preceded by the formation of a second liquid phase (oiling out) which disturbs the crystallization process and often deteriorates the product properties. On the basis of the crystallization of 4,4' dihydroxydiphenylsulfone (DHDPS) from water/acetone mixtures and water/2-propanol mixtures, respectively, this study proved the dependence of the oiling-out behavior on the solvent system. Attempts were made to model the oiling-out phenomenon using a thermodynamic equation of state here: (Perturbed-Chain Statistical Associating Fluid Theory (PC-SAFT)). Applying this model, an oiling-out behavior of the ternary system DHDPS/water/acetone could be predicted qualitatively. Exchanging the water/acetone solvent mixture by a mixture of water and 2-propanol led to a prevention of oiling out. This could be predicted by the calculations using PC-SAFT, as well as confirmed experimentally. Furthermore, micrographs of the crystals obtained revealed the influence of the oiling out on the properties of the solid product. Size, shape and degree of agglomeration of the particles vary depending on whether an oiling out occurred during the cooling process or not.

  10. 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.

  11. 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.

  12. Servers for protein structure prediction.

    PubMed

    Fischer, Daniel

    2006-04-01

    The 1990s cultivated a generation of protein structure human predictors. As a result of structural genomics and genome sequencing projects, and significant improvements in the performance of protein structure prediction methods, a generation of automated servers has evolved in the past few years. Servers for close and distant homology modeling are now routinely used by many biologists, and have already been applied to the experimental structure determination process itself, and to the interpretation and annotation of genome sequences. Because dozens of servers are currently available, it is hard for a biologist to know which server(s) to use; however, the state of the art of these methods is now assessed through the LiveBench and CAFASP experiments. Meta-servers--servers that use the results of other autonomous servers to produce a consensus prediction--have proven to be the best performers, and are already challenging all but a handful of expert human predictors. The difference in performance of the top ten autonomous (non-meta) servers is small and hard to assess using relatively small test sets. Recent experiments suggest that servers will soon free humans from most of the burden of protein structure prediction.

  13. 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.

  14. Water in protein structure prediction

    PubMed Central

    Papoian, Garegin A.; Ulander, Johan; Eastwood, Michael P.; Luthey-Schulten, Zaida; Wolynes, Peter G.

    2004-01-01

    Proteins have evolved to use water to help guide folding. A physically motivated, nonpairwise-additive model of water-mediated interactions added to a protein structure prediction Hamiltonian yields marked improvement in the quality of structure prediction for larger proteins. Free energy profile analysis suggests that long-range water-mediated potentials guide folding and smooth the underlying folding funnel. Analyzing simulation trajectories gives direct evidence that water-mediated interactions facilitate native-like packing of supersecondary structural elements. Long-range pairing of hydrophilic groups is an integral part of protein architecture. Specific water-mediated interactions are a universal feature of biomolecular recognition landscapes in both folding and binding. PMID:14988499

  15. Crystal structures and properties of nylon polymers from theory

    SciTech Connect

    Dasgupta, S.; Goddard, W.A. III; Hammond, W.B.

    1996-12-11

    A complete force field (MSXX) for simulation of all nylon polymers is derived from ab initio quantum calculations. Special emphasis is given to the accuracy of the hydrogen bond potential for the amide unit and the torsional potential between the peptide and alkane fragments. The MSXX force field was used to predict the structures, moduli, and detailed geometries of all nine nylons for which there are experimental crystal data plus one other. For nylon-(2n) with 2n = 6, the {alpha} crystal structure (with all-trans CH{sub 2} chains nearly coplanar with the hydrogen bonding plane) is more stable, while for 2n > 6, {gamma} (with the alkane plane twisted by 70{degree}) is more stable. This change results from the increased importance of methylene packing interactions over H bonds for larger 2n. We find the highest Young`s modulus for nylon-7. 51 refs., 6 figs., 7 tabs.

  16. 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)

  17. 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

  18. 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.

  19. 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.

  20. 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

  1. 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.

  2. Crystal Structure of Cryptosporidium parvum Pyruvate Kinase

    PubMed Central

    Cook, William J.; Senkovich, Olga; Aleem, Khadijah; Chattopadhyay, Debasish

    2012-01-01

    Pyruvate kinase plays a critical role in cellular metabolism of glucose by serving as a major regulator of glycolysis. This tetrameric enzyme is allosterically regulated by different effector molecules, mainly phosphosugars. In response to binding of effector molecules and substrates, significant structural changes have been identified in various pyruvate kinase structures. Pyruvate kinase of Cryptosporidium parvum is exceptional among known enzymes of protozoan origin in that it exhibits no allosteric property in the presence of commonly known effector molecules. The crystal structure of pyruvate kinase from C. parvum has been solved by molecular replacement techniques and refined to 2.5 Å resolution. In the active site a glycerol molecule is located near the γ-phosphate site of ATP, and the protein structure displays a partially closed active site. However, unlike other structures where the active site is closed, the α6' helix in C. parvum pyruvate kinase unwinds and assumes an extended conformation. In the crystal structure a sulfate ion is found at a site that is occupied by a phosphate of the effector molecule in many pyruvate kinase structures. A new feature of the C. parvum pyruvate kinase structure is the presence of a disulfide bond cross-linking the two monomers in the asymmetric unit. The disulfide bond is formed between cysteine residue 26 in the short N-helix of one monomer with cysteine residue 312 in a long helix (residues 303–320) of the second monomer at the interface of these monomers. Both cysteine residues are unique to C. parvum, and the disulfide bond remained intact in a reduced environment. However, the significance of this bond, if any, remains unknown at this time. PMID:23056503

  3. 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.

  4. 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.

  5. 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

  6. 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

  7. TRITIUM RESERVOIR STRUCTURAL PERFORMANCE PREDICTION

    SciTech Connect

    Lam, P.S.; Morgan, M.J

    2005-11-10

    The burst test is used to assess the material performance of tritium reservoirs in the surveillance program in which reservoirs have been in service for extended periods of time. A materials system model and finite element procedure were developed under a Savannah River Site Plant-Directed Research and Development (PDRD) program to predict the structural response under a full range of loading and aged material conditions of the reservoir. The results show that the predicted burst pressure and volume ductility are in good agreement with the actual burst test results for the unexposed units. The material tensile properties used in the calculations were obtained from a curved tensile specimen harvested from a companion reservoir by Electric Discharge Machining (EDM). In the absence of exposed and aged material tensile data, literature data were used for demonstrating the methodology in terms of the helium-3 concentration in the metal and the depth of penetration in the reservoir sidewall. It can be shown that the volume ductility decreases significantly with the presence of tritium and its decay product, helium-3, in the metal, as was observed in the laboratory-controlled burst tests. The model and analytical procedure provides a predictive tool for reservoir structural integrity under aging conditions. It is recommended that benchmark tests and analysis for aged materials be performed. The methodology can be augmented to predict performance for reservoir with flaws.

  8. 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.

  9. 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

  10. Waveguide structures in anisotropic nonlinear crystals

    NASA Astrophysics Data System (ADS)

    Li, Da; Hong, Pengda; Meissner, Helmuth E.

    2017-02-01

    We report on the design and manufacturing parameters of waveguiding structures of anisotropic nonlinear crystals that are employed for harmonic conversions, using Adhesive-Free Bonding (AFB®). This technology enables a full range of predetermined refractive index differences that are essential for the design of single mode or low-mode propagation with high efficiency in anisotropic nonlinear crystals which in turn results in compact frequency conversion systems. Examples of nonlinear optical waveguides include periodically bonded walk-off corrected nonlinear optical waveguides and periodically poled waveguide components, such as lithium triborate (LBO), beta barium borate (β-BBO), lithium niobate (LN), potassium titanyl phosphate (KTP), zinc germanium phosphide (ZGP) and silver selenogallate (AGSE). Simulation of planar LN waveguide shows that when the electric field vector E lies in the k-c plane, the power flow is directed precisely along the propagation direction, demonstrating waveguiding effect in the planar waveguide. Employment of anisotropic nonlinear optical waveguides, for example in combination with AFB® crystalline fiber waveguides (CFW), provides access to the design of a number of novel high power and high efficiency light sources spanning the range of wavelengths from deep ultraviolet (as short as 200 nm) to mid-infrared (as long as about 18 μm). To our knowledge, the technique is the only generally applicable one because most often there are no compatible cladding crystals available to nonlinear optical cores, especially not with an engineer-able refractive index difference and large mode area.

  11. The Crystal Structures of Potentially Tautomeric Compounds

    NASA Astrophysics Data System (ADS)

    Furmanova, Nina G.

    1981-08-01

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

  12. Crystal structure of plant photosystem I

    NASA Astrophysics Data System (ADS)

    Ben-Shem, Adam; Frolow, Felix; Nelson, Nathan

    2003-12-01

    Oxygenic photosynthesis is the principal producer of both oxygen and organic matter on Earth. The conversion of sunlight into chemical energy is driven by two multisubunit membrane protein complexes named photosystem I and II. We determined the crystal structure of the complete photosystem I (PSI) from a higher plant (Pisum sativum var. alaska) to 4.4Å resolution. Its intricate structure shows 12 core subunits, 4 different light-harvesting membrane proteins (LHCI) assembled in a half-moon shape on one side of the core, 45 transmembrane helices, 167 chlorophylls, 3 Fe-S clusters and 2 phylloquinones. About 20 chlorophylls are positioned in strategic locations in the cleft between LHCI and the core. This structure provides a framework for exploration not only of energy and electron transfer but also of the evolutionary forces that shaped the photosynthetic apparatus of terrestrial plants after the divergence of chloroplasts from marine cyanobacteria one billion years ago.

  13. 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

  14. 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.

  15. 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.

  16. 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.

  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. Theoretical investigations of candidate crystal structures for β-carbonic acid.

    PubMed

    Reddy, Sandeep Kumar; Kulkarni, Chidambar H; Balasubramanian, Sundaram

    2011-03-28

    Using multiple computational tools, we examine five candidate crystal structures for β-carbonic acid, a molecular crystal of environmental and astrophysical significance. These crystals comprise of hydrogen bonded molecules in either sheetlike or chainlike topologies. Gas phase quantum calculations, empirical force field based crystal structure search, and periodic density functional theory based calculations and finite temperature simulations of these crystals have been carried out. The infrared spectrum calculated from density functional theory based molecular dynamics simulations compares well with experimental data. Results suggest crystals with one-dimensional hydrogen bonding topologies (chainlike) to be more stable than those with two-dimensional (sheetlike) hydrogen bonding networks. We predict that these structures can be distinguished on the basis of their far infrared spectra.

  19. 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.

  20. 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.

  1. 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.

  2. 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

  3. Clay Mineral Crystal Structure Tied to Composition

    NASA Image and Video Library

    2016-12-13

    This diagram illustrates how the dimensions of clay minerals' crystal structure are affected by which ions are present in the composition of the mineral. Different clay minerals were identified this way at two sites in Mars' Gale Crater: "Murray Buttes" and "Yellowknife Bay." In otherwise identical clay minerals, a composition that includes aluminum and ferric iron ions (red dots) results in slightly smaller crystalline unit cells than one that instead includes magnesium and ferrous iron ions (green dots). Ferric iron is more highly oxidized than ferrous iron. Crystalline cell units are the basic repeating building blocks that define minerals. X-ray diffraction analysis, a capability of the Chemistry and Mineralogy (CheMin) instrument on NASA's Curiosity Mars rover, identifies minerals from their crystalline structure. http://photojournal.jpl.nasa.gov/catalog/PIA21148

  4. 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.

  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. 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.

  7. 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.

  8. 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.

  9. 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.

  10. Crystal Structure of Cold Compressed Graphite

    NASA Astrophysics Data System (ADS)

    Amsler, Maximilian; Flores-Livas, José A.; Lehtovaara, Lauri; Balima, Felix; Ghasemi, S. Alireza; Machon, Denis; Pailhès, Stéphane; Willand, Alexander; Caliste, Damien; Botti, Silvana; San Miguel, Alfonso; Goedecker, Stefan; Marques, Miguel A. L.

    2012-02-01

    Through a systematic structural search we found an allotrope of carbon with Cmmm symmetry which we predict to be more stable than graphite for pressures above 10 GPa. This material, which we refer to as Z-carbon, is formed by pure sp3 bonds and it provides an explanation to several features in experimental x-ray diffraction and Raman spectra of graphite under pressure. The transition from graphite to Z-carbon can occur through simple sliding and buckling of graphene sheets. Our calculations predict that Z-carbon is a transparent wide band-gap semiconductor with a hardness comparable to diamond.

  11. Predictive structural dynamic network analysis.

    PubMed

    Chen, Rong; Herskovits, Edward H

    2015-04-30

    Classifying individuals based on magnetic resonance data is an important task in neuroscience. Existing brain network-based methods to classify subjects analyze data from a cross-sectional study and these methods cannot classify subjects based on longitudinal data. We propose a network-based predictive modeling method to classify subjects based on longitudinal magnetic resonance data. Our method generates a dynamic Bayesian network model for each group which represents complex spatiotemporal interactions among brain regions, and then calculates a score representing that subject's deviation from expected network patterns. This network-derived score, along with other candidate predictors, are used to construct predictive models. We validated the proposed method based on simulated data and the Alzheimer's Disease Neuroimaging Initiative study. For the Alzheimer's Disease Neuroimaging Initiative study, we built a predictive model based on the baseline biomarker characterizing the baseline state and the network-based score which was constructed based on the state transition probability matrix. We found that this combined model achieved 0.86 accuracy, 0.85 sensitivity, and 0.87 specificity. For the Alzheimer's Disease Neuroimaging Initiative study, the model based on the baseline biomarkers achieved 0.77 accuracy. The accuracy of our model is significantly better than the model based on the baseline biomarkers (p-value=0.002). We have presented a method to classify subjects based on structural dynamic network model based scores. This method is of great importance to distinguish subjects based on structural network dynamics and the understanding of the network architecture of brain processes and disorders. Copyright © 2015 Elsevier B.V. All rights reserved.

  12. 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

  13. Niobium hyperfine structure in crystal calcium tungstate

    NASA Technical Reports Server (NTRS)

    Tseng, D. L.; Kikuchi, C.

    1972-01-01

    A study of the niobium hyperfine structure in single crystal calcium tungstate was made by the combination of the technique of electron paramagnetic resonance and electron nuclear double resonance (EPR/ENDOR). The microwave frequency was about 9.4 GHz and the radio frequency from 20MHz to 70 MHz. The rare earth ions Nd(3+), U(3+), or Tm(3+) were added as the charge compensator for Nb(5+). To create niobium paramagnetic centers, the sample was irradiated at 77 deg K with a 10 thousand curie Co-60 gamma source for 1 to 2 hours at a dose rate of 200 K rads per hour and then transferred quickly into the cavity. In a general direction of magnetic field, the spectra showed 4 sets of 10 main lines corresponding to 4 nonequivalent sites of niobium with I = 9/2. These 4 sets of lines coalesced into 2 sets of 10 in the ab-plane and into a single set of 10 along the c-axis. This symmetry suggested that the tungsten ions are substituted by the niobium ions in the crystal.

  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. Protein structural domains: definition and prediction.

    PubMed

    Ezkurdia, Iakes; Tress, Michael L

    2011-11-01

    Recognition and prediction of structural domains in proteins is an important part of structure and function prediction. This unit lists the range of tools available for domain prediction, and describes sequence and structural analysis tools that complement domain prediction methods. Also detailed are the basic domain prediction steps, along with suggested strategies for different protein sequences and potential pitfalls in domain boundary prediction. The difficult problem of domain orientation prediction is also discussed. All the resources necessary for domain boundary prediction are accessible via publicly available Web servers and databases and do not require computational expertise.

  17. 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.

  18. Crystal Structure of the Marburg Virus VP35 Oligomerization Domain

    PubMed Central

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

    2016-01-01

    ABSTRACT 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. IMPORTANCE Marburg virus can cause severe disease, with up to 90% human lethality. Its genome is concise, only producing seven proteins. One of the proteins, VP35, is essential for replication of the viral genome and for evasion of host immune responses. VP35 oligomerizes (self-assembles) in order to function, yet the structure by which it assembles has not been visualized. Here we present two crystal structures of this oligomerization domain. In both structures, three copies of VP35 twist about each other to form a coiled coil. This trimeric assembly is in contrast to tetrameric predictions for VP35 of Ebola virus and to known structures of homologous proteins in the measles, mumps, and Nipah viruses. Distinct oligomeric states of the Marburg and Ebola virus VP35 proteins may explain differences between them in polymerase function and immune evasion. These findings may provide a more accurate understanding of the mechanisms governing VP35's functions and inform the design of therapeutics. PMID:27847355

  19. 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

  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. 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

  2. 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

  3. Controllable Layered Structures in Polyoxomolybdate-Surfactant Hybrid Crystals

    PubMed Central

    Ito, Takeru; Yamase, Toshihiro

    2010-01-01

    Inorganic-organic hybrid crystals containing α-octamolybdate (Mo8) or hexamolybdate (Mo6) were isolated by using hexadecyltrimethylammonium (C16) surfactant. The packing mode of the inorganic layers depended on a difference in the polyoxomolybdate molecular structure. The structure for both crystals consisted of alternate stacking of C16 organic bilayers and polyoxomolybdate inorganic layers with a periodicity of 24.4–24.6 Å. However, the C16-Mo8 crystals contained Mo8 monolayers, while the C16-Mo6 crystals contained Mo6 bilayers. These lattice structures for the polyoxometalate/organic hybrid will be designed by the molecular structures of polyoxometalate.

  4. New Tricks of the Trade for Crystal Structure Refinement.

    PubMed

    Li, Jinjin; Abramov, Yuriy A; Doherty, Michael F

    2017-07-26

    Accurate crystal structures and their experimental uncertainties, determined by X-ray diffraction/neutron diffraction techniques, are vital for crystal engineering studies, such as polymorph stability and crystal morphology calculations. Because of differences in crystal growth and data measurement conditions, crystallographic databases often contain multiple entries of varying quality of the same compound. The choice of the most reliable and best quality crystal structure from many very similar structures remains an unresolved problem, especially for nonexperts. In addition, while crystallographers can make use of some professional software (i.e., Materials Studio) for structure refinement, noncrystallographers may not have access to it. In the present paper, we propose a simple method to study the sensitivity of the crystal lattice energy to changes in the structural parameters, which creates a diagnostic tool to test the quality of crystal structure files and to improve the low-quality structures based on lattice energy distribution. Thus, noncrystallographers could take the proposed idea and program/optimize crystal structure by themselves. They can have their in-house program to determine the reliability of the selected crystal data and then use the best quality data or carry out structural optimization for low-quality data. The proposed method will benefit a broad cross-section of scientific researchers, especially those in solid-state and physical chemistry.

  5. 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)

  6. 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)

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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.

  14. Two-dimensional crystal engineering using halogen and hydrogen bonds: towards structural landscapes.

    PubMed

    Mukherjee, Arijit; Teyssandier, Joan; Hennrich, Gunther; De Feyter, Steven; Mali, Kunal S

    2017-05-01

    Two-dimensional (2D) crystallization on solid surfaces is governed by a subtle balance of supramolecular and interfacial interactions. However, these subtle interactions often make the prediction of supramolecular structure from the molecular structure impossible. As a consequence, surface-based 2D crystallization has often been studied on a case-by-case basis, which hinders the identification of structure-determining relationships between different self-assembling systems. Here we begin the discussion on such structure-determining relationships by comparing the 2D crystallization of two identical building blocks based on a 1,3,5-tris(pyridine-4-ylethynyl)benzene unit at the solution-solid interface. The concepts of supramolecular synthons and structural landscapes are introduced in the context of 2D crystallization on surfaces to identify common structural elements. The systems are characterized using scanning tunneling microscopy (STM). This strategy involves carrying out minor structural modifications on the parent compound to access supramolecular patterns that are otherwise not obtained. We demonstrate that this chemical perturbation strategy translates equally well for 2D co-crystallization experiments with halogen bond donors yielding porous bi-component networks. The holistic approach described here represents a stepping stone towards gaining predictive power over the 2D crystallization of molecules on solid surfaces.

  15. Formamidinium iodide: crystal structure and phase transitions

    PubMed Central

    Goodilin, Eugene A.; Tarasov, Alexey B.; Dorovatovskii, Pavel V.

    2017-01-01

    At a temperature of 100 K, CH5N2 +·I− (I), crystallizes in the monoclinic space group P21/c. The formamidinium cation adopts a planar symmetrical structure [the r.m.s. deviation is 0.002 Å, and the C—N bond lengths are 1.301 (7) and 1.309 (8) Å]. The iodide anion does not lie within the cation plane, but deviates from it by 0.643 (10) Å. The cation and anion of I form a tight ionic pair by a strong N—H⋯I hydrogen bond. In the crystal of I, the tight ionic pairs form hydrogen-bonded zigzag-like chains propagating toward [20-1] via strong N—H⋯I hydrogen bonds. The hydrogen-bonded chains are further packed in stacks along [100]. The thermal behaviour of I was studied by different physicochemical methods (thermogravimetry, differential scanning calorimetry and powder diffraction). Differential scanning calorimetry revealed three narrow endothermic peaks at 346, 387 and 525 K, and one broad endothermic peak at ∼605 K. The first and second peaks are related to solid–solid phase transitions, while the third and fourth peaks are attributed to the melting and decomposition of I. The enthalpies of the phase transitions at 346 and 387 K are estimated as 2.60 and 2.75 kJ mol−1, respectively. The X-ray powder diffraction data collected at different temperatures indicate the existence of I as the monoclinic (100–346 K), ortho­rhom­bic (346–387 K) and cubic (387–525 K) polymorphic modifications. PMID:28435723

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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…

  5. 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…

  6. 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.

  7. 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

  8. Crystal structure of a defective folding protein

    PubMed Central

    Saul, Frederick A.; Mourez, Michaël; Vulliez-le Normand, Brigitte; Sassoon, Nathalie; Bentley, Graham A.; Betton, Jean-Michel

    2003-01-01

    Maltose-binding protein (MBP or MalE) of Escherichia coli is the periplasmic receptor of the maltose transport system. MalE31, a defective folding mutant of MalE carrying sequence changes Gly 32→Asp and Ile 33→Pro, is either degraded or forms inclusion bodies following its export to the periplasmic compartment. We have shown previously that overexpression of FkpA, a heat-shock periplasmic peptidyl-prolyl isomerase with chaperone activity, suppresses MalE31 misfolding. Here, we have exploited this property to characterize the maltose transport activity of MalE31 in whole cells. MalE31 displays defective transport behavior, even though it retains maltose-binding activity comparable with that of the wild-type protein. Because the mutated residues are in a region on the surface of MalE not identified previously as important for maltose transport, we have solved the crystal structure of MalE31 in the maltose-bound state in order to characterize the effects of these changes. The structure was determined by molecular replacement methods and refined to 1.85 Å resolution. The conformation of MalE31 closely resembles that of wild-type MalE, with very small displacements of the mutated residues located in the loop connecting the first α-helix to the first β-strand. The structural and functional characterization provides experimental evidence that MalE31 can attain a wild-type folded conformation, and suggest that the mutated sites are probably involved in the interactions with the membrane components of the maltose transport system. PMID:12592028

  9. Crystal structure of a defective folding protein.

    PubMed

    Saul, Frederick A; Mourez, Michaël; Vulliez-Le Normand, Brigitte; Sassoon, Nathalie; Bentley, Graham A; Betton, Jean-Michel

    2003-03-01

    Maltose-binding protein (MBP or MalE) of Escherichia coli is the periplasmic receptor of the maltose transport system. MalE31, a defective folding mutant of MalE carrying sequence changes Gly 32-->Asp and Ile 33-->Pro, is either degraded or forms inclusion bodies following its export to the periplasmic compartment. We have shown previously that overexpression of FkpA, a heat-shock periplasmic peptidyl-prolyl isomerase with chaperone activity, suppresses MalE31 misfolding. Here, we have exploited this property to characterize the maltose transport activity of MalE31 in whole cells. MalE31 displays defective transport behavior, even though it retains maltose-binding activity comparable with that of the wild-type protein. Because the mutated residues are in a region on the surface of MalE not identified previously as important for maltose transport, we have solved the crystal structure of MalE31 in the maltose-bound state in order to characterize the effects of these changes. The structure was determined by molecular replacement methods and refined to 1.85 A resolution. The conformation of MalE31 closely resembles that of wild-type MalE, with very small displacements of the mutated residues located in the loop connecting the first alpha-helix to the first beta-strand. The structural and functional characterization provides experimental evidence that MalE31 can attain a wild-type folded conformation, and suggest that the mutated sites are probably involved in the interactions with the membrane components of the maltose transport system.

  10. 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)

  11. 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)

  12. Structure prediction: Encoding evolution of porous solids

    NASA Astrophysics Data System (ADS)

    Mellot-Draznieks, Caroline; Cheetham, Anthony K.

    2017-01-01

    The design and prediction of network topology is challenging, even when the components' principle interactions are strong. Now, frameworks with relatively weak 'chiral recognition' between organic building blocks have been synthesized and rationalized in silico -- an important development in the reticular synthesis of molecular crystals.

  13. An Automatic Symmetry-Leveraging Approach for Solving Incomplete Many-Atom Crystal Structures

    NASA Astrophysics Data System (ADS)

    Meredig, Bryce; Wolverton, Chris

    2011-03-01

    We present a new first principles-based method, called a symmetry-leveraging genetic algorithm (SLGA), for fully and automatically solving large crystal structures when experimental diffraction studies do not identify all internal atomic positions. Such incomplete structural refinements may occur when crystals contain light atoms or when the characterization is performed under extreme conditions such as high pressure. We apply our method to solve the crystal structure of the promising hydrogen storage candidate magnesium imide (MgNH), which has remained a mystery for over 40 years. We also confirm via a fully automated procedure a recent specialized ``by hand" prediction for the high-pressure phase of ammonia borane, NH3 BH3 . The MgNH prediction, which involves 36 atoms and a notoriously complex configuration space, to the best of our knowledge represents the largest-ever crystal structure solution derived from first-principles calculations without making simplifying assumptions about atom connectivity. The 32-atom NH3 BH3 prediction is nearly as demanding. Our approach, which takes full advantage of existing experimental information to solve for structural unknowns, has great potential for completing thousands of partially determined crystal structures.

  14. 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.

  15. 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.

  16. Crystal structure of Clostridium difficile toxin A

    SciTech Connect

    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

    2016-01-11

    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 colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. 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.

  17. Crystal structure of Clostridium difficile toxin A.

    PubMed

    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

    2016-01-11

    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 colon. The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host. 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.

  18. Crystal structure of Clostridium difficile toxin A.

    PubMed

    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

    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 colon(1,2). The toxins are large (308 and 270 kDa, respectively), homologous (47% amino acid identity) glucosyltransferases that target small GTPases within the host(3,4). 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.

  19. 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

  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. 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.

  2. 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

  3. Refinement of the crystal structure of rutherfordine.

    SciTech Connect

    Finch, R. J.; Cooper, M. A.; Hawthorne, F. C.; Ewing, R. C.; Chemical Engineering; Univ. of Manitoba; Univ. of Michigan

    1999-01-01

    Rutherfordine, UO{sub 2}CO{sub 3} is orthorhombic, a 4.840(1), b 9.273(2), c 4.298(1) Angstroms, V192.90(7) Angstroms{sup 3}, space group lmm2,Z=2. The structure was refined to an R index of 2.2% on the basis of 306 unique data [|F{sub o}|/{sigma}(|F{sub o}|)>5] measured with MoK{alpha} X-radiation on a single-crystal diffractometer. The structure consists of neutral sheets of edge- and corner-sharing (UO{sub 8}) hexagonal bipyramids and (CO{sub 3}) triangles, as originally proposed by Christ et al. (1955); our refinement, however shows that (CO{sub 3}) groups in alternate layers have the same orientation, not opposite orientations as originally reported. The refined value of the U-O (uranyl) distance is strongly affected by the details of the absorption correction, ranging from 1.71 to 1.80 Angstroms as a function of the plate-glancing angle used in an empirical psi-scan absorption correction and as a function of the type of weighting scheme used in the refinement. The Gaussian-quadrature method of integration also shows similar problems, but they are less extreme. The preferred value for the U-O (uranyl) distance in rutherfordine is {approx}1.745 Angstroms; as rutherfordine contains no H atoms, the O(uranyl) atom is [1]-coordinated, and should have the shortest U-O(uranyl) distance stereochemically possible. The current work suggests that U-O(uranyl) values less than 1.745 Angstrom reported in other studies are adversely affected by less-than-optimum absorption corrections.

  4. 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.

  5. 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

  6. 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.

  7. Novel photonic crystal cavities and related structures.

    SciTech Connect

    Luk, Ting Shan

    2007-11-01

    The key accomplishment of this project is to achieve a much more in-depth understanding of the thermal emission physics of metallic photonic crystal through theoretical modeling and experimental measurements. An improved transfer matrix technique was developed to enable incorporation of complex dielectric function. Together with microscopic theory describing emitter radiative and non-radiative relaxation dynamics, a non-equilibrium thermal emission model is developed. Finally, experimental methodology was developed to measure absolute emissivity of photonic crystal at high temperatures with accuracy of +/-2%. Accurate emissivity measurements allow us to validate the procedure to treat the effect of the photonic crystal substrate.

  8. The PSIPRED protein structure prediction server.

    PubMed

    McGuffin, L J; Bryson, K; Jones, D T

    2000-04-01

    The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method; MEMSAT 2, a new version of a widely used transmembrane topology prediction method; or GenTHREADER, a sequence profile based fold recognition method. Freely available to non-commercial users at http://globin.bio.warwick.ac.uk/psipred/

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Crystal structure and characterization of pyrroloquinoline quinone disodium trihydrate

    PubMed Central

    2012-01-01

    Background Pyrroloquinoline quinone (PQQ), a tricarboxylic acid, has attracted attention as a growth factor, and its application to supplements and cosmetics is underway. The product used for these purposes is a water-soluble salt of PQQ disodium. Although in the past, PQQ disodiumpentahydrates with a high water concentration were used, currently, low hydration crystals of PQQ disodiumpentahydrates are preferred. Results We prepared a crystal of PQQ disodium trihydrate in a solution of ethanol and water, studied its structure, and analyzed its properties. In the prepared crystal, the sodium atom interacted with the oxygen atom of two carboxylic acids as well as two quinones of the PQQ disodium trihydrate. In addition, the hydration water of the prepared crystal was less than that of the conventional PQQ disodium crystal. From the results of this study, it was found that the color and the near-infrared (NIR) spectrum of the prepared crystal changed depending on the water content in the dried samples. Conclusions The water content in the dried samples was restored to that in the trihydrate crystal by placing the samples in a humid environment. In addition, the results of X-ray diffraction (XRD) and X-ray diffraction-differential calorimetry (XRD-DSC) analyses show that the phase of the trihydrate crystal changed when the crystallization water was eliminated. The dried crystal has two crystalline forms that are restored to the original trihydrate crystals in 20% relative humidity (RH). This crystalline (PQQ disodium trihydrate) is stable under normal environment. PMID:22713213

  14. Paramagnetic ionic plastic crystals containing the octamethylferrocenium cation: counteranion dependence of phase transitions and crystal structures.

    PubMed

    Mochida, Tomoyuki; Ishida, Mai; Tominaga, Takumi; Takahashi, Kazuyuki; Sakurai, Takahiro; Ohta, Hitoshi

    2017-05-31

    In recent years, ionic plastic crystals have attracted much attention. Many metallocenium salts exhibit plastic phases, but factors affecting their phase transitions are yet to be elucidated. To investigate these factors, we synthesized octamethylferrocenium salts with various counteranions [Fe(C5Me4H)2]X ([1]X; X(-) = B(CN)4(-), C(CN)3(-), N(CN)2(-), FSA (= (SO2F)2N(-)), FeCl4(-), GaCl4(-) and CPFSA (= CF2(SO2CF2)2N(-))) and elucidated their crystal structures and phase behavior. Correlations between the crystal structures and phase sequences, and the shapes and volumes of the anions are discussed. Except for [1][CPFSA], these salts exhibit phase transitions to plastic phases at or above room temperature (TC = 298-386 K), and the plastic phases exhibit either NaCl- or anti-NiAs-type structures. X-ray crystal structure analyses of these salts at 100 K revealed that they have structures in which cations and anions are alternately arranged, with the exception of [1][CPFSA]. [1][CPFSA] exhibits a structure in which anions and cations are separately stacked to form columns. [1][N(CN)2] exhibits a polar crystal structure that undergoes a monotropic phase transition to a centrosymmetric structure. The magnetic susceptibilities of room-temperature plastic crystals [1][GaCl4] and [1][FeCl4] were investigated; the latter exhibits a small ferromagnetic interaction at low temperatures.

  15. 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.

  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. 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

  18. 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.

  19. Accelerated discovery of two crystal structure types in a complex inorganic phase field

    NASA Astrophysics Data System (ADS)

    Collins, C.; Dyer, M. S.; Pitcher, M. J.; Whitehead, G. F. S.; Zanella, M.; Mandal, P.; Claridge, J. B.; Darling, G. R.; Rosseinsky, M. J.

    2017-06-01

    The discovery of new materials is hampered by the lack of efficient approaches to the exploration of both the large number of possible elemental compositions for such materials, and of the candidate structures at each composition. For example, the discovery of inorganic extended solid structures has relied on knowledge of crystal chemistry coupled with time-consuming materials synthesis with systematically varied elemental ratios. Computational methods have been developed to guide synthesis by predicting structures at specific compositions and predicting compositions for known crystal structures, with notable successes. However, the challenge of finding qualitatively new, experimentally realizable compounds, with crystal structures where the unit cell and the atom positions within it differ from known structures, remains for compositionally complex systems. Many valuable properties arise from substitution into known crystal structures, but materials discovery using this approach alone risks both missing best-in-class performance and attempting design with incomplete knowledge. Here we report the experimental discovery of two structure types by computational identification of the region of a complex inorganic phase field that contains them. This is achieved by computing probe structures that capture the chemical and structural diversity of the system and whose energies can be ranked against combinations of currently known materials. Subsequent experimental exploration of the lowest-energy regions of the computed phase diagram affords two materials with previously unreported crystal structures featuring unusual structural motifs. This approach will accelerate the systematic discovery of new materials in complex compositional spaces by efficiently guiding synthesis and enhancing the predictive power of the computational tools through expansion of the knowledge base underpinning them.

  20. Electronic structure of Cr{sup 3+} in forsterite crystals

    SciTech Connect

    Avanesov, A.G.; Zhorin, V.V.; Pisarenko, V.F.

    1994-11-01

    Specific properties of silicate crystals that make them promising in applications as active media for IR tunable lasers are discussed. The energy level structure of Cr{sup 3+} ions in a forsterite crystal field is analyzed. 4 refs., 3 tabs.

  1. Colloidal crystals: Structure, dynamics, and the importance of dimer bonds

    NASA Astrophysics Data System (ADS)

    Gerbode, Sharon Jane

    Colloidal crystals, periodic arrays of micron-sized solid particles in solution, offer a unique glimpse of the particle-scale structures and dynamics within a true thermodynamic ensemble. Experimental colloidal studies of melting and crystallization [55, 56, 13, 76, 2] as well as non-equilibrium states such as colloidal glasses [67, 68, 29, 49] have uncovered numerous mechanisms that are experimentally inaccessible in atomic systems due to both small timescales and small lengthscales. The great successes of colloidal physics have emerged as a result of technological advances enabling synthesis of large batches of monodisperse spherical particles. Yet, the crystal structures formed by such particles are limited to variations on layers of close-packed spheres. Consequently, one of the current frontiers in colloidal physics is the study of novel crystal structures formed by non-spherical particles. My thesis work has focused on crystals formed by colloidal dimer particles consisting of two connected spherical lobes. Surprisingly, while the structure of two dimensional crystals formed by the dimers are quite similar to those observed for spheres, the motion of defects within the dimer crystals is significantly different. Geometric obstacles formed by interlocking dimers restrict the motion of defects and ultimately introduce a completely unexpected, previously unreported glassy defect dynamics within a colloidal crystal.

  2. Crystal structure and phototransistor behavior of N-substituted heptacence.

    PubMed

    Wu, Yuechao; Yin, Zongyou; Xiao, Jinchong; Liu, Yi; Wei, Fengxia; Tan, Ke Jie; Kloc, Christian; Huang, Ling; Yan, Qingyu; Hu, Fangzhong; Zhang, Hua; Zhang, Qichun

    2012-04-01

    6,8,15,17-Tetraaza-1.18,4.5,9.10,13.14-tetrabenzoheptacene (TTH, 1) has been prepared and characterized by single-crystal X-ray structure analysis. A phototransistor device based on TTH single crystal demonstrated that TTH showed a good performance in signal amplification under the photoconductive effect as well as photocontrolled switches.

  3. 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

  4. 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.

  5. Quantum Chemical Investigations of the Mechanism of Cationic Polymerization and Theoretical Prediction of Crystal Densities and Decomposition Pathways of Energetic Molecules.

    DTIC Science & Technology

    Ab -initio quantum chemical investigations of the mechanism of cationic polymerization; Development, implementation testing of theoretical procedures...for prediction of crystal structures and densities; Ab -initio quantum chemical MODPOT/VRDDO/MERGE calculations on nitroexplosives, including

  6. Crystal growth conditions and structural features of ladder type superconductors

    SciTech Connect

    Leonyuk, L.; Szymczak, R.; Szymczak, H.; Baran, M.; Babonas, G.J.; Maltsev, V.; Shvanskaya, L.; Reza, A.

    1999-12-01

    The single crystals (M{sub 2}Cu{sub 2}O{sub 3}){sub m}(CuO{sub 2}){sub n} (M = Ca, Sr, Y, Bi) containing the ladder-type plane Cu{sub 2}O{sub 3} were obtained by the flux method using Bi- and Ba-cuprates as fluxes. The single crystals with m/n-values 5/7 and 1/1 were found to be superconducting (SC) with the onset of the transition at 80 K. The regularities of the SC crystals with the ladder-type structure were discussed from the viewpoint of the crystal chemistry.

  7. 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.

  8. 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)°.

  9. Interplay between Structure and Size in a Critical Crystal Nucleus

    NASA Astrophysics Data System (ADS)

    Moroni, Daniele; Ten Wolde, Pieter Rein; Bolhuis, Peter G.

    2005-06-01

    We study the kinetics of crystal nucleation of an undercooled Lennard-Jones liquid using various path-sampling methods. We obtain the rate constant and elucidate the pathways for crystal nucleation. Analysis of the path ensemble reveals that crystal nucleation occurs along many different pathways, in which critical solid nuclei can be small, compact, and face centered cubic, but also large, less ordered, and more body centered cubic. The reaction coordinate thus includes, besides the cluster size, also the quality of the crystal structure.

  10. 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.

  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. The MULTICOM toolbox for protein structure prediction.

    PubMed

    Cheng, Jianlin; Li, Jilong; Wang, Zheng; Eickholt, Jesse; Deng, Xin

    2012-04-30

    As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques. The gap between protein sequence and structure continues to enlarge rapidly as the throughput of genome sequencing techniques is much higher than that of protein structure determination techniques. Computational software tools for predicting protein structure and structural features from protein sequences are crucial to make use of this vast repository of protein resources. To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map prediction, disulfide bond prediction, beta-sheet topology prediction, fold recognition, multiple template combination and alignment, template-based tertiary structure modeling, protein model quality assessment, and mutation stability prediction. These tools have been rigorously tested by many users in the last several years and/or during the last three rounds of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7-9) from 2006 to 2010, achieving state-of-the-art or near performance. In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and scientific research. It is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/.

  14. The MULTICOM toolbox for protein structure prediction

    PubMed Central

    2012-01-01

    Background As genome sequencing is becoming routine in biomedical research, the total number of protein sequences is increasing exponentially, recently reaching over 108 million. However, only a tiny portion of these proteins (i.e. ~75,000 or < 0.07%) have solved tertiary structures determined by experimental techniques. The gap between protein sequence and structure continues to enlarge rapidly as the throughput of genome sequencing techniques is much higher than that of protein structure determination techniques. Computational software tools for predicting protein structure and structural features from protein sequences are crucial to make use of this vast repository of protein resources. Results To meet the need, we have developed a comprehensive MULTICOM toolbox consisting of a set of protein structure and structural feature prediction tools. These tools include secondary structure prediction, solvent accessibility prediction, disorder region prediction, domain boundary prediction, contact map prediction, disulfide bond prediction, beta-sheet topology prediction, fold recognition, multiple template combination and alignment, template-based tertiary structure modeling, protein model quality assessment, and mutation stability prediction. Conclusions These tools have been rigorously tested by many users in the last several years and/or during the last three rounds of the Critical Assessment of Techniques for Protein Structure Prediction (CASP7-9) from 2006 to 2010, achieving state-of-the-art or near performance. In order to facilitate bioinformatics research and technological development in the field, we have made the MULTICOM toolbox freely available as web services and/or software packages for academic use and scientific research. It is available at http://sysbio.rnet.missouri.edu/multicom_toolbox/. PMID:22545707

  15. 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.

  16. Universal fragment descriptors for predicting properties of inorganic crystals

    NASA Astrophysics Data System (ADS)

    Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

    2017-06-01

    Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules.

  17. Universal fragment descriptors for predicting properties of inorganic crystals

    PubMed Central

    Isayev, Olexandr; Oses, Corey; Toher, Cormac; Gossett, Eric; Curtarolo, Stefano; Tropsha, Alexander

    2017-01-01

    Although historically materials discovery has been driven by a laborious trial-and-error process, knowledge-driven materials design can now be enabled by the rational combination of Machine Learning methods and materials databases. Here, data from the AFLOW repository for ab initio calculations is combined with Quantitative Materials Structure-Property Relationship models to predict important properties: metal/insulator classification, band gap energy, bulk/shear moduli, Debye temperature and heat capacities. The prediction's accuracy compares well with the quality of the training data for virtually any stoichiometric inorganic crystalline material, reciprocating the available thermomechanical experimental data. The universality of the approach is attributed to the construction of the descriptors: Property-Labelled Materials Fragments. The representations require only minimal structural input allowing straightforward implementations of simple heuristic design rules. PMID:28580961

  18. 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

  19. 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.

  20. 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

  1. 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.

  2. Influence of crystal structure on the compaction properties of n-alkyl 4-hydroxybenzoate esters (parabens).

    PubMed

    Feng, Yushi; Grant, David J W

    2006-07-01

    The aim of the study is to examine the influence of slip planes on the nanoindentation hardness and compaction properties of methyl, ethyl, n-propyl, and n-butyl 4-hydroxybenzoate (parabens). Molecular modeling calculations, embodying the attachment energy concept, were performed to predict the slip planes in the crystal lattices, whereas the nanoindentation hardness of the crystals and the tensile strength of directly compressed compacts were measured. Unlike the other three parabens, methyl paraben has no slip planes in its crystal lattice, and its crystals showed greater nanoindentation hardness, corresponding to lower plasticity, whereas its tablets exhibited substantially lower tensile strength than those of ethyl, propyl, or butyl paraben. The nanoindentation hardness of the crystals and the tensile strength of directly compressed tablets were each found to correlate directly with the absence or presence of slip planes in the crystal structures of the parabens because slip planes confer greater plasticity. This work presents a molecular insight into the influence of crystal structural features on the tableting performance of molecular crystals in general and of crystalline pharmaceuticals in particular.

  3. 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.

  4. The Crystal and Molecular Structure of Dianhydrogossypol

    USDA-ARS?s Scientific Manuscript database

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

  5. Protein structural motifs in prediction and design.

    PubMed

    Mackenzie, Craig O; Grigoryan, Gevorg

    2017-06-01

    The Protein Data Bank (PDB) has been an integral resource for shaping our fundamental understanding of protein structure and for the advancement of such applications as protein design and structure prediction. Over the years, information from the PDB has been used to generate models ranging from specific structural mechanisms to general statistical potentials. With accumulating structural data, it has become possible to mine for more complete and complex structural observations, deducing more accurate generalizations. Motif libraries, which capture recurring structural features along with their sequence preferences, have exposed modularity in the structural universe and found successful application in various problems of structural biology. Here we summarize recent achievements in this arena, focusing on subdomain level structural patterns and their applications to protein design and structure prediction, and suggest promising future directions as the structural database continues to grow. Copyright © 2017 Elsevier Ltd. All rights reserved.

  6. 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

  7. 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.

  8. 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 .

  9. 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.

  10. 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.

  11. Protein structure prediction using hybrid AI methods

    SciTech Connect

    Guan, X.; Mural, R.J.; Uberbacher, E.C.

    1993-11-01

    This paper describes a new approach for predicting protein structures based on Artificial Intelligence methods and genetic algorithms. We combine nearest neighbor searching algorithms, neural networks, heuristic rules and genetic algorithms to form an integrated system to predict protein structures from their primary amino acid sequences. First we describe our methods and how they are integrated, and then apply our methods to several protein sequences. The results are very close to the real structures obtained by crystallography. Parallel genetic algorithms are also implemented.

  12. 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.

  13. Membrane protein structures without crystals, by single particle electron cryomicroscopy

    PubMed Central

    Vinothkumar, Kutti R

    2015-01-01

    It is an exciting period in membrane protein structural biology with a number of medically important protein structures determined at a rapid pace. However, two major hurdles still remain in the structural biology of membrane proteins. One is the inability to obtain large amounts of protein for crystallization and the other is the failure to get well-diffracting crystals. With single particle electron cryomicroscopy, both these problems can be overcome and high-resolution structures of membrane proteins and other labile protein complexes can be obtained with very little protein and without the need for crystals. In this review, I highlight recent advances in electron microscopy, detectors and software, which have allowed determination of medium to high-resolution structures of membrane proteins and complexes that have been difficult to study by other structural biological techniques. PMID:26435463

  14. 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

  15. 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.

  16. A physical approach to protein structure prediction.

    PubMed Central

    Crivelli, Silvia; Eskow, Elizabeth; Bader, Brett; Lamberti, Vincent; Byrd, Richard; Schnabel, Robert; Head-Gordon, Teresa

    2002-01-01

    We describe our global optimization method called Stochastic Perturbation with Soft Constraints (SPSC), which uses information from known proteins to predict secondary structure, but not in the tertiary structure predictions or in generating the terms of the physics-based energy function. Our approach is also characterized by the use of an all atom energy function that includes a novel hydrophobic solvation function derived from experiments that shows promising ability for energy discrimination against misfolded structures. We present the results obtained using our SPSC method and energy function for blind prediction in the 4th Critical Assessment of Techniques for Protein Structure Prediction competition, and show that our approach is more effective on targets for which less information from known proteins is available. In fact our SPSC method produced the best prediction for one of the most difficult targets of the competition, a new fold protein of 240 amino acids. PMID:11751294

  17. Crystal structure of a group I intron splicing intermediate

    PubMed Central

    ADAMS, PETER L.; STAHLEY, MARY R.; GILL, MICHELLE L.; KOSEK, ANNE B.; WANG, JIMIN; STROBEL, SCOTT A.

    2004-01-01

    A recently reported crystal structure of an intact bacterial group I self-splicing intron in complex with both its exons provided the first molecular view into the mechanism of RNA splicing. This intron structure, which was trapped in the state prior to the exon ligation reaction, also reveals the architecture of a complex RNA fold. The majority of the intron is contained within three internally stacked, but sequence discontinuous, helical domains. Here the tertiary hydrogen bonding and stacking interactions between the domains, and the single-stranded joiner segments that bridge between them, are fully described. Features of the structure include: (1) A pseudoknot belt that circumscribes the molecule at its longitudinal midpoint; (2) two tetraloop-tetraloop receptor motifs at the peripheral edges of the structure; (3) an extensive minor groove triplex between the paired and joiner segments, P6-J6/6a and P3-J3/4, which provides the major interaction interface between the intron’s two primary domains (P4-P6 and P3-P9.0); (4) a six-nucleotide J8/7 single stranded element that adopts a μ-shaped structure and twists through the active site, making critical contacts to all three helical domains; and (5) an extensive base stacking architecture that realizes 90% of all possible stacking interactions. The intron structure was validated by hydroxyl radical footprinting, where strong correlation was observed between experimental and predicted solvent accessibility. Models of the pre-first and pre-second steps of intron splicing are proposed with full-sized tRNA exons. They suggest that the tRNA undergoes substantial angular motion relative to the intron between the two steps of splicing. PMID:15547134

  18. 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.

  19. 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.

  20. (PS)2: protein structure prediction server

    PubMed Central

    Chen, Chih-Chieh; Hwang, Jenn-Kang; Yang, Jinn-Moon

    2006-01-01

    Protein structure prediction provides valuable insights into function, and comparative modeling is one of the most reliable methods to predict 3D structures directly from amino acid sequences. However, critical problems arise during the selection of the correct templates and the alignment of query sequences therewith. We have developed an automatic protein structure prediction server, (PS)2, which uses an effective consensus strategy both in template selection, which combines PSI-BLAST and IMPALA, and target–template alignment integrating PSI-BLAST, IMPALA and T-Coffee. (PS)2 was evaluated for 47 comparative modeling targets in CASP6 (Critical Assessment of Techniques for Protein Structure Prediction). For the benchmark dataset, the predictive performance of (PS)2, based on the mean GTD_TS score, was superior to 10 other automatic servers. Our method is based solely on the consensus sequence and thus is considerably faster than other methods that rely on the additional structural consensus of templates. Our results show that (PS)2, coupled with suitable consensus strategies and a new similarity score, can significantly improve structure prediction. Our approach should be useful in structure prediction and modeling. The (PS)2 is available through the website at . PMID:16844981

  1. 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.

  2. 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.

  3. Submicrometer Single Crystal Diffractometry for Highly Accurate Structure Determination

    SciTech Connect

    Yasuda, Nobuhiro; Fukuyama, Yoshimitsu; Kimura, Shigeru; Toriumi, Koshiro; Takata, Masaki

    2010-06-23

    Submicrometer single crystal diffractometry for highly accurate structure determination was developed using the extremely stable and highly brilliant synchrotron radiation from SPring-8. This was achieved using a microbeam focusing system and the submicrometer precision low-eccentric goniometer system. We demonstrated the structure analyses with 2x2x2 {mu}m{sup 3} cytidine, 600x600x300 nm{sup 3} BaTiO{sub 3}, and 1x1x1 {mu}m{sup 3} silicon. The observed structure factors of the silicon crystal were in agreement with the structure factors determined by the Pendelloesung method and do not require absorption and extinction corrections.

  4. 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

  5. Three supramolecular compounds of 1,4-benzeneditetrazole (H2BDT): Syntheses, crystal structures, and crystal to crystal transformation

    NASA Astrophysics Data System (ADS)

    Deng, Ji-Hua; Wen, Ya-Qiong; Luo, Jie; Huang, Zhi-Qiang; Zhong, Di-Chang

    2017-08-01

    Three supramolecular compounds based on 1,4-benzeneditetrazole (H2BDT), (NH4)2(BDT) (1), [Mg(H2O)6](HBDT)2·2H2O (2), and [Mg(CH3OH)4(H2O)2](HBDT)2·2CH3OH (3) have been solvothermally synthesized and structurally characterized by single-crystal/powder X-ray diffraction. Structural analyses indicated that these compounds are 3D supramolecular structures stabilized by electrostatic interactions and intermolecular hydrogen bonds. The crystal to crystal transformation between 2 and 3 were investigated. The result showed that 2 is readily transform to 3 after immersed in methanol solution, while 3 can not be converted to 2 after immersed in distilled water solution.

  6. 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.

  7. 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

  8. 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.

  9. 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.

  10. 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.

  11. Transmembrane beta-barrel protein structure prediction

    NASA Astrophysics Data System (ADS)

    Randall, Arlo; Baldi, Pierre

    Transmembrane β-barrel (TMB) proteins are embedded in the outer membranes of mitochondria, Gram-negative bacteria, and chloroplasts. These proteins perform critical functions, including active ion-transport and passive nutrient intake. Therefore, there is a need for accurate prediction of secondary and tertiary structures of TMB proteins. A variety of methods have been developed for predicting the secondary structure and these predictions are very useful for constructing a coarse topology of TMB structure; however, they do not provide enough information to construct a low-resolution tertiary structure for a TMB protein. In addition, while the overall structural architecture is well conserved among TMB proteins, the amino acid sequences are highly divergent. Thus, traditional homology modeling methods cannot be applied to many putative TMB proteins. Here, we describe the TMBpro: a pipeline of methods for predicting TMB secondary structure, β-residue contacts, and finally tertiary structure. The tertiary prediction method relies on the specific construction rules that TMB proteins adhere to and on the predicted β-residue contacts to dramatically reduce the search space for the model building procedure.

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

    PubMed

    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

    2017-01-26

    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. PAPERCLIP. Copyright © 2017 Elsevier Inc. All rights reserved.

  13. 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.

  14. 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.

  15. Predicting and prioritizing maintenance for concrete structures

    SciTech Connect

    Hertlein, B.H. )

    1991-06-01

    Using nondestructive testing of concrete structures to predict maintenance needs can help schedule maintenance work in advance and prevent unexpected shutdowns. Nondestructive testing methods are described and development of a testing program is discussed.

  16. 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.

  17. 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.

  18. Birefringence property of asymmetric structure photonic crystal fiber

    NASA Astrophysics Data System (ADS)

    Liu, Mingsheng; Yue, Yingjuan; Li, Yan

    2010-12-01

    The random offset of hole-position or random variation of hole-diameter always occur during the actual manufacture process of asymmetric structure photonic crystal fibers. Birefringence of asymmetric photonic crystal fibers with circular air holes and photonic crystal fibers with elliptical air holes are studied numerically based on the finite element method under the perturbation circumstance. The results indicate that when the intrinsic-birefringence of asymmetric photonic crystal fiber is smaller, the random offset of hole-position has larger influence than the variation of hole-diameter. Birefringence resulted from perturbation is less sensitive to asymmetric structures with large pitch or small air-hole. Moreover, the desired birefringence can be obtained by controlling the relative size of the two air holes or the ellipticity of the elliptical-hole.

  19. 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

  20. Screening Libraries of Semifluorinated Arylene Bisimides to Discover and Predict Thermodynamically Controlled Helical Crystallization.

    PubMed

    Ho, Ming-Shou; Partridge, Benjamin E; Sun, Hao-Jan; Sahoo, Dipankar; Leowanawat, Pawaret; Peterca, Mihai; Graf, Robert; Spiess, Hans W; Zeng, Xiangbing; Ungar, Goran; Heiney, Paul A; Hsu, Chain-Shu; Percec, Virgil

    2016-12-12

    Synthesis, structural, and retrostructural analysis of a library containing 16 self-assembling perylene (PBI), 1,6,7,12-tetrachloroperylene (Cl4PBI), naphthalene (NBI), and pyromellitic (PMBI) bisimides functionalized with environmentally friendly AB3 chiral racemic semifluorinated minidendrons at their imide groups via m = 0, 1, 2, and 3 methylene units is reported. These semifluorinated compounds melt at lower temperatures than homologous hydrogenated compounds, permitting screening of all their thermotropic phases via structural analysis to discover thermodynamically controlled helical crystallization from propeller-like, cogwheel, and tilted molecules as well as lamellar-like structures. Thermodynamically controlled helical crystallization was discovered for propeller-like PBI, Cl4PBI and NBI with m = 0. Unexpectedly, assemblies of twisted Cl4PBIs exhibit higher order than those of planar PBIs. PBI with m = 1, 2, and 3 form a thermodynamically controlled columnar hexagonal 2D lattice of tilted helical columns with intracolumnar order. PBI and Cl4PBI with m = 1 crystallize via a recently discovered helical cogwheel mechanism, while NBI and PMBI with m = 1 form tilted helical columns. PBI, NBI and PMBI with m = 2 generate lamellar-like structures. 3D and 2D assemblies of PBI with m = 1, 2, and 3, NBI with m = 1 and PMBI with m = 2 exhibit 3.4 Å π-π stacking. The library approach applied here and in previous work enabled the discovery of six assemblies which self-organize via thermodynamic control into 3D and 2D periodic arrays, and provides molecular principles to predict the supramolecular structure of electronically active components.

  1. 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.

  2. 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.

  3. A genetic algorithm for predicting the structures of interfaces in multicomponent systems.

    PubMed

    Chua, Alvin L-S; Benedek, Nicole A; Chen, Lin; Finnis, Mike W; Sutton, Adrian P

    2010-05-01

    Recent years have seen great advances in our ability to predict crystal structures from first principles. However, previous algorithms have focused on the prediction of bulk crystal structures, where the global minimum is the target. Here, we present a general atomistic approach to simulate in multicomponent systems the structures and free energies of grain boundaries and heterophase interfaces with fixed stoichiometric and non-stoichiometric compositions. The approach combines a new genetic algorithm using empirical interatomic potentials to explore the configurational phase space of boundaries, and thereafter refining structures and free energies with first-principles electronic structure methods. We introduce a structural order parameter to bias the genetic algorithm search away from the global minimum (which would be bulk crystal), while not favouring any particular structure types, unless they lower the energy. We demonstrate the power and efficiency of the algorithm by considering non-stoichiometric grain boundaries in a ternary oxide, SrTiO(3).

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

    PubMed

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

    2017-08-30

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

  5. 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.

  6. Predicting Protein Structure Using Parallel Genetic Algorithms.

    DTIC Science & Technology

    1994-12-01

    34 IEEE Transactions on Systems, Man and Cybernetics, 10(9) (September 1980). 16. De Jong, Kenneth A. "On Using Genetic Algoriths to Search Program...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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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.

  12. Synthesis and Structure Characterization of Forsterite Single Crystal

    NASA Astrophysics Data System (ADS)

    Wang, C.; Jin, S.; Wang, X.; Liu, X.; Fleet, M. E.; Jin, Z.

    2006-12-01

    Forsterite (Mg2SiO4), the low-pressure polymorph of magnesium orthosilicate, is of great importance in the upper mantle due to its aboundance. Up to now, only powder samples of forsterite can be synthesized due to the difficulty of its crystal growth. Therefore, the exact crystal structure of forsterite is still an open question. The crystal structure of forsterite was firstly studied in 1926 by Brown and Bragg. Numerous experimental investigations have been performed in order to get the structure of the olivine group minerals at ambient conditions and a variety of temperature and pressures by using the advent of the computer, the single crystal diffractometer and the diamond cell. However, there are still considerable uncertaintes regarding the accuracy of its unit-cell parameter values. In this study, we synthesized for the first time high quality single crystals of forsterite using the Quickpress piston-cylinder apparatus. The single crystal of forsterite was synthesized by direct reaction of stoichiometric amounts of MgO and amorphous SiO2 (Alfa Aesar, 99.999%) in the presence of ~10-11 wt% distilled water at 2.0GPa, 1723 K for 12h. A colorless single crystal of Mg2SiO4 with size dimensions 0.16×0.11×0.04 mm was selected for single crystal X-ray diffraction analysis. The intensity data were collected with a Rigaku R-AXIS RAPID IP diffractometer by oscillation scans using graphite- monochromated Mo-K?0?6?0?6?7677?0?6?0?6?7699 radiation (λ=0.71073 Å). Cell refinement and data reduction were accomplished with RAPID AUTO program. The crystal structure was solved by direct methods with the SHELXL crystallographic software package. Single crystal X-ray diffraction analysis shows a crystal structure of orthorhombic space group Pnma (No. 62) with a = 10.2073(11) Å, b = 5.9863(5) Å, c = 4.7611(4) Å and Z = 4. Our new data provides new constraints for theoretical investigations of the physical and chemistry properties and behaviors of forsterite under various

  13. 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.

  14. 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.

  15. Formation of lanthanum beryllate real structure under different crystallization conditions

    SciTech Connect

    Tsvetkov, E.G. . E-mail: tsvetkov@uiggm.nsc.ru; Rylov, G.M.; Matrosov, V.N.

    2006-02-02

    The aim of this paper is to characterize the major structural defects of lanthanum beryllate single crystals grown by the Czochralski method, including those doped with rare-earth elements, and to reveal their relationship to specific properties of the crystal structure of La{sub 2}Be{sub 2}O{sub 5} and with their crystallization conditions. As a basic method for research, we used transmission X-ray topography. It was established that the defect state of La{sub 2}Be{sub 2}O{sub 5} crystals prepared by this method can be caused by different types of dislocations and their ordered assemblies, solid-phase inclusions of crucible metal and eutectically co-crystallizing phases, as well as by face growth sectors with elevated content of dopant. We show a possibility for growing single crystals of doped lanthanum beryllate having a minimum quantity of structural defects that could be suitable for manufacture of high quality laser rods.

  16. On the mechanisms of modulation of crystal structures

    NASA Astrophysics Data System (ADS)

    Borisov, S. V.; Magarill, S. A.; Pervukhina, N. V.

    2017-05-01

    Based on the assumption that crystal structures of a number of sulfides are the result of modulation of cationic lattices by anionic lattices, the versions of their conjugation in direct and reciprocal spaces have been analyzed using common translational lattices. The concept of this phenomenon, developed within the superspace formalism, is supplemented by a proposed interpretation of the real modulation of the structures.

  17. On automation of the procedure for crystal structure model refinement

    SciTech Connect

    Dudka, A. P.

    2008-03-15

    The methods of automation of the procedure for crystal structure model refinement from experimental diffraction data, implemented in the ASTRA program package, are described. Such tools as statistical tests, parameter scanning, and data scanning reduce the time necessary for structural investigation. At strong correlations between parameters, especially when the data set is limited, parameter scanning has an advantage over the full-matrix refinement.

  18. 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

  19. 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.

  20. 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.

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

    SciTech Connect

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

    2016-02-15

    The phase field crystal model provides a continual description of the atomic density over the diffusion time of reactions. We consider a homogeneous structure (liquid) and a perfect periodic crystal, which are constructed from the one-mode approximation of the phase field crystal model. A diagram of 2D structures is constructed from the analytic solutions of the model using atomic density functionals. The diagram predicts equilibrium atomic configurations for transitions from the metastable state and includes the domains of existence of homogeneous, triangular, and striped structures corresponding to a liquid, a body-centered cubic crystal, and a longitudinal cross section of 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.

  2. 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.

  3. Prediction of enthalpy of formation based on refined crystal structures of multisite compounds: Part 2. Application to minerals belonging to the system Li 2O-Na 2O-K 2O-BeO-MgO-CaO-MnO-FeO-Fe 2O 3-Al 2O 3-SiO 2-H 2O. Results and discussion

    NASA Astrophysics Data System (ADS)

    Vieillard, Philippe

    1994-10-01

    The method of prediction of enthalpy of formation of a multi-site compound has been developed in Part 1. This method of prediction is based on the use of the following parameters coming from the crystal structure refinements: first by spatial group, bond lengths, shortest bond lengths, molecular volume, and second from the optical properties. Part 2 shows the application of this method with 180 minerals and synthetic compounds belonging to the system Li 2O-Na 2O-K 2O-BeO-MgO-CaO-MnO-FeO-Fe 2O 3-Al 2O 3-SiO 2-H 2O which are gathered in a series of tables according to the spatial group and also to the nature of the family: hydroxides, metasilicates, orthosilicates, pyroxenes, olivines, feldspars, melilites, garnets, aluminates, ferrites, oxoferrates, spinels, phyllosilicates, hydrosilicates, amphiboles, and zeolites. The mean of absolute residual error is 0.59%. Among the twenty-three compounds exhibiting a residual error greater than ±1%, are some hydrogen-bearing minerals which may have a predicted enthalpy of formation from oxides closer to the experimental data by taking into consideration the orientation of water molecules and the hydrogen around the oxygens. This study initially demonstrated for lawsonite, may be applied to other hydrogen-bearing minerals such as natrolite, scolecite, mesolite, yugawaralite, clinochlore, cookeite, carpholite, and chloritoid. From the available recent crystal refinements of some minerals, the enthalpies of formation have been evaluated for the following minerals:

  4. 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.

  5. 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

  6. On the influence of crystal structure on the electromagnetic shower development in the lead tungstate crystals

    NASA Astrophysics Data System (ADS)

    Baryshevsky, V. G.; Haurylavets, V. V.; Korjik, M. V.; Lobko, A. S.; Mechinsky, V. A.; Sytov, A. I.; Tikhomirov, V. V.; Uglov, V. V.

    2017-07-01

    The development of high-energy electromagnetic showers in long oriented lead tungstate crystals, accelerated by the effects induced by the strong field of atomic strings, is simulated for the first time. For that the characteristics of pair production and gamma-radiation by electrons or positrons were first simulated by the direct application of Baier-Katkov formulae in a thin PWO crystal to derive the scaling coefficients of the corresponding Bethe-Heitler cross sections to be incorporated into GEANT4 for the simulation of the electromagnetic shower development in a long crystal. Simulation results demonstrate the significant influence of the crystal structure on the e± and gamma-quanta registration processes in the existing homogeneous electromagnetic calorimeters and gamma-telescopes as well as wide possibilities of improving their performance in future developments.

  7. 'Crystal lattice engineering,' an approach to engineer protein crystal contacts by creating intermolecular symmetry: crystallization and structure determination of a mutant human RNase 1 with a hydrophobic interface of leucines.

    PubMed

    Yamada, Hidenori; Tamada, Taro; Kosaka, Megumi; Miyata, Kohei; Fujiki, Shinya; Tano, Masaru; Moriya, Masayuki; Yamanishi, Mamoru; Honjo, Eijiro; Tada, Hiroko; Ino, Takeshi; Yamaguchi, Hiroshi; Futami, Junichiro; Seno, Masaharu; Nomoto, Takashi; Hirata, Tomoko; Yoshimura, Motonobu; Kuroki, Ryota

    2007-07-01

    A protein crystal lattice consists of surface contact regions, where the interactions of specific groups play a key role in stabilizing the regular arrangement of the protein molecules. In an attempt to control protein incorporation in a crystal lattice, a leucine zipper-like hydrophobic interface (comprising four leucine residues) was introduced into a helical region (helix 2) of the human pancreatic ribonuclease 1 (RNase 1) that was predicted to form a suitable crystallization interface. Although crystallization of wild-type RNase 1 has not yet been reported, the RNase 1 mutant having four leucines (4L-RNase 1) was successfully crystallized under several different conditions. The crystal structures were subsequently determined by X-ray crystallography by molecular replacement using the structure of bovine RNase A. The overall structure of 4L-RNase 1 is quite similar to that of the bovine RNase A, and the introduced leucine residues formed the designed crystal interface. To characterize the role of the introduced leucine residues in crystallization of RNase 1 further, the number of leucines was reduced to three or two (3L- and 2L-RNase 1, respectively). Both mutants crystallized and a similar hydrophobic interface as in 4L-RNase 1 was observed. A related approach to engineer crystal contacts at helix 3 of RNase 1 (N4L-RNase 1) was also evaluated. N4L-RNase 1 also successfully crystallized and formed the expected hydrophobic packing interface. These results suggest that appropriate introduction of a leucine zipper-like hydrophobic interface can promote intermolecular symmetry for more efficient protein crystallization in crystal lattice engineering efforts.

  8. 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.

  9. Band structure peculiarities of magnetic photonic crystals

    NASA Astrophysics Data System (ADS)

    Gevorgyan, A. H.; Golik, S. S.

    2017-10-01

    In this work we studied light diffraction in magneto-photonic crystals (MPC) having large magneto-optical activity and modulation large depth. The case of arbitrary angles between the direction of the external static magnetic field and the normal to the border of the MPC layer is considered. The problem is solved by Ambartsumian's modified layer addition method. It is found that there is a new type of non-reciprocity, namely, the relation R (α) ≠ R (- α) takes place, where R is the reflection coefficient, and α is the incidence angle. It is shown the formation of new photonic band gap (PBG) at oblique incidence of light, which is not selective for the polarization of the incident light, in the case when the external magnetic field is directed along the medium axis. Such a system can be used as: a tunable polarization filter, polarization mirror, circular (elliptical) polarizer, tunable optical diode, etc.

  10. 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

  11. 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

  12. Improving RNA secondary structure prediction with structure mapping data.

    PubMed

    Sloma, Michael F; Mathews, David H

    2015-01-01

    Methods to probe RNA secondary structure, such as small molecule modifying agents, secondary structure-specific nucleases, inline probing, and SHAPE chemistry, are widely used to study the structure of functional RNA. Computational secondary structure prediction programs can incorporate probing data to predict structure with high accuracy. In this chapter, an overview of current methods for probing RNA secondary structure is provided, including modern high-throughput methods. Methods for guiding secondary structure prediction algorithms using these data are explained, and best practices for using these data are provided. This chapter concludes by listing a number of open questions about how to best use probing data, and what these data can provide. © 2015 Elsevier Inc. All rights reserved.

  13. Crystallization by Particle Attachment: New Paradigm for Predicting Influences of Environmental Change on Calcification Processes

    NASA Astrophysics Data System (ADS)

    Dove, P. M.; De Yoreo, J. J.

    2016-02-01

    Traditional approaches to interpreting the formation of marine biominerals were founded on the classical models of crystal growth that were based on observations of mineral systems with high solubility. In these systems growth is dominated by attachment of individual ions to step edges. As Earth scientists began to use high-resolution and in situ TEM methods to investigate the growth of biological minerals and sparingly soluble synthetic materials, the importance of nanoparticle assembly became important. These studies show that the formation of many biominerals cannot be explained solely by the monomer-by-monomer addition of classical models. Rather, the process begins by forming particles that can begin as small molecules, clusters, droplets, or nanocrystals. The particles subsequently interact to give rise to crystalline structures. Evidence from biological and synthetic studies shows crystallization by particle attachment (CPA) processes are widespread (De Yoreo et al., 2015, Science), and possibly a prevailing type of crystal growth. This presentation will outline the dominant pathways for CPA and show evidence for how carbonate mineralization occurs by this process. The revised picture of biominerals is based in evidence from natural and experimental samples and rooted in thermodynamic and kinetic principles. While there is much to be learned about the nature of particle-particle interactions, CPA offers a process-based construct for deciphering chemical signatures and predicting how changing environmental conditions will influence calcification.

  14. Predicting Crystallization of Amorphous Drugs with Terahertz Spectroscopy.

    PubMed

    Sibik, Juraj; Löbmann, Korbinian; Rades, Thomas; Zeitler, J Axel

    2015-08-03

    There is a controversy about the extent to which the primary and secondary dielectric relaxations influence the crystallization of amorphous organic compounds below the glass transition temperature. Recent studies also point to the importance of fast molecular dynamics on picosecond-to-nanosecond time scales with respect to the glass stability. In the present study we provide terahertz spectroscopy evidence on the crystallization of amorphous naproxen well below its glass transition temperature and confirm the direct role of Johari-Goldstein (JG) secondary relaxation as a facilitator of the crystallization. We determine the onset temperature Tβ above which the JG relaxation contributes to the fast molecular dynamics and analytically quantify the level of this contribution. We then show there is a strong correlation between the increase in the fast molecular dynamics and onset of crystallization in several chosen amorphous drugs. We believe that this technique has immediate applications to quantify the stability of amorphous drug materials.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. Predicting structure in nonsymmetric sparse matrix factorizations

    SciTech Connect

    Gilbert, J.R.; Ng, E.

    1991-12-31

    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.

  1. Predicting structure in nonsymmetric sparse matrix factorizations

    SciTech Connect

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

    1991-01-01

    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.

  2. 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.

  3. 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.

  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. 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.

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

    DTIC Science & Technology

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

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. The crystal structure of KR-21042, an analgesic capsaicinoid.

    PubMed

    Park, No Sang; Kim, Yang Bae; Jeong, Eun Ju; Chung, Uoo Tae; Park, I I Yeong

    2002-02-01

    The crystal structure of KR-21042, N-(3-Phenylpropyl)-4-hydroxy-3-methoxyphenylacetamide, was determined by single crystal X-ray diffraction analysis. The compound was recrystallized from a mixture of ethylacetate and n-hexane in monoclinic, space group P21/c, with a = 16.622(1), b = 6.215(1), c = 15.802(1) A, P= 104.97(1), and Z = 4. The calculated density is 1.261 g/cm3. The structure was solved by the direct method and refined by full matrix least-squares procedure to the final R value of 0.068 for 2332 observed reflections.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. Predicting Odor Perceptual Similarity from Odor Structure

    PubMed Central

    Weiss, Tali; Frumin, Idan; Khan, Rehan M.; Sobel, Noam

    2013-01-01

    To understand the brain mechanisms of olfaction we must understand the rules that govern the link between odorant structure and odorant perception. Natural odors are in fact mixtures made of many molecules, and there is currently no method to look at the molecular structure of such odorant-mixtures and predict their smell. In three separate experiments, we asked 139 subjects to rate the pairwise perceptual similarity of 64 odorant-mixtures ranging in size from 4 to 43 mono-molecular components. We then tested alternative models to link odorant-mixture structure to odorant-mixture perceptual similarity. Whereas a model that considered each mono-molecular component of a mixture separately provided a poor prediction of mixture similarity, a model that represented the mixture as a single structural vector provided consistent correlations between predicted and actual perceptual similarity (r≥0.49, p<0.001). An optimized version of this model yielded a correlation of r = 0.85 (p<0.001) between predicted and actual mixture similarity. In other words, we developed an algorithm that can look at the molecular structure of two novel odorant-mixtures, and predict their ensuing perceptual similarity. That this goal was attained using a model that considers the mixtures as a single vector is consistent with a synthetic rather than analytical brain processing mechanism in olfaction. PMID:24068899

  17. 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.

  18. 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.

  19. Crystal Structures of Monomeric Actin Bound to Cytochalasin D

    PubMed Central

    Nair, Usha B.; Joel, Peteranne B.; Wan, Qun; Lowey, Susan; Rould, Mark A.; Trybus, Kathleen M.

    2008-01-01

    The fungal toxin cytochalasin D (CD) interferes with the normal dynamics of the actin cytoskeleton by binding to the barbed end of actin filaments. Despite its widespread use as a tool for studying actin-mediated processes, the exact location and nature of its binding to actin has not been previously determined. Here we describe two crystal structures of an expressed monomeric actin in complex with CD, one obtained by soaking preformed actin crystals with CD, and the other by co-crystallization. The binding site for CD, in the hydrophobic cleft between actin subdomains 1 and 3, is the same in the two structures. Polar and hydrophobic contacts play an equally important role in CD binding, and six hydrogen bonds stabilize the actin-CD complex. Many unrelated actin-binding proteins and marine toxins target this cleft, and the hydrophobic pocket at the front end of the cleft (viewing actin with subdomain 2 in the upper right corner). CD differs in that it binds to the back half of the cleft. The ability of CD to induce actin dimer formation and actin-catalyzed ATP hydrolysis may be related to its unique binding site, and the necessity to fit its bulky macrocycle into this cleft. Contacts with residues lining this cleft appear to be crucial to capping and/or severing. The co-crystallized actin-CD structure also revealed changes in actin conformation. A rotation of ~6° of the smaller actin domain (subdomains 1 and 2) with respect to the larger domain (subdomains 3 and 4) results in small changes in crystal packing that allow the D-loop to adopt an extended loop structure, instead of being disordered as it is in most crystal structures of actin. We speculate that these changes represent a potential conformation that the actin monomer can adopt on the pathway to polymerization or in the filament. PMID:18938176

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  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. 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.

  7. 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.

  8. Ultrasonication as a potential tool to predict solute crystallization in freeze-concentrates.

    PubMed

    Ragoonanan, Vishard; Suryanarayanan, Raj

    2014-06-01

    We hypothesize that ultrasonication can accelerate solute crystallization in freeze-concentrates. Our objective is to demonstrate ultrasonication as a potential predictive tool for evaluating physical stability of excipients in frozen solutions. The crystallization tendencies of lyoprotectants (trehalose, sucrose), carboxylic acid buffers (citric, tartaric, malic, and acetic) and an amino acid buffer (histidine HCl) were studied. Aqueous solutions of buffers, lyoprotectants and mixtures of the two were cooled from room temperature to -20°C and sonicated to induce solute crystallization. The crystallized phases were identified by X-ray diffractometry (laboratory or synchrotron source). Sonication accelerated crystallization of trehalose dihydrate in frozen trehalose solutions. Sonication also enhanced solute crystallization in tartaric (200 mM; pH 5), citric (200 mM pH 4) and malic (200 mM; pH 4) acid buffers. At lower buffer concentrations, longer annealing times following sonication were required to facilitate solute crystallization. The time for crystallization of histidine HCl progressively increased as a function of sucrose concentration. The insonation period required to effect crystallization also increased with sucrose concentration. Sonication can substantially accelerate solute crystallization in the freeze-concentrate. Ultrasonication may be useful in assessing the crystallization tendency of formulation constituents used in long term frozen storage and freeze-drying.

  9. The characterisation of the "X" crystal structure in the Stillinger-Weber potential

    NASA Astrophysics Data System (ADS)

    Fijan, Domagoj; Wilson, Mark

    2017-10-01

    A recently observed crystal structure is characterised by reference to the calculated diffraction patterns. The "X" crystal is related to the β -Sn crystal structure via an atom displacement and a reduction in symmetry from tetragonal to orthorhombic. A further crystal polymorph is identified which retains the tetragonal symmetry of the β -Sn structure but involves a related atom displacement. The unit cells and space groups are reported. The two crystals are labelled as o-X and t-X respectively. The transformation mechanisms from the β -Sn crystal structure to the two structures are identified. No routes to these crystals from other polymorphs are found.

  10. Structure Prediction and Validation of the ERK8 Kinase Domain

    PubMed Central

    Strambi, Angela; Mori, Mattia; Rossi, Matteo; Colecchia, David; Manetti, Fabrizio; Carlomagno, Francesca; Botta, Maurizio; Chiariello, Mario

    2013-01-01

    Extracellular signal-regulated kinase 8 (ERK8) has been already implicated in cell transformation and in the protection of genomic integrity and, therefore, proposed as a novel potential therapeutic target for cancer. In the absence of a crystal structure, we developed a three-dimensional model for its kinase domain. To validate our model we applied a structure-based virtual screening protocol consisting of pharmacophore screening and molecular docking. Experimental characterization of the hit compounds confirmed that a high percentage of the identified scaffolds was able to inhibit ERK8. We also confirmed an ATP competitive mechanism of action for the two best-performing molecules. Ultimately, we identified an ERK8 drug-resistant “gatekeeper” mutant that corroborated the predicted molecular binding mode, confirming the reliability of the generated structure. We expect that our model will be a valuable tool for the development of specific ERK8 kinase inhibitors. PMID:23326322

  11. Protein Structure Prediction with Evolutionary Algorithms

    SciTech Connect

    Hart, W.E.; Krasnogor, N.; Pelta, D.A.; Smith, J.

    1999-02-08

    Evolutionary algorithms have been successfully applied to a variety of molecular structure prediction problems. In this paper we reconsider the design of genetic algorithms that have been applied to a simple protein structure prediction problem. Our analysis considers the impact of several algorithmic factors for this problem: the confirmational representation, the energy formulation and the way in which infeasible conformations are penalized, Further we empirically evaluated the impact of these factors on a small set of polymer sequences. Our analysis leads to specific recommendations for both GAs as well as other heuristic methods for solving PSP on the HP model.

  12. 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.

  13. Protein Structure Prediction by Protein Threading

    NASA Astrophysics Data System (ADS)

    Xu, Ying; Liu, Zhijie; Cai, Liming; Xu, Dong

    The seminal work of Bowie, Lüthy, and Eisenberg (Bowie et al., 1991) on "the inverse protein folding problem" laid the foundation of protein structure prediction by protein threading. By using simple measures for fitness of different amino acid types to local structural environments defined in terms of solvent accessibility and protein secondary structure, the authors derived a simple and yet profoundly novel approach to assessing if a protein sequence fits well with a given protein structural fold. Their follow-up work (Elofsson et al., 1996; Fischer and Eisenberg, 1996; Fischer et al., 1996a,b) and the work by Jones, Taylor, and Thornton (Jones et al., 1992) on protein fold recognition led to the development of a new brand of powerful tools for protein structure prediction, which we now term "protein threading." These computational tools have played a key role in extending the utility of all the experimentally solved structures by X-ray crystallography and nuclear magnetic resonance (NMR), providing structural models and functional predictions for many of the proteins encoded in the hundreds of genomes that have been sequenced up to now.

  14. 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.

  15. 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.…

  16. 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.

  17. 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.…

  18. 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.

  19. 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.

  20. Crystal and molecular structure of lancerodiol–p–hydroxybenzoate

    PubMed Central

    Abd El–Razek, Mohamed H.; Hegazy, Mohamed–Elamir F.; Mohamed, Abou El–Hamd H.

    2010-01-01

    Lancerodiol–p–hydroxybenzoate was isolated from the leaves of Ferula sinaica L. (Apiaceae) as light needle crystals. This work reports for the first time the molecular structure and relative configuration of compound 1, established by X-ray analysis. PMID:21808543

  1. 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.

  2. VO{sub 2} (A): Reinvestigation of crystal structure, phase transition and crystal growth mechanisms

    SciTech Connect

    Rao Popuri, Srinivasa; Artemenko, Alla; Labrugere, Christine; Miclau, Marinela; Villesuzanne, Antoine; Pollet, Michaël

    2014-05-01

    Well crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal reaction in the presence of V{sub 2}O{sub 5} and oxalic acid. With the advantage of high crystalline samples, we propose P4/ncc as an appropriate space group at room temperature. From morphological studies, we found that the oriented attachment and layer by layer growth mechanisms are responsible for the formation of VO{sub 2} (A) micro rods. The structural and electronic transitions in VO{sub 2} (A) are strongly first order in nature, and a marked difference between the structural transition temperatures and electronic transitions temperature was evidenced. The reversible intra- (LTP-A to HTP-A) and irreversible inter- (HTP-A to VO{sub 2} (M1)) structural phase transformations were studied by in-situ powder X-ray diffraction. Attempts to increase the size of the VO{sub 2} (A) microrods are presented and the possible formation steps for the flower-like morphologies of VO{sub 2} (M1) are described. - Graphical abstract: Using a single step and template free hydrothermal synthesis, well crystallized VO{sub 2} (A) microrods were prepared and the P4/ncc space group was assigned to the room temperature crystal structure. Reversible and irreversible phase transitions among different VO{sub 2} polymorphs were identified and their progressive nature was highlighted. Attempts to increase the microrods size, involving layer by layer formation mechanisms, are presented. - Highlights: • Highly crystallized VO{sub 2} (A) microrods were grown via a single step hydrothermal process. • The P4/ncc space group was determined for VO{sub 2} (A) at room temperature. • The electronic structure and progressive nature of the structural phase transition were investigated. • A weak coupling between structural and electronic phase transitions was identified. • Different crystallite morphologies were discussed in relation with growth mechanisms.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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.

  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. 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.

  14. 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.

  15. On calculating the equilibrium structure of molecular crystals.

    SciTech Connect

    Mattsson, Ann Elisabet; Wixom, Ryan R.; Mattsson, Thomas Kjell Rene

    2010-03-01

    The difficulty of calculating the ambient properties of molecular crystals, such as the explosive PETN, has long hampered much needed computational investigations of these materials. One reason for the shortcomings is that the exchange-correlation functionals available for Density Functional Theory (DFT) based calculations do not correctly describe the weak intermolecular van der Waals' forces present in molecular crystals. However, this weak interaction also poses other challenges for the computational schemes used. We will discuss these issues in the context of calculations of lattice constants and structure of PETN with a number of different functionals, and also discuss if these limitations can be circumvented for studies at non-ambient conditions.

  16. 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.

  17. 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.

  18. 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

  19. Crystal Structure of Triosephosphate Isomerase from Trypanosoma cruzi in Hexane

    NASA Astrophysics Data System (ADS)

    Gao, Xiu-Gong; Maldonado, Ernesto; Perez-Montfort, Ruy; Garza-Ramos, Georgina; Tuena de Gomez-Puyou, Marietta; Gomez-Puyou, Armando; Rodriguez-Romero, Adela

    1999-08-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2- angstrom resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 angstrom from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design.

  20. Crystal structure of triosephosphate isomerase from Trypanosoma cruzi in hexane

    PubMed Central

    Gao, Xiu-Gong; Maldonado, Ernesto; Pérez-Montfort, Ruy; Garza-Ramos, Georgina; de Gómez-Puyou, Marietta Tuena; Gómez-Puyou, Armando; Rodríguez-Romero, Adela

    1999-01-01

    To gain insight into the mechanisms of enzyme catalysis in organic solvents, the x-ray structure of some monomeric enzymes in organic solvents was determined. However, it remained to be explored whether the structure of oligomeric proteins is also amenable to such analysis. The field acquired new perspectives when it was proposed that the x-ray structure of enzymes in nonaqueous media could reveal binding sites for organic solvents that in principle could represent the starting point for drug design. Here, a crystal of the dimeric enzyme triosephosphate isomerase from the pathogenic parasite Trypanosoma cruzi was soaked and diffracted in hexane and its structure solved at 2-Å resolution. Its overall structure and the dimer interface were not altered by hexane. However, there were differences in the orientation of the side chains of several amino acids, including that of the catalytic Glu-168 in one of the monomers. No hexane molecules were detected in the active site or in the dimer interface. However, three hexane molecules were identified on the surface of the protein at sites, which in the native crystal did not have water molecules. The number of water molecules in the hexane structure was higher than in the native crystal. Two hexanes localized at <4 Å from residues that form the dimer interface; they were in close proximity to a site that has been considered a potential target for drug design. PMID:10468562

  1. Protein complex compositions predicted by structural similarity

    PubMed Central

    Davis, Fred P.; Braberg, Hannes; Shen, Min-Yi; Pieper, Ursula; Sali, Andrej; Madhusudhan, M.S.

    2006-01-01

    Proteins function through interactions with other molecules. Thus, the network of physical interactions among proteins is of great interest to both experimental and computational biologists. Here we present structure-based predictions of 3387 binary and 1234 higher order protein complexes in Saccharomyces cerevisiae involving 924 and 195 proteins, respectively. To generate candidate complexes, comparative models of individual proteins were built and combined together using complexes of known structure as templates. These candidate complexes were then assessed using a statistical potential, derived from binary domain interfaces in PIBASE (). The statistical potential discriminated a benchmark set of 100 interface structures from a set of sequence-randomized negative examples with a false positive rate of 3% and a true positive rate of 97%. Moreover, the predicted complexes were also filtered using functional annotation and sub-cellular localization data. The ability of the method to select the correct binding mode among alternates is demonstrated for three camelid VHH domain—porcine α–amylase interactions. We also highlight the prediction of co-complexed domain superfamilies that are not present in template complexes. Through integration with MODBASE, the application of the method to proteomes that are less well characterized than that of S.cerevisiae will contribute to expansion of the structural and functional coverage of protein interaction space. The predicted complexes are deposited in MODBASE (). PMID:16738133

  2. 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

  3. 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.

  4. 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.

  5. 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.

  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. 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.

  8. Crystal Structure of High-Pressure Phases V and VI of Potassium Dihydrogen Phosphate

    NASA Astrophysics Data System (ADS)

    Nakamoto, Yuki; Sakata, Masafumi; Fujihisa, Hiroshi; Shimizu, Katsuya; Deguchi, Kiyoshi

    2012-06-01

    Potassium dihydrogen phosphate KH2PO4 is the most typical hydrogen-bonded ferroelectric. The P--T phase diagram and the existence of high-pressure phases V and VI have already been reported. However, their crystal structures remain unknown. We performed a powder x-ray diffraction experiment under high pressure using synchrotron radiation and analyzed the structures from the obtained data. The structures of phases V and VI were determined to be orthorhombic C2221 and triclinic P\\bar{1}. Their hydrogen positions were predicted by a density functional theory calculation.

  9. 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.

  10. 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.

  11. Production, crystallization and structure determination of a mycobacterial glucosylglycerate hydrolase.

    PubMed

    Cereija, Tatiana Barros; Alarico, Susana; Empadinhas, Nuno; Pereira, Pedro José Barbosa

    2017-09-01

    Glucosylglycerate hydrolase is highly conserved among rapidly growing mycobacteria and has been found to be involved in recovery from nitrogen starvation by promoting the rapid mobilization of the glucosylglycerate that accumulates under these conditions. Here, the production, crystallization and structure determination of glucosylglycerate hydrolase from Mycobacterium hassiacum using two-wavelength anomalous diffraction of selenomethionine-substituted crystals are described. The monoclinic (space group P21) crystals diffracted to ∼2.0 Å resolution at a synchrotron-radiation source and contained four molecules in the asymmetric unit, corresponding to a Matthews coefficient of 3.07 Å(3) Da(-1) and a solvent content of 59.9%. The quality of the experimental phases allowed the automated building of 1677 of the 1792 residues in the asymmetric unit.

  12. RNA secondary structure prediction using soft computing.

    PubMed

    Ray, Shubhra Sankar; Pal, Sankar K

    2013-01-01

    Prediction of RNA structure is invaluable in creating new drugs and understanding genetic diseases. Several deterministic algorithms and soft computing-based techniques have been developed for more than a decade to determine the structure from a known RNA sequence. Soft computing gained importance with the need to get approximate solutions for RNA sequences by considering the issues related with kinetic effects, cotranscriptional folding, and estimation of certain energy parameters. A brief description of some of the soft computing-based techniques, developed for RNA secondary structure prediction, is presented along with their relevance. The basic concepts of RNA and its different structural elements like helix, bulge, hairpin loop, internal loop, and multiloop are described. These are followed by different methodologies, employing genetic algorithms, artificial neural networks, and fuzzy logic. The role of various metaheuristics, like simulated annealing, particle swarm optimization, ant colony optimization, and tabu search is also discussed. A relative comparison among different techniques, in predicting 12 known RNA secondary structures, is presented, as an example. Future challenging issues are then mentioned.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. Anisotropic crystal structure of magnetized neutron star crust

    NASA Astrophysics Data System (ADS)

    Baiko, D. A.; Kozhberov, A. A.

    2017-09-01

    Although the crystallized neutron star crust is responsible for many fascinating observational phenomena, its actual microscopic structure in tremendous gravitational and magnetic fields is not understood. Here we show that in a non-uniform magnetic field, three-dimensional ionic Coulomb crystals comprising the crust may stretch or shrink while their electrostatic pressure becomes anisotropic. The pressure depends non-linearly on the magnitude of the stretch, so that a continuous magnetic field evolution may result in an abrupt crystal elongation or contraction. This may provide a trigger for magnetar activity. A phonon-mode instability is revealed, which sets the limits of magnetic field variation beyond which the crystal is destroyed. These limits sometimes correspond to surprisingly large deformations. It is not known what happens to crust matter subjected to a pressure anisotropy exceeding these limits. We hypothesize that the ion system then possesses a long-range order only in one or two dimensions, i.e. becomes a liquid crystal.

  18. Crystallizing Membrane Proteins for Structure Determination using Lipidic Mesophases

    PubMed Central

    Caffrey, Martin; Porter, Christopher

    2010-01-01

    A detailed protocol for crystallizing membrane proteins by using lipidic mesophases is described. This method has variously been referred to as the lipidic cubic phase or in meso method. The method has been shown to be quite versatile in that it has been used to solve X-ray crystallographic structures of prokaryotic and eukaryotic proteins, proteins that are monomeric, homo- and hetero-multimeric, chromophore-containing and chromophore-free, and alpha-helical and beta-barrel proteins. Recent successes using in meso crystallization are the human engineered beta2-adrenergic and adenosine A2a G protein-coupled receptors. Protocols are presented for reconstituting the membrane protein into the monoolein-based mesophase, and for setting up crystallizations in the manual mode. Additional steps in the overall process, such as crystal harvesting, are to be addressed in future video articles. The time required to prepare the protein-loaded mesophase and to set up a crystallization plate manually is about one hour. PMID:21113125

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. Structure-forming components in crystals of ternary and quaternary 3d-metal complex fluorides.

    PubMed

    Peresypkina, E V; Blatov, V A

    2003-06-01

    Crystallochemical analysis and classification were performed for 139 ternary and quaternary complex fluorides with the general formula M1(n)M2(m)M3F(6), belonging to 33 structure types. Using coordination sequences and the uniformity criterion the structure-forming ionic sublattices or their combinations were found, which are responsible for the formation of stable periodic frameworks. Analysis of structure-forming motifs allows the interpretation of the crystal structures of complex fluorides as close packings of F ions with M1, M2 and M3 cations, partially occupying tetrahedral and octahedral voids, or as the packings of [M3F(6)] complex ions with M1 and M2 countercations in the voids. Cationic sublattices are noted to play an essential role, while forming crystal structures of complex fluorides. Relationships between the composition of structure-forming sublattices, the composition of compounds, and the size and charge of ions belonging to the sublattices were analysed under normal conditions, with thermal and high-pressure polymorphic transitions. Rules were formulated to predict the crystal structures of complex fluorides with a given chemical composition.

  4. 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/ PMID:28637268

  5. Predicting structured metadata from unstructured metadata.

    PubMed

    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. © The Author(s) 2016. Published by Oxford University Press.

  6. 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.

  7. Rich parameterization improves RNA structure prediction.

    PubMed

    Zakov, Shay; Goldberg, Yoav; Elhadad, Michael; Ziv-Ukelson, Michal

    2011-11-01

    Current approaches to RNA structure prediction range from physics-based methods, which rely on thousands of experimentally measured thermodynamic parameters, to machine-learning (ML) techniques. While the methods for parameter estimation are successfully shifting toward ML-based approaches, the model parameterizations so far remained fairly constant. We study the potential contribution of increasing the amount of information utilized by RNA folding prediction models to the improvement of their prediction quality. This is achieved by proposing novel models, which refine previous ones by examining more types of structural elements, and larger sequential contexts for these elements. Our proposed fine-grained models are made practical thanks to the availability of large training sets, advances in machine-learning, and recent accelerations to RNA folding algorithms. We show that the application of more detailed models indeed improves prediction quality, while the corresponding running time of the folding algorithm remains fast. An additional important outcome of this experiment is a new RNA folding prediction model (coupled with a freely available implementation), which results in a significantly higher prediction quality than that of previous models. This final model has about 70,000 free parameters, several orders of magnitude more than previous models. Being trained and tested over the same comprehensive data sets, our model achieves a score of 84% according to the F₁-measure over correctly-predicted base-pairs (i.e., 16% error rate), compared to the previously best reported score of 70% (i.e., 30% error rate). That is, the new model yields an error reduction of about 50%. Trained models and source code are available at www.cs.bgu.ac.il/?negevcb/contextfold.

  8. 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

  9. Bankruptcy Prediction with Interfirm Network Structure

    NASA Astrophysics Data System (ADS)

    Kamei, Hideto; Takayasu, Hideki; Kabashima, Yoshiyuki; Takayasu, Misako

    This study examines bankruptcy in terms of financial variables as well as interfirm network structure variables. We first binarize the variables by introducing a threshold and then select the appropriate set of variables that minimize the p-value in Fisher's exact test. Here, the financial variables related to borrowing and savings are strongly correlated with bankruptcy, but the variables of trade network and capital network, including chain bankruptcy effect, have weaker yet significant correlations. Finally, we perform a bankruptcy prediction with the selected variables and a second-order Ising model and confirm that the Ising model has relatively higher predictive power than the logit model.

  10. Coupled melt flow and thermal stress predictions for Czochralski crystal growth

    SciTech Connect

    Zou, Y.F.; Zhang, H.; Prasad, V.

    1995-12-31

    A coupled finite volume-finite element algorithm is developed to simulate the melt flows and predict the temperature distributions and thermal stresses in the Czochralski grown crystals. The computer model employs a multizone adaptive grid generation scheme together with curvilinear finite column discretization (MASTRAPP) to predict the transport phenomena associated with the crystal growth processes as well as the nonplanar melt/crystal interface shape and its dynamics (Zhang and Prasad, 1995a). The MASTRAPP has proven to be a robust and efficient scheme for the problems involving moving interfaces and free surfaces. Thermal stresses in the crystal are obtained by using a commercial finite element code, ALGOR, that uses the curvilinear mesh generated by the MASTRAPP. The numerical results show that the melt flows have a strong influence on thermal stresses in the crystal near the melt/crystal interface, and hence, melt convection must be included in the computer model for accurate stress predictions. The predicted stress phenomena agrees qualitatively with the report results.

  11. 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.

  12. 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).

  13. 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

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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