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Sample records for abstract crystal structure

  1. Deficiencies in structured medical abstracts.

    PubMed

    Froom, P; Froom, J

    1993-07-01

    This study was carried out to determine if the content of structured abstracts conforms with recommendations of the Ad Hoc Working Group for the critical appraisal of the medical literature as adopted by the Annals of Internal Medicine. The study design was a survey. All articles published in Annals of Internal Medicine in 1991, excluding editorials, case-reports, literature reviews, decision analysis, studies in medical education, descriptive studies of clinical and basic phenomena, and papers lacking a structured abstract, were studied. Of a total of 150 articles, 20 were excluded. The abstract and text of each article were assessed for the presence of the following items; patient selection criteria, statements concerning extrapolation of findings, need for further study, and whether or not the information should be used now. Number of refusers, drop outs and reason(s) for drop outs were assessed for intervention and prospective cohort studies only. Deficiencies of assessed items were noted in both abstracts and texts. For abstracts, patient selection criteria, numbers of refusers, number of drop outs and reason(s) for drop outs were reported in 44.6% (58/130), 3.1% (4/130), 16.9% (14/83) and 2.4% (2/83) respectively. These items were reported more frequently in the texts 87.7% (114/130), 9.2% (12/130), 60.2% (50/83) and 37.3% (31/83) respectively (p < 0.05). Statements concerning extrapolation of findings, need for further study and use of information now were also more frequent in texts than abstracts (p < 0.0001). A large number of structured abstracts published in the Annals of Internal Medicine in 1991, lack information recommended by the Ad Hoc Working Group. Our findings should not be extrapolated to other journals requiring structured abstracts.

  2. Typographic Settings for Structured Abstracts.

    ERIC Educational Resources Information Center

    Hartley, James

    2000-01-01

    Lists some of the major typographic variables involved in structured abstracts (containing sub-headings). Illustrates how typography can affect clarity by presenting seven examples that illustrate the effects of these typographic variables in practice. Concludes with a final example of an effective approach. (SR)

  3. Discourse-Level Structure in Abstracts.

    ERIC Educational Resources Information Center

    Liddy, Elizabeth D.

    An investigation was undertaken into the possibility of automatically detecting how concepts exist in relation to each other in abstracts, a text-type commonly used in free-text retrieval. The end goal of this research is to capture these relationships in structured representations of abstracts' contents so that users can require not only that the…

  4. 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.

  5. 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.

  6. Writing a Structured Abstract for the Thesis

    ERIC Educational Resources Information Center

    Hartley, James

    2010-01-01

    This article presents the author's suggestions on how to improve thesis abstracts. The author describes two books on writing abstracts: (1) "Creating Effective Conference Abstracts and Posters in Biomedicine: 500 tips for Success" (Fraser, Fuller & Hutber, 2009), a compendium of clear advice--a must book to have in one's hand as one prepares a…

  7. Strengthening Structured Abstracts for Education Research: The Need for Claim-Based Structured Abstracts

    ERIC Educational Resources Information Center

    Kelly, Anthony E.; Yin, Robert K.

    2007-01-01

    Recent policy recommendations involving the putative primacy of randomized clinical trials in educational settings have reignited research paradigm debates. The authors of this article use the vehicle of strengthening structured journal abstracts to point out the argumentative character of all education research claims. They offer suggestions to…

  8. Abstracts

    ERIC Educational Resources Information Center

    American Biology Teacher, 1977

    1977-01-01

    Included are over 50 abstracts of papers being presented at the 1977 National Association of Biology Teachers Convention. Included in each abstract are the title, author, and summary of the paper. Topics include photographic techniques environmental studies, and biological instruction. (MA)

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

    DTIC Science & Technology

    2009-04-01

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

  10. Introducing structured abstracts for A&A articles

    NASA Astrophysics Data System (ADS)

    Bertout, Claude; Schneider, Peter

    2005-10-01

    Context: Due to their wide availability, abstracts have become the most important part of any astrophysical paper. Aims: Having noticed that abstracts published in astronomical journals are not always optimal, we introduce the concept of structured abstracts for A&A articles. Methods: We explain what structured abstracts are and where they come from, provide examples showing how to structure an abstract, and discuss the advantages and drawbacks of this novel concept. In an on-line appendix, we show what some published abstracts look like once they are structured. Results: We demonstrate the improvements in information content, readability, and style that can be made when writing structured abstracts instead of traditional ones. Conclusions: A new version 6.0 of the A&A LaTeX macro is now available for structuring the abstracts of articles, and A&A authors are kindly invited to use it for their new submissions.

  11. Structured hints : extracting and abstracting domain expertise.

    SciTech Connect

    Hereld, M.; Stevens, R.; Sterling, T.; Gao, G. R.; Mathematics and Computer Science; California Inst. of Tech.; Louisiana State Univ.; Univ. of Delaware

    2009-03-16

    We propose a new framework for providing information to help optimize domain-specific application codes. Its design addresses problems that derive from the widening gap between the domain problem statement by domain experts and the architectural details of new and future high-end computing systems. The design is particularly well suited to program execution models that incorporate dynamic adaptive methodologies for live tuning of program performance and resource utilization. This new framework, which we call 'structured hints', couples a vocabulary of annotations to a suite of performance metrics. The immediate target is development of a process by which a domain expert describes characteristics of objects and methods in the application code that would not be readily apparent to the compiler; the domain expert provides further information about what quantities might provide the best indications of desirable effect; and the interactive preprocessor identifies potential opportunities for the domain expert to evaluate. Our development of these ideas is progressing in stages from case study, through manual implementation, to automatic or semi-automatic implementation. In this paper we discuss results from our case study, an examination of a large simulation of a neural network modeled after the neocortex.

  12. ICCG-10: Tenth International Conference on Crystal Growth. Poster presentation abstracts

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Poster presentation abstracts from the tenth International Conference on Crystal Growth (ICCG) (Aug. 16-21, 1992) are provided. Topics discussed at the conference include crystal growth mechanisms, superconductors, semiconductors, laser materials, optical materials, and biomaterials. Organizing committees, ICCG advisory board and officers, and sponsors of the conference are also included.

  13. ICCG-10: Tenth International Conference on Crystal Growth. Oral presentation abstracts

    NASA Technical Reports Server (NTRS)

    1992-01-01

    Oral presentation abstracts from the tenth International Conference on Crystal Growth (ICCG) (Aug. 16-21, 1992) are provided. Topics discussed at the conference include superconductors, semiconductors, nucleation, crystal growth mechanisms, and laser materials. Organizing committees, ICCG advisory board and officers, and sponsors of the conference are also included.

  14. ICCG-10: Tenth international conference on crystal growth. Poster presentation abstracts

    SciTech Connect

    Not Available

    1992-01-01

    Abstracts from the tenth International Conference on Crystal Growth (ICCG) (Aug. 16-21, 1992) are provided. Topics discussed at the conference include crystal growth mechanisms, superconductors, semiconductors, laser materials, optical materials, and biomaterials. Organizing committees, ICCG advisory board and officers, and sponsors of the conference are also included.

  15. 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.)

  16. 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.

  17. A further characteristic of abstract convexity structures on topological spaces

    NASA Astrophysics Data System (ADS)

    Xiang, Shu-Wen; Xia, Shunyou

    2007-11-01

    In this paper, we give a characteristic of abstract convexity structures on topological spaces with selection property. We show that if a convexity structure defined on a topological space has the weak selection property then satisfies H0-condition. Moreover, in a compact convex subset of a topological space with convexity structure, the weak selection property implies the fixed point property.

  18. 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.

  19. Abstract and concrete concepts have structurally different representational frameworks.

    PubMed

    Crutch, Sebastian J; Warrington, Elizabeth K

    2005-03-01

    The architecture supporting our conceptual knowledge of abstract words has remained almost entirely unexplored. By contrast, a vast neuropsychological, neurolinguistic and neuroimaging literature has addressed questions relating to the structure of the semantic system underpinning our knowledge of concrete items (e.g. artefacts and animals). In the context of semantic refractory access dysphasia, a series of experiments exploring and comparing abstract and concrete word comprehension are described. We demonstrate that semantically associated abstract words reliably interfere with one another significantly more than semantically synonymous abstract words, while concrete words show the reverse pattern. We report the first evidence that abstract and concrete word meanings are based in representational systems that have qualitatively different properties. More specifically, we show that abstract concepts, but not concrete concepts, are represented in an associative neural network. Furthermore, our patient was found to have significantly greater difficulty in identifying high frequency than low frequency abstract words. This observation constitutes the first evidence of an inverse word frequency effect. Our results challenge the generality of many existing models of human conceptual knowledge, which derive their structure from experimental findings in the concrete domain alone.

  20. 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.

  1. 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

  2. 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)

  3. Argument structure and the representation of abstract semantics.

    PubMed

    Rodríguez-Ferreiro, Javier; Andreu, Llorenç; Sanz-Torrent, Mònica

    2014-01-01

    According to the dual coding theory, differences in the ease of retrieval between concrete and abstract words are related to the exclusive dependence of abstract semantics on linguistic information. Argument structure can be considered a measure of the complexity of the linguistic contexts that accompany a verb. If the retrieval of abstract verbs relies more on the linguistic codes they are associated to, we could expect a larger effect of argument structure for the processing of abstract verbs. In this study, sets of length- and frequency-matched verbs including 40 intransitive verbs, 40 transitive verbs taking simple complements, and 40 transitive verbs taking sentential complements were presented in separate lexical and grammatical decision tasks. Half of the verbs were concrete and half were abstract. Similar results were obtained in the two tasks, with significant effects of imageability and transitivity. However, the interaction between these two variables was not significant. These results conflict with hypotheses assuming a stronger reliance of abstract semantics on linguistic codes. In contrast, our data are in line with theories that link the ease of retrieval with availability and robustness of semantic information.

  4. Abstraction and Concreteness in the Everyday Mathematics of Structural Engineers.

    ERIC Educational Resources Information Center

    Gainsburg, Julie

    The everyday mathematics processes of structural engineers were studied and analyzed in terms of abstraction. A main purpose of the study was to explore the degree to which the notion of a gap between school and everyday mathematics holds when the scope of practices considered "everyday" is extended. J. Lave (1988) promoted a methodology…

  5. 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

  6. 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.

  7. 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).

  8. 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

  9. 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

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. 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.

  15. Abstract structural representations of goal-directed behavior.

    PubMed

    Allen, Kachina; Ibara, Steven; Seymour, Amy; Cordova, Natalia; Botvinick, Matthew

    2010-10-01

    Linguistic theory holds that the structure of a sentence can be described in abstract syntactic terms, independent of the specific words the sentence contains. Nonlinguistic behavior, including goal-directed action, is also theorized to have an underlying structural, or "syntactic," organization. We propose that purposive action sequences are represented cognitively in terms of a means-ends parse, which is a formal specification of how actions fit together to accomplish desired outcomes. To test this theory, we leveraged the phenomenon of structural priming in two experiments. As predicted, participants read sentences describing action sequences faster when these sentences were presented amid other sentences sharing the same parse. Results from a second experiment indicate that the underlying representations relevant to observed action sequences are not strictly tied to language processing. Our results suggest that the structure of goal-directed behavior may be represented abstractly, independently of specific actions and goals, just as linguistic syntax is thought to stand independent of other levels of representation.

  16. Modal and temporal logics for abstract space-time structures

    NASA Astrophysics Data System (ADS)

    Uckelman, Sara L.; Uckelman, Joel

    In the fourth century BC, the Greek philosopher Diodoros Chronos gave a temporal definition of necessity. Because it connects modality and temporality, this definition is of interest to philosophers working within branching time or branching space-time models. This definition of necessity can be formalized and treated within a logical framework. We give a survey of the several known modal and temporal logics of abstract space-time structures based on the real numbers and the integers, considering three different accessibility relations between spatio-temporal points.

  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. Structures and Crystal Chemistry of Layered Materials

    NASA Astrophysics Data System (ADS)

    Partin, Daniel Edward

    forming monocapped trigonal prisms, and the copper atoms are coordinated by four oxygen atoms in a square planar arrangement. The crystal structure of BaCuO_2 has been refined many times from X-ray powder data, X-ray single crystal data, and time-of-flight neutron diffraction data, the powder methods have been repeated here. (Abstract shortened by UMI.).

  19. Abstract numeric relations and the visual structure of algebra.

    PubMed

    Landy, David; Brookes, David; Smout, Ryan

    2014-09-01

    Formal algebras are among the most powerful and general mechanisms for expressing quantitative relational statements; yet, even university engineering students, who are relatively proficient with algebraic manipulation, struggle with and often fail to correctly deploy basic aspects of algebraic notation (Clement, 1982). In the cognitive tradition, it has often been assumed that skilled users of these formalisms treat situations in terms of semantic properties encoded in an abstract syntax that governs the use of notation without particular regard to the details of the physical structure of the equation itself (Anderson, 2005; Hegarty, Mayer, & Monk, 1995). We explore how the notational structure of verbal descriptions or algebraic equations (e.g., the spatial proximity of certain words or the visual alignment of numbers and symbols in an equation) plays a role in the process of interpreting or constructing symbolic equations. We propose in particular that construction processes involve an alignment of notational structures across representation systems, biasing reasoners toward the selection of formal notations that maintain the visuospatial structure of source representations. For example, in the statement "There are 5 elephants for every 3 rhinoceroses," the spatial proximity of 5 and elephants and 3 and rhinoceroses will bias reasoners to write the incorrect expression 5E = 3R, because that expression maintains the spatial relationships encoded in the source representation. In 3 experiments, participants constructed equations with given structure, based on story problems with a variety of phrasings. We demonstrate how the notational alignment approach accounts naturally for a variety of previously reported phenomena in equation construction and successfully predicts error patterns that are not accounted for by prior explanations, such as the left to right transcription heuristic.

  20. 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.

  1. 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.

  2. 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.

  3. Abstracted Workow Framework with a Structure from Motion Application

    NASA Astrophysics Data System (ADS)

    Rossi, Adam J.

    In scientific and engineering disciplines, from academia to industry, there is an increasing need for the development of custom software to perform experiments, construct systems, and develop products. The natural mindset initially is to shortcut and bypass all overhead and process rigor in order to obtain an immediate result for the problem at hand, with the misconception that the software will simply be thrown away at the end. In a majority of the cases, it turns out the software persists for many years, and likely ends up in production systems for which it was not initially intended. In the current study, a framework that can be used in both industry and academic applications mitigates underlying problems associated with developing scientific and engineering software. This results in software that is much more maintainable, documented, and usable by others, specifically allowing new users to extend capabilities of components already implemented in the framework. There is a multi-disciplinary need in the fields of imaging science, computer science, and software engineering for a unified implementation model, which motivates the development of an abstracted software framework. Structure from motion (SfM) has been identified as one use case where the abstracted workflow framework can improve research efficiencies and eliminate implementation redundancies in scientific fields. The SfM process begins by obtaining 2D images of a scene from different perspectives. Features from the images are extracted and correspondences are established. This provides a sufficient amount of information to initialize the problem for fully automated processing. Transformations are established between views, and 3D points are established via triangulation algorithms. The parameters for the camera models for all views / images are solved through bundle adjustment, establishing a highly consistent point cloud. The initial sparse point cloud and camera matrices are used to generate a dense

  4. Writing Electron Dot Structures: Abstract of Issue 9905M

    NASA Astrophysics Data System (ADS)

    Magnell, Kenneth R.

    1999-10-01

    "> Screens from Writing Electron Dot Structures Hardware and Software Requirements Hardware and software requirements for Writing Electron Dot Structures are shown in Table 1. Ordering and Information Journal of Chemical Education Software (or JCE Software) is a publication of the Journal of Chemical Education. There is an order form inserted in this issue that provides prices and other ordering information. If this card is not available or if you need additional information, contact: JCE Software, University of Wisconsin­Madison, 1101 University Avenue, Madison, WI 53706-1396; phone; 608/262-5153 or 800/991-5534; fax: 608/265-8094; email: jcesoft@chem.wisc.edu. Information about all of our publications (including abstracts, descriptions, updates) is available from our World Wide Web site at: http://JChemEd.chem.wisc.edu/JCESoft/

  5. Optical and Calorimetric Studies of Cholesterol-Rich Filamentous, Helical Ribbon and Crystal Microstructures (abstract)

    NASA Astrophysics Data System (ADS)

    Miroshnikova, Y. A.; Elsenbeck, M.; Kashuri, K.; Iannacchione, G. S.; Zastavker, Y. V.

    2009-04-01

    Formation of biological self-assemblies at all scales is a focus of studies in fields ranging from biology to physics to biomimetics. Understanding the physico-chemical properties of these self-assemblies may lead to the design of bio-inspired structures and technological applications. Here we examine self-assembled filamentous, helical ribbon, and crystal microstructures formed in chemically defined lipid concentrate (CDLC), a model system for cholesterol crystallization in gallbladder bile. CDLC consists of cholesterol, bilayer-forming amphiphiles, micelle-forming amphiphiles, and water. Phase contrast and differential interference contrast (DIC) microscopy indicate the presence of three microstructure types in all samples studied, and allow for an investigation of the structures' unique geometries. Additionally, confocal microscopy is used for qualitative assessment of surface and internal composition. To complement optical observations, calorimetric (differential-scanning and modulation) experiments, provide the basis for an in-depth understanding of collective and individual thermal behavior. Observed ``transition'' features indicate clustering and ``straightening'' of helical ribbons into short, increasingly thickening, filaments that dissolve with increasing temperature. These results suggest that all microstructures formed in CDLC may coexist in a metastable chemical equilibrium. Further investigation of the CDLC thermal profile should uncover the process of cholesterol crystallization as well as the unique design and function of microstructures formed in this system.

  6. 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.

  7. 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.

  8. 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)

  9. Computational materials science aided design of glass ceramics and crystal properties (abstract only).

    PubMed

    Mannstadt, Wolfgang

    2008-02-13

    Today's high tech materials have in many cases highly specialized properties and designed functionalities. Materials parameters like high temperature stability, high stiffness and certain optical properties have to be optimized and in many cases an adaptation to given processes is necessary. Many materials are compounds or layered structures. Thus, surface and interface properties need to be considered as well. At the same time to some extent just a few atomic layers sometimes determine the properties of the material, as is well known in semiconductor and other thin film technologies. Therefore, a detailed understanding of the materials properties at the atomic scale becomes more and more important. In addition many high tech materials have to be of high purity or selective dopant concentrations have to be adjusted to fulfill the desired functionality. Modern materials developments successfully use computational materials science to achieve that goal. Improved software tools and continuously growing computational power allow us to predict macroscopic properties of materials on the basis of microscopic/atomic ab initio simulation approaches. At Schott, special materials, in particular glasses and glass ceramics, are produced for a variety of applications. For a glass ceramic all the above mentioned difficulties for materials development arise. The properties of a glass ceramic are determined by the interplay of crystalline phases embedded in an amorphous glass matrix. For materials development the understanding of crystal structures and their properties, surfaces and interface phenomena, and amorphous systems are necessary, likewise. Each by itself is already a challenging problem. Many crystal phases that are grown within the glass matrix do not exist as single crystals or are difficult to grow in reasonable amounts for experimental investigations. The only way to obtain the properties of these crystalline phases is through 'ab initio' simulations in the computer

  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. The Discourse Structure and Linguistic Features of Research Article Abstracts in English by Indonesian Academics

    ERIC Educational Resources Information Center

    Arsyad, Safnil

    2014-01-01

    To effectively teach university lecturers or students to write a good research article (RA) abstract for publication in international journals, instructors need to know the present characteristics of abstracts written published in such journals. This study examines the discourse structure and linguistic features of RA abstracts written in English…

  13. (abstract) Characterization of Structural Response for Systems with Loose Joints

    NASA Technical Reports Server (NTRS)

    Bruno, Robin J.

    1995-01-01

    This paper describes a technique to locate and characterize loose joints in a large truss structure to generate an accurate structural model. The joint looseness is modeled as a gap in the member that opens and closes depending on the loading. Arbitrarily placed actuators are used to prestress the structure to first linearize the response. Next the actuator displacements are systematically reduced while monitoring the displacement response. The gap locations are determined by comparing the measured displacements with sets of calculated displacements and the sizes are estimated by monitoring the gap member length changes using the appropriate linear force-displacement relationship for the load level. The effect of measurement error in the truss displacements and the actuator length changes are investigated.

  14. Polymers and Liquid Crystals Symposium held in Boston, Massachusetts on August 19-23, 2007 (Abstracts)

    DTIC Science & Technology

    2007-12-20

    SCLCPs Coleen Pugh, Anirudha Singh 4:35 PM 5 Morphology of side chain liquid crystalline block copolymers: Influence of liquid crystal content Eric...Anirudha Singh, Coleen Pugh 472 Preparation of supramolecular discotic liquid crystals containing hydrogen bonds Seung Jun Lee, Mikyung You, Jin Woo Kim

  15. Mathematical Abstraction in the Solving of Ill-Structured Problems by Elementary School Students in Korea

    ERIC Educational Resources Information Center

    Hong, Jee Yun; Kim, Min Kyeong

    2016-01-01

    Ill-structured problems can be regarded as one of the measures that meet recent social needs emphasizing students' abilities to solve real-life problems. This study aimed to analyze the mathematical abstraction process in solving such problems, and to identify the mathematical abstraction level ([I] Recognition of mathematical structure through…

  16. 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.

  17. Double-crystal monochromator for a PF 60-period soft x-ray undulator (abstract)

    SciTech Connect

    Ishikawa, T.; Maezawa, H.; Nomura, M.; Ando, M.

    1989-07-01

    Since undulator light is sharply collimated itself, it can be effectively monochromatized by a perfect crystal. An x-ray double-crystal monochromator with a fixed exit has been designed and built for the use of undulator light from a 60-period undulator at Photon Factory (beamline 2A). Available Bragg angle ranges from 7/degree/ to 80/degree/. Angle scan is made by means of a goniometer outside the vacuum chamber, with the finest step of 0.1 arcsec. Magnetic fluid is used as the vacuum seal of the feedthrough. The fixed exit beam position is kept by translating the second crystal along the two mechanical guides: one for normal and the other for parallel to the crystal surface. Adjustment of the parallelity of two crystals is made manually with flexible wires. Since a total power in the central coherent portion which is limited by a 1/times/1-mm/sup 2/ slit is not so much, a stable operation is possible without cooling the crystal. Currently, InSb (111) reflection is used. The diffracting planes of the first cyrstal is 1/degree/ off from the surface and the second is the symmetric reflection. At its fifth harmonics, brilliant undulator light of approximately 10/sup 12/ photons/s mm/sup 2/ with 1-eV energy resolution is available (/ital E/=2 keV).

  18. 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.

  19. 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.

  20. Anisotropy and Crystal Structure of the Cocos Plate,

    DTIC Science & Technology

    1973-08-08

    A0785 066 SCRIPPS INSTITUTION OF OCEANOGRAPHY LA JOLLA CA MAR-’ETC F/B 8/10 ANISOTROPY AND CRYSTAL STRUCTURE OF THE COCOS PLATE. (U) U NL AUG 73 6 6...514R. R W RAITT, M HENRYWiCLASSIFIED IGL-U39/73 N -EtohEEE END cIc - .,MPL-U-39/73 ISOTOPYAND CRUSTAL STRUCTURE OFTHE COCOS PLATE* George G. Shor, Jr...of Geophysics, 2525 Correa Road, Honolulu, Hawaii 96822. D P3 -e C7Bl 5 p. 71 R6 P.~- ABSTRACT ~,e~/ L Seismic studies in two locations on the Cocos

  1. 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.

  2. 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.

  3. Nucleation and structural growth of cluster crystals.

    PubMed

    Leitold, Christian; Dellago, Christoph

    2016-08-21

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

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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

  9. Crystal structure of inactive form of Rab3B

    SciTech Connect

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

    2012-02-24

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

  10. 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).

  11. 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.

  12. 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.

  13. 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.

  14. 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.

  15. 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.

  16. 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.

  17. 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.

  18. 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

  19. 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.

  20. 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.

  1. 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).

  2. The crystal structure of {pi}-ErBO{sub 3}: New single-crystal data for an old problem

    SciTech Connect

    Pitscheider, Almut; Kaindl, Reinhard; Oeckler, Oliver; Huppertz, Hubert

    2011-01-15

    Single crystals of the orthoborate {pi}-ErBO{sub 3} were synthesized from Er{sub 2}O{sub 3} and B{sub 2}O{sub 3} under high-pressure/high-temperature conditions of 2 GPa and 800 {sup o}C in a Walker-type multianvil apparatus. The crystal structure was determined on the basis of single-crystal X-ray diffraction data, collected at room temperature. The title compound crystallizes in the monoclinic pseudowollastonite-type structure, space group C2/c, with the lattice parameters a=1128.4(2) pm, b=652.6(2) pm, c=954.0(2) pm, and {beta}=112.8(1){sup o} (R{sub 1}=0.0124 and wR{sub 2}=0.0404 for all data). -- graphical abstract: The first satisfying single-crystal structure determination of {pi}-ErBO{sub 3} sheds light on the extensively discussed structure of {pi}-orthoborates. The application of light pressure during the solid state synthesis yielded in high-quality crystals, due to pressure-induced crystallization. Research highlights: {yields} High-quality single crystals of {pi}-ErBO{sub 3} were prepared via high-pressure-induced crystallization. {yields} At least five different space groups for the rare-earth {pi}-orthoborates are reported. {yields} {pi}-ErBO{sub 3} is isotypic to the pseudowollastonite-type CaSiO{sub 3}. {yields} Remaining ambiguities regarding the structure of the rare-earth {pi}-orthoborates are resolved.

  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. 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.

  5. Crystal Structure and Properties of Tetrathiafulvalenium Triiodide.

    DTIC Science & Technology

    1979-12-03

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

  6. 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

  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. Predicting polymeric crystal structures by evolutionary algorithms

    NASA Astrophysics Data System (ADS)

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

    2014-10-01

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

  9. 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'.

  10. 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.

  11. 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.

  12. 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)

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. The crystal structure of aluminum doped {beta}-rhombohedral boron

    SciTech Connect

    Bykova, Elena; Parakhonskiy, Gleb; Dubrovinskaia, Natalia; Chernyshov, Dmitry; Dubrovinsky, Leonid

    2012-10-15

    A crystal structure of aluminum doped {beta}-rhombohedral boron was studied by single-crystal X-ray diffraction at 80 K. The crystals were synthesized using high-pressure high temperature technique at 3 GPa and 2100 K. The structure is based on three-dimensional framework made of B{sub 12} icosahedra with voids occupied by the B{sub 28}-B-B{sub 28} units, it has the R-3m space group with a=10.9014(3), c=23.7225(7) A lattice dimensions in hexagonal setting. Aluminum atoms are located in A1 and D special positions of the {beta}-B structure with occupancies of 82.7(6)% and 11.3(4)%, respectively. Additional boron atoms are located near the D-site. Their possible distribution is discussed. Finally we have found two appropriate structural models whose refinement suggests two possible chemical compositions, AlB{sub 44.8(5)} and AlB{sub 37.8(5)}, which are in a good agreement with the chemical analysis data obtained from EDX. The crystal structure of AlB{sub 44.8(5)} is described in detail. - Graphical abstract: The atomic distribution near the B(15) atom (non-labeled atom in the center of the picture) shown along the c axis. Anisotropic displacement ellipses for Al(2) (D-site) and B(15) are shown with 50 % probability level. The mirror plane with Miller indices (1 1 0) and related to it (-1 2 0) and (-2 1 0) generated by the 3-fold rotation-inversion axis parallel to the c axis splits the position of B(16) over two sites. Highlights: Black-Right-Pointing-Pointer The crystal structure of the AlB{sub 44.8(5)} has been refined. Black-Right-Pointing-Pointer Aluminum atoms partially fill certain types of voids (the A1- and D-sites). Black-Right-Pointing-Pointer We have got two possible models of atomic distribution near the D-site.

  18. 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.

  19. 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

  20. 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

  1. 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.

  2. Lithium-cation conductivity and crystal structure of lithium diphosphate

    SciTech Connect

    Voronin, V.I.; Sherstobitova, E.A.; Blatov, V.A.; Shekhtman, G.Sh.

    2014-03-15

    The electrical conductivity of lithium diphosphate Li{sub 4}P{sub 2}O{sub 7} has been measured and jump-like increasing of ionic conductivity at 913 K has been found. The crystal structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction at 300–1050 K. At 913 K low temperature triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one, space group P2{sub 1}/n, a=8.8261(4) Å, b=5.2028(4) Å, c=13.3119(2) Å, β=104.372(6)°. The migration maps of Li{sup +} cations based on experimental data implemented into program package TOPOS have been explored. It was found that lithium cations in both low- and high temperature forms of Li{sub 4}P{sub 2}O{sub 7} migrate in three dimensions. Cross sections of the migrations channels extend as the temperature rises, but at the phase transition point have a sharp growth showing a strong “crystal structure – ion conductivity” correlation. -- Graphical abstract: Crystal structure of Li{sub 4}P{sub 2}O{sub 7} at 950 K. Red balls represent oxygen atoms; black lines show Li{sup +} ion migration channels in the layers perpendicular to [001] direction. Highlights: • Structure of Li{sub 4}P{sub 2}O{sub 7} has been refined using high temperature neutron diffraction. • At 913 K triclinic form of Li{sub 4}P{sub 2}O{sub 7} transforms into high temperature monoclinic one. • The migration maps of Li{sup +} implemented into program package TOPOS have been explored. • Cross sections of the migrations channels at the phase transition have a sharp growth.

  3. 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

  4. 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.

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase

    PubMed Central

    Romero, Elvira; Castellanos, J. Rubén Gómez

    2016-01-01

    Abstract Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio‐, chemo‐, and enantioselectivity. However, the low stability of many Baeyer–Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate‐binding cavity explains its preference for small rather than bulky substrates. Small‐scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology. PMID:27873437

  12. Use of Structure as a Basis for Abstraction in Air Traffic Control

    NASA Technical Reports Server (NTRS)

    Davison, Hayley J.; Hansman, R. John

    2004-01-01

    The safety and efficiency of the air traffic control domain is highly dependent on the capabilities and limitations of its human controllers. Past research has indicated that structure provided by the airspace and procedures could aid in simplifying the controllers cognitive tasks. In this paper, observations, interviews, voice command data analyses, and radar analyses were conducted at the Boston Terminal Route Control (TRACON) facility to determine if there was evidence of controllers using structure to simplify their cognitive processes. The data suggest that controllers do use structure-based abstractions to simplify their cognitive processes, particularly the projection task. How structure simplifies the projection task and the implications of understanding the benefits structure provides to the projection task was discussed.

  13. 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.

  14. 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

  15. 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.

  16. 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.

  17. 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.

  18. Summarizing and visualizing structural changes during the evolution of biomedical ontologies using a Diff Abstraction Network.

    PubMed

    Ochs, Christopher; Perl, Yehoshua; Geller, James; Haendel, Melissa; Brush, Matthew; Arabandi, Sivaram; Tu, Samson

    2015-08-01

    Biomedical ontologies are a critical component in biomedical research and practice. As an ontology evolves, its structure and content change in response to additions, deletions and updates. When editing a biomedical ontology, small local updates may affect large portions of the ontology, leading to unintended and potentially erroneous changes. Such unwanted side effects often go unnoticed since biomedical ontologies are large and complex knowledge structures. Abstraction networks, which provide compact summaries of an ontology's content and structure, have been used to uncover structural irregularities, inconsistencies and errors in ontologies. In this paper, we introduce Diff Abstraction Networks ("Diff AbNs"), compact networks that summarize and visualize global structural changes due to ontology editing operations that result in a new ontology release. A Diff AbN can be used to support curators in identifying unintended and unwanted ontology changes. The derivation of two Diff AbNs, the Diff Area Taxonomy and the Diff Partial-area Taxonomy, is explained and Diff Partial-area Taxonomies are derived and analyzed for the Ontology of Clinical Research, Sleep Domain Ontology, and eagle-i Research Resource Ontology. Diff Taxonomy usage for identifying unintended erroneous consequences of quality assurance and ontology merging are demonstrated.

  19. Structure and magnetism in fcc magnetic transition metals on (001) diamond (abstract)

    NASA Astrophysics Data System (ADS)

    Wolf, J. A.; Krebs, J. J.; Idzerda, Y. U.; Prinz, G. A.; Kemner, K. M.

    1996-04-01

    We have prepared single crystal face centered cubic (fcc) magnetic transition metal films (Co,Ni,Fe) on (001) diamonds, the thickness of the films varying between a few tenths of a nanometer to over 100 nm. The crystalline quality and fourfold symmetry of these layers was monitored in situ during the film growth with RHEED and a chemical analysis was performed using Auger spectroscopy. In addition, the structure of the samples was investigated ex situ using X-ray diffraction and EXAFS, demonstrating the single crystal, fcc (001) structure throughout each entire film. The magnetic characterization was performed with Ferromagnetic Resonance (FMR) and Superconducting Quantum Interference Device (SQUID) hysteresis loops. The saturation magnetization of the Co films is only slightly lower than the literature values. The coercive fields are very small (˜25 Oe) and the magnetization reversal very sharp. The FMR yielded a fourfold anisotropy comparable to literature values. The observation of the first standing spinwaves underlines the good quality. The Ni films are tetragonally distorted due to the 1.2% mismatch. The FMR data indicate a significant perpendicular anisotropy slightly smaller than 4πM, the fourfold in-plane anisotropy being comparable to the bulk value. The saturation magnetization is reduced by 30% compared to bulk values, probably due to nickel-carbide which was observed in the XRD data from some samples. Neither the in-plane <110> nor the in-plane <100> axis show an easy axis behavior and both require fields in excess of 6000 Oe to saturate, the coercive fields being about 200 Oe. The RHEED patterns of the Fe films show single crystal growth with a lattice constant comparable to diamond, indicating an fcc structure. A similar structural and magnetic characterization of these films will also be presented.

  20. Visual analysis of large heterogeneous social networks by semantic and structural abstraction.

    PubMed

    Shen, Zeqian; Ma, Kwan-Liu; Eliassi-Rad, Tina

    2006-01-01

    Social network analysis is an active area of study beyond sociology. It uncovers the invisible relationships between actors in a network and provides understanding of social processes and behaviors. It has become an important technique in a variety of application areas such as the Web, organizational studies, and homeland security. This paper presents a visual analytics tool, OntoVis, for understanding large, heterogeneous social networks, in which nodes and links could represent different concepts and relations, respectively. These concepts and relations are related through an ontology (also known as a schema). OntoVis is named such because it uses information in the ontology associated with a social network to semantically prune a large, heterogeneous network. In addition to semantic abstraction, OntoVis also allows users to do structural abstraction and importance filtering to make large networks manageable and to facilitate analytic reasoning. All these unique capabilities of OntoVis are illustrated with several case studies.

  1. 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.

  2. How Structure Sense for Algebraic Expressions or Equations Is Related to Structure Sense for Abstract Algebra

    ERIC Educational Resources Information Center

    Novotna, Jarmila; Hoch, Maureen

    2008-01-01

    Many students have difficulties with basic algebraic concepts at high school and at university. In this paper two levels of algebraic structure sense are defined: for high school algebra and for university algebra. We suggest that high school algebra structure sense components are sub-components of some university algebra structure sense…

  3. Structure and dynamics of European sports science textual contents: Analysis of ECSS abstracts (1996-2014).

    PubMed

    Hristovski, Robert; Aceski, Aleksandar; Balague, Natalia; Seifert, Ludovic; Tufekcievski, Aleksandar; Cecilia, Aguirre

    2017-02-01

    The article discusses general structure and dynamics of the sports science research content as obtained from the analysis of 21998 European College of Sport Science abstracts belonging to 12 science topics. The structural analysis showed intertwined multidisciplinary and unifying tendencies structured along horizontal (scope) and vertical (level) axes. Methodological (instrumental and mode of inquiry) integrative tendencies are dominant. Theoretical integrative tendencies are much less detectable along both horizontal and vertical axes. The dynamic analysis of written abstracts text content over the 19 years reveals the contextualizing and guiding role of thematic skeletons of each sports science topic in forming more detailed contingent research ideas and the role of the latter in stabilizing and procreating the former. This circular causality between both hierarchical levels and functioning on separate characteristic time scales is crucial for understanding how stable research traditions self-maintain and self-procreate through innovative contingencies. The structure of sports science continuously rebuilds itself through use and re-use of contingent research ideas. The thematic skeleton ensures its identity and the contingent conceptual sets its flexibility and adaptability to different research or applicative problems.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. Software abstractions and computational issues in parallel structure adaptive mesh methods for electronic structure calculations

    SciTech Connect

    Kohn, S.; Weare, J.; Ong, E.; Baden, S.

    1997-05-01

    We have applied structured adaptive mesh refinement techniques to the solution of the LDA equations for electronic structure calculations. Local spatial refinement concentrates memory resources and numerical effort where it is most needed, near the atomic centers and in regions of rapidly varying charge density. The structured grid representation enables us to employ efficient iterative solver techniques such as conjugate gradient with FAC multigrid preconditioning. We have parallelized our solver using an object- oriented adaptive mesh refinement framework.

  10. 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

  11. 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

  12. 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.

  13. Research Article Abstracts in Two Subdisciplines of Business--Move Structure and Hedging between Management and Marketing

    ERIC Educational Resources Information Center

    Li, Qian; Pramoolsook, Issra

    2015-01-01

    The importance of RA abstracts lies in their influence on the readers' decision about whether the accompanying article is worth reading. A number of studies have investigated the move structure of abstracts and have generated several influential models. However, little research has been conducted on subdisciplinary variations in move structure of…

  14. 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.

  15. 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)

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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

  5. 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.

  6. 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…

  7. 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.

  8. 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.

  9. 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)

  10. 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.

  11. 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

  12. 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

  13. 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.

  14. 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.

  15. 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.

  16. Abstract algebraic-delay differential systems and age structured population dynamics

    NASA Astrophysics Data System (ADS)

    Kosovalić, N.; Magpantay, F. M. G.; Chen, Y.; Wu, J.

    We consider the abstract algebraic-delay differential system, x'(t)=Ax(t)+F(x(t),a(t)), a(t)=H(xt,at). Here A is a linear operator on D(A)⊂X satisfying the Hille-Yosida conditions, x(t)∈D(A)¯⊂X, and a(t)∈Rn, where X is a real Banach space. With a global Lipschitz condition on F and an appropriate hypothesis on the function H, we show that the corresponding initial value problem gives rise to a continuous semiflow in a subset of the space of continuous functions. We establish the positivity of the x-component and give some examples arising from age structured population dynamics. The examples come from situations where the age of maturity of an individual at a given time is determined by whether or not the resource concentration density, which depends on the immature population, reaches a prescribed threshold within that time.

  17. Research & writing basics: elements of the abstract.

    PubMed

    Krasner, D; Van Rijswijk, L

    1995-04-01

    Writing an abstract is a challenging skill that requires precision and care. Criteria for well-formulated abstracts and abstract guidelines for 2 types of articles (empirical studies and reviews or theoretical articles) as well as a description of the content of a structured abstract are presented. Details were gleaned from a review of the literature including the American Medical Association Manual of Style, Eighth Edition and the Publication Manual of the American Psychological Association, Fourth Edition. A good abstract is like a crystal: it is a clear, sharp synthesis that elucidates meaning for the reader.

  18. 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

    <span class="hlt">ABSTRACT</span>

    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

  19. 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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

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

    SciTech Connect

    Mumbaraddi, Dundappa; Sarkar, Sumanta; Peter, Sebastian C.

    2016-04-15

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

  5. Study of structural and optical properties of YAG and Nd:YAG single crystals

    SciTech Connect

    Kostić, S.; Lazarević, Z.Ž.; Radojević, V.; Milutinović, A.; Romčević, M.; Romčević, N.Ž.; Valčić, A.

    2015-03-15

    Highlights: • Transparent YAG and pale pink Nd:YAG single crystals were produced by the Czochralski technique. • Growth mechanisms and shape of the liquid/solid interface and incorporation of Nd{sup 3+} were studied. • The structure of the crystals was investigated by X-ray diffraction, Raman and IR spectroscopy. • The 15 Raman and 17 IR modes were observed. • The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. - Abstract: Yttrium aluminum garnet (YAG, Y{sub 3}Al{sub 5}O{sub 12}) and yttrium aluminum garnet doped with neodymium (Nd:YAG) single crystals were grown by the Czochralski technique. The critical diameter and the critical rate of rotation were calculated. Suitable polishing and etching solutions were determined. As a result of our experiments, the transparent YAG and pale pink Nd:YAG single crystals were produced. The obtained crystals were studied by X-ray diffraction, Raman and IR spectroscopy. The crystal structure was confirmed by XRD. The 15 Raman and 17 IR modes were observed. The Raman and IR spectroscopy results are in accordance with X-ray diffraction analysis. The obtained YAG and Nd:YAG single crystals were without core and of good optical quality. The absence of a core was confirmed by viewing polished crystal slices. Also, it is important to emphasize that the obtained Nd:YAG single crystal has a concentration of 0.8 wt.% Nd{sup 3+} that is characteristic for laser materials.

  6. 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

  7. 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.

  8. 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

  9. Crystal structure, growth and characterization of LiPbB₉O₁₅: A new congruent melting nonlinear optical crystal

    SciTech Connect

    Xia, M.J.; Li, R.K.

    2013-05-01

    A new congruent-melting crystal LiPbB₉O₁₅ (LPBO) has been grown and its structure was determined by single crystal X-ray diffraction. LPBO crystallizes in a polar space group R3c with a large unit cell of a=b=21.649(11) Å, c=17.193(11) Å, and Z=24. The basic anionic unit, (B₃O₇)⁵⁻ group, is connected by terminal O atoms to build an infinite [(B₃O₅)⁻]ₙ helical chain along the c axis. Second harmonic generation (SHG) measurements of the title compound indicate that LPBO can be phase matchable and its SHG coefficient is almost equal to that of KDP, which is about 3.3 times that of its analog BaLiB₉O₁₅. This significant enhancement of the SHG effect can be tentatively attributed to the lone pair Pb²⁺ cations with severely distorted coordination. LPBO has a wide transparent region from 410 to 2500 nm with a UV absorption edge about 261 nm according to the reflectance spectra. - Graphical abstract: The crystal structure of LiPbB₉O₁₅ composed of the (B₃O₇)⁵⁻ anionic group and the lone pair Pb and Li polyhedra along c axis. Highlights: • A new congruent-melt NLO crystal LiPbB₉O₁₅ (LPBO) has been grown. • The basic structural unit of LPBO is B₃O₇ group same as that found in LiB₃O₅. • LPBO is phase matchable with SHG signal 10 times that of its Ba-analog. • LPBO is highly transparent within 410–1700 nm with a UV cut-off of 261 nm.

  10. 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.

  11. 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.

  12. Missing strings of residues in protein crystal structures

    PubMed Central

    Djinovic-Carugo, Kristina; Carugo, Oliviero

    2015-01-01

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

  13. 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.

  14. 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)°.

  15. 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.

  16. 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.

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. The Crystal and Molecular Structure of Dianhydrogossypol

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  3. 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.

  4. 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.

  5. 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 .

  6. 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

  7. 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

  8. Neural Network Processing of Natural Language: I. Sensitivity to Serial, Temporal, and Abstract Structure of Language in the Infant.

    ERIC Educational Resources Information Center

    Dominey, Peter Ford; Ramus, Franck

    2000-01-01

    Demonstrates how innate representational capabilities for serial and temporal structure of language could arise from a common neural architecture, distinct from that required for the representation of abstract structure, and provides a predictive testable model of the initial computational state of the language learner. (Author/VWL)

  9. 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.

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

    PubMed

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

    2016-01-18

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

  11. Synthesis and crystal structure analysis of uranyl triple acetates

    NASA Astrophysics Data System (ADS)

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

    2016-12-01

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

  12. Growth, structural, optical, thermal and mechanical properties of cytosinium hydrogen selenite: A novel nonlinear optical single crystal

    SciTech Connect

    Jaikumar, P.; Sathiskumar, S.; Balakrishnan, T.; Ramamurthi, K.

    2016-06-15

    Highlights: • Growth of bulk single crystals of cytosinium hydrogen selenite (CHS) is reported. • Dielectric constant of CHS is measured as a function of Frequency and temperature. • Lower cut off value of UV–vis-NIR spectrum of CHS crystal is observed at 210 nm. • Meyer’s index value of CHS crystal calculated identifies it as a soft material. • Powder SHG efficiency of CHS is about 1.5 times that of KDP crystal. - Abstract: A novel nonlinear optical single crystal of cytosinium hydrogen selenite was grown from aqueous solution of cytosinium hydrogen selenite by slow solvent evaporation method at room temperature. The structural properties of grown crystal have been studied by single crystal and powder X-ray diffraction analysis. Presence of various functional groups was identified from Fourier transform infrared spectroscopy. The optical transmittance and absorbance spectra were recorded by UV–vis-NIR spectrometer and the grown crystal possesses good transparency in the entire visible region. The dielectric constant and dielectric loss of the crystal were calculated as a function of frequency at different temperatures. The mechanical strength of the cytosinium hydrogen selenite crystal was estimated using Vicker’s microhardness tester. Etch patterns of the cytosinium hydrogen selenite crystal were obtained using distilled water as etchant for different etching time. Second harmonic generation efficiency tested using Nd:YAG laser is about 1.5 times that of KDP.

  13. 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.

  14. 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.

  15. 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%.

  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. 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

  19. 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.

  20. Revelation of endogenously bound Fe{sup 2+} ions in the crystal structure of ferritin from Escherichia coli

    SciTech Connect

    Thiruselvam, Viswanathan; Sivaraman, Padavattan; Kumarevel, Thirumananseri; Ponnuswamy, Mondikalipudur Nanjappagounder

    2014-10-24

    Highlights: • Crystal structure of ferritin was determined. • Endogenously expressed iron’s were identified. • Binuclear iron sites were observed at A and B active sites. - Abstract: Ferritin is an iron regulatory protein. It is responsible for storage and detoxification of excess iron thereby it regulates iron level in the body. Here we report the crystal structure of ferritin with two endogenously expressed Fe atoms binding in both the sites. The protein was purified and characterized by MALDI-TOF and N-terminal amino acid sequencing. The crystal belongs to I4 space group and it diffracted up to 2.5 Å. The structural analysis suggested that it crystallizes as hexamer and confirmed that it happened to be the first report of endogenously expressed Fe ions incorporated in both the A and B sites, situated in between the helices.

  1. 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.

  2. 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.

  3. 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.

  4. Crystal Structure of the Human Astrovirus Capsid Protein

    PubMed Central

    Toh, Yukimatsu; Harper, Justin; Dryden, Kelly A.; Yeager, Mark; Méndez, Ernesto

    2016-01-01

    ABSTRACT Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. HAstV is a nonenveloped virus with a T=3 capsid and a positive-sense RNA genome. The capsid protein (CP) of HAstV is synthesized as a 90-kDa precursor (VP90) that can be divided into three linear domains: a conserved N-terminal domain, a hypervariable domain, and an acidic C-terminal domain. Maturation of HAstV requires proteolytic processing of the astrovirus CP both inside and outside the host cell, resulting in the removal of the C-terminal domain and the breakdown of the rest of the CP into three predominant protein species with molecular masses of ∼34, 27/29, and 25/26 kDa, respectively. We have now solved the crystal structure of VP9071–415 (amino acids [aa] 71 to 415 of VP90) of human astrovirus serotype 8 at a 2.15-Å resolution. VP9071–415 encompasses the conserved N-terminal domain of VP90 but lacks the hypervariable domain, which forms the capsid surface spikes. The structure of VP9071–415 is comprised of two domains: an S domain, which adopts the typical jelly-roll β-barrel fold, and a P1 domain, which forms a squashed β-barrel consisting of six antiparallel β-strands similar to what was observed in the hepatitis E virus (HEV) capsid structure. Fitting of the VP9071–415 structure into the cryo-electron microscopy (EM) maps of HAstV produced an atomic model for a continuous, T=3 icosahedral capsid shell. Our pseudoatomic model of the human HAstV capsid shell provides valuable insights into intermolecular interactions required for capsid assembly and trypsin-mediated proteolytic maturation needed for virus infectivity. Such information has potential applications in the development of a virus-like particle (VLP) vaccine as well as small-molecule drugs targeting astrovirus assembly/maturation. IMPORTANCE Human astrovirus (HAstV) is a leading cause of viral diarrhea in infants and young children worldwide. As a nonenveloped virus

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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

  10. Crystal structure of cocosin, a potential food allergen from coconut (Cocos nucifera) (abstract)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    RATIONALE: Coconut allergy cases have been reported, but only one coconut allergen has been identified. The 11S seed storage proteins belong to one of a few protein families that contain known food allergens in many food of plant sources. Cocosin, the 11S protein from cocosin remains to be character...

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. 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

  16. 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.

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

    SciTech Connect

    Atuchin, Victor V.; Goloshumova, Alina A.; Isaenko, Ludmila I.; Jiang, Xingxing; Lobanov, Sergey I.; Zhang, Zhaoming; Lin, Zheshuai

    2016-04-15

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. Bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}: New crystal structure type and electronic structure

    SciTech Connect

    Eliziario Nunes, Sayonara; Wang, Chun-Hai; So, Karwei; Evans, John S.O.; Evans, Ivana Radosavljević

    2015-02-15

    We report a combined experimental and computational study of the crystal structure and electronic properties of bismuth zinc vanadate, BiZn{sub 2}VO{sub 6}, known for its visible light photocatalytic activity. The crystal structure has been solved from laboratory powder X-ray diffraction data using the repeated minimisations from random starting values method. BiZn{sub 2}VO{sub 6} adopts a new structure type, based on the following building blocks: corner- and edge-sharing ZnO{sub 4} tetrahedra, ZnO{sub 6} octahedra and VO{sub 4} tetrahedra, and Bi{sub 2}O{sub 12} dimers. It is the only known member of the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family which does not appear to be structurally closely related to others. The electronic structure of BiZn{sub 2}VO{sub 6}, calculated by DFT methods, shows that it is an indirect gap semiconductor with a calculated band gap of 1.6 eV, which compares favourably to the experimentally measured value of 2.4 eV. - Graphical abstract: The crystal structure of BiZn{sub 2}VO{sub 6}, a new structure type in the BiM{sub 2}AO{sub 6} (M=Mg, Ca, Cd, Cu, Pb, Mn, Zn; A=V, P, As) family. - Highlights: • Structure solution from PXRD data by repeated minimisations from random starting values. • New structure type in the BiM{sub 2}AO{sub 6} (M=Pb, Ca, Cd, Mn, Zn, Mg, Cu; A=V, P, As) family. • Electronic structure calculation.

  14. Synthesis, crystal structures and properties of lead phosphite compounds

    SciTech Connect

    Song, Jun-Ling Hu, Chun-Li; Xu, Xiang; Kong, Fang; Mao, Jiang-Gao

    2015-11-15

    Here, we report the preparation and characterization of two lead(II) phosphites, namely, Pb{sub 2}(HPO{sub 3}){sub 2} and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} through hydrothermal reaction or simple solution synthesis, respectively. A new lead phosphite, namely, Pb{sub 2}(HPO{sub 3}){sub 2}, crystallizes in the noncentrosymmetric space group Cmc2{sub 1} (no. 36), which features 3D framework formed by the interconnection of 2D layer of lead(II) phosphites and 1D chain of [Pb(HPO{sub 3}){sub 5}]{sub ∞}. The nonlinear optical properties of Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} have been studied for the first time. The synergistic effect of the stereo-active lone-pairs on Pb{sup 2+} cations and π-conjugated NO{sub 3} units in Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} produces a moderate second harmonic generation (SHG) response of ∼1.8×KDP (KH{sub 2}PO{sub 4}), which is phase matchable (type I). IR, UV–vis spectra and thermogravimetric analysis (TGA) for the two compounds were also measured. - Graphical abstract: Two lead phosphites Pb{sub 2}(HPO{sub 3}){sub 2} and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} are studied. A new lead phosphite Pb{sub 2}(HPO{sub 3}){sub 2} features a unique 3D framework structure and Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} shows a moderate SHG response of ∼1.8×KDP (KH{sub 2}PO{sub 4}). - Highlights: • A new lead phosphite, Pb{sub 2}(HPO{sub 3}){sub 2} is reported. • Pb{sub 2}(HPO{sub 3}){sub 2} features a unique 3D framework structure. • NLO property of Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} is investigated. • Pb{sub 2}(HPO{sub 3})(NO{sub 3}){sub 2} produces a moderate SHG response of ∼1.8×KDP (KH{sub 2}PO{sub 4}).

  15. 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.

  16. 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.…

  17. 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.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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.

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. Sn{sub 4}As{sub 3} revisited: Solvothermal synthesis and crystal and electronic structure

    SciTech Connect

    Kovnir, Kirill Kolen'ko, Yury V.; Baranov, Alexey I.; Neira, Ines S.; Sobolev, Alexey V.; Yoshimura, Masahiro; Presniakov, Igor A.; Shevelkov, Andrei V.

    2009-03-15

    A facile one pot method of synthesis of tin arsenide Sn{sub 4}As{sub 3} starting from metallic tin and elemental arsenic under mild solvothermal conditions in ethylenediamine in the presence of ammonium chloride is offered. The dissolving of the tin metal in ethylenediamine and the role of NH{sub 4}Cl are discussed. The crystal structure of Sn{sub 4}As{sub 3} has been re-determined. It is shown to crystallize in the trigonal non-centrosymmetric space group R3m, (a=4.089(1) A, c=36.059(6) A, Z=3), which differs from the previously reported centrosymmetric structure (R3-barm). The crystal structure of Sn{sub 4}As{sub 3} consists of alternating layers of arsenic and tin atoms that are combined into seven-layer blocks and build up along the c-axis. The major structural feature is the short tin-tin distances (3.24 A) between the adjacent blocks. The analysis of the density of states and band structure reveals that Sn{sub 4}As{sub 3} should have metallic properties, which is in line with the previously reported experimental observations. Analysis of chemical bonding employing the electron localization function shows that only for the shortest Sn-As contacts the bonding is pairwise, while four-center bonds are formed between arsenic and tin atoms at relatively long distances (>2.85 A). Moreover, each tin atom holds an electron lone-pair. - Graphical abstract: Solvothermally synthesized tin arsenide reveals non-centrosymmetric crystal structure and a complicated chemical bonding pattern including multi-center bonds and lone pairs.

  11. On the Synthesis and Characterization of Novel Aluminum-Arsenic Compounds; Crystal Structure of Et2AlAs(SiMe3)22

    DTIC Science & Technology

    1991-10-03

    ARSENIC COMPOUNDS; CRYSTAL STRUCTURE OF [Et2AIAs(SiMe 3 )2 ]2 12 PERSONAL AUTHOR(S) :ells, A.T. McPhail, and T. M. Speer 13a. ’YPE OF REPORT 13b. riME...synthesis, crystal structure , ring compound 19 ABSTRACT (Continue on reverse ir necessary &nd iaenrtiy by 6lOCK numOer) See attached. 91-12706 ITu 20...DU/DC/TR-24 ON THE SYNTHESIS AND CHARACTERIZATION OF NOVEL ALUMINUM-ARSENIC COMPOUNDS- CRYSTAL STRUCTURE OF [Et 2 A1As(SiMe 3)21 2 by R. L. Wells, A. T

  12. 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.

  13. 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.

  14. 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.

  15. Modeling liquid crystal bilayer structures with minimal surfaces.

    PubMed

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

    2004-01-22

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

  16. 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

  17. 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.

  18. 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.

  19. 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.

  20. Myelin structures formed by thermotropic smectic liquid crystals.

    PubMed

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

    2013-12-17

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

  1. Gas and crystal structures of CCl2FSCN

    NASA Astrophysics Data System (ADS)

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

    2017-03-01

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

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

    PubMed

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

    2015-07-15

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

  3. Your kid could not have done that: even untutored observers can discern intentionality and structure in abstract expressionist art.

    PubMed

    Snapper, Leslie; Oranç, Cansu; Hawley-Dolan, Angelina; Nissel, Jenny; Winner, Ellen

    2015-04-01

    Can people with no special knowledge about art detect the skill, intentionality, and expressed meanings in non-representational art? Hawley-Dolan and Winner (2011) showed participants without training in art images of abstract expressionist paintings paired with superficially similar works by children or animals and asked them which they preferred and which was a better work of art. Participants selected the works by artists in response to both questions at a rate above chance. In Study 1, we used the same image pairs but asked a more direct question: which painting is by the artist rather than the child or animal? Individuals with no familiarity with abstract expressionism correctly identified the artists' works at a rate significantly above chance. In Study 2 participants saw each image singly and were asked whether it was by an artist or a child or animal. Participants unfamiliar with abstract expressionism again correctly identified the source of the works at a rate above chance. Study 3 demonstrated that this discrimination is made on the basis of perceived intentionality and perceived structure. People see more than they think they do in abstract art. These findings tell us something about the nature of non-figurative art. They also tell us something about the human tendency to ferret out intentionality.

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

    PubMed

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

    2015-09-01

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

  5. Structure and location of macronutrients in ancient and alternative crops (abstract)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Structure, histochemistry and composition of mature seeds of several ancient or alternative crops were studied by light and electron microscopies to localize specific macronutrients including protein, starch, non-starch carbohydrates and lipid. Botanically, these seeds fall into different classifica...

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

    PubMed

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

    2009-08-21

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

  7. 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.

  8. 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

  9. 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.

  10. 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.

  11. 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.

  12. Developing eThread Pipeline Using SAGA-Pilot Abstraction for Large-Scale Structural Bioinformatics

    PubMed Central

    Ragothaman, Anjani; Feinstein, Wei; Jha, Shantenu; Kim, Joohyun

    2014-01-01

    While most of computational annotation approaches are sequence-based, threading methods are becoming increasingly attractive because of predicted structural information that could uncover the underlying function. However, threading tools are generally compute-intensive and the number of protein sequences from even small genomes such as prokaryotes is large typically containing many thousands, prohibiting their application as a genome-wide structural systems biology tool. To leverage its utility, we have developed a pipeline for eThread—a meta-threading protein structure modeling tool, that can use computational resources efficiently and effectively. We employ a pilot-based approach that supports seamless data and task-level parallelism and manages large variation in workload and computational requirements. Our scalable pipeline is deployed on Amazon EC2 and can efficiently select resources based upon task requirements. We present runtime analysis to characterize computational complexity of eThread and EC2 infrastructure. Based on results, we suggest a pathway to an optimized solution with respect to metrics such as time-to-solution or cost-to-solution. Our eThread pipeline can scale to support a large number of sequences and is expected to be a viable solution for genome-scale structural bioinformatics and structure-based annotation, particularly, amenable for small genomes such as prokaryotes. The developed pipeline is easily extensible to other types of distributed cyberinfrastructure. PMID:24995285

  13. 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.

  14. 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

  15. 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.

  16. Revisiting the crystal structure of rhombohedral lead metaniobate.

    PubMed

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

    2014-09-15

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

  17. 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.

  18. Structural and magnetic characterization of electro-crystallized magnetite nanoparticles under constant current

    SciTech Connect

    Mosivand, Saba; Kazeminezhad, Iraj

    2015-10-15

    Graphical abstract: Structural and magnetic properties of electro-crystallized magnetite nanoparticles under constant current were studied. All samples were characterized using XRD, SEM, VSM, and Mössbauer spectrometry. - Highlights: • The effect of applied current on morphology and properties of Fe{sub 3}O{sub 4} is studied. • The particle size and morphology are controllable by adjusting the current. • The magnetization depends on particle size, type of surfactant and applied current. • The clear correlation between magnetization and the mean particle size is observed. - Abstract: The effect of applied current on the morphology, particle size, structure, and magnetic properties of magnetite nanoparticles prepared by electro-crystallization method was studied. The synthesis was performed in an electrochemical cell containing two iron electrodes and an aqueous solution of sodium sulfate, and either thiourea, sodium butanoate, or β-cyclodextrine as organic stabilizer. All the samples were characterized by XRD, SEM, VSM, and Mössbauer spectroscopy. X-ray diffraction patterns, clearly confirmed that all products have the cubic spinel Fe{sub 3}O{sub 4} crystal structure. Electron microscope images of the samples showed that their mean particle size is in the range 20–80 nm, and depends critically on the applied current and type of the organic additives. Specific magnetization of the samples at room temperature ranges from 60 to 90 A m{sup 2} kg{sup −1}, depending on the growth conditions. Room temperature Mössbauer spectra are typical of nonstoichiometric Fe{sub 3−δ}O{sub 4}, with a small excess of Fe{sup 3+}, 0.06 ≤ δ ≤ 0.17.

  19. Synthesis and crystal structure determination of yttrium ultraphosphate YP{sub 5}O{sub 14}

    SciTech Connect

    Mbarek, A.; Graia, M. Chadeyron, G.; Zambon, D.; Bouaziz, J.; Fourati, M.

    2009-03-15

    The crystal structure of monoclinic YP{sub 5}O{sub 14} (space group C2/c, a=12.919(2) A, b=12.796(4) A, c=12.457(2) A, {beta}=91.30(1){sup o}, Z=8) has been refined from single-crystal X-ray diffraction data. Full-matrix least-squares refinement on F{sup 2} using 2249 independent reflections for 183 refinable parameters results in a final R value of 0.027 ({omega}R=0.069). The structure is isotypic with HoP{sub 5}O{sub 14}. This structure is built up from infinite layers of PO{sub 4} tetrahedra linked through isolated YO{sub 8} polyhedra. The three-dimensional cohesion of the framework results from Y-O-P bridges. This crystal structure refinement leads to the calculated X-ray diffraction powder pattern of this monoclinic polymorph, which has been the starting point of a thorough study of the solid-state synthesis of this ultraphosphate. This investigation further leads to a better outstanding of features observed during the synthesis of powdered samples. The thermal behavior of this ultraphosphate has been studied by DTA and TGA analyses. The infrared and Raman spectroscopic characterizations have been carried out on polycrystalline samples. The luminescence properties of the Eu{sup 3+} ion incorporated in the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} as local structural probe show that in YP{sub 5}O{sub 14}: 5% Eu{sup 3+} sample, the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure. - Graphical Abstract: The crystal structure of the monoclinic C2/c polymorph of YP{sub 5}O{sub 14} has been refined from single-crystal X-ray diffraction data. The luminescence properties of the Eu{sup 3+} ion incorporated in this matrix as local structural probe show that the Eu{sup 3+} ions are distributed over the two Y{sup 3+} crystallographic sites of C{sub 2} symmetry of this structure.

  20. 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

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

    PubMed Central

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

    2015-01-01

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

  2. The Development of Abstract Syntax: Evidence from Structural Priming and the Lexical Boost

    ERIC Educational Resources Information Center

    Rowland, Caroline F.; Chang, Franklin; Ambridge, Ben; Pine, Julian M.; Lieven, Elena V. M.

    2012-01-01

    Structural priming paradigms have been influential in shaping theories of adult sentence processing and theories of syntactic development. However, until recently there have been few attempts to provide an integrated account that explains both adult and developmental data. The aim of the present paper was to begin the process of integration by…

  3. CALL-FOR-ABSTRACTS: SYMPOSIUM ON TECHNOLOGIES FOR PROTECTING AQUATIC ORGANISMS FROM COOLING WATER INTAKE STRUCTURES

    EPA Science Inventory

    Section 316(b) of the Clean Water Act requires EPA to ensure that the location, design, construction, and capacity of cooling water intake structures reflect the best technology available for minimizing adverse environmental impacts. In February 2002, the EPA approved a proposed ...

  4. Synthesis and single crystal structure refinement of the one-layer hydrate of sodium brittle mica

    SciTech Connect

    Kalo, Hussein; Milius, Wolfgang; Braeu, Michael; Breu, Josef

    2013-02-15

    A sodium brittle mica with the ideal composition [Na{sub 4}]{sup inter}[Mg{sub 6}]{sup oct}[Si{sub 4}Al{sub 4}]{sup tet}O{sub 20}F{sub 4} was synthesized via melt synthesis in a gas tight crucible. This mica is unusual inasmuch as the known mica structure holds only room for two interlayer cations per unit cell and inasmuch as it readily hydrates despite the high layer charge while ordinary micas and brittle micas are non-swelling. The crystal structure of one-layer hydrate sodium brittle mica was determined and refined from single crystal X-ray data. Interlayer cations reside at the center of the distorted hexagonal cavities and are coordinated by the three inner basal oxygen atoms. The coordination of the interlayer cation is completed by three interlayer water molecules residing at the center of the interlayer region. The relative position of adjacent 2:1-layers thus is fixed by these octahedrally coordinated interlayer cations. Pseudo-symmetry leads to extensive twinning. In total five twin operations generate the same environment for the interlayer species and are energetically degenerate. - Graphical abstract: The sodium brittle mica has been successfully synthesized by melt synthesis and the crystal structure of the one-layer hydrate of sodium brittle mica was determined from single crystal X-ray diffraction data. Highlights: Black-Right-Pointing-Pointer Melt synthesis yielded coarse grained sodium brittle mica which showed little disorder. Black-Right-Pointing-Pointer Sodium brittle mica hydrated completely to the state of one-layer hydrate. Black-Right-Pointing-Pointer Structure of one-layer hydrate of sodium brittle mica could therefore be determined and refined. Black-Right-Pointing-Pointer Arrangement of upper and lower tetrahedral sheet encompassing interlayer cation were clarified.

  5. 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

  6. Synthesis, growth, structure, mechanical and optical properties of a new semi-organic 2-methyl imidazolium dihydrogen phosphate single crystal

    SciTech Connect

    Nagapandiselvi, P.; Baby, C.; Gopalakrishnan, R.

    2016-09-15

    Highlights: • 2MIDP crystals were grown by slow evaporation solution growth technique. • Single crystal XRD revealed self-assembled supramolecular framework. • Z scan technique is employed for third order nonlinear optical susceptibility. • Structure-property correlation is established. - Abstract: A new semi-organic compound, 2-methyl imidazolium dihydrogen phosphate (2MIDP), was prepared and good quality single crystals of 2MIDP were grown by slow evaporation solution growth technique. Crystal structure elucidated using Single crystal XRD showed that 2MIDP crystallizes in monoclinic system with P2{sub 1}/c space group. FT-IR, UV-Vis-NIR, Fluorescence and FT-NMR spectra confirm the molecular structure of 2MIDP. The UV-Vis-NIR spectra established the suitability of the compound for NLO applications. TG-DSC showed that 2MIDP is thermally stable up to 200 °C. Mechanical characteristics like hardness number (H{sub v}), stiffness constant (C{sub 11}), yield strength (σ{sub v}), fracture toughness (K{sub c}) and brittleness index (B{sub i}) were assessed using Vicker’s microhardness tester. Third order nonlinear optical properties determined from Z-scan measurement using femto and picosecond lasers showed two photon reverse saturable absorption. The enhancement of nonlinear optical properties in femto second laser, revealed the suitability of 2MIDP for optical limiting applications.

  7. Crystal structure of BIS(Betaine) hydrochloride monohydrate

    NASA Astrophysics Data System (ADS)

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

    1990-11-01

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

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

    NASA Astrophysics Data System (ADS)

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

    1990-04-01

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

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

    PubMed

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

    2014-10-01

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

  10. The crystal structure of ice under mesospheric conditions

    NASA Astrophysics Data System (ADS)

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

    2015-05-01

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

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

    SciTech Connect

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

    2015-06-04

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

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

    PubMed

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

    2015-11-01

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

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

    NASA Astrophysics Data System (ADS)

    Schulte, Joachim; Böhm, Michael C.

    1996-04-01

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

  14. Structure development in silicon sheet by shaped crystallization

    NASA Technical Reports Server (NTRS)

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

    1978-01-01

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

  15. Crystal and molecular structures of new enantiopure quinuclidines.

    PubMed

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

    2004-03-01

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

  16. Crystal Structures of Cisplatin Bound to a Human Copper Chaperone

    SciTech Connect

    Boal, Amie K.; Rosenzweig, Amy C.

    2010-08-16

    Copper trafficking proteins, including the chaperone Atox1 and the P{sub 1B}-type ATPase ATP7B, have been implicated in cellular resistance to the anticancer drug cisplatin. We have determined two crystal structures of cisplatin-Atox1 adducts that reveal platinum coordination by the conserved CXXC copper-binding motif. Direct interaction of cisplatin with this functionally relevant site has significant implications for understanding the molecular basis for resistance mediated by copper transport pathways.

  17. Woodpulp Crystal Structure and Its Effect on Nitrocellulose Physical Properties

    DTIC Science & Technology

    1980-09-01

    25963. 10 3. A.M. Hindelah and D.J. Johnson, "Crystallinity and Crystallite Size Treatment in Cellulose I Fibres : 1. Ramie and Fortisan," Polymer , Vol...nitrocellulose from N-7 and N-5 is attributed to the presence of Cellulose 11 crystal structure in the fibre . It does not appear to affect the...13, 1972, pp 42330. 4. V.W. Tripp, "Measurement of Crystallinity," High Polymers : Cellulose and Cellulose Derivatives Part IV, Vol V, 1971, Wiley

  18. Phytases: crystal structures, protein engineering and potential biotechnological applications.

    PubMed

    Yao, M-Z; Zhang, Y-H; Lu, W-L; Hu, M-Q; Wang, W; Liang, A-H

    2012-01-01

    Phytases are a group of enzymes capable of releasing phosphates from phytates, one of the major forms of phosphorus (P) in animal feeds of plant origin. These enzymes have been widely used in animal feed to improve phosphorus nutrition and to reduce phosphorus pollution in animal waste. This review covers the basic nomenclature and crystal structures of phytases and emphasizes both the protein engineering strategies used for the development of new, effective phytases with improved properties and the potential biotechnological applications of phytases.

  19. 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.

  20. Crystal Structures of Aedes Aegypt Alanine Glyoxylate Aminotransferase

    SciTech Connect

    Han,Q.; Robinson, H.; Gao, Y.; Vogelaar, N.; Wilson, S.; Rizzi, M.; Li, J.

    2006-01-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75{angstrom} high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1{angstrom} resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  1. Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.

    PubMed

    Han, Qian; Robinson, Howard; Gao, Yi Gui; Vogelaar, Nancy; Wilson, Scott R; Rizzi, Menico; Li, Jianyong

    2006-12-01

    Mosquitoes are unique in having evolved two alanine glyoxylate aminotransferases (AGTs). One is 3-hydroxykynurenine transaminase (HKT), which is primarily responsible for catalyzing the transamination of 3-hydroxykynurenine (3-HK) to xanthurenic acid (XA). Interestingly, XA is used by malaria parasites as a chemical trigger for their development within the mosquito. This 3-HK to XA conversion is considered the major mechanism mosquitoes use to detoxify the chemically reactive and potentially toxic 3-HK. The other AGT is a typical dipteran insect AGT and is specific for converting glyoxylic acid to glycine. Here we report the 1.75A high-resolution three-dimensional crystal structure of AGT from the mosquito Aedes aegypti (AeAGT) and structures of its complexes with reactants glyoxylic acid and alanine at 1.75 and 2.1A resolution, respectively. This is the first time that the three-dimensional crystal structures of an AGT with its amino acceptor, glyoxylic acid, and amino donor, alanine, have been determined. The protein is dimeric and adopts the type I-fold of pyridoxal 5-phosphate (PLP)-dependent aminotransferases. The PLP co-factor is covalently bound to the active site in the crystal structure, and its binding site is similar to those of other AGTs. The comparison of the AeAGT-glyoxylic acid structure with other AGT structures revealed that these glyoxylic acid binding residues are conserved in most AGTs. Comparison of the AeAGT-alanine structure with that of the Anopheles HKT-inhibitor complex suggests that a Ser-Asn-Phe motif in the latter may be responsible for the substrate specificity of HKT enzymes for 3-HK.

  2. Surface structure of an invariant manifold of a Halo Orbit (extended abstract)

    NASA Technical Reports Server (NTRS)

    Hirani, Anil N.; Lo, Martin W.

    2005-01-01

    We extract the surface structure of the unstable invariant manifold tube projected into position space, of a halo orbit near L2. We do this by using transversal planes to intersect trajectories that approximate the tube. From these intersection points we construct spline-interpolated cross section curves which give a good idea of the structure of the tube. For example, we show that, for the value of (mu) we use, the tube pinches, develops a self-intersection, develops loop-inside-tube structure, pinches some more, and so on. We also construct surfaces made of quadrilaterals and triangles from these cross-sections. The transversal planes are obtained by taking planes orthogonal to a curve that follows the general shape of the tube. One such curve we use, is the unstable invariant manifold of the equilibrium point L2 itself. In another example, we take a circle that follows the tube, as the curve for finding planes transversal to the tube. Our method is complementary to the method of taking cross-sections of constant time (the isochronous method), as used by some other researchers. The isochronous method is good at revealing the temporal structure of trajectories on a tube. However, due to the unequal speeds of different trajectories, it is harder to use for long length surface extraction. In contrast, using our method, we show cross-sections of the tube through an angular extent of nearly (pi) during which the tube becomes extremely convoluted. We also show that tubes of different energies, that start out in certain ordering, do not obey the ordering after a while. Our work is motivated by applications to space mission design.

  3. Subsurface structure of Valles Caldera; a resurgent cauldron in northern New Mexico. [Abstract only

    SciTech Connect

    Goff, F.

    1983-03-01

    Valles Caldera is a 1.1 My old silicic cauldron lying at the intersection of the Rio Grande rift and northeast-trending Jemez Lineament. Geothermal exploration in the caldera region during the last 10 years provides subsurface data which refine our knowledge of deep caldera structure, but raise some questions concerning current models of resurgent cauldrons. For example, a detailed gravity investigation using 730 stations (Segar, 1974) shows a circular negative gravity anomaly centered over the caldera (as expected) but also indicates a strong northeast-trending grain of fault blocks in pre-caldera rocks, that are generally down-faulted to the southeast toward the Rift. Gravity data do not define a diapir structure beneath the resurgent dome attributable to tumescent magma; instead of a northeast-trending horst underlies the Redondo Peak segment of the dome. Interpretation of stratigraphy from many geothermal wells suggests that the caldera and resurgent dome are floored by untilted fault blocks (Hulen and Nielson, 1982). In addition, drilling to Precambrian basement and depths of 3.2 km has not encountered a large intrusive rhyolite that might logically produce tumescence of the dome. The new data indicate that the subsurface structural configuration of Valles Caldera is controlled by pre-caldera tectonics and that a more complicated mechanism is required to explain the resurgent dome standing high inside the caldera. A refined mechanism of resurgence might be one result of CSDP drilling at Valles Caldera.

  4. Crystal structure of lead(II) tartrate: a redetermination.

    PubMed

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ(6) O (1),O (3):O (1'):O (2),O (4):O (4')-lead], [Pb(C4H4O6)] n , were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▶). Acta Cryst. C58, m596-m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb(2+) cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb(2+) cations. The resulting three-dimensional framework is stabilized by O-H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl-ate O atoms of adjacent anions.

  5. Nanoconfinement-induced structures in chiral liquid crystals.

    PubMed

    Melle, Michael; Theile, Madlona; Hall, Carol K; Schoen, Martin

    2013-08-28

    We employ Monte Carlo simulations in a specialized isothermal-isobaric and in the grand canonical ensemble to study structure formation in chiral liquid crystals as a function of molecular chirality. Our model potential consists of a simple Lennard-Jones potential, where the attractive contribution has been modified to represent the orientation dependence of the interaction between a pair of chiral liquid-crystal molecules. The liquid crystal is confined between a pair of planar and atomically smooth substrates onto which molecules are anchored in a hybrid fashion. Hybrid anchoring allows for the formation of helical structures in the direction perpendicular to the substrate plane without exposing the helix to spurious strains. At low chirality, we observe a cholesteric phase, which is transformed into a blue phase at higher chirality. More specifically, by studying the unit cell and the spatial arrangement of disclination lines, this blue phase can be established as blue phase II. If the distance between the confining substrates and molecular chirality are chosen properly, we see a third structure, which may be thought of as a hybrid, exhibiting mixed features of a cholesteric and a blue phase.

  6. Pressure effects on crystal and electronic structure of bismuth tellurohalides

    NASA Astrophysics Data System (ADS)

    Rusinov, I. P.; Menshchikova, T. V.; Sklyadneva, I. Yu; Heid, R.; Bohnen, K.-P.; Chulkov, E. V.

    2016-11-01

    We study the possibility of pressure-induced transitions from a normal semiconductor to a topological insulator (TI) in bismuth tellurohalides using density functional theory and tight-binding method. In BiTeI this transition is realized through the formation of an intermediate phase, a Weyl semimetal, that leads to modification of surface state dispersions. In the topologically trivial phase, the surface states exhibit a Bychkov-Rashba type dispersion. The Weyl semimetal phase exists in a narrow pressure interval of 0.2 GPa. After the Weyl semimetal-TI transition occurs, the surface electronic structure is characterized by gapless states with linear dispersion. The peculiarities of the surface states modification under pressure depend on the band-bending effect. We have also calculated the frequencies of Raman active modes for BiTeI in the proposed high-pressure crystal phases in order to compare them with available experimental data. Unlike BiTeI, in BiTeBr and BiTeCl the topological phase transition does not occur. In BiTeBr, the crystal structure changes with pressure but the phase remains a trivial one. However, the transition appears to be possible if the low-pressure crystal structure is retained. In BiTeCl under pressure, the topological phase does not appear up to 18 GPa due to a relatively large band gap width in this compound.

  7. 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.

  8. Crystal structure of lead(II) tartrate: a redetermination

    PubMed Central

    Weil, Matthias

    2015-01-01

    Single crystals of poly[μ4-tartrato-κ6 O 1,O 3:O 1′:O 2,O 4:O 4′-lead], [Pb(C4H4O6)]n, were grown in a gel medium. In comparison with the previous structure determination of this compound from laboratory powder X-ray diffraction data [De Ridder et al. (2002 ▸). Acta Cryst. C58, m596–m598], the redetermination on the basis of single-crystal data reveals the absolute structure, all atoms with anisotropic displacement parameters and a much higher accuracy in terms of bond lengths and angles. It could be shown that a different space group or incorporation of water as reported for similarly gel-grown lead tartrate crystals is incorrect. In the structure, each Pb2+ cation is bonded to eight O atoms of five tartrate anions, while each tartrate anion links four Pb2+ cations. The resulting three-dimensional framework is stabilized by O—H⋯O hydrogen bonds between the OH groups of one tartrate anion and the carboxyl­ate O atoms of adjacent anions. PMID:25705458

  9. 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.

  10. A novel characterization of organic molecular crystal structures for the purpose of crystal engineering.

    PubMed

    Thomas, Noel W

    2015-08-01

    A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, ϕ2D, of symmetry determined by the space group. Values of ϕ2D reflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parameters aell, bell and χell. The ratio aell/bell allows the established α, β, γ classification to be integrated into the current framework. The values of parameters aell and bell arising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

  11. The first crystal structure of an archaeal helical repeat protein

    SciTech Connect

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-07-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The structure of ST1625p consists of a unique superhelix with a low-level structure resemblance to doamins from other proteins with known three-dimensional structures. The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein.

  12. Structure and functions of simple membrane-water interfaces. [Abstract only

    NASA Technical Reports Server (NTRS)

    Pohorille, A.; Wilson, M. A.

    1994-01-01

    The structure and functions of the earliest ancestors of contemporary cells are focal points in studies of the origin of life. Probably the first cell-like structures were vesicles - closed, spheroidal structures with aqueous medium trapped inside. The membranous walls of vesicles were most likely bilayers composed of simple amphiphilic material available on early earth. The membrane studied was composed of glycerol 1-monooleate (GMO). Glycerol forms the polar head group and the oily tail contains 18 carbon atoms. All head groups have been found to be located in two narrow regions at the interfaces with water. The membrane interior, formed by the hydrophobic tails, is quite fluid with chain disorder increasing towards the center of the bilayer. These results are in agreement with x-ray and neutron scattering data from related bilayers. The width of the membrane is not constant, but fluctuates in time and space. Occasional thinning defects in the membrane, observed during the course of the simulations, may have a significant influence on rates of passive transport of small molecules across membranes. It has been found that water penetrates the head group region but not the oily interior of the membrane. Water molecules near the interface are oriented by dipoles of the head groups. The resulting electrostatic potential across the interface, determined in our simulations, has been found to be markedly larger than across the water-oil interface. This quantity has been implicated as the source of selectivity, with respect to the sign of the charge, as an ion approaches the interface and during transport of hydrophobic ions across membranes.

  13. Gyroid cuticular structures in butterfly wing scales: biological photonic crystals.

    PubMed

    Michielsen, K; Stavenga, D G

    2008-01-06

    We present a systematic study of the cuticular structure in the butterfly wing scales of some papilionids (Parides sesostris and Teinopalpus imperialis) and lycaenids (Callophrys rubi, Cyanophrys remus, Mitoura gryneus and Callophrys dumetorum). Using published scanning and transmission electron microscopy (TEM) images, analytical modelling and computer-generated TEM micrographs, we find that the three-dimensional cuticular structures can be modelled by gyroid structures with various filling fractions and lattice parameters. We give a brief discussion of the formation of cubic gyroid membranes from the smooth endoplasmic reticulum in the scale's cell, which dry and harden to leave the cuticular structure behind when the cell dies. The scales of C. rubi are a potentially attractive biotemplate for producing three-dimensional optical photonic crystals since for these scales the cuticle-filling fraction is nearly optimal for obtaining the largest photonic band gap in a gyroid structure.

  14. Double layer hydroxide minerals as host structures for bioorganic molecules. [Abstract only

    NASA Technical Reports Server (NTRS)

    Lee, Ton; Arrhenius, Meichia L.; Hui, Stella S.-Y.; Ring, Ken M.; Gedulin, Benjamin I.; Orgel, Leslie E.; Arrhenius, Gustaf

    1994-01-01

    A central problem in molecular evolution concerns the selective concentration from dilute, multicomponent solution of source molecules into a reactive environment, where formation of larger molecular assemblages can take place. Minerals consisting of positively charged, separable metal hydroxide sheets have proven capable of these functions. This common structural type is represented by minerals such as pyroaurite (Mg-Fe(3+) hydroxide), hydrotalcite (Mg-Al), green rust Fe(2+)-Fe(3+) and others. Effective interlayer sorption is demonstrated for orthophosphate and condensed phosphates, anionic alkyl compounds, polypeptides, nucleic acids, cyanide complexes and glycolaldehyde phosphate, the latter shown to readily oligomerize to form and selectively retain racemic hexose -2, 4, 6-phosphates, preferentially of altrose (Pitsch, et al, 1993). The selective aldomerization and retention effects correlate with the charge distribution in the host mineral structure and the stereochemistry of the substrate molecules. Interaction between nucleic acid bases, and between the cyanide groups of glycolaldehyde phosphate nitrile at the low water activity in the mineral interlayer is indicated by doubling of the monomeric separation of the hydroxide mineral sheets.

  15. Fusion proteins as alternate crystallization paths to difficult structure problems

    NASA Technical Reports Server (NTRS)

    Carter, Daniel C.; Rueker, Florian; Ho, Joseph X.; Lim, Kap; Keeling, Kim; Gilliland, Gary; Ji, Xinhua

    1994-01-01

    The three-dimensional structure of a peptide fusion product with glutathione transferase from Schistosoma japonicum (SjGST) has been solved by crystallographic methods to 2.5 A resolution. Peptides or proteins can be fused to SjGST and expressed in a plasmid for rapid synthesis in Escherichia coli. Fusion proteins created by this commercial method can be purified rapidly by chromatography on immobilized glutathione. The potential utility of using SjGST fusion proteins as alternate paths to the crystallization and structure determination of proteins is demonstrated.

  16. Band structures in the nematic elastomers phononic crystals

    NASA Astrophysics Data System (ADS)

    Yang, Shuai; Liu, Ying; Liang, Tianshu

    2017-02-01

    As one kind of new intelligent materials, nematic elastomers (NEs) represent an exciting physical system that combines the local orientational symmetry breaking and the entropic rubber elasticity, producing a number of unique physical phenomena. In this paper, the potential application of NEs in the band tuning is explored. The band structures in two kinds of NE phononic crystals (PCs) are investigated. Through changing NE intrinsic parameters, the influence of the porosity, director rotation and relaxation on the band structures in NE PCs are analyzed. This work is a meaningful try for application of NEs in acoustic field and proposes a new intelligent strategy in band turning.

  17. Crystal structure of new AsS{sub 2} compound

    SciTech Connect

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

    2013-01-15

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

  18. 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.

  19. 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.

  20. Relation Between Changes in Pigments' Spectral Properties and Structural Distortions of Pigment Protein Complexes (abstract)

    NASA Astrophysics Data System (ADS)

    Stoitchkova, Katerina; Andreeva, Atanaska; Busheva, Mira

    2009-04-01

    Scientists continue to investigate photosynthesis-nature's process to efficiently regulate and store energy. To explore the mechanisms of regulation we used fluorescence, resonance Raman spectroscopy, and biochemical preparative methods. For detailed analysis we applied decomposition of the low temperature steady-state fluorescence spectra. This allowed us to estimate the emission of distinct pigment protein complexes (PPC) and evaluate the fluorescence of various aggregation forms of the main light harvesting complex (LHCII), which plays a major role in the studied mechanisms. Resonance Raman spectroscopy revealed with precision the relation between changes in pigments' spectral properties and structural distortions of PPC. It was shown that aggregation of LHCII led to out-of-plane distortion, not only of neoxanthin, but also of lutein molecules. This was enhanced when the complex was embedded in thylakoid membranes (TM). It was suggested that lutein molecules are more closely related to the process of aggregation of LHCII in TM than neoxanthin.

  1. Studies on the synthesis, structure, growth and physical properties of an organic NLO crystal: 2-Amino-5-nitropyridinium Phenolsulfonate

    SciTech Connect

    Anandha babu, G.; Ramasamy, P.; Chandramohan, A.

    2011-12-15

    Graphical abstract: 2-Amino-5-nitropyridinium Phenolsulfonate is identified as potential candidate for efficient frequency conversion. Highlights: Black-Right-Pointing-Pointer Single crystals of 2A5NPP have been grown from saturated solution. Black-Right-Pointing-Pointer The high resolution X-ray diffraction curve (DC) measurements substantiate the good quality of the crystals. Black-Right-Pointing-Pointer Powder test with Nd:YAG laser radiation shows a high second harmonic generation. Black-Right-Pointing-Pointer The high value of damage threshold is related to the specific heat of the crystal which is reasonably high. -- Abstract: A noncentrosymmetric crystal was prepared from 2-amino-5-nitropyridine (2A5NP) and p-Phenolsulfonic acid, which was designed for second harmonic generation. Good quality single crystals of 2-amino-5-nitropyridinium Phenolsulfonate (2A5NPP) were successfully grown by the slow evaporation method with dimensions 10 Multiplication-Sign 4 Multiplication-Sign 3 mm{sup 3}. The unit cell dimensions were determined from single crystal X-ray diffraction studies. The structural perfection of the grown crystals has been analyzed by high-resolution X-ray diffraction (HRXRD) rocking curve measurements. Fourier transform infrared (FTIR) spectral studies have been performed to identify the functional groups. The optical transmittance window and the lower cutoff wavelength of the 2A5NPP have been identified by UV-vis-NIR studies. Thermo gravimetric analysis (TGA) and differential thermal analysis (DTA) were used to study its thermal properties. Powder test with Nd:YAG laser radiation shows a high second harmonic generation. The laser induced surface damage threshold for the grown crystal was measured using Nd:YAG laser.

  2. Crystal structure and crystal chemistry of melanovanadite, a natural vanadium bronze.

    USGS Publications Warehouse

    Konnert, J.A.; Evans, H.T.

    1987-01-01

    The crystal structure of melanovanadite from Minas Ragra, Peru, has been determined in space group P1. The triclinic unit cell (non-standard) has a 6.360(2), b 18.090(9), c 6.276(2) A, alpha 110.18(4)o, beta 101.62(3)o, gamma 82.86(4)o. A subcell with b' = b/2 was found by crystal-structure analysis to contain CaV4O10.5H2O. The subcell has a layer structure in which the vanadate sheet consists of corner-shared tetrahedral VO4 and double square-pyramidal V2O8 groups, similar to that previously found in synthetic CsV2O5. Refinement of the full structure (R = 0.056) showed that the Ca atom, which half-occupies a general position in the subcell, is 90% ordered at one of these sites in the whole unit cell. Bond length-bond strength estimates indicate that the tetrahedra contain V5+, and the square pyramids, V4+.-J.A.Z.

  3. Crystal structure of the Rasputin NTF2-like domain from Drosophila melanogaster

    SciTech Connect

    Vognsen, Tina; Kristensen, Ole

    2012-03-30

    Highlights: Black-Right-Pointing-Pointer The crystal structure of the NTF2-like domain of Rasputin protein is presented. Black-Right-Pointing-Pointer Differences to known ligand binding sites of nuclear transport factor 2 are discussed. Black-Right-Pointing-Pointer A new ligand binding site for the Rasputin and G3BP proteins is proposed. -- Abstract: The crystal structure of the NTF2-like domain of the Drosophila homolog of Ras GTPase SH3 Binding Protein (G3BP), Rasputin, was determined at 2.7 A resolution. The overall structure is highly similar to nuclear transport factor 2: It is a homodimer comprised of a {beta}-sheet and three {alpha}-helices forming a cone-like shape. However, known binding sites for RanGDP and FxFG containing peptides show electrostatic and steric differences compared to nuclear transport factor 2. A HEPES molecule bound in the structure suggests a new, and possibly physiologically relevant, ligand binding site.

  4. Manganese oxide minerals: Crystal structures and economic and environmental significance

    PubMed Central

    Post, Jeffrey E.

    1999-01-01

    Manganese oxide minerals have been used for thousands of years—by the ancients for pigments and to clarify glass, and today as ores of Mn metal, catalysts, and battery material. More than 30 Mn oxide minerals occur in a wide variety of geological settings. They are major components of Mn nodules that pave huge areas of the ocean floor and bottoms of many fresh-water lakes. Mn oxide minerals are ubiquitous in soils and sediments and participate in a variety of chemical reactions that affect groundwater and bulk soil composition. Their typical occurrence as fine-grained mixtures makes it difficult to study their atomic structures and crystal chemistries. In recent years, however, investigations using transmission electron microscopy and powder x-ray and neutron diffraction methods have provided important new insights into the structures and properties of these materials. The crystal structures for todorokite and birnessite, two of the more common Mn oxide minerals in terrestrial deposits and ocean nodules, were determined by using powder x-ray diffraction data and the Rietveld refinement method. Because of the large tunnels in todorokite and related structures there is considerable interest in the use of these materials and synthetic analogues as catalysts and cation exchange agents. Birnessite-group minerals have layer structures and readily undergo oxidation reduction and cation-exchange reactions and play a major role in controlling groundwater chemistry. PMID:10097056

  5. From protein structure to function via single crystal optical spectroscopy

    PubMed Central

    Ronda, Luca; Bruno, Stefano; Bettati, Stefano; Storici, Paola; Mozzarelli, Andrea

    2015-01-01

    The more than 100,000 protein structures determined by X-ray crystallography provide a wealth of information for the characterization of biological processes at the molecular level. However, several crystallographic “artifacts,” including conformational selection, crystallization conditions and radiation damages, may affect the quality and the interpretation of the electron density maps, thus limiting the relevance of structure determinations. Moreover, for most of these structures, no functional data have been obtained in the crystalline state, thus posing serious questions on their validity in infereing protein mechanisms. In order to solve these issues, spectroscopic methods have been applied for the determination of equilibrium and kinetic properties of proteins in the crystalline state. These methods are UV-vis spectrophotometry, spectrofluorimetry, IR, EPR, Raman, and resonance Raman spectroscopy. Some of these approaches have been implemented with on-line instruments at X-ray synchrotron beamlines. Here, we provide an overview of investigations predominantly carried out in our laboratory by single crystal polarized absorption UV-vis microspectrophotometry, the most applied technique for the functional characterization of proteins in the crystalline state. Studies on hemoglobins, pyridoxal 5′-phosphate dependent enzymes and green fluorescent protein in the crystalline state have addressed key biological issues, leading to either straightforward structure-function correlations or limitations to structure-based mechanisms. PMID:25988179

  6. Crystal structure of eukaryotic ribosome and its complexes with inhibitors.

    PubMed

    Yusupova, Gulnara; Yusupov, Marat

    2017-03-19

    A high-resolution structure of the eukaryotic ribosome has been determined and has led to increased interest in studying protein biosynthesis and regulation of biosynthesis in cells. The functional complexes of the ribosome crystals obtained from bacteria and yeast have permitted researchers to identify the precise residue positions in different states of ribosome function. This knowledge, together with electron microscopy studies, enhances our understanding of how basic ribosome processes, including mRNA decoding, peptide bond formation, mRNA, and tRNA translocation and cotranslational transport of the nascent peptide, are regulated. In this review, we discuss the crystal structure of the entire 80S ribosome from yeast, which reveals its eukaryotic-specific features, and application of X-ray crystallography of the 80S ribosome for investigation of the binding mode for distinct compounds known to inhibit or modulate the protein-translation function of the ribosome. We also refer to a challenging aspect of the structural study of ribosomes, from higher eukaryotes, where the structures of major distinctive features of higher eukaryote ribosome-the high-eukaryote-specific long ribosomal RNA segments (about 1MDa)-remain unresolved. Presently, the structures of the major part of these high-eukaryotic expansion ribosomal RNA segments still remain unresolved.This article is part of the themed issue 'Perspectives on the ribosome'.

  7. Ionothermal synthesis and crystal structures of metal phosphate chains

    SciTech Connect

    Wragg, David S.; Le Ouay, Benjamin; Beale, Andrew M.; O'Brien, Matthew G.; Slawin, Alexandra M.Z.; Warren, John E.; Prior, Timothy J.; Morris, Russell E.

    2010-07-15

    We have prepared isostructural aluminium and gallium phosphate chains by ionothermal reactions in 1-ethyl-3-methylimidazolium bromide and 1-ethylpyridinium bromide under a variety of conditions. The chains can be prepared as pure phases or along with three dimensional framework phases. The chains are favoured at shorter heating times and the crystallinity can be improved by addition of transition metal acetates and amines which are not included in the final structure. The chain can be prepared with or without the presence of hydrofluoric acid. - Graphical abstract: Chain structures prepared from ionic liquid solvents under a wide variety of synthesis conditions.

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

    SciTech Connect

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

    2009-08-15

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

  9. A versatile instrument for structural studies of interfaces in ultrahigh vacuum (abstract)

    NASA Astrophysics Data System (ADS)

    Clausnitzer, M.; Pauly, T.; Materlik, G.

    1989-07-01

    Structural studies of interfaces with synchrotron x-radiation (SXR) are presently carried out with several different methods which were developed in connection with SXR over the past decade: dynamical x-ray diffraction using standing wavefields (XSW), kinematical surface diffraction (KSD), Fresnel reflection (FR), and absorption spectroscopy (SEXAFS, SXANES). These methods can determine different, and often complementary parameters of a system such as short-/long-range order, relaxation relative to bulk, structure normal/parallel to surface, valence state of surface atoms, roughness of a buried interface, etc. Accordingly, these different principles have also been combined to form new methods such as diffraction of evanescent x rays during total external reflection (DEXTER) and reflection EXAFS (REFLEXAFS). It is, therefore, highly desirable to have the opportunity to study the same interface system with different methods. On the other hand, preparation of a system in ultrahigh vacuum requires in most cases expensive bulky equipment and time consuming techniques. These considerations call for a setup which provides different experimental options. We have, therefore, installed at the beamline ROEMO I at HASYLAB a versatile UHV system for interface studies. A sample can either be prepared inside a chamber with three Knudsen cells for MBE growth and standard equipment for cleaning, heating and surface characterization by RHEED, or inside a chamber for aggressive gases. The first one is installed outside the interlock area providing access also when the ROEMO beam is on and the second one inside the interlock area. From either chamber the sample can be transferred into an analysis chamber at the ROEMO I station or into a transportable baby chamber. The analysis chamber can be used for measurements with standing waves, absorption spectroscopy and reflectivity measurements. Electrons are detected with a spherical analyzer and photons outside the vacuum through Be windows

  10. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction†

    PubMed Central

    Héroux, Annie; Bozinovski, Dragana M.; Valley, Michael P.; Fitzpatrick, Paul F.; Orville, Allen M.

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 Å resolution or better are described of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct. The D402N enzyme has no detectable activity with neutral nitroalkanes (Valley, M. P., and Fitzpatrick, P. F. (2003) J. Am. Chem. Soc. 23, 8738–8739). The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2’-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062–2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2’-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle. PMID:19265437

  11. Crystal Structures of Intermediates in the Nitroalkane Oxidase Reaction

    SciTech Connect

    Heroux, A.; Bozinovski, D; Valley, M; Fitzpatrick, P; Orville, A

    2009-01-01

    The flavoenzyme nitroalkane oxidase is a member of the acyl-CoA dehydrogenase superfamily. Nitroalkane oxidase catalyzes the oxidation of neutral nitroalkanes to nitrite and the corresponding aldehydes or ketones. Crystal structures to 2.2 {angstrom} resolution or better of enzyme complexes with bound substrates and of a trapped substrate-flavin adduct are described. The D402N enzyme has no detectable activity with neutral nitroalkanes. The structure of the D402N enzyme crystallized in the presence of 1-nitrohexane or 1-nitrooctane shows the presence of the substrate in the binding site. The aliphatic chain of the substrate extends into a tunnel leading to the enzyme surface. The oxygens of the substrate nitro group interact both with amino acid residues and with the 2'-hydroxyl of the FAD. When nitroalkane oxidase oxidizes nitroalkanes in the presence of cyanide, an electrophilic flavin imine intermediate can be trapped (Valley, M. P., Tichy, S. E., and Fitzpatrick, P. F. (2005) J. Am. Chem. Soc. 127, 2062-2066). The structure of the enzyme trapped with cyanide during oxidation of 1-nitrohexane shows the presence of the modified flavin. A continuous hydrogen bond network connects the nitrogen of the CN-hexyl-FAD through the FAD 2'-hydroxyl to a chain of water molecules extending to the protein surface. Together, our complementary approaches provide strong evidence that the flavin cofactor is in the appropriate oxidation state and correlates well with the putative intermediate state observed within each of the crystal structures. Consequently, these results provide important structural descriptions of several steps along the nitroalkane oxidase reaction cycle.

  12. Crystal structures of three (trichloromethyl)(carbamoyl)disulfanes.

    PubMed

    Goldenberg, Barbara L; Young, Victor G; Barany, George

    2015-10-01

    The present paper reports crystallographic studies on three related compounds that were of inter-est as precursors for synthetic and mechanistic work in organosulfur chemistry, as well as to model nitro-gen-protecting groups: (N-methyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C3H4Cl3NOS2, (1), (N-benzyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (2), and (N-methyl-N-phenyl-carbamo-yl)(tri-chloro-meth-yl)disulfane, C9H8Cl3NOS2, (3). Their mol-ecular structures, with similar bond lengths and angles for the CCl3SS(C=O)N moieties, are confirmed. Compounds (1) and (3) both crystallized with two independent mol-ecules in the asymmetric unit. Classical hydrogen bonding, as well as chlorine-dense regions, are evident in the crystal packing for (1) and (2). In the crystal of (1), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [110], which are linked by short Cl⋯Cl and S⋯O contacts forming sheets parallel to (001). In the crystal of (2), mol-ecules are linked via N-H⋯O hydrogen bonds forming chains along [001], which in turn are linked by pairs of short O⋯Cl contacts forming ribbons along the c-axis direction. In the crystal of (3), there are no classical hydrogen bonds present and the chlorine-dense regions observed in (1) and (2) are lacking.

  13. Identifying duplicate crystal structures: XTALCOMP, an open-source solution

    NASA Astrophysics Data System (ADS)

    Lonie, David C.; Zurek, Eva

    2012-03-01

    We describe the implementation of XTALCOMP, an efficient, reliable, and open-source library that tests if two crystal descriptions describe the same underlying structure. The algorithm has been tested and found to correctly identify duplicate structures in spite of the "real-world" difficulties that arise from working with numeric crystal representations: degenerate unit cell lattices, numerical noise, periodic boundaries, and the lack of a canonical coordinate origin. The library is portable, open, and not dependent on any external packages. A web interface to the algorithm is publicly accessible at http://xtalopt.openmolecules.net/xtalcomp/xtalcomp.html. Program summaryProgram title: XtalComp Catalogue identifier: AEKV_v1_0 Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEKV_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland Licensing provisions: "New" (3-clause) BSD [1] No. of lines in distributed program, including test data, etc.: 3148 No. of bytes in distributed program, including test data, etc.: 21 860 Distribution format: tar.gz Programming language: C++ Computer: No restrictions Operating system: All operating systems with a compliant C++ compiler. Classification: 7.8 Nature of problem: Computationally identifying duplicate crystal structures taken from the output of modern solid state calculations is a non-trivial exercise for many reasons. The translation vectors in the description are not unique — they may be transformed into linear combinations of themselves and continue to describe the same extended structure. The coordinates and cell parameters contain numerical noise. The periodic boundary conditions at the unit cell faces, edges, and corners can cause very small displacements of atomic coordinates to result in very different representations. The positions of all atoms may be uniformly translated by an arbitrary vector without modifying the underlying structure. Additionally, certain

  14. N-methylcodeinium iodide—Crystal structure and spectroscopic elucidation

    NASA Astrophysics Data System (ADS)

    Seidel, R. W.; Bakalska, B. R.; Kolev, T.; Vassilev, D.; Mayer-Figge, H.; Spiteller, M.; Sheldrick, W. S.; Koleva, B. B.

    2009-07-01

    The correlation between the structure and the spectroscopic properties of N-methylcodeinium iodide ( 1) has been studied, using the methods of single crystal X-ray diffraction, IR-LD spectroscopy of oriented samples as a suspension in nematic liquid crystals, UV-vis spectroscopy and 1H and 13C NMR spectroscopy. HPLC tandem mass spectrometry (HPLC ESI MS/MS) and thermal methods were also employed. Quantum chemical calculations have been performed with a view to obtaining the electronic structure and vibrational properties of the title compound. Compound ( 1) crystallizes in the space group P2 12 12 1 and its cations and anions are joined by moderate intermolecular OH…I - interaction of length 3.442 Å. The codeine molecule exhibits the classical T-shape for opiates. A dihedral angle value of 86.4(5)° between the A/B/C and D/E planes is obtained. Rings A and B are effectively coplanar with an interplanar angle of 3.6(3)°.

  15. Relation between photochromic properties and molecular structures in salicylideneaniline crystals.

    PubMed

    Johmoto, Kohei; Ishida, Takashi; Sekine, Akiko; Uekusa, Hidehiro; Ohashi, Yuji

    2012-06-01

    The crystal structures of the salicylideneaniline derivatives N-salicylidene-4-tert-butyl-aniline (1), N-3,5-di-tert-butyl-salicylidene-3-methoxyaniline (2), N-3,5-di-tert-butyl-salicylidene-3-bromoaniline (3), N-3,5-di-tert-butyl-salicylidene-3-chloroaniline (4), N-3,5-di-tert-butyl-salicylidene-4-bromoaniline (5), N-3,5-di-tert-butyl-salicylidene-aniline (6), N-3,5-di-tert-butyl-salicylidene-4-carboxyaniline (7) and N-salicylidene-2-chloroaniline (8) were analyzed by X-ray diffraction analysis at ambient temperature to investigate the relationship between their photochromic properties and molecular structures. A clear correlation between photochromism and the dihedral angle of the two benzene rings in the salicylideneaniline derivatives was observed. Crystals with dihedral angles less than 20° were non-photochromic, whereas those with dihedral angles greater than 30° were photochromic. Crystals with dihedral angles between 20 and 30° could be either photochromic or non-photochromic. Inhibition of the pedal motion by intra- or intermolecular steric hindrance, however, can result in non-photochromic behaviour even if the dihedral angle is larger than 30°.

  16. Evolution of Structure-Reactivity Correlations for the Hydrogen Abstraction Reaction by Chlorine Atom

    SciTech Connect

    Poutsma, Marvin L

    2013-01-01

    Empirical structure-reactivity correlations are developed for log k298, the gas-phase rate constants for the reaction (Cl + HCR3 ClH + CR3 ). It has long been recognized that correlation with rH is weak. The poor performance of the linear Evans-Polanyi formulation s illustrated and was little improved by adding a quadratic term, e.g., by making its slope smoothly dependent on rH [ ( rH rHmin) / ( rHmax rHmin)]. The polar effect ( -Cl---H---CR3 +) has also been long discussed but there is no formalization of this dependence based on widely available independent variable(s). Using the sum of Hammett constants for the R substituents also gave at best modest correlations, either for para or for its dissection into F (field/inductive) and R (resonance) effects. Much greater success was achieved by combining these approaches with the preferred independent variable set being either [( rH)2, rH, F, and R] or [ , rH, F, and R]. For 64 rate constants which span 7 orders of magnitude, these correlation formulations give r2 > 0.87 and a mean unsigned deviation of <0.5 log k units, with even better performance if primary secondary, and tertiary reaction centers are treated separately.

  17. Crystal structure of 1-methylimidazole 3-oxide monohydrate

    PubMed Central

    Frampton, Christopher S.; Murray, James I.; Spivey, Alan C.

    2017-01-01

    1-Methylimidazole 3-N-oxide (NMI-O) crystallizes as a monohydrate, C4H6N2O·H2O, in the monoclinic space group P21 with Z′ = 2 (mol­ecules A and B). The imidazole rings display a planar geometry (r.m.s. deviations = 0.0008 and 0.0002 Å) and are linked in the crystal structure into infinite zigzag strands of ⋯NMI-O(A)⋯OH2⋯NMI-O(B)⋯OH2⋯ units by O—H⋯O hydrogen bonds. These chains propagate along the b-axis direction of the unit cell. PMID:28316812

  18. Crystal structure and magnetism of UOsAl

    NASA Astrophysics Data System (ADS)

    Andreev, A. V.; Daniš, S.; Šebek, J.; Henriques, M. S.; Vejpravová, J.; Gorbunov, D. I.; Havela, L.

    2017-04-01

    Crystal structure, magnetization, and specific heat were studied on single crystal of uranium intermetallic compound UOsAl. It is a hexagonal Laves phase of MgZn2 type, space group P63/mmc, with lattice parameters a=536.4 pm, c=845.3 pm. Shortest inter-uranium distance 313 pm (along the c-axis) is considerably smaller than the Hill limit (340 pm). The compound is a weakly temperature-dependent paramagnet with magnetic susceptibility of ≈1.5*10-8 m3 mol-1 (at T=2 K), which is slightly higher with magnetic field along the a-axis compared to the c-axis. The Sommerfeld coefficient of electronic specific heat has moderate value of γ=36 mJ mol-1 K-2.

  19. Faceting and commensurability in crystal structures of colloidal thin films.

    PubMed

    Ramiro-Manzano, F; Meseguer, F; Bonet, E; Rodriguez, I

    2006-07-14

    This Letter investigates the influence of finite size effects on the particle arrangement of thin film colloidal crystals. A rich variety of crystallographic faceting with large single domain microcrystallites is shown. Optical reflectance experiments together with scanning electron microscopy permit the identification of the crystal symmetry and the facet orientation, as well as the exact number of monolayers. When the cell thickness is not commensurable with a high symmetry layering, particles arrange themselves in a periodic distribution of (111)- and (100)-orientated face centered cubic (fcc) microcrystallites separated by planar defects. These structures can be described as a fcc ordering orientated along a vicinal surface, modified by a periodic distribution of fcc (111) stacking faults.

  20. Crystal structure of isoflavone reductase from alfalfa (Medicago sativa L.).

    PubMed

    Wang, Xiaoqiang; He, Xianzhi; Lin, Jianqiao; Shao, Hui; Chang, Zhenzhan; Dixon, Richard A

    2006-05-19

    Isoflavonoids play important roles in plant defense and exhibit a range of mammalian health-promoting activities. Isoflavone reductase (IFR) specifically recognizes isoflavones and catalyzes a stereospecific NADPH-dependent reduction to (3R)-isoflavanone. The crystal structure of Medicago sativa IFR with deletion of residues 39-47 has been determined at 1.6A resolution. Structural analysis, molecular modeling and docking, and comparison with the structures of other NADPH-dependent enzymes, defined the putative binding sites for co-factor and substrate and potential key residues for enzyme activity and substrate specificity. Further mutagenesis has confirmed the role of Lys144 as a catalytic residue. This study provides a structural basis for understanding the enzymatic mechanism and substrate specificity of IFRs as well as the functions of IFR-like proteins.

  1. Protein dynamics derived from clusters of crystal structures.

    PubMed Central

    van Aalten, D M; Conn, D A; de Groot, B L; Berendsen, H J; Findlay, J B; Amadei, A

    1997-01-01

    A method is presented to mathematically extract concerted structural transitions in proteins from collections of crystal structures. The "essential dynamics" procedure is used to filter out small-amplitude fluctuations from such a set of structures; the remaining large conformational changes describe motions such as those important for the uptake/release of substrate/ligand and in catalytic reactions. The method is applied to sets of x-ray structures for a number of proteins, and the results are compared with the results from essential dynamics as applied to molecular dynamics simulations of those proteins. A significant degree of similarity is found, thereby providing a direct experimental basis for the application of such simulations to the description of large concerted motions in proteins. Images FIGURE 1 PMID:9414203

  2. The crystal structure of Sr(OD) 2

    NASA Astrophysics Data System (ADS)

    Partin, D. E.; O'Keeffe, M.

    1995-10-01

    The crystal structure of Sr(OD) 2 has been determined from a Reitveld refinement of time-of-flight neutron diffraction data, and the deuterium atom positions have been determined for the first time. The structure is orthorhombic: Pnma, a = 9.8269(5) Å, b = 3.9051(2) Å, c = 6.0733(3) Å, V = 233.06 Å 3, D x = 3.466 g cm -3, Rwp = 3.93%, Rp = 2.95%, reduced X2 = 4.774 for 81 variables. Although the data were collected at 12 K, the H atoms have large thermal parameters suggesting the possibility of some disorder. Relationships of the structure to the structures of YOOH, SrBr 2, SrI 2, and SrBr 2 · H 2O are discussed.

  3. Crystal Structure of a Fructokinase Homolog from Halothermothrix orenii

    SciTech Connect

    Khiang, C.; Seetharaman, J; Kasprzak, J; Cherlyn, N; Patel, B; Love, C; Bujnicki, J; Sivaraman, J

    2010-01-01

    Fructokinase (FRK; EC 2.7.1.4) catalyzes the phosphorylation of D-fructose to D-fructose 6-phosphate (F6P). This irreversible and near rate-limiting step is a central and regulatory process in plants and bacteria, which channels fructose into a metabolically active state for glycolysis. Towards understanding the mechanism of FRK, here we report the crystal structure of a FRK homolog from a thermohalophilic bacterium Halothermothrix orenii (Hore{_}18220 in sequence databases). The structure of the Hore{_}18220 protein reveals a catalytic domain with a Rossmann-like fold and a b-sheet 'lid' for dimerization. Based on comparison of Hore{_}18220 to structures of related proteins, we propose its mechanism of action, in which the lid serves to regulate access to the substrate binding sites. Close relationship of Hore{_}18220 and plant FRK enzymes allows us to propose a model for the structure and function of FRKs.

  4. Single crystal growth and X-ray structure analysis of non-peripheral octahexyl phthalocyanine

    NASA Astrophysics Data System (ADS)

    Ohmori, Masashi; Nakano, Chika; Higashi, Takuya; Miyano, Tetsuya; Tohnai, Norimitsu; Fujii, Akihiko; Ozaki, Masanori

    2016-07-01

    The single-crystal structure of metal-free non-peripheral octahexyl-substituted phthalocyanine (C6PcH2) has been investigated by single-crystal X-ray structure analysis. Two types of C6PcH2 single crystal, bulk and needle crystals, were separately grown by controlling the recrystallization conditions. The structures of the two types of crystal were determined, and were found to be completely different, that is, C6PcH2 exhibits structural polymorphism. It has been clarified that the C6PcH2 microcrystals in thin films used in previously reported electronic devices have the needle structure.

  5. First single crystal growth and structural analysis of superconducting layered bismuth oxyselenide; La(O,F)BiSe{sub 2}

    SciTech Connect

    Tanaka, Masashi; Nagao, Masanori; Matsushita, Yoshitaka; Fujioka, Masaya; Denholme, Saleem J.; Yamaguchi, Takahide; Takeya, Hiroyuki; Takano, Yoshihiko

    2014-11-15

    Single crystals of La(O,F)BiSe{sub 2} were successfully grown for the first time by a CsCl flux method. Single crystal X-ray structural analysis clearly showed that La(O,F)BiSe{sub 2} crystallizes with space group P4/nmm (lattice parameters a=4.1408(2) Å, c=14.1096(6) Å). The structure is composed of alternating BiSe{sub 2} and La(O,F) layers. The bond distances and angles are similar to those of La(O,F)BiS{sub 2}. The bond valence sum calculation indicates the refined structure is slightly cation rich, suggesting the charge neutrality should be kept by modification of valence state of the cations. Magnetic susceptibility and resistivity measurements showed the compound is a superconductor with a transition temperature of 3.6 K, which is higher than that of as-grown La(O,F)BiS{sub 2}. - Graphical abstract: Single crystal La(O,F)BiSe{sub 2} has been prepared by a CsCl flux method. The structural analysis implies that La(O,F)BiSe{sub 2} is a potential superconductor having a higher T{sub c} under high pressure. - Highlights: • Single crystals of La(O,F)BiSe{sub 2} were grown by a CsCl flux method. • Crystal structure of La(O,F)BiSe{sub 2} was determined by single crystal X-ray analysis. • La(O,F)BiSe{sub 2} shows superconductivity with a transition temperature of 3.6 K. • Bonding nature and superconductivity of La(O,F)BiSe{sub 2} are discussed.

  6. Lexical distributional cues, but not situational cues, are readily used to learn abstract locative verb-structure associations.

    PubMed

    Twomey, Katherine E; Chang, Franklin; Ambridge, Ben

    2016-08-01

    Children must learn the structural biases of locative verbs in order to avoid making overgeneralisation errors (e.g., (∗)I filled water into the glass). It is thought that they use linguistic and situational information to learn verb classes that encode structural biases. In addition to situational cues, we examined whether children and adults could use the lexical distribution of nouns in the post-verbal noun phrase of transitive utterances to assign novel verbs to locative classes. In Experiment 1, children and adults used lexical distributional cues to assign verb classes, but were unable to use situational cues appropriately. In Experiment 2, adults generalised distributionally-learned classes to novel verb arguments, demonstrating that distributional information can cue abstract verb classes. Taken together, these studies show that human language learners can use a lexical distributional mechanism that is similar to that used by computational linguistic systems that use large unlabelled corpora to learn verb meaning.

  7. Crystal Structure of the Japanese Encephalitis Virus Envelope Protein

    SciTech Connect

    Luca, Vincent C.; AbiMansour, Jad; Nelson, Christopher A.; Fremont, Daved H.

    2012-03-13

    Japanese encephalitis virus (JEV) is the leading global cause of viral encephalitis. The JEV envelope protein (E) facilitates cellular attachment and membrane fusion and is the primary target of neutralizing antibodies. We have determined the 2.1-{angstrom} resolution crystal structure of the JEV E ectodomain refolded from bacterial inclusion bodies. The E protein possesses the three domains characteristic of flavivirus envelopes and epitope mapping of neutralizing antibodies onto the structure reveals determinants that correspond to the domain I lateral ridge, fusion loop, domain III lateral ridge, and domain I-II hinge. While monomeric in solution, JEV E assembles as an antiparallel dimer in the crystal lattice organized in a highly similar fashion as seen in cryo-electron microscopy models of mature flavivirus virions. The dimer interface, however, is remarkably small and lacks many of the domain II contacts observed in other flavivirus E homodimers. In addition, uniquely conserved histidines within the JEV serocomplex suggest that pH-mediated structural transitions may be aided by lateral interactions outside the dimer interface in the icosahedral virion. Our results suggest that variation in dimer structure and stability may significantly influence the assembly, receptor interaction, and uncoating of virions.

  8. Crystal Structure of Baculovirus RNA Triphosphatase Complexed with Phosphate

    SciTech Connect

    Changela, Anita; Martin, Alexandra; Shuman, Stewart; Mondragon, Alfonso

    2010-03-05

    Baculovirus RNA 5'-triphosphatase (BVP) exemplifies a family of RNA-specific cysteine phosphatases that includes the RNA triphosphatase domains of metazoan and plant mRNA capping enzymes. Here we report the crystal structure of BVP in a phosphate-bound state at 1.5 {angstrom} resolution. BVP adopts the characteristic cysteine-phosphatase {alpha}/{beta} fold and binds two phosphate ions in the active site region, one of which is proposed to mimic the phosphate of the product complex after hydrolysis of the covalent phosphoenzyme intermediate. The crystal structure highlights the role of backbone amides and side chains of the P-loop motif {sup 118}HCTHGXNRT{sup 126} in binding the cleavable phosphate and stabilizing the transition state. Comparison of the BVP structure to the apoenzyme of mammalian RNA triphosphatase reveals a concerted movement of the Arg-125 side chain (to engage the phosphate directly) and closure of an associated surface loop over the phosphate in the active site. The structure highlights a direct catalytic role of Asn-124, which is the signature P-loop residue of the RNA triphosphatase family and a likely determinant of the specificity of BVP for hydrolysis of phosphoanhydride linkages.

  9. The crystal structure of superoxide dismutase from Plasmodium falciparum

    PubMed Central

    Boucher, Ian W; Brzozowski, Andrzej M; Brannigan, James A; Schnick, Claudia; Smith, Derek J; Kyes, Sue A; Wilkinson, Anthony J

    2006-01-01

    Background Superoxide dismutases (SODs) are important enzymes in defence against oxidative stress. In Plasmodium falciparum, they may be expected to have special significance since part of the parasite life cycle is spent in red blood cells where the formation of reactive oxygen species is likely to be promoted by the products of haemoglobin breakdown. Thus, inhibitors of P. falciparum SODs have potential as anti-malarial compounds. As a step towards their development we have determined the crystal structure of the parasite's cytosolic iron superoxide dismutase. Results The cytosolic iron superoxide dismutase from P. falciparum (PfFeSOD) has been overexpressed in E. coli in a catalytically active form. Its crystal structure has been solved by molecular replacement and refined against data extending to 2.5 Å resolution. The structure reveals a two-domain organisation and an iron centre in which the metal is coordinated by three histidines, an aspartate and a solvent molecule. Consistent with ultracentrifugation analysis the enzyme is a dimer in which a hydrogen bonding lattice links the two active centres. Conclusion The tertiary structure of PfFeSOD is very similar to those of a number of other iron-and manganese-dependent superoxide dismutases, moreover the active site residues are conserved suggesting a common mechanism of action. Comparison of the dimer interfaces of PfFeSOD with the human manganese-dependent superoxide dismutase reveals a number of differences, which may underpin the design of parasite-selective superoxide dismutase inhibitors. PMID:17020617

  10. Diterbium hepta­nickel: a crystal structure redetermination

    PubMed Central

    Levytskyy, Volodymyr; Babizhetskyy, Volodymyr; Kotur, Bohdan; Smetana, Volodymyr

    2014-01-01

    The crystal structure of the title compound, Tb2Ni7, was redetermined from single-crystal X-ray diffraction data. In comparison with previous studies based on powder X-ray diffraction data [Lemaire et al. (1967). C. R. Acad. Sci. Ser. B, 265, 1280–1282; Lemaire & Paccard (1969). Bull. Soc. Fr. Mineral. Cristallogr. 92, 9–16; Buschow & van der Goot (1970). J. Less-Common Met. 22, 419–428], the present redetermination affords refined coordinates and anisotropic displacement parameters for all atoms. A partial occupation for one Tb atom results in the non-stoichiometric composition Tb1.962 (4)Ni7. The title compound adopts the Ce2Ni7 structure type and can also be derived from the CaCu5 structure type as an inter­growth structure. The asymmetric unit contains two Tb sites (both site symmetries 3m.) and five Ni sites (.m., mm2, 3m., 3m., -3m.). The two different coordination polyhedra of Tb are a Frank–Kasper polyhedron formed by four Tb and 12 Ni atoms and a pseudo Frank–Kasper polyhedron formed by two Tb and 18 Ni atoms. The four different coordination polyhedra of Ni are Frank–Kasper icosa­hedra formed by five Tb and seven Ni atoms, four Tb and eight Ni atoms, three Tb and nine Ni atoms, and six Tb and six Ni atoms, respectively. PMID:25249871

  11. Crystal Structure of Rat Carnitine Palmitoyltransferase II (CPT-II)

    SciTech Connect

    Hsiao,Y.; Jogl, G.; Esser, V.; Tong, L.

    2006-01-01

    Carnitine palmitoyltransferase II (CPT-II) has a crucial role in the {beta}-oxidation of long-chain fatty acids in mitochondria. We report here the crystal structure of rat CPT-II at 1.9 Angstroms resolution. The overall structure shares strong similarity to those of short- and medium-chain carnitine acyltransferases, although detailed structural differences in the active site region have a significant impact on the substrate selectivity of CPT-II. Three aliphatic chains, possibly from a detergent that is used for the crystallization, were found in the structure. Two of them are located in the carnitine and CoA binding sites, respectively. The third aliphatic chain may mimic the long-chain acyl group in the substrate of CPT-II. The binding site for this aliphatic chain does not exist in the short- and medium-chain carnitine acyltransferases, due to conformational differences among the enzymes. A unique insert in CPT-II is positioned on the surface of the enzyme, with a highly hydrophobic surface. It is likely that this surface patch mediates the association of CPT-II with the inner membrane of the mitochondria.

  12. Crystal Structure of Cruxrhodopsin-3 from Haloarcula vallismortis

    PubMed Central

    Chan, Siu Kit; Kitajima-Ihara, Tomomi; Fujii, Ryudoh; Gotoh, Toshiaki; Murakami, Midori; Ihara, Kunio; Kouyama, Tsutomu

    2014-01-01

    Cruxrhodopsin-3 (cR3), a retinylidene protein found in the claret membrane of Haloarcula vallismortis, functions as a light-driven proton pump. In this study, the membrane fusion method was applied to crystallize cR3 into a crystal belonging to space group P321. Diffraction data at 2.1 Å resolution show that cR3 forms a trimeric assembly with bacterioruberin bound to the crevice between neighboring subunits. Although the structure of the proton-release pathway is conserved among proton-pumping archaeal rhodopsins, cR3 possesses the following peculiar structural features: 1) The DE loop is long enough to interact with a neighboring subunit, strengthening the trimeric assembly; 2) Three positive charges are distributed at the cytoplasmic end of helix F, affecting the higher order structure of cR3; 3) The cytoplasmic vicinity of retinal is more rigid in cR3 than in bacteriorhodopsin, affecting the early reaction step in the proton-pumping cycle; 4) the cytoplasmic part of helix E is greatly bent, influencing the proton uptake process. Meanwhile, it was observed that the photobleaching of retinal, which scarcely occurred in the membrane state, became significant when the trimeric assembly of cR3 was dissociated into monomers in the presence of an excess amount of detergent. On the basis of these observations, we discuss structural factors affecting the photostabilities of ion-pumping rhodopsins. PMID:25268964

  13. Structural chemistry and number theory amalgamized: crystal structure of Na11Hg52.

    PubMed

    Hornfeck, Wolfgang; Hoch, Constantin

    2015-12-01

    The recently elucidated crystal structure of the technologically important amalgam Na11Hg52 is described by means of a method employing some fundamental concept of number theory, namely modular arithmetical (congruence) relations observed between a slightly idealized set of atomic coordinates. In combination with well known ideas from group theory, regarding lattice-sublattice transformations, these allow for a deeper mutual understanding of both and provide the structural chemist with a slightly different kind of spectacles, thus enabling a distinct viw on complex crystal structures in general.

  14. Crystallization, X-Ray Structure Determination and Structure-Based Drug Design for Targeted Malarial Enzymes

    DTIC Science & Technology

    1998-07-01

    COOPERATIVE AGREEMENT NUMBER DAMD17-95-2-5007 TITLE: Crystallization, X-ray Structure Determination and Structure-Based Drug Design for...approach for the develpment of anti-malarial agent using structure-based drug design . This technique will enable us to identify active site inhibitors...based drug design project high resolution three domensional structure of the enzyme - inhibitor complex provides the basis for further modifications

  15. Structure, Hydrodynamics, and Phase Transition of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2000-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enable the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable condensed phase fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new liquid crystal physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and

  16. The crystal structure, electronic, and magnetic properties of NaPd{sub 3}Ge{sub 2}

    SciTech Connect

    Ali, Mazhar N.; Rohr, Fabian von; Campana, C.; Schilling, Andreas; Cava, R.J.

    2015-10-15

    Highlights: • Correct crystal structure of NaPd{sub 3}Ge{sub 2} is solved by single crystal X-ray diffraction. • NaPd{sub 3}Ge{sub 2} is found to crystallize in the ErRh{sub 3}Si{sub 2} structure type. • NaPd{sub 3}Si{sub 2}, NaPd{sub 3}Ge{sub 2} and NaPd{sub 3}Sn{sub 2} are found to be metals down to 2 K. • All three compounds show a weak diamagnetic response down to 2 K. • Trend of p-block atom dimer breaking as function of size. - Abstract: Crystals of NaPd{sub 3}X{sub 2}, (X = Si, Ge, Sn) were synthesized and their crystal structures investigated by single crystal X-ray diffraction. The previously reported structures of NaPd{sub 3}Si{sub 2} and NaPd{sub 3}Sn{sub 2} were confirmed. NaPd{sub 3}Ge{sub 2} was found to have a different unit cell from that originally reported; therefore the structure was solved. It is an orthorhombically distorted version of the hexagonal CeCo{sub 3}Be{sub 2}-type structure, in space group Imma, with cell parameters a = 7.244(1) Å, b = 9.938(1) Å, c = 5.767(2) Å. The originally reported cell is explained through triple twinning of the true cell. The structure of NaPd{sub 3}Ge{sub 2} fits the trend of decreasing X–X dimerization as a function of increasing period from Si–Sn. All three compounds are metals showing weak diamagnetism with increasing resistivity from NaPd{sub 3}Si{sub 2}–NaPd{sub 3}Sn{sub 2}; no superconductivity is observed down to 2 K.

  17. Unusual formation of single-crystal manganese sulfide microboxes co-mediated by the cubic crystal structure and shape.

    PubMed

    Zhang, Lei; Zhou, Liang; Wu, Hao Bin; Xu, Rong; Lou, Xiong Wen David

    2012-07-16

    Kept cubic: MnS microboxes, which act as an anode material for lithium ion batteries, are synthesized by a simple H(2)S gas sulfidation approach (TEM images show porous and hollow microcubes and a microbox). The formation of the single crystals is aided by the intrinsic cubic crystal structure and the nearly cubic shape of the MnCO(3) precursor.

  18. Crystal Structure of the Human Ephrin-A5 Ectodomain

    SciTech Connect

    Nikolov,D.; Li, C.; Lackmann, M.; Jeffrey, P.; Himanen, J.

    2007-01-01

    The Eph receptors, the largest subfamily of receptor tyrosine kinases, and their ephrin ligands are important mediators of cell-cell communication regulating cell attachment, pathfinding, and mobility in the nervous and cardiovascular systems. Recent structural studies have revealed unique molecular features that explain many of the biochemical and signaling properties of Ephs and ephrins. Nevertheless, open questions remain, including understanding the precise molecular mechanism underlining their binding-partner preferences and subclass specificity. In this study, we have determined and present the crystal structure of the extracellular domain of ephrin-A5--the first structure of an unbound A-class ephrin. The structure, determined at 2.1 Angstroms resolution, is a variation of the Greek key {beta}-barrel folding topology, containing eight {beta}-strands, and stabilized by two disulphide bonds. Overall, ephrin-A5 is structurally very similar to ephrin-B1 and ephrin-B2 but, unlike ephrin-B2, it does not show dimerization either in solution or in the crystals. Comparing free ephrin-A5 to the previously published structure of EphB2-bound ephrin-A5 reveals that significant conformational changes occur only around the G-H ephrin loop that upon binding bends toward the receptor. Interestingly, the G-H loop undergoes a very similar conformational rearrangement in ephrin-B2 upon receptor binding. The results of this study further emphasize the importance of the G-H loop for receptor recognition and selectivity, and could serve as a starting point for the development of structure-based Eph antagonists.

  19. On the reliability of peptide nonplanarity seen in ultra‐high resolution crystal structures

    PubMed Central

    Brereton, Andrew E.

    2016-01-01

    Abstract Ultra‐high resolution protein crystal structures have been considered as relatively reliable sources for defining details of protein geometry, such as the extent to which the peptide unit deviates from planarity. Chellapa and Rose (Proteins 2015; 83:1687) recently called this into question, reporting that for a dozen representative protein structures determined at ∼1 Å resolution, the diffraction data could be equally well fit with models restrained to have highly planar peptides, i.e. having a standard deviation of the ω torsion angles of only ∼1° instead of the typically observed value of ∼6°. Here, we document both conceptual and practical shortcomings of that study and show that the more tightly restrained models are demonstrably incorrect and do not fit the diffraction data equally well. We emphasize the importance of inspecting electron density maps when investigating the agreement between a model and its experimental data. Overall, this report reinforces that modern standard refinement protocols have been well‐conceived and that ultra‐high resolution protein crystal structures, when evaluated carefully and used with an awareness of their levels of coordinate uncertainty, are powerful sources of information for providing reliable information about the details of protein geometry. PMID:26779991

  20. 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

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

    ERIC Educational Resources Information Center

    Bindel, Thomas H.

    2008-01-01

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

  2. Supressed Water Crystallization in Nano-Structured Physical Hydrogel

    NASA Astrophysics Data System (ADS)

    Wiener, Clinton; Vogt, Bryan; Weiss, Robert

    2015-03-01

    Suppressed water crystallization occurs in some organisms, such as the common wood frog, which allows it to hibernate in a frozen state without damage to its cells. Knowledge of the behavior of supercooled water and alternate ice forms may have many implications to many fields of science. Supercooling of water by several degrees below the normal freezing point is often observed in hydrogels that have attractive interactions with water, e.g., hydrogen bonding. Repulsive confinement, such as in hydrophobic porous carbon, can have even more significant effects on the supercooling of the entrapped water. This talk describes the freezing behavior in nano-structured, hydrophobically modified poly(dimethyl acrylamide) hydrogels that possess attractive and repulsive interactions with water and are physically crosslinked by hydrophobic nanodomains. Three distinct water freezing regimes were observed in the hydrogel swollen to about 50% water by weight. Differential scanning calorimetry detected three crystallization exotherms at 254K, 244K, and 227K. Quasi-elastic neutron scattering experiments have shown that although the water mobility was suppressed at room temperature, the water remained significantly mobile below the normal freezing point of water. The talk will discuss how tuning the concentration of the hydrophobic composition of the hydrogel affects the porous length scales in the hydrogel, which may alter the state of water and the crystal form produced by supercooling.

  3. Crystal structure and vibrational spectra of betaine hydrogen selenate monohydrate

    NASA Astrophysics Data System (ADS)

    Baran, J.; Drozd, M.; Lis, T.; Śledź, M.; Barnes, A. J.; Ratajczak, H.

    1995-11-01

    The crystal structure of betaine hydrogen selenate monohydrate, (C 5H 12NO 2) +·(HSeO 4) -·(H 2O), BHSeH 2O, has been determined by X-ray diffraction as monoclinic, space group {P2 1}/{c} with a = 6.674(6), b = 11.912(9), c = 14.156(14) A, β = 100.61(4)° and Z = 4. It comprises protonated betaine moieties (betainium cations), hydrogen selenate anions and water molecules which are held together by a number of hydrogen bonds and form infinite chains. Two types of four-membered centrosymmetric rings are distinguished in the chain. The two rings share a common side. Powder FT-IR and FT-Raman spectra were measured for the title crystal, the dehydrated crystal (betaine hydrogen selenate, BHSe) and their deuterated analogues. Assignments of the observed bands to vibrations of the hydrogen bonds and internal vibrations of the hydrogen selenate anions and the betainium cations are proposed. DSC data are also presented.

  4. Natural pseudowollastonite: Crystal structure, associated minerals, and geological context

    NASA Astrophysics Data System (ADS)

    Seryotkin, Yurii V.; Sokol, Ella V.; Kokh, Svetlana N.

    2012-03-01

    Pseudowollastonite, an extremely rare constituent of ultrahigh-temperature combustion metamorphic and igneous rocks, has been found as a rock-forming mineral in Ca-rich paralava veins of Nabi Musa fossil mud volcano (Dead Sea area). Pseudowollastonite-bearing paralavas are the products of combustion metamorphism associated with spontaneous burning of methane. The melt began to crystallize at 1480-1500 °C about the ambient pressure. Pseudowollastonite enters two mineral assemblages: (1) rankinite, larnite, nagelschmidtite, wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, cuspidine, and fluorapatite; (2) parawollastonite (2M), wollastonite (1T), gehlenite-rich melilite, Ti-rich andradite, fluorellestadite. In this study we present the first single-crystal structure determination of natural pseudowollastonite. Pseudowollastonite from Nabi Musa dome is stoichiometric CaSiO3 and belongs to the most widespread four-layer polytype: a = 6.83556(10) Å, b = 11.86962(18) Å, c = 19.6255(3) Å, β = 90.6805(13)°, V = 1592.21(4) Å3, space group C2/c. We argue that pseudowollastonite is so scarce in nature because its formation requires joint action of several uncommon factors: availability of hot melts of T > 1200 °C that bear free calcium but are poor in Mg and Fe (mostly as Fe3 +) and their crystallization in the shallow crust followed by quenching.

  5. Phase-field-crystal methodology for modeling of structural transformations.

    PubMed

    Greenwood, Michael; Rottler, Jörg; Provatas, Nikolas

    2011-03-01

    We introduce and characterize free-energy functionals for modeling of solids with different crystallographic symmetries within the phase-field-crystal methodology. The excess free energy responsible for the emergence of periodic phases is inspired by classical density-functional theory, but uses only a minimal description for the modes of the direct correlation function to preserve computational efficiency. We provide a detailed prescription for controlling the crystal structure and introduce parameters for changing temperature and surface energies, so that phase transformations between body-centered-cubic (bcc), face-centered-cubic (fcc), hexagonal-close-packed (hcp), and simple-cubic (sc) lattices can be studied. To illustrate the versatility of our free-energy functional, we compute the phase diagram for fcc-bcc-liquid coexistence in the temperature-density plane. We also demonstrate that our model can be extended to include hcp symmetry by dynamically simulating hcp-liquid coexistence from a seeded crystal nucleus. We further quantify the dependence of the elastic constants on the model control parameters in two and three dimensions, showing how the degree of elastic anisotropy can be tuned from the shape of the direct correlation functions.

  6. Crystal structure and spectroscopic investigations of an organic monophosphate

    SciTech Connect

    Dhaouadi, H.; Marouani, H. Rzaigui, M.; Madani, A.

    2008-12-01

    Single crystals of (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} are synthesized in water by interaction of H{sub 3}PO{sub 4} and (p-ClC{sub 6}H{sub 4}NH{sub 2}). This compound crystallizes in the orthorhombic system with the Pbca space group. Its unit-cell parameters are a = 9.724(3), b = 7.861(1), c = 25.078(6) A, V = 1917.1(6) A{sup 3} and Z = 8. The crystal structure has been solved and refined to R = 0.039, using 4298 independent reflections. The atomic arrangement can be described by inorganic layers parallel to ab plane, between which the organic cations are located. This compound exhibits a reversible phase transition at 403 K. The electrical conductivity measurements show that the (p-ClC{sub 6}H{sub 4}NH{sub 3})H{sub 2}PO{sub 4} has a conductivity value which goes from {sigma} = 0.88 x 10{sup -6} {omega}{sup -1} cm{sup -1} at room temperature (293 K) to 3.31 x 10{sup -4} {omega}{sup -1} cm{sup -1} at 433 K. Its characterisation by TA, NMR and IR is reported too.

  7. Germanium FCC structure from a colloidal crystal template

    SciTech Connect

    Miguez, H.; Meseguer, F.; Lopez, C.; Holgado, M.; Andreasen, G.; Mifsud, A.; Fornes, V.

    2000-05-16

    Here, the authors show a method to fabricate a macroporous structure in which the pores, essentially identical, arrange regularly in a face-centered cubic (FCC) lattice. The result is a network of air spheres in a germanium medium. This structure presents the highest dielectric contrast ({epsilon}{sub Ge}/{epsilon}{sub air} = 16) ever achieved in the optical regime in such periodic structures, which could result in important applications in photonics. The authors employ solid silica colloidal crystals (opals) as templates within which a cyclic germanium growth process is carried out. Thus, the three-dimensional periodicity of the host is inherited by the guest. Afterward, the silica is removed and a germanium opal replica is obtained.

  8. Syntheses, spectroscopy and crystal structures of new group 4 metallasiloxanes

    NASA Astrophysics Data System (ADS)

    Voigt, Andreas; Murugavel, Ramaswamy; Roesky, Herbert W.; Schmidt, Hans-Georg

    1997-12-01

    The reactions of the organic-soluble (trimethylsilyl)arylaminosilanetriol RSi(OH) 3 (R = (2,6- i-Pr 2C 6H 3)NSiMe 3) (1) with titanocene dichloride and zirconocene dichloride in dimethoxyethane as the solvent leads to the formation of acyclic and cyclic siloxanes [RSi(OH) 2(OTiCp 2Cl)] (2) and [RSi(OH)(OZrCp 2)O] 2 (3), respectively. The molecular structures of the new products 2 and 3 have been established by means of their analytical and spectral data. Further, in each case the solid-state structure of the compounds has been determined by single crystal X-ray diffraction studies. The EI mass spectral data reveal the presence of higher molecular weight compounds in the gas phase corresponding to the bicyclic or cubic structures of 2 and 3, respectively.

  9. Crystal structure solution from experimentally determined atomic pair distribution functions

    SciTech Connect

    Juhas, P.; Granlund, L.; Gujarathi, S.R.; Duxbury, P.M.; Billinge, S.J.L.

    2010-05-25

    An extension of the Liga algorithm for structure solution from atomic pair distribution functions (PDFs), to handle periodic crystal structures with multiple elements in the unit cell, is described. The procedure is performed in three separate steps. First, pair distances are extracted from the experimental PDF. In the second step the Liga algorithm is used to find unit-cell sites consistent with these pair distances. Finally, the atom species are assigned over the cell sites by minimizing the overlap of their empirical atomic radii. The procedure has been demonstrated on synchrotron X-ray PDF data from 16 test samples. The structure solution was successful for 14 samples, including cases with enlarged supercells. The algorithm success rate and the reasons for the failed cases are discussed, together with enhancements that should improve its convergence and usability.

  10. Crystal Structure of a Lipid G Protein-Coupled Receptor

    SciTech Connect

    Hanson, Michael A; Roth, Christopher B; Jo, Euijung; Griffith, Mark T; Scott, Fiona L; Reinhart, Greg; Desale, Hans; Clemons, Bryan; Cahalan, Stuart M; Schuerer, Stephan C; Sanna, M Germana; Han, Gye Won; Kuhn, Peter; Rosen, Hugh; Stevens, Raymond C

    2012-03-01

    The lyso-phospholipid sphingosine 1-phosphate modulates lymphocyte trafficking, endothelial development and integrity, heart rate, and vascular tone and maturation by activating G protein-coupled sphingosine 1-phosphate receptors. Here, we present the crystal structure of the sphingosine 1-phosphate receptor 1 fused to T4-lysozyme (S1P1-T4L) in complex with an antagonist sphingolipid mimic. Extracellular access to the binding pocket is occluded by the amino terminus and extracellular loops of the receptor. Access is gained by ligands entering laterally between helices I and VII within the transmembrane region of the receptor. This structure, along with mutagenesis, agonist structure-activity relationship data, and modeling, provides a detailed view of the molecular recognition and requirement for hydrophobic volume that activates S1P1, resulting in the modulation of immune and stromal cell responses.

  11. The crystal structure and superconducting properties of monatomic bromine.

    PubMed

    Duan, Defang; Meng, Xing; Tian, Fubo; Chen, Changbo; Wang, Liancheng; Ma, Yanming; Cui, Tian; Liu, Bingbing; He, Zhi; Zou, Guangtian

    2010-01-13

    The crystal structure and superconducting properties of monatomic bromine under high pressure have been studied by first-principles calculations. We have found the following phase transition sequence with increasing pressure: from body-centered orthorhombic (bco, phase II) to body-centered tetragonal structure (bct, phase III) at 126 GPa, then to face-centered cubic structure (fcc, phase IV) at 157 GPa, which is stable at least up to 300 GPa. The calculated superconducting critical temperature T(c) = 1.46 K at 100 GPa is consistent with the experimental value of 1.5 K. In addition, our results of T(c) decrease with increasing pressure in all the monatomic phases of bromine, similar to monatomic iodine. Further calculations show that the decrease of λ with pressure in phase IV is mainly attributed to the weakening of the 'soft' vibrational mode caused by pressure.

  12. Crystal structure of the superantigen staphylococcal enterotoxin type A.

    PubMed Central

    Schad, E M; Zaitseva, I; Zaitsev, V N; Dohlsten, M; Kalland, T; Schlievert, P M; Ohlendorf, D H; Svensson, L A

    1995-01-01

    Staphylococcal enterotoxins are prototype superantigens characterized by their ability to bind to major histocompatibility complex (MHC) class II molecules and subsequently activate a large fraction of T-lymphocytes. The crystal structure of staphylococcal enterotoxin type A (SEA), a 27 kDa monomeric protein, was determined to 1.9 A resolution with an R-factor of 19.9% by multiple isomorphous replacement. SEA is a two domain protein composed of a beta-barrel and a beta-grasp motif demonstrating the same general structure as staphylococcal enterotoxins SEB and TSST-1. Unique for SEA, however, is a Zn2+ coordination site involved in MHC class II binding. Four amino acids including Ser1, His187, His225 and Asp227 were found to be involved in direct coordination of the metal ion. SEA is the first Zn2+ binding enterotoxin that has been structurally determined. Images PMID:7628431

  13. Crystal Structure of a Self-Spliced Group ll Intron

    SciTech Connect

    Toor,N.; Keating, K.; Taylor, S.; Pyle, A.

    2008-01-01

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  14. Crystal structure of Homo sapiens protein LOC79017

    SciTech Connect

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

    2010-02-08

    LOC79017 (MW 21.0 kDa, residues 1-188) was annotated as a hypothetical protein encoded by Homo sapiens chromosome 7 open reading frame 24. It was selected as a target by the Center for Eukaryotic Structural Genomics (CESG) because it did not share more than 30% sequence identity with any protein for which the three-dimensional structure is known. The biological function of the protein has not been established yet. Parts of LOC79017 were identified as members of uncharacterized Pfam families (residues 1-95 as PB006073 and residues 104-180 as PB031696). BLAST searches revealed homologues of LOC79017 in many eukaryotes, but none of them have been functionally characterized. Here, we report the crystal structure of H. sapiens protein LOC79017 (UniGene code Hs.530024, UniProt code O75223, CESG target number go.35223).

  15. Crystal Structure of a Self-Spliced Group II Intron

    SciTech Connect

    Toor, Navtej; Keating, Kevin S.; Taylor, Sean D.; Pyle, Anna Marie

    2008-04-10

    Group II introns are self-splicing ribozymes that catalyze their own excision from precursor transcripts and insertion into new genetic locations. Here we report the crystal structure of an intact, self-spliced group II intron from Oceanobacillus iheyensis at 3.1 angstrom resolution. An extensive network of tertiary interactions facilitates the ordered packing of intron subdomains around a ribozyme core that includes catalytic domain V. The bulge of domain V adopts an unusual helical structure that is located adjacent to a major groove triple helix (catalytic triplex). The bulge and catalytic triplex jointly coordinate two divalent metal ions in a configuration that is consistent with a two-metal ion mechanism for catalysis. Structural and functional analogies support the hypothesis that group II introns and the spliceosome share a common ancestor.

  16. Structure and Chemical Durability of Lead Crystal Glass.

    PubMed

    Angeli, Frédéric; Jollivet, Patrick; Charpentier, Thibault; Fournier, Maxime; Gin, Stéphane

    2016-11-01

    Silicate glasses containing lead, also called lead crystal glasses, are commonly used as food product containers, in particular for alcoholic beverages. Lead's health hazards require major attention, which can first be investigated through the understanding of Pb release mechanisms in solution. The behavior of a commercial crystal glass containing 10.6 mol % of PbO (28.3 wt %) was studied in a reference solution of 4% acetic acid at 22, 40, and 70 °C at early and advanced stages of reaction. High-resolution solid-state (17)O and (29)Si NMR was used to probe the local structure of the pristine and, for the first time, of the altered lead crystal glass. Inserted into the vitreous structure between the network formers as Si-O-Pb bonds, Pb does not form Pb-O-Pb clusters which are expected to be more easily leached. A part of K is located near Pb, forming mixed Si-O-(Pb,K) near the nonbridging oxygens. Pb is always released into the solution following a diffusion-controlled dissolution over various periods of time, at a rate between 1 and 2 orders of magnitude lower than the alkalis (K and Na). The preferential release of alkalis is followed by an in situ repolymerization of the silicate network. Pb is only depleted in the outermost part of the alteration layer. In the remaining part, it stays mainly surrounded by Si in a stable structural configuration similar to that of the pristine glass. A simple model is proposed to estimate the Pb concentration as a function of glass surface, solution volume, temperature, and contact time.

  17. Banded Structure and Domain Arrangements in PbTiO3 Single Crystals

    NASA Astrophysics Data System (ADS)

    Chou, Chen-Chia; Chen, Cheng-Sao

    1998-09-01

    In the present work we report the ferroelectric domain arrangements and characteristics of banded structures observed in flux-grown PbTiO3 single crystals. Investigations of etched crystals indicate that most of the specimens show banded structures which may correspond to surface relief characteristics of as-grown crystals. Banded structures, which are different from domain structures, possess structural characteristics similar to those of martensite variants in various alloys and ceramics. The stresses produced during transformation were relieved by the formation of the banded structures and the 90° domain structures, suggesting that the band structures and 90° domains are the products of self-accommodation in as-grown PbTiO3 crystals during the cubic/tetragonal (C/T) transformation. Image characteristics imply that banded-structure-induced domain intersections may store high strain energy in lead titanate crystals and therefore hinder polarization switching of the crystals.

  18. Crystal structure of rofecoxib bound to human cyclooxygenase-2.

    PubMed

    Orlando, Benjamin J; Malkowski, Michael G

    2016-10-01

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7 Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  19. Refinement of the crystal structure of lithium-bearing uvite

    SciTech Connect

    Rozhdestvenskaya, I. V. Frank-Kamenetskaya, O. V.; Kuznetsova, L. G.; Bannova, I. I.; Bronzova, Yu. M.

    2007-03-15

    The crystal structure of a natural calcium tourmaline, i.e., uvite with a high lithium content (0.51 au per formula (aupf) at the Y site, is refined to R = 0.019, R{sub w} = 0.020, and S = 1.11. It is shown that, in nature, there exist uvites in which the charge balance in the case where the Z site is occupied by trivalent cations is provided by the replacement of part of the divalent magnesium cations at the Y site by univalent cations, divalent calcium cations at the X site by sodium cations, and univalent anions at the W site by oxygen anions. The W site is found to be split into two sites, namely, the W1 and W11 sites (the W1-W11 distance is 0.14 A), which are partially occupied by the fluorine and oxygen anions, respectively. An analysis of the results obtained in this study and the data available in the literature on the crystal structure of uvites allows the conclusion that uvite can be considered a superspecies and that the nomenclature of this mineral group needs refinement with the use of structural data.

  20. Crystal structure of the yeast metacaspase Yca1.

    PubMed

    Wong, Ada Hang-Heng; Yan, Chuangye; Shi, Yigong

    2012-08-24

    Yca1, the only metacaspase in Saccharomyces cerevisiae, is thought to be a clan CD cysteine protease that includes the caspase subfamily. Although yeast is a single cell eukaryote, it can undergo a cell death process reminiscent of apoptosis. Yca1 has been reported to play an important role in the regulation of such apoptotic process. However, the structure and functional mechanism of Yca1 remain largely enigmatic. In this study, we report the crystal structure of the Yca1 metacaspase at 1.7 Å resolution, confirming a caspase-like fold. In sharp contrast to canonical caspases, however, Yca1 exists as a monomer both in solution and in the crystals. Canonical caspase contains six β-strands, with strand β6 pairing up with β6 of another caspase molecule to form a homodimerization interface. In Yca1, an extra pair of antiparallel β-strands forms a continuous β-sheet with the six caspase-common β-strands, blocking potential dimerization. Yca1 was reported to undergo autocatalytic processing in yeast; overexpression in bacteria also led to autoprocessing of Yca1 into two fragments. Unexpectedly, we found that both the autocatalytic processing and the proteolytic activity of Yca1 are greatly facilitated by the presence of calcium (Ca(2+)), but not other divalent cations. Our structural and biochemical characterization identifies Yca1 as a Ca(2+)-activated cysteine protease that may cleave specific substrates during stress response in yeast.

  1. 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.

  2. Crystal Structure of the Vanadate-Inhibited Ca(2+)-ATPase.

    PubMed

    Clausen, Johannes D; Bublitz, Maike; Arnou, Bertrand; Olesen, Claus; Andersen, Jens Peter; Møller, Jesper Vuust; Nissen, Poul

    2016-04-05

    Vanadate is the hallmark inhibitor of the P-type ATPase family; however, structural details of its inhibitory mechanism have remained unresolved. We have determined the crystal structure of sarcoplasmic reticulum Ca(2+)-ATPase with bound vanadate in the absence of Ca(2+). Vanadate is bound at the catalytic site as a planar VO3(-) in complex with water and Mg(2+) in a dephosphorylation transition-state-like conformation. Validating bound VO3(-) by anomalous difference Fourier maps using long-wavelength data we also identify a hitherto undescribed Cl(-) site near the dephosphorylation site. Crystallization was facilitated by trinitrophenyl (TNP)-derivatized nucleotides that bind with the TNP moiety occupying the binding pocket that normally accommodates the adenine of ATP, rationalizing their remarkably high affinity for E2P-like conformations of the Ca(2+)-ATPase. A comparison of the configurations of bound nucleotide analogs in the E2·VO3(-) structure with that in E2·BeF3(-) (E2P ground state analog) reveals multiple binding modes to the Ca(2+)-ATPase.

  3. Potassium and magnesium succinatouranilates - Synthesis and crystal structure

    NASA Astrophysics Data System (ADS)

    Novikov, S. A.; Grigoriev, M. S.; Serezhkina, L. B.; Serezhkin, V. N.

    2017-04-01

    Single crystal X-ray diffraction has been applied to determine the structures of two new uranyl coordination polymers: K2[(UO2)2(C4H4O4)3] (1) and [Mg(H2O)6] [(UO2)2(C4H4O4)3]·2H2O (2), where C4H4O42- is succinate anion. Crystals of 1 and 2 contain polymeric complex anions [(UO2)2(C4H4O4)3]2- with the same A2Q023 crystallochemical formula (A=UO22+, Q02=C4O4H42-), and have layered (1) or chain (2) structure. It has been found, that conformation of succinate ions is one of the factors, which affects the structure of [(UO2)2(C4H4O4)3]2- anions. IR spectra of these new compounds are in good agreement with crystallographic data. Topological analysis of the uranium dicarboxylates with A2Q023 crystallochemical formula has shown the presence of five isomers which differ from each other in coordination sequences and / or dimensionality.

  4. Crystal structure of rofecoxib bound to human cyclooxygenase-2

    SciTech Connect

    Orlando, Benjamin J.; Malkowski, Michael G.

    2016-10-26

    Rofecoxib (Vioxx) was one of the first selective cyclooxygenase-2 (COX-2) inhibitors (coxibs) to be approved for use in humans. Within five years after its release to the public, Vioxx was withdrawn from the market owing to the adverse cardiovascular effects of the drug. Despite the widespread knowledge of the development and withdrawal of Vioxx, relatively little is known at the molecular level about how the inhibitor binds to COX-2. Vioxx is unique in that the inhibitor contains a methyl sulfone moiety in place of the sulfonamide moiety found in other coxibs such as celecoxib and valdecoxib. Here, new crystallization conditions were identified that allowed the structural determination of human COX-2 in complex with Vioxx and the structure was subsequently determined to 2.7- Å resolution. The crystal structure provides the first atomic level details of the binding of Vioxx to COX-2. As anticipated, Vioxx binds with its methyl sulfone moiety located in the side pocket of the cyclooxygenase channel, providing support for the isoform selectivity of this drug.

  5. Research Abstracts.

    ERIC Educational Resources Information Center

    Plotnick, Eric

    2001-01-01

    Presents research abstracts from the ERIC Clearinghouse on Information and Technology. Topics include: classroom communication apprehension and distance education; outcomes of a distance-delivered science course; the NASA/Kennedy Space Center Virtual Science Mentor program; survey of traditional and distance learning higher education members;…

  6. Research Abstracts.

    ERIC Educational Resources Information Center

    Plotnik, Eric

    2001-01-01

    Presents six research abstracts from the ERIC (Educational Resources Information Center) database. Topics include: effectiveness of distance versus traditional on-campus education; improved attribution recall from diversification of environmental context during computer-based instruction; qualitative analysis of situated Web-based learning;…

  7. Abstract Constructions.

    ERIC Educational Resources Information Center

    Pietropola, Anne

    1998-01-01

    Describes a lesson designed to culminate a year of eighth-grade art classes in which students explore elements of design and space by creating 3-D abstract constructions. Outlines the process of using foam board and markers to create various shapes and optical effects. (DSK)

  8. Abstract and keywords.

    PubMed

    Peh, W C G; Ng, K H

    2008-09-01

    The abstract of a scientific paper represents a concise, accurate and factual mini-version of the paper contents. Abstract format may vary according to the individual journal. For original articles, a structured abstract usually consists of the following headings: aims (or objectives), materials and methods, results and conclusion. A few keywords that capture the main topics of the paper help indexing in the medical literature.

  9. Characteristics and crystal structure of bacterial inosine-5'-monophosphate dehydrogenase.

    SciTech Connect

    Zhang, R.; Evans, G.; Rotella, F. J.; Westbrook, E. M.; Beno, D.; Huberman, E.; Joachimiak, A.; Collart, F. R.

    1999-01-01

    IMP dehydrogenase (IMPDH) is an essential enzyme that catalyzes the first step unique to GTP synthesis. To provide a basis for the evaluation of IMPDH inhibitors as antimicrobial agents, we have expressed and characterized IMPDH from the pathogenic bacterium Streptococcus pyogenes. Our results show that the biochemical and kinetic characteristics of S. pyogenes IMPDH are similar to other bacterial IMPDH enzymes. However, the lack of sensitivity to mycophenolic acid and the K{sub m} for NAD (1180 {mu}M) exemplify some of the differences between the bacterial and mammalian IMPDH enzymes, making it an attractive target for antimicrobial agents. To evaluate the basis for these differences, we determined the crystal structure of the bacterial enzyme at 1.9 {angstrom} with substrate bound in the catalytic site. The structure was determined using selenomethionine-substituted protein and multiwavelength anomalous (MAD) analysis of data obtained with synchrotron radiation from the undulator beamline (19ID) of the Structural Biology Center at Argonne's Advanced Photon Source. S. pyogenes IMPDH is a tetramer with its four subunits related by a crystallographic 4-fold axis. The protein is composed of two domains: a TIM barrel domain that embodies the catalytic framework and a cystathione {beta}-synthase (CBS) dimer domain of so far unknown function. Using information provided by sequence alignments and the crystal structure, we prepared several site-specific mutants to examine the role of various active site regions in catalysis. These variants implicate the active site flap as an essential catalytic element and indicate there are significant differences in the catalytic environment of bacterial and mammalian IMPDH enzymes. Comparison of the structure of bacterial IMPDH with the known partial structures from eukaryotic organisms will provide an explanation of their distinct properties and contribute to the design of specific bacterial IMPDH inhibitors.

  10. Crystal structure of human tooth enamel studied by neutron diffraction

    NASA Astrophysics Data System (ADS)

    Ouladdiaf, Bachir; Rodriguez-Carvajal, Juan; Goutaudier, Christelle; Ouladdiaf, Selma; Grosgogeat, Brigitte; Pradelle, Nelly; Colon, Pierre

    2015-02-01

    Crystal structure of human tooth enamel was investigated using high-resolution neutron powder diffraction. Excellent agreement between observed and refined patterns is obtained, using the hexagonal hydroxyapatite model for the tooth enamel, where a large hydroxyl deficiency ˜70% is found in the 4e site. Rietveld refinements method combined with the difference Fourier maps have revealed, however, that the hydroxyl ions are not only disordered along the c-axis but also within the basal plane. Additional H ions located at the 6h site and forming HPO42- anions were found.

  11. Crystal structure of tris-(piperidinium) hydrogen sulfate sulfate.

    PubMed

    Lukianova, Tamara J; Kinzhybalo, Vasyl; Pietraszko, Adam

    2015-12-01

    In the title molecular salt, 3C5H12N(+)·HSO4 (-)·SO4 (2-), each cation adopts a chair conformation. In the crystal, the hydrogen sulfate ion is connected to the sulfate ion by a strong O-H⋯O hydrogen bond. The packing also features a number of N-H⋯O hydrogen bonds, which lead to a three-dimensional network structure. The hydrogen sulfate anion accepts four hydrogen bonds from two cations, whereas the sulfate ion, as an acceptor, binds to five separate piperidinium cations, forming seven hydrogen bonds.

  12. Study of the crystal structure of silicon nanoislands on sapphire

    SciTech Connect

    Krivulin, N. O. Pirogov, A. V.; Pavlov, D. A.; Bobrov, A. I.

    2015-02-15

    The results of studies of the crystal structure of silicon nanoislands on sapphire are reported. It is shown that the principal defects in silicon nanoislands on sapphire are twinning defects. As a result of the formation of such defects, different crystallographic orientations are formed in silicon nanoislands on sapphire. In the initial stages of the molecular-beam epitaxy of silicon on sapphire, there are two basic orientations: the (001) orientation parallel to the surface and the (001) orientation at an angle of 70° to the surface.

  13. Electrical and Structural Characterization of Web Dendrite Crystals

    NASA Technical Reports Server (NTRS)

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

    1985-01-01

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

  14. Photonic crystal digital alloys and their band structure properties.

    PubMed

    Lee, Jeongkug; Kim, Dong-Uk; Jeon, Heonsu

    2011-09-26

    We investigated semi-disordered photonic crystals (PCs), digital alloys, and made thorough comparisons with their counterparts, random alloys. A set of diamond lattice PC digital alloys operating in a microwave regime were prepared by alternately stacking two kinds of sub-PC systems composed of alumina and silica spheres of the same size. Measured transmission spectra as well as calculated band structures revealed that when the digital alloy period is short, band-gaps of the digital alloys are practically the same as those of the random alloys. This study indicates that the concept of digital alloys holds for photons in PCs as well.

  15. Structure and Dynamics of Freely Suspended Liquid Crystals

    NASA Technical Reports Server (NTRS)

    Clark, Noel A.

    2004-01-01

    Smectic liquid crystals are phases of rod shaped molecules organized into one dimensionally (1 D) periodic arrays of layers, each layer being between one and two molecular lengths thick. In the least ordered smectic phases, the smectics A and C, each layer is a two dimensional (2D) liquid. Additionally there are a variety of more ordered smectic phases having hexatic short range translational order or 2D crystalline or quasi long range translational order within the layers. The inherent fluid-layer structure and low vapor pressure of smectic liquid crystals enables the long term stabilization of freely suspended, single component, layered fluid films as thin as 30A, a single molecular layer. The layering forces the films to be an integral number of smectic layers thick, quantizing their thickness in layer units and forcing a film of a particular number of layers to be physically homogeneous with respect to its layer structure over its entire area. Optical reflectivity enables the precise determination of the number of layers. These ultrathin freely suspended liquid crystal films are structures of fundamental interest in condensed matter and fluid physics. They are the thinnest known stable fluid structures and have the largest surface-to-volume ratio of any stable fluid preparation, making them ideal for the study of the effects of reduced dimensionality on phase behavior and on fluctuation and interface phenomena. Their low vapor pressure and quantized thickness enable the effective use of microgravity to extend the study of basic capillary phenomena to ultrathin fluid films. Freely suspended films have been a wellspring of new LC physics. They have been used to provide unique experimental conditions for the study of condensed phase transitions in two dimensions. They are the only system in which the hexatic has been unambiguously identified as a phase of matter, and the only physical system in which fluctuations of a 2D XY system and Kosterlitz Thouless phase

  16. Crystal structures of RPt{sub 3-x}Si{sub 1-y}(R=Y, Tb, Dy, Ho, Er, Tm, Yb) studied by single crystal X-ray diffraction

    SciTech Connect

    Gribanov, Alexander; Grytsiv, Andriy; Rogl, Peter; Seropegin, Yurii; Giester, Gerald

    2009-07-15

    The crystal structures of ternary compounds RPt{sub 3-x}Si{sub 1-y}(R=Y, Tb, Dy, Ho, Er, Tm, Yb) have been elucidated from X-ray single crystal CCD data. All compounds are isotypic and crystallize in the tetragonal space group P4/mbm. The general formula RPt{sub 3-x}Si{sub 1-y} arises from defects: x{approx}0.20, y{approx}0.14. The crystal structure of RPt{sub 3-x}Si{sub 1-y} can be considered as a packing of four types of building blocks which derive from the CePt{sub 3}B-type unit cell by various degrees of distortion and Pt, Si-defects. - Graphical Abstract: Electron density in RPt{sub 3-x}Si{sub 1-y} at 0, 1/2 , 0.

  17. Synthesis, crystal structure and electronic structure of the binary phase Rh2Cd5

    NASA Astrophysics Data System (ADS)

    Koley, Biplab; Chatterjee, S.; Jana, Partha P.

    2017-02-01

    A new phase in the Rh-Cd binary system - Rh2Cd5 has been identified and characterized by single crystal X-ray diffraction and Energy dispersive X-ray analysis. The stoichiometric compound Rh2Cd5 crystallizes with a unit cell containing 14 atoms, in the orthorhombic space group Pbam (55). The crystal structure of Rh2Cd5 can be described as a defect form of the In3Pd5 structure with ordered vacancies, formed of two 2D atomic layers with the stacking sequence: ABAB. The A type layers consist of (3.6.3.6)-Kagomé nets of Cd atoms while the B type layers consist of (35) (37)- nets of both Cd and Rh atoms. The stability of this line phase is investigated by first principle electronic structure calculations on the model of ordered Rh2Cd5.

  18. Crystal structure of cbbF from Zymomonas mobilis and its functional implication

    SciTech Connect

    Hwang, Hyo-Jeong; Park, Suk-Youl; Kim, Jeong-Sun

    2014-02-28

    Highlights: • The crystal structure of one cbbF from Zymomonas mobilis was revealed. • Scores of residues form two secondary structures with a non-polar protruded residue. • It exists as a dimeric form in solution. - Abstract: A phosphate group at the C1-atom of inositol-monophosphate (IMP) and fructose-1,6-bisphosphate (FBP) is hydrolyzed by a phosphatase IMPase and FBPase in a metal-dependent way, respectively. The two enzymes are almost indiscernible from each other because of their highly similar sequences and structures. Metal ions are bound to residues on the β1- and β2-strands and one mobile loop. However, FBP has another phosphate and FBPases exist as a higher oligomeric state, which may discriminate FBPases from IMPases. There are three genes annotated as FBPases in Zymomonas mobilis, termed also cbbF (ZmcbbF). The revealed crystal structure of one ZmcbbF shows a globular structure formed by five stacked layers. Twenty-five residues in the middle of the sequence form an α-helix and a β-strand, which occupy one side of the catalytic site. A non-polar Leu residue among them is protruded to the active site, pointing out unfavorable access of a bulky charged group to this side. In vitro assays have shown its dimeric form in solution. Interestingly, two β-strands of β1 and β2 are disordered in the ZmcbbF structure. These data indicate that ZmcbbF might structurally belong to IMPase, and imply that its active site would be reorganized in a yet unreported way.

  19. Incompletely-Condensed Fluorinated Silsesquioxane: Synthesis and Crystal Structure

    DTIC Science & Technology

    2011-11-29

    other provision of law, no person shall be subject to any penalty for failing to comply with a collection of information if it does not display a ...ABSTRACT A recently developed sub-class of POSS, fluorinated polyhedral oligomeric silsesquioxane (F-POSS), consists of a Si-O core with a periphery of...incompletely-condensed silsesquioxane, (CF3(CF2)7CH2CH2)8Si8O11(OH)2, has been synthesized via a multi-step synthesis (52% yield). The structure was

  20. Crystal structure, electronic structure, and photoluminescent properties of SrMoO{sub 4}:Tb{sup 3+} phosphors

    SciTech Connect

    Park, Sung Wook; Moon, Byung Kee; Jeong, Jung Hyun; Bae, Jong Seong; Kim, Jung Hwan

    2015-10-15

    Highlights: • SrMoO{sub 4}:Tb{sup 3+} phosphor samples were synthesized at different temperatures. • The crystal and electronic structures, and luminescence properties were studied. • The excitation peak shifts to red with increasing the sintering temperature. • The luminescence mechanism of SrMoO{sub 4}:Tb{sup 3+} was suggested. - Abstract: The experimental and theoretical studies of the optical properties of SrMoO{sub 4}:Tb{sup 3+} phosphors were carried out. The structural, optical, and electronical properties of the phosphors were systematically studied. The phosphor samples were crystallized at different temperatures via a sol–gel method. Excitation spectra of SrMoO{sub 4}:Tb{sup 3+} powder samples exhibited gradual red shift and luminescent intensity changed with increasing the sintering temperature. Such spectral changes depend strongly on the crystallographic properties such as lattice parameters and crystallinity. The shift of the excitation spectra is mainly ascribed to the covalent bond interaction between Mo−O bonds. An energy band model was demonstrated to describe the luminescence mechanism in the material.

  1. 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.

  2. 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.

  3. Theoretical studies of the crystal structure of rare earths and actinides at zero temperature

    SciTech Connect

    Wills, J.M.; Eriksson, O.

    1993-07-01

    Accurate total energy electronic structure calculations have recently been carried out over a range of volumes for selected rare-earth and actinide elements in crystal structures, experimentally observed in these elements. Correct zero temperature crystal structures are obtained, and calculated equilibrium properties are in reasonable agreement with experiment. Results of these calculations indicate that the interactions underlying crystal structure stability are similar in itinerant f-electron metals and transition metals. The stable crystal structure at a particular volume is determined by a balance between one-electron bandwidths and band fillings and the electrostatic energy of the crystal lattice. Broad bands favor high-symmetry, close-packed structures while narrow bands favor low-symmetry, open structures; allowing for expansion as well as contraction, both transition and actinide elements can be stabilized in both low- and high-symmetry crystal structures.

  4. Theoretical studies of the crystal structure of rare earths and actinides at zero temperature

    SciTech Connect

    Wills, J.M. ); Eriksson, O. . Dept. of Physics)

    1993-01-01

    Accurate total energy electronic structure calculations have recently been carried out over a range of volumes for selected rare-earth and actinide elements in crystal structures, experimentally observed in these elements. Correct zero temperature crystal structures are obtained, and calculated equilibrium properties are in reasonable agreement with experiment. Results of these calculations indicate that the interactions underlying crystal structure stability are similar in itinerant f-electron metals and transition metals. The stable crystal structure at a particular volume is determined by a balance between one-electron bandwidths and band fillings and the electrostatic energy of the crystal lattice. Broad bands favor high-symmetry, close-packed structures while narrow bands favor low-symmetry, open structures; allowing for expansion as well as contraction, both transition and actinide elements can be stabilized in both low- and high-symmetry crystal structures.

  5. Single crystal structures of thallium (I) thorium fluorides and crystal chemistry of monovalent tetravalent cation pentafluorides

    NASA Astrophysics Data System (ADS)

    Oudahmane, Abdelghani; El-Ghozzi, Malika; Jouffret, Laurent; Avignant, Daniel

    2015-12-01

    Two thallium (I) thorium (IV) fluorides, TlTh3F13 and TlThF5 were obtained by solid state synthesis and their crystal structures determined from single crystal X-ray diffraction data recorded at room temperature with an APEX-II CCD diffractometer. TlTh3F13 is orthorhombic, space group Pmc21, with a=8.1801(2) Å, b=7.4479(2) Å, c=8.6375(2) Å, V=526.24(2) Å3, Z=2 and TlThF5 is monoclinic, space group P21/n, with a=8.1128(5) Å, b=7.2250(4) Å, c=8.8493(6) Å, β=116.683(3)°, V=463.46(5) Å3, Z=4. The structure of TlTh3F13 comprises layers of corner and edge-sharing ThF9 polyhedra further linked by chains of trans connected tricapped trigonal prisms ThF9 through corners and edges. The three dimensional thorium frameworks delimits channels parallel to [0 0 1] where the 11-coordinated Tl+ ions are arranged into double columns located in mirror planes of the structure. TlTh3F13 is isotypic with RbTh3F13, RbU3F13 and with one of the two polymorphs of CsTh3F13. The structure of TlThF5 may be regarded as a layer structure built up from the regular succession of 2∞[ M ‧F5 ] - corrugated layers further held by the Tl+ ions along the [1 0 1 ̅] direction. The layers are built up from edge and corner-sharing thorium polyhedra where each (ThF9)5- monocapped square antiprism is connected to five others by sharing three edges and two corners. TlThF5 is isostructural with β-NH4UF5 and with one of the polymorphs of CsThF5. A comparison of the different structural types of MM‧F5 pentafluorides is presented and a diagram of repartition of their structures is given. From the comparison of the Tl structures with their Rb or Cs homologs, where very similar monovalent cation environments are observed it should be concluded to a stereochemically inactivity of the 6s2 lone pair of Tl(I) in both TlTh3F13 and TlThF5, contrary to what is observed in richer Tl(I) content Tl3ThF7 fluorothorate.

  6. Photochemical manipulation of colloidal structures in liquid-crystal colloids

    NASA Astrophysics Data System (ADS)

    Yamamoto, T.; Tabe, Y.; Yokoyama, H.

    2007-05-01

    We investigated photochemical manipulation of physical properties and colloidal structures in liquid-crystal (LC) colloids containing azobenzene compounds. In a LC suspension where polymeric particles were dispersed in a host LC, we achieved photochemical control of light-scattering properties of the suspension. In a nematic phase, when the suspension was sandwiched with two glass plates, the film became opaque. This would be attributable to an appearance of both multidomain structures of LC alignment and mismatches of refractive indices between the materials. The opaque state turned into a transparent one when a nematic-to-isotropic phase transition was induced by the trans-to-cis photoisomerization of the azo-dye. This will result from a disappearance of both the multidomain structures and the refractive-index mismatches in the isotropic phase. The transparent film went back into the initial opaque film when the nematic phase was obtained by the cis-to-trans photoisomerization. In a LC emulsion in which glycerol or water droplets were dispersed in liquid crystals, we examined photochemical change of defect structures and inter-droplet distances by the photochemical manner. At the initial state, Saturn ring and hedgehog defects were formed around the droplets. For the glycerol droplets, we observed structural transformations between Saturn ring and boojums on irradiation with ultra-violet and visible light. For the water droplets, the inter-droplet distances varied by changing defect size on the irradiation. These phenomena would result from modulation of anchoring conditions of the droplets by the photoisomerization of the azo-dyes.

  7. Analysis of zinc binding sites in protein crystal structures.

    PubMed Central

    Alberts, I. L.; Nadassy, K.; Wodak, S. J.

    1998-01-01

    The geometrical properties of zinc binding sites in a dataset of high quality protein crystal structures deposited in the Protein Data Bank have been examined to identify important differences between zinc sites that are directly involved in catalysis and those that play a structural role. Coordination angles in the zinc primary coordination sphere are compared with ideal values for each coordination geometry, and zinc coordination distances are compared with those in small zinc complexes from the Cambridge Structural Database as a guide of expected trends. We find that distances and angles in the primary coordination sphere are in general close to the expected (or ideal) values. Deviations occur primarily for oxygen coordinating atoms and are found to be mainly due to H-bonding of the oxygen coordinating ligand to protein residues, bidentate binding arrangements, and multi-zinc sites. We find that H-bonding of oxygen containing residues (or water) to zinc bound histidines is almost universal in our dataset and defines the elec-His-Zn motif. Analysis of the stereochemistry shows that carboxyl elec-His-Zn motifs are geometrically rigid, while water elec-His-Zn motifs show the most geometrical variation. As catalytic motifs have a higher proportion of carboxyl elec atoms than structural motifs, they provide a more rigid framework for zinc binding. This is understood biologically, as a small distortion in the zinc position in an enzyme can have serious consequences on the enzymatic reaction. We also analyze the sequence pattern of the zinc ligands and residues that provide elecs, and identify conserved hydrophobic residues in the endopeptidases that also appear to contribute to stabilizing the catalytic zinc site. A zinc binding template in protein crystal structures is derived from these observations. PMID:10082367

  8. Crystal structure of Pseudomonas aeruginosa bacteriophytochrome: Photoconversion and signal transduction

    PubMed Central

    Yang, Xiaojing; Kuk, Jane; Moffat, Keith

    2008-01-01

    Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria via reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here we report the crystal structure at 2.9 Å resolution of a bacteriophytochrome from Pseudomonas aeruginosa with an intact, fully photoactive photosensory core domain in its dark-adapted Pfr state. This structure reveals how unusual interdomain interactions, including a knot and an “arm” structure near the chromophore site, bring together the PAS (Per-ARNT-Sim), GAF (cGMP phosphodiesterase/adenyl cyclase/FhlA), and PHY (phytochrome) domains to achieve Pr/Pfr photoconversion. The PAS, GAF, and PHY domains have topologic elements in common and may have a single evolutionary origin. We identify key interactions that stabilize the chromophore in the Pfr state and provide structural and mutational evidence to support the essential role of the PHY domain in efficient Pr/Pfr photoconversion. We also identify a pair of conserved residues that may undergo concerted conformational changes during photoconversion. Modeling of the full-length bacteriophytochrome structure, including its output histidine kinase domain, suggests how local structural changes originating in the photosensory domain modulate interactions between long, cross-domain signaling helices at the dimer interface and are transmitted to the spatially distant effector domain, thereby regulating its histidine kinase activity. PMID:18799746

  9. Crystal structure of the petal death protein from carnation flower.

    PubMed

    Teplyakov, Alexey; Liu, Sijiu; Lu, Zhibing; Howard, Andrew; Dunaway-Mariano, Debra; Herzberg, Osnat

    2005-12-20

    Expression of the PSR132 protein from Dianthus caryophyllus (carnation, clover pink) is induced in response to ethylene production associated with petal senescence, and thus the protein is named petal death protein (PDP). Recent work has established that despite the annotation of PDP in sequence databases as carboxyphosphoenolpyruvate mutase, the enzyme is actually a C-C bond cleaving lyase exhibiting a broad substrate profile. The crystal structure of PDP has been determined at 2.7 A resolution, revealing a dimer-of-dimers oligomeric association. Consistent with sequence homology, the overall alpha/beta barrel fold of PDP is the same as that of other isocitrate lyase/PEP mutase superfamily members, including a swapped eighth helix within a dimer. Moreover, Mg(2+) binds in the active site of PDP with a coordination pattern similar to that seen in other superfamily members. A compound, covalently bound to the catalytic residue, Cys144, was interpreted as a thiohemiacetal adduct resulting from the reaction of glutaraldehyde used to cross-link the crystals. The Cys144-carrying flexible loop that gates access to the active site is in the closed conformation. Models of bound substrates and comparison with the closed conformation of isocitrate lyase and 2-methylisocitrate lyase revealed the structural basis for the broad substrate profile of PDP.

  10. Crystal structures of vortioxetine and its methanol monosolvate

    PubMed Central

    Zhou, Xin-Bo; Gu, Jian-Ming; Sun, Meng-ying; Hu, Xiu-Rong; Wu, Su-Xiang

    2015-01-01

    Vortioxetine, C18H22N2S, (1), systematic name 1-{2-[(2,4-di­methyl­phen­yl)sulfan­yl]phen­yl}piperazine, a new drug used to treat patients with major depressive disorder, has been crystallized as the free base and its methanol monosolvate, C18H22N2S·CH3OH, (2). In both structures, the vortioxetine mol­ecules have similar conformations: in (1), the dihedral angle between the aromatic rings is 80.04 (16)° and in (2) it is 84.94 (13)°. The C—S—C bond angle in (1) is 102.76 (14)° and the corresponding angle in (2) is 103.41 (11)°. The piperazine ring adopts a chair conformation with the exocyclic N—C bond in a pseudo-equatorial orientation in both structures. No directional inter­actions beyond normal van der Waals contacts could be identified in the crystal of (1), whereas in (2), the vortioxetine and methanol mol­ecules are linked by N—H⋯O and O—H⋯N hydrogen bonds, generating [001] chains. PMID:26396746

  11. Structure of carboxymyoglobin in crystals and in solution.

    PubMed Central

    Makinen, M W; Houtchens, R A; Caughey, W S

    1979-01-01

    The configuration of the heme-carbonyl group upon binding of carbon monoxide to sperm whale myoglobin (Mb) in crystals is evaluated on the basis of infrared spectroscopic methods. Multiplets of the totally symmetric C-O stretching mode are observed for the heme-bound ligand near 1933, 1944, and 1967 cm-1, corresponding to three different heme-carbonyl conformers. Variations in the relative proportions of these conformers can be induced by incorporation of small fractions of metMb or deoxyMb into MbCO crystals. The configuration of the iron-carbonyl with respect to the immediate coordination environment of the heme iron is assigned for each v(CO) stretching frequency on the basis of a detailed comparison of the three-dimensional structures of the heme environments of MbCO, metMb, and deoxyMb defined by crystallographic methods. The structures of the three heme-carbonyl conformers account for the v(CO) infrared absorption bands that can be observed for MbCO in solution. PMID:293700

  12. Crystal structure of pyruvate decarboxylase from Zymobacter palmae

    PubMed Central

    Buddrus, Lisa; Andrews, Emma S. V.; Leak, David J.; Danson, Michael J.; Arcus, Vickery L.; Crennell, Susan J.

    2016-01-01

    Pyruvate decarboxylase (PDC; EC 4.1.1.1) is a thiamine pyrophosphate- and Mg2+ ion-dependent enzyme that catalyses the non-oxidative decarboxylation of pyruvate to acetaldehyde and carbon dioxide. It is rare in bacteria, but is a key enzyme in homofermentative metabolism, where ethanol is the major product. Here, the previously unreported crystal structure of the bacterial pyruvate decarboxylase from Zymobacter palmae is presented. The crystals were shown to diffract to 2.15 Å resolution. They belonged to space group P21, with unit-cell parameters a = 204.56, b = 177.39, c = 244.55 Å and R r.i.m. = 0.175 (0.714 in the highest resolution bin). The structure was solved by molecular replacement using PDB entry 2vbi as a model and the final R values were R work = 0.186 (0.271 in the highest resolution bin) and R free = 0.220 (0.300 in the highest resolution bin). Each of the six tetramers is a dimer of dimers, with each monomer sharing its thiamine pyrophosphate across the dimer interface, and some contain ethylene glycol mimicking the substrate pyruvate in the active site. Comparison with other bacterial PDCs shows a correlation of higher thermostability with greater tetramer interface area and number of interactions. PMID:27599861

  13. Crystal Structure of 3S-hydroxy-7 Melleine

    NASA Astrophysics Data System (ADS)

    Liu, Xiao-hong; Xu, Fang; Zhang, Yi; Liu, Li-hong; Huang, Hua-rong; She, Zhi-gang; Lin, Yong-cheng; Chan, Winglai

    2006-10-01

    A new compound, 3S-hydroxy-7 melleine was isolated from the endophytic fungus Xylariasp No.2508 from the mangrove tree on the South China Sea coast. It was the first time that this kind of compound was isolated from marine fungus. The structure was elucidated by NMR data, infrared spectrum (IR) and mass spectrometry (MS). In addition, its structure was determined by the single-crystal X-ray diffraction analysis. It crystallized in monoclinic, space group P21 with a=10.8884(19) Å, b=7.2284(13) Å, c=13.398(2) Å, β=104.217(3)°, C10H10O4·H2O, Mr=212.20, V=1022.2(3) Å3, Z=4, Dc=1.379 mg/m3, F(000)=448, μ=0.112 mm-1, the final R=0.0498, ωR=0.101 for 2407 observed reflections (I>2σ(I)). The molecular backbone of the compound includes a benzopyran ring. By comparing with the melting point and the optical rotation of the known 3R-hydroxy-7 melleine in literature, the absolute configuration of the compound was determined as 3S. It didn't exhibit antibacterial activity against Gram-positive bacterium Staphylococcus aureus at 200 μg/disk in the preliminary test.

  14. Crystal structure of K[Hg(SCN)3] - a redetermination.

    PubMed

    Weil, Matthias; Häusler, Thomas

    2014-09-01

    The crystal structure of the room-temperature modification of K[Hg(SCN)3], potassium tri-thio-cyanato-mercurate(II), was redetermined based on modern CCD data. In comparison with the previous report [Zhdanov & Sanadze (1952 ▶). Zh. Fiz. Khim. 26, 469-478], reliability factors, standard deviations of lattice parameters and atomic coordinates, as well as anisotropic displacement parameters, were revealed for all atoms. The higher precision and accuracy of the model is, for example, reflected by the Hg-S bond lengths of 2.3954 (11), 2.4481 (8) and 2.7653 (6) Å in comparison with values of 2.24, 2.43 and 2.77 Å. All atoms in the crystal structure are located on mirror planes. The Hg(2+) cation is surrounded by four S atoms in a seesaw shape [S-Hg-S angles range from 94.65 (2) to 154.06 (3)°]. The HgS4 polyhedra share a common S atom, building up chains extending parallel to [010]. All S atoms of the resulting (1) ∞[HgS2/1S2/2] chains are also part of SCN(-) anions that link these chains with the K(+) cations into a three-dimensional network. The K-N bond lengths of the distorted KN7 polyhedra lie between 2.926 (2) and 3.051 (3) Å.

  15. Structure of cleaved (001) USb2 single crystal

    SciTech Connect

    Chen, Shao-ping; Hawley, Marilyn; Bauer, Eric D; Stockum, Phil B; Manoharan, Hari C

    2009-01-01

    We have achieved what we believe to be the first atomic resolution STM images for a uranium compound taken at room temperature. The a, b, and c lattice parameters in the images confirm that the USb{sub 2} crystals cleave on the (001) basal plane as expected. The a and b dimensions were equal, with the atoms arranged in a cubic pattern. Our calculations indicate a symmetric cut between Sb planes to be the most favorable cleavage plane and U atoms to be responsible for most of the DOS measured by STM. Some strange features observed in the STM will be discussed in conjunction with ab initio calculations. The purpose of this work is to demonstrate the power of scanning tunneling microscopy (STM) techniques combined with a theoretical underpinning to determine the surface atomic structure and properties of actinide materials, such as the quasi 2-dimensional uranium dipnictide USb{sub 2} single crystal, thereby contributing to the understanding of their surface structural and electronic properties. The members of this interesting UX{sub 2} (X=P, As, Sb, Bi) series of compounds display dual localized and itinerant 5f electron behavior within the same compound due to the hybridization of the 5f orbitals with the conduction band. With the exception of UO{sub 2}, which has to be studied at elevated temperature to generate enough carriers for STM imaging, STM techniques have not been applied successfully to the characterization of the surface atomic structure of any other single crystal actinide compound, to the best of our knowledge. However, STM has been used to a limited extent for the study of some cerium compounds. STM probes electronic properties at the atomic level and can directly provide information about the local density of filled and empty states (LDOS) states simultaneously. A STM topograph provides the local atomic arrangement and spacing of the atoms on the surface, local defect structures (e.g. steps, vacancies, and kink sites) and the presence of contaminants

  16. Crystal structures of type III{sub H} NAD-dependent D-3-phosphoglycerate dehydrogenase from two thermophiles

    SciTech Connect

    Kumar, S.M.; Pampa, K.J.; Manjula, M.; Hemantha Kumar, G.; Kunishima, Naoki; Lokanath, N.K.

    2014-08-15

    Highlights: • Determined the crystal structures of PGDH from two thermophiles. • Monomer is composed of nucleotide binding domain and substrate binding domain. • Crystal structures of type III{sub H} PGDH. - Abstract: In the L-Serine biosynthesis, D-3-phosphoglycerate dehydrogenase (PGDH) catalyzes the inter-conversion of D-3-phosphoglycerate to phosphohydroxypyruvate. PGDH belongs to 2-hydroxyacid dehydrogenases family. We have determined the crystal structures of PGDH from Sulfolobus tokodaii (StPGDH) and Pyrococcus horikoshii (PhPGDH) using X-ray diffraction to resolution of 1.77 Å and 1.95 Å, respectively. The PGDH protomer from both species exhibits identical structures, consisting of substrate binding domain and nucleotide binding domain. The residues and water molecules interacting with the NAD are identified. The catalytic triad residues Glu-His-Arg are highly conserved. The residues involved in the dimer interface and the structural features responsible for thermostability are evaluated. Overall, structures of PGDHs with two domains and histidine at the active site are categorized as type III{sub H} and such PGDHs structures having this type are reported for the first time.

  17. Thermal evolution of the crystal structure of the orthorhombic perovskite LaFeO{sub 3}

    SciTech Connect

    Dixon, Charlotte A.L.; Kavanagh, Christopher M.; Knight, Kevin S.; Kockelmann, Winfried; Morrison, Finlay D.; Lightfoot, Philip

    2015-10-15

    The thermal evolution of the crystal structure of the prototypical orthorhombic perovskite LaFeO{sub 3} has been studied in detail by powder neutron diffraction in the temperature range 25abstract: The unusual thermal evolution of lattice metrics in the perovskite LaFeO{sub 3} is rationalized from a detailed powder neutron diffraction study. - Highlights: • Crystal structure of the perovskite LaFeO{sub 3} studied in detail by powder neutron diffraction. • Unusual thermal evolution of lattice metrics rationalized. • Contrasting behavior to Bi-doped LaFeO{sub 3}. • Octahedral distortion/tilt parameters explain unusual a and c lattice parameter behavior.

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

    DOE PAGES

    Verburg, P. C.; Smillie, L. A.; Römer, G. R. B. E.; ...

    2015-06-04

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

  19. Structural noise tolerance of photonic crystal optical properties

    NASA Astrophysics Data System (ADS)

    Odontsengel, Nyam-Erdene; Cai, DongSheng; Cole, James B.

    2016-12-01

    Using nonstandard (NS) finite difference time domain (FDTD) scheme to perform 2D electromagnetic (EM) simulations, we investigate how the optical properties of 2D photonic crystals (PCs) are affected by various different kinds of structural noises in the PC lattice. While the transmission spectrum is strongly affected by noises, the position and the depth of the band gap in the transmission spectrum are remarkably robust. It is shown that rather coarse numerical grids can be used to evaluate various PC structures in NS-FDTD EM simulations. The combination of noises affects transmission spectrum in the same way as the most influential individual noise. It is shown that reducing the most influential individual noise is a very efficient method to make PC more accurate.

  20. 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.

  1. 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.

  2. Crystal structure of Hg2SO4 – a redetermination

    PubMed Central

    Weil, Matthias

    2014-01-01

    The crystal structure of mercury(I) sulfate (or mercurous sulfate), Hg2SO4, was re-determined based on modern CCD data. In comparison with the previous determination from Weissenberg film data [Dorm (1969 ▶). Acta Chem. Scand. 23, 1607–1615], all atoms were refined with anisotropic displacement parameters, leading to higher precision in terms of bond lengths and angles [e.g. Hg—Hg = 2.5031 (7) compared to 2.500 (3)Å]. The structure consists of alternating rows along [001] of Hg2 2+ dumbbells (generated by inversion symmetry) and SO4 2− tetra­hedra (symmetry 2). The dumbbells are linked via short O—Hg—Hg—O bonds to the sulfate tetra­hedra into chains extending parallel to [20-1]. More remote O—Hg—Hg—O bonds connect these chains into a three-dimensional framework. PMID:25309168

  3. Crystal structure of a family 80 chitosanase from Mitsuaria chitosanitabida.

    PubMed

    Yorinaga, Yutaka; Kumasaka, Takashi; Yamamoto, Masaki; Hamada, Kensaku; Kawamukai, Makoto

    2017-02-01

    Chitosanases belong to glycoside hydrolase families 5, 7, 8, 46, 75 and 80 and hydrolyse glucosamine polymers produced by partial or full deacetylation of chitin. Herein, we determined the crystal structure of chitosanase from the β-proteobacterium, Mitsuaria chitosanitabida, (McChoA) at 1.75 Å resolution; the first structure of a family 80 chitosanase. McChoA is a 34 kDa extracellular protein of 301 amino acids that fold into two (upper and lower) globular domains with an active site cleft between them. Key substrate-binding features are conserved with family 24 lysozymes and family 46 chitosanases. The distance between catalytic residues E41 and E61 (10.8 Å) indicates an inverting type mechanism. Uniquely, three disulphide bridges and the C terminus might contribute to enzyme activity.

  4. Crystal structure of PvdO from Pseudomonas aeruginosa.

    PubMed

    Yuan, Zenglin; Gao, Fei; Bai, Guohui; Xia, Hengchuan; Gu, Lichuan; Xu, Sujuan

    2017-02-26

    Pyoverdine I (PVDI) is a water-soluble fluorescein siderophore with strong iron chelating ability from the gram-negative pathogen Pseudomonas aeruginosa PAO1. Compared to common siderophores, PVDI is a relatively large compound whose synthesis requires a group of enzymes with different catalytic activities. In addition to four nonribosomal peptide synthetases (NRPS) which are responsible for the production of the peptide backbone of PVDI, several additional enzymes are associated with the modification of the side chains. PvdO is one of these enzymes and participates in PVDI precursor maturation in the periplasm. We determined the crystal structure of PvdO at 1.24 Å resolution. The PvdO structure shares a common fold with some FGly-generating enzymes (FGE) and is stabilized by Ca(2+). However, the catalytic residues in FGE are not observed in PvdO, indicating PvdO adopts a unique catalytic mechanism.

  5. The first crystal structure of an archaeal helical repeat protein

    PubMed Central

    Yoneda, Kazunari; Sakuraba, Haruhiko; Tsuge, Hideaki; Katunuma, Nobuhiko; Kuramitsu, Seiki; Kawabata, Takeshi; Ohshima, Toshihisa

    2005-01-01

    The crystal structure of ST1625p, a protein encoded by a hypothetical open reading frame ST1625 in the genome of the hyperthermophilic archaeon Sulfolobus tokodaii, was determined at 2.2 Å resolution. The only sequence similarity exhibited by the amino-acid sequence of ST1625p was a 33% identity with the sequence of SSO0983p from S. solfataricus. The 19 kDa monomeric protein was observed to consist of a right-handed superhelix assembled from a tandem repeat of ten α-­helices. A structural homology search using the DALI and MATRAS algorithms indicates that this protein can be classified as a helical repeat protein. PMID:16511116

  6. Crystal Structure of a Phosphorylation-coupled Saccharide Transporter

    SciTech Connect

    Y Cao; X Jin; E Levin; H Huang; Y Zong; W Hendrickson; J Javitch; K Rajashankar; M Zhou; et al.

    2011-12-31

    Saccharides have a central role in the nutrition of all living organisms. Whereas several saccharide uptake systems are shared between the different phylogenetic kingdoms, the phosphoenolpyruvate-dependent phosphotransferase system exists almost exclusively in bacteria. This multi-component system includes an integral membrane protein EIIC that transports saccharides and assists in their phosphorylation. Here we present the crystal structure of an EIIC from Bacillus cereus that transports diacetylchitobiose. The EIIC is a homodimer, with an expansive interface formed between the amino-terminal halves of the two protomers. The carboxy-terminal half of each protomer has a large binding pocket that contains a diacetylchitobiose, which is occluded from both sides of the membrane with its site of phosphorylation near the conserved His250 and Glu334 residues. The structure shows the architecture of this important class of transporters, identifies the determinants of substrate binding and phosphorylation, and provides a framework for understanding the mechanism of sugar translocation.

  7. Crystal structure of a catalytic intermediate of the maltose transporter

    SciTech Connect

    Oldham, Michael L.; Khare, Dheeraj; Quiocho, Florante A.; Davidson, Amy L.; Chen, Jue

    2008-08-20

    The maltose uptake system of Escherichia coli is a well-characterized member of the ATP-binding cassette transporter superfamily. Here we present the 2.8-{angstrom} crystal structure of the intact maltose transporter in complex with the maltose-binding protein, maltose and ATP. This structure, stabilized by a mutation that prevents ATP hydrolysis, captures the ATP-binding cassette dimer in a closed, ATP-bound conformation. Maltose is occluded within a solvent-filled cavity at the interface of the two transmembrane subunits, about halfway into the lipid bilayer. The binding protein docks onto the entrance of the cavity in an open conformation and serves as a cap to ensure unidirectional translocation of the sugar molecule. These results provide direct evidence for a concerted mechanism of transport in which solute is transferred from the binding protein to the transmembrane subunits when the cassette dimer closes to hydrolyse ATP.

  8. Synthesis, crystal structure, and magnetic properties of two-dimensional divalent metal glutarate/dipyridylamine coordination polymers, with a single crystal-to-single crystal transformation in the copper derivative

    SciTech Connect

    Montney, Matthew R.; Supkowski, Ronald M.; Staples, Richard J.; LaDuca, Robert L.

    2009-01-15

    Hydrothermal reaction of divalent metal chlorides with glutaric acid and 4,4'-dipyridylamine (dpa) has afforded an isostructural family of coordination polymers with formulation [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate). Square pyramidal coordination is seen in 1-3, with semi-ligation of a sixth donor to produce a '5+1' extended coordination sphere. Neighboring metal atoms are linked into 1D [M(glu)]{sub n} neutral chains through chelating/monodentate bridging glutarate moieties with a syn-anti binding mode, and semi-chelation of the pendant carboxylate oxygen. These chains further connect into 2D layers through dipodal dpa ligands. Neighboring layers stack into the pseudo 3D crystal structure of 1-3 through supramolecular hydrogen bonding between dpa amine units and the semi-chelated glutarate oxygen atoms. The variable temperature magnetic behavior of 1-3 was explored and modeled as infinite 1D Heisenberg chains. Notably, complex 3 undergoes a thermally induced single crystal-to-single crystal transformation between centric and acentric space groups, with a conformationally disordered unilayer structure at 293 K and an ordered bilayer structure at 173 K. All materials were further characterized via infrared spectroscopy and elemental and thermogravimetric analyses. - Graphical abstract: The coordination polymers [M(glu)(dpa)]{sub n} (M=Co (1), Ni (2), Cu (3); glu=glutarate, dpa=4,4'-dipyridylamine) exhibit 2D layer structures based on 1D [M(glu)]{sub n} chains linked through dpa tethers. Antiferromagnetic coupling is observed for 2 and 3, while ferromagnetism is predominant in 1. Compound 3 undergoes a thermally induced single crystal-to-single crystal transformation from an acentric to a centrosymmetric space group.

  9. The crystal structure of loparite: a new acentric variety

    NASA Astrophysics Data System (ADS)

    Popova, Elena A.; Lushnikov, Sergey G.; Yakovenchuk, Victor N.; Krivovichev, Sergey V.

    2017-02-01

    The crystal structure of a new structural variety of loparite (Na0.56Ce0.21La0.14Ca0.06Sr0.03Nd0.02Pr0.01)Σ=1.03(Ti0.83Nb0.15)Σ=0.98O3 from the Khibiny alkaline massif, Kola peninsula, Russia, was solved by direct methods and refined to R 1 = 0.029 for 492 unique observed reflections with I > 2σ(I). The mineral is orthorhombic, Ima2, a = 5.5129(2), b = 5.5129(2) and c = 7.7874(5) Å. Similarly to other perovskite-group minerals with the general formula ABO3, the crystal structure of loparite is based upon a three-dimensional framework of distorted corner-sharing BO6. The A cations are coordinated by 12 oxygen atoms and are situated in distorted cuboctahedral cavities. In contrast to the ideal perovskite-type structure ( Pmoverset{-}{3} m ), the unit cell is doubled along the c axis and the a and b axes are rotated in the ab plane at 45o. The BO6 octahedron displays distortion characteristic for the d 0 transition metal cations with the out-of-center shift of the B site. The symmetry reduction is also attributable to the distortion of the BO6 octahedra which are tilted and rotated with respect to the c axis. The occurrence of a new acentric variety of loparite can be explained by the pecularities of its chemical composition characterized by the increased content of Ti compared to the previously studied samples.

  10. Crystal Structure and Inhibition Studies of Transglutaminase from Streptomyces mobaraense*

    PubMed Central

    Yang, Ming-Te; Chang, Cheng-Hsiang; Wang, Jiou Ming; Wu, Tung Kung; Wang, Yu-Kuo; Chang, Chin-Yuan; Li, TienHsiung Thomas

    2011-01-01

    The crystal structure of the microbial transglutaminase (MTGase) zymogen from Streptomyces mobaraense has been determined at 1.9-Å resolution using the molecular replacement method based on the crystal structure of the mature MTGase. The overall structure of this zymogen is similar to that of the mature form, consisting of a single disk-like domain with a deep active cleft at the edge of the molecule. A major portion of the prosequence (45 additional amino acid residues at the N terminus of the mature transglutaminase) folds into an L-shaped structure, consisting of an extended N-terminal segment linked with a one-turn short helix and a long α-helix. Two key residues in the short helix of the prosequence, Tyr-12 and Tyr-16, are located on top of the catalytic triad (Cys-110, Asp-301, and His-320) to block access of the substrate acyl donors and acceptors. Biochemical characterization of the mature MTGase, using N-α-benzyloxycarbonyl-l-glutaminylglycine as a substrate, revealed apparent Km and kcat/Km values of 52.66 mm and 40.42 mm−1 min−1, respectively. Inhibition studies using the partial prosequence SYAETYR and homologous sequence SQAETYR showed a noncompetitive inhibition mechanism with IC50 values of 0.75 and 0.65 mm, respectively, but no cross-linking product formation. Nevertheless, the prosequence homologous oligopeptide SQAETQR, with Tyr-12 and Tyr-16 each replaced with Gln, exhibited inhibitory activity with the formation of the SQAETQR-monodansylcadaverine fluorophore cross-linking product (SQAETQR-C-DNS). MALDI-TOF tandem MS analysis of SQAETQR-C-DNS revealed molecular masses corresponding to those of NSQAETQC-C-DNS and C-DNS-NQRC sequences, suggesting the incorporation of C-DNS onto the C-terminal Gln residue of the prosequence homologous oligopeptide. These results support the putative functional roles of both Tyr residues in substrate binding and inhibition. PMID:21193394

  11. Tetrel Bonds in Infinite Molecular Chains by Electronic Structure Theory and Their Role for Crystal Stabilization.

    PubMed

    George, Janine; Dronskowski, Richard

    2017-02-16

    Intermolecular bonds play a crucial role in the rational design of crystal structures, dubbed crystal engineering. The relatively new term tetrel bonds (TBs) describes a long-known type of such interactions presently in the focus of quantum chemical cluster calculations. Here, we energetically explore the strengths and cooperativity of these interactions in infinite chains, a possible arrangement of such tetrel bonds in extended crystals, by periodic density functional theory. In the chains, the TBs are amplified due to cooperativity by up to 60%. Moreover, we computationally take apart crystals stabilized by infinite tetrel-bonded chains and assess the importance of the TBs for the crystal stabilization. Tetrel bonds can amount to 70% of the overall interaction energy within some crystals, and they can also be energetically decisive for the taken crystal structure; their individual strengths also compete with the collective packing within the crystal structures.

  12. ICCG-10: International Conference on Crystal Growth (10th) Held in San Diego, California on August 16-21, 1992. Oral Presentation Abstracts.

    DTIC Science & Technology

    1992-10-01

    Novel Approaches to Crystal Growth of Bull, 7errwjry Solid Solutions 11:15 Single Crystal Growth of Rare- Earth Gellates an Epitactic Growth Nature J...00 COFFEE BREAK 10:00 Czochralsld Growth of Rare Earth Oxyorthosftscte Single Crystals C. L Meicher, R. A. Manenete, C. A. Peterson. and J. S...Segregation M. M. ft Boutt and C. P. Woensdreot 0. Hofmann. T. Jung and M ule Institute of Earth Sciences Utrecht. The Netherlands Untvesita Eriangan-Numberg

  13. Silicon crystals: Process for manufacturing wafer-like silicon crystals with a columnar structure

    NASA Technical Reports Server (NTRS)

    Authier, B.

    1978-01-01

    Wafer-like crystals suitable for making solar cells are formed by pouring molten Si containing suitable dopants into a mold of the desired shape and allowing it to solidify in a temperature gradient, whereby the large surface of the melt in contact with the mold is kept at less than 200 D and the free surface is kept at a temperature of 200-1000 D higher, but below the melting point of Si. The mold can also be made in the form of a slit, whereby the 2 sides of the mold are kept at different temperatures. A mold was milled in the surface of a cylindrical graphite block 200 mm in diameter. The granite block was induction heated and the bottom of the mold was cooled by means of a water-cooled Cu plate, so that the surface of the mold in contact with one of the largest surfaces of the melt was held at approximately 800 D. The free surface of the melt was subjected to thermal radiation from a graphite plate located 2 mm from the surface and heated to 1500 D. The Si crystal formed after slow cooling to room temperature had a columnar structure and was cut with a diamond saw into wafers approximately 500 mm thick. Solar cells prepared from these wafers had efficiencies of 10 to 11%.

  14. 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.

  15. Crystal structure of dihydroorotate dehydrogenase from Leishmania major.

    PubMed

    Cordeiro, Artur T; Feliciano, Patricia R; Pinheiro, Matheus P; Nonato, M Cristina

    2012-08-01

    Dihydroorotate dehydrogenase (DHODH) is the fourth enzyme in the de novo pyrimidine biosynthetic pathway and has been exploited as the target for therapy against proliferative and parasitic diseases. In this study, we report the crystal structures of DHODH from Leishmania major, the species of Leishmania associated with zoonotic cutaneous leishmaniasis, in its apo form and in complex with orotate and fumarate molecules. Both orotate and fumarate were found to bind to the same active site and exploit similar interactions, consistent with a ping-pong mechanism described for class 1A DHODHs. Analysis of LmDHODH structures reveals that rearrangements in the conformation of the catalytic loop have direct influence on the dimeric interface. This is the first structural evidence of a relationship between the dimeric form and the catalytic mechanism. According to our analysis, the high sequence and structural similarity observed among trypanosomatid DHODH suggest that a single strategy of structure-based inhibitor design can be used to validate DHODH as a druggable target against multiple neglected tropical diseases such as Leishmaniasis, Sleeping sickness and Chagas' diseases.

  16. Crystal structure of the human glucose transporter GLUT1.

    PubMed

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-05

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  17. Crystal Structure of the BARD1 BRCT Domains

    SciTech Connect

    Birrane,G.; Varma, A.; Soni, A.; Ladias, J.

    2007-01-01

    The interaction of the breast tumor suppressor BRCA1 with the protein BARD1 results in the formation of a heterodimeric complex that has ubiquitin ligase activity and plays central roles in cell cycle checkpoint control and DNA repair. Both BRCA1 and BARD1 possess a pair of tandem BRCT domains that interact in a phosphorylation-dependent manner with target proteins. We determined the crystal structure of the human BARD1 BRCT repeats (residues 568-777) at 1.9 {angstrom} resolution. The composition and structure of the BARD1 phosphoserine-binding pocket P{sub 1} are strikingly similar to those of the BRCA1 and MDC1 BRCT domains, suggesting a similar mode of interaction with the phosphate group of the ligand. By contrast, the BARD1 BRCT selectivity pocket P{sub 2} exhibits distinct structural features, including two prominent histidine residues, His685 and His686, which may be important for ligand binding. The protonation state of these histidines has a marked effect on the calculated electrostatic potential in the vicinity of P{sub 2}, raising the possibility that ligand recognition may be regulated by changes in pH. Importantly, the BARD1 BRCT structure provides insights into the mechanisms by which the cancer-associated missense mutations C645R, V695L, and S761N may adversely affect the structure and function of BARD1.

  18. Crystal structure of E. coli lipoprotein diacylglyceryl transferase.

    PubMed

    Mao, Guotao; Zhao, Yan; Kang, Xusheng; Li, Zhijie; Zhang, Yan; Wang, Xianping; Sun, Fei; Sankaran, Krishnan; Zhang, Xuejun C

    2016-01-05

    Lipoprotein biogenesis is essential for bacterial survival. Phosphatidylglycerol:prolipoprotein diacylglyceryl transferase (Lgt) is an integral membrane enzyme that catalyses the first reaction of the three-step post-translational lipid modification. Deletion of the lgt gene is lethal to most Gram-negative bacteria. Here we present the crystal structures of Escherichia coli Lgt in complex with phosphatidylglycerol and the inhibitor palmitic acid at 1.9 and 1.6 Å resolution, respectively. The structures reveal the presence of two binding sites and support the previously reported structure-function relationships of Lgt. Complementation results of lgt-knockout cells with different mutant Lgt variants revealed critical residues, including Arg143 and Arg239, that are essential for diacylglyceryl transfer. Using a GFP-based in vitro assay, we correlated the activities of Lgt with structural observations. Together, the structural and biochemical data support a mechanism whereby substrate and product, lipid-modified lipobox-containing peptide, enter and leave the enzyme laterally relative to the lipid bilayer.

  19. Crystal structure of the human glucose transporter GLUT1

    NASA Astrophysics Data System (ADS)

    Deng, Dong; Xu, Chao; Sun, Pengcheng; Wu, Jianping; Yan, Chuangye; Hu, Mingxu; Yan, Nieng

    2014-06-01

    The glucose transporter GLUT1 catalyses facilitative diffusion of glucose into erythrocytes and is responsible for glucose supply to the brain and other organs. Dysfunctional mutations may lead to GLUT1 deficiency syndrome, whereas overexpression of GLUT1 is a prognostic indicator for cancer. Despite decades of investigation, the structure of GLUT1 remains unknown. Here we report the crystal structure of human GLUT1 at 3.2 Å resolution. The full-length protein, which has a canonical major facilitator superfamily fold, is captured in an inward-open conformation. This structure allows accurate mapping and potential mechanistic interpretation of disease-associated mutations in GLUT1. Structure-based analysis of these mutations provides an insight into the alternating access mechanism of GLUT1 and other members of the sugar porter subfamily. Structural comparison of the uniporter GLUT1 with its bacterial homologue XylE, a proton-coupled xylose symporter, allows examination of the transport mechanisms of both passive facilitators and active transporters.

  20. The crystal structures of potassium and cesium trivanadates

    USGS Publications Warehouse

    Evans, H.T.; Block, S.

    1966-01-01

    Potassium and cesium trivanadates are monoclinic and isomorphous, space group P21/m, with the following dimensions (Z = 2): KV3O8, a = 7.640 A, b = 8.380 A, c = 4.979 A, ??= 96?? 57???; CsV3O8, a = 8.176 A, b = 8.519 A, c = 4.988 A, ?? = 95?? 32???. The crystal structure of KV3O8 has been determined from hk0, 0kl, and h0l Weissenberg data with an R factor of 0.15. The structure of CsV3O8 has been refined with 1273 hkl Weissenberg data to an R factor of 0.089. The structures consist of corrugated sheets based on a linkage of distorted VO6, octahedra. Two of the vanadium atoms lie in double, square-pyramid groups V2O8, which are linked through opposite basal corners into chains along the b axis. The chains are joined laterally along the c axis into sheets by the third vanadium atom in VO groups, also forming part of a square-pyramid coordination. Various aspects of these structures are compared with other known oxovanadate structures.

  1. Crystal and molecular structure of the antimalarial agent enpiroline.

    PubMed Central

    Karle, J M; Karle, I L

    1989-01-01

    To identify common spatial and structural features of amino alcohol antimalarial agents with the eventual goal of designing more effective drugs and a better understanding of the mechanism of action of this class of antimalarial agents, the three-dimensional crystal and molecular structure of enpiroline, a new antimalarial agent active against chloroquine-resistant Plasmodium falciparum, was determined by X-ray crystallography and compared with the crystal structures of the cinchona alkaloids and of the new antimalarial agent WR 194,965. The aromatic rings of the phenyl-pyridine ring system of enpiroline are twisted from each other by approximately 18 degrees. The intramolecular aliphatic N-O distance in enpiroline was 2.80 A (1 A = 0.1 nm), which is close to the N-O distance found in the antimalarial cinchona alkaloids. Enpiroline contains both an intramolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms and an intermolecular hydrogen bond between the aliphatic nitrogen and oxygen atoms of two neighboring molecules. One enantiomer of enpiroline superimposed best with quinine, and the other enantiomer of enpiroline superimposed best with quinidine, suggesting that both enantiomers of enpiroline possess antimalarial activity. Since a common feature of the crystal structures of the amino alcohol antimalarial agents is the formation of intermolecular hydrogen bonds, the common spatial direction of hydrogen bond formation indicates the potential ability of these antimalarial agents to bind to a common receptor site. The crystallographic parameters were as follows: C19H18F6N5O; Mr = 404.3; symmetry of unit cell, monoclinic; space group, P2(1)/a; parameters of unit cell---a = 9.454 +/- 0.004 A, b = 18.908 +/- 0.008 A, c = 10.300 +/- 0.004 A, and beta = 96.55 +/- 0.03 degrees: V (volume of unit cell) = 1829.2 A3; Z (number of molecules per unit cell) = 4; Dchi (calculated density) = 1.46 g cm-3; source of radiation, CuK alpha (lambda = 1.54178 A); mu

  2. A New Approach for Investigating Crystal Stresses that Drive the Initiation of Fatigue-Induced Defects in Structural Alloys

    DTIC Science & Technology

    2008-12-31

    culminated in a novel picture of how the stress evolves at the crystal scale. 1. Using the crystal-based elastoplastic finite element model, we found...None. 14. ABSTRACT We have developed an approach to investigate crystals stresses during cyclic load by coordinating experiments and simulations at ...simulated lattice data culminated in a novel picture of how the stress evolves at the crystal scale. Specifically, using the crystal-based

  3. Single crystal growth and structure of La{sub 4}Cu{sub 3}MoO{sub 12}

    SciTech Connect

    Enterkin, James A.; Maggard, Paul A.; Ishiwata, Shintaro; Marks, Laurence D.; Poeppelmeier, Kenneth R.; Azuma, Masaki; Takano, Mikio

    2010-03-15

    We report the synthesis and structure determination of single crystals of La{sub 4}Cu{sub 3}MoO{sub 12} grown from a CuO/KCl flux. This material, whose structure had previously been reported based solely on polycrystalline diffraction data, shows frustrated magnetic behavior and an anti-ferromagnetic ordering of spin-1/2 triangles at low temperatures. The structural and atomic parameters determined from the single crystal data are in very good agreement with those reported previously. However, HREM data showed evidence for disorder in the stacking of the Cu{sub 3}MoO{sub 4} planes, and thus a twinned structural refinement in space group P2{sub 1}/m was replaced by an equivalent disordered structural model in space group Pm. This development of a synthetic route to single crystals of La{sub 4}Cu{sub 3}MoO{sub 12} will allow a more detailed investigation of its complex electronic and magnetic properties. - Graphical abstract: Structural view of a single layer of the triangular lattice of La{sub 4}Cu{sub 3}MoO{sub 12} perpendicular to the b-axis. The copper atoms are blue, the oxide ions are red and the MoO5 trigonal bipyramids are yellow. The isolated triangular clusters of Cu{sub 3}O are outlined by the thin blue lines.

  4. Exploring protein flexibility: incorporating structural ensembles from crystal structures and simulation into virtual screening protocols.

    PubMed

    Osguthorpe, David J; Sherman, Woody; Hagler, Arnold T

    2012-06-14

    The capacity of proteins to adapt their structure in response to various perturbations including covalent modifications, and interactions with ligands and other proteins plays a key role in biological processes. Here, we explore the ability of molecular dynamics (MD), replica exchange molecular dynamics (REMD), and a library of structures of crystal-ligand complexes, to sample the protein conformational landscape and especially the accessible ligand binding site geometry. The extent of conformational space sampled is measured by the diversity of the shapes of the ligand binding sites. Since our focus here is the effect of this plasticity on the ability to identify active compounds through virtual screening, we use the structures generated by these techniques to generate a small ensemble for further docking studies, using binding site shape hierarchical clustering to determine four structures for each ensemble. These are then assessed for their capacity to optimize enrichment and diversity in docking. We test these protocols on three different receptors: androgen receptor (AR), HIV protease, and CDK2. We show that REMD enhances structural sampling slightly as compared both to MD, and the distortions induced by ligand binding as reflected in the crystal structures. The improved sampling of the simulation methods does not translate directly into improved docking performance, however. The ensemble approach did improve enrichment and diversity, and the ensemble derived from the crystal structures performed somewhat better than those derived from the simulations.

  5. 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

  6. Structures of the OmpF porin crystallized in the presence of foscholine-12

    PubMed Central

    Kefala, Georgia; Ahn, Chihoon; Krupa, Martin; Esquivies, Luis; Maslennikov, Innokentiy; Kwiatkowski, Witek; Choe, Senyon

    2010-01-01

    The endogenous Escherichia coli porin OmpF was crystallized as an accidental by-product of our efforts to express, purify, and crystallize the E. coli integral membrane protein KdpD in the presence of foscholine-12 (FC12). FC12 is widely used in membrane protein studies, but no crystal structure of a protein that was both purified and crystallized with this detergent has been reported in the Protein Data Bank. Crystallization screening for KdpD yielded two different crystals of contaminating protein OmpF. Here, we report two OmpF structures, the first membrane protein crystal structures for which extraction, purification, and crystallization were done exclusively with FC12. The first structure was refined in space group P21 with cell parameters a = 136.7 Å, b = 210.5 Å, c = 137 Å, and β = 100.5°, and the resolution of 3.8 Å. The second structure was solved at the resolution of 4.4 Å and was refined in the P321 space group, with unit cell parameters a = 215.5 Å, b = 215.5 Å, c = 137.5 Å, and γ = 120°. Both crystal forms show novel crystal packing, in which the building block is a tetrahedral arrangement of four trimers. Additionally, we discuss the use of FC12 for membrane protein crystallization and structure determination, as well as the problem of the OmpF contamination for membrane proteins overexpressed in E. coli. PMID:20196071

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

    PubMed Central

    Cole, Jason C.

    2017-01-01

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

  8. Automated High Throughput Protein Crystallization Screening at Nanoliter Scale and Protein Structural Study on Lactate Dehydrogenase

    SciTech Connect

    Li, Fenglei

    2006-08-09

    The purposes of our research were: (1) To develop an economical, easy to use, automated, high throughput system for large scale protein crystallization screening. (2) To develop a new protein crystallization method with high screening efficiency, low protein consumption and complete compatibility with high throughput screening system. (3) To determine the structure of lactate dehydrogenase complexed with NADH by x-ray protein crystallography to study its inherent structural properties. Firstly, we demonstrated large scale protein crystallization screening can be performed in a high throughput manner with low cost, easy operation. The overall system integrates liquid dispensing, crystallization and detection and serves as a whole solution to protein crystallization screening. The system can dispense protein and multiple different precipitants in nanoliter scale and in parallel. A new detection scheme, native fluorescence, has been developed in this system to form a two-detector system with a visible light detector for detecting protein crystallization screening results. This detection scheme has capability of eliminating common false positives by distinguishing protein crystals from inorganic crystals in a high throughput and non-destructive manner. The entire system from liquid dispensing, crystallization to crystal detection is essentially parallel, high throughput and compatible with automation. The system was successfully demonstrated by lysozyme crystallization screening. Secondly, we developed a new crystallization method with high screening efficiency, low protein consumption and compatibility with automation and high throughput. In this crystallization method, a gas permeable membrane is employed to achieve the gentle evaporation required by protein crystallization. Protein consumption is significantly reduced to nanoliter scale for each condition and thus permits exploring more conditions in a phase diagram for given amount of protein. In addition

  9. Crystallization of germanium-carbon alloys -- Structure and electronic transport

    SciTech Connect

    John, T.M.; Blaesing, J.; Veit, P.; Druesedau, T.

    1997-07-01

    Amorphous Ge{sub 1{minus}x}C{sub x} alloys were deposited by rf-magnetron sputtering from a germanium target in methane-argon atmosphere. Structural investigations were performed by means of wide and small angle X-ray scattering, X-ray reflectometry and cross-sectional transmission electron microscopy. The electronic transport properties were characterized using Hall-measurements and temperature depended conductivity. The results of X-ray techniques together with the electron microscopy clearly prove the existence of a segregation of the electronic conductivity in the as-prepared films follows the Mott' T{sup {minus}1/4} law, indicating transport by a hopping process. After annealing at 870 K, samples with x {le} 0.4 show crystallization of the Ge-clusters with a crystallite size being a function of x. After Ge-crystallization, the conductivity increases by 4 to 5 orders of magnitude. Above room temperature, electronic transport is determined by a thermally activated process. For lower temperatures, the {sigma}(T) curves show a behavior which is determined by the crystallite size and the free carrier concentration, both depending on the carbon content.

  10. Birefringence and band structure of CdP2 crystals

    NASA Astrophysics Data System (ADS)

    Beril, S. I.; Stamov, I. G.; Syrbu, N. N.; Zalamai, V. V.

    2013-08-01

    The spatial dispersion in CdP2 crystals was investigated. The dispersion is positive (nk||с>nk||у) at λ>λ0 and negative (nk||сcrystals are isotropic for wavelength λо=896 nm. Indirect transitions in excitonic region Еgx are nonpolarized due to one pair of bands. Minimal direct energy intervals correspond to transitions Г1→Г1 for Е||с and Г2→Г1 for Е⊥с. The temperature coefficient of energy gap sifting in the case of temperature changing between 2 and 4.2 K equals to 10.6 meV/K and 3.2 mev/K for Г1→Г1 and Г2→Г1 band gap correspondingly. Reflectivity spectra were measured for energy interval 1.5-10 eV and optical functions (n, k, ε1, ε2,d2ε1/dE2 and d2ε2/dE2) were calculated by using Kramers-Kronig analyses. All features were interpreted as optical transitions on the basis of both theoretical calculations of band structure.

  11. Modulated crystal structure of Pr2SbO2.

    PubMed

    Magdysyuk, Oxana V; Nuss, Jürgen; Jansen, Martin

    2013-12-01

    The crystal structure of commensurately modulated Pr2SbO2 was solved in the orthorhombic superspace group Immm(0β0)000, q = 3/4b*, a = 13.5790 (15), b = 3.9818 (18), c = 4.0041 (18) Å (T = 40 K) from a crystal twinned by reticular pseudomerohedry applying the twin law (1 0 0, 0 0 1, 0 -1 0), corresponding to a rotation by 90° along the reciprocal a axis. The formation of Zintl-type Sb(2-)-Sb(2-) dumbbells in Pr2(3+)Sb(2-)O2(2-) is considered to be accountable for its semiconducting properties, as observed previously. The space group for the three-dimensional commensurate supercell a = 13.5790 (15), b = 15.9272 (18), c = 4.0041 (18) Å (T = 40 K) is Pmnm.

  12. Crystal and mol-ecular structure of aflatrem.

    PubMed

    Lenta, Bruno N; Ngatchou, Jules; Kenfack, Patrice T; Neumann, Beate; Stammler, Hans-Georg; Sewald, Norbert

    2015-11-01

    The crystal structure of the title compound, C32H39NO4, confirms the absolute configuration of the seven chiral centres in the mol-ecule. The molecule has a 1,1-dimethylprop-2-enyl substituent on the indole nucleus and this nucleus shares one edge with the five-membered ring which is, in turn, connected to a sequence of three edge-shared fused rings. The skeleton is completed by the 7,7-trimethyl-6,8-dioxabi-cyclo-[3.2.1]oct-3-en-2-one group connected to the terminal cyclohexene ring. The two cyclohexane rings adopt chair and half-chair conformations, while in the dioxabi-cyclo-[3.2.1]oct-3-en-2-one unit, the six-membered ring has a half-chair conformation. The indole system of the mol-ecule exhibits a tilt of 2.02 (1)° between its two rings. In the crystal, O-H⋯O hydrogen bonds connect mol-ecules into chains along [010]. Weak N-H⋯π inter-actions connect these chains, forming sheets parallel to (10-1).

  13. Crystal structure of the γ-secretase component nicastrin

    PubMed Central

    Xie, Tian; Yan, Chuangye; Zhou, Rui; Zhao, Yanyu; Sun, Linfeng; Yang, Guanghui; Lu, Peilong; Ma, Dan; Shi, Yigong

    2014-01-01

    γ-Secretase is an intramembrane protease responsible for the generation of amyloid-β (Aβ) peptides. Aberrant accumulation of Aβ leads to the formation of amyloid plaques in the brain of patients with Alzheimer's disease. Nicastrin is the putative substrate-recruiting component of the γ-secretase complex. No atomic-resolution structure had been identified on γ-secretase or any of its four components, hindering mechanistic understanding of γ-secretase function. Here we report the crystal structure of nicastrin from Dictyostelium purpureum at 1.95-Å resolution. The extracellular domain of nicastrin contains a large lobe and a small lobe. The large lobe of nicastrin, thought to be responsible for substrate recognition, associates with the small lobe through a hydrophobic pivot at the center. The putative substrate-binding pocket is shielded from the small lobe by a lid, which blocks substrate entry. These structural features suggest a working model of nicastrin function. Analysis of nicastrin structure provides insights into the assembly and architecture of the γ-secretase complex. PMID:25197054

  14. Crystal Structure of the Human Cannabinoid Receptor CB1.

    PubMed

    Hua, Tian; Vemuri, Kiran; Pu, Mengchen; Qu, Lu; Han, Gye Won; Wu, Yiran; Zhao, Suwen; Shui, Wenqing; Li, Shanshan; Korde, Anisha; Laprairie, Robert B; Stahl, Edward L; Ho, Jo-Hao; Zvonok, Nikolai; Zhou, Han; Kufareva, Irina; Wu, Beili; Zhao, Qiang; Hanson, Michael A; Bohn, Laura M; Makriyannis, Alexandros; Stevens, Raymond C; Liu, Zhi-Jie

    2016-10-20

    Cannabinoid receptor 1 (CB1) is the principal target of Δ(9)-tetrahydrocannabinol (THC), a psychoactive chemical from Cannabis sativa with a wide range of therapeutic applications and a long history of recreational use. CB1 is activated by endocannabinoids and is a promising therapeutic target for pain management, inflammation, obesity, and substance abuse disorders. Here, we present the 2.8 Å crystal structure of human CB1 in complex with AM6538, a stabilizing antagonist, synthesized and characterized for this structural study. The structure of the CB1-AM6538 complex reveals key features of the receptor and critical interactions for antagonist binding. In combination with functional studies and molecular modeling, the structure provides insight into the binding mode of naturally occurring CB1 ligands, such as THC, and synthetic cannabinoids. This enhances our understanding of the molecular basis for the physiological functions of CB1 and provides new opportunities for the design of next-generation CB1-targeting pharmaceuticals.

  15. Crystal structure of substrate free form of glycerol dehydratase

    SciTech Connect

    Liao, Der-Ing; Dotson, Garry; Turner, Jr., Ivan; Reiss, Lisa; Emptage, Mark

    2010-03-08

    Glycerol dehydratase (GDH) and diol dehydratase (DDH) are highly homologous isofunctional enzymes that catalyze the elimination of water from glycerol and 1,2-propanediol (1,2-PD) to the corresponding aldehyde via a coenzyme B{sub 12}-dependent radical mechanism. The crystal structure of substrate free form of GDH in complex with cobalamin and K{sup +} has been determined at 2.5 {angstrom} resolution. Its overall fold and the subunit assembly closely resemble those of DDH. Comparison of this structure and the DDH structure, available only in substrate bound form, shows the expected change of the coordination of the essential K{sup +} from hexacoordinate to heptacoordinate with the displacement of a single coordinated water by the substrate diol. In addition, there appears to be an increase in the rigidity of the K{sup +} coordination (as measured by lower B values) upon the binding of the substrate. Structural analysis of the locations of conserved residues among various GDH and DDH sequences has aided in identification of residues potentially important for substrate preference or specificity of protein-protein interactions.

  16. Understanding surface structure and chemistry of single crystal lanthanum aluminate

    NASA Astrophysics Data System (ADS)

    Pramana, Stevin S.; Cavallaro, Andrea; Qi, Jiahui; Nicklin, Chris L.; Ryan, Mary P.; Skinner, Stephen J.

    2017-03-01

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10‑10 Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10‑6 Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures.

  17. Crystal structure of lipid phosphatase Escherichia coli phosphatidylglycerophosphate phosphatase B.

    PubMed

    Fan, Junping; Jiang, Daohua; Zhao, Yan; Liu, Jianfeng; Zhang, Xuejun Cai

    2014-05-27

    Membrane-integrated type II phosphatidic acid phosphatases (PAP2s) are important for numerous bacterial to human biological processes, including glucose transport, lipid metabolism, and signaling. Escherichia coli phosphatidylglycerol-phosphate phosphatase B (ecPgpB) catalyzes removing the terminal phosphate group from a lipid carrier, undecaprenyl pyrophosphate, and is essential for transport of many hydrophilic small molecules across the membrane. We determined the crystal structure of ecPgpB at a resolution of 3.2 Å. This structure shares a similar folding topology and a nearly identical active site with soluble PAP2 enzymes. However, the substrate binding mechanism appears to be fundamentally different from that in soluble PAP2 enzymes. In ecPgpB, the potential substrate entrance to the active site is located in a cleft formed by a V-shaped transmembrane helix pair, allowing lateral movement of the lipid substrate entering the active site from the membrane lipid bilayer. Activity assays of point mutations confirmed the importance of the catalytic residues and potential residues involved in phosphate binding. The structure also suggests an induced-fit mechanism for the substrate binding. The 3D structure of ecPgpB serves as a prototype to study eukaryotic PAP2 enzymes, including human glucose-6-phosphatase, a key enzyme in the homeostatic regulation of blood glucose concentrations.

  18. Crystal Structure of an Active Form of Human MMP-1

    PubMed Central

    Iyer, Shalini; Visse, Robert; Nagase, Hideaki; Acharya, K. Ravi

    2006-01-01

    The extracellular matrix is a dynamic environment that constantly undergoes remodelling and degradation during vital physiological processes such as angiogenesis, wound healing, and development. Unbalanced extracellular matrix breakdown is associated with many diseases such as arthritis, cancer and fibrosis. Interstitial collagen is degraded by matrix metalloproteinases with collagenolytic activity by MMP-1, MMP-8 and MMP-13, collectively known as the collagenases. Matrix metalloproteinase 1 (MMP-1) plays a pivotal role in degradation of interstitial collagen types I, II, and III. Here, we report the crystal structure of the active form of human MMP-1 at 2.67 Å resolution. This is the first MMP-1 structure that is free of inhibitor and a water molecule essential for peptide hydrolysis is observed coordinated with the active site zinc. Comparing this structure with the human proMMP-1 shows significant structural differences, mainly in the relative orientation of the hemopexin domain, between the pro form and active form of the human enzyme. PMID:16890240

  19. Understanding surface structure and chemistry of single crystal lanthanum aluminate.

    PubMed

    Pramana, Stevin S; Cavallaro, Andrea; Qi, Jiahui; Nicklin, Chris L; Ryan, Mary P; Skinner, Stephen J

    2017-03-02

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10(-10) Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10(-6) Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures.

  20. Understanding surface structure and chemistry of single crystal lanthanum aluminate

    PubMed Central

    Pramana, Stevin S.; Cavallaro, Andrea; Qi, Jiahui; Nicklin, Chris L.; Ryan, Mary P.; Skinner, Stephen J.

    2017-01-01

    The surface crystallography and chemistry of a LaAlO3 single crystal, a material mainly used as a substrate to deposit technologically important thin films (e.g. for superconducting and magnetic devices), was analysed using surface X-ray diffraction and low energy ion scattering spectroscopy. The surface was determined to be terminated by Al-O species, and was significantly different from the idealised bulk structure. Termination reversal was not observed at higher temperature (600 °C) and chamber pressure of 10−10 Torr, but rather an increased Al-O occupancy occurred, which was accompanied by a larger outwards relaxation of Al from the bulk positions. Changing the oxygen pressure to 10−6 Torr enriched the Al site occupancy fraction at the outermost surface from 0.245(10) to 0.325(9). In contrast the LaO, which is located at the next sub-surface atomic layer, showed no chemical enrichment and the structural relaxation was lower than for the top AlO2 layer. Knowledge of the surface structure will aid the understanding of how and which type of interface will be formed when LaAlO3 is used as a substrate as a function of temperature and pressure, and so lead to improved design of device structures. PMID:28252044

  1. Crystal structure of a nuclear actin ternary complex.

    PubMed

    Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng

    2016-08-09

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT-associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus.

  2. Crystal Structure of the MecA Degradation Tag*

    PubMed Central

    Wang, Feng; Mei, Ziqing; Qi, Yutao; Yan, Chuangye; Xiang, Siheng; Zhou, Zhiyuan; Hu, Qi; Wang, Jiawei; Shi, Yigong

    2009-01-01

    MecA is an adaptor protein that regulates the assembly and activity of the ATP-dependent ClpCP protease in Bacillus subtilis. MecA contains two domains. Although the amino-terminal domain of MecA recruits substrate proteins such as ComK and ComS, the carboxyl-terminal domain (residues 121–218) has dual roles in the regulation and function of ClpCP protease. MecA-(121–218) facilitates the assembly of ClpCP oligomer, which is required for the protease activity of ClpCP. This domain was identified to be a non-recycling degradation tag that targets heterologous fusion proteins to the ClpCP protease for degradation. To elucidate the mechanism of MecA, we determined the crystal structure of MecA-(121–218) at 2.2 Å resolution, which reveals a previously uncharacterized α/β fold. Structure-guided mutagenesis allows identification of surface residues that are essential for the function of MecA. We also solved the structure of a carboxyl-terminal domain of YpbH, a paralogue of MecA in B. subtilis, at 2.4 Å resolution. Despite low sequence identity, the two structures share essentially the same fold. The presence of MecA homologues in other bacterial species suggests conservation of a large family of unique degradation tags. PMID:19801546

  3. Crystal structure of a nuclear actin ternary complex

    PubMed Central

    Cao, Tingting; Sun, Lingfei; Jiang, Yuxiang; Huang, Shanjin; Wang, Jiawei; Chen, Zhucheng

    2016-01-01

    Actin polymerizes and forms filamentous structures (F-actin) in the cytoplasm of eukaryotic cells. It also exists in the nucleus and regulates various nucleic acid transactions, particularly through its incorporation into multiple chromatin-remodeling complexes. However, the specific structure of actin and the mechanisms that regulate its polymeric nature inside the nucleus remain unknown. Here, we report the crystal structure of nuclear actin (N-actin) complexed with actin-related protein 4 (Arp4) and the helicase-SANT–associated (HSA) domain of the chromatin remodeler Swr1. The inner face and barbed end of N-actin are sequestered by interactions with Arp4 and the HSA domain, respectively, which prevents N-actin from polymerization and binding to many actin regulators. The two major domains of N-actin are more twisted than those of globular actin (G-actin), and its nucleotide-binding pocket is occluded, freeing N-actin from binding to and regulation by ATP. These findings revealed the salient structural features of N-actin that distinguish it from its cytoplasmic counterpart and provide a rational basis for its functions and regulation inside the nucleus. PMID:27457955

  4. Nanoconfinement crystallization of frustrated alkyl groups: crossover of mesophase to crystalline structure.

    PubMed

    Shi, Haifeng; Wang, Haixia; Xin, John H; Zhang, Xingxiang; Wang, Dujin

    2011-04-07

    Crossover of mesophase to crystalline structure in the nanoconfinement crystallization process of frustrated side groups elucidates the critical crystal thickness d(c) or the length scale of side groups, which defines the transition process from mesophase (hexagonal and monoclinic phase) to crystalline phase (orthorhombic phase) of confined CH(2) sequences in a given crystal size restriction.

  5. Modulation of defect modes intensity by controlled light scattering in photonic crystal with liquid crystal domain structure

    NASA Astrophysics Data System (ADS)

    Gunyakov, V. A.; Krakhalev, M. N.; Zyryanov, V. Ya.; Shabanov, V. F.; Loiko, V. A.

    2016-07-01

    A method to modulate the defect modes intensity in a multilayer photonic crystal with a nematic liquid crystal layer arranged midmost has been proposed. The various electrohydrodynamic domain structures (Williams domains, oblique rolls and grid pattern) were formed in the nematic layer under the action of ac electric field. The domains cause a polarization-sensitive light scattering which leads to an anisotropic reduction of the defect modes intensity. Thus by varying the applied voltage, we can tune gradually the transmittance spectrum of photonic crystal. In addition, the spectrum strongly depends on the light polarization direction above threshold voltage.

  6. m-Xylylenediaminium sulfate: crystal structure and Hirshfeld surface analysis.

    PubMed

    Guesmi, Afef; Gatfaoui, Sofian; Roisnel, Thierry; Marouani, Houda

    2016-06-01

    The crystal structure of the title salt {systematic name: [1,3-phenyl-enebis(methyl-ene)]bis-(aza-nium) sulfate}, C8H14N2 (2+)·SO4 (2-), consists of infinite (100) sheets of alternating organic and inorganic entities The m-xylylenediaminium cations are linked to the sulfate anions by N-H⋯O and asymmetric bifurcated N-H⋯(O,O) hydrogen bonds, generating a three-dimensional network. A weak C-H⋯O inter-action also occurs. The Hirshfeld surface analysis and the two-dimensional fingerprint maps indicate that the packing is dominated by H⋯O/O⋯H and H⋯H contacts.

  7. m-Xylylenediaminium sulfate: crystal structure and Hirshfeld surface analysis

    PubMed Central

    Guesmi, Afef; Gatfaoui, Sofian; Roisnel, Thierry; Marouani, Houda

    2016-01-01

    The crystal structure of the title salt {systematic name: [1,3-phenyl­enebis(methyl­ene)]bis­(aza­nium) sulfate}, C8H14N2 2+·SO4 2−, consists of infinite (100) sheets of alternating organic and inorganic entities The m-xylylenediaminium cations are linked to the sulfate anions by N—H⋯O and asymmetric bifurcated N—H⋯(O,O) hydrogen bonds, generating a three-dimensional network. A weak C—H⋯O inter­action also occurs. The Hirshfeld surface analysis and the two-dimensional fingerprint maps indicate that the packing is dominated by H⋯O/O⋯H and H⋯H contacts. PMID:27308040

  8. Characterization and Crystal Structure of a Robust Cyclohexanone Monooxygenase.

    PubMed

    Romero, Elvira; Castellanos, J Rubén Gómez; Mattevi, Andrea; Fraaije, Marco W

    2016-12-19

    Cyclohexanone monooxygenase (CHMO) is a promising biocatalyst for industrial reactions owing to its broad substrate spectrum and excellent regio-, chemo-, and enantioselectivity. However, the low stability of many Baeyer-Villiger monooxygenases is an obstacle for their exploitation in industry. Characterization and crystal structure determination of a robust CHMO from Thermocrispum municipale is reported. The enzyme efficiently converts a variety of aliphatic, aromatic, and cyclic ketones, as well as prochiral sulfides. A compact substrate-binding cavity explains its preference for small rather than bulky substrates. Small-scale conversions with either purified enzyme or whole cells demonstrated the remarkable properties of this newly discovered CHMO. The exceptional solvent tolerance and thermostability make the enzyme very attractive for biotechnology.

  9. Maximum probability domains in crystals: the rock-salt structure.

    PubMed

    Causà, Mauro; Savin, Andreas

    2011-11-17

    The present paper studies MX crystals in rock-salt structure (M: Li, Na, K; X: F, Cl, Br, I). They are often described as being formed by ions. Pictures based on quantum mechanical calculations sustain and quantify it. The tools used are (i) the Quantum Theory of Atoms in Molecules, (ii) the Electron Localization Function, and (iii) the maximization of the probability to find in a spatial domain a number of electrons equal to that of the ion under consideration. The present paper shows that the images provided by these three different tools to analyze the quantum mechanical calculations yield, for these systems, very similar results, in the sense that the spatial domains and probability distributions are close. While results for the first two methods are already present in the literature, the last of the methods is applied for the first time to these systems, and details about the method of calculation and program are also given.

  10. Crystal structure of (E)-dodec-2-enoic acid

    PubMed Central

    Sonneck, Marcel; Peppel, Tim; Spannenberg, Anke; Wohlrab, Sebastian

    2015-01-01

    The crystal structure of (E)-dodec-2-enoic acid, C12H22O2, an α,β-unsaturated carb­oxy­lic acid with a melting point (295 K) near room temperature, is characterized by carb­oxy­lic acid inversion dimers linked by pairs of O—H⋯O hydrogen bonds. The carb­oxy­lic acid group and the following three carbon atoms of the chain of the (E)-dodec-2-enoic acid mol­ecule lie almost in one plane (r.m.s. deviation for the four C atoms and two O atoms = 0.012 Å), whereas the remaining carbon atoms of the hydro­carbon chain adopt a nearly fully staggered conformation [moduli of torsion angles vary from 174.01 (13) to 179.97 (13)°]. PMID:26279945

  11. Crystal and molecular structure of sodium paratungstate 26 hydrate

    SciTech Connect

    Cruywagen, J.J.; Nassibemi, L.R.; Niven, M.L.; Vander Merwe, I.F.

    1986-08-01

    On standing, an acid solution of tungstate yields single crystals of the paratungstate salt Na/sub 10/(H/sub 2/W/sub 12/O/sub 42/ /SUB sd/ /SUP ./ 26H/sub 2/O. The space group is P1, (No. 2), a 11.811(2), b = 12.486(2), c = 12.206(2) A, ..cap alpha.. = 82.29(1), ..beta.. = 115.12(1), ..gamma.. = 113.76(1) /sup 0/, V = 1485.6 A/sup 3/, Z = 1. The structure was solved by direct methods and refined to R = 0.0397, R /SUB w/ = 0.0403 (w = (sigma/sup 2/F)/sup -1/). The 12 WO/sub 6/ octahedra (shared edges and vertices) are distorted from regular geometry; one of the sodium ions exhibits disorder and there is extensive hydrogen bonding between the water molecules and the oxygens of the paratungstate anion.

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

    PubMed

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

    2015-10-24

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

  13. Optical nonreciprocal transmission in an asymmetric silicon photonic crystal structure

    SciTech Connect

    Wu, Zheng; Chen, Juguang; Ji, Mengxi; Huang, Qingzhong; Xia, Jinsong; Wang, Yi E-mail: ywangwnlo@mail.hust.edu.cn; Wu, Ying E-mail: ywangwnlo@mail.hust.edu.cn

    2015-11-30

    An optical nonreciprocal transmission (ONT) is realized by employing the nonlinear effects in a compact asymmetric direct-coupled nanocavity-waveguide silicon photonic crystal structure with a high loaded quality factor (Q{sub L}) of 42 360 and large extinction ratio exceeding 30 dB. Applying a single step lithography and successive etching, the device can realize the ONT in an individual nanocavity, alleviating the requirement to accurately control the resonance of the cavities. A maximum nonreciprocal transmission ratio of 21.1 dB as well as a working bandwidth of 280 pm in the telecommunication band are obtained at a low input power of 76.7 μW. The calculated results by employing a nonlinear coupled-mode model are in good agreement with the experiment.

  14. Crystal and molecular structure of three biologically active nitroindazoles

    NASA Astrophysics Data System (ADS)

    Cabildo, Pilar; Claramunt, Rosa M.; López, Concepción; García, M. Ángeles; Pérez-Torralba, Marta; Pinilla, Elena; Torres, M. Rosario; Alkorta, Ibon; Elguero, José

    2011-01-01

    3-Bromo-1-methyl-7-nitro-1 H-indazole ( 1), 3-bromo-2-methyl-7-nitro-2 H-indazole ( 2) and 3,7-dinitro-1(2) H-indazole ( 3) have been synthesized and characterized by X-ray diffraction, 13C and 15N NMR spectroscopy in solution and in solid-state. The dihedral angles obtained in the crystal structures are in good agreement with the molecular parameters calculated using DFT B3LYP calculations employing the 6-311++G(d,p) basis set. Compounds 1 and 2 present intermolecular halogen bonds between the bromine and the oxygen atoms of the nitro group and in compound 3 inter- and intramolecular hydrogen bonding exists.

  15. Manufacturing, structure and properties of recycled polyethylene terephthalate /liquid crystal polymer/montmorillonite clay nanocomposites

    NASA Astrophysics Data System (ADS)

    Japins, Guntis; Berzina, Rita; Zicans, Janis; Merijs Meri, Remo; Ivanova, Tatjana; Kalkis, Valdis; Reinholds, Ingars

    2013-12-01

    Polyethylene terephthalate (PET)/liquid crystal polymer (LCP)/monthmorillonite clay (MMT) compositions were obtained by melt mixing. Their mechanical, structural, rheological and thermal properties were investigated.

  16. Crystal Structure of Cindoxin, the P450cin Redox Partner

    PubMed Central

    2015-01-01

    The crystal structure of the flavin mononucleotide (FMN)-containing redox partner to P450cin, cindoxin (Cdx), has been determined to 1.3 Å resolution. The overall structure is similar to that of the FMN domain of human cytochrome P450 reductase. A Brownian dynamics–molecular dynamics docking method was used to produce a model of Cdx with its redox partner, P450cin. This Cdx–P450cin model highlights the potential importance of Cdx Tyr96 in bridging the FMN and heme cofactors as well P450cin Arg102 and Arg346. Each of the single-site Ala mutants exhibits ∼10% of the wild-type activity, thus demonstrating the importance of these residues for binding and/or electron transfer. In the well-studied P450cam system, redox partner binding stabilizes the open low-spin conformation of P450cam and greatly decreases the stability of the oxy complex. In sharp contrast, Cdx does not shift P450cin to a low-spin state, although the stability of oxy-P450cin is decreased 10-fold in the presence of Cdx. This indicates that Cdx may have a modest effect on the open–closed equilibrium in P450cin compared to that in P450cam. It has been postulated that part of the effector role of Pdx on P450cam is to promote a significant structural change that makes available a proton relay network involving Asp251 required for O2 activation. The structure around the corresponding Asp in P450cin, Asp241, provides a possible structural reason for why P450cin is less dependent on its redox partner for functionally important structural changes. PMID:24533927

  17. The crystal structure of iron at the inner core

    NASA Astrophysics Data System (ADS)

    Tateno, S.; Hirose, K.; Ohishi, Y.; Tatsumi, Y.

    2010-12-01

    The Earth’s solid inner core is mainly composed of iron. Thus the crystal structure of iron is of prime importance for understanding the nature of solid inner core. Despite many efforts to investigate phase relations of iron have by dynamic and static compression, and theoretical calculation, consensus on the stable phase at the inner core condition has never been achieved. While hcp-Fe can persist to core pressures at 300 K, a phase transition at elevated temperature is a possibility. Both theory and experiments proposed different forms of iron at simultaneously high P-T conditions, which include bcc, face-centered-cubic (fcc), and hcp structures. The structure of iron has never been examined experimentally at the inner core P-T conditions (>330 GPa and ≥5000 K), because such extreme conditions could only be achieved by shock-wave compression experiments. Based on static compression experiments in a laser-heated diamond-anvil cell (DAC), we determined the structure of iron up to 377 GPa and 5700 K. Iron powder and thermal insulation layers of SiO2 glass were loaded into a hole of a pre-indented rhenium gasket placed in the For experiments beyond 300 GPa, the double-beveled diamond anvils with 40-μm culets were used, and accordingly the sample size was limited to about 20 μm. Heating was performed from both sides of the sample by employing two single mode, Yb fiber lasers with output power up to 100 W each with flat-top beam shaping optics to minimize temperature gradient across the sample. Angle-dispersive x-ray diffraction measurements were conducted at BL10XU of SPring-8. Six separate sets of experiments were conducted in a wide P-T range from 135 GPa and 2690 K to 377 GPa and 5700 K. We observed crystal growth and hence the stability of hcp-Fe at these P-T conditions with no evidence for a phase transition to bcc nor fcc iron phases. The c/a axial ratio of hcp-Fe at high temperature was also studied, which has significant effect on the nature of the

  18. Crystal structure and vibrational properties of RFe3(BO3)4 (R = Ce - Lu) ferroborate crystal: ab initio calculations

    NASA Astrophysics Data System (ADS)

    Petrov, V. P.; Chernyshev, V. A.; Nikiforov, A. E.

    2016-12-01

    The ab initio calculations of the crystal structure and lattice dynamics of ferroborate crystal family RFe3(BO3)4 (R = Ce, Pm, Eu, Gd, Tb, Dy, Ho, Er, Tm, Yb, Lu), S.G. R32, has been carried out within the framework of the MO LCAO approach by using density functional theory and effective 4f-in-core pseudopotential for rare earth element. The fully optimized geometry as well as vibrational frequencies has been calculated.

  19. Crystal structure refinement and hydration behaviour of doped tricalcium aluminate

    SciTech Connect

    Stephan, Dietmar . E-mail: dietmar.stephan@online.de; Wistuba, Sebastian

    2006-11-15

    In this paper analytical evidence on crystal structure and hydration behaviour of C{sub 3}A solid solutions with MgO, SiO{sub 2}, Fe{sub 2}O{sub 3}, Na{sub 2}O and K{sub 2}O is given. Samples were prepared using an innovative sol-gel process as precursor, examined by X-ray powder diffraction, infra-red spectroscopy and the crystal structure was refined by the Rietveld method. A significant shift of lattice parameters was found for C{sub 3}A solid solutions with SiO{sub 2}, Fe{sub 2}O{sub 3} or Na{sub 2}O but only minor changes were detected for K{sub 2}O. The hydration of C{sub 3}A solid solutions in the absence of CaSO{sub 4} was accelerated for samples doped with SiO{sub 2} or K{sub 2}O and it was retarded in the case of MgO, Fe{sub 2}O{sub 3} or Na{sub 2}O. The hydration in the presence of CaSO{sub 4} was accelerated when C{sub 3}A was doped with K{sub 2}O or Na{sub 2}O, whereas Fe{sub 2}O{sub 3} strongly retarded the hydration. The doping with SiO{sub 2} nearly had no influence on the hydration, the effect of MgO was not straight forward.

  20. Syntheses and crystal structures of two new pentaborates

    NASA Astrophysics Data System (ADS)

    Wang, Guo-Ming; Sun, Yan-Qiong; Yang, Guo-Yu

    2005-03-01

    Two new pentaborates, [Zn(DIEN) 2][B 5O 6(OH) 4] 2 (DIEN=diethylenetriamine) ( I) and [B 5O 7(OH) 3Zn(TREN)] (TREN=tris(2-aminoethyl)amine) ( II), have been hydrothermally synthesized and characterized by single crystal X-ray diffraction, FTIR, elemental analysis and thermogravimetric analysis. Compound I crystallizes in the monoclinic system, space group P2 1/c (No. 14), a=8.5686(2) Å, b=11.7883(3) Å, c=14.5407(6) Å, β=91.259(2)°, V=1468.39(8) Å3, Z=2. The structure consists of isolated borate polyanion [B 5O 6(OH) 4] - and zinc complex cation [Zn(DIEN) 2] 2+. The anionic units, [B 5O 6(OH) 4] -, are linked by hydrogen bonds to form a 3D supramolecular network containing large channels, in which the templating [Zn(DIEN) 2] 2+ cation are located. II is monoclinic, P2 1/c (No. 14), a=8.9969(2) Å, b=20.6903(6) Å, c=9.2878(3) Å, β=99.635(2)°, V=1704.52(8) Å3, Z=4. The structure of II is constructed from two distinct motifs, a usual [B 5O 7(OH) 3] 2- cluster and a supporting zinc complex [Zn(TREN)] 2+, which are integrated through Zn-O-B linkage. This compound represents the first example of the combination of B-O cluster with transition-metal complex.

  1. 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.

  2. Crystallization of Stretched Polyimides: A Structure-Property Study

    NASA Technical Reports Server (NTRS)

    Hinkley, Jeffrey A.; Dezern, James F.

    2002-01-01

    A simple rotational isomeric state model was used to detect the degree to which polyimide repeat units might align to give an extended crystal. It was found experimentally that the hallmarks of stretch-crystallization were more likely to occur in materials whose molecules could readily give extended, aligned conformations. A proposed screening criterion was 84% accurate in selecting crystallizing molecules.

  3. Crystal structures and second-order NLO properties of borogermanates

    SciTech Connect

    Zhang, Jian-Han; Kong, Fang; Xu, Xiang; Mao, Jiang-Gao

    2012-11-15

    Borogermanates are a class of very important compounds in materials chemistry. In this paper, the syntheses, structures, and properties of metal borogermanates are reviewed. Organically templated borogermanates with zeolite-like open-frameworks show potential applications as microporous materials. Many compounds in alkali or alkaline-earth borogermanate systems are structurally acentric or polar, some of which exhibit excellent Second Harmonic Generation (SHG) coefficients, wide transparency regions, and high optical-damage thresholds as well as excellent thermal stability. Most of the lanthanide borogermanates are structurally centrosymmetric and not SHG active; however, they are able to emit strong luminescence in visible or near-IR region. In the B-rich compounds, BO{sub 3} and BO{sub 4} groups can be polymerized into a variety of discrete polynuclear anionic cluster units or extended architectures via B-O-B bridges; whereas in the Ge-rich compounds, GeO{sub 4} and GeO{sub 6} polyhedra can also be polymerized. The combinations of borate and germinate afforded rich structural and topological types. - Graphical abstract: Borogermanates are a class of very important compounds in materials chemistry. Both BO{sub x} (x=3, 4) and GeO{sub y} (y=4, 6) polyhedra can be polymerized into a variety of discrete polynuclear anionic cluster units or extended architectures. The combinations of borate and germanate groups in the same oxide framework not only give rise to a rich structural chemistry, but also afford many polar compounds with good SHG properties. Highlights: Black-Right-Pointing-Pointer Borogermanates are a class of new materials. Black-Right-Pointing-Pointer They feature to be the combination of B and Ge atoms into the same oxide framework. Black-Right-Pointing-Pointer They can form a large number of novel 2D and 3D framework structures. Black-Right-Pointing-Pointer Some of them are acentric or polar with moderate strong SHG responses.

  4. Structure of apo acyl carrier protein and a proposal to engineer protein crystallization through metal ions

    SciTech Connect

    Qiu, Xiayang; Janson, Cheryl A.

    2010-11-16

    A topic of current interest is engineering surface mutations in order to improve the success rate of protein crystallization. This report explores the possibility of using metal-ion-mediated crystal-packing interactions to facilitate rational design. Escherichia coli apo acyl carrier protein was chosen as a test case because of its high content of negatively charged carboxylates suitable for metal binding with moderate affinity. The protein was successfully crystallized in the presence of zinc ions. The crystal structure was determined to 1.1 {angstrom} resolution with MAD phasing using anomalous signals from the co-crystallized Zn{sup 2+} ions. The case study suggested an integrated strategy for crystallization and structure solution of proteins via engineering surface Asp and Glu mutants, crystallizing them in the presence of metal ions such as Zn{sup 2+} and solving the structures using anomalous signals.

  5. Crystal structure of HgGa{sub 2}Se{sub 4} under compression

    SciTech Connect

    Gomis, Oscar; Vilaplana, Rosario; Manjón, Francisco Javier; Santamaría-Pérez, David [Departamento de Química Física I, Universidad Complutense de Madrid, MALTA Consolider Team, Avenida Complutense s Departamento de Física Aplicada-ICMUV, MALTA Consolider Team, Universidad de Valencia, Edificio de Investigación, C Errandonea, Daniel [Departamento de Física Aplicada-ICMUV, MALTA Consolider Team, Universidad de Valencia, Edificio de Investigación, C and others

    2013-06-01

    Highlights: ► Single crystals of HgGa{sub 2}Se{sub 4} with defect-chalcopyrite structure were synthesized. ► HgGa{sub 2}Se{sub 4} exhibits a phase transition to a disordered rock salt structure at 17 GPa. ► HgGa{sub 2}Se{sub 4} undergoes a phase transition below 2.1 GPa to a disordered zinc blende. - Abstract: We report on high-pressure x-ray diffraction measurements up to 17.2 GPa in mercury digallium selenide (HgGa{sub 2}Se{sub 4}). The equation of state and the axial compressibilities for the low-pressure tetragonal phase have been determined and compared to related compounds. HgGa{sub 2}Se{sub 4} exhibits a phase transition on upstroke toward a disordered rock-salt structure beyond 17 GPa, while on downstroke it undergoes a phase transition below 2.1 GPa to a phase that could be assigned to a metastable zinc-blende structure with a total cation-vacancy disorder. Thermal annealing at low- and high-pressure shows that kinetics plays an important role on pressure-driven transitions.

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

    PubMed Central

    Hastie, Kathryn M.; Zandonatti, Michelle; Liu, Tong; Li, Sheng; Woods, Virgil L.

    2016-01-01

    ABSTRACT The arenavirus matrix protein Z is highly multifunctional and occurs in both monomeric and oligomeric forms. The crystal structure of a dodecamer of Z from Lassa virus, presented here, illustrates a ring-like structure with a highly basic center. Mutagenesis demonstrates that the dimeric interface within the dodecamer and a Lys-Trp-Lys triad at the center of the ring are important for oligomerization. This structure provides an additional template to explore the many functions of Z. IMPORTANCE The arenavirus Lassa virus causes hundreds of thousands of infections each year, many of which develop into fatal hemorrhagic fever. The arenavirus matrix protein Z is multifunctional, with at least four distinct roles. Z exists in both monomeric and oligomeric forms, each of which likely serves a specific function in the viral life cycle. Here we present the dodecameric form of Lassa virus Z and demonstrate that Z forms a “wreath” with a highly basic center. This structure and that of monomeric Z now provide a pair of critical templates by which the multiple roles of Z in the viral life cycle may be interpreted. PMID:26912609

  7. Crystal structure and elementary electronic properties of Bi-stabilized α-In{sub 2}Se{sub 3}

    SciTech Connect

    Ji, Huiwen; Reijnders, Anjan; Liang, Tian; Schoop, L.M.; Burch, K.S.; Ong, N.P.; Cava, R.J.

    2013-07-15

    Highlights: • The introduction of Bi stabilizes α-In{sub 2}Se{sub 3} and facilitates the crystal growth. • Optical measurements show an indirect band gap. • Transport measurements show semiconducting temperature dependence. - Abstract: The introduction of Bi as a substitution for In at ∼12% in In{sub 2}Se{sub 3} stabilizes the α-polymorph and facilitates the crystal growth by the modified Bridgeman method. The crystal structure (R−3m, Z = 3, a = 3.9978(8) Å, c = 28.276(6) Å) and composition, (In{sub 0.88}Bi{sub 0.12}){sub 2}Se{sub 3}, of the crystals were determined by single crystal X-ray diffraction. The structure, of the tetradymite type, displays positional disorder within the middle Se layer. Optical measurements indicate that (In{sub 0.88}Bi{sub 0.12}){sub 2}Se{sub 3} has an indirect band gap of about 1.19 eV, shown by electronic structure calculations to be from valence band states near the Γ point to conduction band states at the L point. Resistivity and Hall effect measurements on Sn-doped crystals of composition (In{sub 0.88}Bi{sub 0.115}Sn{sub 0.005}){sub 2}Se{sub 3} show it to have a relatively high semiconducting resistivity, about 6 × 10{sup 4} Ω cm at 300 K, with an n-type carrier concentration varying from 10{sup 12}/cm{sup 3} at 300 K to 10{sup 15}/cm{sup 3} at 400 K.

  8. Solvothermal crystal growth of CuSbQ{sub 2} (Q=S, Se) and the correlation between macroscopic morphology and microscopic structure

    SciTech Connect

    Zhou Jian; Bian Guoqing; Zhu Qinyu; Zhang Yong; Li Chunying; Dai Jie

    2009-02-15

    A low temperature solvothermal method has been successfully used for preparation of two semiconductor compounds CuSbQ{sub 2} (Q=S(1), Se(2)) by the reactions of Cu, Sb and S(or Se) powders in 1,2-diaminopropane at 160 deg. C for 10 days. The crystal structure of 2 was determined first time using single crystal X-ray diffraction analyses. The structures of 1 and 2 are discussed in the view of covalent bonds and weak interactions. Double CuSbQ{sub 2} layers are assembled to a 3-D network structure by Cu...Sb and Q...Sb secondary bonds. In contrast with the isostructure of the two materials, the crystal morphology of them is quite different, brick-like crystals for CuSbS{sub 2} and plank-like crystals for CuSbSe{sub 2}. The phenomenon is related to their different inter-planar interactions. Semiconductor properties of the microcrystal samples are measured and the band gaps of 1 and 2 are 1.38 and 1.05 eV, respectively. - Graphical abstract: Two isostructural compounds, CuSbQ{sub 2} (Q=S, Se), display different morphologies in crystals, which is explained by comparing the strength of the interlayer interactions based on the crystal structure data.

  9. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase ll)

    SciTech Connect

    Collard, F.; Zhang, J; Nemet, I; Qanungo, K; Monnier, V; Yee, V

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  10. Crystal structure of the Rous sarcoma virus intasome

    PubMed Central

    Yin, Zhiqi; Shi, Ke; Banerjee, Surajit; Pandey, Krishan K.; Bera, Sibes; Grandgenett, Duane P.; Aihara, Hideki

    2015-01-01

    Integration of the reverse-transcribed viral DNA into the host genome is an essential step in the lifecycle of retroviruses. Retrovirus integrase (IN) catalyzes insertions of both ends of the linear viral DNA into a host chromosome 1. IN from HIV-1 and closely related retroviruses share the three-domain organization, consisting of a catalytic core domain flanked by N- and C-terminal domains essential for the concerted integration reaction. Although structures of the tetrameric IN-DNA complexes have been reported for IN from prototype foamy virus (PFV) featuring an additional DNA-binding domain and longer interdomain linkers 2–5, the architecture of a canonical three-domain IN bound to DNA remained elusive. Here we report a crystal structure of the three-domain IN from Rous sarcoma virus (RSV) in complex with viral and target DNAs. The structure shows an octameric assembly of IN, in which a pair of IN dimers engage viral DNA ends for catalysis while another pair of non-catalytic IN dimers bridge between the two viral DNA molecules and help capture target DNA. The individual domains of the eight IN molecules play varying roles to hold the complex together, making an extensive network of protein-DNA and protein-protein contacts that show both conserved and distinct features compared to those observed for PFV IN. Our work highlights diversity of retrovirus intasome assembly and provides insights into the mechanisms of integration by HIV-1 and related retroviruses. PMID:26887497

  11. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)

    SciTech Connect

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2009-01-12

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6{angstrom} resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12{angstrom} deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates.

  12. 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.

  13. Crystal structure of Bacillus anthracis transpeptidase enzyme CapD.

    SciTech Connect

    Wu, R.; Richter, S.; Zhang, R.; Anderson, V. J.; Missiakas, D.; Joachimiak, A.; Biosciences Division; Univ. of Chicago

    2009-09-04

    Bacillus anthracis elaborates a poly-{gamma}-d-glutamic acid capsule that protects bacilli from phagocytic killing during infection. The enzyme CapD generates amide bonds with peptidoglycan cross-bridges to anchor capsular material within the cell wall envelope of B. anthracis. The capsular biosynthetic pathway is essential for virulence during anthrax infections and can be targeted for anti-infective inhibition with small molecules. Here, we present the crystal structures of the {gamma}-glutamyltranspeptidase CapD with and without {alpha}-l-Glu-l-Glu dipeptide, a non-hydrolyzable analog of poly-{gamma}-d-glutamic acid, in the active site. Purified CapD displays transpeptidation activity in vitro, and its structure reveals an active site broadly accessible for poly-{gamma}-glutamate binding and processing. Using structural and biochemical information, we derive a mechanistic model for CapD catalysis whereby Pro{sup 427}, Gly{sup 428}, and Gly{sup 429} activate the catalytic residue of the enzyme, Thr{sup 352}, and stabilize an oxyanion hole via main chain amide hydrogen bonds.

  14. Crystal structures of phosphoketolase: thiamine diphosphate-dependent dehydration mechanism.

    PubMed

    Suzuki, Ryuichiro; Katayama, Takane; Kim, Byung-Jun; Wakagi, Takayoshi; Shoun, Hirofumi; Ashida, Hisashi; Yamamoto, Kenji; Fushinobu, Shinya

    2010-10-29

    Thiamine diphosphate (ThDP)-dependent enzymes are ubiquitously present in all organisms and catalyze essential reactions in various metabolic pathways. ThDP-dependent phosphoketolase plays key roles in the central metabolism of heterofermentative bacteria and in the pentose catabolism of various microbes. In particular, bifidobacteria, representatives of beneficial commensal bacteria, have an effective glycolytic pathway called bifid shunt in which 2.5 mol of ATP are produced per glucose. Phosphoketolase catalyzes two steps in the bifid shunt because of its dual-substrate specificity; they are phosphorolytic cleavage of fructose 6-phosphate or xylulose 5-phosphate to produce aldose phosphate, acetyl phosphate, and H(2)O. The phosphoketolase reaction is different from other well studied ThDP-dependent enzymes because it involves a dehydration step. Although phosphoketolase was discovered more than 50 years ago, its three-dimensional structure remains unclear. In this study we report the crystal structures of xylulose 5-phosphate/fructose 6-phosphate phosphoketolase from Bifidobacterium breve. The structures of the two intermediates before and after dehydration (α,β-dihydroxyethyl ThDP and 2-acetyl-ThDP) and complex with inorganic phosphate give an insight into the mechanism of each step of the enzymatic reaction.

  15. Crystal Structure of the Epithelial Calcium Channel TRPV6

    PubMed Central

    Saotome, Kei; Singh, Appu K.; Yelshanskaya, Maria V.; Sobolevsky, Alexander I.

    2016-01-01

    Summary Precise regulation of calcium homeostasis is essential for many physiological functions. The Ca2+-selective TRP channels TRPV5 and TRPV6 play vital roles in calcium homeostasis as Ca2+ uptake channels in epithelial tissues. Detailed structural bases for their assembly and Ca2+ permeation remain obscure. Here, we report the crystal structure of rat TRPV6 at 3.25 Å resolution. The overall architecture of TRPV6 reveals shared and unique features compared to other TRP channels. Intracellular domains engage in extensive interactions to form an intracellular “skirt” involved in allosteric modulation. In the K+ channel-like transmembrane domain, Ca2+ selectivity is determined by direct coordination of Ca2+ by a ring of aspartate side chains in the selectivity filter. Based on crystallographically identified cation binding sites at the pore axis and extracellular vestibule, we propose a Ca2+ permeation mechanism. Our results provide a structural foundation to understand the regulation of epithelial Ca2+ uptake and its role in pathophysiology. PMID:27296226

  16. Crystal Structure of Alcohol Oxidase from Pichia pastoris

    PubMed Central

    Valerius, Oliver; Feussner, Ivo; Ficner, Ralf

    2016-01-01

    FAD-dependent alcohol oxidases (AOX) are key enzymes of methylotrophic organisms that can utilize lower primary alcohols as sole source of carbon and energy. Here we report the crystal structure analysis of the methanol oxidase AOX1 from Pichia pastoris. The crystallographic phase problem was solved by means of Molecular Replacement in combination with initial structure rebuilding using Rosetta model completion and relaxation against an averaged electron density map. The subunit arrangement of the homo-octameric AOX1 differs from that of octameric vanillyl alcohol oxidase and other dimeric or tetrameric alcohol oxidases, due to the insertion of two large protruding loop regions and an additional C-terminal extension in AOX1. In comparison to other alcohol oxidases, the active site cavity of AOX1 is significantly reduced in size, which could explain the observed preference for methanol as substrate. All AOX1 subunits of the structure reported here harbor a modified flavin adenine dinucleotide, which contains an arabityl chain instead of a ribityl chain attached to the isoalloxazine ring. PMID:26905908

  17. Crystal structures of the TRIC trimeric intracellular cation channel orthologues

    PubMed Central

    Kasuya, Go; Hiraizumi, Masahiro; Maturana, Andrés D; Kumazaki, Kaoru; Fujiwara, Yuichiro; Liu, Keihong; Nakada-Nakura, Yoshiko; Iwata, So; Tsukada, Keisuke; Komori, Tomotaka; Uemura, Sotaro; Goto, Yuhei; Nakane, Takanori; Takemoto, Mizuki; Kato, Hideaki E; Yamashita, Keitaro; Wada, Miki; Ito, Koichi; Ishitani, Ryuichiro; Hattori, Motoyuki; Nureki, Osamu

    2016-01-01

    Ca2+ release from the sarcoplasmic reticulum (SR) and endoplasmic reticulum (ER) is crucial for muscle contraction, cell growth, apoptosis, learning and memory. The trimeric intracellular cation (TRIC) channels were recently identified as cation channels balancing the SR and ER membrane potentials, and are implicated in Ca2+ signaling and homeostasis. Here we present the crystal structures of prokaryotic TRIC channels in the closed state and structure-based functional analyses of prokaryotic and eukaryotic TRIC channels. Each trimer subunit consists of seven transmembrane (TM) helices with two inverted repeated regions. The electrophysiological, biochemical and biophysical analyses revealed that TRIC channels possess an ion-conducting pore within each subunit, and that the trimer formation contributes to the stability of the protein. The symmetrically related TM2 and TM5 helices are kinked at the conserved glycine clusters, and these kinks are important for the channel activity. Furthermore, the kinks of the TM2 and TM5 helices generate lateral fenestrations at each subunit interface. Unexpectedly, these lateral fenestrations are occupied with lipid molecules. This study provides the structural and functional framework for the molecular mechanism of this ion channel superfamily. PMID:27909292

  18. Crystal structure of the RNA component of bacterial ribonuclease P.

    PubMed

    Torres-Larios, Alfredo; Swinger, Kerren K; Krasilnikov, Andrey S; Pan, Tao; Mondragón, Alfonso

    2005-09-22

    Transfer RNA (tRNA) is produced as a precursor molecule that needs to be processed at its 3' and 5' ends. Ribonuclease P is the sole endonuclease responsible for processing the 5' end of tRNA by cleaving the precursor and leading to tRNA maturation. It was one of the first catalytic RNA molecules identified and consists of a single RNA component in all organisms and only one protein component in bacteria. It is a true multi-turnover ribozyme and one of only two ribozymes (the other being the ribosome) that are conserved in all kingdoms of life. Here we show the crystal structure at 3.85 A resolution of the RNA component of Thermotoga maritima ribonuclease P. The entire RNA catalytic component is revealed, as well as the arrangement of the two structural domains. The structure shows the general architecture of the RNA molecule, the inter- and intra-domain interactions, the location of the universally conserved regions, the regions involved in pre-tRNA recognition and the location of the active site. A model with bound tRNA is in agreement with all existing data and suggests the general basis for RNA-RNA recognition by this ribozyme.

  19. Crystal Structure of the Deglycating Enzyme Fructosamine Oxidase (Amadoriase II)*

    PubMed Central

    Collard, François; Zhang, Jianye; Nemet, Ina; Qanungo, Kaustubha R.; Monnier, Vincent M.; Yee, Vivien C.

    2008-01-01

    Fructosamine oxidases (FAOX) catalyze the oxidative deglycation of low molecular weight fructosamines (Amadori products). These proteins are of interest in developing an enzyme to deglycate proteins implicated in diabetic complications. We report here the crystal structures of FAOX-II from the fungi Aspergillus fumigatus, in free form and in complex with the inhibitor fructosyl-thioacetate, at 1.75 and 1.6Å resolution, respectively. FAOX-II is a two domain FAD-enzyme with an overall topology that is most similar to that of monomeric sarcosine oxidase. Active site residues Tyr-60, Arg-112 and Lys-368 bind the carboxylic portion of the fructosamine, whereas Glu-280 and Arg-411 bind the fructosyl portion. From structure-guided sequence comparison, Glu-280 was identified as a signature residue for FAOX activity. Two flexible surface loops become ordered upon binding of the inhibitor in a catalytic site that is about 12Å deep, providing an explanation for the very low activity of FAOX enzymes toward protein-bound fructosamines, which would have difficulty accessing the active site. Structure-based mutagenesis showed that substitution of Glu-280 and Arg-411 eliminates enzyme activity. In contrast, modification of other active site residues or of amino acids in the flexible active site loops has little effect, highlighting these regions as potential targets in designing an enzyme that will accept larger substrates. PMID:18667417

  20. Crystal structure of an HIV assembly and maturation switch

    SciTech Connect

    Wagner, Jonathan M.; Zadrozny, Kaneil K.; Chrustowicz, Jakub; Purdy, Michael D.; Yeager, Mark; Ganser-Pornillos, Barbie K.; Pornillos, Owen

    2016-07-14

    Virus assembly and maturation proceed through the programmed operation of molecular switches, which trigger both local and global structural rearrangements to produce infectious particles. HIV-1 contains an assembly and maturation switch that spans the C-terminal domain (CTD) of the capsid (CA) region and the first spacer peptide (SP1) of the precursor structural protein, Gag. The crystal structure of the CTD-SP1 Gag fragment is a goblet-shaped hexamer in which the cup comprises the CTD and an ensuing type II β-turn, and the stem comprises a 6-helix bundle. The β-turn is critical for immature virus assembly and the 6-helix bundle regulates proteolysis during maturation. This bipartite character explains why the SP1 spacer is a critical element of HIV-1 Gag but is not a universal property of retroviruses. Our results also indicate that HIV-1 maturation inhibitors suppress unfolding of the CA-SP1 junction and thereby delay access of the viral protease to its substrate.