WorldWideScience

Sample records for chemical structure

  1. Identification numbers for chemical structures

    International Nuclear Information System (INIS)

    Several identification (ID) numbers for chemical structures (connectivity ID number, prime ID number, weighted ID number) are analyzed and tested until a counterexample (a pair of structures with the same ID number) is found. The analysis is carried out for acyclic structures with up to 20 atoms, trees with up to 20 points, benzenoid graphs and polyhexes with up to 10 hexagons, and all connected graphs with up to 6 points. Although all the (chemical) ID numbers studied are highly selective for many families of (molecular) graphs, none of them are unique; in all three cases the counterexamples are found. However, the greatest discriminative power is shown by the weighted ID number

  2. Structure validation in chemical crystallography.

    Science.gov (United States)

    Spek, Anthony L

    2009-02-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions.

  3. Can chemical structure predict reproductive toxicity?

    OpenAIRE

    Maslankiewicz L; Hulzebos EM; Vermeire TG; Muller JJA; Piersma AH; SEC

    2005-01-01

    Structure-Activity Relationships (SARs), including Quantitative SARs, are applied to the hazard assessment of chemicals. This need is all the more urgent considering the proposed new EU policy on chemicals in REACH, which stresses the need for non-animal testing. DEREKfW and the TSCA Chemical Category List of the New Chemicals Program of the US-EPA were chosen to predict reproductive toxicity for REACH purposes. DEREKfW is a software program predicting the toxicological properties using the l...

  4. Protein Structure Determination Using Chemical Shifts

    DEFF Research Database (Denmark)

    Christensen, Anders Steen

    In this thesis, a protein structure determination using chemical shifts is presented. The method is implemented in the open source PHAISTOS protein simulation framework. The method combines sampling from a generative model with a coarse-grained force field and an energy function that includes...... chemical shifts. The method is benchmarked on folding simulations of five small proteins. In four cases the resulting structures are in excellent agreement with experimental data, the fifth case fail likely due to inaccuracies in the energy function. For the Chymotrypsin Inhibitor protein, a structure...

  5. Chemical structure and dynamics: Annual report 1993

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1994-07-01

    The Chemical Structure and Dynamics program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally-important interfaces. The research program is built around the established relationship between structure, thermodynamics, and kinetics. This research effort continues to evolve into a program of rigorous studies of fundamental molecular processes in model systems (e.g., well-characterized surfaces, single-component solutions, clusters, and biological molecules), and studies of complex systems found in the environment. Experimental studies of molecular and supramolecular structures and thermodynamics are key to understanding the nature of matter, and lead to direct comparison with computational results. Kinetic and mechanistic measurements, combined with real-time dynamics measurements of atomic and molecular motions during chemical reactions, provide for a molecular-level description of chemical reactions. The anticipated results of this work are the achievement of a quantitative understanding of chemical processes at complex interfaces, the development of new techniques for the detection and measurement of species at such interfaces, and the interpretation and extrapolation of the observations in terms of models of interfacial chemistry. The Chemical Structure and Dynamics research program includes five areas described in detail in this report: Reaction mechanisms at solid interfaces; Solution and solution interfaces; Structure and dynamics of biological systems; Analytical methods development; and atmospheric chemistry. Extended abstracts are presented for 23 studies.

  6. Chemical structure and dynamics: Annual report 1996

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1997-03-01

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.

  7. Chemical structure and dynamics: Annual report 1996

    International Nuclear Information System (INIS)

    The Chemical Structure and Dynamics (CS ampersand D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species

  8. Chemical structure and dynamics. Annual report 1995

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1996-05-01

    The Chemical Structure and Dynamics program is a major component of Pacific Northwest National Laboratory`s Environmental Molecular Sciences Laboratory (EMSL), providing a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for the characterization of waste tanks and pollutant distributions, and for detection and monitoring of trace atmospheric species.

  9. Annual Report 2000. Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Colson, Steven D.; McDowell, Robin S.

    2001-04-15

    This annual report describes the research and accomplishments of the Chemical Structure and Dynamics Program in the year 2000, one of six research programs at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) - a multidisciplinary, national scientific user facility and research organization. The Chemical Structure and Dynamics (CS&D) program is meeting the need for a fundamental, molecular-level understanding by 1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; 2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and 3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  10. The PubChem chemical structure sketcher

    Directory of Open Access Journals (Sweden)

    Ihlenfeldt Wolf D

    2009-12-01

    Full Text Available Abstract PubChem is an important public, Web-based information source for chemical and bioactivity information. In order to provide convenient structure search methods on compounds stored in this database, one mandatory component is a Web-based drawing tool for interactive sketching of chemical query structures. Web-enabled chemical structure sketchers are not new, being in existence for years; however, solutions available rely on complex technology like Java applets or platform-dependent plug-ins. Due to general policy and support incident rate considerations, Java-based or platform-specific sketchers cannot be deployed as a part of public NCBI Web services. Our solution: a chemical structure sketching tool based exclusively on CGI server processing, client-side JavaScript functions, and image sequence streaming. The PubChem structure editor does not require the presence of any specific runtime support libraries or browser configurations on the client. It is completely platform-independent and verified to work on all major Web browsers, including older ones without support for Web2.0 JavaScript objects.

  11. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson KWAUK

    2007-01-01

    Around the turn of the present century, scholars began to recognize chemical engineering as a complex system, and have been searching for a convenient point of entry for refreshing its knowledge base. From our study of the dynamic structures of dispersed particles in fluidization and the resulting multi-scale method, we have been attempting to extend our findings to structures prevailing in other multiphase systems as well as in the burgeoning industries producing functional materials. Chemical engineering itself is hierarchically structured. Besides structures based on space and time, such hierarchy could be built from ChE history scaled according to science content, or from ChE operation according to the expenditure of manpower and capital investment.

  12. Chemical Structure and Dynamics annual report 1997

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.; McDowell, R.S.

    1998-03-01

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE`s environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous.

  13. Chemical Structure and Dynamics annual report 1997

    International Nuclear Information System (INIS)

    The Chemical Structure and Dynamics (CS and D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. The authors respond to the need for a fundamental, molecular level understanding of chemistry at a wide variety of environmentally important interfaces by: (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing complex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. The focus of the research is defined primarily by DOE's environmental problems: fate and transport of contaminants in the subsurface environment, processing and storage of waste materials, cellular effects of chemical and radiological insult, and atmospheric chemistry as it relates to air quality and global change. Twenty-seven projects are described under the following topical sections: Reaction mechanisms at interfaces; High-energy processes at environmental interfaces; Cluster models of the condensed phase; and Miscellaneous

  14. Annual Report 1998: Chemical Structure and Dynamics

    Energy Technology Data Exchange (ETDEWEB)

    SD Colson; RS McDowell

    1999-05-10

    The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Labo- ratory (EMSL), developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of- the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interracial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in envi- ronmental chemistry and in nuclear waste proc- essing and storage; and (3) developing state-of- the-art analytical methods for characterizing com- plex materials of the types found in stored wastes and contaminated soils, and for detecting and monitoring trace atmospheric species. Our program aims at achieving a quantitative understanding of chemical reactions at interfaces and, more generally, in condensed media, compa- rable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for pre- dicting macroscopic chemical behavior in con- densed and heterogeneous media, which will add significantly to the value of field-scale envi- ronmental models, predictions of short- and long- term nuclear waste storage stabilities, and other areas related to the primary missions of the U.S. Department of Energy (DOE).

  15. Chemical structure and dynamics. Annual report 1994

    Energy Technology Data Exchange (ETDEWEB)

    Colson, S.D.

    1995-07-01

    The Chemical Structure and Dynamics program was organized as a major component of Pacific Northwest Laboratory`s Environmental and Molecular Sciences Laboratory (EMSL), a state-of-the-art collaborative facility for studies of chemical structure and dynamics. Our program responds to the need for a fundamental, molecular-level understanding of chemistry at the wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces, and (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can be brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage. This research effort was initiated in 1989 and will continue to evolve over the next few years into a program of rigorous studies of fundamental molecular processes in model systems, such as well-characterized surfaces, single-component solutions, clusters, and biological molecules; and studies of complex systems found in the environment (multispecies, multiphase solutions; solid/liquid, liquid/liquid, and gas/surface interfaces; colloidal dispersions; ultrafine aerosols; and functioning biological systems). The success of this program will result in the achievement of a quantitative understanding of chemical reactions at interfaces, and more generally in condensed media, that is comparable to that currently available for gas-phase reactions. This understanding will form the basis for the development of a priori theories for predictions of macroscopic chemical behavior in condensed and heterogeneous media, adding significantly to the value of field-scale environmental models, the prediction of short- and long-term nuclear waste storage stabilities, and other problems related to the primary missions of the DOE.

  16. The hierarchical structure of chemical engineering

    Institute of Scientific and Technical Information of China (English)

    Mooson; KWAUK

    2007-01-01

    Around the turn of the present century,scholars began to recognize chemical engineering as a com-plex system,and have been searching for a convenient point of entry for refreshing its knowledge base.From our study of the dynamic structures of dispersed particles in fluidization and the resultingmulti-scale method,we have been attempting to extend our findings to structures prevailing in othermultiphase systems as well as in the burgeoning industries producing functional materials.Chemicalengineering itself is hierarchically structured.Besides structures based on space and time,such hier-archy could be built from ChE history scaled according to science content,or from ChE operation ac-cording to the expenditure of manpower and capital investment.

  17. The chemical bond structure and dynamics

    CERN Document Server

    Zewail, Ahmed

    1992-01-01

    This inspired book by some of the most influential scientists of our time--including six Nobel laureates--chronicles our emerging understanding of the chemical bond through the last nine decades and into the future. From Pauling's early structural work using x-ray and electron diffraction to Zewail's femtosecond lasers that probe molecular dynamics in real time; from Crick's molecular biology to Rich's molecular recognition, this book explores a rich tradition of scientific heritage and accomplishment. The perspectives given by Pauling, Perutz, Rich, Crick, Porter, Polanyi, Herschbach, Zewail,

  18. Trends in information theory-based chemical structure codification.

    Science.gov (United States)

    Barigye, Stephen J; Marrero-Ponce, Yovani; Pérez-Giménez, Facundo; Bonchev, Danail

    2014-08-01

    This report offers a chronological review of the most relevant applications of information theory in the codification of chemical structure information, through the so-called information indices. Basically, these are derived from the analysis of the statistical patterns of molecular structure representations, which include primitive global chemical formulae, chemical graphs, or matrix representations. Finally, new approaches that attempt to go "back to the roots" of information theory, in order to integrate other information-theoretic measures in chemical structure coding are discussed.

  19. Chemical syntheses of inulin and levan structures.

    Science.gov (United States)

    Oscarson, Stefan; Sehgelmeble, Fernando W

    2002-11-29

    A fructofuranosyl thiglycoside donor, ethyl 6-O-acetyl-3-O-benzyl-1,4-O-(1,1,3,3-tetraisopropyldisiloxane-1,3-diyl)-2-thio-beta-D-fructofuranoside (11), designed to yield stereospecifically beta-linkages and also to allow subsequent elongation in the 6- and/or 1-positions, was prepared and used in syntheses of levan and inulin structures. DMTST-promoted glycosylation between 11 (1.3 mol equiv) and methyl beta-D-fructofuranoside 6-OH and 1-OH acceptors (3 and 6) gave stereospecifically the protected methyl levanobioside 12 and inulinobioside 17 in excellent yields (80 and 86%), respectively. Protecting group manipulations on these afforded new disaccharide 6'-OH and 1'-OH acceptors (13 and 19), which were coupled again with donor 11 (1.0 mol equiv) to yield methyl levanotrioside 14 and inulinotrioside 20 in high yields, 65 and 67%, respectively. These were transformed into new acceptors and also fully deprotected to afford the methyl glycosides of levanotriose and inulinotriose, all structures that have earlier not been accessible by chemical synthesis. PMID:12444625

  20. Automated extraction of chemical structure information from digital raster images

    Directory of Open Access Journals (Sweden)

    Shedden Kerby A

    2009-02-01

    Full Text Available Abstract Background To search for chemical structures in research articles, diagrams or text representing molecules need to be translated to a standard chemical file format compatible with cheminformatic search engines. Nevertheless, chemical information contained in research articles is often referenced as analog diagrams of chemical structures embedded in digital raster images. To automate analog-to-digital conversion of chemical structure diagrams in scientific research articles, several software systems have been developed. But their algorithmic performance and utility in cheminformatic research have not been investigated. Results This paper aims to provide critical reviews for these systems and also report our recent development of ChemReader – a fully automated tool for extracting chemical structure diagrams in research articles and converting them into standard, searchable chemical file formats. Basic algorithms for recognizing lines and letters representing bonds and atoms in chemical structure diagrams can be independently run in sequence from a graphical user interface-and the algorithm parameters can be readily changed-to facilitate additional development specifically tailored to a chemical database annotation scheme. Compared with existing software programs such as OSRA, Kekule, and CLiDE, our results indicate that ChemReader outperforms other software systems on several sets of sample images from diverse sources in terms of the rate of correct outputs and the accuracy on extracting molecular substructure patterns. Conclusion The availability of ChemReader as a cheminformatic tool for extracting chemical structure information from digital raster images allows research and development groups to enrich their chemical structure databases by annotating the entries with published research articles. Based on its stable performance and high accuracy, ChemReader may be sufficiently accurate for annotating the chemical database with links

  1. Chemical effects in the mine structure

    International Nuclear Information System (INIS)

    The main objective of the workshop was to bring together, and get talking to each other, long-term safety modellers, geochemical modellers and experimenters working in the field of chemical effects, and to give an insight into their respective activity areas and problem constellations. Lectures on the following subjects were given: modelling of chemical effects in long-term safety analysis; influence of brines; corrosion experiments; sorption experiments; actinide chemistry experiments; geochemical modelling; requirements of safety analyses and geochemical modelling. The workshop concluded with a detailed discussion of the subjects raised and of interdisciplinary aspects. (orig./DG)

  2. Branch structure of corona discharge: experimental simulation and chemical properties

    International Nuclear Information System (INIS)

    The branch structure of corona discharge has been investigated via C2H2 corona discharge. Carbon filament with excellent branch structure is formed in the discharge. This carbon filament offers a direct mimic of the branch structure of corona discharge. It provides a very useful way to study on the average energy, physical and chemical characteristics of corona discharge. On this basis, the chemical property of corona discharge for methane conversion is discussed. (authors)

  3. The double-layered chemical structure in DB white dwarfs

    OpenAIRE

    Althaus, L.G.; Corsico, A. H.

    2004-01-01

    We study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Our treatment of diffusion includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is c...

  4. The Chemical Validation and Standardization Platform (CVSP): large-scale automated validation of chemical structure datasets

    OpenAIRE

    Karapetyan, Karen; Batchelor, Colin; Sharpe, David; Tkachenko, Valery; Williams, Antony J

    2015-01-01

    Background There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical stru...

  5. Chemical isomeric effects on propanol glassy structures

    CERN Document Server

    Cuello, G J; Bermejo, F J; Cabrillo, C

    2002-01-01

    We have studied the structure of both propanol isomers in their glassy and crystalline states by neutron diffraction. The glass-transition temperatures of 1- and 2-propanol are about 98 and 115 K, respectively and, surprisingly, even larger differences are observed for the melting temperatures of the stable crystals, which are 148 and 185 K, respectively. Their supercooled liquid phases show rather different relaxation spectra, 1-propanol manifesting strong deviations from Debye behavior, whereas 2-propanol shows a far weaker effect. We discuss the spectra obtained for the static structure factor and the static pair correlation function D(r). There is a noticeable difference in the position of the first sharp diffraction peak, which clearly indicates a density change, well correlated with the period of the intermolecular oscillations shown by D(r). (orig.)

  6. Bayesian inference of protein structure from chemical shift data

    DEFF Research Database (Denmark)

    Bratholm, Lars Andersen; Christensen, Anders Steen; Hamelryck, Thomas Wim;

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model......, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information...... content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain...

  7. Inferential protein structure determination and refinement using fast, electronic structure based backbone amide chemical shift predictions

    CERN Document Server

    Christensen, Anders S

    2015-01-01

    This report covers the development of a new, fast method for calculating the backbone amide proton chemical shifts in proteins. Through quantum chemical calculations, structure-based forudsiglese the chemical shift for amidprotonen in protein has been parameterized. The parameters are then implemented in a computer program called Padawan. The program has since been implemented in protein folding program Phaistos, wherein the method andvendes to de novo folding of the protein structures and to refine the existing protein structures.

  8. Structural and Chemical Diversity of Tl-Based Cuprate Superconductors

    Institute of Scientific and Technical Information of China (English)

    信赢

    2003-01-01

    The Tl-based cuprate superconductor family is the largest family in crystal structure and chemical composition among all high Tc cuprate superconductors. The Tl family can be divided into two sub-families, the Tl single layer family and the Tl double layer family, based on their crystal structural characteristics. The Tl single layer family is an ideal material for investigating the evolution of crystalline formation, charge carrier density, chemical composition, transport properties, superconductivity and their relationships. The Tl family contains almostall possible crystal structures discovered in high-Tc cuprate superconductors. Tl cuprate superconductors are of great importance not only in studying high-temperature superconductivity but also in commercial applications.

  9. Chemical composition in relation with biomass ash structure

    Science.gov (United States)

    Holubcik, Michal; Jandacka, Jozef

    2014-08-01

    Biomass combustion can be more complicated like combustion of fossil fuels because it is necessary to solve problems with lower ash melting temperature. It can cause a lot of problems during combustion process. Chemical composition of biomass ash has great impact on sinters and slags creation in ash because it affects structure of heated ash. In this paper was solved relation between chemical composition and structure of heated ash from three types of biomass (spruce wood, miscanthus giganteus and wheat straw). Amount of SiO2, CaO, MgO, Al2O3 and K2O was determined. Structure of heated ash was optically determined after heating to 1000 °C or 1200 °C. Results demonstrated that chemical composition has strong effect on structure and color of heated ash.

  10. Chemical composition and structure of sapropelitic coals

    Energy Technology Data Exchange (ETDEWEB)

    Bodoev, N.V. [Inst. of Carbon Material Chemistry, RAS, Kemerovo (Russian Federation); Guet, J.M. [Centre de Recherche sur la Matiere Divisee, Orleans (France); Gruber, R. [Lab. de Thermodynamique et d`Analyse Chimique, Univ. de Metz (France)

    1997-12-31

    Sapropelitic coals of low rank coalification stages were examined using solid state {sup 13}C n.m.r. with cross polarization and magic angle spinning techniques, FT-i.r. spectroscopy and X-ray diffraction (XRD) methods. The FT-i.r., and using solid state {sup 13}C n.m.r. spectra showed that the main constituents of low rank sapropelitic coals are aliphatic chains with carbonyl and carboxylic groups. The XRD analysis of low rank sapropelitic coals has shown very great differences from humic coals. The method of function of radial distribution of atoms (FRDA) was applied to low rank sapropelitic coals. The maxima at 0.5 and 1 nm of FRDA curves of these coals were established, indicating the parallel orientation of aliphatic chains in sapropelitic coals. The sapropelitic structure is probably determined by preservation of microorganisms and algal cell membranes, because it is known that the aliphatic parts of fatty acids of cell membranes have a parallel orientation. (orig.)

  11. Improving 3D structure prediction from chemical shift data

    Energy Technology Data Exchange (ETDEWEB)

    Schot, Gijs van der [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Zhang, Zaiyong [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany); Vernon, Robert [University of Washington, Department of Biochemistry (United States); Shen, Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vranken, Wim F. [VIB, Department of Structural Biology (Belgium); Baker, David [University of Washington, Department of Biochemistry (United States); Bonvin, Alexandre M. J. J., E-mail: a.m.j.j.bonvin@uu.nl [Utrecht University, Computational Structural Biology, Bijvoet Center for Biomolecular Research, Faculty of Science-Chemistry (Netherlands); Lange, Oliver F., E-mail: oliver.lange@tum.de [Technische Universitaet Muenchen, Biomolecular NMR and Munich Center for Integrated Protein Science, Department Chemie (Germany)

    2013-09-15

    We report advances in the calculation of protein structures from chemical shift nuclear magnetic resonance data alone. Our previously developed method, CS-Rosetta, assembles structures from a library of short protein fragments picked from a large library of protein structures using chemical shifts and sequence information. Here we demonstrate that combination of a new and improved fragment picker and the iterative sampling algorithm RASREC yield significant improvements in convergence and accuracy. Moreover, we introduce improved criteria for assessing the accuracy of the models produced by the method. The method was tested on 39 proteins in the 50-100 residue size range and yields reliable structures in 70 % of the cases. All structures that passed the reliability filter were accurate (<2 A RMSD from the reference)

  12. CHANGES IN THE CHEMICAL STRUCTURE OF THERMALLY TREATED WOOD

    Directory of Open Access Journals (Sweden)

    Birol Uner

    2010-07-01

    Full Text Available Changes in the chemical structure of hornbeam and uludag fir woods during thermal treatment were investigated at three temperatures (170, 190, and 210 oC and three durations (4, 8, and 12 hours. After thermal treatment, the extents of degradation in the chemical structure of the samples were determined, and the effects on the chemical composition of hornbeam wood and uludag fir wood were investigated. The data obtained were analyzed using variance analysis, and Tukey’s test was used to determine the changes in the chemical structure of uludag fir and hornbeam woods. The results showed that heating wood permanently changes several of its chemical structures and that the changes are mainly caused by thermal degradation of wood polymers. It was found that decreasing of the cellulose and holocelluloses ratio had a favorable effect on the interaction of the wood with moisture. According to the obtained results, hornbeam wood is affected more than uludag fir wood. For each wood, the maximum decreases of holocellulose and α-cellulose were found at 210oC for 12 hours, and the maximum increase of lignin occurred at the same treatment combination.

  13. Powerful chemical technique. [CSIR uses new x-ray diffractometer for structural chemical analysis

    Energy Technology Data Exchange (ETDEWEB)

    The CSIR's National Chemical Research Laboratory (NCRL) is now using one of the most powerful techniques available to determine the structure of molecules. It has recently acquired a Single Crystal X-ray Diffractometer. This powerful method provides the only means of determining the structure of certain compounds. NCRL scientists often carry out structure determinations to find out the relative or absolute stereochemistry of molecules. This is important when correlating physiological activity and structure, information which is necessary for synthesizing medicines with specific characteristics.

  14. Design of LTCC-based Ceramic Structure for Chemical Microreactor

    OpenAIRE

    D. Belavic; Hrovat, M.; G. Dolanc; Santo Zarnik, M.; Holc, J.; Makarovic, K.

    2012-01-01

    The design of ceramic chemical microreactor for the production of hydrogen needed in portable polymer-electrolyte membrane (PEM) fuel cells is presented. The microreactor was developed for the steam reforming of liquid fuels with water into hydrogen. The complex three-dimensional ceramic structure of the microreactor includes evaporator(s), mixer(s), reformer and combustor. Low-temperature co-fired ceramic (LTCC) technology was used to fabricate the ceramic structures with buried cavities and...

  15. The multifractal structure of chaotically advected chemical fields

    CERN Document Server

    Neufeld, Z; Hernández-García, E; Tél, T; Neufeld, Zoltan; Lopez, Cristobal; Hernandez-Garcia, Emilio; Tel, Tamas

    1999-01-01

    The structure of the concentration field of a decaying substance produced by chemical sources and advected by a smooth incompressible two-dimensional flow is investigated. We focus our attention on the non-uniformities of the Hölder exponent of the resulting filamental chemical field. They appear most evidently in the case of open flows where irregularities of the field exhibit strong spatial intermittency as they are restricted to a fractal manifold. Non-uniformities of the Hölder exponent of the chemical field in closed flows appears as a consequence of the non-uniform stretching of the fluid elements. We study how this affects the scaling exponents of the structure functions, displaying anomalous scaling, and relate the scaling exponents to the distribution of finite-time Lyapunov exponents of the advection dynamics. Theoretical predictions are compared with numerical experiments.

  16. Structural studies of chemical constituents of Thithonia Tagetiflora Desv (Asteraceae)

    DEFF Research Database (Denmark)

    Ngoc Huynh, Vinh; Nguyen Thi Hoai, Thu; Phi Phung Nguyen, Kim;

    2013-01-01

    Tithonia tagetiflora Desv. (Asteraceae) is a widespread plant in Vietnam, and the species of Tithonia are known as plants containing many biologically active compounds. However, T. tagetiflora's chemical composition remains mostly unknown. Therefore, we now report the structural elucidation of two...

  17. Electronic and chemical properties of graphene-based structures:

    DEFF Research Database (Denmark)

    Vanin, Marco

    are easier to remove and therefore only zigzag edges are left. Finally, functionalized graphene has been investigated as catalyst for the electrochemical reduction of CO2 to chemical fuels and comparisons are made with traditional transition-metal surfaces. The investigated porphyrin-like structures...... are attractive candidates although issues regarding the poisoning of the active site remain to be addressed....

  18. Discovering More Chemical Concepts from 3D Chemical Information Searches of Crystal Structure Databases

    Science.gov (United States)

    Rzepa, Henry S.

    2016-01-01

    Three new examples are presented illustrating three-dimensional chemical information searches of the Cambridge structure database (CSD) from which basic core concepts in organic and inorganic chemistry emerge. These include connecting the regiochemistry of aromatic electrophilic substitution with the geometrical properties of hydrogen bonding…

  19. Global Materials Structure Search with Chemically Motivated Coordinates.

    Science.gov (United States)

    Panosetti, Chiara; Krautgasser, Konstantin; Palagin, Dennis; Reuter, Karsten; Maurer, Reinhard J

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces.

  20. Structure activity relationships to assess new chemicals under TSCA

    Energy Technology Data Exchange (ETDEWEB)

    Auletta, A.E. [Environmental Protection Agency, Washington, DC (United States)

    1990-12-31

    Under Section 5 of the Toxic Substances Control Act (TSCA), manufacturers must notify the US Environmental Protection Agency (EPA) 90 days before manufacturing, processing, or importing a new chemical substance. This is referred to as a premanufacture notice (PMN). The PMN must contain certain information including chemical identity, production volume, proposed uses, estimates of exposure and release, and any health or environmental test data that are available to the submitter. Because there is no explicit statutory authority that requires testing of new chemicals prior to their entry into the market, most PMNs are submitted with little or no data. As a result, EPA has developed special techniques for hazard assessment of PMN chemicals. These include (1) evaluation of available data on the chemical itself, (2) evaluation of data on analogues of the PMN, or evaluation of data on metabolites or analogues of metabolites of the PMN, (3) use of quantitative structure activity relationships (QSARs), and (4) knowledge and judgement of scientific assessors in the interpretation and integration of the information developed in the course of the assessment. This approach to evaluating potential hazards of new chemicals is used to identify those that are most in need of addition review of further testing. It should not be viewed as a replacement for testing. 4 tabs.

  1. Structure of adsorbed monolayers. The surface chemical bond

    International Nuclear Information System (INIS)

    This paper attempts to provide a summary of what has been learned about the structure of adsorbed monolayers and about the surface chemical bond from molecular surface science. While the surface chemical bond is less well understood than bonding of molecules in the gas phase or in the solid state, our knowledge of its properties is rapidly accumulating. The information obtained also has great impact on many surface science based technologies, including heterogeneous catalysis and electronic devices. It is hoped that much of the information obtained from studies at solid-gas interfaces can be correlated with molecular behavior at solid-liquid interfaces. 31 references, 42 figures, 1 table

  2. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout.

  3. Applications of the Cambridge Structural Database in chemical education.

    Science.gov (United States)

    Battle, Gary M; Ferrence, Gregory M; Allen, Frank H

    2010-10-01

    The Cambridge Structural Database (CSD) is a vast and ever growing compendium of accurate three-dimensional structures that has massive chemical diversity across organic and metal-organic compounds. For these reasons, the CSD is finding significant uses in chemical education, and these applications are reviewed. As part of the teaching initiative of the Cambridge Crystallographic Data Centre (CCDC), a teaching subset of more than 500 CSD structures has been created that illustrate key chemical concepts, and a number of teaching modules have been devised that make use of this subset in a teaching environment. All of this material is freely available from the CCDC website, and the subset can be freely viewed and interrogated using WebCSD, an internet application for searching and displaying CSD information content. In some cases, however, the complete CSD System is required for specific educational applications, and some examples of these more extensive teaching modules are also discussed. The educational value of visualizing real three-dimensional structures, and of handling real experimental results, is stressed throughout. PMID:20877495

  4. Characterization of iron-phosphate-silicate chemical garden structures.

    Science.gov (United States)

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life.

  5. Electronic and chemical structure of metal-silicon interfaces

    Science.gov (United States)

    Grunthaner, P. J.; Grunthaner, F. J.

    1984-01-01

    This paper reviews our current understanding of the near-noble metal silicides and the interfaces formed with Si(100). Using X-ray photoemission spectroscopy, we compare the chemical composition and electronic structure of the room temperature metal-silicon and reacted silicide-silicon interfaces. The relationship between the interfacial chemistry and the Schottky barrier heights for this class of metals on silicon is explored.

  6. Chemical and structural features influencing the biological activity of curcumin.

    Science.gov (United States)

    Priyadarsini, K Indira

    2013-01-01

    Curcumin, a polyphenolic natural product, exhibits therapeutic activity against a number of diseases, attributed mainly to its chemical structure and unique physical, chemical, and biological properties. It is a diferuloyl methane molecule [1,7-bis (4-hydroxy-3- methoxyphenyl)-1,6-heptadiene-3,5-dione)] containing two ferulic acid residues joined by a methylene bridge. It has three important functionalities: an aromatic o-methoxy phenolic group, α, β-unsaturated β-diketo moiety and a seven carbon linker. Extensive research in the last two decades has provided evidence for the role of these different functional groups in its crucial biological activities. A few highlights of chemical structural features associated with the biological activity of curcumin are: The o-methoxyphenol group and methylenic hydrogen are responsible for the antioxidant activity of curcumin, and curcumin donates an electron/ hydrogen atom to reactive oxygen species. Curcumin interacts with a number of biomolecules through non-covalent and covalent binding. The hydrogen bonding and hydrophobicity of curcumin, arising from the aromatic and tautomeric structures along with the flexibility of the linker group are responsible for the non-covalent interactions. The α, β-unsaturated β-diketone moiety covalently interacts with protein thiols, through Michael reaction. The β-diketo group forms chelates with transition metals, there by reducing the metal induced toxicity and some of the metal complexes exhibit improved antioxidant activity as enzyme mimics. New analogues with improved activity are being developed with modifications on specific functional groups of curcumin. The physico-chemical and structural features associated with some of the biological activities of curcumin and important analogues are summarized in this article. PMID:23116315

  7. Chemical compatibility of structural materials in alkali metals

    International Nuclear Information System (INIS)

    The objectives of this task are to (a) evaluate the chemical compatibility of structural alloys such as V-5 wt.%Cr-5 wt.%Ti alloy and Type 316 stainless steel for application in liquid alkali metals such as lithium and sodium-78 wt.% potassium (NaK) at temperatures in the range that are of interest for International Thermonuclear Experimental Reactor (ITER); (b) evaluate the transfer of nonmetallic elements such as oxygen, nitrogen, carbon, and hydrogen between structural materials and liquid metals; and (c) evaluate the effects of such transfers on the mechanical and microstructural characteristics of the materials for long-term service in liquid-metal-environments

  8. Design of LTCC-based Ceramic Structure for Chemical Microreactor

    Directory of Open Access Journals (Sweden)

    D. Belavic

    2012-04-01

    Full Text Available The design of ceramic chemical microreactor for the production of hydrogen needed in portable polymer-electrolyte membrane (PEM fuel cells is presented. The microreactor was developed for the steam reforming of liquid fuels with water into hydrogen. The complex three-dimensional ceramic structure of the microreactor includes evaporator(s, mixer(s, reformer and combustor. Low-temperature co-fired ceramic (LTCC technology was used to fabricate the ceramic structures with buried cavities and channels, and thick-film technology was used to make electrical heaters, temperature sensors and pressure sensors. The final 3D ceramic structure consists of 45 LTCC tapes. The dimensions of the structure are 75 × 41 × 9 mm3 and the weight is about 73 g.

  9. Chemical and physical structures of proteinoids and related polyamino acids

    Science.gov (United States)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

    Studies of polyamino acid formation pathways in the prebiotic condition are important for the study of the origins of life. Several pathways of prebiotic polyamino acid formation have been reported. Heating of monoammonium malate [1] and heating of amino acids in molten urea [2] are important pathways of the prebiotic peptide formation. The former case, globular structure called proteinoid microsphere is formed in aqueous conditions. The later case, polyamino acids are formed from unrestricted amino acid species. Heating of aqueous aspargine is also interesting pathway for the prebiotic polyamino acid formation, because polyamino acid formation proceeds in aqueous condition [3]. In this study, we analyzed the chemical structure of the proteinoids and related polyamino acids formed in the above three pathways using with mass spectrometer. In addition, their physical structures are analyzed by the electron and optical microscopes, in order to determine the self-organization abilities. We discuss the relation between the chemical and the physical structures for the origins of life. References [1] Harada, K., J. Org. Chem., 24, 1662 (1959), Fox, S. W., Harada, K., and Kendrick, J., Science, 129, 1221 (1959). [2] Terasaki, M., Nomoto, S., Mita, H., and Shimoyama, A., Chem. Lett., 480 (2002), Mita, H., Nomoto, S., Terasaki, M., Shimoyama, A., and Yamamoto, Y., Int. J. Astrobiol., 4, 145 (2005). [3] Kovacs, K and Nagy, H., Nature, 190, 531 (1961), Munegumi, T., Tanikawa, N., Mita, H. and Harada, K., Viva Origino, 22, 109 (1994).

  10. Chemical structure of odorants and perceptual similarity in ants.

    Science.gov (United States)

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity. PMID:23685976

  11. Chemical structure of odorants and perceptual similarity in ants.

    Science.gov (United States)

    Bos, Nick; d'Ettorre, Patrizia; Guerrieri, Fernando J

    2013-09-01

    Animals are often immersed in a chemical world consisting of mixtures of many compounds rather than of single substances, and they constantly face the challenge of extracting relevant information out of the chemical landscape. To this purpose, the ability to discriminate among different stimuli with different valence is essential, but it is also important to be able to generalise, i.e. to treat different but similar stimuli as equivalent, as natural variation does not necessarily affect stimulus valence. Animals can thus extract regularities in their environment and make predictions, for instance about distribution of food resources. We studied perceptual similarity of different plant odours by conditioning individual carpenter ants to one odour, and subsequently testing their response to another, structurally different odour. We found that asymmetry in generalisation, where ants generalise from odour A to B, but not from B to A, is dependent on both chain length and functional group. By conditioning ants to a binary mixture, and testing their reaction to the individual components of the mixture, we show that overshadowing, where parts of a mixture are learned better than others, is rare. Additionally, generalisation is dependent not only on the structural similarity of odorants, but also on their functional value, which might play a crucial role. Our results provide insight into how ants make sense of the complex chemical world around them, for example in a foraging context, and provide a basis with which to investigate the neural mechanisms behind perceptual similarity.

  12. Facile chemical synthesis and structure characterization of copper molybdate nanoparticles

    Science.gov (United States)

    Rahimi-Nasrabadi, Mehdi; Pourmortazavi, Seied Mahdi; Khalilian-Shalamzari, Morteza

    2015-03-01

    Experimental parameters of a synthesis route were optimized by Taguchi robust design for the facile and controllable synthesis of copper molybdate nanoparticles. CuMoO4 nanoparticles were synthesized by chemical precipitation followed by hydrothermal process. Effects of different parameters of synthesis procedure, i.e. concentrations of both reagents, copper feeding flow rate and temperature of reactor on the particle size of prepared copper molybdate nanoparticles were investigated. The results of statistical optimization revealed that the size of copper molybdate particles is dependent on the procedure variables involving copper concentrations, flow rate and temperature of the reactor; while, molybdate concentration has a no considerable role in determining the size of CuMoO4 particles. Based on the results obtained by statistical optimization process, the nanoparticles of copper molybdate were prepared and then their structure and chemical composition were characterized by various techniques, i.e. SEM, TEM, XRD, EDX, FT-IR, UV-Vis and photoluminescence spectroscopy.

  13. The double-layered chemical structure in DB white dwarfs

    CERN Document Server

    Althaus, L G

    2004-01-01

    We study the structure and evolution of white dwarf stars with helium-rich atmospheres (DB) in a self-consistent way with the predictions of time-dependent element diffusion. Our treatment of diffusion includes gravitational settling and chemical and thermal diffusion. OPAL radiative opacities for arbitrary metallicity and carbon-and oxygen-rich compositions are employed. Emphasis is placed on the evolution of the diffusion-modeled double-layered chemical structure. This structure, which is characterized by a pure helium envelope atop an intermediate remnant shell rich in helium, carbon and oxygen, is expected for pulsating DB white dwarfs, assuming that they are descendants of hydrogen-deficient PG1159 post-AGB stars. We find that, depending on the stellar mass, if DB white dwarf progenitors are formed with a helium content smaller than \\approx 10^-3 M_*, a single-layered configuration is expected to emerge during the DB pulsation instability strip. We also explore the consequences of diffusively evolving ch...

  14. Chemical structures and thermochemical properties of bagasse lignin

    Institute of Scientific and Technical Information of China (English)

    Wu Shu-bin; Guo Yi-li; Wang Shao-guang; Li Meng-shi

    2006-01-01

    The chemical structures of bagasse EMAL (enzymatic hydrolysis/mild acidolysis lignin) were revealed quantitatively with 31P-NMR, DFRC (derivatization followed by reductive cleavage). The thermochemical characteristics of bagasse and bagasse EMAL were evaluated with thermogravimetry. The results show that bagasse EMAL is mainly formed by the phenolic hydroxyl group of guaiacyl and syringyl units. The DBDO content in bagasse EMAL was found to be 0.180 mmol·g-1. The decomposition characteristics of bagasse EMAL under elevated temperature were much different from that of bagasse.

  15. EFFECT OF CHEMICAL STRUCTURE OF POLYCARBONATES ON ENTANGLEMENT SPACING

    Institute of Scientific and Technical Information of China (English)

    Wei Ning; Wen-xiang Zhu; Bao-qing Zhang; Chun-cheng Li; Chen-yang Liu; Du-jin Wang

    2012-01-01

    The master curves of a series of aliphatic polycarbonates (APCs) with different lengths of methylene segments in the repeat unit were obtained by dynamic rheological measurements.The plateau modulus and entanglement molecular weight were determined and cross-checked by different methods.Though having distinct difference in chemical structure of repeat units,both APCs and bisphenol-A polycarbonates have the similar entanglement weight and entanglement spacing.On the other side,the plateau modulus decreases with increasing the length of the side group of atiphatic polycarbonates with different side-chain lengths in the literature.The packing length model can explain the relationship between chain structure and entanglements.

  16. Aromatic rings in chemical and biological recognition: energetics and structures.

    Science.gov (United States)

    Salonen, Laura M; Ellermann, Manuel; Diederich, François

    2011-05-16

    This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations. PMID:21538733

  17. Characterization of iron-phosphate-silicate chemical garden structures.

    Science.gov (United States)

    Barge, Laura M; Doloboff, Ivria J; White, Lauren M; Stucky, Galen D; Russell, Michael J; Kanik, Isik

    2012-02-28

    Chemical gardens form when ferrous chloride hydrate seed crystals are added or concentrated solutions are injected into solutions of sodium silicate and potassium phosphate. Various precipitation morphologies are observed depending on silicate and phosphate concentrations, including hollow plumes, bulbs, and tubes. The growth of precipitates is controlled by the internal osmotic pressure, fluid buoyancy, and membrane strength. Additionally, rapid bubble-led growth is observed when silicate concentrations are high. ESEM/EDX analysis confirms compositional gradients within the membranes, and voltage measurements across the membranes during growth show a final potential of around 150-200 mV, indicating that electrochemical gradients are maintained across the membranes as growth proceeds. The characterization of chemical gardens formed with iron, silicate, and phosphate, three important components of an early earth prebiotic hydrothermal system, can help us understand the properties of analogous structures that likely formed at submarine alkaline hydrothermal vents in the Hadean-structures offering themselves as the hatchery of life. PMID:22035594

  18. Integrating chemical footprinting data into RNA secondary structure prediction.

    Directory of Open Access Journals (Sweden)

    Kourosh Zarringhalam

    Full Text Available Chemical and enzymatic footprinting experiments, such as shape (selective 2'-hydroxyl acylation analyzed by primer extension, yield important information about RNA secondary structure. Indeed, since the [Formula: see text]-hydroxyl is reactive at flexible (loop regions, but unreactive at base-paired regions, shape yields quantitative data about which RNA nucleotides are base-paired. Recently, low error rates in secondary structure prediction have been reported for three RNAs of moderate size, by including base stacking pseudo-energy terms derived from shape data into the computation of minimum free energy secondary structure. Here, we describe a novel method, RNAsc (RNA soft constraints, which includes pseudo-energy terms for each nucleotide position, rather than only for base stacking positions. We prove that RNAsc is self-consistent, in the sense that the nucleotide-specific probabilities of being unpaired in the low energy Boltzmann ensemble always become more closely correlated with the input shape data after application of RNAsc. From this mathematical perspective, the secondary structure predicted by RNAsc should be 'correct', in as much as the shape data is 'correct'. We benchmark RNAsc against the previously mentioned method for eight RNAs, for which both shape data and native structures are known, to find the same accuracy in 7 out of 8 cases, and an improvement of 25% in one case. Furthermore, we present what appears to be the first direct comparison of shape data and in-line probing data, by comparing yeast asp-tRNA shape data from the literature with data from in-line probing experiments we have recently performed. With respect to several criteria, we find that shape data appear to be more robust than in-line probing data, at least in the case of asp-tRNA.

  19. Structure of chemical vapor deposition titania/silica gel

    Energy Technology Data Exchange (ETDEWEB)

    Leboda, R.; Gun' ko, V.M.; Marciniak, M.; Malygin, A.A.; Malkin, A.A.; Grzegorczyk, W.; Trznadel, B.J.; Pakhlov, E.M.; Voronin, E.F.

    1999-10-01

    The structure of porous silica gel/titania synthesized using chemical vapor deposition (CVD) of titania via repeated reactions of TiCl{sub 4} with the surface and subsequent hydrolysis of residual Ti-Cl bonds at different temperatures was investigated by means of low-temperature nitrogen adsorption-desorption, X-ray diffraction (XRD), IR spectroscopy, and theoretical methods. A globular model of porous solids with corpuscular structure was applied to estimate the porosity parameters of titania/silica gel adsorbents. The utilization of this model is useful, for example, to predict conditions for synthesis of titania/silica with a specified structure. Analysis of pore parameters and fractal dimension suggests that the porosity and fractality of samples decrease with increasing amount of TiO{sub 2} covering the silica gel surface in a nonuniform layer, which represents small particles embedded in pores and larger particles formed at the outer surface of silica globules. Theoretical simulation shows that the Si-O-Ti linkages between the cover and the substrate can be easily hydrolyzed, which is in agreement with the IR data corresponding to the absence of a band at 950 cm {sup {minus}1} (characteristic of Si-O-Ti bridges) independent of the concentration of CVD-titania.

  20. Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

    International Nuclear Information System (INIS)

    This dissertation reports about studies on the chemical coordination behaviour of uranium of oxidation stages IV and VI with regard to twelve different macrocyclic ligands. For the preparation of the complexes, for every system a different method has been developed. The elementary analysis of the various complexes including the uranium had been done by X-ray fluorescence analysis, and the structural characterization proceeded via vibrational, uv-vis and emission spectroscopy as well as 1H-NMR and 13C-spin-lattice relaxation time studies. Conformational analysis of the polyethers used allowed the structural changes in the complexes to be observed. The structural analysis of the hydrous uranium VI crown ether complexes yielded information of characteristic features of these types of complexes. The first coordination sphere of the uranyl ion with covalently bonded anion remains unchanged. As to the water content, there is a certain range. Depending upon the solvent used, the complexes have two or four H2O molecules per formula unit. (orig./EF)

  1. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    Science.gov (United States)

    Lee, H. V.; Hamid, S. B. A.; Zain, S. K.

    2014-01-01

    Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate's application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein. PMID:25247208

  2. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    Directory of Open Access Journals (Sweden)

    H. V. Lee

    2014-01-01

    Full Text Available Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate’s application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulose crystallinity, which inhibit the digestibility of the biomass for cellulose extraction. This situation offers both challenges and promises for the biomass biorefinery development to utilize the cellulose from lignocellulosic biomass. Thus, multistep biorefinery processes are necessary to ensure the deconstruction of noncellulosic content in lignocellulosic biomass, while maintaining cellulose product for further hydrolysis into nanocellulose material. In this review, we discuss the molecular structure basis for biomass recalcitrance, reengineering process of lignocellulosic biomass into nanocellulose via chemical, and novel catalytic approaches. Furthermore, review on catalyst design to overcome key barriers regarding the natural resistance of biomass will be presented herein.

  3. Designing Allosteric Control into Enzymes by Chemical Rescue of Structure

    Energy Technology Data Exchange (ETDEWEB)

    Deckert, Katelyn; Budiardjo, S. Jimmy; Brunner, Luke C.; Lovell, Scott; Karanicolas, John (Kansas)

    2012-08-07

    Ligand-dependent activity has been engineered into enzymes for purposes ranging from controlling cell morphology to reprogramming cellular signaling pathways. Where these successes have typically fused a naturally allosteric domain to the enzyme of interest, here we instead demonstrate an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. We present two examples, W33G in a {beta}-glycosidase enzyme ({beta}-gly) and W492G in a {beta}-glucuronidase enzyme ({beta}-gluc), in which we engineer indole-dependent activity into enzymes by removing a buried tryptophan side chain that serves as a buttress for the active site architecture. In both cases, we observe a loss of function, and in both cases we find that the subsequent addition of indole can be used to restore activity. Through a detailed analysis of {beta}-gly W33G kinetics, we demonstrate that this rescued enzyme is fully functionally equivalent to the corresponding wild-type enzyme. We then present the apo and indole-bound crystal structures of {beta}-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate {beta}-glycosidase activity in living cells using indole. Disruption and recovery of protein structure may represent a general technique for introducing allosteric control into enzymes, and thus may serve as a starting point for building a variety of bioswitches and sensors.

  4. Wikipedia Chemical Structure Explorer: substructure and similarity searching of molecules from Wikipedia

    OpenAIRE

    Ertl, Peter; Patiny, Luc; Sander, Thomas; Rufener, Christian; Zasso, Michaël

    2015-01-01

    Background Wikipedia, the world’s largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. Results We extracted chemical structures from entries in Wikipedia an...

  5. Chemical etching of deformation sub-structures in quartz

    Science.gov (United States)

    Wegner, M. W.; Christie, J. M.

    1983-02-01

    Chemical etching of dislocations has been studied in natural and synthetic quartz single crystals, in deformed synthetic quartz and in naturally and experimentally deformed quartzites. The ability of different etchants to produce polished or preferentially etched surfaces on quartz is described. Dislocation etching was achieved on all crystal planes examined by using a saturated solution of ammonium bifluoride as the etchant. Appropriate etching times were determined for etching quartzites for grain size, subgrain boundaries, deformation lamellae, dislocations and twins. Growth and polished surfaces of synthetic single crystal quartz were similarly etched and dislocation etch pits, characteristic of various orientations were found. The use of ammonium bifluoride proved to be expecially advantageous for the basal plane, producing a polished surface with etch pits, suitable for dislocation etch pit counting. “Double” etch pits have been found on Dauphiné twin boundaries on the basal plane and the first order prism, using this etchant. Slip lines and deformation bands were suitably etched on deformed synthetic crystal surfaces for identification of the slip planes. Other acidic etchants have been explored and their application to the study of deformation structures in quartz crystals is discussed.

  6. Nepheline structural and chemical dependence on melt composition

    Energy Technology Data Exchange (ETDEWEB)

    Marcial, José; Crum, Jarrod; Neill, Owen; McCloy, John

    2016-02-01

    Nepheline crystallizes upon slow-cooling in some melts concentrated in Na2O and Al2O3, which can result in a residual glass phase of low chemical durability. Nepheline can incorporate many components often found in high-level waste radioactive borosilicate glass, including glass network ions (e.g., Si, Al, Fe), alkali metals (e.g., Cs, K, Na, and possibly Li), alkaline-earth metals (e.g., Ba, Sr, Ca, Mg), and transition metals (e.g., Mn, and possibly Cr, Zn, Ni). When crystallized from melts of different compositions, nepheline chemistry varies as a function of starting glass composition. Five simulated high level nuclear waste borosilicate glasses shown to crystallize large fractions of nepheline on slow cooling, were selected for study. These melts constituted a range of Al2O3, B2O3, CaO, Na2O, K2O, Fe2O3, and SiO2 compositions. Compositional analyses of nepheline crystals in glass by electron probe micro-analysis (EPMA) indicate that boron is unlikely to be present in any significant concentration, if at all, in nepheline. Also, several models are presented for calculating the fraction of vacancies in the nepheline structure.

  7. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    Energy Technology Data Exchange (ETDEWEB)

    Sadtler, Bryce F

    2009-05-20

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or Ag2S lattices were used to calculate interface formation energies. The formation energies indicate the

  8. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    Energy Technology Data Exchange (ETDEWEB)

    Sadtler, Bryce F [Univ. of California, Berkeley, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

    2009-05-01

    Methods are presented for synthesizing nanocrystal heterostructures comprised of two semiconductor materials epitaxially attached within individual nanostructures. The chemical transformation of cation exchange, where the cations within the lattice of an ionic nanocrystal are replaced with a different metal ion species, is used to alter the chemical composition at specific regions ofa nanocrystal. Partial cation exchange was performed in cadmium sulfide (CdS) nanorods of well-defined size and shape to examine the spatial organization of materials within the resulting nanocrystal heterostructures. The selectivity for cation exchange to take place at different facets of the nanocrystal plays an important role in determining the resulting morphology of the binary heterostructure. The exchange of copper (I) (Cu+) cations in CdS nanorods occurs preferentially at the ends of the nanorods. Theoretical modeling of epitaxial attachments between different facets of CdS and Cu2S indicate that the selectivity for cation exchange at the ends of the nanorods is a result of the low formation energy of the interfaces produced. During silver (I) (Ag+) cation exchange in CdS nanorods, non-selective nucleation of silver sulfide (Ag2S), followed by partial phase segregation leads to significant changes in the spatial arrangement of CdS and Ag2S regions at the exchange reaction proceeds through the nanocrystal. A well-ordered striped pattern of alternating CdS and Ag2S segments is found at intermediate fractions of exchange. The forces mediating this spontaneous process are a combination of Ostwald ripening to reduce the interfacial area along with a strain-induced repulsive interaction between Ag2S segments. To elucidate why Cu+ and Ag+ cation exchange with CdS nanorods produce different morphologies, models for epitaxial attachments between various facets of CdS with Cu2S or

  9. [Chemical structure and immunomodulating activities of peptidoglycan from Actinobacillus actinomycetemcomitans].

    Science.gov (United States)

    Kinoshita, F

    1989-12-01

    The chemical structure and immunomodulating activities of the cell wall peptidoglycans isolated from Actinobacillus actinomycetemcomitans were investigated. Peptidoglycans were isolated from A. actinomycetemcomitans strains Y4 and ATCC 29522 by boiling in 4% sodium dodecyl sulfate and by digestion with pronase, trypsin and alpha-amylase. Analysis of amino acids and amino sugars of the peptidoglycans revealed that glucosamine, muramic acid, D-glutamic acid, D-alanine, and meso-2, 6-diaminopimelic acid (A2pm) were the principal components. Serine and glycine were not found. Dinitrophenylation method revealed that about half of A2pm residue had a free aminogroup, and analysis by hydrazinolysis showed that a small part of alanine and A2pm located at the C-terminal. The above results indicate that one of the amino groups of A2pm residue at one strand of the stem peptide subunit crosslinked to the carboxyl group of alanine of the neighboring strand. It was thus revealed that the peptidoglycans of A. actinomycetemcomitans belonged to the Al gamma type of the classification by Schleifer and Kandler. Peptidoglycans isolated from A. actinomycetemcmitans strain Y4 and ATCC 29522 were found to be definitely adjuvant-active in induction of delayed type hypersensitivity against ovalbumin when administered to guinea pigs as water-in oil emulsion and stimulation of increase serum antibody levels was found in both peptidoglycans. Regarding mitogenicity on splenocytes of BALB/c and BALB/c nu/nu mice, peptidoglycans from two strains of A. actinomycetemcomitans were markedly enhanced the uptake [3H] thymidine in dose of 10 micrograms/10(5) cells, however thymocytes were not reactive. Stimulation effects on peritoneal macrophages from a guinea pig to incorporation of 14C-glucosamin were not exhibited on addition of 100 micrograms of both peptidoglycans. These findings indicate that peptidoglycan of A. actinomycetemcomitans might eventually be responsible for destruction of periodontal

  10. Automated Structure-Activity Relationship Mining: Connecting Chemical Structure to Biological Profiles.

    Science.gov (United States)

    Wawer, Mathias J; Jaramillo, David E; Dančík, Vlado; Fass, Daniel M; Haggarty, Stephen J; Shamji, Alykhan F; Wagner, Bridget K; Schreiber, Stuart L; Clemons, Paul A

    2014-06-01

    Understanding the structure-activity relationships (SARs) of small molecules is important for developing probes and novel therapeutic agents in chemical biology and drug discovery. Increasingly, multiplexed small-molecule profiling assays allow simultaneous measurement of many biological response parameters for the same compound (e.g., expression levels for many genes or binding constants against many proteins). Although such methods promise to capture SARs with high granularity, few computational methods are available to support SAR analyses of high-dimensional compound activity profiles. Many of these methods are not generally applicable or reduce the activity space to scalar summary statistics before establishing SARs. In this article, we present a versatile computational method that automatically extracts interpretable SAR rules from high-dimensional profiling data. The rules connect chemical structural features of compounds to patterns in their biological activity profiles. We applied our method to data from novel cell-based gene-expression and imaging assays collected on more than 30,000 small molecules. Based on the rules identified for this data set, we prioritized groups of compounds for further study, including a novel set of putative histone deacetylase inhibitors.

  11. Selectivity on-target of bromodomain chemical probes by structure-guided medicinal chemistry and chemical biology.

    Science.gov (United States)

    Galdeano, Carles; Ciulli, Alessio

    2016-09-01

    Targeting epigenetic proteins is a rapidly growing area for medicinal chemistry and drug discovery. Recent years have seen an explosion of interest in developing small molecules binding to bromodomains, the readers of acetyl-lysine modifications. A plethora of co-crystal structures has motivated focused fragment-based design and optimization programs within both industry and academia. These efforts have yielded several compounds entering the clinic, and many more are increasingly being used as chemical probes to interrogate bromodomain biology. High selectivity of chemical probes is necessary to ensure biological activity is due to an on-target effect. Here, we review the state-of-the-art of bromodomain-targeting compounds, focusing on the structural basis for their on-target selectivity or lack thereof. We also highlight chemical biology approaches to enhance on-target selectivity.

  12. Structure and biological activity of chemically modified nisin A species

    NARCIS (Netherlands)

    Rollema, Harry S.; Metzger, Jörg W.; Both, Paula; Kuipers, Oscar P.; Siezen, Roland J.

    1996-01-01

    Nisin, a 34-residue peptide bacteriocin, contains the less common amino acids lanthionine, β-methyllanthionine, dehydroalanine (Dha), and dehydrobutyrine (Dhb). Several chemically modified nisin A species were purified by reverse-phase HPLC and characterized by two-dimensional NMR and electrospray m

  13. Conversion of Lignocellulosic Biomass to Nanocellulose: Structure and Chemical Process

    OpenAIRE

    Lee, H. V.; S. B. A. Hamid; Zain, S. K.

    2014-01-01

    Lignocellulosic biomass is a complex biopolymer that is primary composed of cellulose, hemicellulose, and lignin. The presence of cellulose in biomass is able to depolymerise into nanodimension biomaterial, with exceptional mechanical properties for biocomposites, pharmaceutical carriers, and electronic substrate’s application. However, the entangled biomass ultrastructure consists of inherent properties, such as strong lignin layers, low cellulose accessibility to chemicals, and high cellulo...

  14. Branch Structure of Corona Discharge:Experimental Simulation and Chemical Properties

    Institute of Scientific and Technical Information of China (English)

    邹吉军; 刘昌俊

    2004-01-01

    The branch structure of corona discharge has been investigated via C2H2 corona discharge. Carbon filament with excellent branch structure is formed in the discharge. This carbon filament offers a direct mimic of the branch structure of corona discharge. It providesa very useful way to study on the average energy, physical and chemical characteristics of coronadischarge. On this basis, the chemical property of corona discharge for methane conversion is discussed.

  15. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    Energy Technology Data Exchange (ETDEWEB)

    Nagaoka, Masataka [Graduate School of Information Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601 (Japan); Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Honmachi, Kawaguchi 332-0012 (Japan); ESICB, Kyoto University, Kyodai Katsura, Nishikyo-ku, Kyoto 615-8520 (Japan)

    2015-12-31

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method.

  16. Computational molecular technology towards macroscopic chemical phenomena-molecular control of complex chemical reactions, stereospecificity and aggregate structures

    International Nuclear Information System (INIS)

    A new efficient hybrid Monte Carlo (MC)/molecular dynamics (MD) reaction method with a rare event-driving mechanism is introduced as a practical ‘atomistic’ molecular simulation of large-scale chemically reactive systems. Starting its demonstrative application to the racemization reaction of (R)-2-chlorobutane in N,N-dimethylformamide solution, several other applications are shown from the practical viewpoint of molecular controlling of complex chemical reactions, stereochemistry and aggregate structures. Finally, I would like to mention the future applications of the hybrid MC/MD reaction method

  17. Effects of chemical treatments on hemp fibre structure

    Science.gov (United States)

    Kabir, M. M.; Wang, H.; Lau, K. T.; Cardona, F.

    2013-07-01

    In this study, hemp fibres were treated with alkali, acetyl and silane chemicals. Fibre constituents such as cellulose, hemicellulose and lignin constituents were separated from treated fibres. The chemical and thermal influences of these constituents on the treated fibres were examined by using scanning electron microscope (SEM), fourier transform infrared (FTIR) spectroscopy, thermogravimetric analysis (TGA), and differential scanning calorimetry (DSC). Experimental results revealed that, hemicellulose was degraded faster than that of cellulose and lignin. Cellulose exhibited better thermal stability and lignin was degraded in a wide range of temperatures. The hydrophilic nature of the fibres was predominantly caused by the presence of hemicellulose and then lignin constituents. Hemicellulose and lignin were mostly removed by the alkalisation with higher concentrations of NaOH, followed by acetylation. Silane treatment could not remove the hemicellulose and lignin, rather this treatment facilitated coupling with the fibre constituents.

  18. Approaches to Establishing the Chemical Structure of Extraterrestrial Organic Solids

    Science.gov (United States)

    Cody, G. D.; Alexander, C. M. OD.; Wirick, Susan

    2003-01-01

    The majority of extraterrestrial organic matter in carbonaceous chondrites resides in a chemically complex, insoluble and perhaps macromolecular phase. We have been applying a series of independent solid state NMR experiments that are designed to provide a self consistent chemical characterization of this complex material. To date we have thoroughly analyzed 8 organic residues from different meteorites, including a CR2 (EET92042), CIl(Orgueil), CM2 (Murchison), Tagish Lake, CM2 (AlH83100), CM2 (Cold Bokkefeld), CM2 (Mighei), CM3 (Y86720). In fig 1. (1)H to (13)C cross polarization NMR spectra of four of these are shown. Note that there exists an enormous range in chemistry exhibited in organic solid [evident by the breadth of the spectral features both in the aliphatic region (sp(sup 3)) and the aromatic region (sp(sup 2))]. There is also considerable differences in the carbon chemistry across the meteorite groups.

  19. Tabletop imaging of structural evolutions in chemical reactions

    CERN Document Server

    Ibrahim, Heide; Beaulieu, Samuel; Schmidt, Bruno E; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T; Wanie, Vincent; Giguére, Mathieu; Kieffer, Jean-Claude; Sanderson, Joseph; Schuurman, Michael S; Légaré, François

    2014-01-01

    The introduction of femto-chemistry has made it a primary goal to follow the nuclear and electronic evolution of a molecule in time and space as it undergoes a chemical reaction. Using Coulomb Explosion Imaging we have shot the first high-resolution molecular movie of a to and fro isomerization process in the acetylene cation. So far, this kind of phenomenon could only be observed using VUV light from a Free Electron Laser [Phys. Rev. Lett. 105, 263002 (2010)]. Here we show that 266 nm ultrashort laser pulses are capable of initiating rich dynamics through multiphoton ionization. With our generally applicable tabletop approach that can be used for other small organic molecules, we have investigated two basic chemical reactions simultaneously: proton migration and C=C bond-breaking, triggered by multiphoton ionization. The experimental results are in excellent agreement with the timescales and relaxation pathways predicted by new and definitively quantitative ab initio trajectory simulations.

  20. Modeling turbulence structure. Chemical kinetics interaction in turbulent reactive flows

    Energy Technology Data Exchange (ETDEWEB)

    Magnussen, B.F. [The Norwegian Univ. of Science and Technology, Trondheim (Norway)

    1997-12-31

    The challenge of the mathematical modelling is to transfer basic physical knowledge into a mathematical formulation such that this knowledge can be utilized in computational simulation of practical problems. The combustion phenomena can be subdivided into a large set of interconnected phenomena like flow, turbulence, thermodynamics, chemical kinetics, radiation, extinction, ignition etc. Combustion in one application differs from combustion in another area by the relative importance of the various phenomena. The difference in fuel, geometry and operational conditions often causes the differences. The computer offers the opportunity to treat the individual phenomena and their interactions by models with wide operational domains. The relative magnitude of the various phenomena therefore becomes the consequence of operational conditions and geometry and need not to be specified on the basis of experience for the given problem. In mathematical modelling of turbulent combustion, one of the big challenges is how to treat the interaction between the chemical reactions and the fluid flow i.e. the turbulence. Different scientists adhere to different concepts like the laminar flamelet approach, the pdf approach of the Eddy Dissipation Concept. Each of these approaches offers different opportunities and problems. All these models are based on a sound physical basis, however none of these have general validity in taking into consideration all detail of the physical chemical interaction. The merits of the models can only be judged by their ability to reproduce physical reality and consequences of operational and geometric conditions in a combustion system. The presentation demonstrates and discusses the development of a coherent combustion technology for energy conversion and safety based on the Eddy Dissipation Concept by Magnussen. (author) 30 refs.

  1. Epithelial structure revealed by chemical dissection and unembedded electron microscopy

    OpenAIRE

    Fey, E G; Capco, D G; Krochmalnic, G; Penman, S

    1984-01-01

    Cytoskeletal structures obtained after extraction of Madin-Darby canine kidney epithelial cell monolayers with Triton X-100 were examined in transmission electron micrographs of cell whole mounts and unembedded thick sections. The cytoskeleton, an ordered structure consisting of a peripheral plasma lamina, a complex network of filaments, and chromatin-containing nuclei, was revealed after extraction of intact cells with a nearly physiological buffer containing Triton X-100. The cytoskeleton w...

  2. Chemical Tuning of the Magnetic Interactions in Layer Structures

    OpenAIRE

    Ronneteg, Sabina

    2005-01-01

    Thin metal films have found their use in many magnetic devices. They form pseudo two-dimensional systems, where the mechanisms for the magnetic interactions between the layers are not completely understood. Layered crystal structures have an advantage over such artificial systems, since the layers can be strictly mono-atomic without any unwanted admixture. In this study, some model systems of layered magnetic crystal structures and their solid solutions have been investigated by x-ray and neu...

  3. WebChem Viewer: a tool for the easy dissemination of chemical and structural data sets

    OpenAIRE

    Durrant, Jacob D; Rommie E Amaro

    2014-01-01

    Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any c...

  4. A robust algorithm for optimizing protein structures with NMR chemical shifts.

    Science.gov (United States)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S

    2015-11-01

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and "PDB worthy". The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca.

  5. A robust algorithm for optimizing protein structures with NMR chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Berjanskii, Mark; Arndt, David; Liang, Yongjie; Wishart, David S., E-mail: david.wishart@ualberta.ca [University of Alberta, Department of Computing Science (Canada)

    2015-11-15

    Over the past decade, a number of methods have been developed to determine the approximate structure of proteins using minimal NMR experimental information such as chemical shifts alone, sparse NOEs alone or a combination of comparative modeling data and chemical shifts. However, there have been relatively few methods that allow these approximate models to be substantively refined or improved using the available NMR chemical shift data. Here, we present a novel method, called Chemical Shift driven Genetic Algorithm for biased Molecular Dynamics (CS-GAMDy), for the robust optimization of protein structures using experimental NMR chemical shifts. The method incorporates knowledge-based scoring functions and structural information derived from NMR chemical shifts via a unique combination of multi-objective MD biasing, a genetic algorithm, and the widely used XPLOR molecular modelling language. Using this approach, we demonstrate that CS-GAMDy is able to refine and/or fold models that are as much as 10 Å (RMSD) away from the correct structure using only NMR chemical shift data. CS-GAMDy is also able to refine of a wide range of approximate or mildly erroneous protein structures to more closely match the known/correct structure and the known/correct chemical shifts. We believe CS-GAMDy will allow protein models generated by sparse restraint or chemical-shift-only methods to achieve sufficiently high quality to be considered fully refined and “PDB worthy”. The CS-GAMDy algorithm is explained in detail and its performance is compared over a range of refinement scenarios with several commonly used protein structure refinement protocols. The program has been designed to be easily installed and easily used and is available at http://www.gamdy.ca http://www.gamdy.ca.

  6. Integrated chemical-thermal and laser treatment of structural and tool steels

    International Nuclear Information System (INIS)

    Using the techniques of autoradiography, radiography, metallography and micro hardness measurement, the distribution of boron and the surface hardening of structural and tool steels under complex chemical, thermal and laser treatment have been investigated

  7. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON THE INTERNET: MOVING TOWARDS A FLAT WORLD

    Science.gov (United States)

    Standardized chemical structure annotation of public toxicity databases and information resources is playing an increasingly important role in the 'flattening' and integration of diverse sets of biological activity data on the Internet. This review discusses public initiatives th...

  8. Structural Analysis Of Alfa Fibers After Chemical Treatment

    Directory of Open Access Journals (Sweden)

    Zakaria Mouallif

    2015-02-01

    Full Text Available Nowadays, natural fibers are used as reinforcement in composite materials. The Alfa fibers have undergone an alkaline treatment with sodium hydroxide NaOH at a concentration of 10%, during an immersion period of two days. After drying, the Fourier transform infrared spectroscopy by attenuated total reflection (FTIR-ATR and X-ray diffraction (XRD were used for the analysis of the chemical properties of these fibers which were extracted from the plant Alfa of the region Al Haouz (Morocco in order to study the modifications resulting from the alkaline treatment. The results proved the presence of the cellulose, with an increase in its proportion in those fibers which have undergone an alkaline treatment with NaOH, the presence of lignin and pectin, as well as their disappearance after the alkaline extraction.

  9. Radial size and chemical structure of nuclear tracks in polymers

    International Nuclear Information System (INIS)

    The radial size of track cores in CR-39 plastics for several types of ions has been determined by two different methods. First, atomic force microscope (AFM) observations were performed on the irradiated CR-39 subsequent to the slight chemical etchings. The track core radii for C, O, Ne and Xe ions evaluated from the intersections of the extrapolated lines, fitted to each growth curve of etch pit radius, were found to be in the range between 2.8 and 4.1 nm, independent of the ion species. Second, ultraviolet (UV)-visible spectra of the irradiated CR-39 were obtained at various fluences. Based on a track overlapping model, the track core radii are evaluated for Ne, Ar, Si and Fe ions. Their core radii were almost proportional to the cube root of the stopping power. The results from the two different measurements are in good agreement with each other. (author)

  10. Recognition and repair of chemically heterogeneous structures at DNA ends.

    Science.gov (United States)

    Andres, Sara N; Schellenberg, Matthew J; Wallace, Bret D; Tumbale, Percy; Williams, R Scott

    2015-01-01

    Exposure to environmental toxicants and stressors, radiation, pharmaceutical drugs, inflammation, cellular respiration, and routine DNA metabolism all lead to the production of cytotoxic DNA strand breaks. Akin to splintered wood, DNA breaks are not "clean." Rather, DNA breaks typically lack DNA 5'-phosphate and 3'-hydroxyl moieties required for DNA synthesis and DNA ligation. Failure to resolve damage at DNA ends can lead to abnormal DNA replication and repair, and is associated with genomic instability, mutagenesis, neurological disease, ageing and carcinogenesis. An array of chemically heterogeneous DNA termini arises from spontaneously generated DNA single-strand and double-strand breaks (SSBs and DSBs), and also from normal and/or inappropriate DNA metabolism by DNA polymerases, DNA ligases and topoisomerases. As a front line of defense to these genotoxic insults, eukaryotic cells have accrued an arsenal of enzymatic first responders that bind and protect damaged DNA termini, and enzymatically tailor DNA ends for DNA repair synthesis and ligation. These nucleic acid transactions employ direct damage reversal enzymes including Aprataxin (APTX), Polynucleotide kinase phosphatase (PNK), the tyrosyl DNA phosphodiesterases (TDP1 and TDP2), the Ku70/80 complex and DNA polymerase β (POLβ). Nucleolytic processing enzymes such as the MRE11/RAD50/NBS1/CtIP complex, Flap endonuclease (FEN1) and the apurinic endonucleases (APE1 and APE2) also act in the chemical "cleansing" of DNA breaks to prevent genomic instability and disease, and promote progression of DNA- and RNA-DNA damage response (DDR and RDDR) pathways. Here, we provide an overview of cellular first responders dedicated to the detection and repair of abnormal DNA termini. PMID:25111769

  11. Combinations of protein-chemical complex structures reveal new targets for established drugs.

    OpenAIRE

    Kalinina, Olga V.; Oliver Wichmann; Gordana Apic; Russell, Robert B.

    2011-01-01

    Biological networks are powerful tools for predicting undocumented relationships between molecules. The underlying principle is that existing interactions between molecules can be used to predict new interactions. Here we use this principle to suggest new protein-chemical interactions via the network derived from three-dimensional structures. For pairs of proteins sharing a common ligand, we use protein and chemical superimpositions combined with fast structural compatibility screens to predi...

  12. The structure and local chemical properties of boron-terminated tetravacancies in hexagonal boron-nitride

    OpenAIRE

    Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H. G.; Liu, Zheng; Suenaga, Kazutomo

    2014-01-01

    Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope (LV-STEM) are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride (h-BN). We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra (EELS) of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sampl...

  13. Corporate Shareholding Structure and Dividend Payout Ratio of Listed Chemical and Paints Companies in Nigeria

    OpenAIRE

    Kabiru Isa Dandago; Musa Adeiza Farouk; Latifat Muhibudeen

    2015-01-01

    This paper is an empirical analysis of influence of Corporate Shareholdings Structure on Dividend payout ratio of listed Chemical and Paints Companies in Nigeria. The study is for the period of 2008-2013. The listed Chemical and Paints Companies are Eight (8) in number as provided by Nigerian stock exchange factbook for 2013. All the eight firms were used for the study. Corporate Shareholdings Structure was proxy with managerial shareholding, institutional shareholding, block shareholding and...

  14. Boron carbide: Consistency of components, lattice parameters, fine structure and chemical composition makes the complex structure reasonable

    Science.gov (United States)

    Werheit, Helmut

    2016-10-01

    The complex, highly distorted structure of boron carbide is composed of B12 and B11C icosahedra and CBC, CBB and B□B linear elements, whose concentration depends on the chemical composition each. These concentrations are shown to be consistent with lattice parameters, fine structure data and chemical composition. The respective impacts on lattice parameters are estimated and discussed. Considering the contributions of the different structural components to the energy of the overall structure makes the structure and its variation within the homogeneity range reasonable; in particular that of B4.3C representing the carbon-rich limit of the homogeneity range. Replacing in B4.3C virtually the B□B components by CBC yields the hypothetical moderately distorted B4.0C (structure formula (B11C)CBC). The reduction of lattice parameters related is compatible with recently reported uncommonly prepared single crystals, whose compositions deviate from B4.3C.

  15. Surface chemical structure of titania-silica nanocomposite powder

    Institute of Scientific and Technical Information of China (English)

    WANG LuYan; SUN YanPing; XU BingShe

    2008-01-01

    Titania-silica (TS) nanocomposite powder with three different composite structures, containing 10-30 mol% SiO2 in each structure, have been prepared by sol-gel processes. The surface characteristics of these titania-silica samples have been investigated by X-ray photo-emission spectroscopy (XPS) and high resolution transmission electron microscopy (HRTEM). The study for all TS oxides annealed at 773 and 1173 K showed: an abnormal surface enrichment in Si increased with increasing annealing tem-perature; the Ti3+, Ti2+, Si3+ and Si2+ oxides coexisted with Ti4+ and Si4+ oxides, and the contents of these TilSi suboxides increased with increasing SiO2 content and annealing temperature; there was a layer rich in O on the topmost surface and the excess O could be attributed to the chem-adsorption of H2O; different composite structures could lead to different contents of Ti/Si suboxides. These results indi-cated that the surface of TS oxide powder derived by sol-gel process was a double layer with enriched O first and then SiOx/TiOy(x, y<2). Ti/Si suboxides could result from the thermal diffusion of Ti4+ and Si4+, which might be induced by the strong interaction between Ti4+ and Si4+.

  16. Shallow nitrogen ion implantation: Evolution of chemical state and defect structure in titanium

    Science.gov (United States)

    Manojkumar, P. A.; Chirayath, V. A.; Balamurugan, A. K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A. K.; Raj, Baldev

    2016-09-01

    Evolution of chemical states and defect structure in titanium during low energy nitrogen ion implantation by Plasma Immersion Ion Implantation (PIII) process is studied. The underlying process of chemical state evolution is investigated using secondary ion mass spectrometry and X-ray photoelectron spectroscopy. The implantation induced defect structure evolution as a function of dose is elucidated using variable energy positron annihilation Doppler broadening spectroscopy (PAS) and the results were corroborated with chemical state. Formation of 3 layers of defect state was modeled to fit PAS results.

  17. Temperature effects on chemical structure and motion in coal. Final report

    Energy Technology Data Exchange (ETDEWEB)

    Maciel, G.E.

    1996-09-30

    The objective of this project was to apply recently developed, state-of-the-art nuclear magnetic resonance (NMR) techniques to examine in situ changes in the chemical structure and molecular/macromolecular motion in coal as the temperature is increased above room temperature. Although alterations in the chemical structure of coal have been studied previously by {sup 13}C NMR, using quenched samples, the goal of this project was to examine these chemical structural changes, and changes in molecular/macromolecular mobility that may precede or accompany the chemical changes, at elevated temperatures, using modern {sup 13}C and {sup 1}H NMR techniques, especially {sup 1}H dipolar-dephasing techniques and related experiments pioneered in the laboratory for examining pyridine-saturated coals. This project consisted of the following four primary segments and related efforts on matters relevant to the first four tasks. (1) {sup 1}H NMR characterization of coal structure and mobility as a function of temperature variation over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (2) {sup 1}H NMR characterization of coal structure, mobility and conversion as a function of temperature variation over a temperature range (240--500 C) for which chemical transformations of coal are known to occur. (3) {sup 13}C NMR investigation of coal structure/mobility as a function of temperature over a temperature range (30--240 C) for which substantial chemical transformations were not anticipated. (4) {sup 13}C NMR investigation of coal structure, dynamics and conversion as a function of temperature variation over a range (240--500 C) for which chemical transformations of coal are known to occur. (5) Related matters relevant to the first four tasks: (a) {sup 1}H CRAMPS NMR characterization of oil shales and their kerogen concentrates; and (b) improved quantitation in {sup 13}C MAS characterization of coals.

  18. Brazilian kefir: structure, microbial communities and chemical composition

    Directory of Open Access Journals (Sweden)

    Karina Teixeira Magalhães

    2011-06-01

    Full Text Available Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5% were the major isolated group identified, followed by yeasts (30.6% and acetic acid bacteria (8.9%. Lactobacillus paracasei (89 isolates, Lactobacillus parabuchneri (41 isolates, Lactobacillus casei (32 isolates, Lactobacillus kefiri (31 isolates, Lactococcus lactis (24 isolates, Acetobacter lovaniensis (32 isolates, Kluyveromyces lactis (31 isolates, Kazachstania aerobia (23 isolates, Saccharomyces cerevisiae (41 isolates and Lachancea meyersii (15 isolates were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml.

  19. CHEMICALS

    CERN Multimedia

    Medical Service

    2002-01-01

    It is reminded that all persons who use chemicals must inform CERN's Chemistry Service (TIS-GS-GC) and the CERN Medical Service (TIS-ME). Information concerning their toxicity or other hazards as well as the necessary individual and collective protection measures will be provided by these two services. Users must be in possession of a material safety data sheet (MSDS) for each chemical used. These can be obtained by one of several means : the manufacturer of the chemical (legally obliged to supply an MSDS for each chemical delivered) ; CERN's Chemistry Service of the General Safety Group of TIS ; for chemicals and gases available in the CERN Stores the MSDS has been made available via EDH either in pdf format or else via a link to the supplier's web site. Training courses in chemical safety are available for registration via HR-TD. CERN Medical Service : TIS-ME :73186 or service.medical@cern.ch Chemistry Service : TIS-GS-GC : 78546

  20. Structural Change of Wood Molecules and Chemorheological Behaviors during Chemical Treatment

    Institute of Scientific and Technical Information of China (English)

    Xie Manhua; Zhao Guangjie

    2004-01-01

    It is very important to clarify the relationship of changes of molecular combinations in wood cell walls and the chemical rheological behavior during various chemical reagent treatments, for it would be helpful to develop new wood modification technologies and to enrich the theory of chemical rheology of wood. Based on previous investigations on the chemorheological properties of wood by chemical treatments and the applied methods in chemical rheology of wool fibers, this paper proposes the study of various additional reagents to wood saturated in water for long periods of time in order to investigate the chemical rheology of wood, which can provide information about the character of combinations between wood molecules and the structural changes of molecules and further put forward the idea of modifying wood in a decrystallized state.

  1. Local Structures and Chemical Properties of Deprotonated Arginine

    Institute of Scientific and Technical Information of China (English)

    Hong-bao Li; Zi-jing Lin; Yi Luo

    2012-01-01

    The potential energy surface of gaseous deprotonated arginine has been systematically investigated by first principles calculations.At the B3LYP/6-31G(d) level,apart from the identification of several stable local structures,a new global minimum is located which is about 6.56 kJ/mol more stable than what has been reported.The deprotonated arginine molecule has two distinct forms with the deprotonation at the carboxylate group (COO-).These two forms are bridged by a very high energy barrier and possess very different IR spectral profiles.Our calculated proton dissociation energy and gas-phase acidity of arginine molecule are found to be in good agreement with the corresponding experimental results.The predicted geometries,dipole moments,rotational constants,vertical ionization energies and IR spectra of low energy conformers will be useful for future experimental measurements.

  2. Chemical bonding and electronic structure of fullerene-based compounds

    International Nuclear Information System (INIS)

    This talk will focus on the nature of bonding of fullerenes with other materials as demonstrated by synchrotron radiation and x-ray photoemission. Adsorption of C60 on metallic and semiconducting substrates occurs via charge transfer from the substrate to a LUMO-derived resonance, resulting in Fermi level alignment and dipole formation. Bonding of metal atoms to C60 depends on the metal work function and bulk cohesive energy. Evaporation of high cohesive energy materials onto a fullerene substrate results in metal cluster nucleation and limited C60 disruption for transition metals. Low cohesive energy metals form compounds with a degree of ionic character related to the metal work function. Photoemission results show the formation of ionic K-fulleride compounds while greater hybridization is observed for Ca-rich fullerides. Finally the electronic structure of fluorinated and hydrogenated fullerenes demonstrate changes in states derived from C60 π bonds due to reaction of dangling bonds

  3. Materials ``alchemy'': Shape-preserving chemical transformation of micro-to-macroscopic 3-D structures

    Science.gov (United States)

    Sandhage, Kenneth H.

    2010-06-01

    The scalable fabrication of nano-structured materials with complex morphologies and tailorable chemistries remains a significant challenge. One strategy for such synthesis consists of the generation of a solid structure with a desired morphology (a “preform”), followed by reactive conversion of the preform into a new chemistry. Several gas/solid and liquid/solid reaction processes that are capable of such chemical conversion into new micro-to-nano-structured materials, while preserving the macroscopic-to-microscopic preform morphologies, are described in this overview. Such shape-preserving chemical transformation of one material into another could be considered a modern type of materials “alchemy.”

  4. Effect of mechanical activation on structure changes and reactivity in further chemical modification of lignin.

    Science.gov (United States)

    Zhao, Xiaohong; Zhang, Yanjuan; Hu, Huayu; Huang, Zuqiang; Yang, Mei; Chen, Dong; Huang, Kai; Huang, Aimin; Qin, Xingzhen; Feng, Zhenfei

    2016-10-01

    Lignin was treated by mechanical activation (MA) in a customized stirring ball mill, and the structure and reactivity in further esterification were studied. The chemical structure and morphology of MA-treated lignin and the esterified products were analyzed by chemical analysis combined with UV/vis spectrometer, FTIR,NMR, SEM and particle size analyzer. The results showed that MA contributed to the increase of aliphatic hydroxyl, phenolic hydroxyl, carbonyl and carboxyl groups but the decrease of methoxyl groups. Moreover, MA led to the decrease of particle size and the increase of specific surface area and roughness of surface in lignin. The reactivity of lignin was enhanced significantly for the increase of hydroxyl content and the improvement of mass transfer in chemical reaction caused by the changes of molecular structure and morphological structure. The process of MA is green and simple, and is an effective method for enhancing the reactivity of lignin. PMID:27344951

  5. The relationship between chemical structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Hao [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States)]. E-mail: hao.jiang@wpafb.af.mil; Hong Lianggou [Materials Sci and Tech Applications, LLC, 409 Maple Springs Drive, Dayton OH 45458 (United States); Venkatasubramanian, N. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Grant, John T. [Research Institute, University of Dayton, 300 College Park, Dayton, OH 45469-0168 (United States); Eyink, Kurt [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Wiacek, Kevin [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Fries-Carr, Sandra [Air Force Research Laboratory, Propulsion Directorate, 1950 Fifth Street, Wright-Patterson Air Force Base, OH 45433-7251 (United States); Enlow, Jesse [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States); Bunning, Timothy J. [Air Force Research Laboratory, Materials Directorate, 3005 Hobson Way, Wright-Patterson Air Force Base, OH 45433-7707 (United States)

    2007-02-26

    Polymer dielectric films fabricated by plasma enhanced chemical vapor deposition (PECVD) have unique properties due to their dense crosslinked bulk structure. These spatially uniform films exhibit good adhesion to a variety of substrates, excellent chemical inertness, high thermal resistance, and are formed from an inexpensive, solvent-free, room temperature process. In this work, we studied the dielectric properties of plasma polymerized (PP) carbon-based polymer thin films prepared from two precursors, benzene and octafluorocyclobutane. Two different monomer feed locations, directly in the plasma zone or in the downstream region (DS) and two different pressures, 80 Pa (high pressure) or 6.7 Pa (low pressure), were used. The chemical structure of the PECVD films was examined by X-ray photoelectron spectroscopy and Fourier-transform infrared spectroscopy. The dielectric constant ({epsilon} {sub r}) and dielectric loss (tan {delta}) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F {sub b}) was characterized by the current-voltage method. Spectroscopic ellipsometry was performed to determine the film thickness and refractive index. Good dielectric properties were exhibited, as PP-benzene films formed in the high pressure, DS region showed a F{sub b} of 610 V/{mu}m, an {epsilon} {sub r} of 3.07, and a tan {delta} of 7.0 x 10{sup -3} at 1 kHz. The PECVD processing pressure has a significant effect on final film structure and the film's physical density has a strong impact on dielectric breakdown strength. Also noted was that the residual oxygen content in the PP-benzene films significantly affected the frequency dependences of the dielectric constant and loss.

  6. Extended Functional Groups (EFG: An Efficient Set for Chemical Characterization and Structure-Activity Relationship Studies of Chemical Compounds

    Directory of Open Access Journals (Sweden)

    Elena S. Salmina

    2015-12-01

    Full Text Available The article describes a classification system termed “extended functional groups” (EFG, which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts of the On-line CHEmical database and Modeling (OCHEM environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models.

  7. Improved Chemical Structure-Activity Modeling Through Data Augmentation.

    Science.gov (United States)

    Cortes-Ciriano, Isidro; Bender, Andreas

    2015-12-28

    Extending the original training data with simulated unobserved data points has proven powerful to increase both the generalization ability of predictive models and their robustness against changes in the structure of data (e.g., systematic drifts in the response variable) in diverse areas such as the analysis of spectroscopic data or the detection of conserved domains in protein sequences. In this contribution, we explore the effect of data augmentation in the predictive power of QSAR models, quantified by the RMSE values on the test set. We collected 8 diverse data sets from the literature and ChEMBL version 19 reporting compound activity as pIC50 values. The original training data were replicated (i.e., augmented) N times (N ∈ 0, 1, 2, 4, 6, 8, 10), and these replications were perturbed with Gaussian noise (μ = 0, σ = σnoise) on either (i) the pIC50 values, (ii) the compound descriptors, (iii) both the compound descriptors and the pIC50 values, or (iv) none of them. The effect of data augmentation was evaluated across three different algorithms (RF, GBM, and SVM radial) and two descriptor types (Morgan fingerprints and physicochemical-property-based descriptors). The influence of all factor levels was analyzed with a balanced fixed-effect full-factorial experiment. Overall, data augmentation constantly led to increased predictive power on the test set by 10-15%. Injecting noise on (i) compound descriptors or on (ii) both compound descriptors and pIC50 values led to the highest drop of RMSEtest values (from 0.67-0.72 to 0.60-0.63 pIC50 units). The maximum increase in predictive power provided by data augmentation is reached when the training data is replicated one time. Therefore, extending the original training data with one perturbed repetition thereof represents a reasonable trade-off between the increased performance of the models and the computational cost of data augmentation, namely increase of (i) model complexity due to the need for optimizing

  8. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics.

    Directory of Open Access Journals (Sweden)

    Anders S Christensen

    Full Text Available We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94. ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3J(NC' spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  9. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    CERN Document Server

    Christensen, Anders S; Borg, Mikael; Boomsma, Wouter; Lindorff-Larsen, Kresten; Hamelryck, Thomas; Jensen, Jan H

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to refine protein structures to this...

  10. Synthesis of Cobalt Oxides Thin Films Fractal Structures by Laser Chemical Vapor Deposition

    Directory of Open Access Journals (Sweden)

    P. Haniam

    2014-01-01

    Full Text Available Thin films of cobalt oxides (CoO and Co3O4 fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures.

  11. Structure-mechanism-based engineering of chemical regulators targeting distinct pathological factors in Alzheimer's disease

    Science.gov (United States)

    Beck, Michael W.; Derrick, Jeffrey S.; Kerr, Richard A.; Oh, Shin Bi; Cho, Woo Jong; Lee, Shin Jung C.; Ji, Yonghwan; Han, Jiyeon; Tehrani, Zahra Aliakbar; Suh, Nayoung; Kim, Sujeong; Larsen, Scott D.; Kim, Kwang S.; Lee, Joo-Yong; Ruotolo, Brandon T.; Lim, Mi Hee

    2016-10-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal-Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs.

  12. ANALYSIS OF THE CHEMICAL COMPOSITION AND MORPHOLOGICAL STRUCTURE OF BANANA PSEUDO-STEM

    OpenAIRE

    Kun Li; Shiyu Fu; Huaiyu Zhan; Yao Zhan; Lucian A. Lucia

    2010-01-01

    An analysis of the chemical composition and anatomical structure of banana pseudo-stem was carried out using Light Microscopy (LM), Scanning Electron Microscopy (SEM), and Confocal Laser Scanning Microscopy (CLSM). The chemical analysis indicated there is a high holocellulose content and low lignin content in banana pseudo-stem compared with some other non-wood fiber resources. These results demonstrate that the banana pseudo-stem has potential value for pulping. In addition, we report for th...

  13. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics

    NARCIS (Netherlands)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert; Dekker, Frans

    2005-01-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architec

  14. The chemical structure of the ZnO/SiC heterointerface as revealed by electron spectroscopies

    International Nuclear Information System (INIS)

    ZnO layers were deposited on 6H-SiC single crystalline wafers by radio frequency magnetron sputtering. The chemical structure of the ZnO/SiC interface was studied by x-ray photoelectron and x-ray excited Auger electron spectroscopy. A complex chemical structure, involving not only silicon–carbon and zinc–oxygen bonds but also silicon–oxygen and zinc–silicon–oxygen bonds was revealed to form at the ZnO/SiC interface. Based on the comparison with the presumably inert (i.e. chemically abrupt) ZnO/Mo interface, it was concluded that a willemite-like zinc silicate (i.e. Zn2SiO4) interface species develops between ZnO and SiC. The presence of this species at the ZnO/SiC interface will affect the electronic structure of the heterojunction and thus needs to be considered for device optimization. (paper)

  15. Surface Nano Structures Manufacture Using Batch Chemical Processing Methods for Tooling Applications

    DEFF Research Database (Denmark)

    Tosello, Guido; Calaon, Matteo; Gavillet, J.;

    2011-01-01

    The patterning of large surface areas with nano structures by using chemical batch processes to avoid using highenergy intensive nano machining processes was investigated. The capability of different surface treatment methods of creating micro and nano structured adaptable mould inserts...... for subsequent polymer replication by injection moulding was analyzed. New tooling solutions to produce nano structured mould surfaces were investigated. Experiments based on three different chemical-based-batch techniques to establish surface nano (i.e. sub-μm) structures on large areas were performed. Three...... approaches were selected: (1) using Ø500 nm nano beads deposition for direct patterning of a 4” silicon wafer; (2) using Ø500 nm nano beads deposition as mask for 4” silicon wafer etching and subsequent nickel electroplating; (3) using the anodizing process to produce Ø500 nm structures on a 30x80 mm2...

  16. Fragment-Based Electronic Structure Approach for Computing Nuclear Magnetic Resonance Chemical Shifts in Molecular Crystals.

    Science.gov (United States)

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

    First-principles chemical shielding tensor predictions play a critical role in studying molecular crystal structures using nuclear magnetic resonance. Fragment-based electronic structure methods have dramatically improved the ability to model molecular crystal structures and energetics using high-level electronic structure methods. Here, a many-body expansion fragment approach is applied to the calculation of chemical shielding tensors in molecular crystals. First, the impact of truncating the many-body expansion at different orders and the role of electrostatic embedding are examined on a series of molecular clusters extracted from molecular crystals. Second, the ability of these techniques to assign three polymorphic forms of the drug sulfanilamide to the corresponding experimental (13)C spectra is assessed. This challenging example requires discriminating among spectra whose (13)C chemical shifts differ by only a few parts per million (ppm) across the different polymorphs. Fragment-based PBE0/6-311+G(2d,p) level chemical shielding predictions correctly assign these three polymorphs and reproduce the sulfanilamide experimental (13)C chemical shifts with 1 ppm accuracy. The results demonstrate that fragment approaches are competitive with the widely used gauge-invariant projector augmented wave (GIPAW) periodic density functional theory calculations. PMID:26584373

  17. Structure and local chemical properties of boron-terminated tetravacancies in hexagonal boron nitride.

    Science.gov (United States)

    Cretu, Ovidiu; Lin, Yung-Chang; Koshino, Masanori; Tizei, Luiz H G; Liu, Zheng; Suenaga, Kazutomo

    2015-02-20

    Imaging and spectroscopy performed in a low-voltage scanning transmission electron microscope are used to characterize the structure and chemical properties of boron-terminated tetravacancies in hexagonal boron nitride. We confirm earlier theoretical predictions about the structure of these defects and identify new features in the electron energy-loss spectra of B atoms using high resolution chemical maps, highlighting differences between these areas and pristine sample regions. We correlate our experimental data with calculations which help explain our observations. PMID:25763963

  18. Application of chemical structure and bonding of actinide oxide materials for forensic science

    Energy Technology Data Exchange (ETDEWEB)

    Wilkerson, Marianne Perry [Los Alamos National Laboratory

    2010-01-01

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO{sub 2} (An: U, Pu) to form non-stoichiometric species described as AnO{sub 2+x}. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  19. Effects of structural differences on the NMR chemical shifts in isostructural dipeptides.

    Science.gov (United States)

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

    Porous crystalline dipeptides have gained recent attention for their potential as gas-storage materials. Within this large class is a group of dipeptides containing alanine, valine, and isoleucine with very similar crystal structures. We report the (13)C (carbonyl and Cα) and (15)N (amine and amide) solid-state NMR isotropic chemical shifts in a series of seven such isostructural porous dipeptides as well as shift tensor data for the carbonyl and amide sites. Using their known crystal structures and aided by ab initio quantum chemical calculations for the resonance assignments, we elucidate trends relating local structure, hydrogen-bonding patterns, and chemical shift. We find good correlation between the backbone dihedral angles and the Cα1 and Cα2 shifts. For the C1 shift tensor, the δ11 value shifts downfield as the hydrogen-bond distance increases, δ22 shifts upfield, and δ33 shows little variation. The C2 shift tensor shows no appreciable correlation with structural parameters. For the N2 tensor, δ11 shows little dependence on the hydrogen-bond length, whereas δ22 and δ33 both show a decrease in shielding as the hydrogen bond shortens. Our analysis teases apart some, but not all, structural contributors to the observed differences the solid-state NMR chemical shifts.

  20. Application of chemical structure and bonding of actinide oxide materials for forensic science

    International Nuclear Information System (INIS)

    We are interested in applying our understanding of actinide chemical structure and bonding to broaden the suite of analytical tools available for nuclear forensic analyses. Uranium- and plutonium-oxide systems form under a variety of conditions, and these chemical species exhibit some of the most complex behavior of metal oxide systems known. No less intriguing is the ability of AnO2 (An: U, Pu) to form non-stoichiometric species described as AnO2+x. Environmental studies have shown the value of utilizing the chemical signatures of these actinide oxide materials to understand transport following release into the environment. Chemical speciation of actinide-oxide samples may also provide clues as to the age, source, or process history of the material. The scientific challenge is to identify, measure and understand those aspects of speciation of actinide analytes that carry information about material origin and history most relevant to forensics. Here, we will describe our efforts in material synthesis and analytical methods development that we will use to provide the fundamental science to characterize actinide oxide molecular structures for forensic science. Structural properties and initial results to measure structural variability of uranium oxide samples using synchrotron-based X-ray Absorption Fine Structure will be discussed.

  1. Influence of Chemical Conditions on the Nanoporous Structure of Silicate Aerogels

    Directory of Open Access Journals (Sweden)

    Katalin Sinkó

    2010-01-01

    Full Text Available Silica or various silicate aerogels can be characterized by highly porous, open cell, low density structures. The synthesis parameters influence the three-dimensional porous structures by modifying the kinetics and mechanism of hydrolysis and condensation processes. Numerous investigations have shown that the structure of porous materials can be tailored by variations in synthesis conditions (e.g., the type of precursors, catalyst, and surfactants; the ratio of water/precursor; the concentrations; the medium pH; and the solvent. The objectives of this review are to summarize and elucidate the effects of chemical conditions on the nanoporous structure of sol-gel derived silicate aerogels.

  2. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    Energy Technology Data Exchange (ETDEWEB)

    Labudde, D.; Leitner, D.; Krueger, M.; Oschkinat, H. [Forschungsinstitut fuer Molekulare Pharmakologie (Germany)], E-mail: oschkinat@fmp-berlin.de

    2003-01-15

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the {alpha}-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely {alpha}-helix, {beta}-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time.

  3. CHEM-PATH-TRACKER: An automated tool to analyze chemical motifs in molecular structures.

    Science.gov (United States)

    Ribeiro, João V; Cerqueira, N M F S A; Fernandes, Pedro A; Ramos, Maria J

    2014-07-01

    In this article, we propose a method for locating functionally relevant chemical motifs in protein structures. The chemical motifs can be a small group of residues or structure protein fragments with highly conserved properties that have important biological functions. However, the detection of chemical motifs is rather difficult because they often consist of a set of amino acid residues separated by long, variable regions, and they only come together to form a functional group when the protein is folded into its three-dimensional structure. Furthermore, the assemblage of these residues is often dependent on non-covalent interactions among the constituent amino acids that are difficult to detect or visualize. To simplify the analysis of these chemical motifs and give access to a generalized use for all users, we developed chem-path-tracker. This software is a VMD plug-in that allows the user to highlight and reveal potential chemical motifs requiring only a few selections. The analysis is based on atoms/residues pair distances applying a modified version of Dijkstra's algorithm, and it makes possible to monitor the distances of a large pathway, even during a molecular dynamics simulation. This tool turned out to be very useful, fast, and user-friendly in the performed tests. The chem-path-tracker package is distributed as an independent platform and can be found at http://www.fc.up.pt/PortoBioComp/database/doku.php?id=chem-path-tracker. PMID:24775806

  4. Prediction algorithm for amino acid types with their secondary structure in proteins (PLATON) using chemical shifts

    International Nuclear Information System (INIS)

    The algorithm PLATON is able to assign sets of chemical shifts derived from a single residue to amino acid types with its secondary structure (amino acid species). A subsequent ranking procedure using optionally two different penalty functions yields predictions for possible amino acid species for the given set of chemical shifts. This was demonstrated in the case of the α-spectrin SH3 domain and applied to 9 further protein data sets taken from the BioMagRes database. A database consisting of reference chemical shift patterns (reference CSPs) was generated from assigned chemical shifts of proteins with known 3D-structure. This reference CSP database is used in our approach for extracting distributions of amino acid types with their most likely secondary structure elements (namely α-helix, β-sheet, and coil) for single amino acids by comparison with query CSPs. Results obtained for the 10 investigated proteins indicates that the percentage of correct amino acid species in the first three positions in the ranking list, ranges from 71.4% to 93.2% for the more favorable penalty function. Where only the top result of the ranking list for these 10 proteins is considered, 36.5% to 83.1% of the amino acid species are correctly predicted. The main advantage of our approach, over other methods that rely on average chemical shift values is the ability to increase database content by incorporating newly derived CSPs, and therefore to improve PLATON's performance over time

  5. Evaluation of chemical and structural properties of germanium-carbon coatings deposited by plasma enhanced chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Jamali, Hossein, E-mail: h.jamali@mut-es.ac.ir; Mozafarinia, Reza; Eshaghi, Akbar

    2015-10-15

    Germanium-carbon coatings were deposited on silicon and glass substrates by plasma enhanced chemical vapor deposition (PECVD) using three different flow ratios of GeH{sub 4} and CH{sub 4} precursors. Elemental analysis, structural evaluation and microscopic investigation of coatings were performed using laser-induced breakdown spectroscopy (LIBS), Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), Raman spectroscopy, field emission scanning electron microscopy (FESEM) and atomic force microscopy (AFM), respectively. Based on the results, the coatings exhibited a homogeneous and dense structure free of pores with a very good adhesion to substrate. The structural evaluation revealed that the germanium-carbon coatings were a kind of a Ge-rich composite material containing the amorphous and crystalline germanium and amorphous carbon with the mixture of Ge–Ge, Ge–C, C–C, Ge–H and C–H bonds. The result suggested that the amorphisation of the coatings could be increased with raising CH{sub 4}:GeH{sub 4} flow rate ratio and subsequently increasing C amount incorporated into the coating. - Highlights: • Germanium-carbon coatings were prepared by PECVD technique. • The germanium-carbon coatings were a kind of composite material. • The amorphisation of the coatings were increased with raising CH{sub 4}:GeH{sub 4} flow ratio.

  6. PPM-One: a static protein structure based chemical shift predictor

    Energy Technology Data Exchange (ETDEWEB)

    Li, Dawei; Brüschweiler, Rafael, E-mail: bruschweiler.1@osu.edu [The Ohio State University, Campus Chemical Instrument Center (United States)

    2015-07-15

    We mined the most recent editions of the BioMagResDataBank and the protein data bank to parametrize a new empirical knowledge-based chemical shift predictor of protein backbone atoms using either a linear or an artificial neural network model. The resulting chemical shift predictor PPM-One accepts a single static 3D structure as input and emulates the effect of local protein dynamics via interatomic steric contacts. Furthermore, the chemical shift prediction was extended to most side-chain protons and it is found that the prediction accuracy is at a level allowing an independent assessment of stereospecific assignments. For a previously established set of test proteins some overall improvement was achieved over current top-performing chemical shift prediction programs.

  7. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin

    OpenAIRE

    Kocsis, Bela; Domokos, J.; Szabo, D.

    2016-01-01

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their...

  8. Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

    OpenAIRE

    Feng Lin; Isaac M. Markus; Doeff, Marca M.; Xin, Huolin L.

    2014-01-01

    The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiati...

  9. Clustering and rule-based classifications of chemical structures evaluated in the biological activity space.

    Science.gov (United States)

    Schuffenhauer, Ansgar; Brown, Nathan; Ertl, Peter; Jenkins, Jeremy L; Selzer, Paul; Hamon, Jacques

    2007-01-01

    Classification methods for data sets of molecules according to their chemical structure were evaluated for their biological relevance, including rule-based, scaffold-oriented classification methods and clustering based on molecular descriptors. Three data sets resulting from uniformly determined in vitro biological profiling experiments were classified according to their chemical structures, and the results were compared in a Pareto analysis with the number of classes and their average spread in the profile space as two concurrent objectives which were to be minimized. It has been found that no classification method is overall superior to all other studied methods, but there is a general trend that rule-based, scaffold-oriented methods are the better choice if classes with homogeneous biological activity are required, but a large number of clusters can be tolerated. On the other hand, clustering based on chemical fingerprints is superior if fewer and larger classes are required, and some loss of homogeneity in biological activity can be accepted.

  10. Electrical conductivity as a constraint on lower mantle thermo-chemical structure

    Science.gov (United States)

    Deschamps, Frédéric; Khan, Amir

    2016-09-01

    Electrical conductivity of the Earth's mantle depends on both temperature and compositional parameters. Radial and lateral variations in conductivity are thus potentially a powerful means to investigate its thermo-chemical structure. Here, we use available electrical conductivity data for the major lower mantle minerals, bridgmanite and ferropericlase, to calculate 3D maps of lower mantle electrical conductivity for two possible models: a purely thermal model, and a thermo-chemical model. Both models derive from probabilistic seismic tomography, and the thermo-chemical model includes, in addition to temperature anomalies, variations in volume fraction of bridgmanite and iron content. The electrical conductivity maps predicted by these two models are clearly different. Compared to the purely thermal model, the thermo-chemical model leads to higher electrical conductivity, by about a factor 2.5, and stronger lateral anomalies. In the lowermost mantle (2000-2891 km) the thermo-chemical model results in a belt of high conductivity around the equator, whose maximum value reaches ∼120% of the laterally-averaged value and is located in the low shear-wave velocity provinces imaged in tomographic models. Based on our electrical conductivity maps, we computed electromagnetic response functions (C-responses) and found, again, strong differences between the C-responses for purely thermal and thermo-chemical models. At periods of 1 year and longer, C-responses based on thermal and thermo-chemical models are easily distinguishable. Furthermore, C-responses for thermo-chemical model vary geographically. Our results therefore show that long-period (1 year and more) variations of the magnetic field may provide key insights on the nature and structure of the deep mantle.

  11. Protein structure similarity clustering (PSSC) and natural product structure as inspiration sources for drug development and chemical genomics.

    Science.gov (United States)

    Dekker, Frank J; Koch, Marcus A; Waldmann, Herbert

    2005-06-01

    Finding small molecules that modulate protein function is of primary importance in drug development and in the emerging field of chemical genomics. To facilitate the identification of such molecules, we developed a novel strategy making use of structural conservatism found in protein domain architecture and natural product inspired compound library design. Domains and proteins identified as being structurally similar in their ligand-sensing cores are grouped in a protein structure similarity cluster (PSSC). Natural products can be considered as evolutionary pre-validated ligands for multiple proteins and therefore natural products that are known to interact with one of the PSSC member proteins are selected as guiding structures for compound library synthesis. Application of this novel strategy for compound library design provided enhanced hit rates in small compound libraries for structurally similar proteins.

  12. Automated assignment of NMR chemical shifts based on a known structure and 4D spectra.

    Science.gov (United States)

    Trautwein, Matthias; Fredriksson, Kai; Möller, Heiko M; Exner, Thomas E

    2016-08-01

    Apart from their central role during 3D structure determination of proteins the backbone chemical shift assignment is the basis for a number of applications, like chemical shift perturbation mapping and studies on the dynamics of proteins. This assignment is not a trivial task even if a 3D protein structure is known and needs almost as much effort as the assignment for structure prediction if performed manually. We present here a new algorithm based solely on 4D [(1)H,(15)N]-HSQC-NOESY-[(1)H,(15)N]-HSQC spectra which is able to assign a large percentage of chemical shifts (73-82 %) unambiguously, demonstrated with proteins up to a size of 250 residues. For the remaining residues, a small number of possible assignments is filtered out. This is done by comparing distances in the 3D structure to restraints obtained from the peak volumes in the 4D spectrum. Using dead-end elimination, assignments are removed in which at least one of the restraints is violated. Including additional information from chemical shift predictions, a complete unambiguous assignment was obtained for Ubiquitin and 95 % of the residues were correctly assigned in the 251 residue-long N-terminal domain of enzyme I. The program including source code is available at https://github.com/thomasexner/4Dassign . PMID:27484442

  13. Protein structure validation and refinement using amide proton chemical shifts derived from quantum mechanics

    DEFF Research Database (Denmark)

    Christensen, Anders Steen; Linnet, Troels Emtekær; Borg, Mikael;

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level...

  14. Physico-Chemical and Structural Properties of DeNOx and SO2 Oxidation Catalysts

    DEFF Research Database (Denmark)

    Masters, Stephen Grenville; Oehlers, Cord; Nielsen, Kurt;

    1996-01-01

    Commercial catalysts for NOx removal and SO2 oxidation and their model systems have been investigated by spectroscopic, thermal, electrochemical and X-ray methods. Structural information on the vanadium complexes and compounds as well as physico-chemical properties for catalyst model systems have...... been obtained. The results are discussed in relation to proposed reaction mechanisms....

  15. Test results of chemical reactivity test (CRT) analysis of structural materials and explosives

    Energy Technology Data Exchange (ETDEWEB)

    Back, P.S.; Barnhart, B.V.; Walters, R.R.; Haws, L.D.; Collins, L.W.

    1980-03-21

    The chemical reactivity test, CRT, is a procedure used to screen the compatibility of component structure materials with explosives. This report contains the results of CRT materials evaluations conducted at Mound Facility. Data about materials combinations are catalogued both under the name of the explosive and the nonexplosive.

  16. Incorporating chemical modification constraints into a dynamic programming algorithm for prediction of RNA secondary structure

    Science.gov (United States)

    Mathews, David H.; Disney, Matthew D.; Childs, Jessica L.; Schroeder, Susan J.; Zuker, Michael; Turner, Douglas H.

    2004-01-01

    A dynamic programming algorithm for prediction of RNA secondary structure has been revised to accommodate folding constraints determined by chemical modification and to include free energy increments for coaxial stacking of helices when they are either adjacent or separated by a single mismatch. Furthermore, free energy parameters are revised to account for recent experimental results for terminal mismatches and hairpin, bulge, internal, and multibranch loops. To demonstrate the applicability of this method, in vivo modification was performed on 5S rRNA in both Escherichia coli and Candida albicans with 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate, dimethyl sulfate, and kethoxal. The percentage of known base pairs in the predicted structure increased from 26.3% to 86.8% for the E. coli sequence by using modification constraints. For C. albicans, the accuracy remained 87.5% both with and without modification data. On average, for these sequences and a set of 14 sequences with known secondary structure and chemical modification data taken from the literature, accuracy improves from 67% to 76%. This enhancement primarily reflects improvement for three sequences that are predicted with <40% accuracy on the basis of energetics alone. For these sequences, inclusion of chemical modification constraints improves the average accuracy from 28% to 78%. For the 11 sequences with <6% pseudoknotted base pairs, structures predicted with constraints from chemical modification contain on average 84% of known canonical base pairs. PMID:15123812

  17. Using NMR chemical shifts to calculate the propensity for structural order and disorder in proteins

    NARCIS (Netherlands)

    Tamiola, Kamil; Mulder, Frans A. A.

    2012-01-01

    NMR spectroscopy offers the unique possibility to relate the structural propensities of disordered proteins and loop segments of folded peptides to biological function and aggregation behaviour. Backbone chemical shifts are ideally suited for this task, provided that appropriate reference data are a

  18. Structures and Chemical Equilibria of Some N-Heterocycles Containing Amide Linkages

    Directory of Open Access Journals (Sweden)

    N. H. Abd El Moneim

    2003-05-01

    Full Text Available Structures and chemical equilibria of 5-carboxy-2-thiouracil (1, 5,6-diphenyl-3-hydroxy-1,2,4-triazine (2, 1-phenyl-3-methyl-5-pyrazolone (3 and 2-mercapto-4,6-dimethylpyrimidine hydrochloride (4 are reported. Their electronic transitions are assigned and pK values are evaluated and discussed.

  19. Physico-Chemical Structural and Electrical Studies of Cu-Zn Ferrites Synthesized by Novel Chemical Route

    Science.gov (United States)

    Lohar, K. S.; Patange, S. M.; Mane, D. R.; Shirsath, Sagar E.; Shinde, N. D.; Kulkarni, Nilesh

    The physico-chemical, structural and electrical properties of zinc substituted copper ferrites having the general formula Cu1-xZnxFe2O4 (x=0.0 to x=0.8) have been studied as a function of zinc ion concentration. The sample was prepared by co-precipitation method from corresponding metal sulphates. X-ray diffraction patterns were used to confirm the structure of synthesized samples. The calculated and theoretical values of average lattice constant, tetrahedral bond, tetrahedral edge and unshared octahedral edge were found to increase, while the shared octahedral edge and octahedral bond decrease as the Zn ion concentration increases. The dielectric constant (ε‧) and dielectric loss tangent (tan δ) were measured at a constant frequency 1 kHz as a function of temperature. The dielectric constant and loss tangent were found to increase with rise in temperature. The conduction mechanism in these ferrites is discussed on the basis of electron exchange between Fe2+ and Fe3+ ions. The temperature dependent dc resistivity was carried out in the temperature range 300 to 800 K. The plots of log ρ versus 103/T are linear showing two regions, corresponding to ferrimagnetic and paramagnetic regions.

  20. Biosynthesis, Chemical Structure, and Structure-Activity Relationship of Orfamide Lipopeptides Produced by Pseudomonas protegens and Related Species

    OpenAIRE

    Ma, Zongwang; Geudens, Niels; Kieu, Nam P.; Sinnaeve, Davy; Ongena, Marc; Martins, José C.; Höfte, Monica

    2016-01-01

    Orfamide type cyclic lipopeptides (CLPs) are biosurfactants produced by Pseudomonas and involved in lysis of oomycete zoospores, biocontrol of Rhizoctonia and insecticidal activity against aphids. In this study, we compared the biosynthesis, structural diversity, in vitro and in planta activities of orfamides produced by rhizosphere-derived Pseudomonas protegens and related Pseudornonas species. Genetic characterization together with chemical identification revealed that the main orfamide com...

  1. Chemical structure and pharmacokinetics of novel quinolone agents represented by avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and nemonoxacin.

    Science.gov (United States)

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-01-01

    Quinolones are potent antimicrobial agents with a basic chemical structure of bicyclic ring. Fluorine atom at position C-6 and various substitutions on the basic quinolone structure yielded fluoroquinolones, namely norfloxacin, ciprofloxacin, levofloxacin, moxifloxacin and numerous other agents. The target molecules of quinolones and fluoroquinolones are bacterial gyrase and topoisomerase IV enzymes. Broad-spectrum and excellent tissue penetration make fluoroquinolones potent agents but their toxic side effects and increasing number of resistant pathogens set limits on their use. This review focuses on recent advances concerning quinolones and fluoroquinolones, we will be summarising chemical structure, mode of action, pharmacokinetic properties and toxicity. We will be describing fluoroquinolones introduced in clinical trials, namely avarofloxacin, delafloxacin, finafloxacin, zabofloxacin and non-fluorinated nemonoxacin. These agents have been proved to have enhanced antibacterial effect even against ciprofloxacin resistant pathogens, and found to be well tolerated in both oral and parenteral administrations. These features are going to make them potential antimicrobial agents in the future. PMID:27215369

  2. Nanostructured PLD-grown gadolinia doped ceria: Chemical and structural characterization by transmission electron microscopy techniques

    DEFF Research Database (Denmark)

    Rodrigo, Katarzyna Agnieszka; Wang, Hsiang-Jen; Heiroth, Sebastian;

    2011-01-01

    The morphology as well as the spatially resolved elemental and chemical characterization of 10 mol% gadolinia doped ceria (CGO10) structures prepared by pulsed laser deposition (PLD) technique are investigated by scanning transmission electron microscopy accompanied with electron energy loss...... spectroscopy and energy dispersive X-ray spectroscopy. A dense, columnar and structurally inhomogeneous CGO10 film, i.e. exhibiting grain size refinement across the film thickness, is obtained in the deposition process. The cerium M4,5 edges, used to monitor the local electronic structure of the grains...

  3. Molecular design chemical structure generation from the properties of pure organic compounds

    CERN Document Server

    Horvath, AL

    1992-01-01

    This book is a systematic presentation of the methods that have been developed for the interpretation of molecular modeling to the design of new chemicals. The main feature of the compilation is the co-ordination of the various scientific disciplines required for the generation of new compounds. The five chapters deal with such areas as structure and properties of organic compounds, relationships between structure and properties, and models for structure generation. The subject is covered in sufficient depth to provide readers with the necessary background to understand the modeling

  4. Quantitative Survey and Structural Classification of Fracking Chemicals Reported in Unconventional Gas Exploitation

    Science.gov (United States)

    Elsner, Martin; Schreglmann, Kathrin

    2015-04-01

    additives reported for use in hydraulic fracturing. For the years 2005-2009 it is based on the Waxman report, and for the years 2011-2013 it relies on the database FracFocus, where it makes use of the data extracted and provided by the website "SkyTruth". For the first time, we list fracking chemicals according to their chemical structure and functional groups, because these properties are important as a starting point for (i) the design of analytical methods, (ii) to assess environmental fate and (iii) to understand why a given chemical is used at a certain stage of the fracturing process and what possible alternatives exist.

  5. Chemical structure of vanadium-based contact formation on n-AlN

    International Nuclear Information System (INIS)

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  6. Structural changes in amorphous organic compounds and their role during chemical transformations

    International Nuclear Information System (INIS)

    Using butanediol vinylacetate and dimetacrylate as an example, it can be shown that structural changes of amorphous-liquid substance play an important part at chemical transformations of amorphous compounds and chemical reaction rate provides an function of local order. When the amorphous polymer is viewed as an system of multiple transformations, each gives birth to the definite local order, the calculation of recombination reaction of active centers accumulated during irradiation of polymer at 77 K is carried out. Concentration of recombinated centers rises steeply near each transformation Tk

  7. Chemical structures of constituents from the whole plant of Bacopa monniera.

    Science.gov (United States)

    Ohta, Tomoe; Nakamura, Seikou; Nakashima, Souichi; Oda, Yoshimi; Matsumoto, Takahiro; Fukaya, Masashi; Yano, Mamiko; Yoshikawa, Masayuki; Matsuda, Hisashi

    2016-07-01

    Two new dammarane-type triterpene oligoglycosides, bacomosaponins A and B, and three new phenylethanoid glycosides, bacomosides A, B1, and B2, were isolated from the whole plant of Bacopa monniera Wettst. The chemical structures of the new constituents were characterized on the basis of chemical and physicochemical evidence. In the present study, bacomosaponins A and B with acyl groups were obtained from the whole plant of B. monniera. This is the first report of acylated dammarane-type triterpene oligoglycosides isolated from B. monniera. In addition, dammarane-type triterpene saponins significantly inhibited the aggregation of 42-mer amyloid β-protein.

  8. Chemical structure of vanadium-based contact formation on n-AlN

    Energy Technology Data Exchange (ETDEWEB)

    Pookpanratana, S.; France, R.; Blum, M.; Bell, A.; Bar, M.; Weinhardt, L.; Zhang, Y.; Hofmann, T.; Fuchs, O.; Yang, W.; Denlinger, J. D.; Mulcahy, S.; Moustakas, T. D.; Heske, Clemens

    2010-05-17

    We have investigated the chemical interaction between a Au/V/Al/V layer structure and n-type AlN epilayers using soft x-ray photoemission, x-ray emission spectroscopy, and atomic force microscopy. To understand the complex processes involved in this multicomponent system, we have studied the interface before and after a rapid thermal annealing step. We find the formation of a number of chemical phases at the interface, including VN, metallic vanadium, aluminum oxide, and metallic gold. An interaction mechanism for metal contact formation on the entire n-(Al,Ga)N system is proposed.

  9. Inclusion compound of vitamin B6 in {beta}-CD. Physico-chemical and structural investigations

    Energy Technology Data Exchange (ETDEWEB)

    Borodi, Gheorghe; Kacso, Irina; Farcas, Sorin I; Bratu, Ioan, E-mail: ioan.bratu@itim-cj.r [National Institute for Research and Development of Isotopic and Molecular Technologies, 65-103 Donath, 400293 Cluj-Napoca (Romania)

    2009-08-01

    Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with {beta}-cyclodextrin ({beta}-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, {sup 1}H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the {sup 1}H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the {beta}-CD-vitamin B6 inclusion complex.

  10. Inclusion compound of vitamin B6 in β-CD. Physico-chemical and structural investigations

    Science.gov (United States)

    Borodi, Gheorghe; Kacso, Irina; Farcaş, Sorin I.; Bratu, Ioan

    2009-08-01

    Structural and physico-chemical characterization of supramolecular assembly of vitamin B6 with β-cyclodextrin (β-CD) prepared by different methods (kneading, co-precipitation and freeze-drying) has been performed by using several spectroscopic techniques (FTIR, 1H NMR, UV-Vis), powder X-ray diffraction and DSC in order to evidence the inclusion compound formation. An analysis of the chemical shifts observed in the 1H-NMR spectra and of the vibrational frequency shifts led to the tentative conclusion that the vitamin B6 probably enters the cyclodextrin torus when forming the β-CD-vitamin B6 inclusion complex.

  11. Modeling the binding affinity of structurally diverse industrial chemicals to carbon using the artificial intelligence approaches.

    Science.gov (United States)

    Gupta, Shikha; Basant, Nikita; Rai, Premanjali; Singh, Kunwar P

    2015-11-01

    Binding affinity of chemical to carbon is an important characteristic as it finds vast industrial applications. Experimental determination of the adsorption capacity of diverse chemicals onto carbon is both time and resource intensive, and development of computational approaches has widely been advocated. In this study, artificial intelligence (AI)-based ten different qualitative and quantitative structure-property relationship (QSPR) models (MLPN, RBFN, PNN/GRNN, CCN, SVM, GEP, GMDH, SDT, DTF, DTB) were established for the prediction of the adsorption capacity of structurally diverse chemicals to activated carbon following the OECD guidelines. Structural diversity of the chemicals and nonlinear dependence in the data were evaluated using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation procedures performed employing a wide series of statistical checks. In complete dataset, the qualitative models rendered classification accuracies between 97.04 and 99.93%, while the quantitative models yielded correlation (R(2)) values of 0.877-0.977 between the measured and the predicted endpoint values. The quantitative prediction accuracies for the higher molecular weight (MW) compounds (class 4) were relatively better than those for the low MW compounds. Both in the qualitative and quantitative models, the Polarizability was the most influential descriptor. Structural alerts responsible for the extreme adsorption behavior of the compounds were identified. Higher number of carbon and presence of higher halogens in a molecule rendered higher binding affinity. Proposed QSPR models performed well and outperformed the previous reports. A relatively better performance of the ensemble learning models (DTF, DTB) may be attributed to the strengths of the bagging and boosting algorithms which enhance the predictive accuracies. The

  12. Protein structure similarity clustering and natural product structure as guiding principles for chemical genomics.

    Science.gov (United States)

    Koch, M A; Waldmann, H

    2006-01-01

    The majority of all proteins are modularly built from a limited set of approximately 1,000 structural domains. The knowledge of a common protein fold topology in the ligand-sensing cores of protein domains can be exploited for the design of small-molecule libraries in the development of inhibitors and ligands. Thus, a novel strategy of clustering protein domain cores based exclusively on structure similarity considerations (protein structure similarity clustering, PSSC) has been successfully applied to the development of small-molecule inhibitors of acetylcholinesterase and the 11beta-hydroxysteroid dehydrogenases based on the structure of a naturally occurring Cdc25 inhibitor. The efficiency of making use of the scaffolds of natural products as biologically prevalidated starting points for the design of compound libraries is further highlighted by the development of benzopyran-based FXR ligands.

  13. Ab initio studies of equations of state and chemical reactions of reactive structural materials

    Science.gov (United States)

    Zaharieva, Roussislava

    The motivations for the research issues addressed in this thesis are based on the needs of the aerospace structural analysis and the design community. The specific focus is related to the characterization and shock induced chemical reactions of multi-functional structural-energetic materials that are also known as the reactive structural materials and their reaction capabilities. Usually motivation for selection of aerospace structural materials is to realize required strength characteristics and favorable strength to weight ratios. The term strength implies resistance to loads experienced during the service life of the structure, including resistance to fatigue loads, corrosion and other extreme conditions. Thus, basically the structural materials are single function materials that resist loads experienced during the service life of the structure. However, it is desirable to select materials that are capable of offering more than one basic function of strength. Very often, the second function is the capability to provide functions of sensing and actuation. In this thesis, the second function is different. The second function is the energetic characteristics. Thus, the choice of dual functions of the material are the structural characteristics and energetic characteristics. These materials are also known by other names such as the reactive material structures or dual functional structural energetic materials. Specifically the selected reactive materials include mixtures of selected metals and metal oxides that are also known as thermite mixtures, reacting intermetallic combinations and oxidizing materials. There are several techniques that are available to synthesize these structural energetic materials or reactive material structures and new synthesis techniques constitute an open research area. The focus of this thesis, however, is the characterization of chemical reactions of reactive material structures that involve two or more solids (or condensed matter). The

  14. NMR crystallography of enzyme active sites: probing chemically detailed, three-dimensional structure in tryptophan synthase.

    Science.gov (United States)

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

    NMR crystallography--the synergistic combination of X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry--offers unprecedented insight into three-dimensional, chemically detailed structure. Initially, researchers used NMR crystallography to refine diffraction data from organic and inorganic solids. Now we are applying this technique to explore active sites in biomolecules, where it reveals chemically rich detail concerning the interactions between enzyme site residues and the reacting substrate. Researchers cannot achieve this level of detail from X-ray, NMR,or computational methodologies in isolation. For example, typical X-ray crystal structures (1.5-2.5 Å resolution) of enzyme-bound intermediates identify possible hydrogen-bonding interactions between site residues and substrate but do not directly identify the protonation states. Solid-state NMR can provide chemical shifts for selected atoms of enzyme-substrate complexes, but without a larger structural framework in which to interpret them only empirical correlations with local chemical structure are possible. Ab initio calculations and molecular mechanics can build models for enzymatic processes, but they rely on researcher-specified chemical details. Together, however, X-ray diffraction, solid-state NMR spectroscopy, and computational chemistry can provide consistent and testable models for structure and function of enzyme active sites: X-ray crystallography provides a coarse framework upon which scientists can develop models of the active site using computational chemistry; they can then distinguish these models by comparing calculated NMR chemical shifts with the results of solid-state NMR spectroscopy experiments. Conceptually, each technique is a puzzle piece offering a generous view of the big picture. Only when correctly pieced together, however, can they reveal the big picture at the highest possible resolution. In this Account, we detail our first steps in the development of

  15. Effect of chemical substituents on the structure of glassy diphenyl polycarbonates.

    Science.gov (United States)

    Sulatha, M S; Natarajan, Upendra

    2011-02-24

    Polycarbonates offer a wide variety of physical property behavior that is difficult to predict due to complexities at the molecular scale. Here, the physical structure of amorphous glassy polycarbonates having aliphatic and cycloaliphatic chemical groups is explored through atomistic simulations. The influence of chemical structure on solubility parameter, torsion distributions, radial distribution function, scattering structure factor, orientation distributions of phenylene rings and carbonate groups, and free volume distributions, leading to interchain packing effects, are shown. The effect of the cyclohexyl ring at the isopropylidene carbon as compared to the effect of the methyl groups positioned on the phenylene rings results in a larger reduction in the solubility parameter (δ). The interchain distance estimated for polycarbonates in this work is in the range of 5-5.8 Å. The o-methyl groups on the phenylene rings, as compared to a cyclohexyl ring, lead to higher interchain distances. The highest interchain distance is observed with a trimethylcyclohexylidene group at the isopropylidene carbon. Atomistic simulations reveal two different types of packing arrangement of nearest-neighbor chains in the glassy state, one type of which agrees with the NMR experimental data. The fundamental insights provided here can be utilized for design of chemical structures for tailored macroscopic properties.

  16. Chemical structure of wood charcoal by infrared spectroscopy and multivariate analysis.

    Science.gov (United States)

    Labbé, Nicole; Harper, David; Rials, Timothy; Elder, Thomas

    2006-05-17

    In this work, the effect of temperature on charcoal structure and chemical composition is investigated for four tree species. Wood charcoal carbonized at various temperatures is analyzed by mid infrared spectroscopy coupled with multivariate analysis and by thermogravimetric analysis to characterize the chemical composition during the carbonization process. The multivariate models of charcoal were able to distinguish between species and wood thermal treatments, revealing that the characteristics of the wood charcoal depend not only on the wood species, but also on the carbonization temperature. This work demonstrates the potential of mid infrared spectroscopy in the whiskey industry, from the identification and classification of the wood species for the mellowing process to the chemical characterization of the barrels after the toasting and charring process. PMID:19127715

  17. Development of new materials and structures based on managed physical-chemical factors of local interaction

    Science.gov (United States)

    Urakov, A. L.

    2016-04-01

    The paper states that assigning certain physical and chemical characteristics to pills and medical drugs solutions can substitute for the development of new drugs (which is essentially equivalent to the creation of new medicines). It is established that the purposeful change of physical and chemical characteristics of the standard ("old") materials (in other words, the known substances) is fundamental for the production of solid and liquid medicines, which allows us to get "new" structures and materials. The paper shows that assigning new physical and chemical properties to "old" materials and their further usage for the production of tablets and solutions from the "old" and well-known medicines can turn even very "old" medicine into very "novel" (moreover, even very fashionable) one with unprecedented (fantastic) pharmacological activity and new mechanisms of action.

  18. Chemical-mechanical stability of the hierarchical structure of shell nacre

    Institute of Scientific and Technical Information of China (English)

    2010-01-01

    The hierarchical structure and mechanical property of shell nacre are experimentally investigated from the new aspects of chemical stability and chemistry-mechanics coupling. Through chemical deproteinization or demineralization methods together with characterization techniques at micro/nano scales,it is found that the nacre of abalone,haliotis discus hannai,contains a hierarchical structure stacked with irregular aragonite platelets and interplatelet organic matrix thin layers. Yet the aragonite platelet itself is a nanocomposite consisting of nanoparticles and intraplatelet organic matrix framework. The mean diameter of the nanoparticles and the distribution of framework are quite different for different platelets. Though the interplatelet and in-traplatelet organic matrix can be both decomposed by sodium hydroxide solution,the chemical stability of individual aragonite platelets is much higher than that of the microstructure stacked with them. Further,macroscopic bending test or nanoindentation experiment is performed on the micro/nanostructure of nacre after sodium hydroxide treatment. It is found that the Young’s modulus of both the stacked microstructure and nanocomposite platelet reduced. The reduction of the microstructure is more remark than that of the platelet. Therefore the chemical-mechanical stability of the nanocomposite platelet itself is much higher than that of the stacked microstructure of nacre.

  19. Chemical diversity among populations of Mikania micrantha: geographic mosaic structure and herbivory.

    Science.gov (United States)

    Bravo-Monzón, Angel Eliezer; Ríos-Vásquez, Eunice; Delgado-Lamas, Guillermo; Espinosa-García, Francisco J

    2014-01-01

    Populations of the same species vary in their secondary metabolite content. This variation has been attributed to biotic and abiotic environmental conditions as well as to historical factors. Some studies have focused on the geographic variation of chemical diversity in plant populations, but whether this structure conforms to a central-marginal model or a mosaic pattern remains unclear. Furthermore, assessing the chemical diversity of invasive plants in their native distribution facilitates the understanding of their relationships with natural enemies. We examined the geographic variation of chemical diversity in Mexican populations of the bittervine weed Mikania micrantha and its relationship to herbivore damage. The foliar volatile terpenoid blend was analyzed in 165 individuals of 14 populations in the Pacific and Gulf of Mexico tropical watersheds. A cluster analysis grouped individuals with similar terpenoid blends into 56 compositional types. Chemical diversity was measured using the number of compounds and their concentration within the blends for individuals, and the number and frequency of compositional types for populations. A stepwise multiple regression analysis performed with geographic, climatic, and chemical diversity variables explained herbivore damage. However, population-level chemical diversity was the only variable found to be significant (β = -0.79, P = 0.042) in the model (R(2) = 0.89). A Mantel test using Euclidean distances did not indicate any separation by geographic origin; however, four barriers were identified using Monmonier's algorithm. We conclude that variation in population-level chemical diversity follows a mosaic pattern in which geographic factors (i.e., natural barriers) have some effect and that variation is also associated with the local intensity of herbivore attack. PMID:23942983

  20. Preparedness of emergency departments in northwest England for managing chemical incidents: a structured interview survey

    Directory of Open Access Journals (Sweden)

    Walter Darren

    2007-12-01

    Full Text Available Abstract Background A number of significant chemical incidents occur in the UK each year and may require Emergency Departments (EDs to receive and manage contaminated casualties. Previously UK EDs have been found to be under-prepared for this, but since October 2005 acute hospital Trusts have had a statutory responsibility to maintain decontamination capacity. We aimed to evaluate the level of preparedness of Emergency Departments in North West England for managing chemical incidents. Methods A face-to-face semi-structured interview was carried out with the Nurse Manager or a nominated deputy in all 18 Emergency Departments in the Region. Results 16/18 departments had a written chemical incident plan but only 7 had the plan available at interview. All had a designated decontamination area but only 11 felt that they were adequately equipped. 12/18 had a current training programme for chemical incident management and 3 had no staff trained in decontamination. 13/18 could contain contaminated water from casualty decontamination and 6 could provide shelter for casualties before decontamination. Conclusion We have identified major inconsistencies in the preparedness of North West Emergency Departments for managing chemical incidents. Nationally recognized standards on incident planning, facilities, equipment and procedures need to be agreed and implemented with adequate resources. Issues of environmental safety and patient dignity and comfort should also be addressed.

  1. THz-Raman: accessing molecular structure with Raman spectroscopy for enhanced chemical identification, analysis, and monitoring

    Science.gov (United States)

    Heyler, Randy A.; Carriere, James T. A.; Havermeyer, Frank

    2013-05-01

    Structural analysis via spectroscopic measurement of rotational and vibrational modes is of increasing interest for many applications, since these spectra can reveal unique and important structural and behavioral information about a wide range of materials. However these modes correspond to very low frequency (~5cm-1 - 200cm-1, or 150 GHz-6 THz) emissions, which have been traditionally difficult and/or expensive to access through conventional Raman and Terahertz spectroscopy techniques. We report on a new, inexpensive, and highly efficient approach to gathering ultra-low-frequency Stokes and anti-Stokes Raman spectra (referred to as "THz-Raman") on a broad range of materials, opening potential new applications and analytical tools for chemical and trace detection, identification, and forensics analysis. Results are presented on explosives, pharmaceuticals, and common elements that show strong THz-Raman spectra, leading to clear discrimination of polymorphs, and improved sensitivity and reliability for chemical identification.

  2. Structural and Optical Properties of Chemical Bath Deposited Silver Oxide Thin Films: Role of Deposition Time

    Directory of Open Access Journals (Sweden)

    A. C. Nwanya

    2013-01-01

    Full Text Available Silver oxide thin films were deposited on glass substrates at a temperature of 50°C by chemical bath deposition technique under different deposition times using pure AgNO3 precursor and triethanolamine as the complexing agent. The chemical analysis based on EDX technique shows the presence of Ag and O at the appropriate energy levels. The morphological features obtained from SEM showed that the AgxO structures varied as the deposition time changes. The X-ray diffraction showed the peaks of Ag2O and AgO in the structure. The direct band gap and the refractive index increased as the deposition time increased and was in the range of 1.64–1.95 eV and 1.02–2.07, respectively. The values of the band gap and refractive index obtained indicate possible applications in photovoltaic and photothermal systems.

  3. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis.

    Science.gov (United States)

    Suyama, Takashi L; Gerwick, William H; McPhail, Kerry L

    2011-11-15

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques.

  4. Neurodevelopmental toxicity of prenatal polychlorinated biphenyls (PCBs) by chemical structure and activity: a birth cohort study

    OpenAIRE

    Park Hye-Youn; Hertz-Picciotto Irva; Sovcikova Eva; Kocan Anton; Drobna Beata; Trnovec Tomas

    2010-01-01

    Abstract Background Polychlorinated biphenyls (PCBs) are ubiquitous environmental toxins. Although there is growing evidence to support an association between PCBs and deficits of neurodevelopment, the specific mechanisms are not well understood. The potentially different roles of specific PCB groups defined by chemical structures or hormonal activities e.g., dioxin-like, non-dioxin like, or anti-estrogenic PCBs, remain unclear. Our objective was to examine the association between prenatal ex...

  5. Studies on chemical constituents of the leaves of Smallantus sonchifolius (yacon): structures of two new diterpenes.

    Science.gov (United States)

    Dou, De-Qiang; Tian, Fang; Qiu, Ying-Kun; Xiang, Zheng; Xu, Bi Xia; Kang, Ting Guo; Dong, Feng

    2010-01-01

    The extract from the leaves of Smallantus sonchifolius (yacon) was found to show potent anti-diabetic activity. Two new diterpenes, named ent-kaurane-3beta,16beta,17, 19-tetrol (1) and ent-kaurane-16beta,17,18,19-tetrol (2), were isolated from the extract, together with six known compounds. The structures of the new compounds were determined on the basis of chemical and physicochemical evidence. PMID:20013471

  6. Preparation and Characterization of Chitosan/Agar Blended Films: Part 1. Chemical Structure and Morphology

    OpenAIRE

    Esam A. El-Hefian; Mohamed Mahmoud NASEF; Yahaya, Abdul Hamid

    2012-01-01

    Chitosan/agar (CS/AG) films were prepared by blending different proportions of chitosan and agar (considering chitosan as the main component) in solution forms. The chemical structure and the morphology of the obtained blended films were investigated using Fourier transform infrared (FTIR) and field emission scanning electron microscope (FESEM). It was revealed that chitosan and agar form a highly compatible blend and their films displayed homogenous and smooth surface properties compared to ...

  7. Understanding the chemical and structural transformations of lignin macromolecule during torrefaction

    International Nuclear Information System (INIS)

    Highlights: • The terrified bamboo has a high energy yield of 85.7% and a HHV of 20.13 MJ/kg. • The structural changes of hemicelluloses, cellulose, and lignin were investigated. • First study on the structural transformations of lignin during torrefaction. • The mechanism of structural changes of lignin has been proposed. - Abstract: Torrefaction is an efficient method to recover energy from biomass. Herein, the characteristics (mass yield, energy yield, physical, and chemical characteristics) of torrefied bamboo at diverse temperatures (200–300 °C) were firstly evaluated by elemental analysis, XRD, and CP–MAS 13C NMR methodologies. Under an optimal condition the terrified bamboo has a relative high energy yield of 85.7% and a HHV of 20.13 MJ/kg. The chemical and structural transformations of lignin induced by thermal treatment were thoroughly investigated by FT-IR and solution-state NMR techniques (quantitative 13C NMR, 2D-HSQC, and 31P-NMR methodologies). The results highlighted the chemical reactions of the native bamboo lignins towards severe torrefaction treatments occurred, such as depolymerization, demethoxylation, bond cleavage, and condensation reactions. NMR results indicated that aryl-ether bonds (β-O-4) and p-coumaric ester in lignin were cleaved during the torrefaction process at mild conditions. The severe treatments of bamboo (275 °C and 300 °C) induced a dramatic enrichment in lignin content together with the almost complete disappearance of β-O-4, β-β, and β-5 linkages. Further analysis of the molecular weight of milled wood lignin (MWL) indicated that the average molecular weights of “torrefied MWL” were lower than those of control MWL. It is believed that understanding of the reactivity and chemical transformations of lignin during torrefaction will contribute to the integrated torrefaction mechanism

  8. Ultra-spatial synchrotron radiation for imaging molecular chemical structure: Applications in plant and animal studies

    OpenAIRE

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very litt...

  9. Analysis of the relationship between the structure and aromatic properties of chemical compounds.

    Science.gov (United States)

    Debska, Barbara; Guzowska-Swider, Barbara

    2003-04-01

    This paper presents the results of research on the relationship between the structure and odour properties of a selection of chemical compounds. The research concerns five groups of esters, each with a different smell: almond, apricot, apple, pineapple and rose. The supposed relationship between the smell and certain selected attributes of each molecule was examined by various pattern recognition techniques using programs developed in the Department of Computer Chemistry at Rzeszów University of Technology.

  10. Relationship between the antitrichinellous effect of seven derivates of benzimidazolecarbamates and their chemical structure.

    Science.gov (United States)

    Spaldonová, R; Corba, J

    1979-01-01

    The efficacy of seven more recently developed anthelmintics of the benzimidazolecarbamate group, i. e., parbendazole, mebendazole, fenbendazole, oxibendazole, cambendazole, oxfendazole and albendazole, has been tested in a series of experiments on white mice artifically infected with Trichinella spiralis. Our results disclosed a relationship between their anthelmintic effect and their chemical structure. This finding might be of importance in a targeted synthesis of new, effective, derivates of benzimidazole, e. g., in the therapy of trichinellosis and in the choice of the most effective drug.

  11. On the Mathematical Structure of Balanced Chemical Reaction Networks Governed by Mass Action Kinetics

    OpenAIRE

    der Schaft, Arjan van; Rao, Shodhan; Jayawardhana, Bayu

    2011-01-01

    Motivated by recent progress on the interplay between graph theory, dynamics, and systems theory, we revisit the analysis of chemical reaction networks described by mass action kinetics. For reaction networks possessing a thermodynamic equilibrium we derive a compact formulation exhibiting at the same time the structure of the complex graph and the stoichiometry of the network, and which admits a direct thermodynamical interpretation. This formulation allows us to easily characterize the set ...

  12. Structural, optical and electrical properties of chemically deposited nonstoichiometric copper indium diselenide films

    Indian Academy of Sciences (India)

    R H Bari; L A Patil; P P Patil

    2006-10-01

    Thin films of copper indium diselenide (CIS) were prepared by chemical bath deposition technique onto glass substrate at temperature, 60°C. The studies on composition, morphology, optical absorption, electrical conductivity and structure of the films were carried out and discussed. Characterization included X-ray diffraction (XRD), scanning electron microscopy (SEM), atomic force microscopy (AFM), energy dispersive X-ray analysis (EDAX) and absorption spectroscopy. The results are discussed and interpreted.

  13. Physico-chemical properties and cytotoxic effects of sugar-based surfactants: Impact of structural variations.

    Science.gov (United States)

    Lu, Biao; Vayssade, Muriel; Miao, Yong; Chagnault, Vincent; Grand, Eric; Wadouachi, Anne; Postel, Denis; Drelich, Audrey; Egles, Christophe; Pezron, Isabelle

    2016-09-01

    Surfactants derived from the biorefinery process can present interesting surface-active properties, low cytotoxicity, high biocompatibility and biodegradability. They are therefore considered as potential sustainable substitutes to currently used petroleum-based surfactants. To better understand and anticipate their performances, structure-property relationships need to be carefully investigated. For this reason, we applied a multidisciplinary approach to systematically explore the effect of subtle structural variations on both physico-chemical properties and biological effects. Four sugar-based surfactants, each with an eight carbon alkyl chain bound to a glucose or maltose head group by an amide linkage, were synthesized and evaluated together along with two commercially available standard surfactants. Physico-chemical properties including solubility, Krafft point, surface-tension lowering and critical micellar concentration (CMC) in water and biological medium were explored. Cytotoxicity evaluation by measuring proliferation index and metabolic activity against dermal fibroblasts showed that all surfactants studied may induce cell death at low concentrations (below their CMC). Results revealed significant differences in both physico-chemical properties and cytotoxic effects depending on molecule structural features, such as the position of the linkage on the sugar head-group, or the orientation of the amide linkage. Furthermore, the cytotoxic response increased with the reduction of surfactant CMC. This study underscores the relevance of a methodical and multidisciplinary approach that enables the consideration of surfactant solution properties when applied to biological materials. Overall, our results will contribute to a better understanding of the concomitant impact of surfactant structure at physico-chemical and biological levels. PMID:27137806

  14. Damascene Array Structure of Phase Change Memory Fabricated with Chemical Mechanical Polishing Method

    Institute of Scientific and Technical Information of China (English)

    LIU Qi-Bin; SONG Zhi-Tang; ZHANG Kai-Liang; WANG Liang-Yong; FENG Song-Lin; CHEN Bomy

    2006-01-01

    @@ A damascene structure of phase change memory (PCM) is fabricated successfully with the chemical mechanical polishing (CMP) method, and the CMP of Ge2Sb2Te5 (GST) and Ti films is investigated. The polished surface of wafer is analysed by scanning electron microscopy (SEM) and an energy dispersive spectrometer (EDS). The measurements show that the damascene device structure of phase change memory is achieved by the CMP process.After the top electrode is deposited, dc sweeping test on PCM reveals that the phase change can be observed.The threshold current of array cells varies between 0.90mA and 1.15mA.

  15. Electronic structure and chemical bonding of Li4Pt3Si

    Science.gov (United States)

    Matar, S. F.; Pöttgen, R.; Al Alam, A. F.; Ouaini, N.

    2012-07-01

    The electronic structure of rhombohedral Li4Pt3Si (space group R32) is examined from ab initio with an assessment of the properties of chemical bonding relating to the presence of different Li and Pt Wyckoff sites. The structure with totally de-intercalated Li keeps the characteristics of the pristine compound with a reduction of the volume albeit with less cohesive energy. The binding energies of Li point to different bonding intensities according to their different Wyckoff sites and indicate the possibility of delithiation.

  16. Probing Structural and Catalytic Characteristics of Galactose Oxidase Confined in Nanoscale Chemical Environments

    DEFF Research Database (Denmark)

    Ikemoto, Hideki; Mossin, Susanne; Ulstrup, Jens;

    2014-01-01

    Galactose oxidase (GAOX) is a special metalloenzyme in terms of its active site structure and catalytic mechanisms. This work reports a study where the enzyme confined in a nanoscale chemical environment provided by mesoporous silicas (MPS) is probed. Two types of MPS, i.e. SBA-15 and MCF, were...... synthesized and used to accommodate GAOX. SBA-15-ROD is rod-shaped particles with periodically ordered nanopores (9.5 nm), while MCF has a mesocellular foam-like structure with randomly distributed pores (23 nm) interconnected by smaller windows (8.8 nm). GAOX is non-covalently confined in SBA-15- ROD, while...

  17. Study and structural and chemical characterization of human dental smalt by electron microscopy

    International Nuclear Information System (INIS)

    The study of human dental smalt has been subject to investigation for this methods with electron microscopy, electron diffraction, X-ray diffraction and image simulation programs have been used with the purpose to determine its chemical and structural characteristics of the organic and inorganic materials. This work has been held mainly for the characterization of hydroxyapatite (Ca)10 (PO4)6 (OH4)2, inorganic material which conforms the dental smalt in 97%, so observing its structural unity which is composed by the prisms and these by crystals and atoms. It was subsequently initiated the study of the organic material, with is precursor of itself. (Author)

  18. Chemical Structure-Biological Activity Models for Pharmacophores' 3D-Interactions.

    Science.gov (United States)

    Putz, Mihai V; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners' (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  19. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Directory of Open Access Journals (Sweden)

    Mihai V. Putz

    2016-07-01

    Full Text Available Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding and quantitative (for predicting mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD as the revived precursor for comparative molecular field analyses (CoMFA and comparative molecular similarity indices analysis (CoMSIA; all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy-methyl]-6-(phenylthiothymine congeners’ (HEPT ligands antiviral activity against Human Immunodeficiency Virus of first type (HIV-1 and new pharmacophores in treating severe genetic disorders (like depression and psychosis, respectively, all involving 3D pharmacophore interactions.

  20. Combined Micro-chemical and Micro-structural Analysis of New Minerals Representing Extreme Conditions

    Science.gov (United States)

    Ma, C.; Tschauner, O. D.

    2015-12-01

    Recent improvements in micro-chemical analysis in combination with novel tools for micrometer-scale structural analysis of minerals from synchrotron X-ray diffraction open a pathway towards studies of mineral paragenesis that were previously not or barely accessible. Often mineral assemblies that represent extreme conditions also pose extreme challenges to analysis: very small size scale, complex matrix, minor amounts of material. Examples of such extreme, but also quite relevant environments are: a) High pressure shock-metamorphic minerals in meteorites and terrestrial impact sites, b) inclusions in diamonds from the deep mantle, c) ultrarefractory phases in Ca-Al-inlcusions from the solar nebula, d) presolar condensates. We show how a combination of synchrotron-based structural and semi-quantitative chemical techniques, with electron-microscopy based high-resolution imaging and fully quantitative chemical analysis and qualitative structural identification establish a powerful tool for discovery and characterization of important and interesting new minerals on micron- to submicron size scale.

  1. Chemical Structure-Biological Activity Models for Pharmacophores’ 3D-Interactions

    Science.gov (United States)

    Putz, Mihai V.; Duda-Seiman, Corina; Duda-Seiman, Daniel; Putz, Ana-Maria; Alexandrescu, Iulia; Mernea, Maria; Avram, Speranta

    2016-01-01

    Within medicinal chemistry nowadays, the so-called pharmaco-dynamics seeks for qualitative (for understanding) and quantitative (for predicting) mechanisms/models by which given chemical structure or series of congeners actively act on biological sites either by focused interaction/therapy or by diffuse/hazardous influence. To this aim, the present review exposes three of the fertile directions in approaching the biological activity by chemical structural causes: the special computing trace of the algebraic structure-activity relationship (SPECTRAL-SAR) offering the full analytical counterpart for multi-variate computational regression, the minimal topological difference (MTD) as the revived precursor for comparative molecular field analyses (CoMFA) and comparative molecular similarity indices analysis (CoMSIA); all of these methods and algorithms were presented, discussed and exemplified on relevant chemical medicinal systems as proton pump inhibitors belonging to the 4-indolyl,2-guanidinothiazole class of derivatives blocking the acid secretion from parietal cells in the stomach, the 1-[(2-hydroxyethoxy)-methyl]-6-(phenylthio)thymine congeners’ (HEPT ligands) antiviral activity against Human Immunodeficiency Virus of first type (HIV-1) and new pharmacophores in treating severe genetic disorders (like depression and psychosis), respectively, all involving 3D pharmacophore interactions. PMID:27399692

  2. Beyond terrestrial biology: charting the chemical universe of α-amino acid structures.

    Science.gov (United States)

    Meringer, Markus; Cleaves, H James; Freeland, Stephen J

    2013-11-25

    α-Amino acids are fundamental to biochemistry as the monomeric building blocks with which cells construct proteins according to genetic instructions. However, the 20 amino acids of the standard genetic code represent a tiny fraction of the number of α-amino acid chemical structures that could plausibly play such a role, both from the perspective of natural processes by which life emerged and evolved, and from the perspective of human-engineered genetically coded proteins. Until now, efforts to describe the structures comprising this broader set, or even estimate their number, have been hampered by the complex combinatorial properties of organic molecules. Here, we use computer software based on graph theory and constructive combinatorics in order to conduct an efficient and exhaustive search of the chemical structures implied by two careful and precise definitions of the α-amino acids relevant to coded biological proteins. Our results include two virtual libraries of α-amino acid structures corresponding to these different approaches, comprising 121 044 and 3 846 structures, respectively, and suggest a simple approach to exploring much larger, as yet uncomputed, libraries of interest.

  3. Magnetism, structure and chemical order in small FeRh clusters

    Energy Technology Data Exchange (ETDEWEB)

    Mokkath, Junais; Pastor, Gustavo [Institut fuer Theoretische Physik, Universitaet Kassel (Germany)

    2010-07-01

    The structural, electronic and magnetic properties of small Fe{sub m}Rh{sub n} clusters having N=m+n{<=}8 atoms are investigated in the framework of a generalized gradient approximation to density-functional theory. The optimized cluster structures are compact with a clear tendency to maximize the number of nearest-neighbor FeRh pairs. For very small sizes the low-lying isomers present a different topology than the optimal structure, while for larger clusters the lowest-energy isomerizations imply mainly changes in the chemical order. The correlation between structure, chemical order, and magnetic behavior is analyzed as a function of size and composition. For all clusters having the optimized most stable structure the magnetic order is found to be Ferromagnetic-like, Antiferromagnetic-like spin arrangements were found in some low-lying isomers. The average magnetic moment per atom anti {mu}{sub N} increases approximately linearly with Fe content. A remarkable enhancement of the local Fe moments is observed as result of Rh doping. This is a consequence of the increase in the number of Fe d holes, due to FeRh charge transfer, combined with the extremely reduced local coordination. The Rh local moments, which are important already in the pure clusters (N{<=}8) are not significantly enhanced by Fe doping. However, the overall stability of magnetism- as measured by the total energy gain upon spin polarization at T=0 increases when Rh is replaced by Fe.

  4. Study on the electronic structure of nickel hydroxide by quantum chemical DV-Xα calculation

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    The electronic structures of atom clusters Ni7O12H122+and Ni7O12H-9 of β-Ni(OH)2 were calculated by quantum chemical DV-Xα method.By analyzing the state densities,orbital populations,net charges and electric charge density differences of the selected clusters,it was indicated that β-Ni(OH)2 was not typical ionic crystal,and the bonds between Ni and O atoms had obvious covalent characteristics.The bonds between H atom and other atoms in the crystal structure were weaker,which ensured that H atoms can easily deintercalate and intercalate into β-Ni(OH)2-The structure of β-Ni(OH)2 was not changed by moderate de-intercalation of H atoms.However,with the excessive de-intercalation of H atoms,the structure of β-Ni(OH)2 changed and the electrochemical active properties were reduced.

  5. Optical and Structural Properties of Nanocrystalline CdS Thin Films Grown by Chemical Bath Deposition

    International Nuclear Information System (INIS)

    Nanocrystalline cadmium sulfide thin films are prepared using chemical bath deposition (CBD) technique in aqueous alkaline bath at 60 degree Celsius and their subsequent condensation on glass substrates. Effects of annealing on structural, morphological and optical properties are presented and discussed. The best annealing temperature for CBD grown CdS films is found to be 350 degree Celsius from optical properties. The optical and structural properties of CdS films are found to be sensitive to annealing temperature and are described in terms of XRD, SEM, transmission spectra and optical studies. The structural parameters such as crystallite size have been evaluated through XRD while SEM micrographs exhibit ordering of grains after annealing. The transmission spectra shift towards higher wavelength upon annealing indicating increase in crystallinity. Annealing over 350 degree Celsius is found to degrade the external structure and optical properties of the film. (author)

  6. Changes in the chemical structure of polytetrafluoroethylene induced by electron beam irradiation in the molten state

    CERN Document Server

    Lappan, U; Lunkwitz, K

    2000-01-01

    Polytetrafluoroethylene (PTFE) was exposed to electron beam radiation at elevated temperature above the melting point under nitrogen atmosphere and in vacuum for comparison. Fourier-transform infrared (FTIR) spectroscopy was used to study the changes in the chemical structure. The irradiation under nitrogen atmosphere leads to the same structures as described recently for PTFE irradiated in vacuum. Trifluoromethyl branches and double bond structures were detected. The concentrations of terminal and internal double bonds are higher after irradiation under nitrogen than in vacuum. Annealing experiments have shown that the thermal oxidative stability of the radiation-modified PTFE is reduced compared to unirradiated PTFE. The reason are the formation of unstable structures such as double bonds.

  7. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Energy Technology Data Exchange (ETDEWEB)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400 (Thailand); Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong [National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Pratontep, Sirapat [College of KMITL Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok (Thailand); Puttipipatkhachorn, Satit, E-mail: uracha@nanotec.or.th [Department of Manufacturing Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400 (Thailand)

    2010-03-26

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of {gamma}-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the {gamma}-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ({sup 1}H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the {sup 1}H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of {gamma}-oryzanol inside the lipid nanoparticles, the {sup 1}H-NMR revealed that the chemical shifts of the liquid lipid in {gamma}-oryzanol loaded systems were found at rather higher field than those in {gamma}-oryzanol free systems, suggesting incorporation of {gamma}-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of {gamma}-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models

  8. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Science.gov (United States)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  9. Screening of 397 chemicals and development of a quantitative structure-activity relationship model for androgen receptor antagonism

    DEFF Research Database (Denmark)

    Vinggaard, Annemarie; Niemelä, Jay Russell; Wedebye, Eva Bay;

    2008-01-01

    We have screened 397 chemicals for human androgen receptor (AR) antagonism by a sensitive reporter gene assay to generate data for the development of a quantitative structure-activity relationship (QSAR) model. A total of 523 chemicals comprising data on 292 chemicals from our laboratory and data...... on 231 chemicals from the literature constituted the training set for the model. The chemicals were selected with the purpose of representing a wide range of chemical structures (e.g., organochlorines and polycyclic aromatic hydrocarbons) and various functions (e.g., natural hormones, pesticides......, plastizicers, plastic additives, brominated flame retardants, and roast mutagens). In addition, the intention was to obtain an equal number of positive and negative chemicals. Among our own data for the training set, 45.7% exhibited inhibitory activity against the transcriptional activity induced...

  10. Chemical control in fabrication of nanometer-scale structures on surfaces

    Science.gov (United States)

    Seshadri, Kannan

    1998-12-01

    The formation of structures with molecular scale organization on surfaces is important for technology development in areas such as microelectronics, optical materials, coatings and biomaterials. The use of alkyl chain molecular assemblies and ultrathin polymer films on solid surfaces represents a step in this direction. Understanding of the chemical issues involved is necessary for controlled engineering and application of these structures. The fabrication and characterization of all these structures involves the application of diverse tools and analytical strategies. Combination of surface sensitive techniques and optical methods such as ellipsometry and infrared spectroscopy, together with quantitative methods of interpretation of the spectra was used in the determination of molecular organization. A new class of ultra-thin polymeric films was developed by the polymerization of diazomethane on gold surfaces. These films are robust and form crystalline, low-dielectric conformal structures on the substrate. Film formation was found to originate by cluster formation at high-energy sites on the gold surface, such as grain boundaries and defect sites. The clusters grow parallel and perpendicular to the surface, and at a certain point, growth spills over to the terraces. These form "nanowell" like structures that have been characterized by electrochemical measurements. These have been used to fabricate novel chemical structures on gold surfaces Self-assembled monolayer films formed from octadecyltrichlorosilane have been used as high-resolution resists for electron beam lithography. The parameters involved in the formation of the siloxy-backbone and the organization of the pendant alkyl chains were investigated using parallel studies on poly(n-alkylsiloxane), The chemistry of the electron beam irradiation has been exhaustively investigated. This has both allowed for, and necessitated the development of protocols for film formation, pattern transfer and surface

  11. Integrating Epistemological Perspectives on Chemistry in Chemical Education: The Cases of Concept Duality, Chemical Language, and Structural Explanations

    Science.gov (United States)

    Kaya, Ebru; Erduran, Sibel

    2013-01-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ("Foundations of Chemistry"…

  12. Iron Isotope Fractionation Reveals Structural Change upon Microbial and Chemical Reduction of Nontronite NAu-1

    Science.gov (United States)

    Liu, K.; Wu, L.; Shi, B.; Smeaton, C. M.; Li, W.; Beard, B. L.; Johnson, C.; Roden, E. E.; Van Cappellen, P.

    2015-12-01

    Iron (Fe) isotope fractionations were determined during reduction of structural Fe(III) in nontronite NAu-1 biologically by Shewanella oneidensis MR-1 and Geobacter sulfurreducens PCA and chemically by dithionite. ~10% reduction was achieved in biological reactors, with similar reduction extents obtained by dithionite. We hypothesize that two stages occurred in our reactors. Firstly, reduction started from edge sites of clays and the produced Fe(II) partially remained in situ and partially was released into solution. Next aqueous Fe(II) adsorbed onto basal planes. The basal sorbed Fe(II) then undergoes electron transfer and atom exchange (ETAE) with octahedral Fe(III) in clays, with the most negative fractionation factor Δ56Febasal Fe(II)-structural Fe(III)of -1.7‰ when basal sorption reached a threshold value. Secondly, when the most reactive Fe(III) was exhausted, bioreduction significantly slowed down and chemical reduction was able to achieve 24% due to diffusion of small size dithionite. Importantly, no ETAE occurred between basal Fe(II) and structural Fe(III) due to blockage of pathways by collapsed clay layers. This two-stage process in our reduction experiments is distinctive from abiotic exchange experiments by mixing aqueous Fe(II) and NAu-1, where no structural change of clay would block ETAE between basal Fe(II) and structural Fe(III). The separation of reduction sites (clay edges) and sorption sites (basal planes) is unique to clay minerals with layered structure. In contrast, reduction and sorption occur on the same sites on the surfaces of Fe oxyhydroxides, where reduction does not induce structure change. Thus, the Fe isotope fractionations are the same for reduction and abiotic exchange experiments for Fe oxides. Our study reveals important changes in electron transfer and atom exchange pathways upon reduction of clay minerals by dissimilatory Fe reducing bacteria, which is prevalent in anoxic soils and sediments.

  13. The influence of chemical composition on structure and mechanical properties of austenitic Cr-Ni steels

    Directory of Open Access Journals (Sweden)

    A. Kurc-Lisiecka

    2013-12-01

    Full Text Available Purpose: The aim of the paper is to investigated the influence of the chemical composition on the structure and mechanical properties of austenitic Cr-Ni steels. Special attention was put on the effect of solution heat treatment on mechanical properties of examined steels. Design/methodology/approach: The examinations of static tensile tests were conducted on ZWICK 100N5A. Hardness measurements were made by Vickers method. The X-ray analyzes were realized with the use of Dron 2.0 diffractometer equipped with the lamp of the cobalt anode. The metallographic observations were carried out on LEICA MEF 4A light microscope. Findings: Results shown that after solution heat treatment the values of strength properties (UTS, YS0.2 and hardness (HV of both investigated steels decrease and their elongation (EL increases. The X5CrNi18-8 steel in delivery state shown austenitic microstructure with twins and numerous non-metallic inclusions, while in steel X10CrNi18-8 revealed a austenitic microstructure with numerous slip bands in areas with deformation martensite α’. The examined steels after solution heat treatment followed by water-cooling has the structure of austenite. Research limitations/implications: To investigate in more detail the influence of chemical composition on structure and mechanical properties the examinations of substructure by TEM should be conducted. Originality/value: The relationship between the solution heat treatment, structure and mechanical properties of investigated steels was specified.

  14. Aged nano-structured platinum based catalyst: effect of chemical treatment on adsorption and catalytic activity.

    Science.gov (United States)

    Shim, Wang Geun; Nahm, Seung Won; Park, Hyuk Ryeol; Yun, Hyung Sun; Seo, Seong Gyu; Kim, Sang Chai

    2011-02-01

    To examine the effect of chemical treatment on the adsorption and catalytic activity of nanostructured platinum based catalyst, the aged commercial Pt/AC catalyst was pretreated with sulfuric acid (H2SO4) and a cleaning agent (Hexane). Several reliable methods such as nitrogen adsorption, X-ray powder diffraction (XRD), scanning electron microscopy (SEM) and inductively coupled plasma (ICP) were employed to characterize the aged Pt/AC catalyst and its chemically pretreated Pt/AC catalysts. The catalytic and adsorption activities of nano-structured heterogeneous Pt/AC catalyst were investigated on the basis of toluene oxidation and adsorption isotherm data. In addition, the adsorption isotherms of toluene were used to calculate the adsorption energy distribution functions for the parent catalyst and its pre-treated nano-structured Pt/AC catalysts. It was found that sulfuric acid aqueous treatment can enhance the catalytic performance of aged Pt/AC catalyst toward catalytic oxidation of toluene. It was also shown that a comparative analysis of the energy distribution functions for nano-structured Pt/AC catalysts as well as the pore size distribution provides valuable information about their structural and energetic heterogeneity.

  15. Heterogeneity of Physico-Chemical Properties in Structured Soils and Its Consequences

    Institute of Scientific and Technical Information of China (English)

    E. JASINSKA; H. WETZEL; T. BAUMGARTL; R. HORN

    2006-01-01

    Structured soils are characterized by the presence of inter- and intra-aggregate pore systems and aggregates, which show varying chemical, physical, and biological properties depending on the aggregate type and land use system. How far these aspects also affect the ion exchange processes and to what extent the interaction between the carbon distribution and kind of organic substances affect the internal soil strength as well as hydraulic properties like wettability are still under discussion. Thus, the objective of this research was to clarify the effect of soil aggregation on physical and chemical properties of structured soils at two scales: homogenized material and single aggregates. Data obtained by sequentially peeling off soil aggregates layers revealed gradients in the chemical composition from the aggregate surface to the aggregatecore. In aggregates from long term untreated forest soils we found lower amounts of carbon in the external layer, while in arable soils the differentiation was not pronounced. However, soil aggregates originating from these sites exhibited a higher concentration of microbial activity in the outer aggregate layer and declined towards the interior. Furthermore,soil depth and the vegetation type affected the wettability. Aggregate strength depended on water suction and differences in tillage treatments.

  16. Quantitative Survey and Structural Classification of Hydraulic Fracturing Chemicals Reported in Unconventional Gas Production.

    Science.gov (United States)

    Elsner, Martin; Hoelzer, Kathrin

    2016-04-01

    Much interest is directed at the chemical structure of hydraulic fracturing (HF) additives in unconventional gas exploitation. To bridge the gap between existing alphabetical disclosures by function/CAS number and emerging scientific contributions on fate and toxicity, we review the structural properties which motivate HF applications, and which determine environmental fate and toxicity. Our quantitative overview relied on voluntary U.S. disclosures evaluated from the FracFocus registry by different sources and on a House of Representatives ("Waxman") list. Out of over 1000 reported substances, classification by chemistry yielded succinct subsets able to illustrate the rationale of their use, and physicochemical properties relevant for environmental fate, toxicity and chemical analysis. While many substances were nontoxic, frequent disclosures also included notorious groundwater contaminants like petroleum hydrocarbons (solvents), precursors of endocrine disruptors like nonylphenols (nonemulsifiers), toxic propargyl alcohol (corrosion inhibitor), tetramethylammonium (clay stabilizer), biocides or strong oxidants. Application of highly oxidizing chemicals, together with occasional disclosures of putative delayed acids and complexing agents (i.e., compounds designed to react in the subsurface) suggests that relevant transformation products may be formed. To adequately investigate such reactions, available information is not sufficient, but instead a full disclosure of HF additives is necessary. PMID:26902161

  17. Advances in Chemical and Structural Characterization of Concretion with Implications for Modeling Marine Corrosion

    Science.gov (United States)

    Johnson, Donald L.; DeAngelis, Robert J.; Medlin, Dana J.; Carr, James D.; Conlin, David L.

    2014-05-01

    The Weins number model and concretion equivalent corrosion rate methodology were developed as potential minimum-impact, cost-effective techniques to determine corrosion damage on submerged steel structures. To apply the full potential of these technologies, a detailed chemical and structural characterization of the concretion (hard biofouling) that transforms into iron bearing minerals is required. The fractions of existing compounds and the quantitative chemistries are difficult to determine from x-ray diffraction. Environmental scanning electron microscopy was used to present chemical compositions by means of energy-dispersive spectroscopy (EDS). EDS demonstrates the chemical data in mapping format or in point or selected area chemistries. Selected-area EDS data collection at precise locations is presented in terms of atomic percent. The mechanism of formation and distribution of the iron-bearing mineral species at specific locations will be presented. Based on water retention measurements, porosity in terms of void volume varies from 15 v/o to 30 v/o (vol.%). The void path displayed by scanning electron microscopy imaging illustrates the tortuous path by which oxygen migrates in the water phase within the concretion from seaside to metalside.

  18. Effects of age and sex on the structural, chemical and technological characteristics of mule duck meat.

    Science.gov (United States)

    Baeza, E; Salichon, M R; Marche, G; Wacrenier, N; Dominguez, B; Culioli, J

    2000-07-01

    1. The aim of the study was to analyse the effect of age and sex on the chemical, structural and technological characteristics of mule duck meat. 2. Ten males and 10 females were weighed and slaughtered at 8, 10, 11, 12 and 13 weeks of age. Weight, pH value, colour, tenderness and juice loss of breast muscle were determined. 3. The activities of 3 enzymes (citrate synthase, beta-hydroxyacyl CoA dehydrogenase, lactate dehydrogenase) which indicate muscular metabolic activity were assayed. 4. Chemical composition (moisture, lipids, proteins, minerals, lipid and phospholipid classes, fatty acid composition) of breast muscle was analysed. 5. Fibre type, fibre type percentage and cross-sectional areas were determined using histochemistry and an image analysis system. 6. For growth performance and muscular structure, the ideal slaughter age of mule ducks is 10 weeks of age. Chemical and technological analysis indicated that muscular maturity in Pectoralis major was reached at 11 weeks of age, but, at this age, breast lipid content is high. Moreover, after 10 weeks of age, food costs rapidly increased. 7. Lastly, sexual dimorphism for body weight is minor. In this study, at any given age, no significant differences between males and females were shown. Thus, it is possible to rear both sexes together and to slaughter them at the same age.

  19. Temporal evolution of the chemical structure during the pattern transfer by ion-beam sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Ha, N.-B.; Jeong, S.; Yu, S.; Ihm, H.-I.; Kim, J.-S.

    2015-01-01

    Highlights: • Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution were performed. • Degradation of the transferred pattern starts before the overlayer is fully removed. • The chemical analysis reveals the severe reduction of the sputter yield of the material forming the overlayer near the interface due to the compound formation, requesting caution in the practice of the pattern transfer. - Abstract: Ru films patterned by ion-beam sputtering (IBS) serve as sacrificial masks for the transfer of the patterns to Si(1 0 0) and metallic glass substrates by continued IBS. Under the same sputter condition, however, both bare substrates remain featureless. Chemical analyses of the individual nano structures simultaneously with the investigation of their morphological evolution reveal that the pattern transfer, despite its apparent success, suffers from premature degradation before the mask is fully removed by IBS. Moreover, the residue of the mask or Ru atoms stubbornly remains near the surface, resulting in unintended doping or alloying of both patterned substrates.

  20. A large scale analysis of information-theoretic network complexity measures using chemical structures.

    Directory of Open Access Journals (Sweden)

    Matthias Dehmer

    Full Text Available This paper aims to investigate information-theoretic network complexity measures which have already been intensely used in mathematical- and medicinal chemistry including drug design. Numerous such measures have been developed so far but many of them lack a meaningful interpretation, e.g., we want to examine which kind of structural information they detect. Therefore, our main contribution is to shed light on the relatedness between some selected information measures for graphs by performing a large scale analysis using chemical networks. Starting from several sets containing real and synthetic chemical structures represented by graphs, we study the relatedness between a classical (partition-based complexity measure called the topological information content of a graph and some others inferred by a different paradigm leading to partition-independent measures. Moreover, we evaluate the uniqueness of network complexity measures numerically. Generally, a high uniqueness is an important and desirable property when designing novel topological descriptors having the potential to be applied to large chemical databases.

  1. Chemical synthesis of porous web-structured CdS thin films for photosensor applications

    International Nuclear Information System (INIS)

    The photo-activity of chemically deposited cadmium sulphide (CdS) thin film has been studied. The simple chemical route nucleates the CdS films with size up to the mean free path of the electron. Growth Kinematics of crystalline hexagonal CdS phase in the thin film form was monitored using X-ray diffraction. The time limitation set for the formation of the amorphous/nano-crystalline material is 40 and 60 min. Thereafter enhancement of the crystalline orientation along the desired plane was identified. Web-like porous structured surface morphology of CdS thin film over the entire area is observed. With decrease in synthesis time, increase of band gap energy i.e., a blue spectral shift was seen. The activation energy of CdS thin film at low and high temperature region was examined. It is considered that this activation energy corresponds to the donor levels associated with shallow traps or surface states of CdS thin film. The photo-electrochemical performance of CdS thin films in polysulphide electrolyte showed diode-like characteristics. Exposure of light on the CdS electrode increases the photocurrent. This suggests the possibility of production of free carriers via excited ions and also the light harvesting mechanism due to porous web-structured morphology. These studies hint that the obtained CdS films can work as a photosensor. - Highlights: • Photoactivity of chemically synthesized cadmium sulphide (CdS) thin films was studied. • Web-like porous structured surface morphology of CdS thin film over the entire area was observed. • Blue spectral shift with lowering of the synthesis time suggests films can act as a window layer over the absorber layer. • Porous web-structured CdS thin films can be useful in light harvesting

  2. Chemical composition and structural transformations of amorphous chromium coatings electrodeposited from Cr(III) electrolytes

    Energy Technology Data Exchange (ETDEWEB)

    Safonova, Olga V. [Swiss-Norwegian Beamlines at European Synchrotron Radiation Facility, 38043 Grenoble Cedex (France); Vykhodtseva, Ludmila N. [Department of Electrochemistry, Faculty of Chemistry, Moscow State University, 119991 Moscow (Russian Federation); Polyakov, Nikolai A. [A.N. Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, 119991 Moscow (Russian Federation); Swarbrick, Janine C. [European Synchrotron Radiation Facility, 38043 Grenoble Cedex (France); Sikora, Marcin [European Synchrotron Radiation Facility, 38043 Grenoble Cedex (France); Department of Solid State Physics, Faculty of Physics and Applied Computer Science, AGH University of Science and Technology, Av. Mickiewicza 30, 30-059 Krakow (Poland); Glatzel, Pieter [European Synchrotron Radiation Facility, 38043 Grenoble Cedex (France); Safonov, Viktor A., E-mail: safon@elch.chem.msu.r [Department of Electrochemistry, Faculty of Chemistry, Moscow State University, 119991 Moscow (Russian Federation)

    2010-12-15

    Amorphous chromium coatings were electrodeposited from Cr(III)-based solutions containing organic (HCOONa) or phosphorus-containing (NaH{sub 2}PO{sub 2}) additives. Their structure was studied by a combination of X-ray diffraction (XRD), valence-to-core X-ray emission spectroscopy (XES) and X-ray absorption spectroscopy (XAS) at the Cr K-edge. Metalloid atoms (C or P) incorporated in electroplates structure are chemically bonded to chromium (i.e. are located in the first coordination shell). Upon annealing at elevated temperatures in vacuum, these amorphous coatings crystallize into a mixture of phases containing metallic chromium and chromium carbides or chromium phosphides. Quantitative analysis of valence-to-core XES data demonstrates that the average local structure of chromium in the amorphous coatings does not change significantly during crystallization.

  3. YNi and its hydrides: Phase stabilities, electronic structures and chemical bonding properties from first principles

    Energy Technology Data Exchange (ETDEWEB)

    Matar, S.F., E-mail: matar@icmcb-bordeaux.cnrs.fr [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France); Nakhl, M. [Universite Libanaise, Laboratoire de Chimie-Physique des Materiaux LCPM, Fanar (Lebanon); Al Alam, A.F.; Ouaini, N. [Universite Saint-Esprit de Kaslik, Faculte des Sciences et de Genie Informatique, Jounieh (Lebanon); Chevalier, B. [CNRS, Universite de Bordeaux, ICMCB, 87 avenue du Docteur Albert Schweitzer, F-33608 Pessac (France)

    2010-11-25

    Graphical abstract: Base centered orthorhombic YNiH{sub X} structure. For x = 3, only H1 and H2 are present. Highest hydrogen content YNiH{sub 4} is obtained when H3 are added. - Abstract: Within density functional theory, establishing the equations of states of YNi in two different controversial structures in the literature, leads to determine the orthorhombic FeB-type as the ground state one with small energy difference. For YNiH{sub 3} and YNiH{sub 4} hydrides crystallizing in the orthorhombic CrB-type structure the geometry optimization and the ab initio determination of the H atomic positions show that the stability of hydrogen decreases from the tri- to the tetra- hydride. New states brought by hydrogen within the valence band lead to its broadening and to enhanced localization of metal density of states. The chemical bonding analysis shows a preferential Ni-H bonding versus Y-H.

  4. Chemical crosslinking and mass spectrometry studies of the structure and dynamics of membrane proteins and receptors.

    Energy Technology Data Exchange (ETDEWEB)

    Haskins, William E.; Leavell, Michael D.; Lane, Pamela; Jacobsen, Richard B.; Hong, Joohee; Ayson, Marites J.; Wood, Nichole L.; Schoeniger, Joseph S.; Kruppa, Gary Hermann; Sale, Kenneth L.; Young, Malin M.; Novak, Petr

    2005-03-01

    Membrane proteins make up a diverse and important subset of proteins for which structural information is limited. In this study, chemical cross-linking and mass spectrometry were used to explore the structure of the G-protein-coupled photoreceptor bovine rhodopsin in the dark-state conformation. All experiments were performed in rod outer segment membranes using amino acid 'handles' in the native protein sequence and thus minimizing perturbations to the native protein structure. Cysteine and lysine residues were covalently cross-linked using commercially available reagents with a range of linker arm lengths. Following chemical digestion of cross-linked protein, cross-linked peptides were identified by accurate mass measurement using liquid chromatography-fourier transform mass spectrometry and an automated data analysis pipeline. Assignments were confirmed and, if necessary, resolved, by tandem MS. The relative reactivity of lysine residues participating in cross-links was evaluated by labeling with NHS-esters. A distinct pattern of cross-link formation within the C-terminal domain, and between loop I and the C-terminal domain, emerged. Theoretical distances based on cross-linking were compared to inter-atomic distances determined from the energy-minimized X-ray crystal structure and Monte Carlo conformational search procedures. In general, the observed cross-links can be explained by re-positioning participating side-chains without significantly altering backbone structure. One exception, between C3 16 and K325, requires backbone motion to bring the reactive atoms into sufficient proximity for cross-linking. Evidence from other studies suggests that residues around K325 for a region of high backbone mobility. These findings show that cross-linking studies can provide insight into the structural dynamics of membrane proteins in their native environment.

  5. On the Comparability of Chemical Structure and Roughness of Nanochannels in Altering Fluid Slippage

    CERN Document Server

    Misra, Chinmay Anand

    2016-01-01

    Interfacial hydrodynamic slippage of water depends on both on surface chemistry and roughness. This study tries to connect the effect of chemical property and the physical structure of the surface on the interfacial slippage of water. By performing molecular dynamics simulations (MDS) of Couette flow of water molecules over a reduced Lennard-Jones (LJ) surface, the velocity profile is obtained and extrapolated to get the slip lengths. The slip lengths are measured for various surface-fluid interactions. These interactions are varied by changing the wettability of the surface (characterized by the static contact angle) and its roughness. The slip length variation with the static contact angle as $(1+cos\\theta)^{-2}$ is observed. However, it is also observed that the presence of surface roughness always reduces the slip length and it is proposed that the slip length varies with non-dimensionalized average surface roughness as $(1+\\alpha^*)^{-2}$ . Thus a relation between the chemical wettability and the physica...

  6. Structural diversity and chemical synthesis of peroxide and peroxide-derived polyketide metabolites from marine sponges.

    Science.gov (United States)

    Norris, Matthew D; Perkins, Michael V

    2016-07-28

    Covering: up to early 2016Marine sponges are widely known as a rich source of natural products, especially of polyketide origin, with a wealth of chemical diversity. Within this vast collection, peroxide and peroxide-derived secondary metabolites have attracted significant interest in the fields of natural product isolation and chemical synthesis for their structural distinction and promising in vitro antimicrobial and anticancer properties. In this review, peroxide and peroxide-derived polyketide metabolites isolated from marine sponges in the past 35 years are summarised. Efforts toward their synthesis are detailed with a focus on methods that utilise or attempt to elucidate the complex biosynthetic interrelationships of these compounds beyond enzymatic polyketide synthesis. Recent isolations, advances in synthetic methodology and theories of biogenesis are highlighted and critically evaluated. PMID:27163115

  7. Tuning the Interfacial Electronic Structure at Organic Heterojunctions by Chemical Design.

    Science.gov (United States)

    Mothy, Sébastien; Guillaume, Maxime; Idé, Julien; Castet, Frédéric; Ducasse, Laurent; Cornil, Jérôme; Beljonne, David

    2012-09-01

    Quantum-chemical techniques are applied to assess the electronic structure at donor/acceptor heterojunctions of interest for organic solar cells. We show that electrostatic effects at the interface of model 1D stacks profoundly modify the energy landscape explored by charge carriers in the photoconversion process and that these can be tuned by chemical design. When fullerene C60 molecules are used as acceptors and unsubstituted oligothiophenes or pentacene are used as donors, the uncompensated quadrupolar electric field at the interface provides the driving force for splitting of the charge-transfer states into free charges. This quadrupolar field can be either enhanced by switching from a C60 to a perylene-tetracarboxylic-dianhydride (PTCDA) acceptor or suppressed by grafting electron-withdrawing groups on the donor. PMID:26292117

  8. Thermopower Wave in Core-Shell Structures of Carbon Nano tube Chemical Fuels

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Wonjoon [Korea Univ., Seoul (Korea, Republic of); Strano, Michael S. [Massachusetts Institute of Technology, Amsden (United States)

    2013-06-15

    There is considerable interest in developing energy sources capable of larger power densities. In our previous works, we proved that by coupling an exothermic chemical reaction with nano structures, a self-propagating reactive wave can be driven along its length with a concomitant electrical pulse of high specific power, which we identified as a thermopower wave. Herein, we discuss details about many different aspects of a thermopower wave. Different alignment degree in vertically aligned CNT films is evaluated in the reactive wave speed and correlated with its thermal reaction that affects the change in the magnitude of energy generation. The effects of the temperature-dependent properties of chemical fuels and CNTs are evaluated. Furthermore, we explore the convection and radiation portions in this thermal wave as well as the synchronization between the thermal reaction transfer and the oscillation of the electrical signal.

  9. Fluctuation Induced Structure in Chemical Reaction with Small Number of Molecules

    Science.gov (United States)

    Suzuki, Yasuhiro

    We investigate the behaviors of chemical reactions of the Lotka-Volterra model with small number of molecules; hence the occurrence of random fluctuations modifies the deterministic behavior and the law of mass action is replaced by a stochastic model. We model it by using Abstract Rewriting System on Multisets, ARMS; ARMS is a stochastic method of simulating chemical reactions and it is based on the reaction rate equation. We confirmed that the magnitude of fluctuations on periodicity of oscillations becomes large, as the number of involved molecules is getting smaller; and these fluctuations induce another structure, which have not observed in the reactions with large number of molecules. We show that the underling mechanism through investigating the coarse grained phase space of ARMS.

  10. Structural, Mechanical and Optical Properties of Plasma-chemical Si-C-N Films

    Directory of Open Access Journals (Sweden)

    A.O. Kozak

    2014-11-01

    Full Text Available An influence of the substrate temperature in the range of 40-400 °C on the properties of the Si-C-N films deposited by plasma enhanced chemical vapor deposition (PECVD technique using hexamethyldisilazane is analyzed. Study of the structure, chemical bonding, surface morphology, mechanical properties and energy gap of the obtained films was carried out using X-ray diffraction, infrared spectroscopy, X-ray photoelectron spectroscopy, atomic force microscopy, optical measurements and nanoindentation. It was established that all the films were X-ray amorphous and had low surface roughness. Intensive hydrogen effusion from the films takes place, when substrate temperature increases up to 400 °C, which promotes a decrease of roughness and an increase in hardness and Young modules more than twice.

  11. The HIFI spectral survey of AFGL 2591 (CHESS). III. Chemical structure of the protostellar envelope

    Science.gov (United States)

    Kaźmierczak-Barthel, M.; Semenov, D. A.; van der Tak, F. F. S.; Chavarría, L.; van der Wiel, M. H. D.

    2015-02-01

    Aims: The aim of this work is to understand the richness of chemical species observed in the isolated high-mass envelope of AFGL 2591, a prototypical object for studying massive star formation. Methods: Based on HIFI and JCMT data, the molecular abundances of species found in the protostellar envelope of AFGL 2591 were derived with a Monte Carlo radiative transfer code (Ratran), assuming a mixture of constant and 1D stepwise radial profiles for abundance distributions. The reconstructed 1D abundances were compared with the results of the time-dependent gas-grain chemical modeling, using the best-fit 1D power-law density structure. The chemical simulations were performed considering ages of 1-5 × 104 years, cosmic ray ionization rates of 5-500 × 10-17 s-1, uniformly-sized 0.1-1 μm dust grains, a dust/gas ratio of 1%, and several sets of initial molecular abundances with C/O 1. The most important model parameters varied one by one in the simulations are age, cosmic ray ionization rate, external UV intensity, and grain size. Results: Constant abundance models give good fits to the data for CO, CN, CS, HCO+, H2CO, N2H+, CCH, NO, OCS, OH, H2CS, O, C, C+, and CH. Models with an abundance jump at 100 K give good fits to the data for NH3, SO, SO2, H2S, H2O, HCl, and CH3OH. For HCN and HNC, the best models have an abundance jump at 230 K. The time-dependent chemical model can accurately explain abundance profiles of 15 out of these 24 species. The jump-like radial profiles for key species like HCO+, NH3, and H2O are consistent with the outcome of the time-dependent chemical modeling. The best-fit model has a chemical age of ~10-50 kyr, a solar C/O ratio of 0.44, and a cosmic-ray ionization rate of ~5 × 10-17 s-1. The grain properties and the intensity of the external UV field do not strongly affect the chemical structure of the AFGL 2591 envelope, whereas its chemical age, the cosmic-ray ionization rate, and the initial abundances play an important role. Conclusions: We

  12. Predicting acute aquatic toxicity of structurally diverse chemicals in fish using artificial intelligence approaches.

    Science.gov (United States)

    Singh, Kunwar P; Gupta, Shikha; Rai, Premanjali

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds.

  13. Chemical tagging can work: Identification of stellar phase-space structures purely by chemical-abundance similarity

    CERN Document Server

    Hogg, David W; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel

    2016-01-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were in fact born together (in the same molecular cloud), long ago. This idea has not previously yielded scientific successes, probably because of the noise and incompleteness in chemical-abundance measurements. However, we have succeeded in substantially improving spectroscopic measurements with The Cannon, which has delivered 15 individual abundances for 100,000 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are...

  14. Chemical Space Mapping and Structure-Activity Analysis of the ChEMBL Antiviral Compound Set.

    Science.gov (United States)

    Klimenko, Kyrylo; Marcou, Gilles; Horvath, Dragos; Varnek, Alexandre

    2016-08-22

    Curation, standardization and data fusion of the antiviral information present in the ChEMBL public database led to the definition of a robust data set, providing an association of antiviral compounds to seven broadly defined antiviral activity classes. Generative topographic mapping (GTM) subjected to evolutionary tuning was then used to produce maps of the antiviral chemical space, providing an optimal separation of compound families associated with the different antiviral classes. The ability to pinpoint the specific spots occupied (responsibility patterns) on a map by various classes of antiviral compounds opened the way for a GTM-supported search for privileged structural motifs, typical for each antiviral class. The privileged locations of antiviral classes were analyzed in order to highlight underlying privileged common structural motifs. Unlike in classical medicinal chemistry, where privileged structures are, almost always, predefined scaffolds, privileged structural motif detection based on GTM responsibility patterns has the decisive advantage of being able to automatically capture the nature ("resolution detail"-scaffold, detailed substructure, pharmacophore pattern, etc.) of the relevant structural motifs. Responsibility patterns were found to represent underlying structural motifs of various natures-from very fuzzy (groups of various "interchangeable" similar scaffolds), to the classical scenario in medicinal chemistry (underlying motif actually being the scaffold), to very precisely defined motifs (specifically substituted scaffolds). PMID:27410486

  15. The interplay between habitat structure and chemical contaminants on biotic responses of benthic organisms.

    Science.gov (United States)

    Mayer-Pinto, Mariana; Matias, Miguel G; Coleman, Ross A

    2016-01-01

    Habitat structure influences the diversity and distribution of organisms, potentially affecting their response to disturbances by either affecting their 'susceptibility' or through the provision of resources that can mitigate impacts of disturbances. Chemical disturbances due to contamination are associated with decreases in diversity and functioning of systems and are also likely to increase due to coastal urbanisation. Understanding how habitat structure interacts with contaminants is essential to predict and therefore manage such effects, minimising their consequences to marine systems. Here, we manipulated two structurally different habitats and exposed them to different types of contaminants. The effects of contamination and habitat structure interacted, affecting species richness. More complex experimental habitats were colonized by a greater diversity of organisms than the less complex habitats. These differences disappeared, however, when habitats were exposed to contaminants, suggesting that contaminants can override effects of habitats structure at small spatial scales. These results provide insight into the complex ways that habitat structure and contamination interact and the need to incorporate evidence of biotic responses from individual disturbances to multiple stressors. Such effects need to be taken into account when designing and planning management and conservation strategies to natural systems. PMID:27168991

  16. Structural, optical and electrical properties of chemically derived nickel substituted zinc ferrite nanocrystals

    Energy Technology Data Exchange (ETDEWEB)

    Chakrabarty, S. [Department of Physics, The University of Burdwan, Burdwan 713 104 (India); Pal, M., E-mail: palm@cgcri.res.in [CSIR-Central Glass and Ceramic Research Institute, Kolkata 700032 (India); Dutta, A., E-mail: adutta@phys.buruniv.ac.in [Department of Physics, The University of Burdwan, Burdwan 713 104 (India)

    2015-03-01

    Single phase spinel Ni substituted nanocrystalline Zn ferrites have been synthesized using a soft chemical route. Effect of Ni substitution on structure, electrical and optical properties has been investigated. X-ray diffraction study confirms the growth of single phase nanocrystalline Ni substituted Zn ferrites. FTIR and UV–Visible studies delineate the change in structure and optical band gap due to inclusion of Ni ions. Substitution of Ni ion has been manifested on lattice parameter which systematically decreases from 8.448 Å to 8.280 Å. An initial increase followed by subsequent decrease in optical band gap with the increase in Ni content is observed. In addition, both ac and dc electrical studies shows anomalous behavior in conductivity and dielectric properties for the samples having Ni content in the range 0.2–0.6 mol fraction which can be attributed to the normal to inverse spinel structural changes. - Highlights: • Pure single phase nanocrystalline Zn/Ni ferrites by facile soft chemical route. • Changes in microstructural parameters of Zn ferrite is observed due to Ni inclusion. • Optical band gap shows a maximum while the concentration of Ni increases. • Inverse to spinal ferrite change is observed in ac and dc electrical properties.

  17. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    Science.gov (United States)

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory. PMID:22999222

  18. STUDIES ON THE CHEMICAL STRUCTURES OF ACTIVATED CARBON FIBERS BY SOLID STATE NMR

    Institute of Scientific and Technical Information of China (English)

    FURuowen; HuangWenqiang; 等

    1999-01-01

    The solid state C13-NMR spectra of different ACFs from various precursor fibers were recorded in this paper,The effects of activation conditions on chemical structures of ACFs,as well as the changes of chemical structures during carbonization and redox reaction were inverstigated by NMR technique,At same time,the soild state P31-NMR spectra of ACFS are studied.The C13-NMR spectra of ACFs can be divided into six bands that are assigned to methyl and methylene groups,hydroxyl and ether groups.acetal (or methylenedioxy) carbon,graphite-like aromatic carbon structure,phenol,and quinone groups,respectively.Only phosphorous pentoxide exists on ACFs and CFs.Moreover,most of them are stuck over the crystal face but not at the edge of graphite-like micro-crystal.The carbonization and activation conditions affect the C13-NMR spectra of ACFs.The experimental rsults indicate that the redox reaction of ACFs with oxidants greatly consumes C-H group.

  19. Optimization of chemical structure of Schottky-type selection diode for crossbar resistive memory.

    Science.gov (United States)

    Kim, Gun Hwan; Lee, Jong Ho; Jeon, Woojin; Song, Seul Ji; Seok, Jun Yeong; Yoon, Jung Ho; Yoon, Kyung Jean; Park, Tae Joo; Hwang, Cheol Seong

    2012-10-24

    The electrical performances of Pt/TiO(2)/Ti/Pt stacked Schottky-type diode (SD) was systematically examined, and this performance is dependent on the chemical structures of the each layer and their interfaces. The Ti layers containing a tolerable amount of oxygen showed metallic electrical conduction characteristics, which was confirmed by sheet resistance measurement with elevating the temperature, transmission line measurement (TLM), and Auger electron spectroscopy (AES) analysis. However, the chemical structure of SD stack and resulting electrical properties were crucially affected by the dissolved oxygen concentration in the Ti layers. The lower oxidation potential of the Ti layer with initially higher oxygen concentration suppressed the oxygen deficiency of the overlying TiO(2) layer induced by consumption of the oxygen from TiO(2) layer. This structure results in the lower reverse current of SDs without significant degradation of forward-state current. Conductive atomic force microscopy (CAFM) analysis showed the current conduction through the local conduction paths in the presented SDs, which guarantees a sufficient forward-current density as a selection device for highly integrated crossbar array resistive memory.

  20. Control of interface nanoscale structure created by plasma-enhanced chemical vapor deposition.

    Science.gov (United States)

    Peri, Someswara R; Akgun, Bulent; Satija, Sushil K; Jiang, Hao; Enlow, Jesse; Bunning, Timothy J; Foster, Mark D

    2011-09-01

    Tailoring the structure of films deposited by plasma-enhanced chemical vapor deposition (PECVD) to specific applications requires a depth-resolved understanding of how the interface structures in such films are impacted by variations in deposition parameters such as feed position and plasma power. Analysis of complementary X-ray and neutron reflectivity (XR, NR) data provide a rich picture of changes in structure with feed position and plasma power, with those changes resolved on the nanoscale. For plasma-polymerized octafluorocyclobutane (PP-OFCB) films, a region of distinct chemical composition and lower cross-link density is found at the substrate interface for the range of processing conditions studied and a surface layer of lower cross-link density also appears when plasma power exceeds 40 W. Varying the distance of the feed from the plasma impacts the degree of cross-linking in the film center, thickness of the surface layer, and thickness of the transition region at the substrate. Deposition at the highest power, 65 W, both enhances cross-linking and creates loose fragments with fluorine content higher than the average. The thickness of the low cross-link density region at the air interface plays an important role in determining the width of the interface built with a layer subsequently deposited atop the first.

  1. The designability of protein switches by chemical rescue of structure: mechanisms of inactivation and reactivation

    Science.gov (United States)

    Xia, Yan; DiPrimio, Nina; Keppel, Theodore R.; Vo, Binh; Fraser, Keith; Battaile, Kevin P.; Egan, Chet; Bystroff, Christopher; Lovell, Scott; Weis, David D.; Anderson, J. Christopher; Karanicolas, John

    2014-01-01

    The ability to selectively activate function of particular proteins via pharmacological agents is a longstanding goal in chemical biology. Recently, we reported an approach for designing a de novo allosteric effector site directly into the catalytic domain of an enzyme. This approach is distinct from traditional chemical rescue of enzymes in that it relies on disruption and restoration of structure, rather than active site chemistry, as a means to achieve modulate function. However, rationally identifying analogous de novo binding sites in other enzymes represents a key challenge for extending this approach to introduce allosteric control into other enzymes. Here we show that mutation sites leading to protein inactivation via tryptophan-to-glycine substitution and allowing (partial) reactivation by the subsequent addition of indole are remarkably frequent. Through a suite of methods including a cell-based reporter assay, computational structure prediction and energetic analysis, fluorescence studies, enzymology, pulse proteolysis, x-ray crystallography and hydrogen-deuterium mass spectrometry we find that these switchable proteins are most commonly modulated indirectly, through control of protein stability. Addition of indole in these cases rescues activity not by reverting a discrete conformational change, as we had observed in the sole previously reported example, but rather rescues activity by restoring protein stability. This important finding will dramatically impact the design of future switches and sensors built by this approach, since evaluating stability differences associated with cavity-forming mutations is a far more tractable task than predicting allosteric conformational changes. By analogy to natural signaling systems, the insights from this study further raise the exciting prospect of modulating stability to design optimal recognition properties into future de novo switches and sensors built through chemical rescue of structure. PMID:24313858

  2. Voting-based consensus clustering for combining multiple clusterings of chemical structures

    Directory of Open Access Journals (Sweden)

    Saeed Faisal

    2012-12-01

    Full Text Available Abstract Background Although many consensus clustering methods have been successfully used for combining multiple classifiers in many areas such as machine learning, applied statistics, pattern recognition and bioinformatics, few consensus clustering methods have been applied for combining multiple clusterings of chemical structures. It is known that any individual clustering method will not always give the best results for all types of applications. So, in this paper, three voting and graph-based consensus clusterings were used for combining multiple clusterings of chemical structures to enhance the ability of separating biologically active molecules from inactive ones in each cluster. Results The cumulative voting-based aggregation algorithm (CVAA, cluster-based similarity partitioning algorithm (CSPA and hyper-graph partitioning algorithm (HGPA were examined. The F-measure and Quality Partition Index method (QPI were used to evaluate the clusterings and the results were compared to the Ward’s clustering method. The MDL Drug Data Report (MDDR dataset was used for experiments and was represented by two 2D fingerprints, ALOGP and ECFP_4. The performance of voting-based consensus clustering method outperformed the Ward’s method using F-measure and QPI method for both ALOGP and ECFP_4 fingerprints, while the graph-based consensus clustering methods outperformed the Ward’s method only for ALOGP using QPI. The Jaccard and Euclidean distance measures were the methods of choice to generate the ensembles, which give the highest values for both criteria. Conclusions The results of the experiments show that consensus clustering methods can improve the effectiveness of chemical structures clusterings. The cumulative voting-based aggregation algorithm (CVAA was the method of choice among consensus clustering methods.

  3. Modulating the electronic structure of chromophores by chemical substituents for efficient energy transfer: application to fluorone.

    Science.gov (United States)

    Sand, Andrew M; Liu, Claire; Valentine, Andrew J S; Mazziotti, David A

    2014-08-01

    Strong electron correlation within a quasi-spin model of chromophores was recently shown to enhance exciton energy transfer significantly. Here we investigate how the modulation of the electronic structure of the chromophores by chemical substitution can enhance energy-transfer efficiency. Unlike previous work that does not consider the direct effect of the electronic structure on exciton dynamics, we add chemical substituents to the fluorone dimer to study the effect of electron-donating and electron-withdrawing substituents on exciton energy transfer. The exciton dynamics are studied from the solution of a quantum Liouville equation for an open system whose model Hamiltonian is derived from excited-state electronic structure calculations. Both van der Waals energies and coupling energies, arising from the Hellmann-Feynman force generated upon transferring the dimers from infinity to a finite separation, are built into the model Hamiltonian. Though these two effects are implicitly treated in dipole-based models, their explicit and separate treatment as discussed here is critical to forging the correct connection with the electronic structure calculations. We find that the addition of electron-donating substituents to the fluorone system results in an increase in exciton-transfer rates by factors ranging from 1.3-1.9. The computed oscillator strength is consistent with the recent experimental results on a larger heterodimer system containing fluorone. The oscillator strength increases with the addition of electron-donating substituents. Our results indicate that the study of chromophore networks via electronic structure will help in the future design of efficient synthetic light-harvesting systems. PMID:25062094

  4. Structural, optical and electrical properties of chemically deposited copper selenide films

    Indian Academy of Sciences (India)

    R H Bari; V Ganesan; S Potadar; L A Patil

    2009-02-01

    Stoichiometric and nonstoichiometric thin films of copper selenide have been prepared by chemical bath deposition technique at temperature below 60°C on glass substrate. The effect of nonstoichiometry on the optical, electrical and structural properties of the film was studied. The bandgap energy was observed to increase with the increase in at % of copper in composition. The grain size was also observed to increase with the decrease of at % of copper in composition. The films were characterized by X-ray diffraction (XRD), scanning electron microscopy (SEM), energy dispersive X-ray analysis (EDS), absorption spectroscopy, and AFM. The results are discussed and interpreted.

  5. Application of Nanocomposite Coatings with Different Structural Physical and Chemical Characteristics in Tissue Engineering

    Directory of Open Access Journals (Sweden)

    A.N. Goltsev

    2013-03-01

    Full Text Available The research covers the results of experimental studies of the effect character of nanocomposite coatings with different physical and chemical parameters (type, roughness, hydrophilic-hydrophobic characteristics on structural and functional properties (adhesive potential, phenotype, gene expression of mesenchymal stem cells (MSCs. On the tested nanocoatings (Al2O3, ZrO2, Ta2O5 the capability of oxide coating Al2O3 to enrich the in vitro cultured bone marrow (BM with the cells of MSCs phenotype markers as well as to increase the expression rate of ido gene in them, which may extend the spectrum of their therapeutic application in clinics, has been found.

  6. Edge Effects on the Electronic Structures of Chemically Modified Armchair Graphene Nanoribbons

    OpenAIRE

    Ren, Hao; Li, Qunxiang; Su, Haibin; Shi, Q. W.; Chen, Jie; Yang, Jinlong

    2007-01-01

    In this paper, we apply the first-principle theory to explore how the electronic structures of armchair graphene nanoribbons (AGNRs) are affected by chemical modifications. The edge addends include H, F, N, NH$_{2}$, and NO$_{2}$. Our theoretical results show that the energy gaps are highly tunable by controlling the widths of AGNRs and addends. The most interesting finding is that N-passivated AGNRs with various widths are metallic due to the unique electronic features of N-N bonds. This pro...

  7. Chemical Structure of Carbon Nitride Films Prepared by MW-ECR Plasma Enhanced Magnetron Sputtering

    Institute of Scientific and Technical Information of China (English)

    XU Jun; GAO Peng; DING Wan-yu; LI Xin; DENG Xin-lu; DONG Chuang

    2004-01-01

    Amorphous carbon nitride thin films were prepared by plasma-enhanced DC magnetron sputtering using twinned microwave electron cyclotron resonance plasma sources. Chemical structure of deposited films was investigated using X-ray photoelectron spectroscopy and Fourier transform infrared spectroscopy. The results indicate that the deposition rate is strongly affected by direct current bias, and the films are mainly composed of a single amorphous carbon nitride phase with N/C ratio close to C3N4, and the bonding is predominantly of C-N type.

  8. Chemical Structure of Carbon Nitride Films Prepared by MW-ECR Plasma Enhanced Magnetron Sputtering

    Institute of Scientific and Technical Information of China (English)

    XUJun,GAOPeng; DINGWan-yu; LIXin; DENGXin-lu; DONGChuang

    2004-01-01

    Amorphous carbon nitride thin films were prepared by plasma-enhanced DC magnetron sputtering using twinned microwave electron cyclotron resonance plasma sources. Chemical structure of deposited films was investigated using X-ray photoelectron spectroscopy and Fourier transtorm infrared spectroscopy. The results indicate that the deposition rate is strongly affected by direct current bias, and the films are mainly composed of a single amorphous carbon nitride phase with N/C ratio close to C3N4, and the bonding is predominantly of C-N type.

  9. CHEMICAL STRUCTURE DEPENDENCE OF THE INTERNAL ENERGY CONTRIBUTION IN RUBBER ELASTICITY

    Institute of Scientific and Technical Information of China (English)

    Juan Sun; Xiao-zhen Yang

    2001-01-01

    Conformational elasticity theory recently developed has been used to explore the internal energy contribution to the elastic force fe/f as a function of strain for poly(cis-1,4-isoprene) and poly(trans-1,4-isoprene). Calculated fe/f values are in good agreement with those obtained experimentally. Results show that behavior of fe/f is mainly contributed by chemical structure, or intramolecular interaction, supporting the experimental observations, and that the internal energy contribution is strain dependent.``

  10. Chemical, electronic, and magnetic structure of LaFeCoSi alloy: Surface and bulk properties

    Energy Technology Data Exchange (ETDEWEB)

    Lollobrigida, V. [Dipartimento di Scienze, Università Roma Tre, I-00146 Rome (Italy); Dipartimento di Matematica e Fisica, Università Roma Tre, I-00146 Rome (Italy); Basso, V.; Kuepferling, M.; Coïsson, M.; Olivetti, E. S.; Celegato, F. [Istituto Nazionale di Ricerca Metrologica (INRIM), I-10135 Torino (Italy); Borgatti, F. [CNR, Istituto per lo Studio dei Materiali Nanostrutturati (ISMN), I-40129 Bologna (Italy); Torelli, P.; Panaccione, G. [CNR, Istituto Officina dei Materiali (IOM), Lab. TASC, I-34149 Trieste (Italy); Tortora, L. [Laboratorio di Analisi di Superficie, Dipartimento di Matematica e Fisica, Università Roma Tre, I-00146 Rome (Italy); Dipartimento di Ingegneria Meccanica, Università Tor Vergata, I-00133 Rome (Italy); Stefani, G.; Offi, F. [Dipartimento di Scienze, Università Roma Tre, I-00146 Rome (Italy)

    2014-05-28

    We investigate the chemical, electronic, and magnetic structure of the magnetocaloric LaFeCoSi compound with bulk and surface sensitive techniques. We put in evidence that the surface retains a soft ferromagnetic behavior at temperatures higher than the Curie temperature of the bulk due to the presence of Fe clusters at the surface only. This peculiar magnetic surface effect is attributed to the exchange interaction between the ferromagnetic Fe clusters located at the surface and the bulk magnetocaloric alloy, and it is used here to monitor the magnetic properties of the alloy itself.

  11. Measuring the Effect of Fuel Chemical Structure on Particulate and Gaseous Emissions using Isotope Tracing

    Energy Technology Data Exchange (ETDEWEB)

    Buchholz, B A; Mueller, C J; Martin, G C; Upatnicks, A; Dibble, R W; Cheng, S

    2003-09-11

    Using accelerator mass spectrometry (AMS), a technique initially developed for radiocarbon dating and recently applied to internal combustion engines, carbon atoms within specific fuel molecules can be labeled and followed in particulate or gaseous emissions. In addition to examining the effect of fuel chemical structure on emissions, the specific source of carbon for PM can be identified if an isotope label exists in the appropriate fuel source. Existing work has focused on diesel engines, but the samples (soot collected on quartz filters or combustion gases captured in bombs or bags) are readily collected from large industrial combustors as well.

  12. Chemical, electronic, and magnetic structure of LaFeCoSi alloy: Surface and bulk properties

    International Nuclear Information System (INIS)

    We investigate the chemical, electronic, and magnetic structure of the magnetocaloric LaFeCoSi compound with bulk and surface sensitive techniques. We put in evidence that the surface retains a soft ferromagnetic behavior at temperatures higher than the Curie temperature of the bulk due to the presence of Fe clusters at the surface only. This peculiar magnetic surface effect is attributed to the exchange interaction between the ferromagnetic Fe clusters located at the surface and the bulk magnetocaloric alloy, and it is used here to monitor the magnetic properties of the alloy itself.

  13. Antibacterial, Structural and Optical Characterization of Mechano-Chemically Prepared ZnO Nanoparticles.

    Science.gov (United States)

    Manzoor, Umair; Siddique, Sumera; Ahmed, Rafay; Noreen, Zobia; Bokhari, Habib; Ahmad, Iftikhar

    2016-01-01

    Structural investigations, optical properties and antibacterial performance of the pure Zinc Oxide (ZnO) nanoparticles (NPs) synthesized by mechano-chemical method are presented. The morphology, dimensions and crystallinity of the ZnO NPs were controlled by tweaking the mechanical agitation of the mixture and subsequent thermal treatment. ZnO nanoparticles in small (resistant Staphylococcus aureus (MRSA), thus potential for medical applications. Scanning electron microscopy and survival assay indicated that most probably ZnO nanoparticles cause changes in cellular morphology which eventually causes bacterial cell death. PMID:27183165

  14. Reassigning the Structures of Natural Products Using NMR Chemical Shifts Computed with Quantum Mechanics: A Laboratory Exercise

    Science.gov (United States)

    Palazzo, Teresa A.; Truong, Tiana T.; Wong, Shirley M. T.; Mack, Emma T.; Lodewyk, Michael W.; Harrison, Jason G.; Gamage, R. Alan; Siegel, Justin B.; Kurth, Mark J.; Tantillo, Dean J.

    2015-01-01

    An applied computational chemistry laboratory exercise is described in which students use modern quantum chemical calculations of chemical shifts to assign the structure of a recently isolated natural product. A pre/post assessment was used to measure student learning gains and verify that students demonstrated proficiency of key learning…

  15. Structure activity studies of an analgesic drug tapentadol hydrochloride by spectroscopic and quantum chemical methods

    Science.gov (United States)

    Arjunan, V.; Santhanam, R.; Marchewka, M. K.; Mohan, S.; Yang, Haifeng

    2015-11-01

    Tapentadol is a novel opioid pain reliever drug with a dual mechanism of action, having potency between morphine and tramadol. Quantum chemical calculations have been carried out for tapentadol hydrochloride (TAP.Cl) to determine the properties. The geometry is optimised and the structural properties of the compound were determined from the optimised geometry by B3LYP method using 6-311++G(d,p), 6-31G(d,p) and cc-pVDZ basis sets. FT-IR and FT-Raman spectra are recorded in the solid phase in the region of 4000-400 and 4000-100 cm-1, respectively. Frontier molecular orbital energies, LUMO-HOMO energy gap, ionisation potential, electron affinity, electronegativity, hardness and chemical potential are also calculated. The stability of the molecule arising from hyperconjugative interactions and charge delocalisation has been analysed using NBO analysis. The 1H and 13C nuclear magnetic resonance chemical shifts of the molecule are analysed.

  16. Chemical compatibility of SiC composite structures with fusion reactor helium coolant at high temperatures

    International Nuclear Information System (INIS)

    The thermodynamic stability of SiC/SiC composite structures proposed for fusion applications is presented in this paper. Minimization of the free energy for reacting species in the temperature range 773-1273 K is achieved by utilizing the NASA-Lewis Chemical Equilibrium Thermodynamics Code (CET). The chemical stability of the matrix (SiC), as well as several fiber coatings (BN and graphite) are studied. Helium coolant is assumed to contain O2 and water moisture impurities in the range 100-1000 ppm. The work is applied to recent Magnetic and Inertial Confinement Conceptual designs. The present study indicates that the upper useful temperature limit for SiC/SiC composites, from the standpoint of high-temperature corrosion, will be in the neighborhood of 1273 K. Up to this temperature, corrosion of SiC is shown to be negligible. The main mechanism of weight loss will be by evaporation to the plasma side. The presence of a protective SiO2 condensed phase is discussed, and is shown to result in further reduction of high-temperature corrosion. The thermodynamic stability of C and BN is shown to be very poor under typical fusion reaction conditions. Further development of chemically stable interface materials is required. (orig.)

  17. Structural and chemical diagnosis of magnetic multilayers by RAFS and XRF techniques

    CERN Document Server

    Mai, Z H; Liu, C X; Li, M H; Jiang, H W; Lai, W Y; Wang, J; Ding, Y F; Hase, T P A; Fulthorpe, B D; Tanner, B K

    2003-01-01

    Elemental distribution of Ni, Mn and Co at the NiMn/Co and Co/NiMn interfaces of ultra-thin NiMn/Co multilayers and that of Bi in the Cu/NiFe/Bi/FeMn/Cu multilayers have been investigated by X-ray reflection anomalous fine structure (RAFS) and X-ray fluorescence (XRF) methods. For the as-grown sample of the NiMn/Co multilayers, a chemical intermixing region with the chemical component varying gradually from Co to CoMn is observed at the Co/NiMn interface, but not at the NiMn/Co interface. After annealing at 250 deg. C for 3, 10 and 20 h respectively, this gradual chemical component variation also appears at the NiMn/Co interface. For the Cu/NiFe/Bi/FeMn/Cu multilayers, the depth distributions of the Bi atoms of the samples with different thicknesses of Bi layer are obtained. The results show that the diffuse ability of Bi is strongly dependent on the thickness of the Bi layer.

  18. Toxicity challenges in environmental chemicals: Prediction of human plasma protein binding through quantitative structure-activity relationship (QSAR) models

    Science.gov (United States)

    The present study explores the merit of utilizing available pharmaceutical data to construct a quantitative structure-activity relationship (QSAR) for prediction of the fraction of a chemical unbound to plasma protein (Fub) in environmentally relevant compounds. Independent model...

  19. Structuring of DLC:Ag nanocomposite thin films employing plasma chemical etching and ion sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Tamulevičius, Tomas, E-mail: Tomas.Tamulevicius@ktu.lt; Tamulevičienė, Asta; Virganavičius, Dainius; Vasiliauskas, Andrius; Kopustinskas, Vitoldas; Meškinis, Šarūnas; Tamulevičius, Sigitas

    2014-12-15

    Highlights: • CF{sub 4}/O{sub 2} dry etching of DLC:Ag films revealed the embedded Ag nanoparticles. • Plasma processed samples with more than 5 at.% Ag demonstrated Ostwald ripening. • 4 μm period patterns in aluminum and photoresist were imposed in the DLC:Ag film. • Different micro patterns are formed depending on the selected processing route. - Abstract: We analyze structuring effects of diamond like carbon based silver nanocomposite (DLC:Ag) thin films by CF{sub 4}/O{sub 2} plasma chemical etching and Ar{sup +} sputtering. DLC:Ag films were deposited employing unbalanced reactive magnetron sputtering of silver target with Ar{sup +} in C{sub 2}H{sub 2} gas atmosphere. Films with different silver content (0.6–12.9 at.%) were analyzed. The films (as deposited and exposed to plasma chemical etching) were characterized employing scanning electron microscopy and energy dispersive X-ray analysis (SEM/EDS), optical microscopy, ultraviolet–visible light (UV–VIS) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. After deposition, the films were plasma chemically etched in CF{sub 4}/O{sub 2} mixture plasma for 2–6 min. It is shown that optical properties of thin films and silver nano particle size distribution can be tailored during deposition changing the magnetron current and C{sub 2}H{sub 2}/Ar ratio or during following plasma chemical etching. The plasma etching enabled to reveal the silver filler particle size distribution and to control silver content on the surface that was found to be dependent on Ostwald ripening process of silver nano-clusters. Employing contact lithography and 4 μm period mask in photoresist or aluminum the films were patterned employing CF{sub 4}/O{sub 2} mixture plasma chemical etching, direct Ar{sup +} sputtering or combined etching processes. It is shown that different processing recipes result in different final grating structures. Selective carbon etching in CF{sub 4}/O{sub 2} gas mixture with

  20. EFFECT OF CHEMICAL STRUCTURE OF SULFOXIDE GRAFTED POLY (VINYL ALCOHOL) ON GAS PERMEABILITY

    Institute of Scientific and Technical Information of China (English)

    JIANG Donglin; ZHANG Yifeng; SHEN Zhiquan

    1994-01-01

    The effects of chemical structure, I. E. Side chain structure and their contents,on thepermeability of pure SO2, N2 and their mixture gases for the sulfoxide grafted poly (vinylalcohol) (RVSO-PVA) membranes have been investigated:(-CH2-CH)2-OH-(CH2-CH)5-OCH2CH2S(O)R where R = Me, Et, Pr, t-Bu and Ph. It was notable that introduction of sulfoxide group into PVA side chain greatly enhanced the permselectivity of sulfur dioxide. SO2 permeability and separation factor of these polymers increased markedly as the size of side chain increased. The sulfoxide content of the polymer also played an important role in the pure and mixture gases permeation. Some explanations have been made to interpret this unique gas separation behaviour.

  1. Structural and optical properties of tellurium films obtained by chemical vapor deposition(CVD)

    Institute of Scientific and Technical Information of China (English)

    MA Yu-tian; GONG Zhu-Qing; XU Wei-Hong; HUANG Jian

    2006-01-01

    Tellurium thin films were prepared by the chemical vapor deposition method. The structure, surface morphology and optical properties of the Te thin films were analyzed by powder X-ray diffraction, scanning electron microscopy, FTIR transmission,UV/VIS/NIR transmission and reflectance. The results show that the films structural and optical properties are influenced by many factors such as film thickness, crystallite size and substrate temperature. The films as thick as 111-133 nm have high IR transmission across the full 8-13 μm band and highly blocking in the solar spectral region elsewhere, which indicates that Te films thickness in this region can be used as good solar radiation shields in radiative cooling devices.

  2. Structural, chemical and deformation changes in friction welded joint of dissimilar steels

    Directory of Open Access Journals (Sweden)

    N. Ratković

    2014-10-01

    Full Text Available Fundamental principles of friction welding of dissimilar steels (high speed and tempering steel from the aspect of metallurgical and chemical processes occurring in the joint zone are presented in this paper. Considering that phenomena accompanying the friction welding are interdependent, it was necessary to experimentally determine the process variable parameters, to establish the optimal welding regime. The experiments were set and realized so that all the variables were analyzed as a function of the friction time. The metallographic investigations included analysis of the joint zone microstructure through structural phases and hardness changes, due to influence of the heat treatment - annealing. The experimental work included analysis of the geometry changes, the joint zone structure and the basic mechanical characteristics of the joint realized by the friction welding.

  3. Band gap and chemically ordered domain structure of a graphene analogue BCN

    Science.gov (United States)

    Venu, K.; Kanuri, S.; Raidongia, K.; Hembram, K. P. S. S.; Waghmare, U. V.; Datta, R.

    2010-12-01

    Chemically synthesized few layer graphene analogues of B xC yN z are characterized by aberration corrected transmission electron microscopy and high resolution electron energy loss spectroscopy (HREELS) to determine the local phase, electronic structure and band gap. HREELS band gap studies of a B xC yN z composition reveal absorption edges at 2.08, 3.43 and 6.01 eV, indicating that the B xC yN z structure may consist of domains of different compositions. The K-absorption edge energy position of the individual elements in B xC yN z is determined and compared with h-BN and graphite. An understanding of these experimental findings is developed with complementary first-principles based calculations of the various ordered configurations of B xC yN z.

  4. Physical and chemical structure of planet-forming disks probed by millimeter observations and modeling

    CERN Document Server

    Dutrey, Anne; Chapillon, Edwige; Gorti, Uma; Guilloteau, Stéphane; Hersant, Franck; Hogerheijde, Michiel; Hughes, Meredith; Meeus, Gwendolyn; Nomura, Hideko; Piétu, Vincent; Qi, Chunhua; Wakelam, Valentine

    2014-01-01

    Protoplanetary disks composed of dust and gas are ubiquitous around young stars and are commonly recognized as nurseries of planetary systems. Their lifetime, appearance, and structure are determined by an interplay between stellar radiation, gravity, thermal pressure, magnetic field, gas viscosity, turbulence, and rotation. Molecules and dust serve as major heating and cooling agents in disks. Dust grains dominate the disk opacities, reprocess most of the stellar radiation, and shield molecules from ionizing UV/X-ray photons. Disks also dynamically evolve by building up planetary systems which drastically change their gas and dust density structures. Over the past decade significant progress has been achieved in our understanding of disk chemical composition thanks to the upgrade or advent of new millimeter/Infrared facilities (SMA, PdBI, CARMA, Herschel, e-VLA, ALMA). Some major breakthroughs in our comprehension of the disk physics and chemistry have been done since PPV. This review will present and discus...

  5. Thermal, chemical and structural characteristics of erbium-doped sodium phosphate glasses

    International Nuclear Information System (INIS)

    Thermal, chemical and structural characteristics of the erbium-doped sodium phosphate glasses with 1-6 mol% Er2O3 were investigated. The glass transition temperature increase, but the thermal expansion coefficient and the dissolution rate of the glasses decrease with increasing Er2O3 content. X-ray photoelectron spectroscopy (XPS) and Fourier transformed infrared (FTIR) spectrometer were used to inspect the structural changes of the glasses. The doping of Er2O3 induces the depolymerization of the glasses at the Q3 tetrahedral sites. The relative content of bridging oxygen (b-O) decreases and that of non-bridging oxygen (nb-O), which is attributed to the forming of the ionic P-O-...Er3+ linkages between phosphate chains, increases with increasing Er2O3 content

  6. Verrucomicrobial community structure and abundance as indicators for changes in chemical factors linked to soil fertility.

    Science.gov (United States)

    Navarrete, Acacio Aparecido; Soares, Tielle; Rossetto, Raffaella; van Veen, Johannes Antonie; Tsai, Siu Mui; Kuramae, Eiko Eurya

    2015-09-01

    Here we show that verrucomicrobial community structure and abundance are extremely sensitive to changes in chemical factors linked to soil fertility. Terminal restriction fragment length polymorphism fingerprint and real-time quantitative PCR assay were used to analyze changes in verrucomicrobial communities associated with contrasting soil nutrient conditions in tropical regions. In case study Model I ("Slash-and-burn deforestation") the verrucomicrobial community structures revealed disparate patterns in nutrient-enriched soils after slash-and-burn deforestation and natural nutrient-poor soils under an adjacent primary forest in the Amazonia (R = 0.819, P = 0.002). The relative proportion of Verrucomicrobia declined in response to increased soil fertility after slash-and-burn deforestation, accounting on average, for 4 and 2 % of the total bacterial signal, in natural nutrient-poor forest soils and nutrient-enriched deforested soils, respectively. In case study Model II ("Management practices for sugarcane") disparate patterns were revealed in sugarcane rhizosphere sampled on optimal and deficient soil fertility for sugarcane (R = 0.786, P = 0.002). Verrucomicrobial community abundance in sugarcane rhizosphere was negatively correlated with soil fertility, accounting for 2 and 5 % of the total bacterial signal, under optimal and deficient soil fertility conditions for sugarcane, respectively. In nutrient-enriched soils, verrucomicrobial community structures were related to soil factors linked to soil fertility, such as total nitrogen, phosphorus, potassium and sum of bases, i.e., the sum of calcium, magnesium and potassium contents. We conclude that community structure and abundance represent important ecological aspects in soil verrucomicrobial communities for tracking the changes in chemical factors linked to soil fertility under tropical environmental conditions. PMID:26184407

  7. Determination of the chemical structures of tandyukisins B-D, isolated from a marine sponge-derived fungus.

    Science.gov (United States)

    Yamada, Takeshi; Umebayashi, Yoshihide; Kawashima, Maiko; Sugiura, Yuma; Kikuchi, Takashi; Tanaka, Reiko

    2015-05-01

    Tandyukisins B-D (1-3), novel decalin derivatives, have been isolated from a strain of Trichoderma harzianum OUPS-111D-4 originally derived from the marine sponge Halichondria okadai, and their structures have been elucidated on the basis of spectroscopic analyses using 1D and 2D NMR techniques. In addition, their chemical structures were established by chemical transformation. They exhibited weak cytotoxicity, but selective growth inhibition on panel screening using 39 human cancer cell lines. PMID:26006715

  8. Insertion of CdSe quantum dots in ZnSe nanowires: Correlation of structural and chemical characterization with photoluminescence

    OpenAIRE

    Den Hertog, Martien; Elouneg-Jamroz, Miryam; Bellet-Amalric, Edith; Bounouar, Samir; Bougerol, Catherine; André, Régis; Genuist, Yann; Poizat, Jean-Philippe; Kheng, Kuntheak; Tatarenko, Serge

    2011-01-01

    ZnSe nanowires with CdSe quantum dot insertions were grown by molecular beam epitaxy using gold as a catalyst. Structural, chemical, and optical properties of the wires and quantum dots were characterized using electron microscopy and photoluminescence spectroscopy. We determined the crystalline structure, the chemical composition, and the size of the quantum dot and established a correlation between quantum dot size and luminescence. As expected, a blueshift of the luminescence was observed ...

  9. Structure and stability of pyrophyllite edge surfaces: Effect of temperature and water chemical potential

    Science.gov (United States)

    Kwon, Kideok D.; Newton, Aric G.

    2016-10-01

    The surfaces of clay minerals, which are abundant in atmospheric mineral dust, serve as an important medium to catalyze ice nucleation. The lateral edge surface of 2:1 clay minerals is postulated to be a potential site for ice nucleation. However, experimental investigations of the edge surface structure itself have been limited compared to the basal planes of clay minerals. Density functional theory (DFT) computational studies have provided insights into the pyrophyllite edge surface. Pyrophyllite is an ideal surrogate mineral for the edge surfaces of 2:1 clay minerals as it possesses no or little structural charge. Of the two most-common hydrated edge surfaces, the AC edge, (1 1 0) surface in the monoclinic polytype notation, is predicted to be more stable than the B edge, (0 1 0) surface. These stabilities, however, were determined based on the total energies calculated at 0 K and did not consider environmental effects such as temperature and humidity. In this study, atomistic thermodynamics based on periodic DFT electronic calculations was applied to examine the effects of environmental variables on the structure and thermodynamic stability of the common edge surfaces in equilibrium with bulk pyrophyllite and water vapor. We demonstrate that the temperature-dependent vibrational energy of sorbed water molecules at the edge surface is a significant component of the surface free energy and cannot be neglected when determining the surface stability of pyrophyllite. The surface free energies were calculated as a function of temperature from 240 to 600 K and water chemical potential corresponding to conditions from ultrahigh vacuum to the saturation vapor pressure of water. We show that at lower water chemical potentials (dry conditions), the AC and B edge surfaces possessed similar stabilities; at higher chemical potentials (humid conditions) the AC edge surface was more stable than the B edge surface. At high temperatures, both surfaces showed similar stabilities

  10. The structural evolution and diffusion during the chemical transformation from cobalt to cobalt phosphide nanoparticles

    KAUST Repository

    Ha, Don-Hyung

    2011-01-01

    We report the structural evolution and the diffusion processes which occur during the phase transformation of nanoparticles (NPs), ε-Co to Co 2P to CoP, from a reaction with tri-n-octylphosphine (TOP). Extended X-ray absorption fine structure (EXAFS) investigations were used to elucidate the changes in the local structure of cobalt atoms which occur as the chemical transformation progresses. The lack of long-range order, spread in interatomic distances, and overall increase in mean-square disorder compared with bulk structure reveal the decrease in the NP\\'s structural order compared with bulk structure, which contributes to their deviation from bulk-like behavior. Results from EXAFS show both the Co2P and CoP phases contain excess Co. Results from EXAFS, transmission electron microscopy, X-ray diffraction, and density functional theory calculations reveal that the inward diffusion of phosphorus is more favorable at the beginning of the transformation from ε-Co to Co2P by forming an amorphous Co-P shell, while retaining a crystalline cobalt core. When the major phase of the sample turns to Co 2P, the diffusion processes reverse and cobalt atom out-diffusion is favored, leaving a hollow void, characteristic of the nanoscale Kirkendall effect. For the transformation from Co2P to CoP theory predicts an outward diffusion of cobalt while the anion lattice remains intact. In real samples, however, the Co-rich nanoparticles continue Kirkendall hollowing. Knowledge about the transformation method and structural properties provides a means to tailor the synthesis and composition of the NPs to facilitate their use in applications. © 2011 The Royal Society of Chemistry.

  11. The influence of chemical composition on the properties and structure Al-Si-Cu(Mg alloys

    Directory of Open Access Journals (Sweden)

    M. Kaczorowski

    2007-04-01

    Full Text Available The mechanical properties of different chemical composition AlSiCuMg type cast alloys after precipitation hardening are presented. The aim of the study was to find out how much the changes in chemistry of aluminum cast alloys permissible by EN-PN standards may influence the mechanical properties of these alloys. Eight AlSi5Cu3(Mg type cast alloys of different content alloying elements were selected for the study. The specimens cut form test castings were subjected to precipitation hardening heat treatment. The age hardened specimens were evaluated using tensile test, hardness measurements and impact test. Moreover, the structure investigation were carried out using either conventional light Metallography and scanning (SEM and transmission (TEM electron microscopy. The two last methods were used for fractography observations and precipitation process observations respectively. It was concluded that the changes in chemical composition which can reach even 2,5wt.% cause essential differences of the structure and mechanical properties of the alloys. As followed from quantitative evaluation and as could be predicted theoretically, copper and silicon mostly influenced the mechanical properties of AlSi5Cu3(Mg type cast alloys. Moreover it was showed that the total concentration of alloying elements accelerated and intensifies the process of decomposition of supersaturated solid solution. The increase of Cu and Mg concentration increased the density of precipitates. It increases of strength properties of the alloys which are accompanied with decreasing in ductility.

  12. Optical and structural properties of PbI2 thin film produced via chemical dipping method

    Science.gov (United States)

    Kariper, İ. A.

    2016-06-01

    PbI2 thin films were deposited on glass substrates via chemical bath deposition. The characteristics of PbI2 thin films were examined through their structural and optical properties. X-ray diffraction spectra showed the presence of rhombohedral structure and atom planes were subject to change with the pH of the bath. Scanning electron microscope indicated uniform distribution of grains. Optical properties were examined via UV-VIS; optical spectrum of the thin films was measured at the range of 200-1100 nm wavelength. Optimum pH levels for producing thin films were found to be pH 4-5. It has been observed that transmission and optical band gap ( E g) increased with the pH of the bath, which varied between 66-95 and 2.24-2.50 %, respectively; on the other hand film thickness of PbI2 thin films was decreased with the pH of the bath. Energy-dispersive X-ray spectroscopy analysis were in accordance with theoretical value of PbI2 at pH = 4 and 5. Refractive index was negatively correlated with pH of the chemical bath; it has been calculated as 1.97, 1.40, 1.29 and 1.24 for the films produced at pH 2, 3, 4 and 5. The results of the study were compared with similar studies in the literature.

  13. DFT modeling of the electronic and magnetic structures and chemical bonding properties of intermetallic hydrides

    International Nuclear Information System (INIS)

    This thesis presents an ab initio study of several classes of intermetallics and their hydrides. These compounds are interesting from both a fundamental and an applied points of view. To achieve this aim two complementary methods, constructed within the DFT, were chosen: (i) pseudo potential based VASP for geometry optimization, structural investigations and electron localization mapping (ELF), and (ii) all-electrons ASW method for a detailed description of the electronic structure, chemical bonding properties following different schemes as well as quantities depending on core electrons such as the hyperfine field. A special interest is given with respect to the interplay between magneto-volume and chemical interactions (metal-H) effects within the following hydrided systems: binary Laves (e.g. ScFe2) and Haucke (e.g. LaNi5) phases on one hand, and ternary cerium based (e.g. CeRhSn) and uranium based (e.g. U2Ni2Sn) alloys on the other hand. (author)

  14. Structure, chemical ordering and thermal stability of Pt-Ni alloy nanoclusters.

    Science.gov (United States)

    Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

    2013-09-01

    Equilibrium structures, chemical ordering and thermal properties of Pt-Ni nanoalloys are investigated by using basin hopping-based global optimization, Monte Carlo (MC) and molecular dynamics (MD) methods, based on the second-moment approximation of the tight-binding potentials (TB-SMA). The TB-SMA potential parameters for Pt-Ni nanoalloys are fitted to reproduce the results of density functional theory calculations for small clusters. The chemical ordering in cuboctahedral (CO) Pt-Ni nanoalloys with 561 and 923 atoms is obtained from the so called semi-grand-canonical ensemble MC simulation at 100 K. Two ordered phases of L12 (PtNi3) and L10 (PtNi) are found for the CO561 and CO923 Pt-Ni nanoalloys, which is in good agreement with the experimental phase diagram of the Pt-Ni bulk alloy. In addition, the order-disorder transition and thermal properties of these nanoalloys are studied by using MC and MD methods, respectively. It is shown that the typical perfect L10 PtNi structure is relatively stable, showing high order-disorder transition temperature and melting point among these CO561 and CO923 Pt-Ni nanoalloys.

  15. Structural interpretation of chemically synthesized ZnO nanorod and its application in lithium ion battery

    Energy Technology Data Exchange (ETDEWEB)

    Kundu, Samapti; Sain, Sumanta [Materials Science Division, Department of Physics, The University of Burdwan, Golapbag, Burdwan 713104, West Bengal (India); Yoshio, Masaki [Advanced Research and Education Centre, Saga University, 1341 Yoga-machi, Saga 840-0047 (Japan); Kar, Tanusree [Department of Materials Science, Indian Association for the Cultivation of Science, Jadavpur, Kolkata 700032, West Bengal (India); Gunawardhana, Nanda, E-mail: nandagunawardhana@pdn.ac.lk [International Research Centre, Senate Building, University of Peradeniya, Peradeniya 20400 (Sri Lanka); Pradhan, Swapan Kumar, E-mail: skpradhan@phys.buruniv.ac.in [Materials Science Division, Department of Physics, The University of Burdwan, Golapbag, Burdwan 713104, West Bengal (India)

    2015-02-28

    Graphical abstract: - Highlights: • ZnO nanorods are synthesized at room temperature via a simple chemical route. • Growth direction of ZnO nanorods has been determined along 〈0 0 2〉. • ZnO nanorods constructed anode shows a high discharge capacity in first cycle. • It retains good reversible capacity compared to other ZnO morphologies. - Abstract: ZnO nanorods are synthesized at room temperature via a simple chemical route without using any template or capping agent and its importance is evaluated as a suitable candidate for anode material in lithium ion battery. Structural and microstructure characterizations of these nanorods are made by analyzing the X-ray diffraction data employing the Rietveld method of powder structure refinement. It reveals that the ZnO nanorods are grown up with a preferred orientation and elongated along 〈0 0 2〉. FESEM images reveal that these uniform cylindrical shaped nanorods are of different lengths and diameters. These synthesized ZnO nanorods are tested as an anode material for lithium ion batteries. The nano grain size of the ZnO rods results in less volume expansion and/or contraction during the alloying/de-alloying process and causes in good cyclability. In addition, synthesized ZnO nanorods deliver high charge/discharge capacities compared to other reported ZnO materials.

  16. Structural, electrical and optical properties of copper selenide thin films deposited by chemical bath deposition technique

    International Nuclear Information System (INIS)

    A low cost chemical bath deposition (CBD) technique has been used for the preparation of Cu2-xSe thin films on glass substrates. Structural, electrical and optical properties of these films were investigated. X-ray diffraction (XRD) study of the Cu2-xSe films annealed at 523K suggests a cubic structure with a lattice constant of 5.697A. Chemical composition was investigated by X-ray photoelectron spectroscopy (XPS). It reveals that absorbed oxygen in the film decreases remarkably on annealing above 423K. The Cu/Se ratio was observed to be the same in as-deposited and annealed films. Both as- deposited and annealed films show very low resistivity in the range of (0.04- 0.15) x 10-5 Ω-m. Transmittance and Reflectance were found in the range of 5-50% and 2-20% respectively. Optical absorption of the films results from free carrier absorption in the near infrared region with absorption coefficient of ∼108 m-1. The band gap for direct transition, Eg.dir varies in the range of 2.0-2.3eV and that for indirect transition Eg.indir is in the range of 1.25-1.5eV.1. (author)

  17. Interactions between structural and chemical biomimetism in synthetic stem cell niches

    International Nuclear Information System (INIS)

    Advancements in understanding stem cell functions and differentiation are of key importance for the clinical success of stem-cell-based therapies. 3D structural niches fabricated by two-photon polymerization are a powerful platform for controlling stem cell growth and differentiation. In this paper, we investigate the possibility of further controlling stem cell fate by tuning the mechanical properties of such niches through coating with thin layers of biomimetic hyaluronan-based and gelatin-based hydrogels. We first assess the biocompatibility of chemical coatings and then study the interactions between structural and chemical biomimetism on the response of MSCs in terms of proliferation and differentiation. We observed a clear effect of the hydrogel coating on otherwise identical 3D scaffolds. In particular, in gelatin-coated niches we observed a stronger metabolic activity and commitment toward the osteo-chondral lineage with respect to hyaluronan-coated niches. Conversely, a reduction in the homing effect was observed in all the coated niches, especially in gelatin-coated niches. This study demonstrates the feasibility of controlling independently different mechanical cues, in bioengineered stem cell niches, i.e. the 3D scaffold geometry and the surface stiffness. This will allow, on the one hand, understanding their specific role in stem cell proliferation and differentiation and, on the other hand, finely tuning their synergistic effect. (paper)

  18. Effects of structural and chemical disorders on the visible/UV spectra of carbonaceous interstellar grains

    CERN Document Server

    Papoular, R J; Roldan, R; Katsnelson, M I; Papoular, R

    2013-01-01

    The recent spectacular progress in the experimental and theoretical understanding of graphene, the basic constituent of graphite, is applied here to compute, from first principles, the UV extinction of nano-particles made of stacks of graphene layers. The theory also covers cases where graphene is affected by structural, chemical or orientation disorder, each disorder type being quantitatively defined by a single parameter. The extinction bumps carried by such model materials are found to have positions and widths falling in the same range as the known astronomical 2175 \\AA features: as the disorder parameter increases, the bump width increases from 0.85 to 2.5 $\\mu$m$^{-1}$, while its peak position shifts from 4.65 to 4.75 $\\mu$m$^{-1}$. Moderate degrees of disorder are enough to cover the range of widths of the vast majority of observed bumps (0.75 to 1.3 $\\mu$m$^{-1}$). Higher degrees account for outliers, also observed in the sky. The introduction of structural or chemical disorder amounts to changing the...

  19. Radiation thermo-chemical models of protoplanetary disks I. Hydrostatic disk structure and inner rim

    CERN Document Server

    Woitke, Peter; Thi, Wing-Fai

    2009-01-01

    This paper introduces a new disk code, called ProDiMo, to calculate the thermo-chemical structure of protoplanetary disks and to interpret gas emission lines from UV to sub-mm. We combine frequency-dependent 2D dust continuum radiative transfer, kinetic gas-phase and UV photo-chemistry, ice formation, and detailed non-LTE heating & cooling balance with the consistent calculation of the hydrostatic disk structure. We include FeII and CO ro-vibrational line heating/cooling relevant for the high-density gas close to the star, and apply a modified escape probability treatment. The models are characterized by a high degree of consistency between the various physical, chemical and radiative processes, where the mutual feedbacks are solved iteratively. In application to a T Tauri disk extending from 0.5AU to 500AU, the models are featured by a puffed-up inner rim and show that the dense, shielded and cold midplane (z/r<0.1, Tg~Td) is surrounded by a layer of hot (5000K) and thin (10^7 to 10^8 cm^-3) atomic ga...

  20. Biomimetic hydrophobic surface fabricated by chemical etching method from hierarchically structured magnesium alloy substrate

    Science.gov (United States)

    Liu, Yan; Yin, Xiaoming; Zhang, Jijia; Wang, Yaming; Han, Zhiwu; Ren, Luquan

    2013-09-01

    As one of the lightest metal materials, magnesium alloy plays an important role in industry such as automobile, airplane and electronic product. However, magnesium alloy is hindered due to its high chemical activity and easily corroded. Here, inspired by typical plant surfaces such as lotus leaves and petals of red rose with super-hydrophobic character, the new hydrophobic surface is fabricated on magnesium alloy to improve anti-corrosion by two-step methodology. The procedure is that the samples are processed by laser first and then immersed and etched in the aqueous AgNO3 solution concentrations of 0.1 mol/L, 0.3 mol/L and 0.5 mol/L for different times of 15 s, 40 s and 60 s, respectively, finally modified by DTS (CH3(CH2)11Si(OCH3)3). The microstructure, chemical composition, wettability and anti-corrosion are characterized by means of SEM, XPS, water contact angle measurement and electrochemical method. The hydrophobic surfaces with microscale crater-like and nanoscale flower-like binary structure are obtained. The low-energy material is contained in surface after DTS treatment. The contact angles could reach up to 138.4 ± 2°, which hydrophobic property is both related to the micro-nano binary structure and chemical composition. The results of electrochemical measurements show that anti-corrosion property of magnesium alloy is improved. Furthermore, our research is expected to create some ideas from natural enlightenment to improve anti-corrosion property of magnesium alloy while this method can be easily extended to other metal materials.

  1. Biomimetic hydrophobic surface fabricated by chemical etching method from hierarchically structured magnesium alloy substrate

    International Nuclear Information System (INIS)

    As one of the lightest metal materials, magnesium alloy plays an important role in industry such as automobile, airplane and electronic product. However, magnesium alloy is hindered due to its high chemical activity and easily corroded. Here, inspired by typical plant surfaces such as lotus leaves and petals of red rose with super-hydrophobic character, the new hydrophobic surface is fabricated on magnesium alloy to improve anti-corrosion by two-step methodology. The procedure is that the samples are processed by laser first and then immersed and etched in the aqueous AgNO3 solution concentrations of 0.1 mol/L, 0.3 mol/L and 0.5 mol/L for different times of 15 s, 40 s and 60 s, respectively, finally modified by DTS (CH3(CH2)11Si(OCH3)3). The microstructure, chemical composition, wettability and anti-corrosion are characterized by means of SEM, XPS, water contact angle measurement and electrochemical method. The hydrophobic surfaces with microscale crater-like and nanoscale flower-like binary structure are obtained. The low-energy material is contained in surface after DTS treatment. The contact angles could reach up to 138.4 ± 2°, which hydrophobic property is both related to the micro–nano binary structure and chemical composition. The results of electrochemical measurements show that anti-corrosion property of magnesium alloy is improved. Furthermore, our research is expected to create some ideas from natural enlightenment to improve anti-corrosion property of magnesium alloy while this method can be easily extended to other metal materials.

  2. Biomimetic hydrophobic surface fabricated by chemical etching method from hierarchically structured magnesium alloy substrate

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Yan; Yin, Xiaoming; Zhang, Jijia [Key Laboratory of Bionic Engineering (Ministry of Education), Jilin University, Changchun 130022 (China); Wang, Yaming [Institute for Advanced Ceramics, Harbin Institute of Technology, Harbin 150001 (China); Han, Zhiwu, E-mail: zwhan@jlu.edu.cn [Key Laboratory of Bionic Engineering (Ministry of Education), Jilin University, Changchun 130022 (China); Ren, Luquan [Key Laboratory of Bionic Engineering (Ministry of Education), Jilin University, Changchun 130022 (China)

    2013-09-01

    As one of the lightest metal materials, magnesium alloy plays an important role in industry such as automobile, airplane and electronic product. However, magnesium alloy is hindered due to its high chemical activity and easily corroded. Here, inspired by typical plant surfaces such as lotus leaves and petals of red rose with super-hydrophobic character, the new hydrophobic surface is fabricated on magnesium alloy to improve anti-corrosion by two-step methodology. The procedure is that the samples are processed by laser first and then immersed and etched in the aqueous AgNO{sub 3} solution concentrations of 0.1 mol/L, 0.3 mol/L and 0.5 mol/L for different times of 15 s, 40 s and 60 s, respectively, finally modified by DTS (CH{sub 3}(CH{sub 2}){sub 11}Si(OCH{sub 3}){sub 3}). The microstructure, chemical composition, wettability and anti-corrosion are characterized by means of SEM, XPS, water contact angle measurement and electrochemical method. The hydrophobic surfaces with microscale crater-like and nanoscale flower-like binary structure are obtained. The low-energy material is contained in surface after DTS treatment. The contact angles could reach up to 138.4 ± 2°, which hydrophobic property is both related to the micro–nano binary structure and chemical composition. The results of electrochemical measurements show that anti-corrosion property of magnesium alloy is improved. Furthermore, our research is expected to create some ideas from natural enlightenment to improve anti-corrosion property of magnesium alloy while this method can be easily extended to other metal materials.

  3. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    Directory of Open Access Journals (Sweden)

    Oscar Martínez-Santiago

    2016-05-01

    Full Text Available This report examines the interpretation of the Graph Derivative Indices (GDIs from three different perspectives (i.e., in structural, steric and electronic terms. It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms.

  4. Structural properties of zinc oxide deposited using atmospheric pressure combustion chemical vapour deposition

    International Nuclear Information System (INIS)

    In this study the deposition of thin zinc oxide (ZnO) films under atmospheric pressure conditions was investigated. The deposition technique applied was combustion chemical vapour deposition (CCVD), at which a propane–air mixture was combusted in a burner. Dissolved zinc nitrate was used as precursor, which was guided as aerosol droplets by the processing gas flow directly into the reaction zone. Fundamental investigations were performed to form undoped ZnO. The structural properties of the films were analysed in dependence of the substrate temperature during the coating process. The presence of crystalline ZnO structures was proved and differences in film growth and crystallite sizes are revealed. Additionally, the particles generated by the CCVD-flame are characterised. The thin films showed a slight excess of Zn and several states of binding energy could be observed by fitting the core level spectra. Scanning and transmission electron microscopy also indicated ordered structures and additionally different orientations of crystallites were observed. - Highlights: • Columnar growth structures of ZnO by CCVD were observed. • The presence of polycrystalline ZnO with (002) as main orientation was confirmed. • Initial particles significantly differ from crystallite sizes of the resulting films. • The films show an excess of Zn with a Zn-to-O ratio of around 1.7

  5. CHEMICAL STRUCTURE AND PYROLYSIS RESPONSE OF BETA-O-4 LIGNIN MODEL POLYMER

    Directory of Open Access Journals (Sweden)

    Jiang-Yan Liu

    2011-04-01

    Full Text Available Hydroxyphenyl (H-type and guaiacyl (G-type lignin model polymers composed of the β–O–4 structure without gamma–hydroxymethyl groups were synthesized. The chemical structures of the H- and G-type lignin models were characterized by 1H- and 13C-NMR, as well as MALDI-TOF/MS. The pyrolysis response was analyzed by means of TG-DTG, Py-GC/MS, and a tube furnace technique. 1H-, 13C-NMR, and MALDI-TOF/MS showed that the lignin models were linear polymers. The polymers included the β–O–4 linkage, as in natural lignin. Pyrolytic products from H-type lignin model only possessed p-hydroxyphenyl structure without methoxyl groups, and the pyrolytic products from G-type lignin model only possessed guaiacyl structure with methoxyl groups. Pyrolysis products from H- and G- type lignin models were classified into char, gas, and liquid (bio-oil, and the gaseous products of two model compounds mainly consisted of H2, CO, CH4, CO2, and C2H4.

  6. Synthesis, structural characterization and quantum chemical studies of silicon-containing benzoic acid derivatives

    Science.gov (United States)

    Zaltariov, Mirela-Fernanda; Cojocaru, Corneliu; Shova, Sergiu; Sacarescu, Liviu; Cazacu, Maria

    2016-09-01

    The present paper is concerned with the synthesis and molecular structure investigation of two new benzoic acid derivatives having trimethylsilyl tails, 4-((trimethylsilyl)methoxy) and 4-(3-(trimethylsilyl)propoxy)benzoic acids. The structures of the novel compounds have been confirmed by X-ray crystallography, Fourier-transform infrared spectroscopy (FTIR) and nuclear magnetic resonance (1H and 13C NMR). The theoretical studies of molecules were conducted by using the quantum chemical methods, such as Density Functional Theory (DFT B3LYP/6-31 + G**), Hartree-Fock (HF/6-31 + G**) and semiempirical computations (PM3, PM6 and PM7). The optimized molecular geometries have been found to be in good agreement with experimental structures resulted from the X-ray diffraction. The maximum electronic absorption bands observed at 272-287 nm (UV-vis spectra) have been assigned to π → π* transitions, which were in reasonable agreement with the time dependent density functional theory (TD-DFT) calculations. The computed vibrational frequencies by DFT method were assigned and compared with the experimental FTIR spectra. The mapped electrostatic potentials revealed the reactive sites, which corroborated the observation of the dimer supramolecular structures formed in the crystals by hydrogen-bonding. The energies of frontier molecular orbitals (HOMO and LUMO), energy gap, dipole moment and molecular descriptors for the new compounds were calculated and discussed.

  7. Structural properties of zinc oxide deposited using atmospheric pressure combustion chemical vapour deposition

    Energy Technology Data Exchange (ETDEWEB)

    Zunke, I., E-mail: iz@innovent-jena.de [Innovent e.V. Technology Development, Department of Surface Engineering, Prüssingstr. 27B, 07745 Jena (Germany); Wolf, S. [University of Jena, Institute for Solid State Physics, Helmholtzweg 3/5, 07745 Jena (Germany); Heft, A.; Schimanski, A.; Grünler, B. [Innovent e.V. Technology Development, Department of Surface Engineering, Prüssingstr. 27B, 07745 Jena (Germany); Ronning, C.; Seidel, P. [University of Jena, Institute for Solid State Physics, Helmholtzweg 3/5, 07745 Jena (Germany)

    2014-08-28

    In this study the deposition of thin zinc oxide (ZnO) films under atmospheric pressure conditions was investigated. The deposition technique applied was combustion chemical vapour deposition (CCVD), at which a propane–air mixture was combusted in a burner. Dissolved zinc nitrate was used as precursor, which was guided as aerosol droplets by the processing gas flow directly into the reaction zone. Fundamental investigations were performed to form undoped ZnO. The structural properties of the films were analysed in dependence of the substrate temperature during the coating process. The presence of crystalline ZnO structures was proved and differences in film growth and crystallite sizes are revealed. Additionally, the particles generated by the CCVD-flame are characterised. The thin films showed a slight excess of Zn and several states of binding energy could be observed by fitting the core level spectra. Scanning and transmission electron microscopy also indicated ordered structures and additionally different orientations of crystallites were observed. - Highlights: • Columnar growth structures of ZnO by CCVD were observed. • The presence of polycrystalline ZnO with (002) as main orientation was confirmed. • Initial particles significantly differ from crystallite sizes of the resulting films. • The films show an excess of Zn with a Zn-to-O ratio of around 1.7.

  8. Physico-Chemical and Structural Interpretation of Discrete Derivative Indices on N-Tuples Atoms

    Science.gov (United States)

    Martínez-Santiago, Oscar; Marrero-Ponce, Yovani; Barigye, Stephen J.; Le Thi Thu, Huong; Torres, F. Javier; Zambrano, Cesar H.; Muñiz Olite, Jorge L.; Cruz-Monteagudo, Maykel; Vivas-Reyes, Ricardo; Vázquez Infante, Liliana; Artiles Martínez, Luis M.

    2016-01-01

    This report examines the interpretation of the Graph Derivative Indices (GDIs) from three different perspectives (i.e., in structural, steric and electronic terms). It is found that the individual vertex frequencies may be expressed in terms of the geometrical and electronic reactivity of the atoms and bonds, respectively. On the other hand, it is demonstrated that the GDIs are sensitive to progressive structural modifications in terms of: size, ramifications, electronic richness, conjugation effects and molecular symmetry. Moreover, it is observed that the GDIs quantify the interaction capacity among molecules and codify information on the activation entropy. A structure property relationship study reveals that there exists a direct correspondence between the individual frequencies of atoms and Hückel’s Free Valence, as well as between the atomic GDIs and the chemical shift in NMR, which collectively validates the theory that these indices codify steric and electronic information of the atoms in a molecule. Taking in consideration the regularity and coherence found in experiments performed with the GDIs, it is possible to say that GDIs possess plausible interpretation in structural and physicochemical terms. PMID:27240357

  9. Chemical Structure-Related Drug-Like Criteria of Global Approved Drugs.

    Science.gov (United States)

    Mao, Fei; Ni, Wei; Xu, Xiang; Wang, Hui; Wang, Jing; Ji, Min; Li, Jian

    2016-01-12

    The chemical structure of a drug determines its physicochemical properties, further determines its ADME/Tox properties, and ultimately affects its pharmacological activity. Medicinal chemists can regulate the pharmacological activity of drug molecules by modifying their structure. Ring systems and functional groups are important components of a drug. The proportion of non-hydrocarbon atoms among non-hydrogen atoms reflects the heavy atoms proportion of a drug. The three factors have considerable potential for the assessment of the drug-like properties of organic molecules. However, to the best of our knowledge, there have been no studies to systematically analyze the simultaneous effects of the number of aromatic and non-aromatic rings, the number of some special functional groups and the proportion of heavy atoms on the drug-like properties of an organic molecule. To this end, the numbers of aromatic and non-aromatic rings, the numbers of some special functional groups and the heavy atoms proportion of 6891 global approved small drugs have been comprehensively analyzed. We first uncovered three important structure-related criteria closely related to drug-likeness, namely: (1) the best numbers of aromatic and non-aromatic rings are 2 and 1, respectively; (2) the best functional groups of candidate drugs are usually -OH, -COOR and -COOH in turn, but not -CONHOH, -SH, -CHO and -SO3H. In addition, the -F functional group is beneficial to CNS drugs, and -NH2 functional group is beneficial to anti-infective drugs and anti-cancer drugs; (3) the best R value intervals of candidate drugs are in the range of 0.05-0.50 (preferably 0.10-0.35), and R value of the candidate CNS drugs should be as small as possible in this interval. We envision that the three chemical structure-related criteria may be applicable in a prospective manner for the identification of novel candidate drugs and will provide a theoretical foundation for designing new chemical entities with good drug

  10. Immunobiological properties of sesquiterpene lactones obtained by chemically transformed structural modifications of trilobolide.

    Science.gov (United States)

    Harmatha, Juraj; Vokáč, Karel; Buděšínský, Miloš; Zídek, Zdeněk; Kmoníčková, Eva

    2015-12-01

    Our previous research on immunostimulatory properties of trilobolide and its structurally related natural analogues isolated from Laser trilobum (L.) Borkh., encouraged us to investigate structurally related guaianolides belonging to a specific group of sesquiterpene lactones with characteristic glycol moiety attached to the lactone ring. Ever increasing attention has been paid to certain guaianolides such as thapsigargin and trilobolide for their promising anti-inflammatory, anticancer, anti-infectious and SERCA inhibitory activities. However, due to their alkylation capabilities, they might be cytotoxic. Search for compounds with preserved immunobiological properties and decreased cytotoxicity led us to transform some of their structural features, particularly those related to their side chain functionality. For this reason, we prepared a series of over 20 various deacylated, acyl modified, or relactonized derivatives of trilobolide. The immunobiological effects were screened in vitro using the rat peritoneal cells primed with lipopolysaccharide. Secretion of interferon-γ (IFN-γ), interleukins (IL) IL-1β, IL-6 and tumour necrosis factor-α (TNF-α) were determined by ELISA, and nitric oxide (NO) production by Griess reagent. Relation between the molecular structure and immunobiological activity was investigated. Acetylation at 7-OH and 11-OH positions of the lactone ring, or acyl modification of the guaianolide functionalities (including relactonization) of trilobolide, led to inability to stimulate secretion of cytokines and production of NO. Interestingly, minor structural changes achieved by catalytic hydrogenation or hydrogenolysis retained the original immunoactivity of trilobolide. It can be concluded that several new chemically transformed sesquiterpene lactones resembling the immunobiological properties of trilobolide or thapsigargin were prepared and identified. The implication of the lactone vicinal diol (glycol) moiety, combined with other structure

  11. Gas separation performance of 6FDA-based polyimides with different chemical structures

    KAUST Repository

    Qiu, Wulin

    2013-10-01

    This work reports the gas separation performance of several 6FDA-based polyimides with different chemical structures, to correlate chemical structure with gas transport properties with a special focus on CO2 and CH 4 transport and plasticization stability of the polyimides membranes relevant to natural gas purification. The consideration of the other gases (He, O2 and N2) provided additional insights regarding effects of backbone structure on detailed penetrant properties. The polyimides studied include 6FDA-DAM, 6FDA-mPDA, 6FDA-DABA, 6FDA-DAM:DABA (3:2), 6FDA-DAM:mPDA (3:2) and 6FDA-mPDA:DABA (3:2). Both pure and binary gas permeation were investigated. The packing density, which is tunable by adjusting monomer type and composition of the various samples, correlated with transport permeability and selectivity. The separation performance of the polyimides for various gas pairs were also plotted for comparison to the upper bound curves, and it was found that this family of materials shows attractive performance. The CO 2 plasticization responses for the un-cross-linked polyimides showed good plasticization resistance to CO2/CH4 mixed gas with 10% CO2; however, only the cross-linked polyimides showed good plasticization resistance under aggressive gas feed conditions (CO 2/CH4 mixed gas with 50% CO2 or pure CO 2). For future work, asymmetric hollow fibers and carbon molecular sieve membranes based on the most attractive members of the family will be considered. © 2013 Elsevier Ltd. All rights reserved.

  12. X-ray photoelectron spectra structure and chemical bonding in AmO2

    Directory of Open Access Journals (Sweden)

    Teterin Yury A.

    2015-01-01

    Full Text Available Quantitative analysis was done of the X-ray photoelectron spectra structure in the binding energy range of 0 eV to ~35 eV for americium dioxide (AmO2 valence electrons. The binding energies and structure of the core electronic shells (~35 eV-1250 eV, as well as the relativistic discrete variation calculation results for the Am63O216 and AmO8 (D4h cluster reflecting Am close environment in AmO2 were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the effects of formation of the outer (0-~15 eV binding energy and the inner (~15 eV-~35 eV binding energy valence molecular orbitals. The filled Am 5f electronic states were shown to form in the AmO2 valence band. The Am 6p electrons participate in formation of both the inner and the outer valence molecular orbitals (bands. The filled Am 6p3/2 and the O 2s electronic shells were found to make the largest contributions to the formation of the inner valence molecular orbitals. Contributions of electrons from different molecular orbitals to the chemical bond in the AmO8 cluster were evaluated. Composition and sequence order of molecular orbitals in the binding energy range 0-~35 eV in AmO2 were established. The experimental and theoretical data allowed a quantitative scheme of molecular orbitals for AmO2, which is fundamental for both understanding the chemical bond nature in americium dioxide and the interpretation of other X-ray spectra of AmO2.

  13. A broad chemical and structural characterization of the damaged region of carbon implanted alumina

    International Nuclear Information System (INIS)

    As candidate materials for future thermonuclear fusion reactors, isolating ceramics will be submitted to high energy gamma and neutron radiation fluxes together with an intense particle flux. Amorphization cannot be tolerated in ceramics for fusion applications, due to the associated volume change and the deterioration of mechanical properties. Therefore, a comprehensive study was carried out to examine the effects of carbon beam irradiation on polycrystalline aluminium oxide (Al2O3), a ceramic component of some diagnostic and plasma heating systems. Complementary techniques have allowed a complete chemical and structural surface analysis of the implanted alumina. Implantation with 75 keV, mono-energetic carbon ions at doses of 1 x 1017 and 5 x 1017 ions/cm2 was performed on polished and thermally treated ceramic discs. The alumina targets were kept below 120 deg. C. The structural modifications induced during ion irradiation were studied by the GXRD and TEM techniques. Under these conditions, alumina is readily amorphized by carbon ions, the thickness of the ion-beam induced disordered area increasing with the ion dose. Matrix elements and ion implanted profiles were followed as a function of depth by using ToF-SIMS, indicating the maximum concentration of implanted ions to be in the deeper half of the amorphous region. Ion distribution and chemical modifications caused in the Al2O3 substrate by carbon irradiation were corroborated with XPS. The amount of oxygen in the vicinity of the implanted alumina surface was reduced, suggesting that this element was selectively sputtered during carbon irradiation. The intensity of those peaks referring to Al-O bonds diminishes, while contributions of reduced aluminium and metal carbides are found at the maximum of the carbon distribution. TEM observations on low temperature thermally annealed specimens indicate partial recovery of the initial crystalline structure.

  14. A broad chemical and structural characterization of the damaged region of carbon implanted alumina

    Science.gov (United States)

    González, M.; Román, R.; Maffiotte, C.; González-Casablanca, J.; Perez, R.; Hole, D.

    2009-05-01

    As candidate materials for future thermonuclear fusion reactors, isolating ceramics will be submitted to high energy gamma and neutron radiation fluxes together with an intense particle flux. Amorphization cannot be tolerated in ceramics for fusion applications, due to the associated volume change and the deterioration of mechanical properties. Therefore, a comprehensive study was carried out to examine the effects of carbon beam irradiation on polycrystalline aluminium oxide (Al2O3), a ceramic component of some diagnostic and plasma heating systems. Complementary techniques have allowed a complete chemical and structural surface analysis of the implanted alumina. Implantation with 75 keV, mono-energetic carbon ions at doses of 1 × 1017 and 5 × 1017 ions/cm2 was performed on polished and thermally treated ceramic discs. The alumina targets were kept below 120 °C. The structural modifications induced during ion irradiation were studied by the GXRD and TEM techniques. Under these conditions, alumina is readily amorphized by carbon ions, the thickness of the ion-beam induced disordered area increasing with the ion dose. Matrix elements and ion implanted profiles were followed as a function of depth by using ToF-SIMS, indicating the maximum concentration of implanted ions to be in the deeper half of the amorphous region. Ion distribution and chemical modifications caused in the Al2O3 substrate by carbon irradiation were corroborated with XPS. The amount of oxygen in the vicinity of the implanted alumina surface was reduced, suggesting that this element was selectively sputtered during carbon irradiation. The intensity of those peaks referring to Al-O bonds diminishes, while contributions of reduced aluminium and metal carbides are found at the maximum of the carbon distribution. TEM observations on low temperature thermally annealed specimens indicate partial recovery of the initial crystalline structure.

  15. Modal structure of chemical mass size distribution in the high Arctic aerosol

    Science.gov (United States)

    Hillamo, Risto; Kerminen, Veli-Matti; Aurela, Minna; MäKelä, Timo; Maenhaut, Willy; Leek, Caroline

    2001-11-01

    Chemical mass size distributions of aerosol particles were measured in the remote marine boundary layer over the central Arctic Ocean as part of the Atmospheric Research Program on the Arctic Ocean Expedition 1996 (AOE-96). An inertial impaction method was used to classify aerosol particles into different size classes for subsequent chemical analysis. The particle chemical composition was determined by ion chromatography and by the particle-induced X-ray emission technique. Continuous particle size spectra were extracted from the raw data using a data inversion method. Clear and varying modal structures for aerosols consisting of primary sea-salt particles or of secondary particles related to dimethyl sulfide emissions were found. Concentration levels of all modes decreased rapidly when the distance from open sea increased. In the submicrometer size range the major ions found by ion chromatography were sulfate, methane sulfonate, and ammonium. They had most of the time a clear Aitken mode and one or two accumulation modes, with aerodynamic mass median diameters around 0.1 μm, 0.3 μm, and between 0.5-1.0 μm, respectively. The overall submicron size distributions of these three ions were quite similar, suggesting that they were internally mixed over most of this size range. The corresponding modal structure was consistent with the mass size distributions derived from the particle number size distributions measured with a differential mobility particle sizer. The Aitken to accumulation mode mass ratio for nss-sulfate and MSA was substantially higher during clear skies than during cloudy periods. Primary sea-salt particles formed a mode with an aerodynamic mass median diameter around 2 μm. In general, the resulting continuous mass size distributions displayed a clear modal structure consistent with our understanding of the two known major source mechanisms. One is the sea-salt aerosol emerging from seawater by bubble bursting. The other is related to

  16. Valence XPS structure and chemical bond in Cs2UO2Cl4

    Directory of Open Access Journals (Sweden)

    Teterin Yury A.

    2016-01-01

    Full Text Available Quantitative analysis was done of the valence electrons X-ray photoelectron spectra structure in the binding energy (BE range of 0 eV to ~35 eV for crystalline dicaesium tetrachloro-dioxouranium (VI (Cs2UO2Cl4. This compound contains the uranyl group UO2. The BE and structure of the core electronic shells (~35 eV-1250 eV, as well as the relativistic discrete variation calculation results for the UO2Cl4(D4h cluster reflecting U close environment in Cs2UO2Cl4 were taken into account. The experimental data show that many-body effects due to the presence of cesium and chlorine contribute to the outer valence (0-~15 eV BE spectral structure much less than to the inner valence (~15 eV-~35 eV BE one. The filled U5f electronic states were theoretically calculated and experimentally confirmed to be present in the valence band of Cs2UO2Cl4. It corroborates the suggestion on the direct participation of the U5f electrons in the chemical bond. Electrons of the U6p atomic orbitals participate in formation of both the inner (IVMO and the outer (OVMO valence molecular orbitals (bands. The filled U6p and the O2s, Cl3s electronic shells were found to make the largest contributions to the IVMO formation. The molecular orbitals composition and the sequence order in the binding energy range 0 eV-~35 eV in the UO2Cl4 cluster were established. The experimental and theoretical data allowed a quantitative molecular orbitals scheme for the UO2Cl4 cluster in the BE range 0-~35 eV, which is fundamental for both understanding the chemical bond nature in Cs2UO2Cl4 and the interpretation of other X-ray spectra of Cs2UO2Cl4. The contributions to the chemical binding for the UO2Cl4 cluster were evaluated to be: the OVMO contribution - 76%, and the IVMO contribution - 24 %.

  17. Filamentary structure in chemical tracer distributions near the subtropical jet following a wave breaking event

    Directory of Open Access Journals (Sweden)

    J. Ungermann

    2013-10-01

    Full Text Available This paper presents a set of observations and analyses of trace gas cross sections in the extratropical upper troposphere/lower stratosphere (UTLS. The spatially highly resolved (≈0.5 km vertically and 12.5 km horizontally cross sections of ozone (O3, nitric acid (HNO3, and peroxyacetyl nitrate (PAN, retrieved from the measurements of the CRISTA-NF infrared limb sounder flown on the Russian M55-Geophysica, revealed intricate layer structures in the region of the subtropical tropopause break. The chemical structure in this region shows an intertwined stratosphere and troposphere. The observed filaments in all discussed trace gases are of a spatial scale of less than 0.8 km vertically and about 200 km horizontally across the jet stream. Backward trajectory calculations confirm that the observed filaments are the result of a breaking Rossby wave in the preceding days. An analysis of the trace gas relationships between PAN and O3 identifies four distinct groups of air mass: polluted subtropical tropospheric air, clean tropical upper-tropospheric air, the lowermost stratospheric air, and air from the deep stratosphere. The tracer relationships further allow the identification of tropospheric, stratospheric, and the transitional air mass made of a mixture of UT and LS air. Mapping of these air mass types onto the geo-spatial location in the cross sections reveals a highly structured extratropical transition layer (ExTL. Finally, the ratio between the measured reactive nitrogen species (HNO3 + PAN + ClONO2 and O3 is analysed to estimate the influence of tropospheric pollution on the extratropical UTLS. In combination, these diagnostics provide the first example of a multi-species two-dimensional picture of the inhomogeneous distribution of chemical species within the UTLS region. Since Rossby wave breaking occurs frequently in the region of the tropopause break, these observed fine-scale filaments are likely ubiquitous in the region. The

  18. Chemical cross-linkers for protein structure studies by mass spectrometry.

    Science.gov (United States)

    Paramelle, David; Miralles, Guillaume; Subra, Gilles; Martinez, Jean

    2013-02-01

    The cross-linking approach combined with MS for protein structure determination is one of the most striking examples of multidisciplinary success. Indeed, it has become clear that the bottleneck of the method was the detection and the identification of low-abundance cross-linked peptides in complex mixtures. Sample treatment or chromatography separation partially addresses these issues. However, the main problem comes from over-represented unmodified peptides, which do not yield any structural information. A real breakthrough was provided by high mass accuracy measurement, because of the outstanding technical developments in MS. This improvement greatly simplified the identification of cross-linked peptides, reducing the possible combinations matching with an observed m/z value. In addition, the huge amount of data collected has to be processed with dedicated software whose role is to propose distance constraints or ideally a structural model of the protein. In addition to instrumentation and algorithms efficiency, significant efforts have been made to design new cross-linkers matching all the requirements in terms of reactivity and selectivity but also displaying probes or reactive systems facilitating the isolation, the detection of cross-links, or the interpretation of MS data. These chemical features are reviewed and commented on in the light of the more recent strategies. PMID:23255214

  19. Structural, energetic and electrical properties of boron nitride nanotubes interacting with DMMP chemical agent

    International Nuclear Information System (INIS)

    Highlights: • ab initio DFT calculations were used for interaction of DMMP with BNNTs. • Full structural optimization was performed for several possible active sites. • Electronic structure of the energetically favorable complexes was analyzed. • The stability of the most stable complex was evaluated at ambient condition. • First-principles calculations showed that DMMP is strongly bound to the small diameter BNNTs. - Abstract: The adsorption of DMMP as an intoxicating chemical warfare agent onto the boron nitride nanotube has been investigated by using density functional theory calculations. Several active sites were considered for both interacting systems and full structural optimization was performed to accurately find the energetically favorable state. It is found that DMMP molecule prefers to be adsorbed strongly on the top site above the B atom of a (5, 0) BNNT with a binding energy of about −103.24 kJ mol−1 and an O–B binding distance of 1.641 Å. We have performed a comparative investigation of BNNTs with different diameters and the results indicate that the DMMP adsorption ability for the side wall of the tubes significantly decreases for higher diameters BNNTs. Furthermore, the adsorption properties of DMMP molecule onto the BNNT have been investigated using the ab initio MD simulation at room temperature. Our result showed that BNNTs facilitates the DMMP detection at ambient conditions for practical applications

  20. Structure and photoluminescence of molybdenum selenide nanomaterials grown by hot filament chemical vapor deposition

    Energy Technology Data Exchange (ETDEWEB)

    Wang, B.B. [College of Chemistry and Chemical Engineering, Chongqing University of Technology, 69 Hongguang Rd, Lijiatuo, Banan District, Chongqing 400054 (China); Plasma Nanoscience Laboratories, Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organization, P. O. Box 218, Lindfield, NSW 2070 (Australia); Zhu, M.K. [College of Materials Science and Engineering, Beijing University of Technology, Beijing 100124 (China); Ostrikov, K., E-mail: kostya.ostrikov@qut.edu.au [Plasma Nanoscience Laboratories, Manufacturing Flagship, Commonwealth Scientific and Industrial Research Organization, P. O. Box 218, Lindfield, NSW 2070 (Australia); Institute for Future Environments, School of Chemistry, Physics and Mechanical Engineering, Queensland University of Technology, Brisbane, QLD 4000 (Australia); Plasma Nanoscience, School of Physics, The University of Sydney, Sydney, NSW 2006 (Australia); Shao, R.W.; Zheng, K. [Institute of Microstructure and Properties of Advanced Materials, Beijing University of Technology, Beijing 100124 (China)

    2015-10-25

    Molybdenum selenide nanomaterials with different structures are synthesized on silicon substrates coated with gold films by hot filament chemical vapor deposition (HFCVD) in nitrogen environment, where molybdenum trioxide and selenium powders are used as source materials. The structure and composition of the synthesized molybdenum selenide nanomaterials are studied using field emission scanning electron microscopy, transmission electron microscopy, micro-Raman spectroscopy and X-ray photoelectron spectroscopy. The results indicate that the structures of molybdenum selenide change from nanoflakes to nanoparticles with the increase of content of molybdenum trioxide precursor. The photoluminescence (PL) excitation using the 325 nm line of He–Cd laser as the excitation source generates green light with the wavelength of about 512–516 nm. The formation of molybdenum selenide nanomaterials is determined by the decomposition rates of molybdenum trioxide in HFCVD. The possible factors that affect the generation of green PL bands are analyzed. These outcomes of this work enrich our knowledge on the synthesis of transition metal dichalcogenides and contribute to the development of applications of these materials in optoelectronic devices. - Highlights: • Molybdenum selenide nanoflakes, nanoparticles and hybrids produced by HFCVD. • Uncommon MoO{sub 3} and Se precursor co-location and mixing and effective MoO{sub 3} decomposition. • Morphology change from nanoflakes to nanoparticles with higher ratio of MoO{sub 3} precursor. • Strong photoluminescence emission of green light with a wavelength of ∼512–516 nm.

  1. Structural, Optical and Electrical Properties of Nanocrystalline Cuprous Oxide Thin Film Deposited By Chemical Method

    Directory of Open Access Journals (Sweden)

    Prakash Bansilal Ahirrao

    2010-06-01

    Full Text Available Cuprous oxide (Cu2O is an interesting p-type semiconductor material used in solar cell applications.  The Modified Chemical Bath Deposition (M-CBD method is suitable for growing thin multilayer structure due to low deposition temperature. This method does not require any sophisticated instrument and substrate need not to be conductive. The nanocrystalline Cu2O thin films were deposited on glass substrates by M-CBD method. The deposited films were characterized by different characterization techniques to study structural, surface morphological, optical and electrical properties. The structural studies show that, the formation of Cu2O thin films with an average crystallite size of 14 nm. Optical studies show a direct band gap 2.48 eV. The room temperature electrical resistivity is of the order of 1.3 kW-cm and activation energy 0.33 eV. The films exhibit p-type electrical conductivity as seen by thermo-emf measurements.

  2. An ab initio quantum chemical investigation of the structure and stability of ozone-water complexes

    Energy Technology Data Exchange (ETDEWEB)

    Kumar, Pradeep [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Sathyamurthy, N., E-mail: nsath@iitk.ac.in [Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur 208016 (India); Indian Institute of Science Education and Research Mohali, Sector 81, SAS Nagar, Manauli 140306 (India)

    2013-03-29

    Highlights: ► Eclipse geometry most stable for the 1:1 ozone-water complex. ► Cyclic structure most stable for the 1:2 complex. ► Shift in the vertical electronic excitation energy of ozone due to hydration. - Abstract: Ab initio quantum chemical calculations have been carried out to investigate the structure and stability of 1:1 and 1:2 ozone-water complexes. All the geometries have been optimized at the CCSD level of theory using aug-cc-pVDZ and aug-cc-pVTZ basis sets. The importance of correlation-consistent basis sets in deciding the nature of critical points on these complexes is emphasized. An analysis based on the dipole moment of the complexes and the charge distribution on atoms follows. The effect of ozone molecule on the structure and properties of water dimer is also investigated. Values of the vertical electronic excitation energy and the corresponding transition dipole moment have been calculated for the ozone-water complexes using the multi-reference-configuration-interaction method and the aug-cc-pVTZ basis set. The calculated shift in vibrational frequencies due to complex formation is compared with the earlier reported experimental and theoretical values.

  3. EDCs DataBank: 3D-Structure database of endocrine disrupting chemicals.

    Science.gov (United States)

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

    Endocrine disrupting chemicals (EDCs) are a group of compounds that affect the endocrine system, frequently found in everyday products and epidemiologically associated with several diseases. The purpose of this work was to develop EDCs DataBank, the only database of EDCs with three-dimensional structures. This database was built on MySQL using the EU list of potential endocrine disruptors and TEDX list. It contains the three-dimensional structures available on PubChem, as well as a wide variety of information from different databases and text mining tools, useful for almost any kind of research regarding EDCs. The web platform was developed employing HTML, CSS and PHP languages, with dynamic contents in a graphic environment, facilitating information analysis. Currently EDCs DataBank has 615 molecules, including pesticides, natural and industrial products, cosmetics, drugs and food additives, among other low molecular weight xenobiotics. Therefore, this database can be used to study the toxicological effects of these molecules, or to develop pharmaceuticals targeting hormone receptors, through docking studies, high-throughput virtual screening and ligand-protein interaction analysis. EDCs DataBank is totally user-friendly and the 3D-structures of the molecules can be downloaded in several formats. This database is freely available at http://edcs.unicartagena.edu.co.

  4. Chemical structure and intra-molecular effects on NMR-NQR tensors of harmine and harmaline alkaloids

    Science.gov (United States)

    Ahmadinejad, Neda; Tahan, Arezoo; Talebi Tari, Mostafa

    2016-02-01

    Density functional theory (DFT) methods were used to analyze the effects of molecular structure and ring currents on the NMR chemical shielding tensors and NQR frequencies of harmine and harmaline alkaloids in the gas phase. The results demonstrated that NMR tensors and NQR frequencies of 15N nuclei in these compounds depend on chemical environment and resonance interactions. Hence, their values are obviously different in the mentioned structures. The interpretation of natural bond orbital (NBO) data suggests that in harmine structure, the lone pair participation of N9 in π-system electron clouds causes to development of aromaticity nature in pyrrole ring. However, the chemical shielding around N9 atom in harmine structure is higher than in harmaline, while in harmaline structure, lone pair participation of N2 in π-system electron clouds causes to development of aromaticity nature in pyridine ring. Hence, chemical shielding around N2 atom in harmaline structure is higher than in harmine. It can be deduced that by increasing lone pair electrons contribution of nitrogen atoms in ring resonance interactions and aromaticity development, the values of NMR chemical shielding around them increase, while χ and q zz values of these nuclei decrease.

  5. Regioisomers of octanoic acid-containing structured triacylglycerols analyzed by tandem mass spectrometry using ammonia negative ion chemical ionization

    DEFF Research Database (Denmark)

    Kurvinen, J.P.; Mu, Huiling; Kallio, H.;

    2001-01-01

    Tandem mass spectrometry based on ammonia negative ion chemical ionization and sample introduction via direct exposure probe was applied to analysis of regioisomeric structures of octanoic acid containing structured triacylglycerols (TAG) of type MML, MLM, MLL, and LML (M, medium-chain fatty acid...

  6. X-rays in protoplanetary disks : Their impact on the thermal and chemical structure, a grid of models

    NARCIS (Netherlands)

    Aresu, G.; Kamp, I.; Meijerink, R.; Woitke, P.; Thi, W. F.; Spaans, M.

    2011-01-01

    X-rays impact protoplanetary disks hydrostatic, thermal and chemical structure. The range of efficiency of X-rays is explored using a grid modelling approach: different parameters affects the structure of the disk, this determines different contribution of the X-ray radiation to the chemistry and th

  7. Nanoscale carbon materials from hydrocarbons pyrolysis: Structure, chemical behavior, utilisation for non-aqueous supercapacitors

    Energy Technology Data Exchange (ETDEWEB)

    Savilov, Serguei V., E-mail: savilov@chem.msu.ru [Lomonosov Moscow State University, Chemistry Department (Russian Federation); Strokova, Natalia E.; Ivanov, Anton S.; Arkhipova, Ekaterina A. [Lomonosov Moscow State University, Chemistry Department (Russian Federation); Desyatov, Andrey V. [D. Mendeleyev University of Chemical Technology of Russia (Russian Federation); Hui, Xia [Herbert Gleiter Institute of Nanoscience, School of Materials Science and Engineering, Nanjing University of Science and Technology (China); Aldoshin, Serguei M. [Lomonosov Moscow State University, Faculty of Fundamental Physical and Chemical Engineering (Russian Federation); Lunin, Valery V. [Lomonosov Moscow State University, Chemistry Department (Russian Federation)

    2015-09-15

    Highlights: • N-doped and regular carbon nanomaterials were obtained by pyrolitic technique. • Dynamic vapor sorption of different solvents reveals smaller S{sub BET} values. • Steric hindrance and specific chemical interactions are the reasons for this. • Nitrogen doping leads to raise of capacitance and coulombic efficiency with non-aqueous N-containing electrolyte. - Abstract: This work systematically studies adsorption properties of carbon nanomaterials that are synthesized through hydrocarbons that is a powerful technique to fabricate different kinds of carbon materials, e.g., nanotubes, nanoshells, onions, including nitrogen substituted. The adsorption properties of the as-synthesized carbons are achieved by low temperature nitrogen adsorption and organic vapors sorption. Heptane, acetonitrile, water, ethanol, benzene and 1-methylimidazole, which are of great importance for development of supercapacitors, are used as substrates. It is discovered that while nitrogen adsorption reveals a high specific surface area, this parameter for most of organic compounds is rather small depending not only on the size of its molecule but also on chemical interactions for a pair adsorbent–adsorbate. The experimental values of heat of adsorption for carbon and N-substituted structures, when Coulomb cross-coupling of nitrogen atoms in adsorbent and adsorbate takes place, confirms this supposition.

  8. The Influence of the Chemical Structures of Chitosan and Acid Dye on the Adsorption Process

    Directory of Open Access Journals (Sweden)

    Hayet Ben Ali

    2012-01-01

    Full Text Available The objective of this paper is the study of the influence of the chemical structures of adsorbent and adsorbate on the adsorption process. By using of crab shell chitosan (CC and deep-pink shrimp chitosan (CP for removal of acid 183 and AR114 from aqueous solutions, it is shown that CP, which corresponds to the highest molecular weight, is the most efficient adsorbent material. In addition, the best extent of decolorization is obtained for AR 183 that is the smallest molecule. Langmuir model represents the best fit of the experimental data, indicating monolayer coverage of chitosan outer surface. Pseudo-second order kinetic model describes accurately the adsorption processes, suggesting chemical rate limiting steps. The positive values of the enthalpy changes indicated endothermic attachment of dyes to the biomaterials. CP/AR183 system corresponds to the most energetically favorable phenomenon. Besides, desorption of AR from chitosan was found to be very low in acidic aqueous medium for all couples.

  9. Chemical, physical, structural and morphological characterization of the electric arc furnace dust.

    Science.gov (United States)

    Machado, Janaína G M S; Brehm, Feliciane Andrade; Moraes, Carlos Alberto Mendes; Santos, Carlos Alberto Dos; Vilela, Antônio Cezar Faria; Cunha, João Batista Marimon da

    2006-08-25

    Electric arc furnace dust (EAFD) is a hazardous industrial waste generated in the collection of particulate material during steelmaking process via electric arc furnace. Important elements to the industry such as, Fe and Zn are the main ones in EAFD. Due to their presence, it becomes very important to know how these elements are combined before studying new technologies for its processing. The aim of this work was to carry out a chemical, physical, structural and morphological characterization of the EAFD. The investigation was carried out by using granulometry analysis, chemical analysis, scanning electron microscopy (SEM), energy dispersive spectroscopy via SEM (EDS), X-ray mapping analysis via SEM, X-ray diffraction (XRD) and Mössbauer spectroscopy. By XRD the following phases were detected: ZnFe(2)O(4), Fe(3)O(4), MgFe(2)O(4), FeCr(2)O (4), Ca(0.15)Fe(2.85)O(4), MgO, Mn(3)O(4), SiO(2) and ZnO. On the other hand, the phases detected by Mössbauer spectroscopy were: ZnFe(2)O(4), Fe(3)O(4), Ca(0.15)Fe(2.85)O(4) and FeCr(2)O(4). Magnesium ferrite (MgFe(2)O(4)), observed in the XRD pattern as overlapped peaks, was not identified in the Mössbauer spectroscopy analysis.

  10. Research Update: Mechanical properties of metal-organic frameworks – Influence of structure and chemical bonding

    Directory of Open Access Journals (Sweden)

    Wei Li

    2014-12-01

    Full Text Available Metal-organic frameworks (MOFs, a young family of functional materials, have been attracting considerable attention from the chemistry, materials science, and physics communities. In the light of their potential applications in industry and technology, the fundamental mechanical properties of MOFs, which are of critical importance for manufacturing, processing, and performance, need to be addressed and understood. It has been widely accepted that the framework topology, which describes the overall connectivity pattern of the MOF building units, is of vital importance for the mechanical properties. However, recent advances in the area of MOF mechanics reveal that chemistry plays a major role as well. From the viewpoint of materials science, a deep understanding of the influence of chemical effects on MOF mechanics is not only highly desirable for the development of novel functional materials with targeted mechanical response, but also for a better understanding of important properties such as structural flexibility and framework breathing. The present work discusses the intrinsic connection between chemical effects and the mechanical behavior of MOFs through a number of prototypical examples.

  11. X-ray chemical imaging and the electronic structure of a single nanoplatelet Ni/graphene composite.

    Science.gov (United States)

    Zhou, Chunyu; Wang, Jian; Szpunar, Jerzy A

    2014-03-01

    Chemical imaging and quantitative analysis of a single graphene nanoplatelet grown with Ni nanoparticles (Ni/graphene) has been performed by scanning transmission X-ray microscopy (STXM). Local electronic and chemical structure of Ni/graphene has been investigated by spatially resolved C, O K-edges and Ni L-edge X-ray absorption near edge structure (XANES) spectroscopy, revealing the covalent anchoring of Ni(0) on graphene. This study facilitates the understanding of the structure modification of host materials for hydrogen storage and offers a better understanding of interaction between Ni particles and graphene.

  12. Quantum chemical calculation of the equilibrium structures of small metal atom clusters

    Science.gov (United States)

    Kahn, L. R.

    1981-01-01

    A decomposition of the molecular energy is presented that is motivated by the atom superposition and electron delocalization physical model of chemical binding. The energy appears in physically transparent form consisting of a classical electrostatic interaction, a zero order two electron exchange interaction, a relaxation energy, and the atomic energies. Detailed formulae are derived in zero and first order of approximation. The formulation extends beyond first order to any chosen level of approximation leading, in principle, to the exact energy. The structure of this energy decomposition lends itself to the fullest utilization of the solutions to the atomic sub problems to simplify the calculation of the molecular energy. If nonlinear relaxation effects remain minor, the molecular energy calculation requires at most the calculation of two center, two electron integrals. This scheme thus affords the prospects of substantially reducing the computational effort required for the calculation of molecular energies.

  13. The chemical and magnetic structures of holmium-yttrium and holmium-lutetium superlattices

    DEFF Research Database (Denmark)

    McMorrow, D.F.; Jehan, D.A.; Swaddling, P.P.;

    1993-01-01

    We present the results of a study of the chemical and magnetic structures of Ho/Y and Ho/Lu superlattices, all grown by molecular beam epitaxy. By combining the results of high-resolution X-ray diffraction with detailed modelling we show that the superlattices have high crystallographic integrity...... to depend on n(Ho), the number of atomic planes in the Ho block. If n(Ho) > 20, then the Ho3+ Moments form a basal-plane helix down to the lowest temperatures. For n(Ho) less-than-or-equal-to 20, the Ho3+ moments undergo a phase transition at low temperatures from a helix to a state where...

  14. Electronic Structures and Chemical Bonds of Cobaltite and Ni-Doped

    Institute of Scientific and Technical Information of China (English)

    MIN Xinmin; XING Xueling; ZHU Lei

    2005-01-01

    The relation among electronic structure, chemical bond and thermoelectric property of Ca3 Co2 O6 and Ni-doped was studied by density function theory and discrete variation method(DFT-DVM). The results indicate that the highest valence band (HVB) and the lowest conduction band(LCB) are mainly attributed to Co3 d, Ni3 d and O2 p atomic orbitals. The property of a semiconductor is shown from the gap between HVB and LCB. The gap of Ni-doped one is less than that of Ca3 Co2 O6. The non-metal bond or ceramic characteristic of Ni-doped one is weaker than that of Ca3 Co2 O6, but the metal characteristics of Ni-doped one are stronger than those of Ca3 Co2O6. The thermoelectric property should be improved by adding Ni element into the system of Ca3 Co2 O6.

  15. ZnO-coated SMS structure interrogated by a fiber ring laser for chemical sensing

    Science.gov (United States)

    Wen, X. Y.; Huang, J.; Xiao, H.; Yang, M. H.

    2014-11-01

    A zinc oxide (ZnO)-coated single mode-multimode-single mode fiber (SMS) structure interrogated by a fiber ring laser has been developed as a chemical sensor. Response to relative humidity (RH) and ethanol volatilization was evaluated by tracking the wavelength shifts of the output laser line in different moisture environments and ethanol solutions, respectively. For humidity sensing a linear response with a measurement range of 4-96% RH, and a sensitivity of 0.06 nm per %RH were obtained. As for ethanol volatilization sensing obvious wavelength blue shift was observed for the sensor immersed in 50% and 62% ethanol solution, while no variation could be detected in pure ethanol solution (purity larger than 97%). With the advantages of low cost, ease of fabrication and sensitive response, ZnO-coated SMS interrogated with a fiber ring laser was demonstrated to be an effective sensor for humidity and ethanol volatilization sensing.

  16. ZnO-coated SMS structure interrogated by a fiber ring laser for chemical sensing

    International Nuclear Information System (INIS)

    A zinc oxide (ZnO)-coated single mode–multimode–single mode fiber (SMS) structure interrogated by a fiber ring laser has been developed as a chemical sensor. Response to relative humidity (RH) and ethanol volatilization was evaluated by tracking the wavelength shifts of the output laser line in different moisture environments and ethanol solutions, respectively. For humidity sensing a linear response with a measurement range of 4–96% RH, and a sensitivity of 0.06 nm per %RH were obtained. As for ethanol volatilization sensing obvious wavelength blue shift was observed for the sensor immersed in 50% and 62% ethanol solution, while no variation could be detected in pure ethanol solution (purity larger than 97%). With the advantages of low cost, ease of fabrication and sensitive response, ZnO-coated SMS interrogated with a fiber ring laser was demonstrated to be an effective sensor for humidity and ethanol volatilization sensing. (paper)

  17. Raman imaging to study structural and chemical features of the dentin enamel junction

    Science.gov (United States)

    Alebrahim, M. Anwar; Krafft, C.; Popp, J.

    2015-10-01

    The structure and chemical features of the human dentin enamel junction (DEJ) were characterized using Raman spectroscopic imaging. Slices were prepared from 10 German, and 10 Turkish teeth. Raman images were collected at 785 nm excitation and the average Raman spectra were calculated for analysis. Univariate and multivariate spectral analysis were applied for investigation. Raman images were obtained based on the intensity ratios of CH at 1450 cm-1 (matrix) to phosphate at 960 cm-1 (mineral), and carbonate to phosphate (1070/960) ratios. Different algorithms (HCA, K-means cluster and VCA) also used to study the DEJ. The obtained results showed that the width of DEJ is about 5 pm related to univariate method while it varies from 6 to 12 μm based on multivariate spectral technique. Both spectral analyses showed increasing in carbonate content inside the DEJ compared to the dentin, and the amide I (collagen) peak in dentin spectra is higher than DEJ spectra peak.

  18. Chemical structures and hepatoprotective effects of constituents from Cassia auriculata leaves.

    Science.gov (United States)

    Nakamura, Seikou; Xu, Fengming; Ninomiya, Kiyofumi; Nakashima, Souichi; Oda, Yoshimi; Morikawa, Toshio; Muraoka, Osamu; Yoshikawa, Masayuki; Matsuda, Hisashi

    2014-01-01

    An 80% aqueous acetone extract of Cassia auriculata leaves was found to show a protective effect on D-galactosamine-induced cytotoxicity in primary cultured mouse hepatocytes. From the 80% aqueous acetone extract, we isolated a new benzocoumarin glycoside, avaraoside I (1), and a new flavanol dimer, avaraol I (2), together with 29 known constituents. The structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. In addition, three isolated compounds, pseudosemiglabrin (15, 0.0011%), (2S)-7,4'-dihydroxyflavan(4β→8)-catechin (22, 0.00075%), and (2S)-7,4'-dihydroxyflavan(4β→8)-gallocatechin (23, 0.092%), displayed hepatoprotective effects equivalent to that of the hepatoprotective agent, silybin.

  19. Structural analysis of CdS thin films obtained by multiple dips of oscillating chemical bath

    Energy Technology Data Exchange (ETDEWEB)

    Gutierrez Lazos, C.D. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Rosendo, E., E-mail: erosendo@siu.buap.m [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Ortega, M. [Seccion de Electronica del Estado Solido, Centro de Investigacion y de Estudios Avanzados, Av. Instituto Politecnico Nacional 2508, Col. San Pedro Zacatenco, 07360 Mexico, D.F. (Mexico); Oliva, A.I. [Departamento de Fisica Aplicada, Centro de Investigacion y de Estudios Avanzados, Unidad Merida, A.P. 73 Cordemex, 97310 Merida, Yucatan (Mexico); Tapia, O.; Diaz, T.; Juarez, H.; Garcia, G. [Centro de Investigacion en Dispositivos Semiconductores, Universidad Autonoma de Puebla, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico); Rubin, M. [Facultad de Ciencias de la Computacion, 14 Sur y San Claudio, Col. San Manuel, C.P. 72570, Puebla (Mexico)

    2009-11-25

    Highly oriented CdS thin films with thicknesses greater than 1 mum were deposited by multiple dips, using oscillating chemical bath deposition (OCBD) at the bath temperature of 75 deg. C, and deposition time ranging from 15 to 75 min for a single dip. Samples with different thickness were prepared by repeating the deposition process for two and three times. The films deposited by a single dip have the alpha-greenockite structure showing the (0 0 2) as preferred orientation, as indicated by the X-ray diffraction measurements. This notable characteristic is preserved in the samples obtained from two or three dips. The crystallite size for the samples deposited by a single dip depends on the deposition time, because it varied from 23 to 37 nm as the deposition time increased. Nevertheless for samples deposited by two and three dips, the grain size shows no noticeable change, being about 22 nm.

  20. Geometrical and substituent effects in conical intersections: Linking chemical structure and photoreactivity in polyenes

    International Nuclear Information System (INIS)

    The knowledge of the intersection space topography of electronic states is essential for deciphering and predicting photoinduced reactions. Michl and Bonacic-Koutecky developed a two-electron two-orbital model that allowed first systematic studies of the chemical origin of conical intersections in strongly polar systems. We generalize this approach to arbitrary functionalized and unfunctionalized polyene systems. For the extended model, a set of mathematical conditions for the formation of conical intersections are derived. These conditions are translated into geometrical motions and electronic effects, which help to explain and predict the structure and energetics of conical intersections. A three-step strategy for the conceptual search of conical intersections is outlined. Its universal validity is demonstrated using the textbook example cyclohexadiene and its functionalized derivative trifluoromethyl-indolylfulgide, a chromophore studied for possible application as a molecular switch.

  1. Structural, Chemical and Biological Aspects of Antioxidants for Strategies Against Metal and Metalloid Exposure

    Directory of Open Access Journals (Sweden)

    Swaran J. S. Flora

    2009-01-01

    Full Text Available Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties.

  2. Corrosion resistance, composition and structure of RE chemical conversion coating on magnesium alloy

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Golden yellow rare earths chemical conversion coating was obtained on the surface of magnesium alloy by immersing in cerium sulfate solution.The corrosion resistance of RE conversion coating was evaluated using immersion test and potentiodynamic polarization measurements in 3.5%NaCl solution.The morphologies of samples before corrosion and after corrosion were observed by SEM.The structures and compositions of the RE conversion coating were studied by means of XPS.XRD and IR.The results show that,the conversion coating consists of mainly two kinds of element Ce and O,the valences of cerium are+3 and+4.and OH exists in the coating.The anti-corrosion property of magnesium alloy is increased obviously by rare earths conversion coating,Its self-corrosion current density decreases and the coating has self-repairing capability in the corrosion process in 3.5%NaCl solution.

  3. Review of selective accumudation of photosensitizers with different chemical structure in tumor tissue

    Directory of Open Access Journals (Sweden)

    E. A. Machinskaya

    2013-01-01

    Full Text Available The review of available theories explaining mechanisms of photosensitizer selective accumulation in tumor tissue is represented in the article. Variants associated with both targeted delivery of compounds with different chemical structure to tumor and low elimination rate of photosensitizers in the tumor are described. Details of tumor cell up-take of photosensitizer bounded with lipoproteins due to increased expression of low solidity lipoproteins receptors comparing with normal cells; mechanisms of photosensitizer accumulation in tumor tissue due to phagocytosis by macrophages localized in this area; mechanisms of binding of porphyrin-based photosensitizer by collagen fibers, production of which is increased in tumor cells, and other mechanisms are reviewed. Perspectives of practical application of knowledge about mechanisms of selective accumulation for induced increase in selectiveness of photosensitizer accumulation in tumor through targeted delivery of agent to pathological tissues are shown. Analysis of world trends in the search of transport systems for photosensitizers is performed. 

  4. Structural Changes of a Doubly Spin-Labeled Chemically Driven Molecular Shuttle Probed by PELDOR Spectroscopy.

    Science.gov (United States)

    Franchi, Paola; Bleve, Valentina; Mezzina, Elisabetta; Schäfer, Christian; Ragazzon, Giulio; Albertini, Marco; Carbonera, Donatella; Credi, Alberto; Di Valentin, Marilena; Lucarini, Marco

    2016-06-20

    Gaining detailed information on the structural rearrangements associated with stimuli-induced molecular movements is of utmost importance for understanding the operation of molecular machines. Pulsed electron-electron double resonance (PELDOR) was employed to monitor the geometrical changes arising upon chemical switching of a [2]rotaxane that behaves as an acid-base-controlled molecular shuttle. To this aim, the rotaxane was endowed with stable nitroxide radical units in both the ring and axle components. The combination of PELDOR data and molecular dynamic calculations indicates that in the investigated rotaxane, the ring displacement along the axle, caused by the addition of a base, does not alter significantly the distance between the nitroxide labels, but it is accompanied by a profound change in the geometry adopted by the macrocycle. PMID:27123774

  5. Plasma enhanced chemical vapor deposition of iron doped thin dioxide films, their structure and photowetting effect

    Energy Technology Data Exchange (ETDEWEB)

    Sobczyk-Guzenda, A., E-mail: anna.sobczyk-guzenda@p.lodz.pl [Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz (Poland); Owczarek, S.; Szymanowski, H. [Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz (Poland); Wypych-Puszkarz, A. [Department of Molecular Physics, Lodz University of Technology, Zeromskiego 116, 90-924 Lodz (Poland); Volesky, L. [Technical University of Liberec, Institute for Nanomaterials, Advanced Technologies and Innovation, Studentska 1402/2, 461 17 Liberec 1 (Czech Republic); Gazicki-Lipman, M. [Institute of Materials Science and Engineering, Lodz University of Technology, Stefanowskiego 1/15, 90-924 Lodz (Poland)

    2015-08-31

    Radio frequency plasma enhanced chemical vapor deposition (RF PECVD) technique was applied for the purpose of deposition of iron doped titanium dioxide coatings from a gaseous mixture of oxygen with titanium (IV) chloride and iron (0) pentacarbonyl. Glass slides and silicon wafers were used as substrates. The coatings morphology was investigated using scanning electron microscopy (SEM) and atomic force microscopy (AFM). Their elemental and chemical composition was studied with the help of X-ray energy dispersive spectroscopy (EDS) and Fourier transform infrared (FTIR) spectroscopy, respectively, while their phase composition was analyzed with the Raman spectroscopy. For the determination of the film optical properties, ultraviolet (UV–Vis) spectroscopy techniques were used. Iron content in the range of 0.07 to 11.5 at.% was found in the coatings. FTIR studies showed that iron was built-in in the structure of TiO{sub 2} matrix. Surface roughness, assessed with the SEM and AFM techniques, increases with an increasing content of this element. Trace amounts of iron resulted in a lowering of an absorption threshold of the films and their optical gap, but the tendency was reversed for high concentrations of that element. The effect of iron doping on UV photowettability of the films was also studied and, for coatings containing up to 5% of iron, it was stronger than that exhibited by pure TiO{sub 2}. - Highlights: • Iron doped TiO{sub 2} films were deposited with the PECVD method. • Differences of surface morphology of the films with different iron content were shown. • Depending on the iron content, the film structure is either amorphous or crystalline. • A parabolic character of the optical gap dependence on the concentration of iron was observed. • Up to a concentration of 5% of iron, doped TiO{sub 2} films exhibit a super-hydrophilic effect.

  6. Theoretical study of the electronic structure of f-element complexes by quantum chemical methods

    International Nuclear Information System (INIS)

    This thesis is related to comparative studies of the chemical properties of molecular complexes containing lanthanide or actinide trivalent cations, in the context of the nuclear waste disposal. More precisely, our aim was a quantum chemical analysis of the metal-ligand bonding in such species. Various theoretical approaches were compared, for the inclusion of correlation (density functional theory, multiconfigurational methods) and of relativistic effects (relativistic scalar and 2-component Hamiltonians, relativistic pseudopotentials). The performance of these methods were checked by comparing computed structural properties to published experimental data, on small model systems: lanthanide and actinide tri-halides and on X3M-L species (X=F, Cl; M=La, Nd, U; L = NH3, acetonitrile, CO). We have thus shown the good performance of density functionals combined with a quasi-relativistic method, as well as of gradient-corrected functionals associated with relativistic pseudopotentials. In contrast, functionals including some part of exact exchange are less reliable to reproduce experimental trends, and we have given a possible explanation for this result . Then, a detailed analysis of the bonding has allowed us to interpret the discrepancies observed in the structural properties of uranium and lanthanides complexes, based on a covalent contribution to the bonding, in the case of uranium(III), which does not exist in the lanthanide(III) homologues. Finally, we have examined more sizeable systems, closer to experimental species, to analyse the influence of the coordination number, of the counter-ions and of the oxidation state of uranium, on the metal-ligand bonding. (author)

  7. Dependence of SERS enhancement on the chemical composition and structure of Ag/Au hybrid nanoparticles.

    Science.gov (United States)

    Chaffin, Elise; O'Connor, Ryan T; Barr, James; Huang, Xiaohua; Wang, Yongmei

    2016-08-01

    Noble metal nanoparticles (NPs) such as silver (Ag) and gold (Au) have unique plasmonic properties that give rise to surface enhanced Raman scattering (SERS). Generally, Ag NPs have much stronger plasmonic properties and, hence, provide stronger SERS signals than Au NPs. However, Ag NPs lack the chemical stability and biocompatibility of comparable Au NPs and typically exhibit the most intense plasmonic resonance at wavelengths much shorter than the optimal spectral region for many biomedical applications. To overcome these issues, various experimental efforts have been devoted to the synthesis of Ag/Au hybrid NPs for the purpose of SERS detections. However, a complete understanding on how the SERS enhancement depends on the chemical composition and structure of these nanoparticles has not been achieved. In this study, Mie theory and the discrete dipole approximation have been used to calculate the plasmonic spectra and near-field electromagnetic enhancements of Ag/Au hybrid NPs. In particular, we discuss how the electromagnetic enhancement depends on the mole fraction of Au in Ag/Au alloy NPs and how one may use extinction spectra to distinguish between Ag/Au alloyed NPs and Ag-Au core-shell NPs. We also show that for incident laser wavelengths between ∼410 nm and 520 nm, Ag/Au alloyed NPs provide better electromagnetic enhancement than pure Ag, pure Au, or Ag-Au core-shell structured NPs. Finally, we show that silica-core Ag/Au alloy shelled NPs provide even better performance than pure Ag/Au alloy or pure solid Ag and pure solid Au NPs. The theoretical results presented will be beneficial to the experimental efforts in optimizing the design of Ag/Au hybrid NPs for SERS-based detection methods.

  8. Determination of contact maps in proteins: A combination of structural and chemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Wołek, Karol; Cieplak, Marek, E-mail: mc@ifpan.edu.pl [Institute of Physics, Polish Academy of Science, Al. Lotników 32/46, 02-668 Warsaw (Poland); Gómez-Sicilia, Àngel [Instituto Cajal, Consejo Superior de Investigaciones Cientificas (CSIC), Av. Doctor Arce, 37, 28002 Madrid (Spain); Instituto Madrileño de Estudios Avanzados en Nanociencia (IMDEA-Nanociencia), C/Faraday 9, 28049 Cantoblanco (Madrid) (Spain)

    2015-12-28

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles.

  9. Determination of contact maps in proteins: A combination of structural and chemical approaches

    International Nuclear Information System (INIS)

    Contact map selection is a crucial step in structure-based molecular dynamics modelling of proteins. The map can be determined in many different ways. We focus on the methods in which residues are represented as clusters of effective spheres. One contact map, denoted as overlap (OV), is based on the overlap of such spheres. Another contact map, named Contacts of Structural Units (CSU), involves the geometry in a different way and, in addition, brings chemical considerations into account. We develop a variant of the CSU approach in which we also incorporate Coulombic effects such as formation of the ionic bridges and destabilization of possible links through repulsion. In this way, the most essential and well defined contacts are identified. The resulting residue-residue contact map, dubbed repulsive CSU (rCSU), is more sound in its physico-chemical justification than CSU. It also provides a clear prescription for validity of an inter-residual contact: the number of attractive atomic contacts should be larger than the number of repulsive ones — a feature that is not present in CSU. However, both of these maps do not correlate well with the experimental data on protein stretching. Thus, we propose to use rCSU together with the OV map. We find that the combined map, denoted as OV+rCSU, performs better than OV. In most situations, OV and OV+rCSU yield comparable folding properties but for some proteins rCSU provides contacts which improve folding in a substantial way. We discuss the likely residue-specificity of the rCSU contacts. Finally, we make comparisons to the recently proposed shadow contact map, which is derived from different principles

  10. Electronic structure and chemical bond nature in Cs2PuO2Cl4

    Directory of Open Access Journals (Sweden)

    Teterin Yury A.

    2015-01-01

    Full Text Available X-ray photoelectron spectral analysis of dicaesiumtetrachlorodioxoplutonate (Cs2PuO2Cl4 single crystal was done in the binding energy range 0-~35 eV on the basis of binding energies and structure of the core electronic shells (~35 eV-1250 eV, as well as the relativistic discrete variation calculation results for the PuO2Cl4 (D4h. This cluster reflects Pu close environment in Cs2PuO2Cl4 containing the plutonyl group PuO2. The many-body effects due to the presence of cesium and chlorine were shown to contribute to the outer valence (0-~15 eV binding energy spectral structure much less than to the inner valence (~15 eV- ~35 eV binding energy one. The filled Pu 5f electronic states were theoretically calculated and experimentally con- firmed to present in the valence band of Cs2PuO2Cl4. It corroborates the suggestion on the direct participation of the Pu 5f electrons in the chemical bond. The Pu 6p atomic orbitals were shown to participate in formation of both the inner and the outer valence molecular orbitals (bands, while the filled Pu 6p and O 2s, Cl 3s electronic shells were found to take the largest part in formation of the inner valence molecular orbitals. The composition of molecular orbitals and the sequence order in the binding energy range 0-~35 eV in Cs2PuO2Cl4 were established. The quantitative scheme of molecular orbitals for Cs2PuO2Cl4 in the binding energy range 0-~15 eV was built on the basis of the experimental and theoretical data. It is fundamental for both understanding the chemical bond nature in Cs2PuO2Cl4 and the interpretation of other X-ray spectra of Cs2PuO2Cl4. The contributions to the chemical binding for the PuO2Cl4 cluster were evaluated to be: the contribution of the outer valence molecular orbitals -66 %, the contribution of the inner valence molecular orbitals -34 %.

  11. Structure and properties of braided sleeve preforms for chemical vapor infiltration

    Energy Technology Data Exchange (ETDEWEB)

    Starr, T.L.; Fiadzo, O.G.; Hablutzel, N. [Georgia Inst. of Tech., Atlanta, GA (United States). School of Materials Science and Technology

    1998-04-01

    In all composites the properties and structure of the reinforcement strongly influence the performance of the material. For some composites, however, the reinforcement also affects the fabrication process itself exerting an additional, second order influence on performance. This is the case for the chemical vapor infiltration (CVI) process for fabrication of ceramic matrix composites. In this process the matrix forms progressively as a solid deposit, first onto the fiber surfaces, then onto the previous layer of deposit, ultimately growing to fill the inter-fiber porosity. The transport of reactants to the surfaces and the evolved morphology of the matrix depend on the initial reinforcement structure. This structure can vary greatly and is controlled by such factors as fiber size and cross-section, the number of filaments and amount of twist per tow or yarn, and the weave or braid architecture. Often the choice of reinforcement is based on mechanical performance analysis or on the cost and availability of the material or on the temperature stability of the fiber. Given this choice, the composite densification process--CVI--must be optimized to attain a successful material. Ceramic fiber in the form of cylindrical braided sleeve is an attractive choice for fabrication of tube-form ceramic matrix composites. Multiple, concentric layers of sleeve can be placed over a tubular mandrel, compressed and fixed with a binder to form a freestanding tube preform. This fiber architecture is different than that created by layup of plain weave cloth--the material used in most previous CVI development. This report presents the results of the investigation of CVI densification of braided sleeve preforms and the evolution of their structure and transport properties during processing.

  12. Pure magnetic hard fct FePt nanoparticles: Chemical synthesis, structural and magnetic properties correlations

    Energy Technology Data Exchange (ETDEWEB)

    Suber, L., E-mail: lorenza.suber@ism.cnr.it [ISM-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Marchegiani, G. [ISM-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Olivetti, E.S.; Celegato, F.; Coïsson, M.; Tiberto, P. [INRIM, Electromagnetism Division, Strada delle Cacce 91, 10135 Torino (Italy); Allia, P. [DISAT Politecnico di Torino, Corso Duca degli Abruzzi 24, 10129 Torino (Italy); Barrera, G. [Dipartimento di Chimica, Università di Torino, Via Pietro Giuria 7, 10125 Torino (Italy); Pilloni, L. [UTTMAT-CHI, Via Anguillarese 10, 00123 S. Maria di Galeria, Roma (Italy); Barba, L. [IC-CNR, Area Science Park, SS 14 Km 163.5 Basovizza, 34149 Trieste (Italy); Padella, F. [UTTMAT-CHI, Via Anguillarese 10, 00123 S. Maria di Galeria, Roma (Italy); Cossari, P. [IGAG-CNR, Area della Ricerca di Roma 1, Via Salaria km 29.300, 00015 Monterotondo Scalo, RM (Italy); Chiolerio, A. [Istituto Italiano di Tecnologia, Center for Space Human Robotics, Corso Trento 21, 10129 Torino (Italy)

    2014-03-01

    FePt nanoparticles, containing a near-equal atomic percentage of Fe and Pt, with a face centered tetragonal structure (fct), are challenging for potential applications in high performance permanent magnets and high density data storage. In this study, we report on the chemical synthesis, carried out both solvothermally and hydrothermally in autoclave reacting iron (III) acetylacetonate and platinum (II) acetylacetonate with tri- or tetra-ethylene glycol, these employed as solvents, reducers and particle surface protecting agents as well. In both methods, a subsequent thermal treatment at high temperatures is necessary to transform the magnetic soft face centered cubic (fcc) phase to the hard fct one. Organic low-weight molecules, generally used to protect the nanoparticle surface and avoid particle aggregation, are decomposed by the thermal treatment resulting in particle aggregation and coalescence phenomena; on the contrary, in this case, a polymer matrix is formed as particle protecting agent and, by thermally treating the hydrothermally prepared nanoparticles up to 750 °C for 1 h, the pure magnetic hard fct phase is obtained while preserving the nanostructure. A detailed study is carried out on FePt nanoparticle structure (fcc and fct phases) and correlated to the magnetic properties of the system. - Highlights: • fct FePt nanoparticles for hard magnetic nanotechnology applications. • Influence of synthesis parameters on the precursor fcc FePt nanoparticle structure. • Easy hydrothermal method for preparing pure fct FePt nanoparticles. • Monitoring the role of temperature and time on the FePt fcc–fct phase transformation. • Correlation between FePt nanoparticle structural and magnetic properties.

  13. Predicting the redox state and secondary structure of cysteine residues using multi-dimensional classification analysis of NMR chemical shifts.

    Science.gov (United States)

    Wang, Ching-Cheng; Lai, Wen-Chung; Chuang, Woei-Jer

    2016-09-01

    A tool for predicting the redox state and secondary structure of cysteine residues using multi-dimensional analyses of different combinations of nuclear magnetic resonance (NMR) chemical shifts has been developed. A data set of cysteine [Formula: see text], (13)C(α), (13)C(β), (1)H(α), (1)H(N), and (15)N(H) chemical shifts was created, classified according to redox state and secondary structure, using a library of 540 re-referenced BioMagResBank (BMRB) entries. Multi-dimensional analyses of three, four, five, and six chemical shifts were used to derive rules for predicting the structural states of cysteine residues. The results from 60 BMRB entries containing 122 cysteines showed that four-dimensional analysis of the C(α), C(β), H(α), and N(H) chemical shifts had the highest prediction accuracy of 100 and 95.9 % for the redox state and secondary structure, respectively. The prediction of secondary structure using 3D, 5D, and 6D analyses had the accuracy of ~90 %, suggesting that H(N) and [Formula: see text] chemical shifts may be noisy and made the discrimination worse. A web server (6DCSi) was established to enable users to submit NMR chemical shifts, either in BMRB or key-in formats, for prediction. 6DCSi displays predictions using sets of 3, 4, 5, and 6 chemical shifts, which shows their consistency and allows users to draw their own conclusions. This web-based tool can be used to rapidly obtain structural information regarding cysteine residues directly from experimental NMR data.

  14. Biosynthesis, Chemical Structure, and Structure-Activity Relationship of Orfamide Lipopeptides Produced by Pseudomonas protegens and Related Species.

    Science.gov (United States)

    Ma, Zongwang; Geudens, Niels; Kieu, Nam P; Sinnaeve, Davy; Ongena, Marc; Martins, José C; Höfte, Monica

    2016-01-01

    Orfamide-type cyclic lipopeptides (CLPs) are biosurfactants produced by Pseudomonas and involved in lysis of oomycete zoospores, biocontrol of Rhizoctonia and insecticidal activity against aphids. In this study, we compared the biosynthesis, structural diversity, in vitro and in planta activities of orfamides produced by rhizosphere-derived Pseudomonas protegens and related Pseudomonas species. Genetic characterization together with chemical identification revealed that the main orfamide compound produced by the P. protegens group is orfamide A, while the related strains Pseudomonas sp. CMR5c and CMR12a produce orfamide B. Comparison of orfamide fingerprints led to the discovery of two new orfamide homologs (orfamide F and orfamide G) in Pseudomonas sp. CMR5c. The structures of these two CLPs were determined by nuclear magnetic resonance (NMR) and mass spectrometry (MS) analysis. Mutagenesis and complementation showed that orfamides determine the swarming motility of parental Pseudomonas sp. strain CMR5c and their production was regulated by luxR type regulators. Orfamide A and orfamide B differ only in the identity of a single amino acid, while orfamide B and orfamide G share the same amino acid sequence but differ in length of the fatty acid part. The biological activities of orfamide A, orfamide B, and orfamide G were compared in further bioassays. The three compounds were equally active against Magnaporthe oryzae on rice, against Rhizoctonia solani AG 4-HGI in in vitro assays, and caused zoospore lysis of Phytophthora and Pythium. Furthermore, we could show that orfamides decrease blast severity in rice plants by blocking appressorium formation in M. oryzae. Taken all together, our study shows that orfamides produced by P. protegens and related species have potential in biological control of a broad spectrum of fungal plant pathogens. PMID:27065956

  15. Biosynthesis, chemical structure and structure-activity relationship of orfamide lipopeptides produced by Pseudomonas protegens and related species

    Directory of Open Access Journals (Sweden)

    Zongwang eMa

    2016-03-01

    Full Text Available Orfamide-type cyclic lipopeptides (CLPs are biosurfactants produced by Pseudomonas and involved in lysis of oomycete zoospores, biocontrol of Rhizoctonia and insecticidal activity against aphids. In this study we compared the biosynthesis, structural diversity, in vitro and in planta activities of orfamides produced by rhizosphere-derived Pseudomonas protegens and related Pseudomonas species. Genetic characterization together with chemical identification revealed that the main orfamide compound produced by the P. protegens group is orfamide A, while the related strains Pseudomonas sp. CMR5c and CMR12a produce orfamide B. Comparison of orfamide fingerprints led to the discovery of two new orfamide homologues (orfamide F and orfamide G in Pseudomonas sp. CMR5c. The structures of these two CLPs were determined by nuclear magnetic resonance (NMR and mass spectrometry (MS analysis. Mutagenesis and complementation showed that orfamides determine the swarming motility of parental Pseudomonas sp. strain CMR5c and their production was regulated by luxR type regulators. Orfamide A and orfamide B differ only in the identity of a single amino acid, while orfamide B and orfamide G share the same amino acid sequence but differ in length of the fatty acid part. The biological activities of orfamide A, orfamide B and orfamide G were compared in further bioassays. The three compounds were equally active against Magnaporthe oryzae on rice, against Rhizoctonia solani AG 4-HGI in in vitro assays, and caused zoospore lysis of Phytophthora and Pythium. Furthermore we could show that orfamides decrease blast severity in rice plants by blocking appressorium formation in M. oryzae. Taken all together, our study shows that orfamides produced by P. protegens and related species have potential in biological control of a broad spectrum of fungal plant pathogens.

  16. Synthesis and the Structural Transformation of fcc to hcp in Ni-Graphene Nanocomposite by Simple Chemical Route via Sonication

    OpenAIRE

    N. K. Mahale; R. D. Ladhe; Attarde, S. B.; S. T. Ingle

    2014-01-01

    We report the synthesis and structural transformation of fcc to hcp in Ni-graphene (Ni-Gr) composite by simple chemical route via sonication. The syntheses of Ni-Gr composite by simultaneous reduction method, and the effect of different composition ratio on morphology and crystal structure were examined in our present study. The results indicated that the graphene ratio played an important role in crystal structure and d-spacing in nickel crystals. Different compositions have shown different ...

  17. Quantum chemical and experimental studies on the structure and vibrational spectra of an alkaloid-Corlumine

    Science.gov (United States)

    Mishra, Rashmi; Joshi, Bhawani Datt; Srivastava, Anubha; Tandon, Poonam; Jain, Sudha

    2014-01-01

    The study concentrates on an important natural product, phthalide isoquinoline alkaloid Corlumine (COR) [(6R)-6-[(1S)-1,2,3,4-Tetrahydro-6,7-dimethoxy-2-methylisoquinolin-1-yl] furo [3,4-e]-1,3-benzodioxol-8(6H)-one] well known to exhibit spasmolytic and GABA antagonist activity. It was fully characterized by a variety of experimental methods including vibrational spectroscopy (IR and Raman), thermal analysis (DSC), UV and SEM. For a better interpretation and analysis of the results quantum chemical calculations employing DFT were also performed. TD-DFT was employed to elucidate electronic properties for both gaseous and solvent environment using IEF-PCM model. Graphical representation of HOMO and LUMO would provide a valuable insight into the nature of reactivity and some of the structural and physical properties of the title molecule. The structure-activity relationship have been interpreted by mapping electrostatic potential surface (MEP), which is valuable information for the quality control of medicines and drug-receptor interactions. Stability of the molecule arising from hyper conjugative interactions, charge delocalisation has been analyzed using natural bond orbital (NBO) analysis. Computation of thermodynamical properties would help to have a deep insight into the molecule for further applications.

  18. Structural and morphological evolution of gallium nitride nanorods grown by chemical beam epitaxy

    International Nuclear Information System (INIS)

    The morphological and structural evolution is presented for GaN nanorods grown by chemical beam epitaxy on (0001) Al2O3 substrates. Their structural and optical properties are investigated by x-ray diffraction, scanning and transmission electron microscopy, and temperature-dependent photoluminescence measurements. While increasing the growth temperature and the flow rate of radio-frequency nitrogen radical, the three-dimensional growth mode will be enhanced to form one-dimensional nanostructures. The high density of well-aligned nanorods with a diameter of 30-50 nm formed uniformly over the entire sapphire substrate. The x-ray diffraction patterns and transmission electron microscopic images indicate that the self-assembled GaN nanorods are a pure single crystal and preferentially oriented in the c-axis direction. Particularly, the ''S-shape'' behavior with localization of ∼10 meV observed in the temperature-dependent photoluminescence might be ascribed to the fluctuation in crystallographic defects and composition.

  19. Structural and spectroscopic evidence for stable chemical bonds and the correlation with high Tc superconductivity

    International Nuclear Information System (INIS)

    It is discovered that in the high-Tc superconducting YBa2−xLaxCu3Oz system, by structural analysis and Raman spectroscopy, a stable ‘fixed triangle’ structure exists in the CuO2 planes. All chemical bonds and angles constituting the O(3)–Cu(2)–O(2) triangle are almost constant with doping. The frequencies and linewidths of the out-of-phase c-axis O(2)–O(3) buckling modes around 337 cm−1 and the in-plane Cu(2)–O(2) bond stretching modes around 534 cm−1 are both independent of the doping level, providing direct evidence for the stability of this fixed triangle. It was previously revealed that just these two phonons couple strongly with the antinodal and nodal electronic states, respectively, resulting in an anisotropic electron–phonon interaction in the cuprates. This work implies that the stability of the CuO2 subunit and phonons related to it might be quite important in inducing the d-wave high-Tc superconductivity and should be paid more attention. (paper)

  20. The Effect of Sterilization Methods on the Structural and Chemical Properties of Fibrin Microthread Scaffolds.

    Science.gov (United States)

    Grasman, Jonathan M; O'Brien, Megan P; Ackerman, Kevin; Gagnon, Keith A; Wong, Gregory M; Pins, George D

    2016-06-01

    A challenge for the design of scaffolds in tissue engineering is to determine a terminal sterilization method that will retain the structural and biochemical properties of the materials. Since commonly used heat and ionizing energy-based sterilization methods have been shown to alter the material properties of protein-based scaffolds, the effects of ethanol and ethylene oxide (EtO) sterilization on the cellular compatibility and the structural, chemical, and mechanical properties of uncrosslinked, UV crosslinked, or 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC) crosslinked fibrin microthreads in neutral (EDCn) or acidic (EDCa) buffers are evaluated. EtO sterilization significantly reduces the tensile strength of uncrosslinked microthreads. Surface chemistry analyses show that EtO sterilization induces alkylation of EDCa microthreads leading to a significant reduction in myoblast attachment. The material properties of EDCn microthreads do not appear to be affected by the sterilization method. These results significantly enhance the understanding of how sterilization or crosslinking techniques affect the material properties of protein scaffolds. PMID:26847494

  1. The Effect of Perfluorooctane Sulfonate, Exposure Time, and Chemical Mixtures on Methanogenic Community Structure and Function.

    Science.gov (United States)

    McNamara, Patrick J; LaPara, Timothy M; Novak, Paige J

    2015-01-01

    A plethora of organic micropollutant mixtures are found in untreated municipal wastewater. Anaerobic digesters receive large loadings of hydrophobic micropollutants that sorb to wastewater biosolids. Despite micropollutants being pervasive as mixtures, little research is available to explain the impact that mixtures of compounds, as well as exposure time, have on microbial communities in anaerobic digesters. Perfluorooctane sulfonate (PFOS) was added to anaerobic enrichment cultures in both short-term (14 days) and long-term (140 days) studies to determine the impact of exposure time. Additionally, triclosan was added during the experiments to investigate the impact of mixtures on community structure and function. PFOS did not alter methane production in short-term studies, but in long-term studies, methane production increased, consistent with our hypothesis that PFOS may act as a metabolic uncoupler. The impact of triclosan on methane production was exacerbated when PFOS was already present in the anaerobic enrichment cultures. Triclosan also had greater impacts on microbial community structures in the bottles that had been exposed to PFOS long-term. These results demonstrate that both chemical mixtures and exposure time are important parameters to address when trying to define the impacts of micropollutants on anaerobic microbial communities. PMID:26462249

  2. The Effect of Perfluorooctane Sulfonate, Exposure Time, and Chemical Mixtures on Methanogenic Community Structure and Function

    Science.gov (United States)

    McNamara, Patrick J; LaPara, Timothy M; Novak, Paige J

    2015-01-01

    A plethora of organic micropollutant mixtures are found in untreated municipal wastewater. Anaerobic digesters receive large loadings of hydrophobic micropollutants that sorb to wastewater biosolids. Despite micropollutants being pervasive as mixtures, little research is available to explain the impact that mixtures of compounds, as well as exposure time, have on microbial communities in anaerobic digesters. Perfluorooctane sulfonate (PFOS) was added to anaerobic enrichment cultures in both short-term (14 days) and long-term (140 days) studies to determine the impact of exposure time. Additionally, triclosan was added during the experiments to investigate the impact of mixtures on community structure and function. PFOS did not alter methane production in short-term studies, but in long-term studies, methane production increased, consistent with our hypothesis that PFOS may act as a metabolic uncoupler. The impact of triclosan on methane production was exacerbated when PFOS was already present in the anaerobic enrichment cultures. Triclosan also had greater impacts on microbial community structures in the bottles that had been exposed to PFOS long-term. These results demonstrate that both chemical mixtures and exposure time are important parameters to address when trying to define the impacts of micropollutants on anaerobic microbial communities. PMID:26462249

  3. Local atomic and electronic structure of boron chemical doping in monolayer graphene.

    Science.gov (United States)

    Zhao, Liuyan; Levendorf, Mark; Goncher, Scott; Schiros, Theanne; Pálová, Lucia; Zabet-Khosousi, Amir; Rim, Kwang Taeg; Gutiérrez, Christopher; Nordlund, Dennis; Jaye, Cherno; Hybertsen, Mark; Reichman, David; Flynn, George W; Park, Jiwoong; Pasupathy, Abhay N

    2013-10-01

    We use scanning tunneling microscopy and X-ray spectroscopy to characterize the atomic and electronic structure of boron-doped and nitrogen-doped graphene created by chemical vapor deposition on copper substrates. Microscopic measurements show that boron, like nitrogen, incorporates into the carbon lattice primarily in the graphitic form and contributes ~0.5 carriers into the graphene sheet per dopant. Density functional theory calculations indicate that boron dopants interact strongly with the underlying copper substrate while nitrogen dopants do not. The local bonding differences between graphitic boron and nitrogen dopants lead to large scale differences in dopant distribution. The distribution of dopants is observed to be completely random in the case of boron, while nitrogen displays strong sublattice clustering. Structurally, nitrogen-doped graphene is relatively defect-free while boron-doped graphene films show a large number of Stone-Wales defects. These defects create local electronic resonances and cause electronic scattering, but do not electronically dope the graphene film. PMID:24032458

  4. The effect of chemical structure of dimethyl ether (DME) on NOx formation in nonpremixed counterflow flames

    International Nuclear Information System (INIS)

    To clarify the effect of chemical structure of Dimethyl ether(DME) on NOx formation in nonpremixed counterflow flame, DME flame was investigated numerically to compare the flame structures and NOx emissions with C2H6 and Mixed-fuel. Numerically, the governing equations were solved using the Oppdif code coupled with CHEMKIN package, and DME flames were calculated by Kaiser's mechanism, while the C2H6 flames and Mixed-fuel flames were calculated by the C3 mechanism. These mechanisms were combined with the modified Miller-Bowman mechanism for the analysis of NOx. Numerical results of nonpremixed counterflow flames show that the EINO of DME nonpremixed flame is low as much as 50 % of the C2H6 nonpremixed flame. The cause of EINO reduction is attributed mainly to the characteristics of partial premixed flame due to the existence of oxygen atom in DME and partly to the O-C bond in DME, instead of C-C bond in hydrocarbon fuels

  5. Expanding the chemical space of polyketides through structure-guided mutagenesis of Vitis vinifera stilbene synthase.

    Science.gov (United States)

    Bhan, Namita; Cress, Brady F; Linhardt, Robert J; Koffas, Mattheos

    2015-08-01

    Several natural polyketides (PKs) have been associated with important pharmaceutical properties. Type III polyketide synthases (PKS) that generate aromatic PK polyketides have been studied extensively for their substrate promiscuity and product diversity. Stilbene synthase-like (STS) enzymes are unique in the type III PKS class as they possess a hydrogen bonding network, furnishing them with thioesterase-like properties, resulting in aldol condensation of the polyketide intermediates formed. Chalcone synthases (CHS) in contrast, lack this hydrogen-bonding network, resulting primarily in the Claisen condensation of the polyketide intermediates formed. We have attempted to expand the chemical space of this interesting class of compounds generated by creating structure-guided mutants of Vitis vinifera STS. Further, we have utilized a previously established workflow to quickly compare the wild-type reaction products to those generated by the mutants and identify novel PKs formed by using XCMS analysis of LC-MS and LC-MS/MS data. Based on this approach, we were able to generate 15 previously unreported PK molecules by exploring the substrate promiscuity of the wild-type enzyme and all mutants using unnatural substrates. These structures were specific to STSs and cannot be formed by their closely related CHS-like counterparts. PMID:26048582

  6. The structural, chemical, and electrical properties of He-implantation-induced nanocavities in silicon

    Energy Technology Data Exchange (ETDEWEB)

    Seager, C.H.; Myers, S.M.; Follstaedt, D.M.; Stein, H.J.; Wampler, W.R.

    1993-11-01

    Si implanted with He to doses of about 2 {times} 10{sup 16}cm{sup {minus}2} and greater and annealed at high temperatures develops a layer of internal nanocavities near the end of the He range. Above an annealing temperature of 700 C, all the implanted He escapes from these implanted samples, and the resultant internal cavity surfaces can be shown to possess a high density of chemically reactive Si dangling orbitals. These structures, in addition to possessing a variety of interesting electronic properties, have recently been shown to hold great promise as getters for removing undesirable impurities from the silicon matrix. Here the authors describe some of the structural features of these nanocavities and studies which have been used to accurately determine the binding energy of H and Cu to Si atoms at the cavity walls. Recently, they have also demonstrated that these nanocavities capture large densities of majority carriers in n- and p-type silicon. These electrical measurements have demonstrated that the nanocavity electronic states possess both acceptor and donor levels in the Si forbidden gap. The approximate location of these levels has been determined by a variety of different types of capacitance transient spectroscopy.

  7. Biodegradation of PAHs in soil: Influence of chemical structure, concentration and multiple amendment

    Energy Technology Data Exchange (ETDEWEB)

    Couling, Natalie R.; Towell, Marcie G. [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom); Semple, Kirk T., E-mail: k.semple@lancaster.ac.u [Lancaster Environment Centre, Lancaster University, Lancaster LA1 4YQ (United Kingdom)

    2010-11-15

    The influence of PAH chemical structure and concentration, added in either single (75 or 300 mg kg{sup -1}) or multiple (2 x 75, 2 x 150 or 4 x 75 mg kg{sup -1}) applications as single- or multiple-contaminant systems, on the development of PAH biodegradation in a pristine soil was investigated. Development in microbial catabolic ability was assessed at 0, 28, 56 and 84 d by monitoring {sup 14}C-naphthalene, {sup 14}C-phenanthrene and {sup 14}C-pyrene mineralisation over 14 d in respirometric assays. The presence of other contaminants influenced the ability of the indigenous microflora to mineralise structurally different contaminants over time. {sup 14}C-Naphthalene mineralisation was inhibited by the presence of other contaminants; whereas the presence of naphthalene significantly enhanced rates of mineralisation in multiple-contaminant systems containing {sup 14}C-phenanthrene and {sup 14}C-pyrene. Generally, increasing the number of contaminant applications has implications for catabolic activity of soil microbes. It is suggested the toxic nature of PAHs retarded mineralisation at increased contaminant concentrations. - The simultaneous effects of PAH concentration, contaminant mixture and repeated application on the development of catabolic activity in soil.

  8. Structural Plasticity of Malaria Dihydroorotate Dehydrogenase Allows Selective Binding of Diverse Chemical Scaffolds

    Energy Technology Data Exchange (ETDEWEB)

    Deng, Xiaoyi; Gujjar, Ramesh; El Mazouni, Farah; Kaminsky, Werner; Malmquist, Nicholas A.; Goldsmith, Elizabeth J.; Rathod, Pradipsinh K.; Phillips, Margaret A.; (UWASH); (UTSMC)

    2010-01-20

    Malaria remains a major global health burden and current drug therapies are compromised by resistance. Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) was validated as a new drug target through the identification of potent and selective triazolopyrimidine-based DHODH inhibitors with anti-malarial activity in vivo. Here we report x-ray structure determination of PfDHODH bound to three inhibitors from this series, representing the first of the enzyme bound to malaria specific inhibitors. We demonstrate that conformational flexibility results in an unexpected binding mode identifying a new hydrophobic pocket on the enzyme. Importantly this plasticity allows PfDHODH to bind inhibitors from different chemical classes and to accommodate inhibitor modifications during lead optimization, increasing the value of PfDHODH as a drug target. A second discovery, based on small molecule crystallography, is that the triazolopyrimidines populate a resonance form that promotes charge separation. These intrinsic dipoles allow formation of energetically favorable H-bond interactions with the enzyme. The importance of delocalization to binding affinity was supported by site-directed mutagenesis and the demonstration that triazolopyrimidine analogs that lack this intrinsic dipole are inactive. Finally, the PfDHODH-triazolopyrimidine bound structures provide considerable new insight into species-selective inhibitor binding in this enzyme family. Together, these studies will directly impact efforts to exploit PfDHODH for the development of anti-malarial chemotherapy.

  9. Chemical constituents of Chinese natural medicine, morindae radix, the dried roots of morinda officinalis how.: structures of morindolide and morofficinaloside.

    Science.gov (United States)

    Yoshikawa, M; Yamaguchi, S; Nishisaka, H; Yamahara, J; Murakami, N

    1995-09-01

    A new iridoid lactone, morindolide, and a new iridoid glucoside, morofficinaloside, have been isolated from a Chinese natural medicine, Morindae Radix, the dried root of Morinda officinalis How. together with a number of known compounds: five anthraquinones, four iridoid glucosides, a monoterpene glycoside, two sterols, an ursane-type triterpene, and a lactone compound. The chemical structures of the new compounds were determined on the basis of chemical and physicochemical evidence. PMID:7586069

  10. Quantum chemical investigation on structures and energetics of Tungsten Fluoride (WF$_{n}^{f}$) species ( = 0, ±1; < 6)

    Indian Academy of Sciences (India)

    Ambrish Kumar Srivastava; Anoop Kumar Pandey; Neeraj Misra

    2015-10-01

    The present work deals with a systematic study on WF species using ab initio density functional method. The geometrical features related to the equilibrium structures of WF species up to = 5 are highlighted and the effect of addition as well as removal of an electron is discussed. The chemical stability of these species is discussed by calculating their HOMO-LUMO energy gap and binding energy per atom. The frontier molecular orbital surfaces are also analyzed. The energy based electronic properties such as ionization potential, electron affinity, absolute electronegativity and chemical hardness are also evaluated which provide insights into chemical reactivity of these species.

  11. Coordination compounds of tetravalent silicon, germanium and tin: the structure, chemical bonding and intermolecular interactions in them

    Science.gov (United States)

    Korlyukov, A. A.

    2015-04-01

    The review is devoted to analysis and generalization of the results of (i) quantum chemical studies on the structure, chemical bonding and intermolecular interactions in coordination compounds of tetravalent silicon, germanium and tin in crystals, in solutions and in the gas phase and (ii) experimental investigations of the electron density distribution in these systems. The bibliography includes 147 references. In memoriam of Corresponding Member of the Russian Academy of Sciences M Yu Antipin (1951 - 2013), Academician of the Russian Academy of Sciences M G Voronkov (1921 - 2014) and Dr. S P Knyazev, Lomonosov Moscow University of Fine Chemical Technology (1949 - 2012).

  12. THE INFLUENCE OF THE COMPLEX CHEMICAL ADDITIVE CONTAINING THE STRUCTURED CARBON NANOMATERIAL ON PROPERTIES OF CEMENT

    Directory of Open Access Journals (Sweden)

    O. Yu. Sheyda

    2015-01-01

    Full Text Available The paper presents results of investigations on influence of domestic complex chemical additive containing structured carbon nanomaterial and characterized by a combination effect (curing acceleration and plasticizing on cement and cement stone properties. The purpose of the investigations, on the one hand, has been to confirm efficacy of УКД-1additive from the perspective for increasing the rate of gain, strength growth of cement concrete and additive influence on setting time with the purpose to preserve molding properties of concrete mixes in time, and on the other hand, that is to assess “mechanism” of the УКД-1 additive action in the cement concrete. The research results have revealed regularities in changes due to the additive of water requirements and time period of the cement setting. The reqularities are considered as a pre-requisite for relevant changes in molding properties of the concrete mixes. The paper also experimentally substantiates the possibility to decrease temperature of cement concrete heating with the УДК-1 additive. It has been done with the purpose to save energy resources under production conditions. In addition to this the paper proves the efficiency of the additive which is expressed in strength increase of cement stone up to 20–40 % in the rated age (28 days that is considered as a basis for strength growth of cement concrete. The paper confirms a hypothesis on physical nature of this phenomenon because the X-ray phase analysis method has shown that there are no changes in morphology of portland cement hydration products under the action of the additive agent containing a structured carbon nanomaterial. Results of theoretical and experimental investigations on УКД-1 additive efficiency have been proved by industrial approbation while fabricating precast concrete products and construction of monolithic structures under plant industrial conditions (Minsk, SS “Stroyprogress” JSC MAPID and on

  13. Mashed potatoes enriched with soy protein isolate and inulin: chemical, rheological and structural basis.

    Science.gov (United States)

    Alvarez, M D; Olivares, M D; Blanch, M; Canet, W

    2013-10-01

    Soy protein isolate is typical vegetable protein with health-enhancing activities. Inulin, a prebiotic no digestible carbohydrate, has functional properties. A mashed potato serving of 200 g with added soy protein isolate and/or inulin concentrations of 15-60 g/kg provides from 3 to 12 g of soy protein isolate and/or inulin, respectively. Currently, no information is available about the possible texture-modifying effect of this non-ionizable polar carbohydrate in different soy-based food systems. In this study, the effect of the addition of soy protein isolate and inulin blends at different soy protein isolate: inulin ratios on the degree of inulin polymerization and the rheological and structural properties of fresh mashed and frozen/thawed mashed potatoes were evaluated. The inulin chemical structure remained intact throughout the various treatments, and soy protein isolate did not affect inulin composition being a protein compatible with this fructan. Small-strain rheology showed that both ingredients behaved like soft fillers. In the frozen/thawed mashed potatoes samples, addition of 30 : 30 and 15 : 60 blend ratios significantly increased elasticity (G' value) compared with 0 : 0 control, consequently reducing the freeze/thaw stability conferred by the cryoprotectants. Inulin crystallites caused a significant strengthening effect on soy protein isolate gel. Micrographs revealed that soy protein isolate supports the inulin structure by building up a second fine-stranded network. Thereby, possibility of using soy protein isolate and inulin in combination with mashed potatoes to provide a highly nutritious and healthy product is promising.

  14. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    Science.gov (United States)

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  15. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

  16. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

    Science.gov (United States)

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

  17. An IR and Calorimetric Investigation of the Structural, Crystal-Chemical and Thermodynamic Properties of Hydrogrossular

    Science.gov (United States)

    Geiger, C. A.; Dachs, E.

    2012-04-01

    The garnet class of phases is extremely broad in terms of composition and structural properties. Garnet is found in nature and various synthetic garnet phases have a number of important technical applications. There exist the rock-forming silicate garnets that are so widespread geologically. An additional class is given by the so-called "hydrogarnets" in which the tetrahedral site (Wyckoff position 24d) is empty. At relatively low temperatures there is complete solid solution between Ca3Al2Si3O12 and Ca3Al2H12O12, for example. The substitution mechanism can be written as O4H4 \\lrarr SiO4. The latter, pure OH-containing end-member, which has not been found in nature, is termed katoite/hydrogrossular. Its structure has been investigated by various workers by X-ray and neutron diffraction and by proton NMR, IR and Raman spectroscopic methods. At ambient conditions the structure has the "standard" garnet cubic symmetry of Ia-3d. At high pressures, and possibly at low temperatures, a different structure may occur. We measured the low temperature IR spectra and heat capacity of katoite in order to understand its structural, crystal-chemical and thermophysical properties. A sample of Ca3Al2H12O12 was synthesized hydrothermally in Au capsules at 250 °C and 3 kb water pressure. X-ray powder measurements show that about 98-99% katoite was obtained. Powder IR spectra were recorded between 298 K and 10 K. The measured spectra are considerably different in the high wavenumber region, where O-H stretching modes occur, between 298 K and 10 K. At room temperature the IR-active O-H band located around 3662 cm-1 is broad and it narrows and shifts to higher wavenumbers and also develops structure below about 80 K. Concomitantly, additional weak intensity O-H bands located around 3600 cm-1 begin to appear and they become sharper and increase in intensity with further decreases in temperature down to 10 K. The spectra indicate that the vibrational behavior of individual OH groups and

  18. The magnetic and chemical structural property of the epitaxially-grown multilayered thin film

    Science.gov (United States)

    Lee, Hwachol

    L10 FePt- and Fe-related alloys such as FePtRh, FeRh and FeRhPd have been studied for the high magnetocrystalline anisotropy and magnetic phase transition property for the future application. In this work, the thin film structural and magnetic property is investigated for the selected FePtRh and FeRhPd alloys. The compositionally-modulated L10 FePtRh multilayered structure is grown epitaxially on a-plane Al2O3 with Cr and Pt buffer layer at 600degC growth temperature by DC sputtering technique and examined for the structural, interfacial and magnetic property. For the epitaxially grown L10 [Fe50Pt45Rh5 (FM) (10nm) / Fe50Pt25Rh25 (AFM) (20nm)]x8 superlattice, the magnetically and chemically sharp interface formation between layers was observed in X-ray diffraction, transmission electron microscopy and polarized neutron reflectivity measurements with the negligible exchange bias at room and a slight coupling effect at lower temperature regime. For FeRhPd, the magnetic phase transition of epitaxially-grown 111-oriented Fe46Rh48Pd6 thin film is studied. The applied Rhodium buffer layer on a-plane Al2O3 (11 20) at 600degC shows the extraordinarily high quality of epitaxial film in (111) orientation, where two broad and coherent peak in rocking curve, and Laue oscillations are observed. The epitaxially-grown Pd-doped FeRh on Pt (111) grown at 600degC, 700degC exhibits the co-existing stable L10 (111) and B2 (110) structures and magnetic phase transition around 300degC. On the other hand, the partially-ordered FeRhPd structure grown at 400degC, 500degC shows background high ferromagnetic state over 5K˜350K temperature. For the reduced thickness of Fe46Rh48Pd 6, the ferromagnetic state becomes dominant with a reduced portion of the film undergoing a magnetic phase transition. For some epitaxial FeRhPd film, the spin-glass-like disordered state is also observed in field dependent SQUID measurement. For the tri-layered FeRhPd with thin Pt spacer, the background

  19. Effect of chemical permeation enhancers on stratum corneum barrier lipid organizational structure and interferon alpha permeability.

    Science.gov (United States)

    Moghadam, Shadi H; Saliaj, Evi; Wettig, Shawn D; Dong, Chilbert; Ivanova, Marina V; Huzil, J Torin; Foldvari, Marianna

    2013-06-01

    The outermost layer of the skin, known as the stratum corneum (SC), is composed of dead corneocytes embedded in an intercellular lipid matrix consisting of ceramides, free fatty acids, and cholesterol. The high level of organization within this matrix protects the body by limiting the permeation of most compounds through the skin. While essential for its protective functions, the SC poses a significant barrier for the delivery of topically applied pharmaceutical agents. Chemical permeation enhancers (CPEs) can increase delivery of small drug compounds into the skin by interacting with the intercellular lipids through physical processes including extraction, fluidization, increased disorder, and phase separation. However, it is not clear whether these same mechanisms are involved in delivery of biotherapeutic macromolecules, such as proteins. Here we describe the effect of three categories of CPEs {solvents [ethanol, propylene glycol, diethylene glycol monoethyl ether (transcutol), oleic acid], terpenes [menthol, nerol, camphor, methyl salicylate], and surfactants [Tween 80, SDS, benzalkonium chloride, polyoxyl 40 hydrogenated castor oil (Cremophor RH40), didecyldimethylammonium bromide (DDAB), didecyltrimethylammonium bromide (DTAB)]} on the lipid organizational structure of human SC as determined by X-ray scattering studies. Small- and wide-angle X-ray scattering studies were conducted to correlate the degree of structural changes and hydrocarbon chain packing in SC lipids caused by these various classes of CPEs to the extent of permeation of interferon alpha-2b (IFNα), a 19 kDa protein drug, into human skin. With the exception of solvents, propylene glycol and ethanol, all classes of CPEs caused increased disordering of lamellar and lateral packing of lipids. We observed that the highest degree of SC lipid disordering was caused by surfactants (especially SDS, DDAB, and DTAB) followed by terpenes, such as nerol. Interestingly, in vitro skin permeation studies

  20. Change of free radicals and chemical structure of Moso bamboo with 60Co γ radiation

    International Nuclear Information System (INIS)

    After 60Co γ radiation, absolutely dry bamboo powder produced free radicals and its chemical composition and structure changed. Electron spin resonance (ESR) and X-ray photoelectron spectroscopy (XPS) techniques were used to measure the spectrum of the free radicals and X-ray photoelectron spectroscopy of the γ-ray radiated bamboo powder. The test results reveal that when the spectral splitting factor (g) of the bamboo free radicals is 2.0033, and the intensity of free radicals increase with the absorbed dosage of irradiation according to exponential law. After irradiation of 200 kGy, the O/C atomic number ratio in the bamboo surface increases slightly, C-C and C-H content increases, C-O and C=O content decreases, and -O-C=O content increases to 1.5 times over that of the original, which indicates some oxygen-containing functional groups occur and oxidation state of carbon increases in the bamboo surface. (authors)

  1. Influences of the chemical structure of entrainers on the activity coefficients in presence of biodiesel

    International Nuclear Information System (INIS)

    In this work we analyzed the strength of the intermolecular forces between biodiesel and the entrainer and their influence on the entrainer's ability to interact with biodiesel. Furthermore we investigated the influence of the chemical structure of an entrainer to the interaction with biodiesel. For this purpose the activity coefficients γ∞ at infinite dilution of acids, aldehydes, ketones and alcohols in biodiesel were measured with the method of headspace gas chromatography (HSGC). Short-chained acids showed the highest interaction of the analyzed entrainers caused by their ability to build hydrogen bonds with biodiesel. Increased chain length of the acids cause reduced interaction with biodiesel, which is mainly due to the higher obstruction of the acid molecule and therefore the reduced ability to build hydrogen bonds with biodiesel. Aldehydes, ketones and alcohols showed lower interaction with biodiesel compared to the acids. Longer-chained alcohols showed increased interaction with biodiesel due to the raised London Forces and an inductive +I effect of the molecule chain.

  2. Effect of Chemical Structure on Polymer-Templated Growth of Graphitic Nanoribbons.

    Science.gov (United States)

    Liu, Nan; Kim, Kwanpyo; Jeong, Hu Young; Hsu, Po-Chun; Cui, Yi; Bao, Zhenan

    2015-09-22

    Graphene nanoribbon (GNR) is an important candidate for future nanoelectronics due to its high carrier mobility and dimension-controlled band gap. Polymer-templated growth is a promising method toward high quality and massive production of GNRs. However, the obtained GNRs so far are still quite defective. In order to rationally control the crystallinity of the synthesized GNRs, herein we systematically investigate the effect of polymer chemical structure on their templated growth of GNRs. We studied the morphology/dimensions, composition, graphitization degree, and electrical conductivity of GNRs derived from four different types of electrospun polymers. The four polymers polystyrene (PS), poly(vinyl alcohol) (PVA), polyvinylphenol (PVP), and Novolac (a phenolic resin) are chosen to investigate the effect of metal binding and the effect of aromatic moieties. We found that metal-binding functional groups are crucial for obtaining uniform and continuous GNRs. On the other hand, a polymer with aromatic moieties leads to a higher sp(2) percentage in the resulting GNRs, showing a higher graphitization degree and electrical conductivity. PMID:26267798

  3. Electronic Structure and Chemical Bond of Ti3SiC2 and Adding Al Element

    Institute of Scientific and Technical Information of China (English)

    MIN Xinmin; LU Ning; MEI Bingchu

    2006-01-01

    The relation among electronic structure, chemical bond and property of Ti3SiC2 and Al-doped was studied by density function and discrete variation (DFT-DVM) method. When Al element is added into Ti3SiC2, there is a less difference of ionic bond, which does not play a leading role to influent the properties. After adding Al, the covalent bond of Al and the near Ti becomes somewhat weaker, but the covalent bond of Al and the Si in the same layer is obviously stronger than that of Si and Si before adding. Therefore, in preparation of Ti3SiC2, adding a proper quantity of Al can promote the formation of Ti3SiC2. The density of state shows that there is a mixed conductor character in both of Ti3SiC2 and adding Al element. Ti3SiC2 is with more tendencies to form a semiconductor. The total density of state near Fermi lever after adding Al is larger than that before adding, so the electric conductivity may increase after adding Al.

  4. Physico-chemical studies of hardened cement paste structure with micro-reinforcing fibers

    Energy Technology Data Exchange (ETDEWEB)

    Steshenko, Aleksei, E-mail: steshenko.alexey@gmail.com; Kudyakov, Aleksander; Konusheva, Viktoriya [Tomsk State University of Architecture and Building, 2 Solyanaya Sq., Tomsk, 634003 (Russian Federation)

    2016-01-15

    The results of physico-chemical studies of modified hardened cement paste with micro-reinforcing fibers are given in this article. The goal was to study the reasons of the increase of strength properties of modified hardened cement paste by the method of X-ray diffraction and electron microscopy. It is shown that the use of mineral fibers in the production of cement based material has positive effect on its properties. The study found out that the increase in the strength of the hardened cement paste with micro-reinforcing fibers is due to the increase of the rate of hydration of cement without a significant change in the phase composition in comparison with hardened cement paste without additive. The results of microstructure investigation (of control samples and samples of the reinforced hardened cement paste) have shown that introduction of mineral fibers in the amount of 0.1-2 % by weight of cement provides the structure of the homogeneous microporous material with uniform distribution of the crystalline phase provided by densely packed hydrates.

  5. A comparative chemical-structural study of fossil humic acids and those extracted from urban wastes

    Energy Technology Data Exchange (ETDEWEB)

    Garcia, C.; Hernandez, T.; Costa, F.; Ceccanti, B.; Polo, A. (Centro de Edafologia y Biologia Aplicada del Segura, Murcia (Spain))

    1992-05-01

    Chemical-structural features of commercial humic acids (HAs) from leonardite or lignite were studied and the data obtained were compared with those of humic acids extracted from composted urban wastes. The greatest differences showed by the elemental analysis between the three HAs were in N and H contents, both of which diminished with the oxidation degree of the starting materials. FTIR spectra did not show differences between HAs from evolved materials such as leonardite or lignite. However, differences were found between these HAs and those extracted from composts of urban wastes, which showed a greater aliphatic character and a more pronounced peak in the absorption band attributed to secondary amides and in that of carbohydrates. The {sup 13}C-NMR spectra were similar for both HAs from leonardite regardless of their oxidation degree. The percentage of aromaticity of these HAs was 45%. The spectra of compost HAs showed a low aromaticity degree for these HAs as a consequence of the pronounced peak appearing at 73 ppm corresponding to carbon of carbohydrates and/or polyalcohols and aminoacids. Py-GC revealed a high content of benzene and toluene in all the commercial HAs. The values of these fragments as well as those of the ratios between pyrolitic fragments, used as humification index for soils, were the highest in the HA extracted from the more oxidized leonardite. 17 refs., 1 fig., 5 tabs.

  6. Different patterns of developmental toxicity in the rat following prenatal administration of structurally diverse chemicals

    Energy Technology Data Exchange (ETDEWEB)

    Simmons, D.L.; Valentine, D.M.; Bradshaw, W.S.

    1984-01-01

    Differences in the profiles of developmental toxicity for four structurally diverse chemical compounds have been defined following prenatal exposure in the rat. Diethylstilbestrol (DES), 3,4,3',4'-tetrachlorobiphenyl (4CB), zeranol, and cadmium were administered by gavage to Sprague-Dawley rats daily from d 6 through d 18 of gestation. Dams were sacrificed at four prenatal endpoints and the numbers of live and dead fetuses and resorbed embryos were counted. Additional dams were allowed to bring their litters to term, and their offspring were monitored until they reached adulthood. DES induced prenatal death primarily in early embryonic life, and also during parturition. 4CB increased mortality from late in gestation up to 24 h after birth, and altered the sex ratio of survivors by selectively acting against males in utero. Exposure to zeranol resulted in embryolethality only. Cadmium was not lethal to the conceptus at any dose below the dose that caused maternal mortality. Only 4CB had an obvious teratogenic effect, causing intestinal hemorrhage. All compounds produced transient perinatal decreases in the weight of the offspring. 30 references, 6 tables.

  7. The chemical synthesis of α-conotoxins and structurally modified analogs with enhanced biological stability.

    Science.gov (United States)

    Banerjee, Jayati; Gyanda, Reena; Chang, Yi-Pin; Armishaw, Christopher J

    2013-01-01

    α-Conotoxins are peptide neurotoxins isolated from the venom ducts of carnivorous marine cone snails that exhibit exquisite pharmacological potency and selectivity for various nicotinic acetylcholine receptor subtypes. As such, they are important research tools and drug leads for treating various diseases of the central nervous system, including pain and tobacco addiction. Despite their therapeutic potential, the chemical synthesis of α-conotoxins for use in structure-activity relationship studies is complicated by the possibility of three disulfide bond isomers, where inefficient folding methods can lead to a poor recovery of the pharmacologically active isomer. In order to achieve higher yields of the native isomer, especially in high-throughput syntheses it is necessary to select appropriate oxidative folding conditions. Moreover, the poor biochemical stability exhibited by α-conotoxins limits their general therapeutic applicability in vivo. Numerous strategies to enhance their stability including the substitution of disulfide bond with diselenide bond and N-to-C cyclization via an oligopeptide spacer have successfully overcome these limitations. This chapter describes methods for performing both selective and nonselective disulfide bond oxidation strategies for controlling the yields and formation of α-conotoxin disulfide bond isomers, as well as methods for the production of highly stable diselenide-containing and N-to-C cyclized conotoxin analogs. PMID:24014431

  8. Structural and chemical characterization of hardwood from tree species with applications as bioenergy feedstocks.

    Science.gov (United States)

    Cetinkol, Özgül Persil; Smith-Moritz, Andreia M; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A; Heazlewood, Joshua L; Holmes, Bradley M

    2012-01-01

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks. PMID:23300786

  9. Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

    Energy Technology Data Exchange (ETDEWEB)

    Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A.; Heazlewood, Joshua L.; Holmes, Bradley M.; Zabotina, Olga A.

    2012-12-28

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks.

  10. Electronic and physico-chemical properties of nanometric boron delta-doped diamond structures

    Energy Technology Data Exchange (ETDEWEB)

    Chicot, G., E-mail: gauthier.chicot@neel.cnrs.fr; Fiori, A.; Tran Thi, T. N.; Bousquet, J.; Delahaye, J.; Grenet, T.; Eon, D.; Omnès, F.; Bustarret, E. [Université Grenoble Alpes, Institut NEEL, 38042 Grenoble (France); CNRS, Institut NEEL, 38042 Grenoble (France); Volpe, P. N.; Tranchant, N.; Mer-Calfati, C.; Arnault, J. C. [CEA, LIST, Diamond Sensors Laboratory, 91191 Gif-sur-Yvette (France); Gerbedoen, J. C.; Soltani, A.; De Jaeger, J. C. [IEMN, UMR-CNRS 8520, Avenue Poincaré, Université de Lille 1, 59652 Villeneuve d' Ascq (France); Alegre, M. P.; Piñero, J. C.; Araújo, D. [Dpto Ciencia de los Materiales, Facultad de Ciencias, Universidad de Cádiz, 11510 Puerto Real (Cádiz) (Spain); Jomard, F. [Groupe d' Étude de la Matière Condensée (GEMaC), UMR 8635 du CNRS, UVSQ, 45 Avenue des États-Unis, 78035 Versailles Cedex (France); and others

    2014-08-28

    Heavily boron doped diamond epilayers with thicknesses ranging from 40 to less than 2 nm and buried between nominally undoped thicker layers have been grown in two different reactors. Two types of [100]-oriented single crystal diamond substrates were used after being characterized by X-ray white beam topography. The chemical composition and thickness of these so-called delta-doped structures have been studied by secondary ion mass spectrometry, transmission electron microscopy, and spectroscopic ellipsometry. Temperature-dependent Hall effect and four probe resistivity measurements have been performed on mesa-patterned Hall bars. The temperature dependence of the hole sheet carrier density and mobility has been investigated over a broad temperature range (6 K < T < 450 K). Depending on the sample, metallic or non-metallic behavior was observed. A hopping conduction mechanism with an anomalous hopping exponent was detected in the non-metallic samples. All metallic delta-doped layers exhibited the same mobility value, around 3.6 ± 0.8 cm{sup 2}/Vs, independently of the layer thickness and the substrate type. Comparison with previously published data and theoretical calculations showed that scattering by ionized impurities explained only partially this low common value. None of the delta-layers showed any sign of confinement-induced mobility enhancement, even for thicknesses lower than 2 nm.

  11. Electronic and physico-chemical properties of nanometric boron delta-doped diamond structures

    International Nuclear Information System (INIS)

    Heavily boron doped diamond epilayers with thicknesses ranging from 40 to less than 2 nm and buried between nominally undoped thicker layers have been grown in two different reactors. Two types of [100]-oriented single crystal diamond substrates were used after being characterized by X-ray white beam topography. The chemical composition and thickness of these so-called delta-doped structures have been studied by secondary ion mass spectrometry, transmission electron microscopy, and spectroscopic ellipsometry. Temperature-dependent Hall effect and four probe resistivity measurements have been performed on mesa-patterned Hall bars. The temperature dependence of the hole sheet carrier density and mobility has been investigated over a broad temperature range (6 K 2/Vs, independently of the layer thickness and the substrate type. Comparison with previously published data and theoretical calculations showed that scattering by ionized impurities explained only partially this low common value. None of the delta-layers showed any sign of confinement-induced mobility enhancement, even for thicknesses lower than 2 nm

  12. Physico-chemical studies of hardened cement paste structure with micro-reinforcing fibers

    Science.gov (United States)

    Steshenko, Aleksei; Kudyakov, Aleksander; Konusheva, Viktoriya

    2016-01-01

    The results of physico-chemical studies of modified hardened cement paste with micro-reinforcing fibers are given in this article. The goal was to study the reasons of the increase of strength properties of modified hardened cement paste by the method of X-ray diffraction and electron microscopy. It is shown that the use of mineral fibers in the production of cement based material has positive effect on its properties. The study found out that the increase in the strength of the hardened cement paste with micro-reinforcing fibers is due to the increase of the rate of hydration of cement without a significant change in the phase composition in comparison with hardened cement paste without additive. The results of microstructure investigation (of control samples and samples of the reinforced hardened cement paste) have shown that introduction of mineral fibers in the amount of 0.1-2 % by weight of cement provides the structure of the homogeneous microporous material with uniform distribution of the crystalline phase provided by densely packed hydrates.

  13. Influence of the pore structure and surface chemical properties of activated carbon on the adsorption of mercury from aqueous solutions

    International Nuclear Information System (INIS)

    Highlights: • Activated carbons with different pore structure and surface chemical properties were prepared by modification process. • HgCl2 as a pollution target to evaluate the adsorption performance. • Influence of pore structure and surface chemical properties of activated carbon on adsorption of mercury was investigated. -- Abstract: Reactivation and chemical modification were used to obtain modified activated carbons with different pore structure and surface chemical properties. The samples were characterized by nitrogen absorption–desorption, Fourier transform infrared spectroscopy and the Bothem method. Using mercury chloride as the target pollutant, the Hg2+ adsorption ability of samples was investigated. The results show that the Hg2+ adsorption capacity of samples increased significantly with increases in micropores and acidic functional groups and that the adsorption process was exothermic. Different models and thermodynamic parameters were evaluated to establish the mechanisms. It was concluded that the adsorption occurred through a monolayer mechanism by a two-speed process involving both rapid adsorption and slow adsorption. The adsorption rate was determined by chemical reaction

  14. Spectroscopic and quantum chemical study of the structure of a new paramagnetic dimeric palladium(II,III) complex with creatine

    Science.gov (United States)

    Mitewa, Mariana; Enchev, Venelin; Bakalova, Tatyana

    2002-05-01

    The structure and coordination mode of the newly synthesized dimeric paramagnetic Pd(II,III) complex are studied using magneto-chemical, EPR and IR spectroscopic methods. In order to perform reliable assignment of the IR bands, the structure and IR spectrum of the free creatine were calculated using ab initio method. For calculation of the configuration of its deprotonated and doubly deprotonated forms the semiempirical AM1 method was used.

  15. Effects of chemical contaminants on growth, age-structure, and reproduction of Mytilus edulis complex from Puget sound, Washington.

    Science.gov (United States)

    Kagley, Anna N; Kardong, Kyle E; Snider, Robert G; Casillas, Edmundo

    2014-07-01

    Bivalves are used as sentinel species to detect chemical contaminants in the marine environment, but biological effects on indigenous populations that result from chemical exposure are largely unknown. We assessed age-weight, length-weight relationships, age structure, and reproductive status (i.e. fecundity, egg size) of the blue mussel Mytilus edulis complex from six sites in central Puget Sound, Washington, and one site in the relatively pristine area of northern Puget Sound. Results of this study suggest that mussels from urban areas of Puget Sound exhibit a lower growth rate, altered population age-structure, and potential reproductive impairment as a result of exposure to chemical contaminants. These findings support the use of mussels as sentinel species to assess the biological effects of contaminants on invertebrate populations.

  16. Effect of chemical fertilization and green manure on the abundance and community structure of ammonia oxidizers in a paddy soil

    Directory of Open Access Journals (Sweden)

    Yu Fang

    2015-12-01

    Full Text Available Ammonia oxidization is a critical step in the soil N cycle and can be affected by the fertilization regimes. Chinese milk-vetch (Astragalus sinicus L., MV is a major green manure of rice (Oryza sativa L. fields in southern China, which is recommended as an important agronomic practice to improve soil fertility. Soil chemical properties, abundance and community structures of ammonia-oxidizing bacteria (AOB and ammonia-oxidizing archaea (AOA in a MV-rice rotation field under different fertilization regimes were investigated. The field experiment included six treatments: control, without MV and chemical fertilizer (CK; 100% chemical fertilizer (NPK; 18 000 kg MV ha-1 plus 100% chemical fertilizer (NPKM1; 18 000 kg MV ha-1 plus 40% chemical fertilizer (NPKM2; 18 000 kg MV ha-1 alone (MV; and 18 000 kg MV ha-1 plus 40% chemical fertilizer plus straw (NPKMS. Results showed that NPKMS treatment could improve the soil fertility greatly although the application of 60% chemical fertilizer. The abundance of AOB only in the MV treatment had significant difference with the control; AOA were more abundant than AOB in all corresponding treatments. The NPKMS treatment had the highest AOA abundance (1.19 x 10(8 amoA gene copies g-1 and the lowest abundance was recorded in the CK treatment (3.21 x 10(7 amoA gene copies g-1. The abundance of AOA was significantly positively related to total N, available N, NH4+-N, and NO3--N. The community structure of AOA exhibited little variation among different fertilization regimes, whereas the community structure of AOB was highly responsive. Phylogenetic analysis showed that all AOB sequences were affiliated with Nitrosospira or Nitrosomonas and all AOA denaturing gradient gel electrophoresis (DGGE bands belonged to the soil and sediment lineage. These findings could be fundamental to improve our understanding of AOB and AOA in the N cycle in the paddy soil.

  17. Nano-structural and Nano-chemical analysis of dissimilar metal weld interfaces

    Energy Technology Data Exchange (ETDEWEB)

    Choi, Kyoung Joon; Shin, Sang Hoon; Kim, Jong Jin; Jung, Ju Ang; Kim, Ji Hyun [Ulsan National Institute of Science and Technology, Ulsan (Korea, Republic of)

    2012-05-15

    Dissimilar Metal Welds (DMWs) is generally applied to nuclear power plants for manufacturing and machining in structural components such as reactor pressure vessels and pressurizer nozzles. Alloy 152 is used frequently as filler metal in the manufacture of the DMW in light water reactors to join the low alloy steel pressure vessel nozzles and steam generator nozzles to nickel-based wrought alloy or austenitic stainless steel components. However, in recent years cracking phenomena has been observed in the welded joints. Concerns have been raised to the integrity and reliability in the joint transition zone due to the high susceptibility of the heat affected zone (HAZ) and the fusion boundary (FB) to stress corrosion cracking in combination with thermal aging. Since the material microstructure and chemical composition are key parameters affecting the stress corrosion cracking, improving the understanding of stress corrosion cracking at the FB region requires fundamental understanding of the unique microstructure of the FB region in DMW. Despite the potential degradation and consequent risk in the DMW, there is still a lack of the fundamental understanding of microstructure in the FB region, in particular the region containing unidentified band structures near the FB. The scale of the microstructure in modern metallic materials is becoming increasingly smaller. The 3-dimensional atom probe tomography (3D APT) has a truly quantitative analytical capability to characterize nanometer scale particles in metallic materials, thus its application to the microstructural analysis in multi-component metallic materials provides critical information on the mechanism of nanoscale microstructural evolution. The 3D APT is a microscope that allows the reconstruction of 3D 'atom maps'. These reconstructions can be interrogated and interpreted to determine the nanoscale chemistry of the material. Therefore, the current study is aiming at the establishment of detail procedure

  18. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    Science.gov (United States)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

  19. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs: the role of the aromatic ring.

    NARCIS (Netherlands)

    Handoko, K.B.; Puijenbroek, E.P. van; Bijl, A.H.; Hermens, W.A.; Rijkom, JE Zwart-van; Hekster, Y.A.; Egberts, T.C.G.

    2008-01-01

    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  20. Influence of chemical structure on hypersensitivity reactions induced by antiepileptic drugs : the role of the aromatic ring

    NARCIS (Netherlands)

    Handoko, Kim B; van Puijenbroek, Eugène P; Bijl, Annemarie H; Hermens, Walter A J J; Zwart-van Rijkom, Jeannette E F; Hekster, Yechiel A; Egberts, Toine C G

    2008-01-01

    OBJECTIVE: Antiepileptic drugs (AEDs) can cause various 'idiosyncratic' hypersensitivity reactions, i.e. the mechanism by which AEDs induce hypersensitivity is unknown. The aim of this study was to assess whether the presence of an aromatic ring as a commonality in chemical structures of AEDs can ex

  1. SPECIES DIFFERENCES IN ANDROGEN AND ESTROGEN RECEPTOR STRUCTURE AND FUNCTION AMONG VERTEBRATES AND INVERTEBRATES: INTERSPECIES EXTRAPOLATIONS REGARDING ENDOCRINE DISRUPTING CHEMICALS

    Science.gov (United States)

    Species Differences in Androgen and Estrogen Receptor Structure and Function Among Vertebrates and Invertebrates: Interspecies Extrapolations regarding Endocrine Disrupting Chemicals VS Wilson1, GT Ankley2, M Gooding 1,3, PD Reynolds 1,4, NC Noriega 1, M Cardon 1, P Hartig1,...

  2. [New biological active derivatives of indomethacin and acetylsalicylic acid. Synthesis, physico-chemical characterisation and structure validation].

    Science.gov (United States)

    Stan, Catalina; Stefanache, Alina; Dumitrache, M

    2006-01-01

    It is well known that niflumic acid glycinamide has a good antiinflammatory action useful in gum inflammatory diseases. The objective of this study was to obtain new glycinamides of acetylsalicylic acid and indomethacin, which could have a better antiinflammatory action than niflumic acid glycinamide. The study presents the synthesis, physico-chemical characterisation and structure validation of these glycinamides.

  3. THE GALACTIC STRUCTURE AND CHEMICAL EVOLUTION TRACED BY THE POPULATION OF PLANETARY NEBULAE

    International Nuclear Information System (INIS)

    Planetary nebulae (PNe) derive from the evolution of ∼1-8 Msun mass stars, corresponding to a wide range of progenitor ages, and thus are essential probes of the chemical evolution of galaxies, and indispensable to constrain the results from chemical models. We use an extended and homogeneous data set of Galactic PNe to study the metallicity gradients and the Galactic structure and evolution. The most up-to-date abundances, distances (calibrated with Magellanic Cloud PNe), and other parameters have been employed, together with a novel homogeneous morphological classification, to characterize the different PN populations. We confirm that morphological classes have a strong correlation with Peimbert's type PN, and also with their distribution on the Galactic landscape. We studied the α-element distribution within the Galactic disk, and found that the best selected disk population (i.e., excluding bulge and halo component), together with the most reliable PN distance scale yields to a radial oxygen gradient of Δlog(O/H)/ΔRG = -0.023 ± 0.006 dex kpc-1 for the whole disk sample, and of Δlog(O/H)/ΔRG = -0.035 ± 0.024, -0.023 ± 0.005, and -0.011 ± 0.013 dex kpc-1, respectively for Type I, II, and III PNe, i.e., for high-, intermediate-, and low-mass progenitors. Neon gradients for the same PN types confirm the trend. Accurate statistical analysis shows moderately high uncertainties in the slopes, but also confirms the trend of steeper gradient for PNe with more massive progenitors, indicating a possible steepening with time of the Galactic disk metallicity gradient for what the α-elements are concerned. We found that the metallicity gradients are almost independent on the distance scale model used, as long as these scales are equally well calibrated with the Magellanic Clouds. The PN metallicity gradients presented here are consistent with the local metallicity distribution; furthermore, oxygen gradients determined with young and intermediate age PNe show good

  4. CPUF - a chemical-structure-based polyurethane foam decomposition and foam response model.

    Energy Technology Data Exchange (ETDEWEB)

    Fletcher, Thomas H. (Brigham Young University, Provo, UT); Thompson, Kyle Richard; Erickson, Kenneth L.; Dowding, Kevin J.; Clayton, Daniel (Brigham Young University, Provo, UT); Chu, Tze Yao; Hobbs, Michael L.; Borek, Theodore Thaddeus III

    2003-07-01

    A Chemical-structure-based PolyUrethane Foam (CPUF) decomposition model has been developed to predict the fire-induced response of rigid, closed-cell polyurethane foam-filled systems. The model, developed for the B-61 and W-80 fireset foam, is based on a cascade of bondbreaking reactions that produce CO2. Percolation theory is used to dynamically quantify polymer fragment populations of the thermally degrading foam. The partition between condensed-phase polymer fragments and gas-phase polymer fragments (i.e. vapor-liquid split) was determined using a vapor-liquid equilibrium model. The CPUF decomposition model was implemented into the finite element (FE) heat conduction codes COYOTE and CALORE, which support chemical kinetics and enclosure radiation. Elements were removed from the computational domain when the calculated solid mass fractions within the individual finite element decrease below a set criterion. Element removal, referred to as ?element death,? creates a radiation enclosure (assumed to be non-participating) as well as a decomposition front, which separates the condensed-phase encapsulant from the gas-filled enclosure. All of the chemistry parameters as well as thermophysical properties for the CPUF model were obtained from small-scale laboratory experiments. The CPUF model was evaluated by comparing predictions to measurements. The validation experiments included several thermogravimetric experiments at pressures ranging from ambient pressure to 30 bars. Larger, component-scale experiments were also used to validate the foam response model. The effects of heat flux, bulk density, orientation, embedded components, confinement and pressure were measured and compared to model predictions. Uncertainties in the model results were evaluated using a mean value approach. The measured mass loss in the TGA experiments and the measured location of the decomposition front were within the 95% prediction limit determined using the CPUF model for all of the

  5. Secondary structural analysis of proteins based on 13C chemical shift assignments in unresolved solid-state NMR spectra enhanced by fragmented structure database

    International Nuclear Information System (INIS)

    Magic-angle-spinning solid-state 13C NMR spectroscopy is useful for structural analysis of non-crystalline proteins. However, the signal assignments and structural analysis are often hampered by the signal overlaps primarily due to minor structural heterogeneities, especially for uniformly-13C,15N labeled samples. To overcome this problem, we present a method for assigning 13C chemical shifts and secondary structures from unresolved two-dimensional 13C–13C MAS NMR spectra by spectral fitting, named reconstruction of spectra using protein local structures (RESPLS). The spectral fitting was conducted using databases of protein fragmented structures related to 13Cα, 13Cβ, and 13C′ chemical shifts and cross-peak intensities. The experimental 13C–13C inter- and intra-residue correlation spectra of uniformly isotope-labeled ubiquitin in the lyophilized state had a few broad peaks. The fitting analysis for these spectra provided sequence-specific Cα, Cβ, and C′ chemical shifts with an accuracy of about 1.5 ppm, which enabled the assignment of the secondary structures with an accuracy of 79 %. The structural heterogeneity of the lyophilized ubiquitin is revealed from the results. Test of RESPLS analysis for simulated spectra of five different types of proteins indicated that the method allowed the secondary structure determination with accuracy of about 80 % for the 50–200 residue proteins. These results demonstrate that the RESPLS approach expands the applicability of the NMR to non-crystalline proteins exhibiting unresolved 13C NMR spectra, such as lyophilized proteins, amyloids, membrane proteins and proteins in living cells.

  6. Neurodevelopmental toxicity of prenatal polychlorinated biphenyls (PCBs by chemical structure and activity: a birth cohort study

    Directory of Open Access Journals (Sweden)

    Park Hye-Youn

    2010-08-01

    Full Text Available Abstract Background Polychlorinated biphenyls (PCBs are ubiquitous environmental toxins. Although there is growing evidence to support an association between PCBs and deficits of neurodevelopment, the specific mechanisms are not well understood. The potentially different roles of specific PCB groups defined by chemical structures or hormonal activities e.g., dioxin-like, non-dioxin like, or anti-estrogenic PCBs, remain unclear. Our objective was to examine the association between prenatal exposure to defined subsets of PCBs and neurodevelopment in a cohort of infants in eastern Slovakia enrolled at birth in 2002-2004. Methods Maternal and cord serum samples were collected at delivery, and analyzed for PCBs using high-resolution gas chromatography. The Bayley Scales of Infant Development -II (BSID were administered at 16 months of age to over 750 children who also had prenatal PCB measurements. Results Based on final multivariate-adjusted linear regression model, maternal mono-ortho-substituted PCBs were significantly associated with lower scores on both the psychomotor (PDI and mental development indices (MDI. Also a significant association between cord mono-ortho-substituted PCBs and reduced PDI was observed, but the association with MDI was marginal (p = 0.05. Anti-estrogenic and di-ortho-substituted PCBs did not show any statistically significant association with cognitive scores, but a suggestive association between di-ortho-substituted PCBs measured in cord serum and poorer PDI was observed. Conclusion Children with higher prenatal mono-ortho-substituted PCB exposures performed more poorly on the Bayley Scales. Evidence from this and other studies suggests that prenatal dioxin-like PCB exposure, including mono-ortho congeners, may interfere with brain development in utero. Non-dioxin-like di-ortho-substituted PCBs require further investigation.

  7. [Chemical structure and immunobiological activities of peptidoglycan isolated from Capnocytophaga species].

    Science.gov (United States)

    Hanagata, T

    1990-12-01

    The chemical structure and immunobiological activities of the cell wall peptidoglycan isolated from Capnocytophaga species was investigated. Peptidoglycan was isolated from Capnocytophaga species strain SE2-2 by boiling in 4% sodium dodecyl sulfate and by digestion with pronase, trypsin and alpha-amylase. Analysis of amino acids and amino sugars of the peptidoglycan revealed that glucosamine, muramic acid, D-glutamic acid, alanine, and diaminopimelic acid (A2pm) were the principal components. Serine and glycine were not found. Dinitrophenylation method revealed that about half of A2pm residue had a free amino group, and analysis by hydrazinolysis showed that a small part of alanine and A2pm located at the C-terminal. The above results indicate that one of the amino groups of A2pm residue at one strand of the stem peptide subunit cross-linked to the carboxyl group of alanine of the neighboring strand. It was thus revealed that the peptidoglycan of Capnocytophaga species belonged to the Al gamma type of the classification by Schleifer and Kandler. Peptidoglycan isolated from Capnocytophaga species strain SE2-2 was found to be definitely adjuvant-active in induction of delayed type hypersensitivity against ovalbumin when administered to guinea pigs as water-in-oil emulsion and in stimulation of increase serum antibody levels. Regarding mitogenicity on splenocytes of BALB/c and BALB/c nu/nu mice, peptidoglycan from Capnocytophaga species was markedly enhanced the uptake [3H] thymidine in dose of 10 micrograms/10(5) cells, however thymocytes were not reactive. Stimulation effects on peritoneal macrophages from a guinea pig to incorporation of 14C-glucosamin was exhibited by addition of 100 micrograms of this peptidoglycan. These findings indicate that peptidoglycan of Capnocytophaga species might eventually be responsible for destruction of periodontal tissue by host mediated activities.

  8. Chemical-Structural Changes of Organic Matter in a Semi-Arid Soil After Organic Amendment

    Institute of Scientific and Technical Information of China (English)

    C.NICOL(A)S; G.MASCIANDARO; T.HERN(A)NDEZ; C.GARCIA

    2012-01-01

    A 9-month incubation experiment using composted and non-composted amendments derived from vine pruning waste and sewage sludge was carried out to study the effects of the nature and stability of organic amendments on the structural composition of organic matter (OM) in a semi-arid soil. The changes of soil OM,both in the whole soil and in the extractable carbon with pyrophosphate,were evaluated by pyrolysis-gas chromatography and chemical analyses.By the end of the experiment,the soils amended with pruning waste exhibited less organic carbon loss than those receiving sewage sludge.The non-composted residues increased the aliphatic-pyrolytic products of the OM,both in the whole soil and also in the pyrophosphate extract,with the products derived from peptides and proteins being significantly higher.After 9 months,in the soils amended with pruning waste the relative abundance of phenolic-pyrolytic products derived from phenolic compounds,lignin and proteins in the whole soil tended to increase more than those in the soils amended with sewage sludge.However,the extractable OM with pyrophosphate in the soils amended with composted residues tended to have higher contents of these phenolic-pyrolytic products than that in non-composted ones.Thus,despite the stability of pruning waste,the composting of this material promoted the incorporation of phenolic compounds to the soil OM.The pyrolytic indices (furfural/pyrrole and aliphatic/aromatic ratios) showed the diminution of aliphatic compounds and the increase of aromatic compounds,indicating the stabilization of the OM in the amended soils after 9 months.In conclusion,the changes of soil OM depend on the nature and stability of the organic amendments,with composted vine pruning waste favouring humification.

  9. Chemical Structure and Immunomodulating Activities of an α-Glucan Purified from Lobelia chinensis Lour

    Directory of Open Access Journals (Sweden)

    Xiao-Jun Li

    2016-06-01

    Full Text Available A neutral α-glucan, named BP1, with a molecular mass of approximately 9.45 kDa, was isolated from Lobelia chinensis by hot-water extraction, a Q-Sepharose Fast Flow column and Superdex-75 column chromatography. Its chemical structure was characterized by monosaccharide analysis, methylation analysis and analysis of its FT-IR, high performance gel permeation chromatography (HPGPC and 1D/2D-NMR spectra data. The backbone of BP1 consists of →6α-d-Glcp1→6,3α-d-Glcp1→(6α-d-Glcp1x-6,3α-d-Glcp1-(6α-d-Glcp1y→. The side chains were terminal α-d-Glcp1→ and α-d-Glcp1→ (6α-d-Glcp1z→4α-d-Glcp1→3α-d-Glcp1→4α-d-Glcp1→ (x + y + z = 5, which are attached to the backbone at O-3 of 3,6α-d-Glcp1. The results of the effect of BP1 on mouse macrophage cell line RAW 264.7 indicate that BP1 enhances the cell proliferation, phagocytosis, nitric oxide production and cytokine secretion in a dose-dependent manner. Because the inhibitor of Toll-like receptor 4 blocks the BP1-induced secretion of TNF-α and IL-6, we hypothesize that α-glucan BP1 activates TLR4, which mediates the above-mentioned immunomodulating effects.

  10. Chemical Structure and Immunomodulating Activities of an α-Glucan Purified from Lobelia chinensis Lour.

    Science.gov (United States)

    Li, Xiao-Jun; Bao, Wan-Rong; Leung, Chung-Hang; Ma, Dik-Lung; Zhang, Ge; Lu, Ai-Ping; Wang, Shun-Chun; Han, Quan-Bin

    2016-01-01

    A neutral α-glucan, named BP1, with a molecular mass of approximately 9.45 kDa, was isolated from Lobelia chinensis by hot-water extraction, a Q-Sepharose Fast Flow column and Superdex-75 column chromatography. Its chemical structure was characterized by monosaccharide analysis, methylation analysis and analysis of its FT-IR, high performance gel permeation chromatography (HPGPC) and 1D/2D-NMR spectra data. The backbone of BP1 consists of →₆α-d-Glcp¹→6,3α-d-Glcp¹→(₆α-d-Glcp¹)x-6,3α-d-Glcp¹-(₆α-d-Glcp¹)y→. The side chains were terminal α-d-Glcp¹→ and α-d-Glcp¹→ (₆α-d-Glcp¹)z→₄α-d-Glcp¹→₃α-d-Glcp¹→₄α-d-Glcp¹→ (x + y + z = 5), which are attached to the backbone at O-3 of 3,6α-d-Glcp¹. The results of the effect of BP1 on mouse macrophage cell line RAW 264.7 indicate that BP1 enhances the cell proliferation, phagocytosis, nitric oxide production and cytokine secretion in a dose-dependent manner. Because the inhibitor of Toll-like receptor 4 blocks the BP1-induced secretion of TNF-α and IL-6, we hypothesize that α-glucan BP1 activates TLR4, which mediates the above-mentioned immunomodulating effects. PMID:27314319

  11. Structure and Chemical Bond of Thermoelectric Ce-Co-Sb Skutterudites

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The correlations among composition,structure,chemical bond and thermoelectric property of skutterudites CoSb3 and CeCo5Fe3Sb12 have been studied by using density function and discrete variation (DFT-DVM) method.Three models for this study were proposed and calculated by which the "rattling" pattern was described.Model 1 is with Ce in the center,model 2 is with Ce away the center and near to Sb,and model 3 is also with Ce away the center but near to Fe.The calculated results show that in model 3,the ionic bond is the strongest,but the covalent bond is the weakest.Due to the different changes between ionic and covalent bond,there is less difference in the stability among the models 1,2 and 3.Therefore,these different models can exist at the same time,or can translate from one to another more easily.In other words,the "rattling" pattern has taken place.Unfilled model of CoSb3,without Ce and Fe,is called model 4.The covalent bond of Co-Sb or Fe-Sb in models 1,2 and 3 is weaker than that of Co-Sb in model 4,as some electrical cloud of Sb takes part in the covalent bond of Ce-Sb in the filled models.The result is consistent with the experimental result that the thermal conductivity of CeCo5Fe3Sb12 is lower than that of CoSb3,and the thermoelectric property of CeCo5Fe3Sb12 is superior to that of CoSb3.

  12. Structure, topology and chemical order in Ge-As-Te glasses: a high-energy x-ray diffraction study

    Energy Technology Data Exchange (ETDEWEB)

    Sen, S; Soyer Uzun, S [Department of Chemical Engineering and Materials Science, University of California at Davis, Davis, CA 95616 (United States); Benmore, C J [Argonne National Laboratory, Argonne, IL 60439 (United States); Aitken, B G [Glass Research Division, Corning Incorporated, Corning, NY 14831 (United States)

    2010-10-13

    High-energy x-ray diffraction is employed to study the atomic structure of bulk Ge{sub x}As{sub 2x}Te{sub 100-3x} glasses with compositions in the range 25 {<=} 3x {<=} 70. The coordination environments of Te atoms suggest significant violation of chemical order in these glasses. Analyses of the nearest-neighbor coordination environments and the parameters for the first sharp diffraction peak indicate that these telluride glasses are structurally and chemically more disordered as compared with their sulfide or selenide analogs. The compositional evolution of the structural parameters is shown to be consistent with the corresponding variation in molar volume and glass transition temperature.

  13. Structural and chemical properties of the nitrogen-rich energetic material triaminoguanidinium 1-methyl-5-nitriminotetrazolate under pressure.

    Science.gov (United States)

    McWilliams, R Stewart; Kadry, Yasmin; Mahmood, Mohammad F; Goncharov, Alexander F; Ciezak-Jenkins, Jennifer

    2012-08-01

    The structural and chemical properties of the bi-molecular, hydrogen-bonded, nitrogen-rich energetic material triaminoguanidinium 1-methyl-5-nitriminotetrazolate C(3)H(12)N(12)O(2) (TAG-MNT) have been investigated at room pressure and under high pressure isothermal compression using powder x-ray diffraction and Raman and infrared spectroscopy. A stiffening of the equation of state and concomitant structural relaxation between 6 and 14 GPa are found to correlate with Raman mode disappearances, frequency discontinuities, and changes in the pressure dependence of modes. These observations manifest the occurrence of a reversible martensitic structural transformation to a new crystalline phase. The onset and vanishing of Fermi resonance in the nitrimine group correlate with the stiffening of the equation of state and phase transition, suggesting a possible connection between these phenomena. Beyond 15 GPa, pressure induces irreversible chemical reactions, culminating in the formation of a polymeric phase by 60 GPa. PMID:22894358

  14. Structural and chemical determination of the new nanolaminated carbide Mo2Ga2C from first principles and materials analysis

    International Nuclear Information System (INIS)

    Following our recent discovery of a new nanolaminated carbide, Mo2Ga2C, we herein present a detailed structural and chemical analysis of this phase based on ab initio calculations, X-ray photoelectron spectroscopy, high resolution scanning transmission electron microscopy, and neutron powder diffraction. Calculations suggest an energetically and dynamically stable structure for C in the octahedral sites between the Mo layers, with Ga bilayers – stacked in a simple hexagonal arrangement – between the Mo2C layers. The predicted elastic properties are below those of the related nanolaminate Mo2GaC. The predicted structure, including lattice parameters and atomic positions, is experimentally confirmed

  15. Wet chemical treatments of high purity Ge crystals for γ-ray detectors: Surface structure, passivation capabilities and air stability

    Energy Technology Data Exchange (ETDEWEB)

    Carturan, S., E-mail: carturan@lnl.infn.it [Department of Physics and Astronomy, University of Padova, Padova (Italy); INFN, Laboratori Nazionali di Legnaro, Legnaro, Padova (Italy); Maggioni, G. [Department of Physics and Astronomy, University of Padova, Padova (Italy); INFN, Laboratori Nazionali di Legnaro, Legnaro, Padova (Italy); Rezvani, S.J. [Department of Physics, University of Camerino, Camerino, Macerata (Italy); Gunnella, R. [Department of Physics, University of Camerino, Camerino, Macerata (Italy); INFN, Laboratori Nazionali di Frascati, Frascati (Italy); Pinto, N. [Department of Physics, University of Camerino, Camerino, Macerata (Italy); INFN, Sezione di Perugia, Perugia (Italy); Gelain, M. [Department of Physics and Astronomy, University of Padova, Padova (Italy); INFN, Laboratori Nazionali di Legnaro, Legnaro, Padova (Italy); Napoli, D.R. [INFN, Laboratori Nazionali di Legnaro, Legnaro, Padova (Italy)

    2015-07-01

    Aiming at the production of HPGe diodes for γ-ray detection, surface passivation of the pristine Germanium surface is pursued by treatment of freshly etched, highly reactive Ge (100) surface by different chemicals, to obtain chemisorbed species with sufficient insulating properties for allowing high voltage application (up to 1100 V) with low leakage currents (lower than 30 pA). (100) surface termination of Ge crystal with hydride, methoxide, and sulphide is carried out by wet chemical treatments using suitable reactants. The chemical composition of the newly formed monolayers is investigated with regards to the nature of chemical bonding with Ge atop atoms. To this aim Fourier Transform Infrared Spectrometry (FTIR) and X-ray Photoelectron Spectroscopy (XPS) were used; the performance as dielectric layer of each native Ge compound/complex is measured directly from I–V measurements of a HPGe diode. Atomic stability of each surface layer is monitored detecting structural changes after air exposure by XPS and FTIR spectroscopies and by relevant leakage current variations. - Highlights: • Different surface passivations were applied to HPGe by wet chemical methods. • New chemical bonds were characterized by FTIR and XPS. • Air stability: hydride and sulphide treatments display the best oxidation resistance. • I–V measurements: all the treatments provided efficient passivation.

  16. Complex, dynamic combination of physical, chemical and nutritional variables controls spatio-temporal variation of sandy beach community structure.

    Directory of Open Access Journals (Sweden)

    Kelly Ortega Cisneros

    Full Text Available Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean

  17. Poly(ADP-ribose)--a unique natural polymer structural features, biological role and approaches to the chemical synthesis.

    Science.gov (United States)

    Drenichev, Mikhail S; Mikhailov, Sergey N

    2015-01-01

    Poly(ADP-ribose) (PAR) is a natural polymer, taking part in numerous important cellular processes. Several enzymes are involved in biosynthesis and degradation of PAR. One of them, poly(ADP-ribose)polymerase-1 (PARP-1) is considered to be a perspective target for the design of new drugs, affecting PAR metabolism. The structure of PAR was established by enzymatic hydrolysis and further analysis of the products, but total chemical synthesis of PAR hasn't been described yet. Several approaches have been developed on the way to chemical synthesis of this unique biopolymer.

  18. ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions.

    Science.gov (United States)

    Sushko, Iurii; Salmina, Elena; Potemkin, Vladimir A; Poda, Gennadiy; Tetko, Igor V

    2012-08-27

    The article presents a Web-based platform for collecting and storing toxicological structural alerts from literature and for virtual screening of chemical libraries to flag potentially toxic chemicals and compounds that can cause adverse side effects. An alert is uniquely identified by a SMARTS template, a toxicological endpoint, and a publication where the alert was described. Additionally, the system allows storing complementary information such as name, comments, and mechanism of action, as well as other data. Most importantly, the platform can be easily used for fast virtual screening of large chemical datasets, focused libraries, or newly designed compounds against the toxicological alerts, providing a detailed profile of the chemicals grouped by structural alerts and endpoints. Such a facility can be used for decision making regarding whether a compound should be tested experimentally, validated with available QSAR models, or eliminated from consideration altogether. The alert-based screening can also be helpful for an easier interpretation of more complex QSAR models. The system is publicly accessible and tightly integrated with the Online Chemical Modeling Environment (OCHEM, http://ochem.eu). The system is open and expandable: any registered OCHEM user can introduce new alerts, browse, edit alerts introduced by other users, and virtually screen his/her data sets against all or selected alerts. The user sets being passed through the structural alerts can be used at OCHEM for other typical tasks: exporting in a wide variety of formats, development of QSAR models, additional filtering by other criteria, etc. The database already contains almost 600 structural alerts for such endpoints as mutagenicity, carcinogenicity, skin sensitization, compounds that undergo metabolic activation, and compounds that form reactive metabolites and, thus, can cause adverse reactions. The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly

  19. Chemical sensor

    Science.gov (United States)

    Rauh, R. David (Inventor)

    1990-01-01

    A sensor for detecting a chemical substance includes an insertion element having a structure which enables insertion of the chemical substance with a resulting change in the bulk electrical characteristics of the insertion element under conditions sufficient to permit effective insertion; the change in the bulk electrical characteristics of the insertion element is detected as an indication of the presence of the chemical substance.

  20. Chemical and Electronic Structure Studies of Refractory and Dielectric Thin Films.

    Science.gov (United States)

    Corneille, Jason Stephen

    This study presents the synthesis and characterization of oxide and refractory thin films under varying conditions. The deposition of the thin films is performed under vacuum conditions. The characterization of the growth, as well as the chemical and electronic properties of the thin films was accomplished using a broad array of surface analytical techniques. These model studies describe the relationship between the preparative processes and the stoichiometry, structure and electronic properties of the film products. From these efforts, the optimal deposition conditions for the production of high quality films have been established. The thin film oxides synthesized and studied here include magnesium oxide, silicon oxide and iron oxide. These oxides were synthesized on a refractory substrate using both post oxidation of thin films as well as reactive vapor deposition of the metals in the presence of an oxygen background. Comparisons and contrasts are presented for the various systems. Metallic magnesium films were grown and characterized as a preliminary study to the synthesis of magnesium oxide. Magnesium oxide (MgO(100)) was synthesized on Mo(100) by evaporating magnesium at a rate of one monolayer per minute in an oxygen background pressure of 1 times 10 ^{-6} Torr at room temperature. The resulting film was found to exhibit spectroscopic characteristics quite similar to those observed for bulk MgO. The acid/base characteristics of the films were studied using carbon monoxide, water and methanol as probe molecules. The film was found to exhibit essentially the same chemical properties as found in analogous powdered catalysts. Silicon dioxide was synthesized by evaporating silicon onto Mo(100) in an oxygen ambient. It is shown that the silicon oxide prepared at room temperature with a silicon deposition rate of {~ }{1.2}A/min and an oxygen pressure of 2 times 10^{ -8} Torr, consisted of predominantly silicon dioxide with a small fraction of suboxides. Annealing to

  1. At the brink of supercoloniality: genetic, behavioral and chemical assessments of population structure of the desert ant Cataglyphis niger

    Directory of Open Access Journals (Sweden)

    Maya eSaar

    2014-05-01

    Full Text Available The nesting habits of ants play an important role in structuring ant populations. They vary from monodomy, a colony occupies a single nest, via polydomy, a colony occupies multiple adjacent nests, to supercoloniality, a colony spans over large territories comprising dozen to thousands nests without having any boundaries. The population structure of the desert ant Cataglyphis niger, previously considered to form supercolonies, was studied using genetic, chemical and behavioral tools in plots of 50x50 meters at two distinct populations. At the Palmahim site, the plot comprised 15 nests that according to the genetic analysis constituted three colonies. Likewise at the Rishon Leziyyon site 14 nests constituted 5 genetic colonies. In both sites, both chemical analysis and the behavioral (aggression tests confirmed the colony genetic architecture. The behavioral tests also revealed that aggression between colonies within a population was higher than that exhibited between colonies of different populations, suggesting the occurrence of the nasty neighbor phenomenon. In contrast to supercolony structure previously reported in another population of this species, the presently studied populations were composed of polydomous colonies. However, both the genetic and chemical data revealed that the inter-colonial differences between sites were larger than those within site, suggesting some within-site population viscosity. Thus, C. niger exhibits flexible nesting characteristics, from polydomy to supercoloniality, and can be considered at the brink of supercoloniality. We attribute the differences in population structure among sites to the intensity of intraspecific competition.

  2. Growth of a Novel Periodic Structure of SiC/AlN Multilayers by Low Pressure Chemical Vapour Deposition

    Institute of Scientific and Technical Information of China (English)

    ZHAO Yong-Mei; SUN Guo-Sheng; LI Jia-Ye; LIU Xing-Fang; WANG Lei; ZHAO Wan-Shun; LI Jin-Min

    2007-01-01

    A novel 10-period SiC/AlN multilayered structure with a SiC cap layer is prepared by low pressure chemical vapour deposition (LPCVD). The structure with total Sim thickness of about 1.45μm is deposited on a Si (111) substrate and shows good surface morphology with a smaller rms surface roughness of 5.3 nm. According to the secondary ion mass spectroscopy results, good interface of the 10 period SiC/AlN structure and periodic changes of depth profiles of C, Si, Al, N components are obtained by controlling the growth procedure. The structure exhibits the peak reflectivity close to 30% near the wavelength of 322 nm. To the best of our knowledge, this is the first report of growth of the SiC/AlN periodic structure using the home-made LPCVD system.

  3. Toward epitaxially grown two-dimensional crystal hetero-structures: Single and double MoS2/graphene hetero-structures by chemical vapor depositions

    Science.gov (United States)

    Lin, Meng-Yu; Chang, Chung-En; Wang, Cheng-Hung; Su, Chen-Fung; Chen, Chi; Lee, Si-Chen; Lin, Shih-Yen

    2014-08-01

    Uniform large-size MoS2/graphene hetero-structures fabricated directly on sapphire substrates are demonstrated with layer-number controllability by chemical vapor deposition (CVD). The cross-sectional high-resolution transmission electron microscopy (HRTEM) images provide the direct evidences of layer numbers of MoS2/graphene hetero-structures. Photo-excited electron induced Fermi level shift of the graphene channel are observed on the single MoS2/graphene hetero-structure transistors. Furthermore, double hetero-structures of graphene/MoS2/graphene are achieved by CVD fabrication of graphene layers on top of the MoS2, as confirmed by the cross-sectional HRTEM. These results have paved the possibility of epitaxially grown multi-hetero-structures for practical applications.

  4. Chemical sensing by band modulation of a black phosphorus/molybdenum diselenide van der Waals hetero-structure

    Science.gov (United States)

    Feng, Zhihong; Chen, Buyun; Qian, Shuangbei; Xu, Linyan; Feng, Liefeng; Yu, Yuanyuan; Zhang, Rui; Chen, Jiancui; Li, Qianqian; Li, Quanning; Sun, Chongling; Zhang, Hao; Liu, Jing; Pang, Wei; Zhang, Daihua

    2016-09-01

    We report on a new chemical sensor based on black phosphorus/molybdenum diselenide van der Waals hetero-junctions. Due to the atomically thin nature of two-dimensional (2D) materials, surface adsorption of gas molecules can effectively modulate the band alignment at the junction interface, making the device a highly sensitive detector for chemical adsorptions. Compared to sensors made of homogeneous nanomaterials, the hetero-junction demonstrates considerably lower detection limit and higher sensitivity toward nitrogen dioxide. Kelvin probe force microscopy and finite element simulations have provided experimental and theoretical explanations for the enhanced performance, proving that chemical adsorption can induce significant changes in band alignment and carrier transport behaviors. The study demonstrates the potential of van der Waals hetero-junction as a new platform for sensing applications, and provides more insights into the interaction between gaseous molecules and 2D hetero-structures.

  5. Economic Crisis and Industrial Structure of the Chemical Sector in Italy

    OpenAIRE

    Vitali Giampaolo

    2010-01-01

    The paper aim is to highlight the transformation of the chemical industry in Italy, after the declining of the large companies (Montedison, Enimont, Snia, etc.) and the rising of many medium- sized firms that have a good international competitiveness. The paper explores the characteristics of the sector: large presence of foreign MNEs, strong links between chemical industry and industrial district productions, high company specialization. The focus is on the competitive advantage of the Itali...

  6. Preparedness of emergency departments in northwest England for managing chemical incidents: a structured interview survey

    OpenAIRE

    Walter Darren; Williams Jane; Challen Kirsty

    2007-01-01

    Abstract Background A number of significant chemical incidents occur in the UK each year and may require Emergency Departments (EDs) to receive and manage contaminated casualties. Previously UK EDs have been found to be under-prepared for this, but since October 2005 acute hospital Trusts have had a statutory responsibility to maintain decontamination capacity. We aimed to evaluate the level of preparedness of Emergency Departments in North West England for managing chemical incidents. Method...

  7. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    International Nuclear Information System (INIS)

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary

  8. Structural, chemical surface and transport modifications of regenerated cellulose dense membranes due to low-dose {gamma}-radiation

    Energy Technology Data Exchange (ETDEWEB)

    Vazquez, M.I. [Grupo de Caracterizacion Electrocinetica en Membranas e Interfases, Departamento de Fisica Aplicada I, Facultad de Ciencias, Universidad de Malaga, E-29071 Malaga (Spain); Heredia-Guerrero, J.A., E-mail: jose.alejandro@icmse.csic.es [Instituto de Ciencia de Materiales de Sevilla, Centro Mixto CSIC-Universidad de Sevilla, Avda, Americo Vespuccio 49, 41092 Sevilla (Spain); Galan, P. [Grupo de Caracterizacion Electrocinetica en Membranas e Interfases, Departamento de Fisica Aplicada I, Facultad de Ciencias, Universidad de Malaga, E-29071 Malaga (Spain); Benitez, J.J. [Instituto de Ciencia de Materiales de Sevilla, Centro Mixto CSIC-Universidad de Sevilla, Avda, Americo Vespuccio 49, 41092 Sevilla (Spain); Benavente, J. [Grupo de Caracterizacion Electrocinetica en Membranas e Interfases, Departamento de Fisica Aplicada I, Facultad de Ciencias, Universidad de Malaga, E-29071 Malaga (Spain)

    2011-04-15

    Research highlights: {yields} Low dose {gamma}-radiation causes slight structural, chemical and morphological changes on regenerated cellulose films. {yields} Induced structural changes increase the fragility of irradiated films. {yields} Structural modifications reduce ion permeability of films. - Abstract: Modifications caused in commercial dense regenerated cellulose (RC) flat membranes by low-dose {gamma}-irradiation (average photons energy of 1.23 MeV) are studied. Slight structural, chemical and morphological surface changes due to irradiation in three films with different RC content were determined by ATR-FTIR, XRD, XPS and AFM. Also, the alteration of their mechanical elasticity has been studied. Modification of membrane performance was determined from solute diffusion coefficient and effective membrane fixed charge concentration obtained from NaCl diffusion measurements. Induced structural changes defining new and effective fracture propagation directions are considered to be responsible for the increase of fragility of irradiated RC membranes. The same structural changes are proposed to explain the reduction of the membrane ion permeability through a mechanism involving either ion pathways elongation and/or blocking.

  9. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

    Science.gov (United States)

    Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H

    2015-11-17

    Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.

  10. NMR structure calculation for all small molecule ligands and non-standard residues from the PDB Chemical Component Dictionary

    Energy Technology Data Exchange (ETDEWEB)

    Yilmaz, Emel Maden; Güntert, Peter, E-mail: guentert@em.uni-frankfurt.de [Goethe University Frankfurt am Main, Center for Biomolecular Magnetic Resonance, Institute of Biophysical Chemistry (Germany)

    2015-09-15

    An algorithm, CYLIB, is presented for converting molecular topology descriptions from the PDB Chemical Component Dictionary into CYANA residue library entries. The CYANA structure calculation algorithm uses torsion angle molecular dynamics for the efficient computation of three-dimensional structures from NMR-derived restraints. For this, the molecules have to be represented in torsion angle space with rotations around covalent single bonds as the only degrees of freedom. The molecule must be given a tree structure of torsion angles connecting rigid units composed of one or several atoms with fixed relative positions. Setting up CYANA residue library entries therefore involves, besides straightforward format conversion, the non-trivial step of defining a suitable tree structure of torsion angles, and to re-order the atoms in a way that is compatible with this tree structure. This can be done manually for small numbers of ligands but the process is time-consuming and error-prone. An automated method is necessary in order to handle the large number of different potential ligand molecules to be studied in drug design projects. Here, we present an algorithm for this purpose, and show that CYANA structure calculations can be performed with almost all small molecule ligands and non-standard amino acid residues in the PDB Chemical Component Dictionary.

  11. Nontarget effects of chemical pesticides and biological pesticide on rhizospheric microbial community structure and function in Vigna radiata.

    Science.gov (United States)

    Singh, Sunil; Gupta, Rashi; Kumari, Madhu; Sharma, Shilpi

    2015-08-01

    Intensive agriculture has resulted in an indiscriminate use of pesticides, which demands in-depth analysis of their impact on indigenous rhizospheric microbial community structure and function. Hence, the objective of the present work was to study the impact of two chemical pesticides (chlorpyrifos and cypermethrin) and one biological pesticide (azadirachtin) at two dosages on the microbial community structure using cultivation-dependent approach and on rhizospheric bacterial communities involved in nitrogen cycle in Vigna radiata rhizosphere through cultivation-independent technique of real-time PCR. Cultivation-dependent study highlighted the adverse effects of both chemical pesticide and biopesticide on rhizospheric bacterial and fungal communities at different plant growth stages. Also, an adverse effect on number of genes and transcripts of nifH (nitrogen fixation); amoA (nitrification); and narG, nirK, and nirS (denitrification) was observed. The results from the present study highlighted two points, firstly that nontarget effects of pesticides are significantly detrimental to soil microflora, and despite being of biological origin, azadirachtin exerted negative impact on rhizospheric microbial community of V. radiata behaving similar to chemical pesticides. Hence, such nontarget effects of chemical pesticide and biopesticide in plants' rhizosphere, which bring out the larger picture in terms of their ecotoxicological effect, demand a proper risk assessment before application of pesticides as agricultural amendments. PMID:25801369

  12. Dissecting the chemical interactions and substrate structural signatures governing RNA polymerase II trigger loop closure by synthetic nucleic acid analogues

    DEFF Research Database (Denmark)

    Xu, Liang; Butler, Kyle Vincent; Chong, Jenny;

    2014-01-01

    The trigger loop (TL) of RNA polymerase II (Pol II) is a conserved structural motif that is crucial for Pol II catalytic activity and transcriptional fidelity. The TL remains in an inactive open conformation when the mismatched substrate is bound. In contrast, TL switches from an inactive open...... state to a closed active state to facilitate nucleotide addition upon the binding of the cognate substrate to the Pol II active site. However, a comprehensive understanding of the specific chemical interactions and substrate structural signatures that are essential to this TL conformational change...... II. This study reveals novel insights into understanding the molecular basis of TL conformational transition upon substrate binding during Pol II transcription. This synthetic chemical biology approach may be extended to understand the mechanisms of other RNA polymerases as well as other nucleic acid...

  13. A chemically stable electrolyte with a novel sandwiched structure for proton-conducting solid oxide fuel cells (SOFCs)

    KAUST Repository

    Bi, Lei

    2013-11-01

    A chemically stable electrolyte structure was developed for proton-conducting SOFCs by using two layers of stable BaZr0.7Pr 0.1Y0.2O3 -δ to sandwich a highly-conductive but unstable BaCe0.8Y0.2O 3 -δ electrolyte layer. The sandwiched electrolyte structure showed good chemical stability in both CO2 and H2O atmosphere, indicating that the BZPY layers effectively protect the inner BCY electrolyte, while the BCY electrolyte alone decomposed completely under the same conditions. Fuel cell prototypes fabricated with the sandwiched electrolyte achieved a relatively high performance of 185 mW cm- 2 at 700 C, with a high electrolyte film conductivity of 4 × 10- 3 S cm- 1 at 600 C. © 2013 Elsevier B.V.

  14. Chemical composition and molecular structure of polysaccharide-protein biopolymer from Durio zibethinus seed: extraction and purification process

    Directory of Open Access Journals (Sweden)

    Amid Bahareh

    2012-10-01

    Full Text Available Abstract Background The biological functions of natural biopolymers from plant sources depend on their chemical composition and molecular structure. In addition, the extraction and further processing conditions significantly influence the chemical and molecular structure of the plant biopolymer. The main objective of the present study was to characterize the chemical and molecular structure of a natural biopolymer from Durio zibethinus seed. A size-exclusion chromatography coupled to multi angle laser light-scattering (SEC-MALS was applied to analyze the molecular weight (Mw, number average molecular weight (Mn, and polydispersity index (Mw/Mn. Results The most abundant monosaccharide in the carbohydrate composition of durian seed gum were galactose (48.6-59.9%, glucose (37.1-45.1%, arabinose (0.58-3.41%, and xylose (0.3-3.21%. The predominant fatty acid of the lipid fraction from the durian seed gum were palmitic acid (C16:0, palmitoleic acid (C16:1, stearic acid (C18:0, oleic acid (C18:1, linoleic acid (C18:2, and linolenic acid (C18:2. The most abundant amino acids of durian seed gum were: leucine (30.9-37.3%, lysine (6.04-8.36%, aspartic acid (6.10-7.19%, glycine (6.07-7.42%, alanine (5.24-6.14%, glutamic acid (5.57-7.09%, valine (4.5-5.50%, proline (3.87-4.81%, serine (4.39-5.18%, threonine (3.44-6.50%, isoleucine (3.30-4.07%, and phenylalanine (3.11-9.04%. Conclusion The presence of essential amino acids in the chemical structure of durian seed gum reinforces its nutritional value.

  15. Delayed stage-structured predator-prey model with impulsive perturbations on predator and chemical control on prey

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    We consider a delayed stage-structured pest management predator-prey system with impulsive transmitting on predator and chemical control on prey. Sufficient conditions of the global attractiveness of the pest-extinction boundary periodic solution and permanence of the system are obtained. We also prove that all solutions of the system are uniformly ultimately bounded. Our results provide reliable tactical basis for practical pest management.

  16. Correlation between magnetic spin structure and the three-dimensional geometry in chemically synthesized nanoscale magnetite rings

    DEFF Research Database (Denmark)

    Eltschka, M.; Klaui, M.; Rudiger, U;

    2008-01-01

    The correlation between magnetic spin structure and geometry in nanoscale chemically synthesized Fe3O4 rings has been investigated by transmission electron microscopy. We find primarily the flux closure vortex states but in rings with thickness variations, an effective stray field occurs. Using t...... interaction between exchange coupled rings leads to antiparallel vortex states and extended onion states. (c) 2008 American Institute of Physics....

  17. Computer modelling system of the chemical composition and treatment parameters influence on mechanical properties of structural steels

    OpenAIRE

    L.A. Dobrzański; R. Honysz

    2009-01-01

    Purpose: This paper presents Neuro-Lab. It is an authorship programme, which use algorithms of artificial intelligence for structural steels mechanical properties estimation.Design/methodology/approach: On the basis of chemical composition, parameters of heat and mechanical treatment and elements of geometrical shape and size this programme has the ability to calculate the mechanical properties of examined steel and introduce them as raw numeric data or in graphic as influence charts. Possibl...

  18. Chemical Structure, Property and Potential Applications of Biosurfactants Produced by Bacillus subtilis in Petroleum Recovery and Spill Mitigation

    OpenAIRE

    Jin-Feng Liu; Serge Maurice Mbadinga; Shi-Zhong Yang; Ji-Dong Gu; Bo-Zhong Mu

    2015-01-01

    Lipopeptides produced by microorganisms are one of the five major classes of biosurfactants known and they have received much attention from scientific and industrial communities due to their powerful interfacial and biological activities as well as environmentally friendly characteristics. Microbially produced lipopeptides are a series of chemical structural analogues of different families and, among them, 26 families covering about 90 lipopeptide compounds have been reported in the last tw...

  19. The Molecular Surface Structure of Ammonium and Potassium Dinitramide : A Vibrational Sum Frequency Spectroscopy and Quantum Chemical Study

    OpenAIRE

    Rahm, Martin; Tyrode, Eric; Brinck, Tore; Johnson, Magnus

    2011-01-01

    Vibrational sum frequency spectroscopy (VSFS) and quantum chemical modeling have been employed to investigate the molecular surface structure of ammonium and potassium dinitramide (ADN and KDN) crystals. Identification of key vibrational modes was made possible by performing density functional theory calculations of molecular clusters. The surface of KDN was found to be partly covered with a thin layer of the decomposition product KNO3, which due to its low thickness was not detectable by inf...

  20. Structural and stability investigation of the anticancer drug Cyclophosphamide via quantum chemical calculations :A nanotube drug delivery

    Directory of Open Access Journals (Sweden)

    Z. Felegari

    2014-12-01

    Full Text Available Cyclophosphamide is a medicine used to interfere with the growth and spread of tumor cells and treat cancers and autoimmune disorders.This work reports the study of anticancer drugs with density functional theory (DFT and electronic structures.Its structure was optimized with B3LYP/6-311G* level in the gas phase and different solvents (SCRF calculation. NBO analysis,NMR parameter,thermodynamic properties,HOMO and LUMO,HOMO-LUMO band gap, and the electronic chemical potential (µ were calculated. The results indicated that the Cyclophosphamide in water solvent is more stable than the gas phase orother solvents.

  1. Investigation of Welding Processes of Multilayers Structures Composed from Different Chemical Composition Crystallites by Vacuum Hot Rolling

    International Nuclear Information System (INIS)

    Promising method of laminated composite materials production is the method of metal pack rolling in vacuum. The proposed method is based on the welding of heterogeneous materials in solid phase, that contain easily oxidized metals and alloys. Processes occurring during multi layer structures of different chemical composition welding are examined. On the example of multi layer structure Ti-Nb-Cu steel forces operating on the materials in the pack are studied. The welding of strata of laminas is studied on a metallographic microscope and with help of an electronic raster microscopy is learnt mass transfer of one material in other

  2. Effect of acetylene flow rate on morphology and structure of carbon nanotube thick films grown by thermal chemical vapor deposition

    Institute of Scientific and Technical Information of China (English)

    CAO Zhangyi; SUN Zhuo; GUO Pingsheng; CHEN Yiwei

    2007-01-01

    Carbon nanotube (CNT) films were grown on nickel foil substrates by thermal chemical vapor deposition (CVD) with acetylene and hydrogen as the precursors. The morphology and structure of CNTs depending on the acetylene flow rate were characterized by a scanning electron microscope (SEM),a transmission electron microscope (TEM) and a Raman spectrometer,respectively.The effect of acetylene flow rate on the morphology and structure of CNT films was investigated.By increasing the acetylene flow rate from 10 to 90 sccm (standard cubic centimeter perminute),the yield and the diameter of CNTs increase.Also, the defects and amorphous phase in CNT films increase with increasing acetylene flow rate.

  3. First-principles study of magnetism, structure and chemical order in small FeRh alloy clusters

    OpenAIRE

    Mokkath, Junais Habeeb; Pastor, G. M.

    2011-01-01

    The structural, electronic and magnetic properties of small ${\\rm Fe}_m {\\rm Rh}_n$ clusters having $N = m+n \\leq 8$ atoms are studied in the framework of a generalized-gradient approximation to density-functional theory. The correlation between structure, chemical order, and magnetic behavior is analyzed as a function of size and composition. For $N = m+n \\leq 6$ a thorough sampling of all cluster topologies has been performed, while for N = 7 and 8 only a few representative topologies are c...

  4. Optimizing the Binding Energy of Hydrogen on Nanostructured Carbon Materials through Structure Control and Chemical Doping

    Energy Technology Data Exchange (ETDEWEB)

    Jie Liu

    2011-02-01

    The DOE Hydrogen Sorption Center of Excellence (HSCoE) was formed in 2005 to develop materials for hydrogen storage systems to be used in light-duty vehicles. The HSCoE and two related centers of excellence were created as follow-on activities to the DOE Office of Energy Efficiency and Renewable Energy’s (EERE’s) Hydrogen Storage Grand Challenge Solicitation issued in FY 2003. The Hydrogen Sorption Center of Excellence (HSCoE) focuses on developing high-capacity sorbents with the goal to operate at temperatures and pressures approaching ambient and be efficiently and quickly charged in the tank with minimal energy requirements and penalties to the hydrogen fuel infrastructure. The work was directed at overcoming barriers to achieving DOE system goals and identifying pathways to meet the hydrogen storage system targets. To ensure that the development activities were performed as efficiently as possible, the HSCoE formed complementary, focused development clusters based on the following four sorption-based hydrogen storage mechanisms: 1. Physisorption on high specific surface area and nominally single element materials 2. Enhanced H2 binding in Substituted/heterogeneous materials 3. Strong and/or multiple H2 binding from coordinated but electronically unsatruated metal centers 4. Weak Chemisorption/Spillover. As a member of the team, our group at Duke studied the synthesis of various carbon-based materials, including carbon nanotubes and microporous carbon materials with controlled porosity. We worked closely with other team members to study the effect of pore size on the binding energy of hydrogen to the carbon –based materials. Our initial project focus was on the synthesis and purification of small diameter, single-walled carbon nanotubes (SWNTs) with well-controlled diameters for the study of their hydrogen storage properties as a function of diameters. We developed a chemical vapor deposition method that synthesized gram quantities of carbon nanotubes with

  5. Exploiting Chemical Libraries, Structure, and Genomics in the Search for Kinase Inhibitors

    NARCIS (Netherlands)

    Gray, Nathanael S.; Wodicka, Lisa; Thunnissen, Andy-Mark W.H.; Norman, Thea C.; Kwon, Soojin; Espinoza, F. Hernan; Morgan, David O.; Barnes, Georjana; LeClerc, Sophie; Meijer, Laurent; Kim, Sung-Hou; Lockhart, David J.; Schultz, Peter G.

    1998-01-01

    Selective protein kinase inhibitors were developed on the basis of the unexpected binding mode of 2,6,9-trisubstituted purines to the adenosine triphosphate-binding site of the human cyclin-dependent kinase 2 (CDK2). By iterating chemical library synthesis and biological screening, potent inhibitors

  6. Heterogeneity in physical, chemical and plankton-community structures in Lake Tanganyika

    NARCIS (Netherlands)

    Langenberg, V.T.; Tumba, J.M.; Tshibangu, K.; Lukwesa, C.; Chitamwebwa, D.; Bwebwa, D.; Makasa, L.; Roijackers, R.M.M.

    2008-01-01

    From 28 August to 6 September 1995, we monitored the lake-wide physical, chemical and biological properties of the pelagic waters in Lake Tanganyika. The aim of this study was to examine the spatial environmental variability and its relation to fluctuations in plankton abundance and community assemb

  7. Structural, chemical and magnetic properties of secondary phases in Co-doped ZnO

    DEFF Research Database (Denmark)

    Ney, A; Kovács, András; Ney, V;

    2011-01-01

    , chemical and magnetic properties of Co-doped ZnO samples. It can be established on a quantitative basis that the superparamagnetic (SPM) behavior observed by integral superconducting quantum interference device magnetometry is not an intrinsic property of the material but stems from precipitations...

  8. Structural, chemical and optical evaluation of Cu-doped ZnO nanoparticles synthesized by an aqueous solution method

    Energy Technology Data Exchange (ETDEWEB)

    Iribarren, A., E-mail: augusto@imre.oc.uh.cu [Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, Zapata y G, Vedado, Plaza, La Habana 10400 (Cuba); Hernández-Rodríguez, E. [Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, Zapata y G, Vedado, Plaza, La Habana 10400 (Cuba); Maqueira, L. [Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, Zapata y G, Vedado, Plaza, La Habana 10400 (Cuba); Facultad de Química, Universidad de La Habana, Zapata y G, Vedado, Plaza, La Habana 10400 (Cuba)

    2014-12-15

    Highlights: • Cu-doped ZnO nanoparticles obtained by chemical synthesis. • Substitutional or interstitial Cu into ZnO lead specific structural, chemical, and optical changes. • Incorporation efficiency of Cu atoms in ZnO as a function of the Cu concentration in the precursor dissolution. - Abstract: In this work a study of ZnO and Cu-doped ZnO nanoparticles obtained by chemical synthesis in aqueous media was carried out. Structural analysis gave the dominant presence of wurtzite ZnO phase forming a solid solution Zn{sub 1−x}Cu{sub x}O. For high Cu doping CuO phase is also present. For low Cu concentration the lattice shrinks due to Cu atoms substitute Zn atoms. For high Cu concentration the lattice enlarges due to predominance of interstitial Cu. From elemental analysis we determined and analyzed the incorporation efficiency of Cu atoms in Zn{sub 1−x}Cu{sub x}O as a function of the Cu concentration in the precursor dissolution. Combining structural and chemical results we described the Cu/Zn precursor concentrations r{sub w} in which the solid solution of Cu in ZnO is predominant. In the region located at r{sub w} ≈ 0.2–0.3 it is no longer valid. For Cu/Zn precursor concentration r{sub w} > 0.3 interstitial Cu dominates, and some amount of copper oxide appears. As the Cu concentration increases, the effective size of nanoparticles decreases. Photoluminescence (PL) measurements of the Cu-doped ZnO nanoparticles were carried out and analyzed.

  9. Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

    Science.gov (United States)

    Kravchenko, Alexandra; Grandy, Stuart A.

    2014-05-01

    Understanding chemical structure of soil organic matter (SOM) and factors that affect it are vital for gaining understanding of mechanisms of C sequestration by soil. Physical protection of C by adsorption to mineral particles and physical disconnection between C sources and microbial decomposers is now regarded as the key component of soil C sequestration. Both of the processes are greatly influenced by micro-scale structure and distribution of soil pores. However, because SOM chemical structure is typically studied in disturbed (ground and sieved) soil samples the experimental evidence of the relationships between soil pore structure and chemical structure of SOM are still scarce. Our study takes advantage of the X-ray computed micro-tomography (µ-CT) tools that enable non-destructive analysis of pore structure in intact soil samples. The objective of this study is to examine the relationship between SOM chemical structure and pore-characteristics in intact soil macro-aggregates from two contrasting long-term land uses. The two studied land use treatments are a conventionally tilled corn-soybean-wheat rotation treatment and a native succession vegetation treatment removed from agricultural use >20 years ago. The study is located in southwest Michigan, USA, on sandy-loam Typic Hapludalfs. For this study we used soil macro-aggregates 4-6 mm in size collected at 0-15 cm depth. The aggregate size was selected so as both to enable high resolution of µ-CT and to provide sufficient amount of soil for C measurements. X-ray µ-CT scanning was conducted at APS Argonne at a scanning resolution of 14 µm. Two scanned aggregates (1 per treatment) were used in this preliminary study. Each aggregate was cut into 7 "geo-referenced" sections. Analyses of pore characteristics in each section were conducted using 3DMA and ImageJ image analysis tools. SOM chemistry was analyzed using pyrolysis/gas chromatography-mass spectroscopy. Results demonstrated that the relationships

  10. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso). PMID:26787258

  11. Elucidating the Link between NMR Chemical Shifts and Electronic Structure in d(0) Olefin Metathesis Catalysts.

    Science.gov (United States)

    Halbert, Stéphanie; Copéret, Christophe; Raynaud, Christophe; Eisenstein, Odile

    2016-02-24

    The nucleophilic carbon of d(0) Schrock alkylidene metathesis catalysts, [M] = CHR, display surprisingly low downfield chemical shift (δ(iso)) and large chemical shift anisotropy. State-of-the-art four-component relativistic calculations of the chemical shift tensors combined with a two-component analysis in terms of localized orbitals allow a molecular-level understanding of their orientations, the magnitude of their principal components (δ11 > δ22 > δ33) and associated δ(iso). This analysis reveals the dominating influence of the paramagnetic contribution yielding a highly deshielded alkylidene carbon. The largest paramagnetic contribution, which originates from the coupling of alkylidene σ(MC) and π*(MC) orbitals under the action of the magnetic field, is analogous to that resulting from coupling σ(CC) and π*(CC) in ethylene; thus, δ11 is in the MCH plane and is perpendicular to the MC internuclear direction. The higher value of carbon-13 δ(iso) in alkylidene complexes relative to ethylene is thus due to the smaller energy gap between σ(MC) and π*(MC) vs this between σ(CC) and π*(CC) in ethylene. This effect also explains why the highest value of δ(iso) is observed for Mo and the lowest for Ta, the values for W and Re being in between. In the presence of agostic interaction, the chemical shift tensor principal components orientation (δ22 or δ33 parallel or perpendicular to π(MX)) is influenced by the MCH angle because it determines the orientation of the alkylidene CHR fragment relative to the MC internuclear axis. The orbital analysis shows how the paramagnetic terms, understood with a localized bond model, determine the chemical shift tensor and thereby δ(iso).

  12. Optical properties and surface structure comparison of tooth whitening using four laser systems and chemical action agents

    Science.gov (United States)

    Dostalova, Tatjana; Jelinkova, Helena; Koranda, Pavel; Nemec, Michal; Sulc, Jan; Housova, Devana; Miyagi, Mitsunobu; Kokta, Milan R.

    2003-06-01

    The purpose of the study is to evaluate the effect of various laser techniques for bleaching teeth in office vital whitening. Hydrogen peroxide (30% concentration) and carbamide peroxide (10% solution) were used for chemical activation of bleaching process. Extracted non-carcious upper central incisors were exposed to laser radiation. Four different laser systems (Nd:YAG laser SHG, wavelength 0.53 μm, CTE:YAG laser, wavelength 2.7 μm, Nd:YAG laser, wavelength 1.06 μm, and alexandrite laser, wavelength 0.75 μm) were applied to accelerate the speed of the process. The end of chemical exposition was verified by the change of bleaching agent color. The color change was determined by stereomicroscope (Nikon SMZ 2T, Japan), the quality of surface structure was checked by scanning electron microscope Joel, Japan). The speed of bleaching rnaged from 630 s (chemical methods only) to 250-340 s (chemicals + alexandrite laser radiation). The Alexandrite laser application was considered an elective process to decrease the time of bleaching without modifying the surface.

  13. Survey of marine natural product structure revisions: a synergy of spectroscopy and chemical synthesis

    OpenAIRE

    Suyama, Takashi L.; Gerwick, William H.; McPhail, Kerry L.

    2011-01-01

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of m...

  14. Quantum Chemical Study on Structure-activity Relationship of Several Kinds of Drugs

    Institute of Scientific and Technical Information of China (English)

    LI Xiao-Hong; CHENG Xin-Lu; ZHANG Rui-Zhou; YANG Xiang-Dong

    2005-01-01

    The structure-activity relationship of several drugs with similar structure has been investigated by using ab initio method.The relation between the dipole moments and biological activities of these drugs was judged after comparing their geometric structures, dipole moments and inhibitory concentrations.In principle, new drug molecule could be reasonably designed by altering the place of groups and ultimately, the potential drug could be screened by comparing the dipole moments of obtained molecules.

  15. Effects of LiCl/DMSO dissolution and enzymatic hydrolysis on the chemical composition and lignin structure of rice straw

    International Nuclear Information System (INIS)

    The exploration of solvent system to completely dissolve lignocellulosic biomass is of great important for the development of biomass based materials and chemicals. Dimethyl sulfoxide containing certain amount of lithium chloride (LiCl/DMSO) was proved an effective solvent system for the dissolution of ball-milled wood. In this paper, four samples of rice straw, internode (stem without node), stem, leaf (leaf and sheath) and whole straw, with and without 1 h of ball milling treatment, were used to investigate the effects of their dissolution in LiCl/DMSO solvent on the chemical composition of regenerated and enzymatically hydrolyzed materials. Because of the structural difference from wood, samples expose d to 1 h of milling were almost completely dissolved. The chemical nature of the regenerated material and of residual after enzymatic hydrolysis of rice straw was analyzed and the susceptibility of this rice straw to the enzymatic hydrolysis was evaluated. - Highlights: • Rice straw with 1 h ball milling can be completely dissolved in 8% LiCl/DMSO. • About 1/4 of lignin lost after ball milling and LiCl/DMSO dissolution/regeneration. • The efficiency of enzymatic hydrolysis was effectively improved. • The structure of lignin in stem is rather different with that in leaf. • It is probably that straw lignin in LCC has a higher degree of condensation

  16. Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

    Energy Technology Data Exchange (ETDEWEB)

    Singh, Sunil; Gupta, Rashi; Sharma, Shilpi, E-mail: shilpi@dbeb.iitd.ac.in

    2015-06-30

    Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture.

  17. Effects of chemical and biological pesticides on plant growth parameters and rhizospheric bacterial community structure in Vigna radiata

    International Nuclear Information System (INIS)

    Highlights: • Non-target effects of pesticides employing qualitative and quantitative approaches. • Qualitative shifts in resident and active bacterial community structure. • Abundance of 16S rRNA gene and transcripts were reduced significantly. • Effects of biological pesticide similar to chemical pesticides on rhizospheric bacteria. - Abstract: With increasing application of pesticides in agriculture, their non-target effects on soil microbial communities are critical to soil health maintenance. The present study aimed to evaluate the effects of chemical pesticides (chlorpyrifos and cypermethrin) and a biological pesticide (azadirachtin) on growth parameters and the rhizospheric bacterial community of Vigna radiata. Qualitative and quantitative analysis by PCR-denaturing gradient gel electrophoresis (DGGE) and q-PCR, respectively, of the 16S rRNA gene and transcript were performed to study the impact of these pesticides on the resident and active rhizospheric bacterial community. While plant parameters were not affected significantly by the pesticides, a shift in the bacterial community structure was observed with an adverse effect on the abundance of 16S rRNA gene and transcripts. Chlorpyrifos showed almost complete degradation toward the end of the experiment. These non-target impacts on soil ecosystems and the fact that the effects of the biopesticide mimic those of chemical pesticides raise serious concerns regarding their application in agriculture

  18. Structural and XPS studies of PSi/TiO2 nanocomposites prepared by ALD and Ag-assisted chemical etching

    International Nuclear Information System (INIS)

    Highlights: • Porous silicon/TiO2 nanocomposites have been investigated. • Morphology and chemical composition of PSi/TiO2 nanocomposites were established. • Valence-band XPS maximums for PSi/TiO2 nanocomposites were found and analyzed. - Abstract: PSi/TiO2 nanocomposites fabricated by atomic layer deposition (ALD) and metal-assisted chemical etching (MACE) were investigated. The morphology and phase structure of PSi/TiO2 nanocomposites were studied by means of scanning electron microscopy (SEM), transmission electron microscopy (TEM) with an energy dispersive X-ray spectroscopy (EDX) and Raman spectroscopy. The mean size of TiO2 nanocrystals was determined by TEM and Raman spectroscopy. X-ray photoelectron spectroscopy (XPS) was used to analyze the chemical elemental composition by observing the behavior of the Ti 2p, O 1s and Si 2p lines. TEM, Raman spectroscopy and XPS binding energy analysis confirmed the formation of TiO2 anatase phase inside the PSi matrix. The XPS valence band analysis was performed in order to investigate the modification of PSi/TiO2 nanocomposites electronic structure. Surface defects states of Ti3+ at PSi/TiO2 nanocomposites were identified by analyzing of XPS valence band spectra

  19. Fabrication of broadband antireflective black metal surfaces with ultra-light-trapping structures by picosecond laser texturing and chemical fluorination

    Science.gov (United States)

    Zheng, Buxiang; Wang, Wenjun; Jiang, Gedong; Mei, Xuesong

    2016-06-01

    A hybrid method consisting of ultrafast laser-assisted texturing and chemical fluorination treatment was applied for efficiently enhancing the surface broadband antireflection to fabricate black titanium alloy surface with ultra-light-trapping micro-nanostructure. Based on the theoretical analysis of surface antireflective principle of micro-nanostructures and fluoride film, the ultra-light-trapping micro-nanostructures have been processed using a picosecond pulsed ultrafast laser on titanium alloy surfaces. Then fluorination treatment has been performed by using fluoroalkyl silane solution. According to X-ray diffraction phase analysis of the surface compositions and measurement of the surface reflectance using spectrophotometer, the broadband antireflective properties of titanium alloy surface with micro-nano structural characteristics were investigated before and after fluorination treatment. The results show that the surface morphology of micro-nanostructures processed by picosecond laser has significant effects on the antireflection of light waves to reduce the surface reflectance, which can be further reduced using chemical fluorination treatment. The high antireflection of over 98 % in a broad spectral range from ultraviolet to infrared on the surface of metal material has been achieved for the surface structures, and the broadband antireflective black metal surfaces with an extremely low reflectance of ultra-light-trapping structures have been obtained in the wavelength range from ultraviolet-visible to near-infrared, middle-wave infrared. The average reflectance of microgroove groups structured surface reaches as low as 2.43 % over a broad wavelength range from 200 to 2600 nm. It indicates that the hybrid method comprising of picosecond laser texturing and chemical fluorination can effectively induce the broadband antireflective black metal surface. This method has a potential application for fabricating antireflective surface used to improve the

  20. Effect of anatomical and chemical structure in the permeability of "Amapá" wood

    Directory of Open Access Journals (Sweden)

    Edy Eime Pereira Baraúna

    2014-12-01

    Full Text Available This paper aimed to study the permeability to air and liquid, in the longitudinal direction of "amapá" wood (Brosimum parinarioides Ducke, originating from the Amazon Forest. Furthermore, the influence of anatomical and chemical characteristics in the permeability of the wood was investigated. For this study, samples were collected from three trees, in the state of Pará, Brazil, and submitted to permeability test, anatomical characterization, and chemical analyses. The permeability to the air of the "amapá" wood was estimated at 63.7.10-9 m3.[m.(N.m-2.s]-1 and to the liquid was 2.07.10-9 m3.[m.(N.m-2.s]-1. There were low correlations between air and liquid permeability and the anatomical features.

  1. Structural, optical and photocatalytic properties of flower-like ZnO nanostructures prepared by a facile wet chemical method

    Directory of Open Access Journals (Sweden)

    Sini Kuriakose

    2013-11-01

    Full Text Available Flower-like ZnO nanostructures were synthesized by a facile wet chemical method. Structural, optical and photocatalytic properties of these nanostructures have been studied by X-ray diffraction (XRD, scanning electron microscopy (SEM, transmission electron microscopy (TEM, photoluminescence (PL and UV–vis absorption spectroscopy. SEM and TEM studies revealed flower-like structures consisting of nanosheets, formed due to oriented attachment of ZnO nanoparticles. Flower-like ZnO structures showed enhanced photocatalytic activity towards sun-light driven photodegradation of methylene blue dye (MB as compared to ZnO nanoparticles. XRD, UV–vis absorption, PL, FTIR and TEM studies revealed the formation of Zn(OH2 surface layer on ZnO nanostructures upon ageing. We demonstrate that the formation of a passivating Zn(OH2 surface layer on the ZnO nanostructures upon ageing deteriorates their efficiency to photocatalytically degrade of MB.

  2. Structure and physico-chemical properties in mixed aqueoussolution of sodium alkylcarboxylate-alkyltrimethylammoniumbromide

    Institute of Scientific and Technical Information of China (English)

    HUANG, Jian-Bin(黄建滨); ZHAO, Guo-Xi(赵国玺); HE, Xu(何煦); ZHU, Bu-Yao(朱步瑶); FU, Hong-Lan(付宏兰)

    2000-01-01

    The physico-chemical properties of organized assemblies (micelle or vesicle) from sodium alkylcarboxylate-alkyltrimethyl-ammonium bromide mixture have been investigated systematically. In different mixed cationic-anionic surfactant systems, micelles and vesicles can coexist or be transformed into each other on different conditions. The experimental results are explained prelimilarily from the viewpoint of molecular packing geometry. The solubilization of organic compound in the mixed surfactant system was also studied in detail.

  3. Structural, chemical and deformation changes in friction welded joint of dissimilar steels

    OpenAIRE

    Ratković, N.; R. Nikolić; I. Samardžić

    2014-01-01

    Fundamental principles of friction welding of dissimilar steels (high speed and tempering steel) from the aspect of metallurgical and chemical processes occurring in the joint zone are presented in this paper. Considering that phenomena accompanying the friction welding are interdependent, it was necessary to experimentally determine the process variable parameters, to establish the optimal welding regime. The experiments were set and realized so that all the variables were analyzed as a func...

  4. THERMAL AND CHEMICAL STRUCTURE VARIATIONS IN TITAN'S STRATOSPHERE DURING THE CASSINI MISSION

    Energy Technology Data Exchange (ETDEWEB)

    Bampasidis, Georgios; Coustenis, A.; Vinatier, S. [Laboratoire d' Etudes Spatiales et d' Instrumentation en Astrophysique (LESIA), Observatoire de Paris, CNRS, UPMC Univ. Paris 06, Univ. Paris-Diderot, 5, place Jules Janssen, F-92195 Meudon Cedex (France); Achterberg, R. K. [Department of Astronomy, University of Maryland, College Park, MD 20742 (United States); Lavvas, P. [GSMA, Universite Reims Champagne-Ardenne, F-51687 Reims Cedex 2 (France); Nixon, C. A.; Jennings, D. E.; Flasar, F. M.; Carlson, R. C.; Romani, P. N.; Guandique, E. A. [Goddard Space Flight Center, Greenbelt, MD 20771 (United States); Teanby, N. A. [School of Earth Sciences, University of Bristol, Bristol BS8 1RJ (United Kingdom); Moussas, X.; Preka-Papadema, P.; Stamogiorgos, S., E-mail: gbabasid@phys.uoa.gr [Faculty of Physics, National and Kapodistrian University of Athens, Panepistimioupolis, GR 15783 Zographos, Athens (Greece)

    2012-12-01

    We have developed a line-by-line Atmospheric Radiative Transfer for Titan code that includes the most recent laboratory spectroscopic data and haze descriptions relative to Titan's stratosphere. We use this code to model Cassini Composite Infrared Spectrometer data taken during the numerous Titan flybys from 2006 to 2012 at surface-intercepting geometry in the 600-1500 cm{sup -1} range for latitudes from 50 Degree-Sign S to 50 Degree-Sign N. We report variations in temperature and chemical composition in the stratosphere during the Cassini mission, before and after the Northern Spring Equinox (NSE). We find indication for a weakening of the temperature gradient with warming of the stratosphere and cooling of the lower mesosphere. In addition, we infer precise concentrations for the trace gases and their main isotopologues and find that the chemical composition in Titan's stratosphere varies significantly with latitude during the 6 years investigated here, with increased mixing ratios toward the northern latitudes. In particular, we monitor and quantify the amplitude of a maximum enhancement of several gases observed at northern latitudes up to 50 Degree-Sign N around mid-2009, at the time of the NSE. We find that this rise is followed by a rapid decrease in chemical inventory in 2010 probably due to a weakening north polar vortex with reduced lateral mixing across the vortex boundary.

  5. Chemical Structure and Properties: A Modified Atoms-First, One-Semester Introductory Chemistry Course

    Science.gov (United States)

    Schaller, Chris P.; Graham, Kate J.; Johnson, Brian J.; Jakubowski, Henry V.; McKenna, Anna G.; McIntee, Edward J.; Jones, T. Nicholas; Fazal, M. A.; Peterson, Alicia A.

    2015-01-01

    A one-semester, introductory chemistry course is described that develops a primarily qualitative understanding of structure-property relationships. Starting from an atoms-first approach, the course examines the properties and three-dimensional structure of metallic and ionic solids before expanding into a thorough investigation of molecules. In…

  6. STRUCTURAL FEATURES OF ECONOMICALLY-ALLOYED STEEL 20HGNMB AFTER CHEMICAL AND THERMAL HARDENING

    Directory of Open Access Journals (Sweden)

    S. P. Rudenko

    2014-01-01

    Full Text Available It is established that structural characteristics of the parts produced of industrial steel melting correspond to the requirements rendered to quality of the cemented layer and core of high-intense gear wheels according to the results of spectral, metallographic, X-ray structural and durometric analyses.

  7. A crystal-chemical classification of borate structures with emphasis on hydrated borates

    Science.gov (United States)

    Christ, C.L.; Clark, J.R.

    1977-01-01

    The rules governing formation of hydrated borate polyanions that were proposed by C.L. Christ in 1960 are critically reviewed and new rules added on the basis of recent crystal structure determinations. Principles and classifications previously published by others are also critically reviewed briefly. The fundamental building blocks from which borate polyanions can be constructed are defined on the basis of the number n of boron atoms, and the fully hydrated polyanions are illustrated. Known structures are grouped accordingly, and a shorthand notation using n and symbols ?? = triangle, T = tetrahedron is introduced so that the polyanions can be easily characterized. For example, 3:??+2T describes [B3O3(OH)5]2-. Correct structural formulas are assigned borates with known structures whereas borates of unknown structure are grouped separately. ?? 1977 Springer-Verlag.

  8. A comparative study of blue, green and yellow light emitting diode structures grown by metal organic chemical vapor deposition

    Science.gov (United States)

    Ramaiah, Kodigala Subba; Su, Y. K.; Chang, S. J.; Chen, C. H.

    2006-02-01

    The blue, green and yellow light emitting diode (LED) structures have been fabricated by metal organic chemical vapor deposition (MOCVD), and characterized by using different techniques, in order to understand the mechanism between these LEDs. Atomic force microscopy (AFM) analysis revealed that the surface roughness value and density of etch pits were different in the blue, green and yellow LEDs. The threading, misfit dislocations, interfacial dislocations, nano-pipe-like structures and quantum dot-like structures, which determine quality of the structures, were observed by transmission electron microscope (TEM) in the LED structures. The reasons for their formation in the layers are now elucidated. The indium composition, period width such as well and barrier widths were determined by simulating experimental high resolution X-ray diffraction (HRXRD) spectra. The In composition obtained by HRXRD and photoluminescence (PL) measurements for the same LED structure was not one and the same due to several reasons. In fact, the InGaN quantum well emission peaks at 2.667 and 2.544 eV of the blue and green LEDs, respectively showed S-shaped character shift, whereas the quantum well peak at 2.219 eV of yellow LEDs did not show any shift in the PL spectra with decreasing temperature. The blue, green and yellow LEDs showed different activation energies.

  9. Relationship between structure and ''decorporative'' efficiency in the diphosphonate chemical series

    International Nuclear Information System (INIS)

    Molecular structure of some diphosphonates was studied by topological analysis. The investigated activity was the efficiency of the molecules to remove injected plutonium from the organism, in order to correlate some topological properties of these molecules to their decorporating ability. The studied polyphosphonates have been divided into two families: unprotected and protected compounds. Only unprotected compounds clearly show structure activity relationships. Though structurally different from the rest of the family, LICAM (C) well fits the correlation. An interpretation was that a better efficiency might be related to the branching of the molecules

  10. Structural and chemical properties of the nitrogen-rich energetic material triaminoguanidinium 1-methyl-5-nitriminotetrazolate under pressure

    Energy Technology Data Exchange (ETDEWEB)

    McWilliams, R. Stewart; Kadry, Yasmin; Mahmood, Mohammad F.; Goncharov, Alexander F.; Ciezak-Jenkins, Jennifer (Howard); (CIW); (USARL)

    2012-12-10

    The structural and chemical properties of the bi-molecular, hydrogen-bonded, nitrogen-rich energetic material triaminoguanidinium 1-methyl-5-nitriminotetrazolate C{sub 3}H{sub 12}N{sub 12}O{sub 2} (TAG-MNT) have been investigated at room pressure and under high pressure isothermal compression using powder x-ray diffraction and Raman and infrared spectroscopy. A stiffening of the equation of state and concomitant structural relaxation between 6 and 14 GPa are found to correlate with Raman mode disappearances, frequency discontinuities, and changes in the pressure dependence of modes. These observations manifest the occurrence of a reversible martensitic structural transformation to a new crystalline phase. The onset and vanishing of Fermi resonance in the nitrimine group correlate with the stiffening of the equation of state and phase transition, suggesting a possible connection between these phenomena. Beyond 15 GPa, pressure induces irreversible chemical reactions, culminating in the formation of a polymeric phase by 60 GPa.

  11. Micro structural evaluation of fuel clad chemical interaction for metallic fuels for fast reactor

    International Nuclear Information System (INIS)

    The neutronic performance of metal fuel based on binary U-Pu alloy or ternary U-Pu-Zr alloys are better than conventional uranium plutonium mixed oxide or high density carbide ceramic fuel. The growing energy demand in India needs faster growth of nuclear power and warrants introduction of fast reactors based on metallic fuels because of higher breeding ratio and lower doubling time. Two design concepts have been proposed: one based on sodium bonded ternary alloy fuel of U-Pu-Zr ( 2-10 wt%) in modified T91 cladding material and the other is U-Pu binary alloy mechanically bonded to modified T91 cladding material with 'Zircaloy', as a liner between the fuel alloy and the clad. The Zircaloy liner act as a barrier in reducing the fuel clad chemical interaction. It also helps in transfer of heat from the fuel to the clad. Fuel clad chemical interaction is a serious issue limiting the life of a fuel pin as a result of formation of low temperature eutectic between the fuel and components of the cladding material. The eutectic reaction temperature between T91 and Uranium were estimated by dilatometry, differential thermal analysis and high temperature microscopy. Diffusion couple experiments were also carried out between U/Zr/T91 and U/T91 by isothermal annealing of the couples between 550 deg C to 750 deg C for times up to 1500 hrs. to find out the extent of chemical interaction. These studies were supported by metallographic examination, micro hardness measurement, XRD, SEM/EDAX and EPMA. The eutectic temperature was found to be higher than the estimated fuel clad interface temperature under the reactor operating condition. The paper highlights the results of these studies and attempts to analyze them in the light of performance. The outcome of these studies has been useful to the fuel designer in optimizing the design features and predicting the in-reactor fuel behavior. (author)

  12. Topoisomerase I and II inhibitors: chemical structure, mechanisms of action and role in cancer chemotherapy

    Science.gov (United States)

    Dezhenkova, L. G.; Tsvetkov, V. B.; Shtil, A. A.

    2014-01-01

    The review summarizes and analyzes recent published data on topoisomerase I and II inhibitors as potential antitumour agents. Functions and the mechanism of action of topoisomerases are considered. The molecular mechanism of interactions between low-molecular-weight compounds and these proteins is discussed. Topoisomerase inhibitors belonging to different classes of chemical compounds are systematically covered. Assays for the inhibition of topoisomerases and the possibilities of using the computer-aided modelling for the rational design of novel drugs for cancer chemotherapy are presented. The bibliography includes 127 references.

  13. Structural and chemical analysis of gadolinium halides encapsulated within WS2 nanotubes

    Science.gov (United States)

    Anumol, E. A.; Enyashin, Andrey N.; Batra, Nitin M.; Costa, Pedro M. F. J.; Deepak, Francis Leonard

    2016-06-01

    The hollow cavities of nanotubes serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of WS2 nanotubes by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is non-trivial due to the presence of multiple high atomic number elements. Therefore, energy dispersive X-ray spectroscopy (EDS) tomography was employed revealing the three dimensional chemical composition. Molecular dynamics simulations of the filling procedure shed light into the mechanics behind the formation of the confined gadolinium halide crystals. The quasi-1D system employed here serves as an example of a TEM-based chemical nanotomography method that could be extended to other materials, including beam-sensitive soft materials.The hollow cavities of nanotubes serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of WS2 nanotubes by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is non-trivial due to the

  14. Phase structure of two-flavor QCD at finite chemical potential.

    Science.gov (United States)

    Braun, Jens; Haas, Lisa M; Marhauser, Florian; Pawlowski, Jan M

    2011-01-14

    We study the phase diagram of two-flavor QCD at imaginary chemical potentials in the chiral limit. To this end we compute order parameters for chiral symmetry breaking and quark confinement. The interrelation of quark confinement and chiral symmetry breaking is analyzed with a new order parameter for the confinement phase transition. We show that it is directly related to both the quark density as well as the Polyakov loop expectation value. Our analytical and numerical results suggest a close relation between the chiral and the confinement phase transition. PMID:21405221

  15. Visible photoluminescence of MWCNT/CdS nanohybrid structure synthesized by a simple chemical process

    Energy Technology Data Exchange (ETDEWEB)

    Paul, Rima; Kumbhakar, P. [Department of Physics, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur 713209, West Bengal (India); Mitra, A.K., E-mail: akmrecdgp@yahoo.co [Department of Physics, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur 713209, West Bengal (India)

    2010-03-15

    The authors report a simple wet chemical technique to prepare hybrid nanostructures of multiwalled carbon nanotubes (MWCNT) and cadmium sulphide (CdS) nanoparticles. In a solution containing cadmium acetate and sodium sulphide, purified MWCNTs are added. Cadmium sulphide nanocrystals of average size 5 nm are synthesized and they decorate the walls of the MWCNTs. The hybrid material is characterized by scanning electron microscopy (SEM), high resolution transmission electron microscopy (HRTEM), X-ray diffraction (XRD) and Raman spectroscopy. Interesting optical properties of the composite are revealed through UV-vis and photoluminescence (PL) spectroscopy.

  16. The influence of chemical composition on the properties and structure Al-Si-Cu(Mg) alloys

    OpenAIRE

    M. Kaczorowski; A. Krzyńska

    2007-01-01

    The mechanical properties of different chemical composition AlSiCuMg type cast alloys after precipitation hardening are presented. The aim of the study was to find out how much the changes in chemistry of aluminum cast alloys permissible by EN-PN standards may influence the mechanical properties of these alloys. Eight AlSi5Cu3(Mg) type cast alloys of different content alloying elements were selected for the study. The specimens cut form test castings were subjected to precipitation hardening ...

  17. Earle K. Plyler Prize for Molecular Spectroscopy & Dynamics Lecture: Broadband Rotational Spectroscopy for Chemical Kinetics, Molecular Structure, and Analytical Chemistry

    Science.gov (United States)

    Pate, Brooks

    2013-03-01

    Advances in high-speed digital electronics have enabled a new generation of molecular rotational spectroscopy techniques that provide instantaneous broadband spectral coverage. These techniques use a chirped excitation pulse to coherently excite the molecular sample over a spectral bandwidth of 10 GHz or larger through rapid passage. The subsequent time-domain emission is recorded using high-speed digitizers (up to 100 Gigasample/s) and the frequency domain spectrum is produced by fast Fourier transformation. The chirped-pulse Fourier transform (CP-FT) method has been implemented in the microwave frequency range (2-40 GHz) for studies of cold samples in pulsed jet sources and in the mm-wave/terahertz (THz) frequency range for studies of samples at room-temperature. The method has opened new applications for molecular rotational spectroscopy in the area of chemical kinetics where dynamic rotational spectroscopy is used to measure the rates of unimolecular isomerization reactions in highly excited molecules prepared by pulsed infrared laser excitation. In these applications, the isomerization rate is obtained from an analysis of the overall line shapes which are modified by chemical exchange leading to coalescence behavior similar to the effect in NMR spectroscopy. The sensitivity of the method and the ability to extend it to low frequency (2-8 GHz) have significantly increased the size range of molecules and molecular clusters for structure determination using isotopic substitution to build up the 3D molecular structures atom-by-atom. Application to the structure of water clusters with up to 15 water molecules will be presented. When coupled with advances in solid-state mm-wave/THz devices, this method provides a direct digital technique for analytical chemistry of room-temperature gases based on molecular rotational spectroscopy. These high-throughput methods can analyze complex sample mixtures with unmatched chemical selectivity and short analysis times. Work

  18. Electronic structure and the properties of solids the physics of the chemical bond

    CERN Document Server

    Harrison, Walter A

    1980-01-01

    "Should be widely read by practicing physicists, chemists and materials scientists." - Philosophical Magazine In this comprehensive and innovative text, Professor Harrison (Stanford University) offers a basic understanding of the electronic structure of covalent and ionic solids, simple metals, transition metals, and their compounds. The book illuminates the relationships of the electronic structures of these materials and shows how to calculate dielectric, conducting, and bonding properties for each.

  19. Synthesis and Characterization of Carbon Based One-Dimensional Structures : Tuning Physical and Chemical Properties

    OpenAIRE

    Barzegar, HamidReza

    2015-01-01

    Carbon nanostructures have been extensively used in different applications; ranging from electronic and optoelectronic devices to energy conversion. The interest stems from the fact that covalently bonded carbon atoms can form a wide variety of structures with zero-, one- and two-dimensional configuration with different physical properties. For instance, while fullerene molecules (zero-dimensional carbon structures) realize semiconductor behavior, two-dimensional graphene shows metallic behav...

  20. Structure, stability, and dynamics of canonical and noncanonical base pairs: quantum chemical studies.

    Science.gov (United States)

    Roy, Ashim; Panigrahi, Swati; Bhattacharyya, Malyasri; Bhattacharyya, Dhananjay

    2008-03-27

    The importance of non-Watson-Crick base pairs in the three-dimensional structure of RNA is now well established. The structure and stability of these noncanonical base pairs are, however, poorly understood. We have attempted to understand structural features of 33 frequently occurring base pairs using density functional theory. These are of three types, namely (i) those stabilized by two or more polar hydrogen bonds between the bases, (ii) those having one polar and another C-H...O/N type interactions, and (iii) those having one H-bond between the bases and another involving one of the sugars linked to the bases. We found that the base pairs having two polar H-bonds are very stable as compared to those having one C-H...O/N interaction. Our quantitatively analysis of structures of these optimized base pairs indicates that they possess a different amount of nonplanarity with large propeller or buckle values as also observed in the crystal structures. We further found that geometry optimization does not modify the hydrogen-bonding pattern, as values of shear and open angle of the base pairs remain conserved. The structures of initial crystal geometry and final optimized geometry of some base pairs having only one polar H-bond and a C-H...O/N interaction, however, are significantly different, indicating the weak nature of the nonpolar interaction. The base pair flexibility, as measured from normal-mode analysis, in terms of the intrinsic standard deviations of the base pair structural parameters are in conformity with those calculated from RNA crystal structures. We also noticed that deformation of a base pair along the stretch direction is impossible for all of the base pairs, and movements of the base pairs along shear and open are also quite restricted. The base pair opening mode through alteration of propeller or buckle is considerably less restricted for most of the base pairs. PMID:18318519

  1. Structural and Functional Difference of Pheromone Binding Proteins in Discriminating Chemicals in the Gypsy Moth, Lymantria Dispar

    Directory of Open Access Journals (Sweden)

    Yanxue Yu, Fei Ma, Yixia Cao, Junhua Zhang, Yongan Zhang, Shengnan Duan, Yadong Wei, Shuifang Zhu, Naizhong Chen

    2012-01-01

    Full Text Available Pheromone-binding proteins (PBPs of the gypsy moth, Lymantria dispar L., play an important role in olfaction. Here structures of PBPs were first built by Homology Modeling, and each model of PBPs had seven α-helices and a large hydrophobic cavity including 25 residues for PBP1 and 30 residues for PBP2. Three potential semiochemicals were first screened by CDOCKER program based on the PBP models and chemical database. These chemicals were Palmitic acid n-butyl ester (Pal, Bis(3,4-epoxycyclohexylmethyl adipate (Bis, L-trans-epoxysuccinyl-isoleucyl-proline methyl ester propylamide (CA-074. The analysis of chemicals docking the proteins showed one hydrogen bond was established between the residues Lys94 and (+-Disparlure ((+-D, and л-л interactions were present between Phe36 of PBP1 and (+-D. The Lys94 of PBP1 formed two and three hydrogen bonds with Bis and CA-074, respectively. There was no residue of PBP2 interacting with these four chemicals except Bis forming one hydrogen bond with Lys121. After simulating the conformational changes of LdisPBPs at pH7.3 and 5.5 by constant pH molecular dynamics simulation in implicit solvent, the N-terminal sequences of PBPs was unfolded, only having five α-helices, and PBP2 had larger binding pocket at 7.3 than PBP1. To investigate the changes of α-helices at different pH, far-UV and near-UV circular dichroism showed PBPs consist of α-helices, and the tertiary structures of PBP1 and PBP2 were influenced at pH7.3 and 5.5. The fluorescence binding assay indicated that PBP1 and PBP2 have similarly binding affinity to (+-D at pH 5.5 and 7.3, respectively. At pH 5.5, the dissociation constant of the complex between PBP1 and 2-decyl-1-oxaspiro [2.2] pentane (OXP1 was 0.68±0.01μM, for (+-D was 5.32±0.11μM, while PBP2 with OXP1 and (+-D were 1.88±0.02μM and 5.54±0.04μM, respectively. Three chemicals screened had higher affinity to PBP1 than (+-D except Pal at pH5.5, and had lower affinity than (+-D at p

  2. Quantum chemical calculations on structure of Mo8 O4-26

    Institute of Scientific and Technical Information of China (English)

    吴争平; 尹周澜; 陈启元; 张平民

    2002-01-01

    Two possible structures of Mo8O4-26 were optimized using the Polak-Ribiere method of Molecular Mechanics Optimization and the termination condition is RMS (Root-mean-square) gradient of 0.42kJ/mol. Based on the calculations of the molecular dynamics, Lengevin dynamics and Monte Carlo dynamics simulation, the structure models of Mo8O4-26 with the lowest energy were acquired respectively according to the energy of the systems calculated using the ZIDO/1 and PM3 methods. The total energy, energies of some frontier molecular orbitals and atomic charges of Mo8O4-26 were computed at the HF/3-21G and HF/STO-3G levels. The calculation results show that the contortion of the structure with eight MoO6 is smaller than that of the structure with six MoO6 and two MoO4. The total energies of the two structures are nearly equal because the contortion of the structure with six MoO6 and two MoO4 would make the exclusion force decreased.

  3. Impact of the physical and chemical environment on the molecular structure of Coprinus cinereus peroxidase.

    Science.gov (United States)

    Houborg, Karen; Harris, Pernille; Petersen, Jens; Rowland, Paul; Poulsen, Jens-Christian Navarro; Schneider, Palle; Vind, Jesper; Larsen, Sine

    2003-06-01

    The structure of the peroxidase from Coprinus cinereus (CiP) has been determined in three different space groups and crystalline environments. Two of these are of the recombinant glycosylated form (rCiP), which crystallized in space groups P2(1)2(1)2(1) and C2. The third crystal form was obtained from a variant of CiP in which the glycosylation sites have been removed (rCiPON). It crystallizes in space group P2(1) with beta approximately 90 degrees; the structure was determined from room-temperature data and low-temperature data obtained from twinned crystals. Two independent molecules of CiP related by non-crystallographic symmetry are contained in the three crystal forms. The packing in the two structures of the glycosylated form of rCiP is closely related, but differs from the packing in the unglycosylated rCiPON. A database search based on small-molecule porphinato iron (III) complexes has been performed and related to observations of the spin states and coordination numbers of the iron ion. The room-temperature structures of CiP and one structure of the almost identical peroxidase from Arthromyces ramosus (ARP) have been used to identify 66 conserved water molecules and to assign a structural role to most of them.

  4. The hyperfine structure in the rotational spectra of bromofluoromethane: Lamb-dip technique and quantum-chemical calculations

    OpenAIRE

    Cazzoli, Gabriele; Puzzarini, Cristina; Stopkowicz, Stella; Gauss, Jürgen

    2008-01-01

    Abstract The hyperfine structure in the rotational spectra of six isotopic species of bromofluoromethane, namely CH2{79}BrF, CH2{81}BrF, CDH{79}BrF, CDH{81}BrF, CD2{79}BrF, and CD2{81}BrF, has been investigated using the Lamb-dip technique in the submillimeter-wave frequency range. Measurements as well as assignment procedures have been supported by high-level quantum-chemical calculations of the hyperfine parameters at the coupled-cluster level. For all species, the accuracy of th...

  5. Quantitative structure activity relationship model for predicting the depletion percentage of skin allergic chemical substances of glutathione.

    Science.gov (United States)

    Si, Hongzong; Wang, Tao; Zhang, Kejun; Duan, Yun-Bo; Yuan, Shuping; Fu, Aiping; Hu, Zhide

    2007-05-22

    A quantitative model was developed to predict the depletion percentage of glutathione (DPG) compounds by gene expression programming (GEP). Each kind of compound was represented by several calculated structural descriptors involving constitutional, topological, geometrical, electrostatic and quantum-chemical features of compounds. The GEP method produced a nonlinear and five-descriptor quantitative model with a mean error and a correlation coefficient of 10.52 and 0.94 for the training set, 22.80 and 0.85 for the test set, respectively. It is shown that the GEP predicted results are in good agreement with experimental ones, better than those of the heuristic method. PMID:17481417

  6. 1H NMR study of the solvent THF concerning their structural and dynamical properties in chemically Li-intercalated SWNT

    KAUST Repository

    Schmid, Marc R.

    2011-09-01

    Structural and dynamical properties of the THF solvent in single-walled carbon nanotubes intercalated with lithium are investigated by NMR. 1H NMR experiments reveal the existence of two types of inequivalent THF solvent molecules with different chemical environments and dynamical behavior. At low temperatures THF molecules perpendicularly arranged in between adjacent SWNT presumably exhibit a restricted rotation around their dipolar axis. At higher temperatures THF molecules are isotropically rotating and diffusing along the interstitial channels of the SWNT bundles. © 2011 Elsevier B.V. All rights reserved.

  7. Effects of pore structure on the high-performance capacitive deionization using chemically activated carbon nanofibers.

    Science.gov (United States)

    Im, Ji Sun; Kim, Jong Gu; Lee, Young-Seak

    2014-03-01

    Capacitive deionization (CDI) electrodes were constructed from activated carbon fibers prepared using electrospinning and chemical activation. The CDI efficiencies of these electrodes were studied as a function of their specific surface areas, pore volumes and pore sizes via salt ion adsorption. The specific surface areas increased approximately 90 fold and the pore volume also increased approximately 26 fold with the use of greater amounts of the chemical activation agent. There was a relative increase in the mesopore fraction with higher porosity. A NaCI solution was passed through a prepared CDI system, and the salt removal efficiency of the CDI system was determined by the separation of the Na+ and Cl- ions toward the anode and cathode. The CDI efficiency increased with greater specific surface areas and pore volumes. In addition, the efficiency per unit pore volume increased with a reduction in the micropore fraction, resulting in the suppressed overlapping effect. In conclusion, the obtained improvements in CDI efficiency were mainly attributed to mesopores, but the micropores also played an important role in the high-performance CDI under conditions of high applied potential and high ion concentrations. PMID:24745222

  8. Structural and Chemical Analysis of Gadolinium Halides Encapsulated within WS 2 Nanotubes

    KAUST Repository

    Anumol, E A

    2016-05-18

    The hollow cavities of nanotubes could serve as templates for the growth of size- and shape-confined functional nanostructures, giving rise to novel materials and properties. In this work, considering their potential application as MRI contrast agents, gadolinium halides are encapsulated within the hollow cavities of inorganic nanotubes of WS2 by capillary filling to obtain GdX3@WS2 nanotubes (where X = Cl, Br or I and @ means encapsulated in). Aberration corrected scanning/transmission electron microscopy (S/TEM) and spectroscopy is employed to understand the morphology and composition of the GdI3@WS2 nanotubes. The three dimensional morphology is studied with STEM tomography but understanding the compositional information is a non-trivial matter due to the presence of multiple high atomic number elements. Therefore, energy dispersive X-ray spectroscopy (EDS) tomography was employed revealing the three dimensional chemical composition. Molecular dynamics simulations of the filling procedure shed light into the mechanics behind the formation of the confined gadolinium halide crystals. The quasi-1D system employed here serves as an example of a TEM-based chemical nanotomography method that could be extended to other materials, including beam-sensitive soft materials.

  9. Chemical and structural characterization of glass ionomer cements indicated for atraumatic restorative treatment.

    Science.gov (United States)

    Guedes, Orlando Aguirre; Borges, Álvaro Henrique; Bandeca, Matheus Coelho; Nakatani, Mariana Kyosen; de Araújo Estrela, Cyntia Rodrigues; de Alencar, Ana Helena Gonçalves; Estrela, Carlos

    2015-01-01

    Glass ionomer cements (GICs) are restorative materials, which clinical use has increased significantly during the last decade. The aim of the present study was to analyze the chemical constitution and surface morphology of four glass ionomer cements: Maxxion R, VitroFill, Vidrion R and Vitremer. Twelve polyethylene tubes with an internal diameter of 3 and 3 mm in length were prepared, filled and then transferred to a chamber with 95% relative humidity and a temperature of 37°C. The surface morphology of the tested materials was examined by scanning electron microscopy (SEM) and main components were investigated by energy-dispersive X-ray microanalysis (EDX). Scanning electron microscopy revealed irregular and rough external surface. Cracking was not observed. The main constituents were found to be aluminum, silicon, calcium, sodium and fluoride. Phosphorus, sulfur and barium were only observed in Vidrion R, while chlorine were only observed in Maxxion R. Elemental mapping of the outer surface revealed high concentration of aluminum and silicon. Significant irregularities on the surface of the tested materials were observed. The chemical constitution of all GIC was similar. PMID:25876952

  10. Chemical method of assessing the degree of biodegradation of wooden structural elements

    Directory of Open Access Journals (Sweden)

    T.A. Serova

    2014-05-01

    Full Text Available Wood is an environmentally friendly and lightweight building material that is sensible to the destrustion of various biological agents at non-observance of proper temperature and humidity regime. Wood-destroying white-rot and brown-rot fungi and micromycetes (mold have a leading position among biodestructors. This organisms use wood as the trophic base changing it’s chemical composition and correspondingly it’s mechanical properties. We investigated changes in the content of the main biopolymers of wood (cellulose and lignin and changes in ash content and moisture of the material under the influence of mold and wood fungi. We analyzed samples of wooden constructions with different biodestruction degree. We used chemical methods of extraction of cellulose and lignin from intact and diseased by fungi wood, method of calculation of material’s moisture and ash content. It was found that, with the development of deep destructions cellulose content is reduced by 20%, lignin content is reduced by 40%. Moisture and ash content of wood can also be used as markers of a certain degree of biodegradation.

  11. The HIFI spectral survey of AFGL 2591 (CHESS). III. Chemical structure of the protostellar envelope

    CERN Document Server

    Kazmierczak-Barthel, Maja; van der Tak, Floris; Chavarría, Luis; van der Wiel, Matthijs

    2014-01-01

    We aim to understand the rich chemical composition of AFGL 2591, a prototypical isolated high-mass star-forming region. Based on HIFI and JCMT data, the molecular abundances of species found in the protostellar envelope of AFGL 2591 were derived with the Monte Carlo radiative transfer code RATRAN, assuming either constant values or 1D stepwise radial profiles as abundance distributions. The reconstructed 1D abundances were compared with the results of time-dependent gas-grain chemical modeling, considering ages of 10,000 to 50,000 years, cosmic-ray ionization rates of 0.5 to 50 times 10^-16 s^-1, uniformly-sized 0.1-1 micron dust grains, a dust/gas ratio of 1%, and several sets of initial molecular abundances with C/O 1. Constant abundance models give good fits to the data for CO, CN, CS, HCO+, H2CO, N2H+, C2H, NO, OCS, OH, H2CS, O, C, C+, and CH. Models with an abundance jump at 100 K give good fits to the data for NH3, SO, SO2, H2S, H2O, HCl, and CH3OH. For HCN and HNC, the best models have an abundance jum...

  12. Magnetism, structure and chemical order in small CoPd clusters: A first-principles study

    International Nuclear Information System (INIS)

    The structural, electronic and magnetic properties of small ComPdn(N=m+n=8,m=0−N) nanoalloy clusters are studied in the framework of a generalized-gradient approximation to density-functional theory. The optimized cluster structures have a clear tendency to maximize the number of nearest-neighbor CoCo pairs. The magnetic order is found to be ferromagnetic-like (FM) for all the ground-state structures. Antiferromagnetic-like spin arrangements were found in some low-lying isomers. The average magnetic moment per atom μ¯N increases approximately linearly with Co content. A remarkable enhancement of the local Co moments is observed as a result of Pd doping. This is a consequence of the increase in the number of Co d holes, due to CoPd charge transfer, combined with the reduced local coordination. The influence of spin–orbit interactions on the cluster properties is also discussed. - Highlights: • This work analyses the structural and magnetic properties of CoPd nanoclusters. • The magnetic order is found to be ferromagnetic-like for all the ground-state structures. • The average magnetic moment per atom increases approximately linearly with Co content. • The influence of spin–orbit interactions on the cluster properties is discussed

  13. Comprehensive comparison of the chemical and structural characterization of landfill leachate and leonardite humic fractions.

    Science.gov (United States)

    Tahiri, Abdelghani; Richel, Aurore; Destain, Jacqueline; Druart, Philippe; Thonart, Philippe; Ongena, Marc

    2016-03-01

    Humic substances (HS) are complex and heterogeneous mixtures of organic compounds that occur everywhere in the environment. They represent most of the dissolved organic matter in soils, sediments (fossil), water, and landfills. The exact structure of HS macromolecules has not yet been determined because of their complexity and heterogeneity. Various descriptions of HS are used depending on specific environments of origin and research interests. In order to improve the understanding of the structure of HS extracted from landfill leachate (LHS) and commercial HS from leonardite (HHS), this study sought to compare the composition and characterization of the structure of LHS and HHS using elemental composition, chromatographic (high-performance liquid chromatography (HPLC)), and spectroscopic techniques (UV-vis, FTIR, NMR, and MALDI-TOF). The results showed that LHS molecules have a lower molecular weight and less aromatic structure than HHS molecules. The characteristics of functional groups of both LHS and HHS, however, were basically similar, but there was some differences in absorbance intensity. There were also less aliphatic and acidic functional groups and more aromatic and polyphenolic compounds in the humic acid (HA) fraction than in the fulvic acid (FA) and other molecules (OM) fractions of both origins. The differences between LHS and HHS might be due to the time course of humification. Combining the results obtained from these analytical techniques cold improve our understanding of the structure of HS of different origins and thus enhance their potential use. PMID:26781101

  14. Magnetism, structure and chemical order in small CoPd clusters: A first-principles study

    Energy Technology Data Exchange (ETDEWEB)

    Mokkath, Junais Habeeb, E-mail: Junais.Mokkath@kaust.edu.sa

    2014-01-15

    The structural, electronic and magnetic properties of small Co{sub m}Pd{sub n}(N=m+n=8,m=0−N) nanoalloy clusters are studied in the framework of a generalized-gradient approximation to density-functional theory. The optimized cluster structures have a clear tendency to maximize the number of nearest-neighbor CoCo pairs. The magnetic order is found to be ferromagnetic-like (FM) for all the ground-state structures. Antiferromagnetic-like spin arrangements were found in some low-lying isomers. The average magnetic moment per atom μ{sup ¯}{sub N} increases approximately linearly with Co content. A remarkable enhancement of the local Co moments is observed as a result of Pd doping. This is a consequence of the increase in the number of Co d holes, due to CoPd charge transfer, combined with the reduced local coordination. The influence of spin–orbit interactions on the cluster properties is also discussed. - Highlights: • This work analyses the structural and magnetic properties of CoPd nanoclusters. • The magnetic order is found to be ferromagnetic-like for all the ground-state structures. • The average magnetic moment per atom increases approximately linearly with Co content. • The influence of spin–orbit interactions on the cluster properties is discussed.

  15. Structural and Physico-Chemical Interpretation (SPCI) of QSAR Models and Its Comparison with Matched Molecular Pair Analysis.

    Science.gov (United States)

    Polishchuk, Pavel; Tinkov, Oleg; Khristova, Tatiana; Ognichenko, Ludmila; Kosinskaya, Anna; Varnek, Alexandre; Kuz'min, Victor

    2016-08-22

    This paper describes the Structural and Physico-Chemical Interpretation (SPCI) approach, which is an extension of a recently reported method for interpretation of quantitative structure-activity relationship (QSAR) models. This approach can efficiently be used to reveal structural motifs and the major physicochemical factors affecting the investigated properties. Its efficacy was demonstrated both on the classical Free-Wilson data set and on several data sets with different end points (permeability of the blood-brain barrier, fibrinogen receptor antagonists, acute oral toxicity). Structure-activity patterns extracted from QSAR models with SPCI were in good correspondence with experimentally observed relationships and molecular docking, regardless of the machine learning method used. Comparison of SPCI with the matched molecular pair (MMP) method clearly shows an advantage of our approach over MMP, especially for small or structurally diverse data sets. The developed approach has been implemented in the SPCI software tool with a graphical user interface, which is publicly available at http://qsar4u.com/pages/sirms_qsar.php . PMID:27419846

  16. Effects of particle size and edge structure on the electronic structure, spectroscopic features, and chemical properties of Au(111)-supported MoS2 nanoparticles.

    Science.gov (United States)

    Bruix, Albert; Lauritsen, Jeppe V; Hammer, Bjørk

    2016-07-01

    Materials based on MoS2 are widely used as catalysts and their structure usually consists of single-layered MoS2 nanoparticles whose edges are known to constitute the catalytically active sites. Methods based on density functional theory are used in this work to calculate the electronic structure of representative computational models of MoS2 nanoparticles supported on Au(111). By considering nanoparticles with different edge-terminations, compositions, and sizes, we describe how the electronic structure, Mo3d core-level shifts, and chemical properties (i.e. H adsorption and S vacancy formation) depend on the MoS2 nanoparticle size and structure. In addition, site-specific properties, largely inaccessible when using only slab models of MoS2 edges, are reported, which reveal that the edge sites are not uniform along the nanoparticle and largely depend on the proximity to the corners of the triangular NPs, especially when interacting with a metallic support. Furthermore, a structural motif where H atoms adsorb favourably in a bridging position between two Mo atoms is proposed as an active site for the hydrogen evolution reaction. PMID:27076269

  17. The structural properties of CdS deposited by chemical bath deposition and pulsed direct current magnetron sputtering

    Energy Technology Data Exchange (ETDEWEB)

    Lisco, F., E-mail: F.Lisco@lboro.ac.uk [Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Leicestershire, LE11 3TU (United Kingdom); Kaminski, P.M.; Abbas, A.; Bass, K.; Bowers, J.W.; Claudio, G. [Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Leicestershire, LE11 3TU (United Kingdom); Losurdo, M. [Institute of Inorganic Methodologies and of Plasmas, IMIP-CNR, via Orabona 4, 70126 Bari (Italy); Walls, J.M. [Centre for Renewable Energy Systems Technology (CREST), School of Electronic, Electrical and Systems Engineering, Loughborough University, Leicestershire, LE11 3TU (United Kingdom)

    2015-05-01

    Cadmium sulphide (CdS) thin films were deposited by two different processes, chemical bath deposition (CBD), and pulsed DC magnetron sputtering (PDCMS) on fluorine doped-tin oxide coated glass to assess the potential advantages of the pulsed DC magnetron sputtering process. The structural, optical and morphological properties of films obtained by CBD and PDCMS were investigated using X-ray photoelectron spectroscopy, X-ray diffraction, scanning and transmission electron microscopy, spectroscopic ellipsometry and UV-Vis spectrophotometry. The as-grown films were studied and comparisons were drawn between their morphology, uniformity, crystallinity, and the deposition rate of the process. The highest crystallinity is observed for sputtered CdS thin films. The absorption in the visible wavelength increased for PDCMS CdS thin films, due to the higher density of the films. The band gap measured for the as-grown CBD-CdS is 2.38 eV compared to 2.34 eV for PDCMS-CdS, confirming the higher density of the sputtered thin film. The higher deposition rate for PDCMS is a significant advantage of this technique which has potential use for high rate and low cost manufacturing. - Highlights: • Pulsed DC magnetron sputtering (PDCMS) of CdS films • Chemical bath deposition of CdS films • Comparison between CdS thin films deposited by chemical bath and PDCMS techniques • High deposition rate deposition for PDCMS deposition • Uniform, pinhole free CdS thin films.

  18. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    Science.gov (United States)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  19. How Clean is Safe? Improving the Effectiveness of Decontamination of Structures and People Following Chemical and Biological Incidents

    Energy Technology Data Exchange (ETDEWEB)

    Vogt (Sorensen), B.M.

    2003-04-03

    This report describes a U.S. Department of Energy, (DOE) Chemical and Biological National Security Program project that sought to establish what is known about decontamination of structures, objects, and people following an exposure to chemical or biological materials. Specifically we sought to identify the procedures and protocols used to determine when and how people or buildings are considered ''clean'' following decontamination. To fulfill this objective, the study systematically examined reported decontamination experiences to determine what procedures and protocols are currently employed for decontamination, the timeframe involved to initiate and complete the decontamination process, how the contaminants were identified, the factors determining when people were (or were not) decontaminated, the problems encountered during the decontamination process, how response efforts of agencies were coordinated, and the perceived social psychological effects on people who were decontaminated or who participated in the decontamination process. Findings and recommendations from the study are intended to aid decision-making and to improve the basis for determining appropriate decontamination protocols for recovery planners and policy makers for responding to chemical and biological events.

  20. Relationships between chemical structures and functions of triterpene glycosides isolated from sea cucumbers

    Directory of Open Access Journals (Sweden)

    Joo-In ePark

    2014-09-01

    Full Text Available Many marine triterpene glycosides have in vitro and in vivo activities with very low toxicity, suggesting that they are suitable agents for the prevention and treatment of different diseases, particularly cancer. However, the molecular mechanisms of action of natural marine compounds in cancer, immune and other various cells are not fully known. This review focuses on the structural characteristics of marine triterpene glycosides and how these affect their biological activities and molecular mechanisms. In particular, the membranotropic and membranolytic activities of frondoside A and cucumariosides from sea cucumbers and their ability to induce cytotoxicity and apoptosis have been discussed, with a focus on structure-activity relationships. In addition, the structural characteristics and antitumor effects of stichoposide C and stichoposide D have been reviewed along with underlying their molecular mechanisms.

  1. Structural and chemical modifications of typical South African biomasses during torrefaction.

    Science.gov (United States)

    Mafu, Lihle D; Neomagus, Hein W J P; Everson, Raymond C; Carrier, Marion; Strydom, Christien A; Bunt, John R

    2016-02-01

    Torrefaction experiments were carried out for three typical South African biomass samples (softwood chips, hardwood chips and sweet sorghum bagasse) to a weight loss of 30 wt.%. During torrefaction, moisture, non-structural carbohydrates and hemicelluloses were reduced, resulting in a structurally modified torrefaction product. There was a reduction in the average crystalline diameter (La) (XRD), an increase in the aromatic fraction and a reduction in aliphatics (substituted and unsubstituted) (CPMAS (13)C NMR). The decrease in the aliphatic components of the lignocellulosic material under the torrefaction conditions also resulted in a slight ordering of the carbon lattice. The degradation of hemicelluloses and non-structural carbohydrates increased the inclusive surface area of sweet sorghum bagasse, while it did not change significantly for the woody biomasses.

  2. Structural and Chemical Analysis of the Zirconia-Veneering Ceramic Interface.

    Science.gov (United States)

    Inokoshi, M; Yoshihara, K; Nagaoka, N; Nakanishi, M; De Munck, J; Minakuchi, S; Vanmeensel, K; Zhang, F; Yoshida, Y; Vleugels, J; Naert, I; Van Meerbeek, B

    2016-01-01

    The interfacial interaction of veneering ceramic with zirconia is still not fully understood. This study aimed to characterize morphologically and chemically the zirconia-veneering ceramic interface. Three zirconia-veneering conditions were investigated: 1) zirconia-veneering ceramic fired on sandblasted zirconia, 2) zirconia-veneering ceramic on as-sintered zirconia, and 3) alumina-veneering ceramic (lower coefficient of thermal expansion [CTE]) on as-sintered zirconia. Polished cross-sectioned ceramic-veneered zirconia specimens were examined using field emission gun scanning electron microscopy (Feg-SEM). In addition, argon-ion thinned zirconia-veneering ceramic interface cross sections were examined using scanning transmission electron microscopy (STEM)-energy dispersive X-ray spectrometry (EDS) at high resolution. Finally, the zirconia-veneering ceramic interface was quantitatively analyzed for tetragonal-to-monoclinic phase transformation and residual stress using micro-Raman spectroscopy (µRaman). Feg-SEM revealed tight interfaces for all 3 veneering conditions. High-resolution transmission electron microscopy (HRTEM) disclosed an approximately 1.0-µm transformed zone at sandblasted zirconia, in which distinct zirconia grains were no longer observable. Straight grain boundaries and angular grain corners were detected up to the interface of zirconia- and alumina-veneering ceramic with as-sintered zirconia. EDS mapping disclosed within the zirconia-veneering ceramic a few nanometers thick calcium/aluminum-rich layer, touching the as-sintered zirconia base, with an equally thick silicon-rich/aluminum-poor layer on top. µRaman revealed t-ZrO2-to-m-ZrO2 phase transformation and residual compressive stress at the sandblasted zirconia surface. The difference in CTE between zirconia- and the alumina-veneering ceramic resulted in residual tensile stress within the zirconia immediately adjacent to its interface with the veneering ceramic. The rather minor chemical

  3. Ellipsometric study of metal-organic chemically vapor deposited III-V semiconductor structures

    Science.gov (United States)

    Alterovitz, Samuel A.; Sekula-Moise, Patricia A.; Sieg, Robert M.; Drotos, Mark N.; Bogner, Nancy A.

    1992-01-01

    An ellipsometric study of MOCVD-grown layers of AlGaAs and InGaAs in thick films and strained layer complex structures is presented. It is concluded that the ternary composition of thick nonstrained layers can be accurately determined to within experimental errors using numerical algorithms. In the case of complex structures, thickness of all layers and the alloy composition of nonstrained layers can be determined simultaneously, provided that the correlations between parameters is no higher than 0.9.

  4. One-dimensional structures of Bi 2O 3 synthesized via metalorganic chemical vapor deposition process

    Science.gov (United States)

    Kim, Hyoun Woo; Myung, Ju Hyun; Shim, Seung Hyun

    2006-01-01

    We have demonstrated the synthesis of one-dimensional (1D) structures of bismuth oxide (Bi 2O 3) by a reaction of a trimethylbismuth (TMBi) and oxygen (O 2) mixture at 450 °C. Scanning electron microscopy showed that the product consisted of 1D materials with width or diameters less than 1 μm and lengths up to several tens of micrometers. The X-ray energy dispersive spectroscopy revealed that the materials contained elements of Bi and O. The results of X-ray diffraction and selected area electron diffraction pattern indicated that the obtained Bi 2O 3 were crystalline with monoclinic structure.

  5. Structure and Electrical Study of New Chemically Modified Poly(vinyl chloride

    Directory of Open Access Journals (Sweden)

    F. Ammari

    2015-01-01

    Full Text Available The aim of this work was to study the structural and electrical properties of a new polymer obtained by functionalization of a commercial poly(vinyl chloride (PVC (Mw = 48000 by grafting aminoalkyl and aminoaryl groups. Modified poly(vinyl chloride was prepared in two steps. The structural properties of the polymer were systematically investigated by varieties of techniques as differential scanning calorimetric (DSC, thermogravimetry analysis (TG, X-ray diffraction (XRD, and Fourier transform infrared (FTIR spectroscopy. The electrical properties of the polymer were studied by electrochemical impedance spectroscopy (EIS.

  6. Chemical profiling of the major components in natural waxes to elucidate their role in liquid oil structuring.

    Science.gov (United States)

    Doan, Chi Diem; To, Chak Ming; De Vrieze, Mike; Lynen, Frederic; Danthine, Sabine; Brown, Allison; Dewettinck, Koen; Patel, Ashok R

    2017-01-01

    Elucidating the composition of waxes is of utmost importance to explain their behavior in liquid oil structuring. The chemical components (hydrocarbons - HCs, free fatty acids - FFAs, free fatty alcohols - FALs and wax esters - WEs) of natural waxes were analyzed using HPLC-ELSD and GC-MS followed by evaluation of their oil structuring properties. The gel strength, including the average storage modulus and oscillation yield stress, displayed a negative correlation with FALs and a positive correlation with HCs, FFAs and WEs. The components dictating the gel strength are HCs, FFAs and WEs in a descending order of importance. The consistency of the oleogels increased with the increasing amount of FFAs and HCs and the decreasing amount of WEs and FALs. The presence of more WEs results in a strong but brittle gel with a high initial flow yield stress. We believe these results might be useful in selecting the right waxes to combine in certain fat-based food products. PMID:27507530

  7. Effect of ethanol on the chemical structure of the soot extractable material of an ethylene inverse diffusion flame

    Energy Technology Data Exchange (ETDEWEB)

    Santamaria, Alexander; Mondragon, Fanor [Institute of Chemistry, University of Antioquia, A.A. 1226, Medellin (Colombia); Eddings, Eric G. [Department of Chemical Engineering, University of Utah, Salt Lake City, UT 84112 (United States)

    2007-10-15

    The effect of fuel-side ethanol addition on the chemical structure of the soot extractable material generated in an ethylene inverse diffusion flame was evaluated by means of average structural parameters. The results indicate that the ethanol effect on the aromatic components was more pronounced, with an increase of about 40% in the average number of aromatic fused rings (R{sub a}) as compared to the results of a neat flame. This observation also helps explain the low percentage of chloroform-extractable material in the soot samples obtained from the flame with ethanol addition. In contrast, the aliphatic component of the extractable material did not demonstrate significant changes with ethanol addition. (author)

  8. Chemical structure-optical property understanding in bisphenyls and substituted polycarbonates by molecular simulations: Role of polarizabilities and conformations

    Science.gov (United States)

    Natarajan, Upendra; Sulatha, M. S.

    2005-03-01

    We present calculations of polarizability tensors, optical anisotropy of organic molecules, repeating units and polymer chains of several bisphenyls, bisphenol carbonates and polycarbonates with a variety of chemical substitutions.^1,2 Theoretical calculations of polarizabilities and optical birefringence of several newer structures having specific side-group substitutions which render low birefringence, not previously reported, is also shown here. Our method combines VOSRIS scheme^3, molecular geometry and conformations from force-field simulations and accurate anisotropic polarizability tensors. Aliphatic, aliphatic aromatic and cycloaliphatic substitutions reduce optical anisotropy in relation to bisphenol A polycarbonate. Calculated /x of these structurally modified polycarbonates^2 follows linear behavior with respect to experimentally observed melt stress-optical coefficient (Cm). *J. Phys. Chem. A, 107, 97 (2003) *Macromolecules, 36, 2944 (2003) *P.J. Flory, Statistical Mechanics of Chain Molecules, Wiley Interscience, New York (1969)

  9. Structural and electronic characterization of graphene grown by chemical vapor deposition and transferred onto sapphire

    Science.gov (United States)

    Joucken, Frédéric; Colomer, Jean-François; Sporken, Robert; Reckinger, Nicolas

    2016-08-01

    We present a combination of magnetotransport and local probe measurements on graphene grown by chemical vapor deposition on copper foil and subsequently transferred onto a sapphire substrate. A rather strong p-doping is observed (∼9 × 1012 cm-2) together with quite low carrier mobility (∼1350 cm2/V s). Atomic force and tunneling imaging performed on the transport devices reveals the presence of contaminants between sapphire and graphene, explaining the limited performance of our devices. The transferred graphene displays ridges similar to those observed whilst graphene is still on the copper foil. We show that, on sapphire, these ridges are made of different thicknesses of the contamination layer and that, contrary to what was reported for hBN or certain transition metal dichalcogenides, no self-cleansing process of the sapphire substrate is observed.

  10. Effect of chemical composition and alumina content on structure and properties of ceramic insulators

    Indian Academy of Sciences (India)

    Arman Sedghi; Nastaran Riahi-Noori; Naser Hamidnezhad; Mohammad Reza Salmani

    2014-04-01

    In the present work, six electrical porcelain compositions with different amount of alumina and silica have been prepared and fired in an industrial furnace at 1300°C. Density, porosity, bending strength and electrical strength were measured in the samples. In order to find a relationship between properties and sample microstructures, samples were analyzed by scanning electron microscope (SEM) and x-ray diffraction (XRD) techniques. The results showed that, with chemical composition of 53.5 wt.% SiO2 and 37.5 wt.% alumina, highest electrical strength of 21.97 kV/mm was achieved in fabricated electrical porcelains. Increasing amount of alumina up to 30 wt.% decreases quartz and cristobalite phases, but increases corundum phase 3 to 5 times. SEM observation revealed that dense particles and uniform distribution of long and thin needle shaped mullite are predominant in sample microstructures with highest electrical strength.

  11. Chemical structures and reactivities of coal as an organic natural product

    Energy Technology Data Exchange (ETDEWEB)

    Collins, C J; Hombach, H P; Benjamin, B M; Roark, W H; Maxwell, B; Raaen, V F

    1979-01-01

    Some chemical reactions involved in coal liquefaction have been studied using carbon 14 labelled compounds and nuclear magnetic resonance. On the basis of these studies it is concluded that the role of tetralin during coal conversion is (1) to act as a dispersion vehicle; (2) to supply hydrogen radicals, when needed, to trap coal radicals, and (3) in a very minor way to undergo intermolecular reaction with the coal through making and breaking of C--C (and possibly other) bonds. As a result of other experiments it is concluded that to the methods previously employed for breaking bonds in coal molecules and thereby lowering their molecular weights, must now be added the use of solvated-electrons for breaking -CH/sub 2/--CH/sub 2/- linkages. A possible mechanism for the cleavage of bibenzyl (used as a model compound for coal) is given. (LTN)

  12. The Virtual Product-Process Design Laboratory for Structured Chemical Product Design and Analysis

    DEFF Research Database (Denmark)

    Mattei, Michele; Yunus, Nor Alafiza Binti; Kalakul, Sawitree;

    2014-01-01

    The objective of this paper is to present new methods for design of chemicals based formulated products and their implementation in the software, the Virtual Product-Process Design Laboratory. The new products are tailor-made blended liquid products and emulsion-based products. The new software...... employs a template approach, where each template follows the same common steps in the workflow for design of formulated products, but has the option to employ different product specific property models, data and calculation routines, when necessary. With the new additions, the software is able to support....... Output from the software is a small set of most promising product candidates and a short list of recommended experiments that can validate and further fine-tune the product composition. The application of the new features is highlighted through two case studies relative to an emulsion-based product...

  13. Spectroscopic and quantum chemical electronic structure investigations of 3,4-dihydrocoumarin and 3-methylcoumarin

    Science.gov (United States)

    Arivazhagan, M.; Kavitha, R.; Subhasini, V. P.

    2014-09-01

    A complete vibrational analysis of 3,4-dihydrocoumarin and 3-methylcoumarin have been performed according to SQM force field method based on ab initio and DFT calculation 6-311++G(d,p) basis set and their frequencies are compared. The influences of carbon-oxygen bond and methyl group to the vibrational frequencies of the title compounds have been discussed. The pronounced decrease of the lone pair orbital occupancy and the molecular stabilization energy show the hyperconjugation interaction from the NBO analysis. Calculations of molecular orbital geometry show that the visible absorption maxima of DHC and 3MC correspond to the electron transition between frontier orbitals such as translation from HOMO to LUMO. Gauge-including atomic orbital (GIAO) 1H and 13C chemical shift calculations have been calculated. Area of high, neutral and low electrostatic potential is determined for DHC and 3MC.

  14. Isolated and synergistic effects of chemical and structural defenses of two species of Tethya (Porifera: Demospongiae)

    Science.gov (United States)

    Ribeiro, Suzi Meneses; Cassiano, Keila Mara; Cavalcanti, Diana Negrão; Teixeira, Valéria Laneuville; Pereira, Renato Crespo

    2012-02-01

    Sponges are an important source of many interesting secondary metabolites with multiple ecological roles. Sponges can also use their spicules as a means of deterring consumers. The present study investigated the importance of chemicals and spicules as defensive strategies against predation for two congeneric sponge species from the Brazilian coast, Tethya rubra and Tethya maza. Crude extract and spicules differed somewhat in their effectiveness between these sponge species, with T. maza better defended than T. rubra against predation by the hermit crab Calcinus tibicen and synergistic effects stronger in T. rubra. These results show that defensive strategies may be similar between sponge species possessing monophyletic origin, and reveal the importance of research on congeneric species to understand the ecology and evolution of defensive strategies.

  15. Microbial Mineralization of Soil Organic Matter: Role of Chemical Composition and Structural Organization

    Science.gov (United States)

    Khalaf, M. M. R.; Chilom, G.; Rice, J. A.

    2014-12-01

    The purpose of this study is to quantitatively assess the effect of organic matter self-assembly on its resistance to microbial mineralization. Humic acids isolated from leonardite, two peats and a mineral soil were used as organic matter samples because they provide a broad range of variability in terms of the origin and nature of their organic components. Using a solvent-based fractionation method, humic acid samples were disassembled into a humic-like component and a humic-lipid composite. The humic-lipid composite was further disassembled into an amphiphilic and a lipid component using an alkaline aqueous solution. Mixtures that reproduced the composition of self-assembled samples were prepared by mixing the solid individual fractions in the exact proportions that they were present in the original material. The original humic acids or their corresponding mixtures were added as the sole carbon source in separate aerobic cultures containing a microbial consortium isolated from a mineral soil. After incubation for 125 days mineralization of the self-assembled samples was shown to be higher by as much as 70% compared to their corresponding physical mixtures. The extent of mineralization of the self-assembled samples was not correlated to the material's chemical composition or hydrophobicity index obtained from their 13C solid-state NMR spectra. In contrast, mineralization of the physical mixtures and the individual fractions did vary with chemical composition and was accompanied by preferential mineralization of alkyl carbon. These results suggest the microbial mineralization of humic acids is related to their self-assembly.

  16. Development of standards for chemical and biological decontamination of buildings and structures affected by terrorism

    Energy Technology Data Exchange (ETDEWEB)

    Lumley, T.C.; Volchek, K.; Fingas, M. [Environment Canada, Ottawa, ON (Canada). Emergencies Science and Technology Division, Environmental Technology Centre, Science and Technology Branch; Hay, A.W.M. [Leeds Univ., Leeds (United Kingdom)

    2006-07-01

    Currently, there are no suitable standards for determining levels of safety when reoccupying a building that has been recommissioned following a biological or chemical attack. For that reason, this study focused on developing clean-up standards for decontaminating buildings and construction materials after acts of terrorism. Several parameters must be assessed when determining the course of action to decontaminate toxic agents and to rehabilitate facilities. First, the hazardous substance must be positively identified along with the degree of contamination and information on likely receptors. Potential exposure route is also a key consideration in the risk assessment process. A key objective of the study was to develop specific guidelines for ascertaining and defining clean. In particular, standards for chemical and biological agents that pose a real or potential risk for use as agents of terrorism will be developed. The selected agents for standards development were ammonia, fentanyl, malathion, mustard gas, potassium cyanide, ricin, sarin, hepatitis A virus, and bacillus anthracis. The standards will be developed by establishing the relationship between the amount of exposure and expected health effects; assessing real and potential risks by identifying individuals at risk and consideration of all exposure routes; and, characterizing the risk to determine the potential for toxicity or infectivity. For non-carcinogens, this was done through the analysis of other known guidelines. Cancer-slope factors will be considered for carcinogens. The standards will be assessed in the laboratory using animal models. The guidelines and standards are intended for first-responders and are scheduled for development by the end of 2006. 15 refs., 3 tabs.

  17. mzGroupAnalyzer--predicting pathways and novel chemical structures from untargeted high-throughput metabolomics data.

    Directory of Open Access Journals (Sweden)

    Hannes Doerfler

    Full Text Available The metabolome is a highly dynamic entity and the final readout of the genotype x environment x phenotype (GxExP relationship of an organism. Monitoring metabolite dynamics over time thus theoretically encrypts the whole range of possible chemical and biochemical transformations of small molecules involved in metabolism. The bottleneck is, however, the sheer number of unidentified structures in these samples. This represents the next challenge for metabolomics technology and is comparable with genome sequencing 30 years ago. At the same time it is impossible to handle the amount of data involved in a metabolomics analysis manually. Algorithms are therefore imperative to allow for automated m/z feature extraction and subsequent structure or pathway assignment. Here we provide an automated pathway inference strategy comprising measurements of metabolome time series using LC- MS with high resolution and high mass accuracy. An algorithm was developed, called mzGroupAnalyzer, to automatically explore the metabolome for the detection of metabolite transformations caused by biochemical or chemical modifications. Pathways are extracted directly from the data and putative novel structures can be identified. The detected m/z features can be mapped on a van Krevelen diagram according to their H/C and O/C ratios for pattern recognition and to visualize oxidative processes and biochemical transformations. This method was applied to Arabidopsis thaliana treated simultaneously with cold and high light. Due to a protective antioxidant response the plants turn from green to purple color via the accumulation of flavonoid structures. The detection of potential biochemical pathways resulted in 15 putatively new compounds involved in the flavonoid-pathway. These compounds were further validated by product ion spectra from the same data. The mzGroupAnalyzer is implemented in the graphical user interface (GUI of the metabolomics toolbox COVAIN (Sun & Weckwerth, 2012

  18. Accelerated structure-based design of chemically diverse allosteric modulators of a muscarinic G protein-coupled receptor.

    Science.gov (United States)

    Miao, Yinglong; Goldfeld, Dahlia Anne; Moo, Ee Von; Sexton, Patrick M; Christopoulos, Arthur; McCammon, J Andrew; Valant, Celine

    2016-09-20

    Design of ligands that provide receptor selectivity has emerged as a new paradigm for drug discovery of G protein-coupled receptors, and may, for certain families of receptors, only be achieved via identification of chemically diverse allosteric modulators. Here, the extracellular vestibule of the M2 muscarinic acetylcholine receptor (mAChR) is targeted for structure-based design of allosteric modulators. Accelerated molecular dynamics (aMD) simulations were performed to construct structural ensembles that account for the receptor flexibility. Compounds obtained from the National Cancer Institute (NCI) were docked to the receptor ensembles. Retrospective docking of known ligands showed that combining aMD simulations with Glide induced fit docking (IFD) provided much-improved enrichment factors, compared with the Glide virtual screening workflow. Glide IFD was thus applied in receptor ensemble docking, and 38 top-ranked NCI compounds were selected for experimental testing. In [(3)H]N-methylscopolamine radioligand dissociation assays, approximately half of the 38 lead compounds altered the radioligand dissociation rate, a hallmark of allosteric behavior. In further competition binding experiments, we identified 12 compounds with affinity of ≤30 μM. With final functional experiments on six selected compounds, we confirmed four of them as new negative allosteric modulators (NAMs) and one as positive allosteric modulator of agonist-mediated response at the M2 mAChR. Two of the NAMs showed subtype selectivity without significant effect at the M1 and M3 mAChRs. This study demonstrates an unprecedented successful structure-based approach to identify chemically diverse and selective GPCR allosteric modulators with outstanding potential for further structure-activity relationship studies. PMID:27601651

  19. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches

    International Nuclear Information System (INIS)

    Identification of endocrine disrupting chemicals is one of the important goals of environmental chemical hazard screening. We report on the development of validated in silico predictors of chemicals likely to cause estrogen receptor (ER)-mediated endocrine disruption to facilitate their prioritization for future screening. A database of relative binding affinity of a large number of ERα and/or ERβ ligands was assembled (546 for ERα and 137 for ERβ). Both single-task learning (STL) and multi-task learning (MTL) continuous quantitative structure–activity relationship (QSAR) models were developed for predicting ligand binding affinity to ERα or ERβ. High predictive accuracy was achieved for ERα binding affinity (MTL R2 = 0.71, STL R2 = 0.73). For ERβ binding affinity, MTL models were significantly more predictive (R2 = 0.53, p < 0.05) than STL models. In addition, docking studies were performed on a set of ER agonists/antagonists (67 agonists and 39 antagonists for ERα, 48 agonists and 32 antagonists for ERβ, supplemented by putative decoys/non-binders) using the following ER structures (in complexes with respective ligands) retrieved from the Protein Data Bank: ERα agonist (PDB ID: 1L2I), ERα antagonist (PDB ID: 3DT3), ERβ agonist (PDB ID: 2NV7), and ERβ antagonist (PDB ID: 1L2J). We found that all four ER conformations discriminated their corresponding ligands from presumed non-binders. Finally, both QSAR models and ER structures were employed in parallel to virtually screen several large libraries of environmental chemicals to derive a ligand- and structure-based prioritized list of putative estrogenic compounds to be used for in vitro and in vivo experimental validation. - Highlights: • This is the largest curated dataset inclusive of ERα and β (the latter is unique). • New methodology that for the first time affords acceptable ERβ models. • A combination of QSAR and docking enables prediction of affinity and function. • The results have

  20. Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Liying; Sedykh, Alexander; Tripathi, Ashutosh [Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC (United States); Zhu, Hao [The Rutgers Center for Computational and Integrative Biology, Rutgers University, Camden, NJ (United States); Department of Chemistry, Rutgers University, Camden, NJ (United States); Afantitis, Antreas; Mouchlis, Varnavas D.; Melagraki, Georgia [NovaMechanics Ltd., Nicosia (Cyprus); Rusyn, Ivan, E-mail: iir@unc.edu [Department of Environmental Sciences and Engineering, University of North Carolina, Chapel Hill, NC (United States); Tropsha, Alexander, E-mail: alex_tropsha@unc.edu [Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC (United States)

    2013-10-01

    Identification of endocrine disrupting chemicals is one of the important goals of environmental chemical hazard screening. We report on the development of validated in silico predictors of chemicals likely to cause estrogen receptor (ER)-mediated endocrine disruption to facilitate their prioritization for future screening. A database of relative binding affinity of a large number of ERα and/or ERβ ligands was assembled (546 for ERα and 137 for ERβ). Both single-task learning (STL) and multi-task learning (MTL) continuous quantitative structure–activity relationship (QSAR) models were developed for predicting ligand binding affinity to ERα or ERβ. High predictive accuracy was achieved for ERα binding affinity (MTL R{sup 2} = 0.71, STL R{sup 2} = 0.73). For ERβ binding affinity, MTL models were significantly more predictive (R{sup 2} = 0.53, p < 0.05) than STL models. In addition, docking studies were performed on a set of ER agonists/antagonists (67 agonists and 39 antagonists for ERα, 48 agonists and 32 antagonists for ERβ, supplemented by putative decoys/non-binders) using the following ER structures (in complexes with respective ligands) retrieved from the Protein Data Bank: ERα agonist (PDB ID: 1L2I), ERα antagonist (PDB ID: 3DT3), ERβ agonist (PDB ID: 2NV7), and ERβ antagonist (PDB ID: 1L2J). We found that all four ER conformations discriminated their corresponding ligands from presumed non-binders. Finally, both QSAR models and ER structures were employed in parallel to virtually screen several large libraries of environmental chemicals to derive a ligand- and structure-based prioritized list of putative estrogenic compounds to be used for in vitro and in vivo experimental validation. - Highlights: • This is the largest curated dataset inclusive of ERα and β (the latter is unique). • New methodology that for the first time affords acceptable ERβ models. • A combination of QSAR and docking enables prediction of affinity and function.

  1. Diagnosis of chemical attack of concrete structures: The role of microscopy

    NARCIS (Netherlands)

    Larbi, J.A.; Visser, J.H.M.

    1999-01-01

    Microscopical analysis of concrete in a deteriorating structure involves investigative techniques that make use of various analytical methods to solve specific problems related to the concrete. The technique is quick and particularly useful for diagnosing concrete deterioration and damage problems s

  2. The quaternary structure of the recombinant bovine odorant-binding protein is modulated by chemical denaturants.

    Directory of Open Access Journals (Sweden)

    Olga V Stepanenko

    Full Text Available A large group of odorant-binding proteins (OBPs has attracted great scientific interest as promising building blocks in constructing optical biosensors for dangerous substances, such as toxic and explosive molecules. Native tissue-extracted bovine OBP (bOBP has a unique dimer folding pattern that involves crossing the α-helical domain in each monomer over the other monomer's β-barrel. In contrast, recombinant bOBP maintaining the high level of stability inherent to native tissue bOBP is produced in a stable native-like state with a decreased tendency for dimerization and is a mixture of monomers and dimers in a buffered solution. This work is focused on the study of the quaternary structure and the folding-unfolding processes of the recombinant bOBP in the absence and in the presence of guanidine hydrochloride (GdnHCl. Our results show that the recombinant bOBP native dimer is only formed at elevated GdnHCl concentrations (1.5 M. This process requires re-organizing the protein structure by progressing through the formation of an intermediate state. The bOBP dimerization process appears to be irreversible and it occurs before the protein unfolds. Though the observed structural changes for recombinant bOBP at pre-denaturing GdnHCl concentrations show a local character and the overall protein structure is maintained, such changes should be considered where the protein is used as a sensitive element in a biosensor system.

  3. Semiempirical Predictions of Chemical Degradation Reaction Mechanisms of CL-20 as Related to Molecular Structure

    Energy Technology Data Exchange (ETDEWEB)

    Qasim, Mohammad M.; Furey, John; Fredrickson, Herbert L.; Szecsody, Jim E.; Mcgrath, Chris J.; Bajpai, Rakesh

    2004-10-01

    Quantum mechanical methods and force field molecular mechanics were used to characterize cage cyclic nitramines and to predict environmental degradation mechanisms. Due to structural similarities it is predicted that, under homologous circumstances, the major environmental RDX degradation pathways should also be effective for CL-20 and similar cyclic nitramines.

  4. Mineralogical, physical and chemical characteristics of historic brick-made structures

    Science.gov (United States)

    El-Midany, A. A.; Mahmoud, H. M.

    2015-12-01

    Brick-structured historic buildings represent one of the common monument types. Although they stand till now due to their fused structure, they are subjected to weathering and are affected by environmental deterioration. To perform any conservation/restortation process, a detailed characterization of the current conditions of the bricks is needed for identification of major threats and choosing a suitable material for conservation. In this study, historic brick-made structures was subjected to detailed characterization to identify the composition and quality of raw materials as well as environmental impacts on their original structure. Different characterization techniques such as mineralogical and petrographic examination, scanning electron microscopy (SEM), and determination of physical and mechanical properties were used. The results of the characterization indicate that the bricks were manufactured from low-quality clay and treated at a temperature lower than 900 °C. In addition, environment pollution enhanced the presence of some ions, which affected the mechanical properties of bricks and lead to their deterioration and damage.

  5. Hydramycin, a new antitumor antibiotic. Taxonomy, isolation, physico-chemical properties, structure and biological activity.

    Science.gov (United States)

    Hanada, M; Kaneta, K; Nishiyama, Y; Hoshino, Y; Konishi, M; Oki, T

    1991-08-01

    A new antitumor antibiotic hydramycin was isolated from the fermentation broth of Streptomyces violaceus P950-4 (ATCC 53807). It showed potent antibacterial and cytotoxic activity and increased the survival time of mice inoculated with P388 leukemia. A new structure related to the pluramycin group antibiotics was assigned by its spectroscopic experiments. PMID:1833366

  6. Coal Liquefaction characteristics and chemical structure of product oil; Sekitan ekika hanno tokusei to seiseibutsu no kagaku kozo

    Energy Technology Data Exchange (ETDEWEB)

    Endo, H.; Sato, M.; Chiba, T.; Hattori, H. [Hokkaido University, Sapporo (Japan). Center for Advanced Research of Energy Technology; Sasaki, M. [Hokkaido National Industrial Research Institute, Sapporo (Japan)

    1996-10-28

    Through the hydrogenolysis of Wandoan coal and Tanito Harum coal which are used for the NEDOL process, differences of liquefaction characteristics between them were found. The purpose of this study is to grasp these differences as differences of chemical structures of oil fractions. The compound type analysis was conducted for oil fractions obtained at varied reaction temperature for varied reaction time. Coal liquefaction characteristics of these coals were discussed by relating oil yields and chemical structures. For Tanito Harum coal, yields of gas and oil were considered to be lower than those for Wandoan coal, which reflected that the contents of partially hydrogenated hydroaromatics in oil fraction from the former were lower than those from the latter, and that the remarkable change of composition did not occur with the progress of the reaction. For both the coals, the remarkable changes in the average molecular weight of oil fraction were not observed with the progress of the reaction. While, the content of methane gradually increased with the progress of the reaction, which suggested that oil was gradually dealkylated. 5 figs.

  7. Growth control, structure, chemical state, and photoresponse of CuO-CdS core-shell heterostructure nanowires.

    Science.gov (United States)

    El Mel, A A; Buffière, M; Bouts, N; Gautron, E; Tessier, P Y; Henzler, K; Guttmann, P; Konstantinidis, S; Bittencourt, C; Snyders, R

    2013-07-01

    The growth of single-crystal CuO nanowires by thermal annealing of copper thin films in air is studied. We show that the density, length, and diameter of the nanowires can be controlled by tuning the morphology and structure of the copper thin films deposited by DC magnetron sputtering. After identifying the optimal conditions for the growth of CuO nanowires, chemical bath deposition is employed to coat the CuO nanowires with CdS in order to form p-n nanojunction arrays. As revealed by high-resolution TEM analysis, the thickness of the polycrystalline CdS shell increases when decreasing the diameter of the CuO core for a given time of CdS deposition. Near-edge x-ray absorption fine-structure spectroscopy combined with transmission x-ray microscopy allows the chemical analysis of isolated nanowires. The absence of modification in the spectra at the Cu L and O K edges after the deposition of CdS on the CuO nanowires indicates that neither Cd nor S diffuse into the CuO phase. We further demonstrate that the core-shell nanowires exhibit the I-V characteristic of a resistor instead of a diode. The electrical behavior of the device was found to be photosensitive, since increasing the incident light intensity induces an increase in the collected electrical current. PMID:23732175

  8. A phenomenological model for the structure-composition relationship of the high Tc cuprates based on simple chemical principles

    International Nuclear Information System (INIS)

    A simple phenomenological model for the relationship between structure and composition of the high Tc cuprates is presented. The model is based on two simple crystal chemistry principles: unit cell doping and charge balance within unit cells. These principles are inspired by key experimental observations of how the materials accommodate large deviations from stoichiometry. Consistent explanations for significant HTSC properties can be explained without any additional assumptions while retaining valuable insight for geometric interpretation. Combining these two chemical principles with a review of Crystal Field Theory (CFT) or Ligand Field Theory (LFT), it becomes clear that the two oxidation states in the conduction planes (typically d8 and d9) belong to the most strongly divergent d-levels as a function of deformation from regular octahedral coordination. This observation offers a link to a range of coupling effects relating vibrations and spin waves through application of Hund’s rules. An indication of this model’s capacity to predict physical properties for HTSC is provided and will be elaborated in subsequent publications. Simple criteria for the relationship between structure and composition in HTSC systems may guide chemical syntheses within new material systems.

  9. Atomic-scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-ray Spectroscopy

    Science.gov (United States)

    Lu, Ping; Zhou, Lin; Kramer, M. J.; Smith, David J.

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L21 phase with Ni0.48Co0.52 at A-sites, Al at BΙ-sites and Fe0.20Ti0.80 at BΙΙ-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  10. Atomic-Scale Chemical Imaging and Quantification of Metallic Alloy Structures by Energy-Dispersive X-Ray Spectroscopy

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ping [Sandia National Laboratories; Zhou, Lin [Ames Laboratory; Kramer, Matthew J. [Ames Laboratory; Smith, David J. [Arizona State University

    2014-02-04

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L21 phase with Ni0.48Co0.52 at A-sites, Al at BΙ-sites and Fe0.20Ti0.80 at BΙΙ-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems.

  11. Crystallization, phase evolution and corrosion of Fe-based metallic glasses: An atomic-scale structural and chemical characterization study

    International Nuclear Information System (INIS)

    Understanding phase changes, including their formation and evolution, is critical for the performance of functional as well as structural materials. We analyze in detail microstructural and chemical transformations of the amorphous steel Fe50Cr15Mo14C15B6 during isothermal treatments at temperatures ranging from 550 to 800 °C. By combining high-resolution transmission electron microscopy and Rietveld analyses of X-ray diffraction patterns together with the local chemical data obtained by atom probe tomography, this research provides relevant information at the atomic scale about the mechanisms of crystallization and the subsequent phases evolution. During the initial stages of crystallization a stable (Fe,Cr)23(C,B)6 precipitates as well as two metastable intermediates of M3(C,B) and the intermetallic χ-phase. When full crystallization is reached, only a percolated nano-scale Cr-rich (Fe,Cr)23(C,B)6 and Mo-rich η-Fe3Mo3C structure is detected, with no evidence to suggest that other phases appear at any subsequent time. Finally, the corrosion behavior of the developed phases is discussed from considerations of the obtained atomic information

  12. Chemical Structure, Property and Potential Applications of Biosurfactants Produced by Bacillus subtilis in Petroleum Recovery and Spill Mitigation

    Directory of Open Access Journals (Sweden)

    Jin-Feng Liu

    2015-03-01

    Full Text Available Lipopeptides produced by microorganisms are one of the five major classes of biosurfactants known and they have received much attention from scientific and industrial communities due to their powerful interfacial and biological activities as well as environmentally friendly characteristics. Microbially produced lipopeptides are a series of chemical structural analogues of different families and, among them, 26 families covering about 90 lipopeptide compounds have been reported in the last two decades. This paper reviews the chemical structural characteristics and molecular behaviors of surfactin, one of the representative lipopeptides of the 26 families. In particular, two novel surfactin molecules isolated from cell-free cultures of Bacillus subtilis HSO121 are presented. Surfactins exhibit strong self-assembly ability to form sphere-like micelles and larger aggregates at very low concentrations. The amphipathic and surface properties of surfactins are related to the existence of the minor polar and major hydrophobic domains in the three 3-D conformations. In addition, the application potential of surfactin in bioremediation of oil spills and oil contaminants, and microbial enhanced oil recovery are discussed.

  13. Growth control, structure, chemical state, and photoresponse of CuO-CdS core-shell heterostructure nanowires.

    Science.gov (United States)

    El Mel, A A; Buffière, M; Bouts, N; Gautron, E; Tessier, P Y; Henzler, K; Guttmann, P; Konstantinidis, S; Bittencourt, C; Snyders, R

    2013-07-01

    The growth of single-crystal CuO nanowires by thermal annealing of copper thin films in air is studied. We show that the density, length, and diameter of the nanowires can be controlled by tuning the morphology and structure of the copper thin films deposited by DC magnetron sputtering. After identifying the optimal conditions for the growth of CuO nanowires, chemical bath deposition is employed to coat the CuO nanowires with CdS in order to form p-n nanojunction arrays. As revealed by high-resolution TEM analysis, the thickness of the polycrystalline CdS shell increases when decreasing the diameter of the CuO core for a given time of CdS deposition. Near-edge x-ray absorption fine-structure spectroscopy combined with transmission x-ray microscopy allows the chemical analysis of isolated nanowires. The absence of modification in the spectra at the Cu L and O K edges after the deposition of CdS on the CuO nanowires indicates that neither Cd nor S diffuse into the CuO phase. We further demonstrate that the core-shell nanowires exhibit the I-V characteristic of a resistor instead of a diode. The electrical behavior of the device was found to be photosensitive, since increasing the incident light intensity induces an increase in the collected electrical current.

  14. THE EFFECT OF CHARGE AND CHEMICAL STRUCTURE OF CATIONIC SURFACTANTS ON LASER TONER AGGLOMERATION UNDER ALKALINE PULPING CONDITIONS

    Directory of Open Access Journals (Sweden)

    Jie Jiang,

    2012-02-01

    Full Text Available Laboratory-scale agglomeration experiments followed by image analysis were used to evaluate the effectiveness of different cationic surfactants on the 1-octadecanol agglomeration of a negatively charged laser toner. Various types of surfactants with different geometric structures were investigated. It was found that this toner became agglomerated under neutral pulping conditions, but it did not agglomerate under alkaline conditions at all. A small amount of the cationic surfactant compensated for the agglomeration disruption caused by the negative surface charge of the toner and made this toner agglomerate very well. These cationic surfactants consist of a chemical structure of C12 to C18 saturated alkyl hydrophobic chains. The positive charge of these surfactants played the major role in alleviating agglomeration disruption. Additionally, an extra phenol group on these surfactants contributed only minor advantages for toner agglomeration in the presence of 1-octadecanol. The best co-agglomeration performance occurred within a very narrow range of similar total positive charge densities based on the total toner weight. It was also found that this positive charge effect could not be applied to the chemical compounds of high molecular weight polymeric materials.

  15. Chemical structure, property and potential applications of biosurfactants produced by Bacillus subtilis in petroleum recovery and spill mitigation.

    Science.gov (United States)

    Liu, Jin-Feng; Mbadinga, Serge Maurice; Yang, Shi-Zhong; Gu, Ji-Dong; Mu, Bo-Zhong

    2015-01-01

    Lipopeptides produced by microorganisms are one of the five major classes of biosurfactants known and they have received much attention from scientific and industrial communities due to their powerful interfacial and biological activities as well as environmentally friendly characteristics. Microbially produced lipopeptides are a series of chemical structural analogues of different families and, among them, 26 families covering about 90 lipopeptide compounds have been reported in the last two decades. This paper reviews the chemical structural characteristics and molecular behaviors of surfactin, one of the representative lipopeptides of the 26 families. In particular, two novel surfactin molecules isolated from cell-free cultures of Bacillus subtilis HSO121 are presented. Surfactins exhibit strong self-assembly ability to form sphere-like micelles and larger aggregates at very low concentrations. The amphipathic and surface properties of surfactins are related to the existence of the minor polar and major hydrophobic domains in the three 3-D conformations. In addition, the application potential of surfactin in bioremediation of oil spills and oil contaminants, and microbial enhanced oil recovery are discussed. PMID:25741767

  16. Atomic-scale chemical imaging and quantification of metallic alloy structures by energy-dispersive X-ray spectroscopy.

    Science.gov (United States)

    Lu, Ping; Zhou, Lin; Kramer, M J; Smith, David J

    2014-01-01

    Determination of atomic-scale crystal structure for nanostructured intermetallic alloys, such as magnetic alloys containing Al, Ni, Co (alnico) and Fe, is crucial for understanding physical properties such as magnetism, but technically challenging due to the small interatomic distances and the similar atomic numbers. By applying energy-dispersive X-ray spectroscopy (EDS) mapping to the study of two intermetallic phases of an alnico alloy resulting from spinodal decomposition, we have determined atomic-scale chemical composition at individual lattice sites for the two phases: one is the B2 phase with Fe0.76Co0.24 -Fe0.40Co0.60 ordering and the other is the L2(1) phase with Ni0.48Co0.52 at A-sites, Al at B(Ι)-sites and Fe0.20Ti0.80 at B(ΙΙ)-sites, respectively. The technique developed through this study represents a powerful real-space approach to investigate structure chemically at the atomic scale for a wide range of materials systems. PMID:24492747

  17. Chemical and structural characterization of interstrand cross-links formed between abasic sites and adenine residues in duplex DNA

    Science.gov (United States)

    Price, Nathan E.; Catalano, Michael J.; Liu, Shuo; Wang, Yinsheng; Gates, Kent S.

    2015-01-01

    A new type of interstrand DNA–DNA cross-link between abasic (Ap) sites and 2′-deoxyadenosine (dA) residues was recently reported, but the chemical structure and properties of this lesion were not rigorously established. Here we characterized the nucleoside cross-link remnant released by enzymatic digestion of duplex DNA containing the dA-Ap cross-link. A synthetic standard was prepared for the putative nucleoside cross-link remnant 6 in which the anomeric carbon of the 2-deoxyribose residue was connected to the exocyclic N6-amino group of dA. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis showed that the synthetic material 6 matched the authentic cross-link remnant released by enzymatic digestion of cross-linked DNA. These findings establish the chemical structure of the dA-Ap cross-link released from duplex DNA and may provide methods for the detection of this lesion in cellular DNA. Both the nucleoside cross-link remnant 6 and the cross-link in duplex DNA were quite stable at pH 7 and 37°C, suggesting that the dA-Ap cross-link could be a persistent lesion with the potential to block the action of various DNA processing enzymes. PMID:25779045

  18. Aluminum germanides of the divalent lanthanoides Eu and Yb. Synthesis, structural chemistry and chemical bonding

    International Nuclear Information System (INIS)

    In the course of attempts to substitute Ca by Yb and Sr by Eu in known alkaline earth Al-germanides, the four new ternary compounds Eu3Al1.8Ge2.2, Eu3Al2Ge4, Yb2AlGe3, and Yb17Al8Ge19 have been synthesized from mixtures of the elements and their crystal structures determined by means of single-crystal X-ray data. The two europium compounds Eu3Al1.8Ge2.2 (Ta3B4 structure type, orthorhombic, space group Immm, a = 417.68(3), b = 470.70(3), c = 1897.2(2) pm, Z = 2, R1 = 0.0439) and Eu3Al2Ge4 (Sr3Al2Ge4 structure type, monoclinic, space group C2/m, a = 1235.9(6), b = 416.8(2), c = 878.4(4) pm, β = 110.615(13) , Z = 2, R1 = 0.0978) are isotypic with the corresponding strontium phases. After ionic decomposition, the layers [Al-2Ge-4]6- in Eu3Al2Ge4 with four-bonded Al and three-bonded Ge atoms can be interpreted as electron-precise Zintl anions. In contrast, the planar ribbons 1∞[Al2/2Ge2Al2/2] of condensed six-membered rings in Eu3Al1.8Ge2.2 exhibit considerably shorter Al-Ge bonds and an Al-Al bond length of only 251 pm. Yb2AlGe3 (orthorhombic, space group Pnma, a = 682.20(10), b = 417.87(9), c = 1813.9(3) pm, Z = 4, R1 = 0.0415) crystallizes with the Y2AlGe3 structure type. Folded [Al2Ge2] ladders, also found in Eu3Al2Ge4 and the known compound Yb7Al5Ge8, are connected by planar cis/trans chains of Ge atoms. The total density of states calculated within the FP-LAPW DFT band structure approach shows a distinct minimum at the Fermi level for the electron precise Zintl compound Eu3Al2Ge4, whereas π-bonding contributions are evident from the band structures of Eu3Al2Ge2 and Yb2AlGe3. In full accordance, the tDOS of both compounds exhibits no minimum at EF, small phase widths are possible for Eu3Al2Ge2 and related alkaline earth compounds, and Yb2AlGe3 is isotypic with several other more electron-rich LnIII compounds. The complicated structure of the new compound Yb17Al8Ge19 (tetragonal, space group P4/nmm, a = 1542.50(2), c = 788.285(8) pm, Z = 2, R1 = 0.0282) contains

  19. Sensitivity of chemical reaction networks: a structural approach 3. Regular multimolecular systems

    CERN Document Server

    Brehm, Bernhard

    2016-01-01

    We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions, multiple reaction products, nonmonotone rate functions, and non-closed autonomous systems. Our structural sensitivity analysis is based on the stoichiometry of the reaction network, only. It does not require numerical data on reaction rates. Instead, we impose mild and generic nondegeneracy conditions of algebraic type. From the structural data, only, we derive which steady-state concentrations are sensitive to, and hence influenced by, changes of any particular reaction rate - and which are not. We also establish transitivity properties for influences involving rate perturbations. This allows us to derive an influence graph which globally summarizes the influence pattern of the given network. The influence graph allows the computational, but meaningful, automatic identification ...

  20. Organic chemistry as a language and the implications of chemical linguistics for structural and retrosynthetic analyses.

    Science.gov (United States)

    Cadeddu, Andrea; Wylie, Elizabeth K; Jurczak, Janusz; Wampler-Doty, Matthew; Grzybowski, Bartosz A

    2014-07-28

    Methods of computational linguistics are used to demonstrate that a natural language such as English and organic chemistry have the same structure in terms of the frequency of, respectively, text fragments and molecular fragments. This quantitative correspondence suggests that it is possible to extend the methods of computational corpus linguistics to the analysis of organic molecules. It is shown that within organic molecules bonds that have highest information content are the ones that 1) define repeat/symmetry subunits and 2) in asymmetric molecules, define the loci of potential retrosynthetic disconnections. Linguistics-based analysis appears well-suited to the analysis of complex structural and reactivity patterns within organic molecules.