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.

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).

ACToR Chemical Structure processing using Open Source ...

Science.gov (United States)

ACToR (Aggregated Computational Toxicology Resource) is a centralized database repository developed by the National Center for Computational Toxicology (NCCT) at the U.S. Environmental Protection Agency (EPA). Free and open source tools were used to compile toxicity data from over 1,950 public sources. ACToR contains chemical structure information and toxicological data for over 558,000 unique chemicals. The database primarily includes data from NCCT research programs, in vivo toxicity data from ToxRef, human exposure data from ExpoCast, high-throughput screening data from ToxCast and high quality chemical structure information from the EPA DSSTox program. The DSSTox database is a chemical structure inventory for the NCCT programs and currently has about 16,000 unique structures. Included are also data from PubChem, ChemSpider, USDA, FDA, NIH and several other public data sources. ACToR has been a resource to various international and national research groups. Most of our recent efforts on ACToR are focused on improving the structural identifiers and Physico-Chemical properties of the chemicals in the database. Organizing this huge collection of data and improving the chemical structure quality of the database has posed some major challenges. Workflows have been developed to process structures, calculate chemical properties and identify relationships between CAS numbers. The Structure processing workflow integrates web services (PubChem and NIH NCI Cactus) to d

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.

From glass structure to its chemical durability

International Nuclear Information System (INIS)

Angeli, F.

2009-01-01

The author gives an overview of his research activities. He more precisely reports studies related to glass structure based on nuclei observed by NMR and present in glasses of interest for nuclear activities. He discusses the influence of chemical composition on structure, and discusses information which can be extracted from network formers (Al, B) and modifiers (Na, Ca), and from oxygen present in the network linkages of oxide glasses. He discusses the different experimental and modelling approaches which enable structural and morphological information to be obtained at a mesoscopic scale. The last part deals with the investigation of the long term behaviour of confinement matrices (glassy matrix for medium-activity wastes, ceramic matrix)

Structural-chemical characteristics of implanted metals

International Nuclear Information System (INIS)

Kozejkin, B.V.; Pavlov, P.V.; Pitirimova, E.A.; Frolov, A.I.

1988-01-01

Corrosion and structural characteristics of metallic layers implanted by ions of chemically active impurities and noble gases are studied. Dependence of experimental results on parameters of initial materials and technological conditions of implantation is established. In studying corrosion characteristics of implanted metals a strong dependence of chemical passivation effect on technological conditions of ion-implantation and structure of initial material is stated. On the basis of developed mathematical model of chemical passivation effect it is shown that increase of corrosion characteristics of implanted metals is defined by superposition of surface and volumetric mechanisms

Conservation-dissipation structure of chemical reaction systems.

Science.gov (United States)

Yong, Wen-An

2012-12-01

In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics.

Structure alerts for carcinogenicity, and the Salmonella assay system: a novel insight through the chemical relational databases technology.

Science.gov (United States)

Benigni, Romualdo; Bossa, Cecilia

2008-01-01

In the past decades, chemical carcinogenicity has been the object of mechanistic studies that have been translated into valuable experimental (e.g., the Salmonella assays system) and theoretical (e.g., compilations of structure alerts for chemical carcinogenicity) models. These findings remain the basis of the science and regulation of mutagens and carcinogens. Recent advances in the organization and treatment of large databases consisting of both biological and chemical information nowadays allows for a much easier and more refined view of data. This paper reviews recent analyses on the predictive performance of various lists of structure alerts, including a new compilation of alerts that combines previous work in an optimized form for computer implementation. The revised compilation is part of the Toxtree 1.50 software (freely available from the European Chemicals Bureau website). The use of structural alerts for the chemical biological profiling of a large database of Salmonella mutagenicity results is also reported. Together with being a repository of the science on the chemical biological interactions at the basis of chemical carcinogenicity, the SAs have a crucial role in practical applications for risk assessment, for: (a) description of sets of chemicals; (b) preliminary hazard characterization; (c) formation of categories for e.g., regulatory purposes; (d) generation of subsets of congeneric chemicals to be analyzed subsequently with QSAR methods; (e) priority setting. An important aspect of SAs as predictive toxicity tools is that they derive directly from mechanistic knowledge. The crucial role of mechanistic knowledge in the process of applying (Q)SAR considerations to risk assessment should be strongly emphasized. Mechanistic knowledge provides a ground for interaction and dialogue between model developers, toxicologists and regulators, and permits the integration of the (Q)SAR results into a wider regulatory framework, where different types of

Computational Study on Atomic Structures, Electronic Properties, and Chemical Reactions at Surfaces and Interfaces and in Biomaterials

Science.gov (United States)

Takano, Yu; Kobayashi, Nobuhiko; Morikawa, Yoshitada

2018-06-01

Through computer simulations using atomistic models, it is becoming possible to calculate the atomic structures of localized defects or dopants in semiconductors, chemically active sites in heterogeneous catalysts, nanoscale structures, and active sites in biological systems precisely. Furthermore, it is also possible to clarify physical and chemical properties possessed by these nanoscale structures such as electronic states, electronic and atomic transport properties, optical properties, and chemical reactivity. It is sometimes quite difficult to clarify these nanoscale structure-function relations experimentally and, therefore, accurate computational studies are indispensable in materials science. In this paper, we review recent studies on the relation between local structures and functions for inorganic, organic, and biological systems by using atomistic computer simulations.

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.

Molecule database framework: a framework for creating database applications with chemical structure search capability.

Science.gov (United States)

Kiener, Joos

2013-12-11

Research in organic chemistry generates samples of novel chemicals together with their properties and other related data. The involved scientists must be able to store this data and search it by chemical structure. There are commercial solutions for common needs like chemical registration systems or electronic lab notebooks. However for specific requirements of in-house databases and processes no such solutions exist. Another issue is that commercial solutions have the risk of vendor lock-in and may require an expensive license of a proprietary relational database management system. To speed up and simplify the development for applications that require chemical structure search capabilities, I have developed Molecule Database Framework. The framework abstracts the storing and searching of chemical structures into method calls. Therefore software developers do not require extensive knowledge about chemistry and the underlying database cartridge. This decreases application development time. Molecule Database Framework is written in Java and I created it by integrating existing free and open-source tools and frameworks. The core functionality includes:•Support for multi-component compounds (mixtures)•Import and export of SD-files•Optional security (authorization)For chemical structure searching Molecule Database Framework leverages the capabilities of the Bingo Cartridge for PostgreSQL and provides type-safe searching, caching, transactions and optional method level security. Molecule Database Framework supports multi-component chemical compounds (mixtures).Furthermore the design of entity classes and the reasoning behind it are explained. By means of a simple web application I describe how the framework could be used. I then benchmarked this example application to create some basic performance expectations for chemical structure searches and import and export of SD-files. By using a simple web application it was shown that Molecule Database Framework

Research of chemical structure of atmospheric precipitation

International Nuclear Information System (INIS)

Korenyak, D.

2001-01-01

The structure of atmospheric precipitation changes in its passing through the air medium. Thus, the atmospheric precipitation is one of the ecological factors, acting regularly. The research of chemical structure of atmospheric precipitation is closely connected with the problems of turnover of elements, with sanitary - ecological conditions of regions, with the matters of agricultural equipment and of salt balance of the soils. In paper the author for the first time represents the data on chemical structure of precipitation in the town. The data of chemical analysis of 18 samples are given. Obtained results permitted, to a certain extent, to determine the mechanisms of formation of atmospheric precipitation in the region investigated and its genesis. (authors)

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector; Kiani, Narsis A.; Shang, Ming-mei; Tegner, Jesper

2018-01-01

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector

2018-02-16

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

Algorithmic Complexity and Reprogrammability of Chemical Structure Networks

KAUST Repository

Zenil, Hector

2018-04-02

Here we address the challenge of profiling causal properties and tracking the transformation of chemical compounds from an algorithmic perspective. We explore the potential of applying a computational interventional calculus based on the principles of algorithmic probability to chemical structure networks. We profile the sensitivity of the elements and covalent bonds in a chemical structure network algorithmically, asking whether reprogrammability affords information about thermodynamic and chemical processes involved in the transformation of different compound classes. We arrive at numerical results suggesting a correspondence between some physical, structural and functional properties. Our methods are capable of separating chemical classes that reflect functional and natural differences without considering any information about atomic and molecular properties. We conclude that these methods, with their links to chemoinformatics via algorithmic, probability hold promise for future research.

De novo protein structure generation from incomplete chemical shift assignments

Energy Technology Data Exchange (ETDEWEB)

Shen Yang [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States); Vernon, Robert; Baker, David [University of Washington, Department of Biochemistry and Howard Hughes Medical Institute (United States); Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)], E-mail: bax@nih.gov

2009-02-15

NMR chemical shifts provide important local structural information for proteins. Consistent structure generation from NMR chemical shift data has recently become feasible for proteins with sizes of up to 130 residues, and such structures are of a quality comparable to those obtained with the standard NMR protocol. This study investigates the influence of the completeness of chemical shift assignments on structures generated from chemical shifts. The Chemical-Shift-Rosetta (CS-Rosetta) protocol was used for de novo protein structure generation with various degrees of completeness of the chemical shift assignment, simulated by omission of entries in the experimental chemical shift data previously used for the initial demonstration of the CS-Rosetta approach. In addition, a new CS-Rosetta protocol is described that improves robustness of the method for proteins with missing or erroneous NMR chemical shift input data. This strategy, which uses traditional Rosetta for pre-filtering of the fragment selection process, is demonstrated for two paramagnetic proteins and also for two proteins with solid-state NMR chemical shift assignments.

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.

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

Synthesis, vibrational, NMR, quantum chemical and structure-activity relation studies of 2-hydroxy-4-methoxyacetophenone.

Science.gov (United States)

Arjunan, V; Devi, L; Subbalakshmi, R; Rani, T; Mohan, S

2014-09-15

The stable geometry of 2-hydroxy-4-methoxyacetophenone is optimised by DFT/B3LYP method with 6-311++G(∗∗) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry have been determined. The effects of substituents (hydroxyl, methoxy and acetyl groups) on the benzene ring vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of 2-hydroxy-4-methoxyacetophenone have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and assignments made are compared with the experimental values. The energies of important MO's, the total electron density and electrostatic potential of the compound are determined. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities are calculated. Copyright © 2014 Elsevier B.V. All rights reserved.

Fragmentation pathways and structural characterization of organophosphorus compounds related to the Chemical Weapons Convention by electron ionization and electrospray ionization tandem mass spectrometry.

Science.gov (United States)

Hosseini, Seyed Esmaeil; Saeidian, Hamid; Amozadeh, Ali; Naseri, Mohammad Taghi; Babri, Mehran

2016-12-30

For unambiguous identification of Chemical Weapons Convention (CWC)-related chemicals in environmental samples, the availability of mass spectra, interpretation skills and rapid microsynthesis of suspected chemicals are essential requirements. For the first time, the electron ionization single quadrupole and electrospray ionization tandem mass spectra of a series of O-alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates (Scheme 1, cpd 4) were studied for CWC verification purposes. O-Alkyl N-[bis(dimethylamino)methylidene]-P-methylphosphonamidates were prepared through a microsynthetic method and were analyzed using electron ionization and electrospray ionization mass spectrometry with gas and liquid chromatography, respectively, as MS-inlet systems. General EI and ESI fragmentation pathways were proposed and discussed, and collision-induced dissociation studies of the protonated derivatives of these compounds were performed to confirm proposed fragment ion structures by analyzing mass spectra of deuterated analogs. Mass spectrometric studies revealed some interesting fragmentation pathways during the ionization process, such as McLafferty rearrangement, hydrogen rearrangement and a previously unknown intramolecular electrophilic aromatic substitution reaction. The EI and ESI fragmentation routes of the synthesized compounds 4 were investigated with the aim of detecting and identifying CWC-related chemicals during on-site inspection and/or off-site analysis and toxic chemical destruction monitoring. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

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.

Temporal Control over Transient Chemical Systems using Structurally Diverse Chemical Fuels.

Science.gov (United States)

Chen, Jack L-Y; Maiti, Subhabrata; Fortunati, Ilaria; Ferrante, Camilla; Prins, Leonard J

2017-08-25

The next generation of adaptive, intelligent chemical systems will rely on a continuous supply of energy to maintain the functional state. Such systems will require chemical methodology that provides precise control over the energy dissipation process, and thus, the lifetime of the transiently activated function. This manuscript reports on the use of structurally diverse chemical fuels to control the lifetime of two different systems under dissipative conditions: transient signal generation and the transient formation of self-assembled aggregates. The energy stored in the fuels is dissipated at different rates by an enzyme, which installs a dependence of the lifetime of the active system on the chemical structure of the fuel. In the case of transient signal generation, it is shown that different chemical fuels can be used to generate a vast range of signal profiles, allowing temporal control over two orders of magnitude. Regarding self-assembly under dissipative conditions, the ability to control the lifetime using different fuels turns out to be particularly important as stable aggregates are formed only at well-defined surfactant/fuel ratios, meaning that temporal control cannot be achieved by simply changing the fuel concentration. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Chemical structure-based predictive model for methanogenic anaerobic biodegradation potential.

Science.gov (United States)

Meylan, William; Boethling, Robert; Aronson, Dallas; Howard, Philip; Tunkel, Jay

2007-09-01

Many screening-level models exist for predicting aerobic biodegradation potential from chemical structure, but anaerobic biodegradation generally has been ignored by modelers. We used a fragment contribution approach to develop a model for predicting biodegradation potential under methanogenic anaerobic conditions. The new model has 37 fragments (substructures) and classifies a substance as either fast or slow, relative to the potential to be biodegraded in the "serum bottle" anaerobic biodegradation screening test (Organization for Economic Cooperation and Development Guideline 311). The model correctly classified 90, 77, and 91% of the chemicals in the training set (n = 169) and two independent validation sets (n = 35 and 23), respectively. Accuracy of predictions of fast and slow degradation was equal for training-set chemicals, but fast-degradation predictions were less accurate than slow-degradation predictions for the validation sets. Analysis of the signs of the fragment coefficients for this and the other (aerobic) Biowin models suggests that in the context of simple group contribution models, the majority of positive and negative structural influences on ultimate degradation are the same for aerobic and methanogenic anaerobic biodegradation.

Protein Structure Determination Using Chemical Shifts

DEFF Research Database (Denmark)

Christensen, Anders Steen

is determined using only chemical shifts recorded and assigned through automated processes. The CARMSD to the experimental X-ray for this structure is 1.1. Å. Additionally, the method is combined with very sparse NOE-restraints and evolutionary distance restraints and tested on several protein structures >100...

Chemical structure and dynamics: Annual report 1996

International Nuclear Information System (INIS)

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

1997-03-01

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

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.

Nucleic acid helix structure determination from NMR proton chemical shifts

Energy Technology Data Exchange (ETDEWEB)

Werf, Ramon M. van der; Tessari, Marco; Wijmenga, Sybren S., E-mail: S.Wijmenga@science.ru.nl [Radboud University Nijmegen, Department of Biophysical Chemistry, Institute of Molecules and Materials (Netherlands)

2013-06-15

We present a method for de novo derivation of the three-dimensional helix structure of nucleic acids using non-exchangeable proton chemical shifts as sole source of experimental restraints. The method is called chemical shift de novo structure derivation protocol employing singular value decomposition (CHEOPS) and uses iterative singular value decomposition to optimize the structure in helix parameter space. The correct performance of CHEOPS and its range of application are established via an extensive set of structure derivations using either simulated or experimental chemical shifts as input. The simulated input data are used to assess in a defined manner the effect of errors or limitations in the input data on the derived structures. We find that the RNA helix parameters can be determined with high accuracy. We finally demonstrate via three deposited RNA structures that experimental proton chemical shifts suffice to derive RNA helix structures with high precision and accuracy. CHEOPS provides, subject to further development, new directions for high-resolution NMR structure determination of nucleic acids.

Quantum chemical and spectroscopic analysis of calcium hydroxyapatite and related materials

International Nuclear Information System (INIS)

Khavryuchenko, V.D.; Khavryuchenko, O.V.; Lisnyak, V.V.

2007-01-01

Amorphous calcium hydroxyapatite was examined by vibrational spectroscopy (Raman and infra-red (IR)) and quantum chemical simulation techniques. The structures and vibrational (IR, Raman and inelastic neutron scattering) spectra of PO 4 3- ion, Ca 3 (PO 4 ) 2 , [Ca 3 (PO 4 ) 2 ] 3 , Ca 5 (PO 4 ) 3 OH, CaHPO 4 , [CaHPO 4 ] 2 , Ca 3 (PO 4 ) 2 .H 2 O, Ca 3 (PO 4 ) 2 .2H 2 O and Ca 3 (PO 4 ) 2 .3H 2 O clusters were quantum chemically simulated at ab initio and semiempirical levels of approximation. A complete coordinate analysis of the vibrational spectra was performed. The comparison of the theoretically simulated spectra with the experimental ones allows to identify correctly the phase composition of the amorphous calcium hydroxyapatite and related materials. The shape of the bands in the IR spectra of the hydroxoapatite can be used in order to characterize the structural properties of the material, e.g., the PO 4 3- ion status, the degree of hydrolysis of the material and the presence of hydrolysis products. - Graphical abstract: The structure of the quantum chemically optimized Ca 5 (PO 4 ) 3 (OH) cluster, which was used for vibrations spectra simulation

Annual Report 2000. Chemical Structure and Dynamics; FINAL

International Nuclear Information System (INIS)

Colson, Steve D; McDowell, Rod S

2001-01-01

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 and 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

ESC resistance of commercial grade polycarbonates during exposure to butter and related chemicals

DEFF Research Database (Denmark)

Kjellander, Carina Koch; Nielsen, Tenna B; Ghanbari-Siahkali, Afshin

2008-01-01

differences in ESC resistance could be related to their structural or chemical properties. MALDI-TOF mass spectrometry revealed that Makrolon Rx:1805 contains a low molar mass material characterised as poly(propylene glycol)p, which was confirmed by ATR-FTIR and H-1 NMR. Some "non-absorbing" chemicals......, such as butter, cause the PCs to be less resistant to ESC under stress. The reason for this is that these chemicals and the PCs have sufficiently similar Hansen solubility parameters to allow surface conformational changes even though absorption is non-existent or extremely small. ATR-FTIR was used to detect...

Dislocations and related defects in niobium oxide structures

Energy Technology Data Exchange (ETDEWEB)

Anderson, J S; Hutchinson, J L; Lincoln, F J [Oxford Univ. (UK). Inorganic Chemistry Lab.

1977-01-07

Lattice images of the niobium oxides, structures based on the linkage of octahedral groups in continuous networks, occasionally contain features recognizable as dislocations. Since lattice imaging enables the microstructure to be resolved in greater detail, at the level of local structural organization, it is possible to determine the configuration, and also to infer the chemical composition, of dislocated areas. By treating the niobium oxide 'block' structures as superstructures of the ReO/sub 3/ (DO/sub 9/) type, the topology of dislocations can be expressed by relations between the insertion (or deletion) of one or more half-planes of cations, or of oxygen atoms only, changes in the number of crystallographic shear plane interfaces between blocks or columns, changes in (idealized) dimensions and any requisite distortion in the third dimension. Mapping the structure around a dislocation, from the lattice image, is directly equivalent to plotting the Burgers' circuit. In this way, the precise nature of a dislocating perturbation and its implications for the local chemical composition of the crystal can be directly identified. The method is exemplified by analysis of dislocations and of related extended defects of several types, associated with twinning phenomena, semicoherent intergrowth between different ReO/sub 3/-type superstructures and arrays building up a low angle boundary. The essential features of the analysis are not restricted to structures of the niobium oxide type, but can be extended to other types of polyhedron networks.

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.

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

Visualizing tissue molecular structure of a black type of canola (Brassica) seed with a thick seed coat after heat-related processing in a chemical way.

Science.gov (United States)

Yu, Peiqiang

2013-02-20

Heat-related processing of cereal grains, legume seeds, and oil seeds could be used to improve nutrient availability in ruminants. However, different types of processing may have a different impact on intrinsic structure of tissues. To date, there is little research on structure changes after processing within intact tissues. The synchrotron-based molecular imaging technique enables us to detect inherent structure change on a molecular level. The objective of this study was to visualize tissue of black-type canola (Brassica) seed with a thick seed coat after heat-related processing in a chemical way using the synchrotron imaging technique. The results showed that the chemical images of protein amides were obtained through the imaging technique for the raw, wet, and dry heated black type of canola seed tissues. It seems that different types of processing have a different impact on the protein spectral profile in the black type of canola tissues. Wet heating had a greater impact on the protein α-helix to β-sheet ratio than dry heating. Both dry and wet heating resulted in different patterns in amide I, the second derivative, and FSD spectra. However, the exact differences in the tissue images are relatively difficult to be obtained through visual comparison. Future studies should focus on (1) comparing the response and sensitivity of canola seeds to various processing methods between the yellow-type and black-type of canola seeds; (2) developing a sensitive method to compare the image difference between tissues and between treatments; (3) developing a method to link images to nutrient digestion, and (4) revealing how structure changes affect nutrient absorption in humans and animals.

Chemical review and studies related to species from the genus Tynanthus (Bignoniaceae

Directory of Open Access Journals (Sweden)

Fernanda Colombi Cansian

2015-09-01

Full Text Available Species from the Bignoniaceae Family, including the genus Tynanthus, are very prevalent in the tropical Americas, with specimens found in a large part of the Brazilian territory. These plants are commonly used in traditional medicine for several purposes, and some studies have described their chemical structure, in addition to other reports related to some species from this genus. This review aimed to gather information from published works concerning species of the genus Tynanthus, as well as to detect flaws in research related to these plants, which may have great biological and pharmaceutical importance. Also, this review points out some common chemical characteristics of these species, providing information that may help new researchers to improve their knowledge about these plants.

Effect of chemical structure on the radioactive decay rate of 71Ge

International Nuclear Information System (INIS)

Makariunas, K.; Makariuniene, E.; Dragunas, A.

1979-01-01

The influence of the chemical structure on the electron capture radioactive decay rate of 71 Ge was observed. 71 Ge nuclei in bivalent sulphide GeS decay faster than in quadrivalent sulphide GeS 2 . The relative change Δlambda/lambda of the decay constant lambda is + (11.4 +- 1.7) X 10 -4 . A possibility to use the experimental values of Δlambda/lambda to determine the chemical changes in the electron density at germanium nuclei in germanium chemical compounds is discussed. Quantitative determination of the changes in the electron density is complicated because of insufficient reliability of the published values of exchange and overlap corrections to the electron capture probabilities. (Auth.)

Structural and chemical transformations in SnS thin films used in chemically deposited photovoltaic cells

International Nuclear Information System (INIS)

Avellaneda, David; Delgado, Guadalupe; Nair, M.T.S.; Nair, P.K.

2007-01-01

Chemically deposited SnS thin films possess p-type electrical conductivity. We report a photovoltaic structure: SnO 2 :F-CdS-SnS-(CuS)-silver print, with V oc > 300 mV and J sc up to 5 mA/cm 2 under 850 W/m 2 tungsten halogen illumination. Here, SnO 2 :F is a commercial spray-CVD (Pilkington TEC-8) coating, and the rest deposited from different chemical baths: CdS (80 nm) at 333 K, SnS (450 nm) and CuS (80 nm) at 293-303 K. The structure may be heated in nitrogen at 573 K, before applying the silver print. The photovoltaic behavior of the structure varies with heating: V oc ∼ 400 mV and J sc 2 , when heated at 423 K in air, but V oc decreases and J sc increases when heated at higher temperatures. These photovoltaic structures have been found to be stable over a period extending over one year by now. The overall cost of materials, simplicity of the deposition process, and possibility of easily varying the parameters to improve the cell characteristics inspire further work. Here we report two different baths for the deposition of SnS thin films of about 500 nm by chemical deposition. There is a considerable difference in the nature of growth, crystalline structure and chemical stability of these films under air-heating at 623-823 K or while heating SnS-CuS layers, evidenced in XRF and grazing incidence angle XRD studies. Heating of SnS-CuS films results in the formation of SnS-Cu x SnS y . 'All-chemically deposited photovoltaic structures' involving these materials are presented

From glass structure to its chemical durability; De la structure du verre a sa durabilite chimique

Energy Technology Data Exchange (ETDEWEB)

Angeli, F.

2009-07-01

The author gives an overview of his research activities. He more precisely reports studies related to glass structure based on nuclei observed by NMR and present in glasses of interest for nuclear activities. He discusses the influence of chemical composition on structure, and discusses information which can be extracted from network formers (Al, B) and modifiers (Na, Ca), and from oxygen present in the network linkages of oxide glasses. He discusses the different experimental and modelling approaches which enable structural and morphological information to be obtained at a mesoscopic scale. The last part deals with the investigation of the long term behaviour of confinement matrices (glassy matrix for medium-activity wastes, ceramic matrix)

Understanding the chemical and structural transformations of lignin macromolecule during torrefaction

International Nuclear Information System (INIS)

Wen, Jia-Long; Sun, Shao-Long; Yuan, Tong-Qi; Xu, Feng; Sun, Run-Cang

2014-01-01

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 13 C 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 13 C NMR, 2D-HSQC, and 31 P-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

Structural and morphological properties of electroceramics for chemical sensors

International Nuclear Information System (INIS)

Tor Vergata, Via della Ricerca Scientifica, Roma (Italy). Dipartimento di Scienze e Tecnologie Chimiche)" data-affiliation=" (Universita' di Roma Tor Vergata, Via della Ricerca Scientifica, Roma (Italy). Dipartimento di Scienze e Tecnologie Chimiche)" >Enrico Traversa

1996-01-01

Ceramic materials possess a unique structure consisting of grains, grain boundaries, surfaces and pores, which makes them suitable for chemical sensors. The control of the chemical composition and microstructure of electrochemicals is fundamental for controlling their properties. Ceramics with a given composition and microstructure can be produced by controlling the different steps of their processing. The chemical processing of ceramics offer many advantages in terms of control and reproducibility, with respect to the conventional ceramics processing. Results are reported about the chemical processing of perovskite-type oxides for gas sensors and about the novel humidity-sensitive electrical properties of sol-gel processed alkali-doped titania films. The structural and morphological characterization of these materials permits the understanding of the sensitive electrical properties of the ceramics (71 refs.)

Chemical structure of the Chromophoric Dissolved Organic Matter (CDOM) fluorescent matter.

Science.gov (United States)

Blough, N. V.; Del Vecchio, R.; Cartisano, C. M.; Bianca, M.

2017-12-01

The structure(s), distribution and dynamics of CDOM have been investigated over the last several decades largely through optical spectroscopy (including both absorption and fluorescence) due to the fairly inexpensive instrumentation and the easy-to-gather data (over thousands published papers from 1990-2016). Yet, the chemical structure(s) of the light absorbing and emitting species or constituents within CDOM has only recently being proposed and tested through chemical manipulation of selected functional groups (such as carbonyl and carboxylic/phenolic containing molecules) naturally occurring within the organic matter pool. Similarly, fitting models (among which the PArallel FACtor analysis, PARAFAC) have been developed to better understand the nature of a subset of DOM, the CDOM fluorescent matter (FDOM). Fluorescence spectroscopy coupled with chemical tests and PARAFAC analyses could potentially provide valuable insights on CDOM sources and chemical nature of the FDOM pool. However, despite that applications (and publications) of PARAFAC model to FDOM have grown exponentially since its first application/publication (2003), a large fraction of such publications has misinterpreted the chemical meaning of the delivered PARAFAC `components' leading to more confusion than clarification on the nature, distribution and dynamics of the FDOM pool. In this context, we employed chemical manipulation of selected functional groups to gain further insights on the chemical structure of the FDOM and we tested to what extent the PARAFAC `components' represent true fluorophores through a controlled chemical approach with the ultimate goal to provide insights on the chemical nature of such `components' (as well as on the chemical nature of the FDOM) along with the advantages and limitations of the PARAFAC application.

The chemical structure of the insoluble organic matter from carbonaceous meteorites

Science.gov (United States)

Derenne, S.; Robert, F.

2008-09-01

Carbonaceous chondrites are the most primitive objects of the solar system. They contain substantial amounts of carbon (up to 3%), mostly occurring in macromolecular insoluble organic matter (IOM). This IOM is generally considered as a record of interstellar synthesis and may contain precursors of prebiotic molecules possibly deposited on earth by meteoritic bombardments. For these reasons, chondritic IOM has been raising interest for long and it is therefore of special interest to decipher its chemical structure. It is now well established that the chemical structure of this macromolecular material is based on aromatic moieties linked by short aliphatic chains and comprising substantial amounts of heteroatoms. However, its precise chemical structure could only be recently specified. The aim of this presentation is to propose a molecular model for the chemical structure of IOM isolated from non-metamorphosed carbonaceous chondrites. This model is derived from a large set of data obtained through a combination of techniques including various spectrocopies, high resolution transmission electron microscopy (HRTEM) and chemical and thermal degradations. Cosmochemical implications of such a structure will also be discussed.

Relation Between Sustainability‑Related Communication and Competitiveness in the Chemical Industry

Directory of Open Access Journals (Sweden)

Jaroslava Hyršlová

2017-01-01

Full Text Available Interests of companies in the sustainability‑related communication have risen considerably in recent years. This paper focuses on the current state of sustainability‑related reporting in chemical industry companies registered in the Association of Chemical Industry in the Czech Republic. It deals with the form and the content of reporting, the importance of different stakeholders in this process as well as benefits of the sustainability‑related communication and its impacts on competitiveness of the company. This paper summarizes the results of a research executed in the year 2014. The results of the research showed that chemical industry companies were aware of the significance of sustainability‑related communication and they utilized various types of sustainability‑related reports for this communication. Companies prefer to report on the environmental and social aspects of their activities primarily in their annual reports, or they issue separate environmental reports. The research verified the relationship between the sustainability‑related communication and competitiveness. A suitable established high quality system of communication that provides sufficient information and meets the information requirements of the key stakeholders may significantly contribute to reputation improvement, to increased attractiveness of the company as an employer and thereby to maintain, to improve respectively, the level of a company’s competitiveness.

Identification of chemicals related to the chemical weapons convention during an interlaboratory proficiency test

NARCIS (Netherlands)

Hooijschuur, E.W.J.; Hulst, A.G.; Jong, A.L. de; Reuver, L.P. de; Krimpen, S.H. van; Baar, B.L.M. van; Wils, E.R.J.; Kientz, C.E.; Brinkman, U.A.Th

2002-01-01

In order to test the ability of laboratories to detect and identify chemicals related to the Chemical Weapons Convention (CWC), which prohibits the development, production, stockpiling and use of chemical weapons, and to designate laboratories for this task, the Technical Secretariat of the

Physical-chemical structure of VIPRO

International Nuclear Information System (INIS)

Lauri, L.

1986-01-01

PELF is a manufacturer of rigid expanded PVC in the form of panels of different density. There are only three manufacturers of this product in the world. This material is used in self-supporting structures of forms of transport, refrigerator trucks, busses, in the naval industry, for the construction of boats up to 40-50 meters in length, in the aeronautical and military industries. The research was developed in the two following phases: 1st phase: construction of a PVC panel with the density of approximately 1.000 Kg/cm. doped with extremely pure Boron using the base formula of rigid expanded PVC 2nd phase: construction of a completely new panel using for the first time in the world in the sector of plastic matters, the formula 'in alloy' where the absorbing material Boron or Lead become part of the chemical link. Only a simple and at the same time extremely resistant physical-chemical structure, a determined increase of resistance to temperatures, a considerable increase also of the number of Hydrogen atoms/c.m. could give the hoped for results. This is how VIPRO was born

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)

Chemical compositions, methods of making the chemical compositions, and structures made from the chemical compositions

Science.gov (United States)

Yang, Lei; Cheng, Zhe; Liu, Ze; Liu, Meilin

2015-01-13

Embodiments of the present disclosure include chemical compositions, structures, anodes, cathodes, electrolytes for solid oxide fuel cells, solid oxide fuel cells, fuel cells, fuel cell membranes, separation membranes, catalytic membranes, sensors, coatings for electrolytes, electrodes, membranes, and catalysts, and the like, are disclosed.

Protein structure refinement using a quantum mechanics-based chemical shielding predictor

DEFF Research Database (Denmark)

Bratholm, Lars Andersen; Jensen, Jan Halborg

2017-01-01

The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor...... of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic...

Chemical structures and characteristics of animal manures and composts during composting and assessment of maturity indices.

Directory of Open Access Journals (Sweden)

Jieying Huang

Full Text Available Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different.

Relationships between chemical structure, mechanical properties and materials processing in nanopatterned organosilicate fins

Directory of Open Access Journals (Sweden)

Gheorghe Stan

2017-04-01

Full Text Available The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM to investigate the fabrication of 20–500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10–20 nm. While the observed structure–property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential.

[Construction of chemical information database based on optical structure recognition technique].

Science.gov (United States)

Lv, C Y; Li, M N; Zhang, L R; Liu, Z M

2018-04-18

To create a protocol that could be used to construct chemical information database from scientific literature quickly and automatically. Scientific literature, patents and technical reports from different chemical disciplines were collected and stored in PDF format as fundamental datasets. Chemical structures were transformed from published documents and images to machine-readable data by using the name conversion technology and optical structure recognition tool CLiDE. In the process of molecular structure information extraction, Markush structures were enumerated into well-defined monomer molecules by means of QueryTools in molecule editor ChemDraw. Document management software EndNote X8 was applied to acquire bibliographical references involving title, author, journal and year of publication. Text mining toolkit ChemDataExtractor was adopted to retrieve information that could be used to populate structured chemical database from figures, tables, and textual paragraphs. After this step, detailed manual revision and annotation were conducted in order to ensure the accuracy and completeness of the data. In addition to the literature data, computing simulation platform Pipeline Pilot 7.5 was utilized to calculate the physical and chemical properties and predict molecular attributes. Furthermore, open database ChEMBL was linked to fetch known bioactivities, such as indications and targets. After information extraction and data expansion, five separate metadata files were generated, including molecular structure data file, molecular information, bibliographical references, predictable attributes and known bioactivities. Canonical simplified molecular input line entry specification as primary key, metadata files were associated through common key nodes including molecular number and PDF number to construct an integrated chemical information database. A reasonable construction protocol of chemical information database was created successfully. A total of 174 research

Device for collecting chemical compounds and related methods

Science.gov (United States)

Scott, Jill R.; Groenewold, Gary S.; Rae, Catherine

2013-01-01

A device for sampling chemical compounds from fixed surfaces and related methods are disclosed. The device may include a vacuum source, a chamber and a sorbent material. The device may utilize vacuum extraction to volatilize the chemical compounds from the fixed surfaces so that they may be sorbed by the sorbent material. The sorbent material may then be analyzed using conventional thermal desorption/gas chromatography/mass spectrometry (TD/GC/MS) instrumentation to determine presence of the chemical compounds. The methods may include detecting release and presence of one or more chemical compounds and determining the efficacy of decontamination. The device may be useful in collection and analysis of a variety of chemical compounds, such as residual chemical warfare agents, chemical attribution signatures and toxic industrial chemicals.

Identifying secondary structures in proteins using NMR chemical shift 3D correlation maps

Science.gov (United States)

Kumari, Amrita; Dorai, Kavita

2013-06-01

NMR chemical shifts are accurate indicators of molecular environment and have been extensively used as aids in protein structure determination. This work focuses on creating empirical 3D correlation maps of backbone chemical shift nuclei for use as identifiers of secondary structure elements in proteins. A correlated database of backbone nuclei chemical shifts was constructed from experimental structural data gathered from entries in the Protein Data Bank (PDB) as well as isotropic chemical shift values from the RefDB database. Rigorous statistical analysis of the maps led to the conclusion that specific correlations between triplets of backbone chemical shifts are best able to differentiate between different secondary structures such as α-helices, β-strands and turns. The method is compared with similar techniques that use NMR chemical shift information as aids in biomolecular structure determination and performs well in tests done on experimental data determined for different types of proteins, including large multi-domain proteins and membrane proteins.

NMR determination of chemically related metals in solution as a new method of inorganic analysis

International Nuclear Information System (INIS)

Fedorov, L.A.

1989-01-01

An NMR spectroscopic method for the determination of chemically related metals in solution is suggested. The metals are determined in complexes with specially selected polydentate ligands. Structural requirements to ligands, analytical properties and general limits of the application of the method are discussed. (orig.)

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.

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

Current Challenges in Development of a Database of Three-Dimensional Chemical Structures

Science.gov (United States)

Maeda, Miki H.

2015-01-01

We are developing a database named 3DMET, a three-dimensional structure database of natural metabolites. There are two major impediments to the creation of 3D chemical structures from a set of planar structure drawings: the limited accuracy of computer programs and insufficient human resources for manual curation. We have tested some 2D–3D converters to convert 2D structure files from external databases. These automatic conversion processes yielded an excessive number of improper conversions. To ascertain the quality of the conversions, we compared IUPAC Chemical Identifier and canonical SMILES notations before and after conversion. Structures whose notations correspond to each other were regarded as a correct conversion in our present work. We found that chiral inversion is the most serious factor during the improper conversion. In the current stage of our database construction, published books or articles have been resources for additions to our database. Chemicals are usually drawn as pictures on the paper. To save human resources, an optical structure reader was introduced. The program was quite useful but some particular errors were observed during our operation. We hope our trials for producing correct 3D structures will help other developers of chemical programs and curators of chemical databases. PMID:26075200

Evaluation of the influence of fluoroquinolone chemical structure on stability: forced degradation and in silico studies

Directory of Open Access Journals (Sweden)

André Valle de Bairros

2018-05-01

Full Text Available ABSTRACT Fluoroquinolones are a known antibacterial class commonly used around the world. These compounds present relative stability and they may show some adverse effects according their distinct chemical structures. The chemical hydrolysis of five fluoroquinolones was studied using alkaline and photolytic degradation aiming to observe the differences in molecular reactivity. DFT/B3LYP-6.31G* was used to assist with understanding the chemical structure degradation. Gemifloxacin underwent degradation in alkaline medium. Gemifloxacin and danofloxacin showed more degradation perceptual indices in comparison with ciprofloxacin, enrofloxacin and norfloxacin in photolytic conditions. Some structural features were observed which may influence degradation, such as the presence of five member rings attached to the quinolone ring and the electrostatic positive charges, showed in maps of potential electrostatic charges. These measurements may be used in the design of effective and more stable fluoroquinolones as well as the investigation of degradation products from stress stability assays.

21 CFR 1300.02 - Definitions relating to listed chemicals.

Science.gov (United States)

2010-04-01

... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Definitions relating to listed chemicals. 1300.02 Section 1300.02 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE DEFINITIONS § 1300.02 Definitions relating to listed chemicals. (a) Any term not defined in this part shall have the...

DFT simulation, quantum chemical electronic structure, spectroscopic and structure-activity investigations of 2-benzothiazole acetonitrile.

Science.gov (United States)

Arjunan, V; Thillai Govindaraja, S; Jose, Sujin P; Mohan, S

2014-07-15

The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. Copyright © 2014 Elsevier B.V. All rights reserved.

Relation between molecular electronic structure and nuclear spin-induced circular dichroism

DEFF Research Database (Denmark)

Štěpánek, Petr; Coriani, Sonia; Sundholm, Dage

2017-01-01

with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates...... with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state....... The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes...

Applications of the Cambridge Structural Database in chemical education1

Science.gov (United States)

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

2010-01-01

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

Chemical and Biological Significance of Oenothein B and Related Ellagitannin Oligomers with Macrocyclic Structure

Directory of Open Access Journals (Sweden)

Takashi Yoshida

2018-03-01

Full Text Available In 1990, Okuda et al. reported the first isolation and characterization of oenothein B, a unique ellagitannin dimer with a macrocyclic structure, from the Oenothera erythrosepala leaves. Since then, a variety of macrocyclic analogs, including trimeric–heptameric oligomers have been isolated from various medicinal plants belonging to Onagraceae, Lythraceae, and Myrtaceae. Among notable in vitro and in vivo biological activities reported for oenothein B are antioxidant, anti-inflammatory, enzyme inhibitory, antitumor, antimicrobial, and immunomodulatory activities. Oenothein B and related oligomers, and/or plant extracts containing them have thus attracted increasing interest as promising targets for the development of chemopreventive agents of life-related diseases associated with oxygen stress in human health. In order to better understand the significance of this type of ellagitannin in medicinal plants, this review summarizes (1 the structural characteristics of oenothein B and related dimers; (2 the oxidative metabolites of oenothein B up to heptameric oligomers; (3 the distribution of oenotheins and other macrocyclic analogs in the plant kingdom; and (4 the pharmacological activities hitherto documented for oenothein B, including those recently found by our laboratory.

Chemical probes of metal cluster structure--Fe, Co, Ni, and Cu

International Nuclear Information System (INIS)

Parks, E.K.; Zhu, L.; Ho, J.; Riley, S.J.

1992-01-01

Chemical reactivity is one of the few methods currently available for investigating the geometrical structure of isolated transition metal clusters. In this paper we summarize what is currently known about the structures of clusters of four transition metals, Fe, Co, Ni, and Cu, in the size range from 13 to 180 atoms. Chemical probes used to determine structural information include reactions with H 2 (D 2 ), H 2 0, NH 3 and N 2 . Measurements at both low coverage and at saturation are discussed

Chemical-induced disease relation extraction with various linguistic features.

Science.gov (United States)

Gu, Jinghang; Qian, Longhua; Zhou, Guodong

2016-01-01

Understanding the relations between chemicals and diseases is crucial in various biomedical tasks such as new drug discoveries and new therapy developments. While manually mining these relations from the biomedical literature is costly and time-consuming, such a procedure is often difficult to keep up-to-date. To address these issues, the BioCreative-V community proposed a challenging task of automatic extraction of chemical-induced disease (CID) relations in order to benefit biocuration. This article describes our work on the CID relation extraction task on the BioCreative-V tasks. We built a machine learning based system that utilized simple yet effective linguistic features to extract relations with maximum entropy models. In addition to leveraging various features, the hypernym relations between entity concepts derived from the Medical Subject Headings (MeSH)-controlled vocabulary were also employed during both training and testing stages to obtain more accurate classification models and better extraction performance, respectively. We demoted relation extraction between entities in documents to relation extraction between entity mentions. In our system, pairs of chemical and disease mentions at both intra- and inter-sentence levels were first constructed as relation instances for training and testing, then two classification models at both levels were trained from the training examples and applied to the testing examples. Finally, we merged the classification results from mention level to document level to acquire final relations between chemicals and diseases. Our system achieved promisingF-scores of 60.4% on the development dataset and 58.3% on the test dataset using gold-standard entity annotations, respectively. Database URL:https://github.com/JHnlp/BC5CIDTask. © The Author(s) 2016. Published by Oxford University Press.

Pollen source effects on growth of kernel structures and embryo chemical compounds in maize.

Science.gov (United States)

Tanaka, W; Mantese, A I; Maddonni, G A

2009-08-01

Previous studies have reported effects of pollen source on the oil concentration of maize (Zea mays) kernels through modifications to both the embryo/kernel ratio and embryo oil concentration. The present study expands upon previous analyses by addressing pollen source effects on the growth of kernel structures (i.e. pericarp, endosperm and embryo), allocation of embryo chemical constituents (i.e. oil, protein, starch and soluble sugars), and the anatomy and histology of the embryos. Maize kernels with different oil concentration were obtained from pollinations with two parental genotypes of contrasting oil concentration. The dynamics of the growth of kernel structures and allocation of embryo chemical constituents were analysed during the post-flowering period. Mature kernels were dissected to study the anatomy (embryonic axis and scutellum) and histology [cell number and cell size of the scutellums, presence of sub-cellular structures in scutellum tissue (starch granules, oil and protein bodies)] of the embryos. Plants of all crosses exhibited a similar kernel number and kernel weight. Pollen source modified neither the growth period of kernel structures, nor pericarp growth rate. By contrast, pollen source determined a trade-off between embryo and endosperm growth rates, which impacted on the embryo/kernel ratio of mature kernels. Modifications to the embryo size were mediated by scutellum cell number. Pollen source also affected (P embryo chemical compounds. Negative correlations among embryo oil concentration and those of starch (r = 0.98, P embryos with low oil concentration had an increased (P embryo/kernel ratio and allocation of embryo chemicals seems to be related to the early established sink strength (i.e. sink size and sink activity) of the embryos.

Closing in on chemical bonds by opening up relativity theory.

Science.gov (United States)

Whitney, Cynthia K

2008-03-01

This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization potentials in elements. Striking patterns in ionization potentials are revealed when the data are viewed in an element-independent way, where element-specific details are removed via an appropriate scaling law. The scale factor involved is not explained by quantum mechanics; it is revealed only when one goes back further, to the development of Einstein's special relativity theory.

Chemical ecotoxicology

International Nuclear Information System (INIS)

Paasivirta, J.

1991-01-01

This book discusses risk assessment, chemical cycles, structure-activity relations, organohalogens, oil residues, mercury, sampling and analysis of trace chemicals, and emissions from the forestry industry. Topics include: Cycles of chemicals in the environment. Rick assessment and management, strucuture and toxicity, sampling and analysis of trace chemicals in environment, interpretation of the environmental analysis results, mercury in the environment, organohalogen compounds in the environment, emissions from forestry industry, oil residues in the environment: oil spills in the marine environment

Chemical structure investigation on SFEF fractions of Dagang vacuum residue

Energy Technology Data Exchange (ETDEWEB)

Zhang, Z.; Yan, G.; Zhao, S.; Guo, S. [China Univ. of Petroleum, Beijing (China). State Key Laboratory of Heavy Oil Processing; Zhang, Z. [Beijing Aeronautical Technology Research Center, Beijing (China)

2006-07-01

One of the most important problems in petroleum chemistry is the molecular structure and composition of heavy oil fractions and its importance in applications pertaining to the recovery, refining, and upgrading of petroleum. This paper presented an investigation into the chemical structure on supercritical fluid extraction and fraction (SFEF) factions of Dagang vacuum residue. Dagang vacuum residue was cut into sixteen fractions and a tailing with SFEF instrument. Then, using a chromatography, all SFEF fractions were further separated into four group compositions, notably saturated hydrocarbons, aromatic hydrocarbons, resins and asphaltenes (SARA). Last, the chemical structure was explored through a thorough analysis of the products from the ruthenium ions-catalyzed oxidation (RICO) reaction of those aromatics, resins and asphaltenes. The paper discussed the experiment in terms of samples and chemicals; supercritical fluid extraction and fraction; SARA separation; and RICO. The results and discussions focused on alkyl side chains attached to aromatic carbon; polymethylene bridges connecting two aromatic units; benzenecarboxylic acids an aromatic units; and others. The study has brought to light useful characterization on covalent molecular structure of two typical SFEF fractions, notably the tenth and fifteen fraction. 17 refs., 6 tabs., 16 figs., 1 appendix.

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.

Advanced photonic structures for biological and chemical detection

CERN Document Server

Fan, Xudong

2009-01-01

One of a series of books on Integrated Microanalytical Systems, this text discusses the latest applications of photonic technologies in bio/chemical sensing. The book is divided into four sections, each one being based on photonic structures.

Structural, optical and electrical properties of chemically deposited ...

Indian Academy of Sciences (India)

Structural, optical and electrical properties of chemically deposited nonstoichiometric copper ... One of these compounds, CuInSe2, with its optical absorption .... is clear from SEM images that the number of grains goes on increasing with the ...

Protein Structure Validation and Refinement Using Chemical Shifts Derived from Quantum Mechanics

DEFF Research Database (Denmark)

Bratholm, Lars Andersen

to within 3 A. Furthermore, a fast quantum mechanics based chemical shift predictor was developed together with methodology for using chemical shifts in structure simulations. The developed predictor was used for renement of several protein structures and for reducing the computational cost of quantum...... mechanics / molecular mechanics (QM/MM) computations of chemical shieldings. Several improvements to the predictor is ongoing, where among other things, kernel based machine learning techniques have successfully been used to improve the quantum mechanical level of theory used in the predictions....

Strain-induced structural changes and chemical reactions. 1: Thermomechanical and kinetic models

International Nuclear Information System (INIS)

Levitas, V.I.; Nesterenko, V.F.; Meyers, M.A.

1998-01-01

Strain-induced chemical reactions were observed recently (Nesterenko et al) in experiments in the shear band in both Ti-Si and Nb-Si mixtures. Reactions can start in the solid state or after melting of at least one component. One of the aims is to find theoretically whether there are possible macroscopic mechanisms of mechanical intensification of the above and other chemical reactions due to plastic shear in the solid state. Continuum thermodynamical theory of structural changes with an athermal kinetics, which includes martensitic phase transformations, plastic strain-induced chemical reactions and polymorphic transformations, is developed at finite strains. The theory includes kinematics, criterion of structural change and extremum principle for determination of all unknown variable parameters for the case with neglected elastic strains. Thermodynamically consistent kinetic theory of thermally activated structural changes is suggested. The concept of the effective temperature is introduced which takes into account that temperature can vary significantly (on 1,000 K) during the chemical reactions under consideration. The theory will be applied in Part 2 of the paper for the description of chemical reactions in the shear band

Influence of chemical structure on carbon isotope composition of lignite

Science.gov (United States)

Erdenetsogt, Bat-Orshikh; Lee, Insung; Ko, Yoon-Joo; Mungunchimeg, Batsaikhan

2017-04-01

During the last two decades, a number of studies on carbon isotopes in terrestrial organic matter (OM) have been carried out and used to determine changes in paleoatmospheric δ13C value as well as assisting in paleoclimate analysis. Coal is abundant terrestrial OM. However, application of its δ13C value is very limited, because the understanding of changes in isotopic composition during coalification is relatively insufficient. The purpose of this study was to examine the influence of the chemical structure on the carbon isotope composition of lignite. Generally, lignite has more complex chemical structures than other higher rank coal because of the existence of various types of oxygen-containing functional groups that are eliminated at higher rank level. A total of sixteen Lower Cretaceous lignite samples from Baganuur mine (Mongolia) were studied by ultimate, stable carbon isotope and solid-state 13C CP/MAS NMR analyses. The carbon contents of the samples increase with increase in depth, whereas oxygen content decreases continuously. This is undoubtedly due to normal coalification process and also consistent with solid state NMR results. The δ13C values of the samples range from -23.54‰ to -21.34‰ and are enriched in 13C towards the lowermost samples. Based on the deconvolution of the NMR spectra, the ratios between carbons bonded to oxygen (60-90 ppm and 135-220 ppm) over carbons bonded to carbon and hydrogen (0-50 ppm and 90-135 ppm) were calculated for the samples. These correlate well with δ13C values (R2 0.88). The results indicate that the δ13C values of lignite are controlled by two mechanisms: (i) depletion in 13C as a result of loss of isotopically heavy oxygen-bounded carbons and (ii) enrichment in 13C caused by a loss of isotopically light methane from aliphatic and aromatic carbons. At the rank of lignite, coal is enriched in 13C because the amount of isotopically heavy CO2 and CO, released from coal as a result of changes in the chemical

Properties of thin optical Ge films related to their technology dependent structure

Energy Technology Data Exchange (ETDEWEB)

Schirmer, G; Duparre, A; Heerdegen, W; Kuehn, H J; Lehmann, A; Richter, W; Schroeter, B [Dept. of Physics, Friedrich-Schiller Univ., Jena (Germany, F.R.); Hacker, E; Meyer, J [Jenaoptik GmbH Carl Zeiss, Jena (Germany, F.R.)

1991-03-16

Sputtered and evaporated optical Ge films are investigated using electron microscopy and diffraction, total integrated scattering, infrared reflection absorption spectroscopy. Auger electron spectroscopy, and optical transmission measurements to observe differences of the chemical composition, atomic structure, morphology, optical constants, and degradation in relation to the parameters of technology during preparation. (orig.).

Several new phases in RE-Mg-Ge systems (RE = rare earth metal) - syntheses, structures, and chemical bonding

International Nuclear Information System (INIS)

Suen, Nian-Tzu; Bobev, Svilen

2012-01-01

Reported are the synthesis and structural characterization of Ce_5Mg_8Ge_8 (its own structure type), CeMg_2_-_xGe_2_+_x (BaAl_4-type structure), RE_4Mg_7Ge_6 (RE = Ce-Nd, Sm; La_4Mg_7Ge_6-type structure), and RE_4Mg_5Ge_6 (RE = Ce, Pr; Tm_4Zn_5Ge_6-type structure). The structures of these compounds have been established by single-crystal and powder X-ray diffraction. These compounds are closely related to each other not only in their chemical compositions but also in their structures. A common structural feature of all are MgGe_4 tetrahedra, which are connected by corner- and/or edge-sharing into complex polyanionic frameworks with the rare-earth metal atoms filling the ''empty'' space. The structures are compared to known types of structures, and we have investigated the chemical bonding in Ce_5Mg_8Ge_8 with electronic structure calculations, which were carried out by the tight-bonding linear muffin-tin orbital (TB-LMTO) method. (Copyright copyright 2012 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim)

Chemical modulation of electronic structure at the excited state

Science.gov (United States)

Li, F.; Song, C.; Gu, Y. D.; Saleem, M. S.; Pan, F.

2017-12-01

Spin-polarized electronic structures are the cornerstone of spintronics, and have thus attracted a significant amount of interest; in particular, researchers are looking into how to modulate the electronic structure to enable multifunctional spintronics applications, especially in half-metallic systems. However, the control of the spin polarization has only been predicted in limited two-dimensional systems with spin-polarized Dirac structures and is difficult to achieve experimentally. Here, we report the modulation of the electronic structure in the light-induced excited state in a typical half-metal, L a1 /2S r1 /2Mn O3 -δ . According to the spin-transport measurements, there appears a light-induced increase in magnetoresistance due to the enhanced spin scattering, which is closely associated with the excited spin polarization. Strikingly, the light-induced variation can be enhanced via alcohol processing and reduced by oxygen annealing. X-ray photoelectron spectroscopy measurements show that in the chemical process, a redox reaction occurs with a change in the valence of Mn. Furthermore, first-principles calculations reveal that the change in the valence of Mn alters the electronic structure and consequently modulates the spin polarization in the excited state. Our findings thus report a chemically tunable electronic structure, demonstrating interesting physics and the potential for multifunctional applications and ultrafast spintronics.

How to tackle chemical communication? Relative proportions versus semiquantitative determination of compounds in lizard chemical secretions.

Science.gov (United States)

García-Roa, Roberto; Sáiz, Jorge; Gómara, Belén; López, Pilar; Martín, José

2018-02-01

Knowledge about chemical communication in some vertebrates is still relatively limited. Squamates are a glaring example of this, even when recent evidences indicate that scents are involved in social and sexual interactions. In lizards, where our understanding of chemical communication has considerably progressed in the last few years, many questions about chemical interactions remain unanswered. A potential reason for this is the inherent complexity and technical limitations that some methodologies embody when analyzing the compounds used to convey information. We provide here a straightforward procedure to analyze lizard chemical secretions based on gas chromatography coupled to mass spectrometry that uses an internal standard for the semiquantification of compounds. We compare the results of this method with those obtained by the traditional procedure of calculating relative proportions of compounds. For such purpose, we designed two experiments to investigate if these procedures allowed revealing changes in chemical secretions 1) when lizards received previously a vitamin dietary supplementation or 2) when the chemical secretions were exposed to high temperatures. Our results show that the procedure based on relative proportions is useful to describe the overall chemical profile, or changes in it, at population or species levels. On the other hand, the use of the procedure based on semiquantitative determination can be applied when the target of study is the variation in one or more particular compounds of the sample, as it has proved more accurate detecting quantitative variations in the secretions. This method would reveal new aspects produced by, for example, the effects of different physiological and climatic factors that the traditional method does not show.

Relative Configuration of Natural Products Using NMR Chemical Shifts

Science.gov (United States)

By comparing calculated with experimental NMR chemical shifts, we were able to determine the relative configurations of three monoterpene diastereomers produced by the walkingstick Anisomorpha buprestoides. The combined RMSDs of both 1H and 13C quantum chemically calculated shifts were able to predi...

Weighted voting-based consensus clustering for chemical structure databases

Science.gov (United States)

Saeed, Faisal; Ahmed, Ali; Shamsir, Mohd Shahir; Salim, Naomie

2014-06-01

The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures.

Chemical graph-theoretic cluster expansions

International Nuclear Information System (INIS)

Klein, D.J.

1986-01-01

A general computationally amenable chemico-graph-theoretic cluster expansion method is suggested as a paradigm for incorporation of chemical structure concepts in a systematic manner. The cluster expansion approach is presented in a formalism general enough to cover a variety of empirical, semiempirical, and even ab initio applications. Formally such approaches for the utilization of chemical structure-related concepts may be viewed as discrete analogues of Taylor series expansions. The efficacy of the chemical structure concepts then is simply bound up in the rate of convergence of the cluster expansions. In many empirical applications, e.g., boiling points, chromatographic separation coefficients, and biological activities, this rate of convergence has been observed to be quite rapid. More note will be made here of quantum chemical applications. Relations to questions concerning size extensivity of energies and size consistency of wave functions are addressed

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

between SOM chemical structure and pore characteristics differed in the aggregates of the two treatments. For example, in the agricultural treatment, the aggregate sections with prevalence of small pores had lower relative lignin abundance, while higher lignin abundances occurred in aggregate sections with more large pores. This relationship could be reflecting the low accessibility of the sections dominated by small pores to plant roots. It is interesting to note that no relationship between pores and lignin were observed in the aggregate from the native succession treatment. In the native succession aggregate we found that a larger presence of protein and N-bearing compounds was associated with sections with greater presence of 35-90 µm pores. This could be a result of fungal activities, as pores of this size constitute a primary fungal habitat and fungi are known for secreting proteins. Fewer fungi in the soil under agricultural management are likely the reason that no such relationship was observed in the aggregate from the agricultural treatment. Our preliminary results indicate that substantial spatial variability patterns in SOM chemical structure can exist even within a single macro-aggregate and that pores are likely a main driver of intra-aggregate SOM chemistry.

Quantum chemical calculations in the structural analysis of phloretin

Science.gov (United States)

Gómez-Zavaglia, Andrea

2009-07-01

In this work, a conformational search on the molecule of phloretin [2',4',6'-Trihydroxy-3-(4-hydroxyphenyl)-propiophenone] has been performed. The molecule of phloretin has eight dihedral angles, four of them taking part in the carbon backbone and the other four, related with the orientation of the hydroxyl groups. A systematic search involving a random variation of the dihedral angles has been used to generate input structures for the quantum chemical calculations. Calculations at the DFT(B3LYP)/6-311++G(d,p) level of theory permitted the identification of 58 local minima belonging to the C 1 symmetry point group. The molecular structures of the conformers have been analyzed using hierarchical cluster analysis. This method allowed us to group conformers according to their similarities, and thus, to correlate the conformers' stability with structural parameters. The dendrogram obtained from the hierarchical cluster analysis depicted two main clusters. Cluster I included all the conformers with relative energies lower than 25 kJ mol -1 and cluster II, the remaining conformers. The possibility of forming intramolecular hydrogen bonds resulted the main factor contributing for the stability. Accordingly, all conformers depicting intramolecular H-bonds belong to cluster I. These conformations are clearly favored when the carbon backbone is as planar as possible. The values of the νC dbnd O and νOH vibrational modes were compared among all the conformers of phloretin. The redshifts associated with intramolecular H-bonds were correlated with the H-bonds distances and energies.

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

International Nuclear Information System (INIS)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei

2013-01-01

We introduce a Python-based program that utilizes the large database of 13 C and 15 N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D 13 C– 13 C, 15 N– 13 C, or 3D 15 N– 13 C– 13 C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D 13 C– 13 C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the Cα and Cβ chemical shifts, the highest-ranked PLUQ assignments were 40–60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO–Cα–Cβ or N–Cα–Cβ), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

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.

Human Metabolism and Interactions of Deployment-Related Chemicals

National Research Council Canada - National Science Library

Hodgson, Ernest; Brimfield, Alan A; Goldstein, Joyce E; Rose, Randy L; Wallace, Andrew D

2008-01-01

.... The metabolism of chlorpyrifos, DEET, permethrin, pyridostigmine bromide, sulfur mustard, naphthalene and nonane as well as a number of their metabolites and related chemicals was investigated...

Human Metabolism and Interactions of Deployment-Related Chemicals

National Research Council Canada - National Science Library

Hodgson, Ernest

2003-01-01

This study examines the human-metabolism and metabolic interactions of a subset of deployment-related chemicals, including chlorpyrifos, DEET, permethrin, pyridostigmine bromide, and sulfur mustard metabolites...

Prediction of proton chemical shifts in RNA - Their use in structure refinement and validation

International Nuclear Information System (INIS)

Cromsigt, Jenny A.M.T.C.; Hilbers, Cees W.; Wijmenga, Sybren S.

2001-01-01

An analysis is presented of experimental versus calculated chemical shifts of the non-exchangeable protons for 28 RNA structures deposited in the Protein Data Bank, covering a wide range of structural building blocks. We have used existing models for ring-current and magnetic-anisotropy contributions to calculate the proton chemical shifts from the structures. Two different parameter sets were tried: (i) parameters derived by Ribas-Prado and Giessner-Prettre (GP set) [(1981) J. Mol. Struct.,76, 81-92.]; (ii) parameters derived by Case [(1995) J. Biomol. NMR, 6, 341-346]. Both sets lead to similar results. The detailed analysis was carried using the GP set. The root-mean-square-deviation between the predicted and observed chemical shifts of the complete database is 0.16 ppm with a Pearson correlation coefficient of 0.79. For protons in the usually well-defined A-helix environment these numbers are, 0.08 ppm and 0.96, respectively. As a result of this good correspondence, a reliable analysis could be made of the structural dependencies of the 1 H chemical shifts revealing their physical origin. For example, a down-field shift of either H2' or H3' or both indicates a high-syn/syn χ-angle. In an A-helix it is essentially the 5'-neighbor that affects the chemical shifts of H5, H6 and H8 protons. The H5, H6 and H8 resonances can therefore be assigned in an A-helix on the basis of their observed chemical shifts. In general, the chemical shifts were found to be quite sensitive to structural changes. We therefore propose that a comparison between calculated and observed 1 H chemical shifts is a good tool for validation and refinement of structures derived from NOEs and J-couplings

Chemical structures and theoretical models of lean premixed ...

African Journals Online (AJOL)

To better understand the chemistry involved in the lean-fuel combustion, the chemical structure of lean premixed propene-oxygen-nitrogen flames stabilized on a flat-flame burner at atmospheric pressure was determined experimentally. The species mole fraction profiles were also computed by the Premix code and three ...

Practical use of chemical shift databases for protein solid-state NMR: 2D chemical shift maps and amino-acid assignment with secondary-structure information

Energy Technology Data Exchange (ETDEWEB)

Fritzsching, K. J.; Yang, Y.; Schmidt-Rohr, K.; Hong Mei, E-mail: mhong@iastate.edu [Iowa State University, Department of Chemistry (United States)

2013-06-15

We introduce a Python-based program that utilizes the large database of {sup 13}C and {sup 15}N chemical shifts in the Biological Magnetic Resonance Bank to rapidly predict the amino acid type and secondary structure from correlated chemical shifts. The program, called PACSYlite Unified Query (PLUQ), is designed to help assign peaks obtained from 2D {sup 13}C-{sup 13}C, {sup 15}N-{sup 13}C, or 3D {sup 15}N-{sup 13}C-{sup 13}C magic-angle-spinning correlation spectra. We show secondary-structure specific 2D {sup 13}C-{sup 13}C correlation maps of all twenty amino acids, constructed from a chemical shift database of 262,209 residues. The maps reveal interesting conformation-dependent chemical shift distributions and facilitate searching of correlation peaks during amino-acid type assignment. Based on these correlations, PLUQ outputs the most likely amino acid types and the associated secondary structures from inputs of experimental chemical shifts. We test the assignment accuracy using four high-quality protein structures. Based on only the C{alpha} and C{beta} chemical shifts, the highest-ranked PLUQ assignments were 40-60 % correct in both the amino-acid type and the secondary structure. For three input chemical shifts (CO-C{alpha}-C{beta} or N-C{alpha}-C{beta}), the first-ranked assignments were correct for 60 % of the residues, while within the top three predictions, the correct assignments were found for 80 % of the residues. PLUQ and the chemical shift maps are expected to be useful at the first stage of sequential assignment, for combination with automated sequential assignment programs, and for highly disordered proteins for which secondary structure analysis is the main goal of structure determination.

Indirect radiation effects related to the environmental structure of targets

International Nuclear Information System (INIS)

Frankenberg, D.

1976-01-01

It is supposed, that in biological systems there are direct as well as indirect radiation effects. Their contributions to lethal effects depend mainly on two different kinds of structures within irradiated systems: the microscopic energy deposition patterns of radiation and the environmental structures of targets. The approach to determine these contributions of the lethal action of ionizing radiation in yeast cells was, to use chemical compounds, which specifically change the radical spectrum of water radiolysis. The efficiency of such chemical compounds in scavenging specifically water radicals was tested in aqueous solutions of thymine molecules, in which indirect radiation effects occur exclusively. The main result is, that the OH'-radical is by far the most effective radical to destroy thymine molecules. The relative contributions of direct and indirect radiation effects to lethal actions of ionizing radiation was investigated in yeast cells. The radical spectrum of water radiolysis was changed by bubbling the cell suspensions with different gases. The main result is, that there are no lethal radiation effects du to the action of water radicals

Symmetry Relations in Chemical Kinetics Arising from Microscopic Reversibility

Science.gov (United States)

Adib, Artur B.

2006-01-01

It is shown that the kinetics of time-reversible chemical reactions having the same equilibrium constant but different initial conditions are closely related to one another by a directly measurable symmetry relation analogous to chemical detailed balance. In contrast to detailed balance, however, this relation does not require knowledge of the elementary steps that underlie the reaction, and remains valid in regimes where the concept of rate constants is ill defined, such as at very short times and in the presence of low activation barriers. Numerical simulations of a model of isomerization in solution are provided to illustrate the symmetry under such conditions, and potential applications in protein folding or unfolding are pointed out.

Fault detection in nonlinear chemical processes based on kernel entropy component analysis and angular structure

Energy Technology Data Exchange (ETDEWEB)

Jiang, Qingchao; Yan, Xuefeng; Lv, Zhaomin; Guo, Meijin [East China University of Science and Technology, Shanghai (China)

2013-06-15

Considering that kernel entropy component analysis (KECA) is a promising new method of nonlinear data transformation and dimensionality reduction, a KECA based method is proposed for nonlinear chemical process monitoring. In this method, an angle-based statistic is designed because KECA reveals structure related to the Renyi entropy of input space data set, and the transformed data sets are produced with a distinct angle-based structure. Based on the angle difference between normal status and current sample data, the current status can be monitored effectively. And, the confidence limit of the angle-based statistics is determined by kernel density estimation based on sample data of the normal status. The effectiveness of the proposed method is demonstrated by case studies on both a numerical process and a simulated continuous stirred tank reactor (CSTR) process. The KECA based method can be an effective method for nonlinear chemical process monitoring.

Fault detection in nonlinear chemical processes based on kernel entropy component analysis and angular structure

International Nuclear Information System (INIS)

Jiang, Qingchao; Yan, Xuefeng; Lv, Zhaomin; Guo, Meijin

2013-01-01

Considering that kernel entropy component analysis (KECA) is a promising new method of nonlinear data transformation and dimensionality reduction, a KECA based method is proposed for nonlinear chemical process monitoring. In this method, an angle-based statistic is designed because KECA reveals structure related to the Renyi entropy of input space data set, and the transformed data sets are produced with a distinct angle-based structure. Based on the angle difference between normal status and current sample data, the current status can be monitored effectively. And, the confidence limit of the angle-based statistics is determined by kernel density estimation based on sample data of the normal status. The effectiveness of the proposed method is demonstrated by case studies on both a numerical process and a simulated continuous stirred tank reactor (CSTR) process. The KECA based method can be an effective method for nonlinear chemical process monitoring

Chemical substructure analysis in toxicology

Energy Technology Data Exchange (ETDEWEB)

Beauchamp, R.O. Jr. [Center for Information on Toxicology and Environment, Raleigh, NC (United States)

1990-12-31

A preliminary examination of chemical-substructure analysis (CSA) demonstrates the effective use of the Chemical Abstracts compound connectivity file in conjunction with the bibliographic file for relating chemical structures to biological activity. The importance of considering the role of metabolic intermediates under a variety of conditions is illustrated, suggesting structures that should be examined that may exhibit potential activity. This CSA technique, which utilizes existing large files accessible with online personal computers, is recommended for use as another tool in examining chemicals in drugs. 2 refs., 4 figs.

Structure of adsorbed monolayers. The surface chemical bond

International Nuclear Information System (INIS)

Somorjai, G.A.; Bent, B.E.

1984-06-01

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

Radiological and related Chemical Health Impact Assessments of ...

African Journals Online (AJOL)

Ogunjo Samuel

concentrations obtained and the relation from United State Environmental Protection Agency (USEPA), the chemical ... radioactive elements uranium-238 and thorium-232 decay .... Using Equation 2, the elemental concentrations in pipe.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

OpenAIRE

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster reson...

Electronic structure and chemical bond in technetium dimer

International Nuclear Information System (INIS)

Klyagina, A.P.; Fursova, V.D.; Levin, A.A.; Gutsev, G.L.

1987-01-01

DV-X α method is used to study electron structure and peculiarities of chemical bond in Tc 2 and Tc 2 2+ dimers. Electron state characteristics are calculated in the basis of numerical Hartree-Fock functions for d 6 s 1 - and d 5 s 2 -configurations of Tc atom and for Tc 2 2+ ion d 5 s 1 -configuration. Disposition order for valence MO in Tc and Tc 2 2+ calculated for the given configurations is presented. It is shown that quinary bond with π u 4 dσ g 2 σ g 4 sσ g 2 δ u 2 configuration corresponds to the ground state of Tc 2 molecule. In Tc 2 some weakening of binding for π- and δ-orbitals and strengthening of total σ-binding in comparison with Mo 2 takes place. In Tc + and Tc 2+ MO composition is slightly changed, but a shift of 2σ-MO relatively MO consisting of d-AO is occured

Ab initio/GIAO-CCSD(T) study of structures, energies, and 13C NMR chemical shifts of C4H7(+) and C5H9(+) ions: relative stability and dynamic aspects of the cyclopropylcarbinyl vs bicyclobutonium ions.

Science.gov (United States)

Olah, George A; Surya Prakash, G K; Rasul, Golam

2008-07-16

The structures and energies of the carbocations C 4H 7 (+) and C 5H 9 (+) were calculated using the ab initio method. The (13)C NMR chemical shifts of the carbocations were calculated using the GIAO-CCSD(T) method. The pisigma-delocalized bisected cyclopropylcarbinyl cation, 1 and nonclassical bicyclobutonium ion, 2 were found to be the minima for C 4H 7 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level the structure 2 is 0.4 kcal/mol more stable than the structure 1. The (13)C NMR chemical shifts of 1 and 2 were calculated by the GIAO-CCSD(T) method. Based on relative energies and (13)C NMR chemical shift calculations, an equilibrium involving the 1 and 2 in superacid solutions is most likely responsible for the experimentally observed (13)C NMR chemical shifts, with the latter as the predominant equilibrating species. The alpha-methylcyclopropylcarbinyl cation, 4, and nonclassical bicyclobutonium ion, 5, were found to be the minima for C 5H 9 (+) at the MP2/cc-pVTZ level. At the MP4(SDTQ)/cc-pVTZ//MP2/cc-pVTZ + ZPE level ion 5 is 5.9 kcal/mol more stable than the structure 4. The calculated (13)C NMR chemical shifts of 5 agree rather well with the experimental values of C 5H 9 (+).

TSCA Chemical Data Reporting Fact Sheet: Reporting Manufactured Chemical Substances from Metal Mining and Related Activities

Science.gov (United States)

This fact sheet provides guidance on the Chemical Data Reporting (CDR) rule requirements related to the reporting of mined metals, intermediates, and byproducts manufactured during metal mining and related activities.

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

International Nuclear Information System (INIS)

Li, Dawei; Brüschweiler, Rafael

2015-01-01

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

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

International Nuclear Information System (INIS)

Wilkerson, Marianne Perry

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 2 (An: U, Pu) to form non-stoichiometric species described as AnO 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.

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.

Book of abstracts Chemical Engineering: IV All-Russian Conference on chemical engineering, All-Russian Youth Conference on chemical engineering, All-Russian school on chemical engineering for young scientists and specialists. Chemical engineering of nanomaterials. Energy- and resource-saving chemical-engineering processes and problems of their intensification. Processes and apparatuses of chemical engineering, chemical cybernetics. Ecological problems of chemical engineering and related fields

International Nuclear Information System (INIS)

Zakhodyaeva, Yu.A.; Belova, V.V.

2012-01-01

In the given volume of abstracts of the IV All-Russian Conference on chemical engineering, All-Russian Youth Conference on chemical engineering, All-Russian school on chemical engineering for young scientists and specialists (Moscow, March 18-23, 2012) there are the abstracts of the reports concerning chemical engineering of nanomaterials, energy- and resource-saving chemical-engineering processes, processes and apparatuses of chemical engineering, chemical cybernetics, ecological problems of chemical engineering and related fields. The abstracts deal with state-of-the-art and future development of theoretical and experimental investigations as well as with experience in practical realization of development works in the field of chemical engineering and relative areas [ru

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape.

Science.gov (United States)

Ferreon, Allan Chris M; Moosa, Mahdi Muhammad; Gambin, Yann; Deniz, Ashok A

2012-10-30

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson's disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 21 [urea][TMAO] ratio has a net neutral effect on the protein's dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments.

Counteracting chemical chaperone effects on the single-molecule α-synuclein structural landscape

Science.gov (United States)

Ferreon, Allan Chris M.; Moosa, Mahdi Muhammad; Deniz, Ashok A.

2012-01-01

Protein structure and function depend on a close interplay between intrinsic folding energy landscapes and the chemistry of the protein environment. Osmolytes are small-molecule compounds that can act as chemical chaperones by altering the environment in a cellular context. Despite their importance, detailed studies on the role of these chemical chaperones in modulating structure and dimensions of intrinsically disordered proteins have been limited. Here, we used single-molecule Förster resonance energy transfer to test the counteraction hypothesis of counterbalancing effects between the protecting osmolyte trimethylamine-N-oxide (TMAO) and denaturing osmolyte urea for the case of α-synuclein, a Parkinson’s disease-linked protein whose monomer exhibits significant disorder. The single-molecule experiments, which avoid complications from protein aggregation, do not exhibit clear solvent-induced cooperative protein transitions for these osmolytes, unlike results from previous studies on globular proteins. Our data demonstrate the ability of TMAO and urea to shift α-synuclein structures towards either more compact or expanded average dimensions. Strikingly, the experiments directly reveal that a 2∶1 [urea]∶[TMAO] ratio has a net neutral effect on the protein’s dimensions, a result that holds regardless of the absolute osmolyte concentrations. Our findings shed light on a surprisingly simple aspect of the interplay between urea and TMAO on α-synuclein in the context of intrinsically disordered proteins, with potential implications for the biological roles of such chemical chaperones. The results also highlight the strengths of single-molecule experiments in directly probing the chemical physics of protein structure and disorder in more chemically complex environments. PMID:22826265

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

Energy Technology Data Exchange (ETDEWEB)

Manojkumar, P.A., E-mail: manoj@igcar.gov.in [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Chirayath, V.A.; Balamurugan, A.K.; Krishna, Nanda Gopala; Ilango, S.; Kamruddin, M.; Amarendra, G.; Tyagi, A.K. [Indira Gandhi Centre for Atomic Research, Kalpakkam 603102 (India); Raj, Baldev [National Institute of Advanced Studies, Bangalore 560 012 (India)

2016-09-15

Highlights: • Low energy nitrogen ion implantation in titanium was studied. • Chemical and defect states were analyzed using SIMS, XPS and PAS. • SIMS and depth resolved XPS data showed good agreement. • Depth resolved defect and chemical states information were revealed. • Formation of 3 layers of defect states proposed to fit PAS results. - Abstract: 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.

Guidelines for terms related to chemical speciations and fractionation of elements : definitions, structural aspects, and methodological approaches (IUPAC Recommendations 2000)

NARCIS (Netherlands)

Templeton, D.M.; Ariese, F.; Cornelis, R.; Danielsson, L.G.; Muntau, H.; Leeuwen, van H.P.; Lobínski, R.

2000-01-01

This paper presents definitions of concepts related to speciation of elements, more particularly speciation analysis and chemical species. Fractionation is distinguished from speciation analysis, and a general outline of fractionation procedures is given. We propose a categorization of species

Structure-Antioxidative and Anti-Inflammatory Activity Relationships of Purpurin and Related Anthraquinones in Chemical and Cell Assays

Directory of Open Access Journals (Sweden)

Woo Nam

2017-02-01

Full Text Available Anthraquinone (9,10-anthraquinone and several hydroxy derivatives, including purpurin (1,2,4-trihydroxyanthraquinone, anthrarufin (1,5-dihydroxyanthraquinone, and chrysazin (1,8-dihydroxyanthraquinone, were evaluated for antioxidative and anti-inflammatory activities in chemical assays and mammalian cells (murine macrophage RAW 264.7 cells. Several tests were used to assess their activities: 1,1-diphenyl-2-picrylhydrazyl (DPPH free radical; ABTS radical cation; hydrogen peroxide scavenging; reduction of potassium ferricyanide; chelation of ferrous ions; inhibition of lipid peroxidation; inhibition of nitric oxide generation; scavenging of the intracellular hydroxyl radical; expression of NLRP3 polypeptide for inflammasome assembly; and quantitation of proinflammatory cytokine interleukin 1β (IL-1β for inflammasome activation. The results show that purpurin, from the root of the madder plant (Rubia tinctorum L., exhibited the highest antioxidative activity in both chemical and cultured cell antioxidant assays. The antioxidative activities of the other three anthraquinones were lower than that of purpurin. In addition, purpurin could down-regulate NLRP3 inflammasome assembly and activation, suggesting that it might protect foods against oxidative damage and prevent in vivo oxidative stress and inflammation. Structure-activity relationships and the significance of the results for food quality and human health are discussed.

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.

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.

Structure and chemical composition of layers adsorbed at interfaces with champagne.

Science.gov (United States)

Aguié-Béghin, V; Adriaensen, Y; Péron, N; Valade, M; Rouxhet, P; Douillard, R

2009-11-11

The structure and the chemical composition of the layer adsorbed at interfaces involving champagne have been investigated using native champagne, as well as ultrafiltrate (UFch) and ultraconcentrate (UCch) obtained by ultrafiltration with a 10(4) nominal molar mass cutoff. The layer adsorbed at the air/liquid interface was examined by surface tension and ellipsometry kinetic measurements. Brewster angle microscopy demonstrated that the layer formed on polystyrene by adsorption or drop evaporation was heterogeneous, with a domain structure presenting similarities with the layer adsorbed at the air/liquid interface. The surface chemical composition of polystyrene with the adlayer was determined by X-ray photoelectron spectroscopy (XPS). The contribution of champagne constituents varied according to the liquid (native, UFch, and UCch) and to the procedure of adlayer formation (evaporation, adsorption, and adsorption + rinsing). However, their chemical composition was not significantly influenced either by ultrafiltration or by the procedure of deposition on polystyrene. Modeling this composition in terms of classes of model compounds gave approximately 35% (w/w) of proteins and 65% (w/w) of polysaccharides. In the adlayer, the carboxyl groups or esters represent about 18% of carbon due to nonpolypeptidic compounds, indicating the presence of either uronic acids in the complex structure of pectic polysaccharides or of polyphenolic esters. This structural and chemical information and its relationship with the experimental procedures indicate that proteins alone cannot be used as a realistic model for the macromolecules forming the adsorption layer of champagne. Polysaccharides, the other major macromolecular components of champagne wine, are assembled with proteins at the interfaces, in agreement with the heterogeneous character of the adsorbed layer at interfaces.

Evaluation of quantum-chemical methods of radiolysis stability for macromolecular structures

International Nuclear Information System (INIS)

Postolache, Cristian; Matei, Lidia

2005-01-01

The behavior of macromolecular structures in ionising fields was analyzed by quantum-chemical methods. In this study the primary radiolytic effect was analyzed using a two-step radiolytic mechanism: a) ionisation of molecule and spatial redistribution of atoms in order to reach a minimum value of energy, characteristic to the quantum state; b) neutralisation of the molecule by electron capture and its rapid dissociation into free radicals. Chemical bonds suspected to break are located in the distribution region of LUMO orbital and have minimal homolytic dissociation energies. Representative polymer structures (polyethylene, polypropylene, polystyrene, poly α and β polystyrene, polyisobutylene, polytetrafluoroethylene, poly methylsiloxanes) were analyzed. (authors)

Automated detection of structural alerts (chemical fragments in (ecotoxicology

Directory of Open Access Journals (Sweden)

Ronan Bureau

2013-02-01

Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

AUTOMATED DETECTION OF STRUCTURAL ALERTS (CHEMICAL FRAGMENTS IN (ECOTOXICOLOGY

Directory of Open Access Journals (Sweden)

Alban Lepailleur

2013-02-01

Full Text Available This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (ecotoxicological endpoints. These structural alerts correspond to one of the most interesting approach of in silico toxicology due to their direct link with specific toxicological mechanisms. A number of expert systems are already available but, since the first work in this field which considered a binomial distribution of chemical fragments between two datasets, new data miners were developed and applied with success in chemoinformatics. The frequency of a chemical fragment in a dataset is often at the core of the process for the definition of its toxicological relevance. However, recent progresses in data mining provide new insights into the automated discovery of new rules. Particularly, this review highlights the notion of Emerging Patterns that can capture contrasts between classes of data.

Model abstraction addressing long-term simulations of chemical degradation of large-scale concrete structures

International Nuclear Information System (INIS)

Jacques, D.; Perko, J.; Seetharam, S.; Mallants, D.

2012-01-01

This paper presents a methodology to assess the spatial-temporal evolution of chemical degradation fronts in real-size concrete structures typical of a near-surface radioactive waste disposal facility. The methodology consists of the abstraction of a so-called full (complicated) model accounting for the multicomponent - multi-scale nature of concrete to an abstracted (simplified) model which simulates chemical concrete degradation based on a single component in the aqueous and solid phase. The abstracted model is verified against chemical degradation fronts simulated with the full model under both diffusive and advective transport conditions. Implementation in the multi-physics simulation tool COMSOL allows simulation of the spatial-temporal evolution of chemical degradation fronts in large-scale concrete structures. (authors)

Chemical compatibility of structural materials in alkali metals

International Nuclear Information System (INIS)

Natesan, K.; Rink, D.L.; Haglund, R.

1995-01-01

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

Vibronic coupling in ionized organic molecules: structural distortions and chemical reactions

International Nuclear Information System (INIS)

Williams, Ffrancon

2003-01-01

Ionized organic molecules (radical cations) in radiation chemistry are liable to undergo vibronic coupling whenever there is a relatively small energy gap (∼0.5-1.5 eV) between their ground and excited states. As a result of this mixing, the force constant for the symmetry-allowed vibrational mode that couples these states is lowered in the ground state of the radical cation so that deformation can take place more easily along this specific mode. This pseudo-Jahn-Teller effect can then result in a permanent structural distortion of the radical cation relative to the symmetry of the parent neutral molecule. It can also bring about an energetically favored pathway for a facile chemical rearrangement along a reaction coordinate defined by the coupling mode. Examples taken from matrix-isolation studies are used to illustrate these dramatic consequences of vibronic coupling in radical cations. Thus, the bicyclo[2.2.2]oct-2-ene and tetramethylurea radical cations are found to have twisted structures departing from the C 2v symmetry of their parent molecules, while the oxirane and bicyclo[1.1.1]pentane radical cations undergo ring-opening rearrangements along reaction coordinates that correspond to the deformational modes predicted by the pseudo-Jahn-Teller effect

Predicting oil and gas compositional yields via chemical structure-chemical yield modeling (CS-CYM): Part 1 - Concepts and implementation

Energy Technology Data Exchange (ETDEWEB)

Freund, H.; Walters, C.C.; Kelemen, S.R.; Siskin, M.; Gorbaty, M.L.; Curry, D.J.; Bence, A.E. [ExxonMobil Research & Engineering Co., Annandale, NJ (United States)

2007-07-01

We have developed a method to calculate the amounts and composition of products resulting from the thermal decomposition of a solid complex carbonaceous material. This procedure provides a means of using laboratory measurements of complex carbonaceous solids to construct a representative model of its chemical structure (CS) that is then coupled with elementary reaction pathways to predict the chemical yield (CY) upon thermal decomposition. Data from elemental analysis, H, N, O, S, solid state {sup 13}C NMR, X-ray photoelectron spectroscopy (XPS), sulfur X-ray absorption structure spectroscopy (XANES), and pyrolysis-gas chromatography (GC) are used to constrain the construction of core molecular structures representative of the complex carbonaceous material. These core structures are expanded stochastically to describe large macromolecules ({gt} 10{sup 6} cores with similar to 10{sup 6} atoms) with bulk properties that match the experimental results. Gas, liquid and solid product yields, resulting from thermal decomposition, are calculated by identifying reactive functional groups within the CS stochastic ensemble and imposing a reaction network constrained by fundamental thermodynamics and kinetics. An expulsion model is added to the decomposition model to calculate the chemical products in open and closed systems. Product yields may then be predicted under a wide range of time-temperature conditions used in rapid laboratory pyrolysis experiments, refinery processes, or geologic maturation.

Structural Consequences of Duplicitous Chemical Relation of Cobalt and Fullerene in Mixture

Czech Academy of Sciences Publication Activity Database

Lavrentiev, Vasyl; Vacík, Jiří; Naramoto, H.

2012-01-01

Roč. 20, 4-7 (2012), s. 328-335 ISSN 1536-383X R&D Projects: GA AV ČR(CZ) KAN400480701; GA ČR GA106/09/1264; GA ČR GAP107/11/1856 Institutional support: RVO:61389005 Keywords : fullerene * cobalt * chemical bonding * nanostructure * self- organization Subject RIV: BG - Nuclear, Atomic and Molecular Physics, Colliders Impact factor: 0.764, year: 2012

The direct measurement of the heteronuclear chemical shifts relative to tetramethylsilane

International Nuclear Information System (INIS)

Moritz, A.G.

1988-12-01

The measurement of heteronuclear chemical shifts using absolute frequencies of the heteronucleus and the 1 H resonance of tetramethylsilane has been examined. This method avoids the problems associated with external standards and gives results which can be obtained quickly and with high precision. The method has a number of advantages in the accurate measurement of chemical shifts, as for example 31 P in chemical warfare agents and related chemicals and allows multinuclear data to be obtained without dynamic range or potential interference problems. 15 refs., 4 tabs

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...... it is covalently immobilized in MCF. Relatively high loadings in the range of 50–60 mg g1 are achieved. Electron spin resonance (ESR) spectroscopy is used to probe the active site structures of the enzyme. The similar ESR spectra observed for GAOX in the free and immobilized states support that the electronic...

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. Copyright © 2013 Elsevier Inc. All rights reserved.

Chemical equilibrium relations used in the fireball model of relativistic heavy ion reactions

International Nuclear Information System (INIS)

Gupta, S.D.

1978-01-01

The fireball model of relativistic heavy-ion collision uses chemical equilibrium relations to predict cross sections for particle and composite productions. These relations are examined in a canonical ensemble model where chemical equilibrium is not explicitly invoked

Student Teachers' Knowledge about Chemical Representations

Science.gov (United States)

Taskin, Vahide; Bernholt, Sascha; Parchmann, Ilka

2017-01-01

Chemical representations serve as a communication tool not only in exchanges between scientists but also in chemistry lessons. The goals of the present study were to measure the extent of student teachers' knowledge about chemical representations, focusing on chemical formulae and structures in particular, and to explore which factors related to…

Validation of archived chemical shifts through atomic coordinates

Science.gov (United States)

Rieping, Wolfgang; Vranken, Wim F

2010-01-01

The public archives containing protein information in the form of NMR chemical shift data at the BioMagResBank (BMRB) and of 3D structure coordinates at the Protein Data Bank are continuously expanding. The quality of the data contained in these archives, however, varies. The main issue for chemical shift values is that they are determined relative to a reference frequency. When this reference frequency is set incorrectly, all related chemical shift values are systematically offset. Such wrongly referenced chemical shift values, as well as other problems such as chemical shift values that are assigned to the wrong atom, are not easily distinguished from correct values and effectively reduce the usefulness of the archive. We describe a new method to correct and validate protein chemical shift values in relation to their 3D structure coordinates. This method classifies atoms using two parameters: the per-atom solvent accessible surface area (as calculated from the coordinates) and the secondary structure of the parent amino acid. Through the use of Gaussian statistics based on a large database of 3220 BMRB entries, we obtain per-entry chemical shift corrections as well as Z scores for the individual chemical shift values. In addition, information on the error of the correction value itself is available, and the method can retain only dependable correction values. We provide an online resource with chemical shift, atom exposure, and secondary structure information for all relevant BMRB entries (http://www.ebi.ac.uk/pdbe/nmr/vasco) and hope this data will aid the development of new chemical shift-based methods in NMR. Proteins 2010. © 2010 Wiley-Liss, Inc. PMID:20602353

Structure-charge mobility relation for hexabenzocoronene derivatives

Energy Technology Data Exchange (ETDEWEB)

Kirkpatrick, James [Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128 (Germany); Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW (United Kingdom); Marcon, Valentina; Kremer, Kurt [Max Planck Institute for Polymer Research, Ackermannweg 10, Mainz 55128 (Germany); Nelson, Jenny [Department of Physics, Imperial College London, Prince Consort Road, London SW7 2BW (United Kingdom); Andrienko, Denis

2008-05-15

Charge mobilities of several derivatives of discotic liquid crystals have been determined by combining three methods into one scheme: (i) quantum chemical methods for the calculation of molecular electronic structures and reorganization energies (ii) molecular dynamics for simulation of the relative positions and orientations of molecules in a columnar mesophase, and (iii) kinetic Monte Carlo simulations and Master Equation approach to simulate charge transport. Applying this scheme to differently substituted hexabenzocoronene derivatives we reproduce the trends and magnitudes of mobilities as measured by pulse-radiolysis time-resolved microwave conductivity (PR-TRMC) and connect mobility directly to the microscopic morphology of the columns. Our study also shows that it is possible to understand and reproduce experimental charge transport parameters, and, in some cases, accurately predict them. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Aging of nuclear safety related concrete structures

International Nuclear Information System (INIS)

Cerny, R.; Vydra, V.; Toman, J.; Vodak, F.

1994-01-01

An analysis of aging processes in nuclear-safety-related concrete structures (NSRCS) is presented. The major environmental stressor and aging factors affecting the performance of NSRCS are summarized, as are drying and plastic shrinkage, expansion of water during the freeze-thaw cycle, water passing through cracks dissolving or leaching the soluble calcium hydroxide, attack of acid rain and ground water, chemical reactions between particular aggregates and the alkaline solution within cement paste, reaction of calcium hydroxide in cement paste hydration products with atmospheric carbon dioxide, and physical radiation effects of neutrons and gamma radiation. The current methods for aging management in NSRCS are analyzed and evaluated. A new treatment is presented for the monitoring, evaluation and prediction of aging processes, consisting in a combination of theoretical methods, laboratory experiments, in-situ measurements and numerical simulations. 24 refs

Lincosamides: Chemical structure, biosynthesis, mechanism of action, resistance, and applications

Czech Academy of Sciences Publication Activity Database

Spížek, Jaroslav; Řezanka, Tomáš

2017-01-01

Roč. 133, June 1 SI (2017), s. 20-28 ISSN 0006-2952 Institutional support: RVO:61388971 Keywords : Lincosamides * Chemical structure * Biosynthesis and mechanism of action Subject RIV: EE - Microbiology, Virology OBOR OECD: Microbiology Impact factor: 4.581, year: 2016

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 subse...

Chemical imaging of structured SAMs with a novel SFG microscope

Science.gov (United States)

Hoffmann, Dominik M. P.; Kuhnke, Klaus; Kern, Klaus

2002-11-01

We present a newly developed microscope for sum frequency generation (SFG) imaging of opaque and reflecting interfaces. The sample is viewed at an angle of 60° with respect to the surface normal in order to increase the collected SFG intensity. Our setup is designed to keep the whole field of view (FOV) in focus and to compensate for the distortion usually related to oblique imaging by means of a blazed grating. The separation of the SFG intensity and the reflected visible beam is accomplished by a suitable combination of spectral filters. The sum frequency microscope (SFM) is capable of in-situ chemically selective imaging by tuning the IR-beam to vibrational transitions of the respective molecules. The SFM is applied to imaging of structured self-assembled monolayers (SAM) of thiol molecules on a gold surface.

Effect of chemical structure on the cloud point of some new non-ionic surfactants based on bisphenol in relation to their surface active properties

Directory of Open Access Journals (Sweden)

A.M. Al-Sabagh

2011-06-01

Full Text Available A series of non-ionic surfactants were prepared from bisphenol derived from acetone (A, acetophenone (AC and cyclohexanone (CH. The prepared bisphenols were ethoxylated at different degrees of ethylene oxide (27, 35, 43. The ethoxylated bisphenols were non-esterified by fatty acids; decanoic, lauric, myristic, palmitic, stearic, oleic, linoloic and linolinic. Some surface active properties for these surfactants were measured and calculated such as, surface tension [γ], critical micelle concentration [CMC], minimum area per molecule [Amin], surface excess [Cmax], free energy of micellization and adsorption [ΔGmic] and [ΔGads]. At a certain temperature, the cloud point was measured for these surfactants. From the obtained data it was found that; the cloud point is very sensitive to the increase of the alkyl chain length, content of ethylene oxide and degree of unsaturation. The core of bisphenol affected the cloud point sharply and they are ranked regarding bisphenol structure as BA > BCH > BAC. By inspection of the surface active properties of these surfactants, a good relation was obtained with their cloud points. The data were discussed on the light of their chemical structures.

Algorithm for advanced canonical coding of planar chemical structures that considers stereochemical and symmetric information.

Science.gov (United States)

Koichi, Shungo; Iwata, Satoru; Uno, Takeaki; Koshino, Hiroyuki; Satoh, Hiroko

2007-01-01

We describe a rigorous and fast algorithm for advanced canonical coding of planar chemical structures based on the algorithm of Faulon et al. (J. Chem. Inf. Comput. Sci. 2004, 44, 427-436). Our algorithm works well even for highly symmetric structures; moreover, an advantage of our algorithm includes providing a rigorous canonical numbering of atoms with a consideration of stereochemistry and recognizing symmetric moieties. The planar structural line notation with the canonical numbering is also fit for use with stereochemical line notation. These capabilities are usable for general purposes in chemical structural coding and are particularly essential for detecting equivalent atoms in NMR studies. This algorithm was implemented on a 13C NMR chemical shift prediction system CAST/CNMR. Applications of the algorithm to several organic compounds demonstrate the practical efficiency of the rigorous coding.

Chemical approaches toward graphene-based nanomaterials and their applications in energy-related areas.

Science.gov (United States)

Luo, Bin; Liu, Shaomin; Zhi, Linjie

2012-03-12

A 'gold rush' has been triggered all over the world for exploiting the possible applications of graphene-based nanomaterials. For this purpose, two important problems have to be solved; one is the preparation of graphene-based nanomaterials with well-defined structures, and the other is the controllable fabrication of these materials into functional devices. This review gives a brief overview of the recent research concerning chemical and thermal approaches toward the production of well-defined graphene-based nanomaterials and their applications in energy-related areas, including solar cells, lithium ion secondary batteries, supercapacitors, and catalysis. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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 tw...

Biophysical insight into structure-function relation of Allium sativum Protease Inhibitor by thermal, chemical and pH-induced modulation using comprehensive spectroscopic analysis.

Science.gov (United States)

Shamsi, Tooba Naz; Parveen, Romana; Naz, Huma; Haque, Md Anzarul; Fatima, Sadaf

2017-10-01

In this study, we have analyzed the structural and functional changes in the nature of Allium sativum Protease Inhibitor (ASPI) on undergoing various denaturation with variable range of pH, temperature and urea (at pH 8.2). ASPI being anti-tryptic in nature has native molecular mass of ∼15kDa. The conformational stability, functional parameters and their correlation were estimated under different conditions using circular dichroism, fluorescence and activity measurements. ASPI was found to fall in belongs to α+β protein. It demonstrated structural and functional stability in the pH range 5.0-12.0 and up to70°C temperature. Further decrease in pH and increase in temperature induces unfolding followed by aggregation. Chemical induced denaturation was found to be cooperative and transitions were reversible and sigmoid. T m (midpoint of denaturation), ΔC p (constant pressure heat capacity change) and ΔH m (van't Hoff enthalpy change at T m were calculated to be 41.25±0.2°C, 1.3±0.07kcalmol -1 K -1 and 61±2kcalmol -1 respectively for thermally denatured ASPI earlier. The reversibility of the protein was confirmed for both thermally and chemically denatured ASPI. The results obtained from trypsin inhibitory activity assay and structural studies are found to be in a significant correlation and hence established structure-function relationship of ASPI. Copyright © 2017 Elsevier B.V. All rights reserved.

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.

[Nanometer scale exciton spectroscopy and photochemistry: Dynamic imaging of DNA structure-activity relations and radiation signatures

International Nuclear Information System (INIS)

1992-01-01

Our aim is to investigate, on the molecular level at a spatially resolved mode of operation, structure-activity relations of DNA and their sensitivity to ionizing radiation. This entails in-vitro (and later in-vivo) ultra-resolved microscopy, spectroscopy and chemical sensing, with non-destructive probing

A crowdsourcing workflow for extracting chemical-induced disease relations from free text.

Science.gov (United States)

Li, Tong Shu; Bravo, Àlex; Furlong, Laura I; Good, Benjamin M; Su, Andrew I

2016-01-01

Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available athttps://github.com/SuLab/crowd_cid_relexDatabase URL:https://github.com/SuLab/crowd_cid_relex. © The Author(s) 2016. Published by Oxford University Press.

A crowdsourcing workflow for extracting chemical-induced disease relations from free text

Science.gov (United States)

Li, Tong Shu; Bravo, Àlex; Furlong, Laura I.; Good, Benjamin M.; Su, Andrew I.

2016-01-01

Relations between chemicals and diseases are one of the most queried biomedical interactions. Although expert manual curation is the standard method for extracting these relations from the literature, it is expensive and impractical to apply to large numbers of documents, and therefore alternative methods are required. We describe here a crowdsourcing workflow for extracting chemical-induced disease relations from free text as part of the BioCreative V Chemical Disease Relation challenge. Five non-expert workers on the CrowdFlower platform were shown each potential chemical-induced disease relation highlighted in the original source text and asked to make binary judgments about whether the text supported the relation. Worker responses were aggregated through voting, and relations receiving four or more votes were predicted as true. On the official evaluation dataset of 500 PubMed abstracts, the crowd attained a 0.505 F-score (0.475 precision, 0.540 recall), with a maximum theoretical recall of 0.751 due to errors with named entity recognition. The total crowdsourcing cost was $1290.67 ($2.58 per abstract) and took a total of 7 h. A qualitative error analysis revealed that 46.66% of sampled errors were due to task limitations and gold standard errors, indicating that performance can still be improved. All code and results are publicly available at https://github.com/SuLab/crowd_cid_relex Database URL: https://github.com/SuLab/crowd_cid_relex PMID:27087308

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.

Bioremediation performance as related to chemical availability

International Nuclear Information System (INIS)

Loehr, R.; Olivera, F.; Webster, M.

1995-01-01

Two side-by-side field prepared bed land treatment units (PBLTU) were evaluated. One PBLTU (H unit) treated soils containing chemicals from a diesel spill that had occurred about 12 months earlier. The other PBLTU (G unit) treated soils containing crude oil that had been in the soil for many decades. Laboratory slurry treatability studies and indicated that the hydrocarbons in both soils could be bioremediated if adequate nutrients were provided. The PBLTU had nutrients applied periodically, and were operated in a manner consistent with good operational guidelines. PBLTU performance was based on reductions in mobility, toxicity, and chemical concentration. Spatially random soil samples were taken from the two field PBLTU monthly and analyzed for the above parameters as well as nutrients and pH. Periodically, microbial numbers and type in the soil samples also were evaluated. Performance was monitored over an 18 month period. In the H unit, no detectable TPH reductions occurred although petroleum hydrocarbon degrading microorganisms existed in the soil and other conditions were appropriate for bioremediation. GC/MS analyses indicated reduction in some specific hydrocarbons. The H unit soils had low chemical mobility as determined by leachability tests (TCLP, SPLP) and had low relative toxicity as determined by Microtox trademark

Denaturation of collagen structures and their transformation under the physical and chemical effects

Science.gov (United States)

Ivankin, A.; Boldirev, V.; Fadeev, G.; Baburina, M.; Kulikovskii, A.; Vostrikova, N.

2017-11-01

The process of denaturation of collagen structures under the influence of physical and chemical factors play an important role in the manufacture of food technology and the production of drugs for medicine and cosmetology. The paper discussed the problem of the combined effects of heat treatment, mechanical dispersion and ultrasonic action on the structural changes of the animal collagen in the presence of weak protonated organic acids. Algorithm combined effects of physical and chemical factors as a result of the formation of the technological properties of products containing collagen has been shown.

Correlating the vibrational spectra of structurally related molecules: A spectroscopic measure of similarity.

Science.gov (United States)

Tao, Yunwen; Zou, Wenli; Cremer, Dieter; Kraka, Elfi

2018-03-05

Using catastrophe theory and the concept of a mutation path, an algorithm is developed that leads to the direct correlation of the normal vibrational modes of two structurally related molecules. The mutation path is defined by weighted incremental changes in mass and geometry of the molecules in question, which are successively applied to mutate a molecule into a structurally related molecule and thus continuously converting their normal vibrational spectra from one into the other. Correlation diagrams are generated that accurately relate the normal vibrational modes to each other by utilizing mode-mode overlap criteria and resolving allowed and avoided crossings of vibrational eigenstates. The limitations of normal mode correlation, however, foster the correlation of local vibrational modes, which offer a novel vibrational measure of similarity. It will be shown how this will open new avenues for chemical studies. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Influence of chemical structures on biodegradation of azo dyes by ...

African Journals Online (AJOL)

Influence of chemical structures on biodegradation of azo dyes by Pseudomonas sp. NA Oranusi, CJ Ogugbue. Abstract. No Abstract. Global Journal of Environmental Sciences Vol. 5(1) 2006: 19-25. Full Text: EMAIL FREE FULL TEXT EMAIL FREE FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL TEXT.

Development of activated carbon pore structure via physical and chemical activation of biomass fibre waste

International Nuclear Information System (INIS)

Williams, Paul T.; Reed, Anton R.

2006-01-01

Biomass waste in the form of biomass flax fibre, produced as a by-product of the textile industry was processed via both physical and chemical activation to produce activated carbons. The surface area of the physically activated carbons were up to 840 m 2 g -1 and the carbons were of mesoporous structure. Chemical activation using zinc chloride produced high surface area activated carbons up to 2400 m 2 g -1 and the pore size distribution was mainly microporous. However, the process conditions of temperature and zinc chloride concentration could be used to manipulate the surface area and porosity of the carbons to produce microporous, mesoporous and mixed microporous/mesoporous activated carbons. The physically activated carbons were found to be a mixture of Type I and Type IV carbons and the chemically activated carbons were found to be mainly Type I carbons. The development of surface morphology of physically and chemically activated carbons observed via scanning electron microscopy showed that physical activation produced activated carbons with a nodular and pitted surface morphology whereas activated carbons produced through chemical activation had a smooth surface morphology. Transmission electron microscopy analysis could identify mesopore structures in the physically activated carbon and microporous structures in the chemically activated carbons

Federal agencies active in chemical industry-related research and development

Energy Technology Data Exchange (ETDEWEB)

NONE

1995-09-29

The Energy Policy Act of 1992 calls for a program to further the commercialization of renewable energy and energy efficient technologies for the industrial sector.. The primary objective of the Office of Industrial Technologies Chemical Industry Team is to work in partnership with the US chemical industry to maximize economic, energy, and environmental benefits through research and development of innovative technologies. This document was developed to inventory organizations within the federal government on current chemical industry-related research and development. While an amount of funding or number of projects specifically relating to chemical industry research and development was not defined in all organizations, identified were about 60 distinct organizations representing 7 cabinet-level departments and 4 independent agencies, with research efforts exceeding $3.5 billion in fiscal year 1995. Effort were found to range from less than $500 thousand per year at the Departments of Agriculture and the Interior to over $100 million per year at the Departments of Commerce, Defense, Energy, and Health and Human Services and the National Aeronautics and Space Administration. The total number of projects in these programs exceeded 10,000. This document is complete to the extent that agencies volunteered information. Additions, corrections, and changes are encouraged and will be incorporated in future revisions.

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.

Calculating the dermal flux of chemicals with OELs based on their molecular structure: An attempt to assign the skin notation.

Science.gov (United States)

Kupczewska-Dobecka, Małgorzata; Jakubowski, Marek; Czerczak, Sławomir

2010-09-01

Our objectives included calculating the permeability coefficient and dermal penetration rates (flux value) for 112 chemicals with occupational exposure limits (OELs) according to the LFER (linear free-energy relationship) model developed using published methods. We also attempted to assign skin notations based on each chemical's molecular structure. There are many studies available where formulae for coefficients of permeability from saturated aqueous solutions (K(p)) have been related to physicochemical characteristics of chemicals. The LFER model is based on the solvation equation, which contains five main descriptors predicted from chemical structure: solute excess molar refractivity, dipolarity/polarisability, summation hydrogen bond acidity and basicity, and the McGowan characteristic volume. Descriptor values, available for about 5000 compounds in the Pharma Algorithms Database were used to calculate permeability coefficients. Dermal penetration rate was estimated as a ratio of permeability coefficient and concentration of chemical in saturated aqueous solution. Finally, estimated dermal penetration rates were used to assign the skin notation to chemicals. Defined critical fluxes defined from the literature were recommended as reference values for skin notation. The application of Abraham descriptors predicted from chemical structure and LFER analysis in calculation of permeability coefficients and flux values for chemicals with OELs was successful. Comparison of calculated K(p) values with data obtained earlier from other models showed that LFER predictions were comparable to those obtained by some previously published models, but the differences were much more significant for others. It seems reasonable to conclude that skin should not be characterised as a simple lipophilic barrier alone. Both lipophilic and polar pathways of permeation exist across the stratum corneum. It is feasible to predict skin notation on the basis of the LFER and other published

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.

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

International Nuclear Information System (INIS)

Jiang Hao; Hong Lianggou; Venkatasubramanian, N.; Grant, John T.; Eyink, Kurt; Wiacek, Kevin; Fries-Carr, Sandra; Enlow, Jesse; Bunning, Timothy J.

2007-01-01

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 (ε r ) and dielectric loss (tan δ) of the films were investigated over a range of frequencies up to 1 MHz and the dielectric strength (breakdown voltage) (F 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 b of 610 V/μm, an ε r of 3.07, and a tan δ of 7.0 x 10 -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

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

2016-10-13

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.

Hierarchically structured photonic crystals for integrated chemical separation and colorimetric detection.

Science.gov (United States)

Fu, Qianqian; Zhu, Biting; Ge, Jianping

2017-02-16

A SiO 2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO 2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

Shining Light on the Differences in Molecular Structural Chemical Makeup and the Cause of Distinct Degradation Behavior Between Malting- and Feed- Type Barley Using Synchrotorn FTIR Microspectroscopy: A Novel Approach

International Nuclear Information System (INIS)

Yu, P.; Doiron, K.; Liu, D.

2008-01-01

The objective of this study was to use advanced synchrotron-sourced FTIR microspectroscopy (SFTIRM) as a novel approach to identify the differences in protein and carbohydrate molecular structure (chemical makeup) between these two varieties of barley and illustrate the exact causes for their significantly different degradation kinetics. Items assessed included (1) molecular structural differences in protein amide I to amide II intensities and their ratio within cellular dimensions, (2) molecular structural differences in protein secondary structure profile and their ratios, and (3) molecular structural differences in carbohydrate component peak profile. Our hypothesis was that molecular structure (chemical makeup) affects barley quality, fermentation, and degradation behavior in both humans and animals. Using SFTIRM, the protein and carbohydrate molecular structural chemical makeup of barley was revealed and identified. The protein molecular structural chemical makeup differed significantly between the two varieties of barleys. No difference in carbohydrate molecular structural chemical makeup was detected. Harrington was lower than Valier in protein amide I, amide II, and protein amide I to amide II ratio, while Harrington was relatively higher in model-fitted protein a-helix and β-sheet, but lower in the others (β-turn and random coil). These results indicated that it is the molecular structure of protein (chemical makeup) that may play a major role in the different degradation kinetics between the two varieties of barleys (not the molecular structure of carbohydrate). It is believed that use of the advanced synchrotron technology will make a significant step and an important contribution to research in examining the molecular structure (chemical makeup) of plant, feed, and seeds.

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. Copyright © 2016 Elsevier B.V. All rights reserved.

Physico-Chemical Alternatives in Lignocellulosic Materials in Relation to the Kind of Component for Fermenting Purposes

Directory of Open Access Journals (Sweden)

Alberto Coz

2016-07-01

Full Text Available The complete bioconversion of the carbohydrate fraction is of great importance for a lignocellulosic-based biorefinery. However, due to the structure of the lignocellulosic materials, and depending basically on the main parameters within the pretreatment steps, numerous byproducts are generated and they act as inhibitors in the fermentation operations. In this sense, the impact of inhibitory compounds derived from lignocellulosic materials is one of the major challenges for a sustainable biomass-to-biofuel and -bioproduct industry. In order to minimise the negative effects of these compounds, numerous methodologies have been tested including physical, chemical, and biological processes. The main physical and chemical treatments have been studied in this work in relation to the lignocellulosic material and the inhibitor in order to point out the best mechanisms for fermenting purposes. In addition, special attention has been made in the case of lignocellulosic hydrolysates obtained by chemical processes with SO2, due to the complex matrix of these materials and the increase in these methodologies in future biorefinery markets. Recommendations of different detoxification methods have been given.

20180318 - Sharing chemical structures with peer-reviewed publications. Are we there yet? (ACS Spring)

Science.gov (United States)

In the domain of chemistry one of the greatest benefits to publishing research is that data are shared. Unfortunately, the vast majority of chemical structure data remain locked up in document form, primarily as PDF files. Despite the explosive growth of online chemical databases...

Chemical structure and physical properties of radiation-induced crosslinking of polytetrafluoroethylene

International Nuclear Information System (INIS)

Oshima, Akihiro; Ikeda, Shigetoshi; Katoh, Etsuko; Tabata, Yoneho

2001-01-01

The chemical structure and physical properties of polytetrafluoroethylene (PTFE) that has been crosslinked by radiation have been studied by various methods. It has been found that a Y-type crosslinking structure and a Y-type structure incorporating a double bond (modified Y-type) is formed in PTFE by radiation-crosslinking in the molten state. In addition, various types of double bond structures, excluding the crosslinking site, have been identified. The crosslinked PTFE has a good light transparency due to the loss of crystallites, whilst it retains the excellent properties of electrical insulation and heat resistance. The coefficient of abrasion and the permanent creep are also greatly improved by crosslinking

Photoluminescence study of ZnO structures grown by aqueous chemical growth

International Nuclear Information System (INIS)

Kenanakis, G.; Androulidaki, M.; Vernardou, D.; Katsarakis, N.; Koudoumas, E.

2011-01-01

ZnO micro-structures were deposited by aqueous chemical growth on Si (100) substrates, their morphology and size depending on the growth period. Characterization of the structures was performed using X-ray diffraction, scanning electron microscopy and Raman spectroscopy. Photoluminescence spectra recorded at 18 and 295 K for 325 nm CW excitation indicated that these are strongly affected by the morphology of the structures. Rods and tubes emit stronger UV radiation, in contrast to stronger yellow-green emission observed for flower-like structures. A red shift of the UV emission was found for increasing input power, while, thermal annealing of the samples induced stimulated emission for quite high excitation intensities.

Sensitivity of ab Initio vs Empirical Methods in Computing Structural Effects on NMR Chemical Shifts for the Example of Peptides.

Science.gov (United States)

Sumowski, Chris Vanessa; Hanni, Matti; Schweizer, Sabine; Ochsenfeld, Christian

2014-01-14

The structural sensitivity of NMR chemical shifts as computed by quantum chemical methods is compared to a variety of empirical approaches for the example of a prototypical peptide, the 38-residue kaliotoxin KTX comprising 573 atoms. Despite the simplicity of empirical chemical shift prediction programs, the agreement with experimental results is rather good, underlining their usefulness. However, we show in our present work that they are highly insensitive to structural changes, which renders their use for validating predicted structures questionable. In contrast, quantum chemical methods show the expected high sensitivity to structural and electronic changes. This appears to be independent of the quantum chemical approach or the inclusion of solvent effects. For the latter, explicit solvent simulations with increasing number of snapshots were performed for two conformers of an eight amino acid sequence. In conclusion, the empirical approaches neither provide the expected magnitude nor the patterns of NMR chemical shifts determined by the clearly more costly ab initio methods upon structural changes. This restricts the use of empirical prediction programs in studies where peptide and protein structures are utilized for the NMR chemical shift evaluation such as in NMR refinement processes, structural model verifications, or calculations of NMR nuclear spin relaxation rates.

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors.

Science.gov (United States)

Nandi, Sisir; Monesi, Alessandro; Drgan, Viktor; Merzel, Franci; Novič, Marjana

2013-10-30

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software. Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q2 and predictive R2 values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers. A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

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.

Including chemical-related impact categories in LCA on printed matter does it matter?

DEFF Research Database (Denmark)

Larsen, Henrik Fred; Hansen, Morten Søes; Hauschild, Michael Zwicky

2004-01-01

global warming, acidification and nutrification. The studies focus on energy consumption including the emissions and impact categories related to energy. The chemical-related impact categories comprising ecotoxicity and human toxicity are not included at all or only to a limited degree. In this paper we...... include these chemical-related impact categories by making use of some of the newest knowledge about emissions from the production at the printing industry combined with knowledge about the composition of the printing materials used during the production of offset printed matter. This paper is based...... printed matter produced on a fictitious sheet feed offset printing industry in Europe has been identified and shown in Figure 1 (light bars). „Ï The effect of including the chemical related impact categories is substantial as shown in Figure 1, e.g. the importance of paper is reduced from 67% to 31...

Electronic structure and chemical bonding in LaIrSi-type intermetallics

Energy Technology Data Exchange (ETDEWEB)

Matar, Samir F. [Bordeaux Univ., Pessac (France). CNRS; Poettgen, Rainer [Muenster Univ. (Germany). Inst. fuer Anorganische und Analytische Chemie; Nakhl, Michel [Univ. Libanaise, Fanar (Lebanon). Ecole Doctorale Sciences et Technologies

2017-05-01

The cubic LaIrSi type has 23 representatives in aluminides, gallides, silicides, germanides, phosphides, and arsenides, all with a valence electron count of 16 or 17. The striking structural motif is a three-dimensional network of the transition metal (T) and p element (X) atoms with TX{sub 3/3} respectively XT{sub 3/3} coordination. Alkaline earth or rare earth atoms fill cavities within the polyanionic [TX]{sup δ-} networks. The present work presents a detailed theoretical study of chemical bonding in LaIrSi-type representatives, exemplarily for CaPtSi, BaIrP, BaAuGa, LaIrSi, CeRhSi, and CeIrSi. DFT-GGA-based electronic structure calculations show weakly metallic compounds with itinerant small magnitude DOSs at E{sub F} except for CeRhSi whose large Ce DOS at E{sub F} leads to a finite magnetization on Ce (0.73 μ{sub B}) and induced small moments of opposite sign on Rh and Si in a ferromagnetic ground state. The chemical bonding analyses show dominant bonding within the [TX]{sup δ-} polyanionic networks. Charge transfer magnitudes were found in accordance with the course of the electronegativites of the chemical constituents.

Micro-chemical and micro-structural investigation of archaeological bronze weapons from the Ayanis fortress (lake Van, Eastern Anatolia, Turkey)

Science.gov (United States)

Faraldi, F.; Çilingirǒglu, A.; Angelini, E.; Riccucci, C.; De Caro, T.; Batmaz, A.; Mezzi, A.; Caschera, D.; Cortese, B.

2013-12-01

Bronze weapons (VII cen BC) found during the archaeological excavation of the Ayanis fortress (lake Van, eastern Anatolia, Turkey) are investigated in order to determine their chemical composition and metallurgical features as well as to identify the micro-chemical and micro-structural nature of the corrosion products grown during long-term burial. Small fragments were sampled from the artefacts and analysed by means of the combined use of optical microscopy (OM), X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), scanning electron microscopy (SEM) and energy dispersive spectrometry (EDS). The results show that the bronze artefacts have been manufactured by using alloys with a controlled and refined chemical composition demonstrating the high level metallurgical competence and skill of the Urartian craftsmen and artists. Furthermore, the micro-structural and metallurgical investigations evidence the presence of equiaxed grains in the matrix, indicating that the artefact were produced by repeated cycles of mechanical shaping and thermal annealing treatments to restore the alloy ductility. From the degradation point of view, the results show the structures and the chemical composition of the stratified corrosion layers (i.e. the patina) where the copper or tin depletion phenomenon is commonly observed with the surface enrichment of some elements coming from the burial soil, mainly Cl, which is related to the high concentration of chlorides in the Ayanis soil. The results reveal also that another source of degradation is the inter-granular corrosion phenomenon likely increased by the metallurgical features of the alloys caused by the high temperature manufacturing process that induces crystallisation and segregation phenomena along the grain boundaries.

Structural, chemical and electrical characterisation of conductive graphene-polymer composite films

Energy Technology Data Exchange (ETDEWEB)

Brennan, Barry; Spencer, Steve J.; Belsey, Natalie A. [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom); Faris, Tsegie [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Cronin, Harry [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Advanced Technology Institute (ATI), University of Surrey, Guildford, GU2 7XH (United Kingdom); Silva, S. Ravi P. [Advanced Technology Institute (ATI), University of Surrey, Guildford, GU2 7XH (United Kingdom); Sainsbury, Toby; Gilmore, Ian S. [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom); Stoeva, Zlatka [DZP Technologies Ltd., Future Business Centre, Cambridge, CB4 2HY (United Kingdom); Pollard, Andrew J., E-mail: andrew.pollard@npl.co.uk [National Physical Laboratory, Teddington, TW11 0LW (United Kingdom)

2017-05-01

Graphical abstract: Secondary Ion Mass Spectrometry (SIMS) imaging of the dispersion of graphene within graphene-polymer composites using the Na{sup +} signal. - Highlights: • Relation of properties of graphene flakes with electrical properties of composite. • Standardised characterisation method for structural properties of graphene flakes. • Structural and chemical characterisation of commercial graphene flakes. • ToF-SIMS used to determine dispersion of graphene in polymer. - Abstract: Graphene poly-acrylic and PEDOT:PSS nanocomposite films were produced using two alternative commercial graphene powders to explore how the graphene flake dimensions and chemical composition affected the electrical performance of the film. A range of analytical techniques, including scanning electron microscopy (SEM), atomic force microscopy (AFM), Raman spectroscopy, X-ray photoelectron spectroscopy (XPS) and time-of-flight secondary ion mass spectrometry (ToF-SIMS), were employed to systematically analyse the initial graphene materials as well as the nanocomposite films. Electrical measurements indicated that the sheet resistance of the films was affected by the properties of the graphene flakes used. To further explore the composition of the films, ToF-SIMS mapping was employed and provided a direct means to elucidate the nature of the graphene dispersion in the films and to correlate this with the electrical analysis. These results reveal important implications for how the dispersion of the graphene material in films produced from printable inks can be affected by the type of graphene powder used and the corresponding effect on electrical performance of the nanocomposites. This work provides direct evidence for how accurate and comparable characterisation of the graphene material is required for real-world graphene materials to develop graphene enabled films and proposes a measurement protocol for comparing graphene materials that can be used for international

Structural investigation of chemically synthesized ferrite magnetic nanomaterials

Science.gov (United States)

Uyanga, E.; Sangaa, D.; Hirazawa, H.; Tsogbadrakh, N.; Jargalan, N.; Bobrikov, I. A.; Balagurov, A. M.

2018-05-01

In recent times, interest in ferrite magnetic nanomaterials has considerably grown, mainly due to their highly promising medical and biological applications. Spinel ferrite powder samples, with high heat generation abilities in AC magnetic fields, were studied for their application to the hyperthermia treatment of cancer tumors. These properties of ferrites strongly depend on their chemical composition, ion distribution between crystallographic positions, magnetic structure and method of preparation. In this study, crystal and magnetic structures of several magnetic spinels were investigated by neutron diffraction. The explanation of the mechanism triggering the heat generation ability in the magnetic materials, and the electronic and magnetic states of ferrite-spinel type structures, were theoretically defined by a first-principles method. Ferrites with the composition of CuxMg1-xFe2O4 have been investigated as a heat generating magnetic nanomaterial. Atomic fraction of copper in ferrite was varied between 0 and 100% (that is, x between 0 and 1.0 with 0.2 steps), with the copper dope limit corresponding to appear a tetragonal phase.

Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

Science.gov (United States)

Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

2015-12-01

First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

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.

Structural and chemical aspects of HPMA copolymers as drug carriers.

Science.gov (United States)

Ulbrich, Karel; Subr, Vladimír

2010-02-17

Synthetic strategies and chemical and structural aspects of the synthesis of HPMA copolymer conjugates with various drugs and other biologically active molecules are described and discussed in this chapter. The discussion is held from the viewpoint of design and structure of the polymer backbone and biodegradable spacer between a polymer and drug, structure and methods of attachment of the employed drugs to the carrier and structure and methods of conjugation with targeting moieties. Physicochemical properties of the water-soluble polymer-drug conjugates and polymer micelles including mechanisms of drug release are also discussed. Detailed description of biological behavior of the polymer-drug conjugates as well as application of the copolymers for surface modification and targeting of gene delivery vectors are not included, they are presented and discussed in separate chapters of this issue. Copyright 2009 Elsevier B.V. All rights reserved.

Accumulation of radium in relation to some chemical analogues in Dicranopteris linearis

International Nuclear Information System (INIS)

Chao, J.H.; Chuang, C.Y.

2011-01-01

This study elucidates the uptake and accumulation of radium in the field-growing fern Dicranopteris linearis by relating the radium concentration to some potential chemical analogues, including alkaline earth metals, rare earth elements, and some important heavy metals. Time-dependent accumulation of radium and these chemical analogues for D. linearis were described by the 228 Th/ 228 Ra activity ratio, an index for inferring plant age. The correlation between radium and these elements was assessed by statistical analysis and used as a reference to elucidate the uptake and accumulation of radium in relation to the chemical analogues. Analytical and statistical results showed that the concentrations of alkaline earth metals (except for Mg) rare earth elements and some heavy metals in D. linearis increased linearly with plant age. These elements, exhibiting a similar accumulation pattern to radium and significant correlation coefficients with radium, were considered as the chemical analogues to radium. Additionally, the plant/soil concentration ratios (CRs) for radium and most of these analogues in D. linearis exceeded 1, consistent with the definition of hyper-accumulator plants.

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.

Exploring the structure-activity relations of N-carbethoxyphthalimide by combining FTIR, FT-Raman and NMR spectroscopy with DFT electronic structure method.

Science.gov (United States)

Arjunan, V; Govindaraja, S Thillai; Ravindran, P; Mohan, S

2014-01-01

The complete vibrational assignment and analysis of N-carbethoxyphthalimide were carried out using the experimental FTIR and FT-Raman data in the range 4000-450 and 4000-100 cm(-1), respectively along with quantum chemical studies of the compound using DFT-B3LYP gradient calculations employing the 6-31G**, 6-311++G** and cc-pVDZ basis sets. The 1H (400 MHz; CDCl3) and 13C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra were also recorded. Due to the partial ionic nature of the carbonyl group, the carbon atoms C1 and C3 in NCEP show downfield effect and the corresponding observed chemical shift of both are observed at 163.76 ppm and the carbon atom C16 in the carbethoxy group also give signal in the downfield at 148.45 ppm. The active sites are determined by molecular electrostatic potential. The possible electronic transitions are determined by HOMO and LUMO orbital shapes and their energies. The structure-chemical reactivity relations of the compound were determined through chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. Copyright © 2013 Elsevier B.V. All rights reserved.

AI AND SAR APPROACHES FOR PREDICTING CHEMICAL CARCINOGENICITY: SURVEY AND STATUS REPORT

Science.gov (United States)

A wide variety of artificial intelligence (AI) and structure-activity relationship (SAR approaches have been applied to tackling the general problem of predicting rodent chemical carcinogenicity. Given the diversity of chemical structures and mechanisms relative to this endpoin...

Determination of the thickness of chemically removed thin layers on GaAs VPE structures

Energy Technology Data Exchange (ETDEWEB)

Somogyi, K.; Nemeth-Sallay, M.; Nemcsics, A. (Research Inst. for Technical Physics, Hungarian Academy of Sciences, Budapest (Hungary))

1991-01-01

Thinning of epitaxial GaAs layers was studied during the surface etching, with a special attention to submicron epitaxial structures, like MESFET or varactor-type structures. Each chemical treatment influences the crystal surface during the device preparation processes, though the possible thinning of the active layer is small. Therefore a method allowing determination of thicknesses as small as at about 20 nm of the layer removed by chemical etching from GaAs VPE structures was applied. Using special multilayered structures and a continuous electrochemical carrier concentration depth profiling, the influence of the layer thickness inhomogeneity and of some measurement errors can be minimized. Some frequently used etchants and the influence of different - so called - non-etching processes were compared in different combinations. It was shown that besides the direct etching a change of the surface conditions occurs, which influences the etch rate in the succeeding etching procedure. (orig.).

Chemical equilibrium. [maximizing entropy of gas system to derive relations between thermodynamic variables

Science.gov (United States)

1976-01-01

The entropy of a gas system with the number of particles subject to external control is maximized to derive relations between the thermodynamic variables that obtain at equilibrium. These relations are described in terms of the chemical potential, defined as equivalent partial derivatives of entropy, energy, enthalpy, free energy, or free enthalpy. At equilibrium, the change in total chemical potential must vanish. This fact is used to derive the equilibrium constants for chemical reactions in terms of the partition functions of the species involved in the reaction. Thus the equilibrium constants can be determined accurately, just as other thermodynamic properties, from a knowledge of the energy levels and degeneracies for the gas species involved. These equilibrium constants permit one to calculate the equilibrium concentrations or partial pressures of chemically reacting species that occur in gas mixtures at any given condition of pressure and temperature or volume and temperature.

Relative influence of soil chemistry and topography on soil available micronutrients by structural equation modeling

OpenAIRE

Zhu, Hongfen; Zhao, Ying; Nan, Feng; Duan, Yonghong; Bi, Rutian

2016-01-01

Soil chemical and topographic properties are two important factors influencing available micronutrient distribution of soil in the horizontal dimension. The objective of this study was to explore the relative influence of soil chemistry (including soil pH, soil organic matter, total nitrogen, available phosphorus, and available potassium) and topography (including elevation, slope, aspect, and wetness index) on the availability of micronutrients (Fe, Mn, Cu, Zn, and B) using structural equati...

Native chemical ligation at Asx-Cys, Glx-Cys: chemical synthesis and high-resolution X-ray structure of ShK toxin by racemic protein crystallography.

Science.gov (United States)

Dang, Bobo; Kubota, Tomoya; Mandal, Kalyaneswar; Bezanilla, Francisco; Kent, Stephen B H

2013-08-14

We have re-examined the utility of native chemical ligation at -Gln/Glu-Cys- [Glx-Cys] and -Asn/Asp-Cys- [Asx-Cys] sites. Using the improved thioaryl catalyst 4-mercaptophenylacetic acid (MPAA), native chemical ligation could be performed at -Gln-Cys- and Asn-Cys- sites without side reactions. After optimization, ligation at a -Glu-Cys- site could also be used as a ligation site, with minimal levels of byproduct formation. However, -Asp-Cys- is not appropriate for use as a site for native chemical ligation because of formation of significant amounts of β-linked byproduct. The feasibility of native chemical ligation at -Gln-Cys- enabled a convergent total chemical synthesis of the enantiomeric forms of the ShK toxin protein molecule. The D-ShK protein molecule was ~50,000-fold less active in blocking the Kv1.3 channel than the L-ShK protein molecule. Racemic protein crystallography was used to obtain high-resolution X-ray diffraction data for ShK toxin. The structure was solved by direct methods and showed significant differences from the previously reported NMR structures in some regions of the ShK protein molecule.

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

Effect of pH on the chemical modification of quercetin and structurally related flavonoids characterized by optical (UV-visible and Raman) spectroscopy.

Science.gov (United States)

Jurasekova, Z; Domingo, C; Garcia-Ramos, J V; Sanchez-Cortes, S

2014-07-07

In this work we report the study of the chemical modifications undergone by flavonoids, especially by quercetin (QUC), under alkaline conditions by UV-visible absorption, Raman and surface-enhanced Raman scattering (SERS) spectroscopy, the study was performed in aqueous solution and also on Ag nanoparticles (AgNPs). Several processes are involved in the effect of alkaline pH both in solution and on AgNPs: autoxidation affecting mainly the C-ring of the molecule and giving rise to the molecular fragmentation leading to simpler molecular products, and/or the dimerization and further polymerization leading to species with a higher molecular weight. In addition, there exists a clear structure-instability correlation concerning mainly particular groups in the molecule: the C3-OH group in the C-ring, the catechol moiety in the B-ring and the C2=C3 bond also existing in the C-ring. QUC possesses all these groups and exhibits high instability in alkaline solution. The SERS spectra registered at different pH revealed a change in the dimerization protocol of QUC going from the A- and C-rings-like-condensation to B-ring-like-condensation. Increasing the knowledge of the chemical properties of these compounds and determining the structure-activity relationship under specific environmental factors allow us to improve their beneficial properties for health as well as the preservation of Cultural Heritage objects, for example, by preventing their degradation.

Chemical synthesis and structure elucidation of bovine κ-casein (1-44)

International Nuclear Information System (INIS)

Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F.

2006-01-01

The caseins (α s1 , α s2 , β, and κ) are phosphoproteins present in bovine milk that have been studied for over a century and whose structures remain obscure. Here we describe the chemical synthesis and structure elucidation of the N-terminal segment (1-44) of bovine κ-casein, the protein which maintains the micellar structure of the caseins. κ-Casein (1-44) was synthesised by highly optimised Boc solid-phase peptide chemistry and characterised by mass spectrometry. Structure elucidation was carried out by circular dichroism and nuclear magnetic resonance spectroscopy. CD analysis demonstrated that the segment was ill defined in aqueous medium but in 30% trifluoroethanol it exhibited considerable helical structure. Further, NMR analysis showed the presence of a helical segment containing 26 residues which extends from Pro 8 to Arg 34 . This is First report which demonstrates extensive secondary structure within the casein class of proteins

Chemical investigation, isolation and structural analysis of flavones from primula veris

International Nuclear Information System (INIS)

Huck, Ch.

1998-01-01

The chemical investigation, isolation and structural analysis of six flavones present in flowers of Primula veris is described. Sample preparation of substances G from Primula veris comprised methanol extraction, low pressure chromatography on aluminum oxide, medium pressure chromatography on silica gel, and RP-HPLC on ODS. The six flavones, which were identified by their blue fluorescence after separation by thin layer chromatography, were named substance G1, G2, G3, G4, G5 and G6 according to their Rf-values. Fractions were collected during each of the separation processes and the fractions were analyzed by NP-HPLC and RP-HPLC. Higher resolution was obtained by NP-HPLC on a silica gel column and an n-hexane/ isopropanol (92:8 v/v) eluent, where 6 peaks (G1, G2, G3, G4, G5 and G6) were obtained. Diode array detection from 190 - 350 nm was utilized for the recording of UV-spectra for peak identification and peak-purity-analysis. The structures of Substance G4 and Substance G6 were established on the basis of UV, NMR, EI-MS and APCI-MS. The structure of the isolated substance G4 was verified by chemical synthesis. (author)

Structural Logical Relations

DEFF Research Database (Denmark)

Schürmann, Carsten; Sarnat, Jeffrey

2008-01-01

Tait's method (a.k.a. proof by logical relations) is a powerful proof technique frequently used for showing foundational properties of languages based on typed lambda-calculi. Historically, these proofs have been extremely difficult to formalize in proof assistants with weak meta-logics......, such as Twelf, and yet they are often straightforward in proof assistants with stronger meta-logics. In this paper, we propose structural logical relations as a technique for conducting these proofs in systems with limited meta-logical strength by explicitly representing and reasoning about an auxiliary logic...

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships.

Science.gov (United States)

Arnau, E G; Andersen, K E; Bruze, M; Frosch, P J; Johansen, J D; Menné, T; Rastogi, S C; White, I R; Lepoittevin, J P

2000-12-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application test on the pre-sensitized patient. The chemical composition of the fractions giving a positive patch-test response and repeated open application test reactions was obtained by gas chromatography-mass spectrometry. From the compounds identified, those that contained a "structural alert" in their chemical structure, indicating an ability to modify skin proteins and thus behave as a skin sensitizer, were tested on the patient. The patient reacted positively to the synthetic fragrance p-t-butyl-alpha-methylhydrocinnamic aldehyde (Lilial), a widely used fragrance compound not present in the fragrance mix. The combination of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships seems to be a valuable tool for the investigation of contact allergy to fragrance materials.

Structural changes in γ-irradiated Brucella strain chemical vaccine

International Nuclear Information System (INIS)

Dranovskaya, E.A.; Kulikov, V.I.

1986-01-01

It was shown that γ-irradiation of Brucella strain chemical vaccine stimulated phospholipid peroxidation therein: the content of extractable total phospholipids in the exposed vaccine decreased mainly due to diminution of phosphatidynatidylcholines and phosphatidylethanolamines. A relative content of high- and low-molecular weight protein componets increase in the γ-irradiated vaccine

Integrative Chemical-Biological Read-Across Approach for Chemical Hazard Classification

Science.gov (United States)

Low, Yen; Sedykh, Alexander; Fourches, Denis; Golbraikh, Alexander; Whelan, Maurice; Rusyn, Ivan; Tropsha, Alexander

2013-01-01

Traditional read-across approaches typically rely on the chemical similarity principle to predict chemical toxicity; however, the accuracy of such predictions is often inadequate due to the underlying complex mechanisms of toxicity. Here we report on the development of a hazard classification and visualization method that draws upon both chemical structural similarity and comparisons of biological responses to chemicals measured in multiple short-term assays (”biological” similarity). The Chemical-Biological Read-Across (CBRA) approach infers each compound's toxicity from those of both chemical and biological analogs whose similarities are determined by the Tanimoto coefficient. Classification accuracy of CBRA was compared to that of classical RA and other methods using chemical descriptors alone, or in combination with biological data. Different types of adverse effects (hepatotoxicity, hepatocarcinogenicity, mutagenicity, and acute lethality) were classified using several biological data types (gene expression profiling and cytotoxicity screening). CBRA-based hazard classification exhibited consistently high external classification accuracy and applicability to diverse chemicals. Transparency of the CBRA approach is aided by the use of radial plots that show the relative contribution of analogous chemical and biological neighbors. Identification of both chemical and biological features that give rise to the high accuracy of CBRA-based toxicity prediction facilitates mechanistic interpretation of the models. PMID:23848138

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

International Nuclear Information System (INIS)

Gusakovskaya, I.G.

1994-01-01

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 T k

Chemical interaction of B4C, B, and C with Mo/Si layered structures

International Nuclear Information System (INIS)

Rooij-Lohmann, V. I. T. A. de; Veldhuizen, L. W.; Zoethout, E.; Yakshin, A. E.; Kruijs, R. W. E. van de; Thijsse, B. J.; Gorgoi, M.; Schaefers, F.; Bijkerk, F.

2010-01-01

To enhance the thermal stability, B 4 C diffusion barrier layers are often added to Mo/Si multilayer structures for extreme ultraviolet optics. Knowledge about the chemical interaction between B 4 C and Mo or Si, however is largely lacking. Therefore, the chemical processes during annealing up to 600 deg. C of a Mo/B 4 C/Si layered structure have been investigated in situ with hard x-ray photoelectron spectroscopy and ex situ with depth profiling x-ray photoelectron spectroscopy. Mo/B/Si and Mo/C/Si structures have also been analyzed as reference systems. The chemical processes in these systems have been identified, with two stages being distinguished. In the first stage, B and C diffuse and react predominantly with Mo. MoSi x forms in the second stage. If the diffusion barrier consists of C or B 4 C, a compound forms that is stable up to the maximum probed temperature and annealing time. We suggest that the diffusion barrier function of B 4 C interlayers as reported in literature can be caused by the stability of the formed compound, rather than by the stability of B 4 C itself.

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

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.

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.

Structural and chemical variations in phlogopite from lamproitic rocks of the Central Mediterranean region

Science.gov (United States)

Lepore, Giovanni O.; Bindi, Luca; Pedrazzi, Giuseppe; Conticelli, Sandro; Bonazzi, Paola

2017-08-01

Micas from mafic ultrapotassic rocks with lamproitic affinity from several localities of the Central Mediterranean region were studied through single-crystal X-ray diffraction (SC-XRD), electron microprobe analysis (EMPA) and Secondary Ion Mass Spectrometry (SIMS); Mössbauer Spectroscopy (MöS), when feasible, was also applied to minimise the number of unknown variables and uncertainties. Analysed lamproitic samples cover the most important Central Mediterranean type localities, from Plan d'Albard (Western Alps) to Sisco (Corsica), Montecatini Val di Cecina and Orciatico (Tuscany, Italy) and Torre Alfina (Northern Latium, Italy). The studied crystals show distinctive chemical and structural features; all of them belong to the phlogopite-annite join and crystallise in the 1M polytype, except for micas from Torre Alfina, where both 1M and 2M1 polytypes were found. Studied micas have variable but generally high F and Ti contents, with Mg/(Mg + Fe) ranging from 0.5 to 0.9; 2M1 crystals from Torre Alfina radically differ in chemical composition, showing high contents of Ti and Fe as well as of Al in both tetrahedra and octahedra, leading to distinctive structural distortions, especially in tetrahedral sites. SIMS data indicate that studied micas are generally dehydrogenated with OH contents ranging from 0.2 apfu (atoms per formula unit) for Orciatico and Torre Alfina to 1.4 for Plan d'Albard crystals; this feature is also testified by the length of the c parameter, which decreases with the loss of hydrogen and/or the increase of the F → OH substitution. Chemical and structural data suggest that the entry of high charge octahedral cations is mainly balanced by an oxy mechanism and, to a lesser extent, by a M3 +,4 +-Tschermak substitution. Our data confirm that Ti preferentially partitions into the M2 site and that different Ti and F contents, as well as different K/Al values, are both dependant upon fH2O and the composition of magma rather than controlled by P and T

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

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

Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

Energy Technology Data Exchange (ETDEWEB)

Bai, Rekha, E-mail: rekha.mittal07@gmail.com; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K. [Thin Film Laboratory, Physics Department, Indian Institute of Technology Delhi, New Delhi-110016 (India)

2016-05-06

Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.

Structural and optical properties of nano-structured CdS thin films prepared by chemical bath deposition

International Nuclear Information System (INIS)

Bai, Rekha; Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K.

2016-01-01

Cadmium sulfide (CdS) thin films have been deposited on conducting glass substrates by chemical bath deposition (CBD) technique. The effect of precursor concentration on the structural, morphological, compositional, and optical properties of the CdS films has been studied. Crystal structure of these CdS films is characterized by X-ray diffraction (XRD) and it reveals polycrystalline structure with mixture of cubic and wurtzite phases with grain size decreasing as precursor concentration is increased. Optical studies reveal that the CdS thin films have high transmittance in visible spectral region reaching 90% and the films possess direct optical band gap that decreases from 2.46 to 2.39 eV with decreasing bath concentration. Our study suggests that growth is nucleation controlled.

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. �

Identification of putative estrogen receptor-mediated endocrine disrupting chemicals using QSAR- and structure-based virtual screening approaches

International Nuclear Information System (INIS)

Zhang, Liying; Sedykh, Alexander; Tripathi, Ashutosh; Zhu, Hao; Afantitis, Antreas; Mouchlis, Varnavas D.; Melagraki, Georgia; Rusyn, Ivan; Tropsha, Alexander

2013-01-01

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 2 = 0.71, STL R 2 = 0.73). For ERβ binding affinity, MTL models were significantly more predictive (R 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. • The results

Quinones from plants of northeastern Brazil: structural diversity, chemical transformations, NMR data and biological activities.

Science.gov (United States)

Lemos, Telma L G; Monte, Francisco J Q; Santos, Allana Kellen L; Fonseca, Aluisio M; Santos, Hélcio S; Oliveira, Mailcar F; Costa, Sonia M O; Pessoa, Otilia D L; Braz-Filho, Raimundo

2007-05-20

The present review focus in quinones found in species of Brazilian northeastern Capraria biflora, Lippia sidoides, Lippia microphylla and Tabebuia serratifolia. The review cover ethnopharmacological aspects including photography of species, chemical structure feature, NMR datea and biological properties. Chemical transformations of lapachol to form enamine derivatives and biological activities are discussed.

Structure and behavior as determinants: United States nuclear test ban and chemical and biological arms control policy

International Nuclear Information System (INIS)

Reich, J.C.

1991-01-01

US efforts to control chemical and biological warfare and nuclear testing are examined with the aim of explaining the paucity of US backed agreements in these areas. Two theoretical perspectives, the behavioral and structural approaches, are used to explore US arms control outcomes. In the behavioral approach, the effects of governmental organization and the bargaining dynamics of policy-making elites with different cognitive styles are posited as important influences on US nuclear test ban and chemical and biological arms control policy outcomes. The behavioral perspective accounts for the timing of all US failed and successful entries (with one exception) into nuclear test bans and chemical and biological warfare restraints. A shortcoming of the behavior approach, however, is that it tends to overemphasize the chances for successful US entry into nuclear test and chemical and biological warfare limitations. Analysis of the same events from the structural perspective helps to correct for expectations generated by behavioral variables for a higher success rate than ultimately resulted. In the structural approach, the focus is on the effect of the organization of international politics on US nuclear test ban and chemical and biological arms control policy outcomes

Relation between structure and properties of modified starches. Application to the formulation of non-polluting drilling fluids; Relation structure/proprietes d'amidons modifies. Application a la formulation de fluides de forage non polluants

Energy Technology Data Exchange (ETDEWEB)

Dubois, I

1999-12-06

Starch is a polymeric carbohydrate derivative with anhydro-glucose units and is extracted from the tissues of certain plants. In its native form, starch granule is non soluble in cold water and therefore most applications need a cooking period in the presence of an excess of water. The cooking treatment is therefore associated with large changes in viscosity. Overall, starch suspensions properties are strongly influenced by starch botanical origins, shearing and heating conditions under which they are prepared. Their properties can be modulated though chemical modifications depending on their uses in the petroleum industry. This study focuses on the relations between structure and physico-chemical, rheological and filtration properties of modified starches. These starches are originated from native potato, i. e. hydroxy-propyl and/or crosslinked starches above or below the gelatinization temperature. The samples were characterised in terms of swelling capacity, average granule size distribution and molecular weight. Microscopic methods were used to investigate starch structure. Relations were established between the rheological properties and the physico-chemical parameters. These properties are governed by the deformability and rigidity parameters as a function of the concentration. The best samples were then chosen and were submitted to the high temperature (140 deg. C - 160 deg. C), high shearing (16000 tr/ mn) and salinity (CaCl{sub 2}, 1M). The physico-chemical and rheological studies showed that the starch system which is crosslinked below the gelatinization temperature is more resistant that the samples crosslinked above the gelatinization temperature. Then, a drilling fluid formulation was investigated. The filtration results evidenced an increase of the cake permeability in the presence of starch particles but the good stability of these samples permits their uses for high temperature. Thus, non crosslinked / crosslinked starch mixtures were investigated

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

Energy Technology Data Exchange (ETDEWEB)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States); Assadi, Amir [University of Wisconsin-Madison, Mathematics Department (United States); Markley, John L. [National Magnetic Resonance Facility at Madison, Biochemistry Department (United States)], E-mail: eghbalni@nmrfam.wisc.edu

2005-05-15

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states.

Protein energetic conformational analysis from NMR chemical shifts (PECAN) and its use in determining secondary structural elements

International Nuclear Information System (INIS)

Eghbalnia, Hamid R.; Wang Liya; Bahrami, Arash; Assadi, Amir; Markley, John L.

2005-01-01

We present an energy model that combines information from the amino acid sequence of a protein and available NMR chemical shifts for the purposes of identifying low energy conformations and determining elements of secondary structure. The model ('PECAN', Protein Energetic Conformational Analysis from NMR chemical shifts) optimizes a combination of sequence information and residue-specific statistical energy function to yield energetic descriptions most favorable to predicting secondary structure. Compared to prior methods for secondary structure determination, PECAN provides increased accuracy and range, particularly in regions of extended structure. Moreover, PECAN uses the energetics to identify residues located at the boundaries between regions of predicted secondary structure that may not fit the stringent secondary structure class definitions. The energy model offers insights into the local energetic patterns that underlie conformational preferences. For example, it shows that the information content for defining secondary structure is localized about a residue and reaches a maximum when two residues on either side are considered. The current release of the PECAN software determines the well-defined regions of secondary structure in novel proteins with assigned chemical shifts with an overall accuracy of 90%, which is close to the practical limit of achievable accuracy in classifying the states

Influence of encapsulated functional lipids on crystal structure and chemical stability in solid lipid nanoparticles: Towards bioactive-based design of delivery systems.

Science.gov (United States)

Salminen, Hanna; Gömmel, Christina; Leuenberger, Bruno H; Weiss, Jochen

2016-01-01

We investigated the influence of physicochemical properties of encapsulated functional lipids--vitamin A, β-carotene and ω-3 fish oil--on the structural arrangement of solid lipid nanoparticles (SLN). The relationship between the crystal structure and chemical stability of the incorporated bioactive lipids was evaluated with different emulsifier compositions of a saponin-rich, food-grade Quillaja extract alone or combined with high-melting or low-melting lecithins. The major factors influencing the structural arrangement and chemical stability of functional lipids in solid lipid dispersions were their solubility in the aqueous phase and their crystallization temperature in relation to that of the carrier lipid. The results showed that the stabilization of the α-subcell crystals in the lattice of the carrier lipid is a key parameter for forming stable solid lipid dispersions. This study contributes to a better understanding of SLN as a function of the bioactive lipid. Copyright © 2015 Elsevier Ltd. All rights reserved.

The 5S rRNA loop E: chemical probing and phylogenetic data versus crystal structure.

Science.gov (United States)

Leontis, N B; Westhof, E

1998-09-01

A significant fraction of the bases in a folded, structured RNA molecule participate in noncanonical base pairing interactions, often in the context of internal loops or multi-helix junction loops. The appearance of each new high-resolution RNA structure provides welcome data to guide efforts to understand and predict RNA 3D structure, especially when the RNA in question is a functionally conserved molecule. The recent publication of the crystal structure of the "Loop E" region of bacterial 5S ribosomal RNA is such an event [Correll CC, Freeborn B, Moore PB, Steitz TA, 1997, Cell 91:705-712]. In addition to providing more examples of already established noncanonical base pairs, such as purine-purine sheared pairings, trans-Hoogsteen UA, and GU wobble pairs, the structure provides the first high-resolution views of two new purine-purine pairings and a new GU pairing. The goal of the present analysis is to expand the capabilities of both chemical probing and phylogenetic analysis to predict with greater accuracy the structures of RNA molecules. First, in light of existing chemical probing data, we investigate what lessons could be learned regarding the interpretation of this widely used method of RNA structure probing. Then we analyze the 3D structure with reference to molecular phylogeny data (assuming conservation of function) to discover what alternative base pairings are geometrically compatible with the structure. The comparisons between previous modeling efforts and crystal structures show that the intricate involvements of ions and water molecules in the maintenance of non-Watson-Crick pairs render the process of correctly identifying the interacting sites in such pairs treacherous, except in cases of trans-Hoogsteen A/U or sheared A/G pairs for the adenine N1 site. The phylogenetic analysis identifies A/A, A/C, A/U and C/A, C/C, and C/U pairings isosteric with sheared A/G, as well as A/A and A/C pairings isosteric with both G/U and G/G bifurcated pairings

Imaging, structural, and chemical analysis of silicon nanowires

International Nuclear Information System (INIS)

Barsotti, R.J. Jr.; Fischer, J.E.; Lee, C.H.; Mahmood, J.; Adu, C.K.W.; Eklund, P.C.

2002-01-01

Laser ablation has been used to grow silicon nanowires with an average silicon crystal core diameter of 6.7 nm±2.9 nm surrounded by an amorphous SiO x sheath of 1-2 nm, the smallest silicon wires reported in the literature. Imaging, chemical, and structural analysis of these wires are reported. Due to the growth temperature and the presence of calcium impurities and trace oxygen, two distinct types of wires are found. They appear to grow by two different processes. One requires a metal catalyst, the other is catalyzed by oxygen. Suggestions for controlled synthesis based on these growth mechanisms are made

Anti-trypanosomal activities and structural chemical properties of selected compound classes.

Science.gov (United States)

Ponte-Sucre, Alicia; Bruhn, Heike; Schirmeister, Tanja; Cecil, Alexander; Albert, Christian R; Buechold, Christian; Tischer, Maximilian; Schlesinger, Susanne; Goebel, Tim; Fuß, Antje; Mathein, Daniela; Merget, Benjamin; Sotriffer, Christoph A; Stich, August; Krohne, Georg; Engstler, Markus; Bringmann, Gerhard; Holzgrabe, Ulrike

2015-02-01

Potent compounds do not necessarily make the best drugs in the market. Consequently, with the aim to describe tools that may be fundamental for refining the screening of candidates for animal and preclinical studies and further development, molecules of different structural classes synthesized within the frame of a broad screening platform were evaluated for their trypanocidal activities, cytotoxicities against murine macrophages J774.1 and selectivity indices, as well as for their ligand efficiencies and structural chemical properties. To advance into their modes of action, we also describe the morphological and ultrastructural changes exerted by selected members of each compound class on the parasite Trypanosoma brucei. Our data suggest that the potential organelles targeted are either the flagellar pocket (compound 77, N-Arylpyridinium salt; 15, amino acid derivative with piperazine moieties), the endoplasmic reticulum membrane systems (37, bisquaternary bisnaphthalimide; 77, N-Arylpyridinium salt; 68, piperidine derivative), or mitochondria and kinetoplasts (88, N-Arylpyridinium salt; 68, piperidine derivative). Amino acid derivatives with fumaric acid and piperazine moieties (4, 15) weakly inhibiting cysteine proteases seem to preferentially target acidic compartments. Our results suggest that ligand efficiency indices may be helpful to learn about the relationship between potency and chemical characteristics of the compounds. Interestingly, the correlations found between the physico-chemical parameters of the selected compounds and those of commercial molecules that target specific organelles indicate that our rationale might be helpful to drive compound design toward high activities and acceptable pharmacokinetic properties for all compound families.

Chemical and structural order in silicon oxynitrides by methods of surface physics

Science.gov (United States)

Finster, J.; Heeg, J.; Klinkenberg, E.-D.

A large number of thin amorphous layers of SiO xN y and several (crystalline) reference compounds (SiO 2, Si 3N 4, Si 2N 2O) are studied. Although XANES and SEXAFS are well sulted to derive structural and chemical order, for these compounds many problems remain to be solved. We show how core level spectra (XPS, AES) can be used to gain such information (e.g. random bonding structure, N coordination, oxidation behaviour).

Reactions driving conformational movements (molecular motors) in gels: conformational and structural chemical kinetics.

Science.gov (United States)

Otero, Toribio F

2017-01-18

In this perspective the empirical kinetics of conducting polymers exchanging anions and solvent during electrochemical reactions to get dense reactive gels is reviewed. The reaction drives conformational movements of the chains (molecular motors), exchange of ions and solvent with the electrolyte and structural (relaxation, swelling, shrinking and compaction) gel changes. Reaction-driven structural changes are identified and quantified from electrochemical responses. The empirical reaction activation energy (E a ), the reaction coefficient (k) and the reaction orders (α and β) change as a function of the conformational energy variation during the reaction. This conformational energy becomes an empirical magnitude. E a , k, α and β include and provide quantitative conformational and structural information. The chemical kinetics becomes structural chemical kinetics (SCK) for reactions driving conformational movements of the reactants. The electrochemically stimulated conformational relaxation model describes empirical results and some results from the literature for biochemical reactions. In parallel the development of an emerging technological world of soft, wet, multifunctional and biomimetic tools and anthropomorphic robots driven by reactions of the constitutive material, as in biological organs, can be now envisaged being theoretically supported by the kinetic model.

Physico-chemical findings related to the resilience of different soils ...

African Journals Online (AJOL)

As part of an interdisciplinary study on Sustainable Agriculture in semiarid Areas (SASA) in south-central Tanzania, soils from five different locations were investigated for their mineralogical composition and physico-chemical characteristics in order to determine their resilience in relation to land use. The results of the ...

Cell behavior related to implant surfaces with different microstructure and chemical composition: an in vitro analysis.

Science.gov (United States)

Conserva, Enrico; Lanuti, Anna; Menini, Maria

2010-01-01

This paper reports on an in vitro comparison of osteoblast and mesenchymal stem cell (MSC) adhesion, proliferation, and differentiation related to two different surface treatments applied to the same implant design to determine whether the interaction between cells and implants is influenced by surface structure and chemical composition of the implants. Thirty-nine implants with a sandblasted (SB) surface and 39 implants with a grit-blasted and high-temperature acid-etched (GBAE) surface were used. The implant macrostructures and microstructures were analyzed by high- and low-voltage scanning electron microscopy (SEM) and by stereo-SEM. The surface chemical composition was investigated by energy dispersive analysis and x-ray photoemission spectroscopy. SaOS-2 osteoblasts and human MSCs were used for the evaluation of cell proliferation and alkaline phosphatase enzymatic activity in contact with the two surfaces. The GBAE surface showed fewer contaminants and a very high percentage of titanium (19.7%) compared to the SB surface (14.2%). The two surfaces showed similar mean roughness (Ra), but the depth (Rz) and density (RSm) of the porosity were significantly increased in the GBAE surface. The GBAE surface presented more osteoblast and MSC proliferation than the SB surface. No statistically significant differences in alkaline phosphatase activity were found between surfaces for either cellular line. The GBAE surface showed less surface contaminants and a higher percentage of titanium (19.7%) than the SB surface. The macro/micropore structured design and chemical composition of the GBAE surface allowed greater cell adhesion and proliferation and an earlier cell spreading but did not play an obvious role in in vitro cellular differentiation.

Electronic structure imperfections and chemical bonding at graphene interfaces

Science.gov (United States)

Schultz, Brian Joseph

The manifestation of novel phenomena upon scaling to finite size has inspired a paradigm shift in materials science that takes advantage of the distinctive electrical and physical properties of nanomaterials. Remarkably, the simple honeycomb arrangement of carbon atoms in a single atomic layer has become renowned for exhibiting never-before-seen electronic and physical phenomena. This archetypal 2-dimensional nanomaterial is known as graphene, a single layer of graphite. Early reports in the 1950's eluded to graphene-like nanostructures that were evidenced from exfoliation of oxidized graphite followed by chemical reduction, absorbed carbon on transition metals, and thermal decomposition of SiC. Furthermore, the earliest tight binding approximation calculations in the 1950's held clues that a single-layer of graphite would behave drastically different than bulk graphite. Not until 2004, when Giem and Novoselov first synthesized graphene by mechanical exfoliation from highly-oriented pyrolytic graphite did the field of graphene-based research bloom within the scientific community. Since 2004, the availability and relatively straight forward synthesis of single-layer graphene (SLG) enabled the observation of remarkable phenomena including: massless Dirac fermions, extremely high mobilities of its charge carriers, room temperature half-integer quantum Hall effect, the Rashba effect, and the potential for ballistic conduction over macroscopic distances. These enticing electronic properties produce the drive to study graphene for use in truly nanoscale electrical interconnects, integrated circuits, transparent conducting electrodes, ultra-high frequency transistors, and spintronic devices, just to name a few. Yet, for almost all real world applications graphene will need to be interfaced with other materials, metals, dielectrics, organics, or any combination thereof that in turn are constituted from various inorganic and organic components. Interfacing graphene, a

Modelling of structural effects on chemical reactions in turbulent flows

Energy Technology Data Exchange (ETDEWEB)

Gammelsaeter, H.R.

1997-12-31

Turbulence-chemistry interactions are analysed using algebraic moment closure for the chemical reaction term. The coupling between turbulence and chemical length and time scales generate a complex interaction process. This interaction process is called structural effects in this work. The structural effects are shown to take place on all scales between the largest scale of turbulence and the scales of the molecular motions. The set of equations describing turbulent correlations involved in turbulent reacting flows are derived. Interactions are shown schematically using interaction charts. Algebraic equations for the turbulent correlations in the reaction rate are given using the interaction charts to include the most significant couplings. In the frame of fundamental combustion physics, the structural effects appearing on the small scales of turbulence are proposed modelled using a discrete spectrum of turbulent scales. The well-known problem of averaging the Arrhenius law, the specific reaction rate, is proposed solved using a presumed single variable probability density function and a sub scale model for the reaction volume. Although some uncertainties are expected, the principles are addressed. Fast chemistry modelling is shown to be consistent in the frame of algebraic moment closure when the turbulence-chemistry interaction is accounted for in the turbulent diffusion. The modelling proposed in this thesis is compared with experimental data for an laboratory methane flame and advanced probability density function modelling. The results show promising features. Finally it is shown a comparison with full scale measurements for an industrial burner. All features of the burner are captured with the model. 41 refs., 33 figs.

Chemical constituents of Sweetpotato genotypes in relation to textural characteristics of processed French fries

Science.gov (United States)

Sweetpotato French fries (SPFF) are growing in popularity but limited information is available on SPFF textural properties in relation to chemical composition. This study aimed to investigate the relationship between chemical components of different sweetpotato varieties and textural characteristics...

Predicting allergic contact dermatitis: a hierarchical structure activity relationship (SAR) approach to chemical classification using topological and quantum chemical descriptors

Science.gov (United States)

Basak, Subhash C.; Mills, Denise; Hawkins, Douglas M.

2008-06-01

A hierarchical classification study was carried out based on a set of 70 chemicals—35 which produce allergic contact dermatitis (ACD) and 35 which do not. This approach was implemented using a regular ridge regression computer code, followed by conversion of regression output to binary data values. The hierarchical descriptor classes used in the modeling include topostructural (TS), topochemical (TC), and quantum chemical (QC), all of which are based solely on chemical structure. The concordance, sensitivity, and specificity are reported. The model based on the TC descriptors was found to be the best, while the TS model was extremely poor.

Weighted similarity-based clustering of chemical structures and bioactivity data in early drug discovery.

Science.gov (United States)

Perualila-Tan, Nolen Joy; Shkedy, Ziv; Talloen, Willem; Göhlmann, Hinrich W H; Moerbeke, Marijke Van; Kasim, Adetayo

2016-08-01

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

Physical and chemical processes for the generation of 1-μm-structures

International Nuclear Information System (INIS)

Mader, L.

1979-01-01

The following processes for the realization of fine structures in isolator and metal layers on silicon wafers have been studied: Wet chemical etching of silicon dioxide and aluminum layers; plasma etching of polysilicon layers; ion beam etching of silicon dioxide and polysilicon layers, lift-off technique for metal pattern generation. Test structures and functioning integrated circuits (memory cells, CCDs) with minimum dimensions of 1.5 μm were realized using these methods of pattern generation. (orig.) 891 ORU/orig. 892 MB [de

Plant Sterols: Chemical and Enzymatic Structural Modifications and Effects on Their Cholesterol-Lowering Activity.

Science.gov (United States)

He, Wen-Sen; Zhu, Hanyue; Chen, Zhen-Yu

2018-03-28

Plant sterols have attracted increasing attention due to their excellent cholesterol-lowering activity. However, free plant sterols have some characteristics of low oil solubility, water insolubility, high melting point, and low bioavailability, which greatly limit their application in foods. Numerous studies have been undertaken to modify their chemical structures to improve their chemical and physical properties in meeting the needs of various applications. The present review is to summarize the literature and update the progress on structural modifications of plant sterols in the following aspects: (i) synthesis of plant sterol esters by esterification and transesterification with hydrophobic fatty acids and triacylglycerols to improve their oil solubility, (ii) synthesis of plant sterol derivatives by coupling with various hydrophilic moieties to enhance their water solubility, and (iii) mechanisms by which plant sterols reduce plasma cholesterol and the effect of structural modifications on plasma cholesterol-lowering activity of plant sterols.

Relation between structure and properties of modified starches. Application to the formulation of non-polluting drilling fluids; Relation structure/proprietes d'amidons modifies. Application a la formulation de fluides de forage non polluants

Energy Technology Data Exchange (ETDEWEB)

Dubois, I.

1999-12-06

Starch is a polymeric carbohydrate derivative with anhydro-glucose units and is extracted from the tissues of certain plants. In its native form, starch granule is non soluble in cold water and therefore most applications need a cooking period in the presence of an excess of water. The cooking treatment is therefore associated with large changes in viscosity. Overall, starch suspensions properties are strongly influenced by starch botanical origins, shearing and heating conditions under which they are prepared. Their properties can be modulated though chemical modifications depending on their uses in the petroleum industry. This study focuses on the relations between structure and physico-chemical, rheological and filtration properties of modified starches. These starches are originated from native potato, i. e. hydroxy-propyl and/or crosslinked starches above or below the gelatinization temperature. The samples were characterised in terms of swelling capacity, average granule size distribution and molecular weight. Microscopic methods were used to investigate starch structure. Relations were established between the rheological properties and the physico-chemical parameters. These properties are governed by the deformability and rigidity parameters as a function of the concentration. The best samples were then chosen and were submitted to the high temperature (140 deg. C - 160 deg. C), high shearing (16000 tr/ mn) and salinity (CaCl{sub 2}, 1M). The physico-chemical and rheological studies showed that the starch system which is crosslinked below the gelatinization temperature is more resistant that the samples crosslinked above the gelatinization temperature. Then, a drilling fluid formulation was investigated. The filtration results evidenced an increase of the cake permeability in the presence of starch particles but the good stability of these samples permits their uses for high temperature. Thus, non crosslinked / crosslinked starch mixtures were investigated

Chemical engineering and structural and pharmacological characterization of the α-scorpion toxin OD1.

Science.gov (United States)

Durek, Thomas; Vetter, Irina; Wang, Ching-I Anderson; Motin, Leonid; Knapp, Oliver; Adams, David J; Lewis, Richard J; Alewood, Paul F

2013-01-01

Scorpion α-toxins are invaluable pharmacological tools for studying voltage-gated sodium channels, but few structure-function studies have been undertaken due to their challenging synthesis. To address this deficiency, we report a chemical engineering strategy based upon native chemical ligation. The chemical synthesis of α-toxin OD1 was achieved by chemical ligation of three unprotected peptide segments. A high resolution X-ray structure (1.8 Å) of synthetic OD1 showed the typical βαββ α-toxin fold and revealed important conformational differences in the pharmacophore region when compared with other α-toxin structures. Pharmacological analysis of synthetic OD1 revealed potent α-toxin activity (inhibition of fast inactivation) at Nav1.7, as well as Nav1.4 and Nav1.6. In addition, OD1 also produced potent β-toxin activity at Nav1.4 and Nav1.6 (shift of channel activation in the hyperpolarizing direction), indicating that OD1 might interact at more than one site with Nav1.4 and Nav1.6. Investigation of nine OD1 mutants revealed that three residues in the reverse turn contributed significantly to selectivity, with the triple OD1 mutant (D9K, D10P, K11H) being 40-fold more selective for Nav1.7 over Nav1.6, while OD1 K11V was 5-fold more selective for Nav1.6 than Nav1.7. This switch in selectivity highlights the importance of the reverse turn for engineering α-toxins with altered selectivity at Nav subtypes.

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.

Chemical and structural properties of polymorphous silicon thin films grown from dichlorosilane

Energy Technology Data Exchange (ETDEWEB)

Álvarez-Macías, C.; Monroy, B.M.; Huerta, L.; Canseco-Martínez, M.A. [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico); Picquart, M. [Departamento de Física, Universidad Autónoma Metropolitana, Iztapalapa, A.P. 55-534, 09340 México, D.F. (Mexico); Santoyo-Salazar, J. [Departamento de Física, CINVESTAV-IPN, A.P. 14-740, C.P. 07000 México, D.F. (Mexico); Sánchez, M.F. García [Unidad Profesional Interdisciplinaria en Ingeniería y Tecnologías Avanzadas, Instituto Politécnico Nacional, Av. I.P.N. 2580, Gustavo A. Madero, 07340 México .D.F. (Mexico); Santana, G., E-mail: gsantana@iim.unam.mx [Instituto de Investigaciones en Materiales, Universidad Nacional Autónoma de México, A.P. 70-360, Coyoacán, C.P. 04510 México, D.F. (Mexico)

2013-11-15

We have examined the effects of hydrogen dilution (R{sub H}) and deposition pressure on the morphological, structural and chemical properties of polymorphous silicon thin films (pm-Si:H), using dichlorosilane as silicon precursor in the plasma enhanced chemical vapor deposition (PECVD) process. The use of silicon chlorinated precursors enhances the crystallization process in as grown pm-Si:H samples, obtaining crystalline fractions from Raman spectra in the range of 65–95%. Atomic Force Microscopy results show the morphological differences obtained when the chlorine chemistry dominates the growth process and when the plasma–surface interactions become more prominent. Augmenting R{sub H} causes a considerable reduction in both roughness and topography, demonstrating an enhancement of ion bombardment and attack of the growing surface. X-ray Photoelectron Spectroscopy results show that, after ambient exposure, there is low concentration of oxygen inside the films grown at low R{sub H}, present in the form of Si-O, which can be considered as structural defects. Instead, oxidation increases with deposition pressure and dilution, along with film porosity, generating a secondary SiO{sub x} phase. For higher pressure and dilution, the amount of chlorine incorporated to the film decreases congruently with HCl chlorine extraction processes involving atomic hydrogen interactions with the surface. In all cases, weak silicon hydride (Si-H) bonds were not detected by infrared spectroscopy, while bonding configurations associated to the silicon nanocrystal surface were clearly observed. Since these films are generally used in photovoltaic devices, analyzing their chemical and structural properties such as oxygen incorporation to the films, along with chlorine and hydrogen, is fundamental in order to understand and optimize their electrical and optical properties.

Double-Layer Structured CO2 Adsorbent Functionalized with Modified Polyethyleneimine for High Physical and Chemical Stability.

Science.gov (United States)

Jeon, Sunbin; Jung, Hyunchul; Kim, Sung Hyun; Lee, Ki Bong

2018-06-18

CO 2 capture using polyethyleneimine (PEI)-impregnated silica adsorbents has been receiving a lot of attention. However, the absence of physical stability (evaporation and leaching of amine) and chemical stability (urea formation) of the PEI-impregnated silica adsorbent has been generally established. Therefore, in this study, a double-layer impregnated structure, developed using modified PEI, is newly proposed to enhance the physical and chemical stabilities of the adsorbent. Epoxy-modified PEI and diepoxide-cross-linked PEI were impregnated via a dry impregnation method in the first and second layers, respectively. The physical stability of the double-layer structured adsorbent was noticeably enhanced when compared to the conventional adsorbents with a single layer. In addition to the enhanced physical stability, the result of simulated temperature swing adsorption cycles revealed that the double-layer structured adsorbent presented a high potential working capacity (3.5 mmol/g) and less urea formation under CO 2 -rich regeneration conditions. The enhanced physical and chemical stabilities as well as the high CO 2 working capacity of the double-layer structured adsorbent were mainly attributed to the second layer consisting of diepoxide-cross-linked PEI.

THE CHEMICAL EVOLUTION OF THE MONOCEROS RING/GALACTIC ANTICENTER STELLAR STRUCTURE

International Nuclear Information System (INIS)

Chou Meiyin; Majewski, Steven R.; Patterson, Richard J.; Cunha, Katia; Smith, Verne V.; MartInez-Delgado, David

2010-01-01

The origin of the Galactic Anticenter Stellar Structure (GASS) or 'Monoceros Ring' - a low-latitude overdensity at the edge of the Galactic disk spanning at least the second and third Galactic quadrants-remains controversial. Models for the origin of GASS generally fall into scenarios where either it is a part (e.g., warp) of the Galactic disk or it represents tidal debris from the disruption of a Milky Way (MW) satellite galaxy. To further constrain models for the origin of GASS, we derive chemical abundance patterns from high-resolution spectra for 21 M giants spatially and kinematically identified with it. The abundances of the (mostly) α-element, titanium, and s-process elements, yttrium and lanthanum, for these GASS stars are found to be lower at the same [Fe/H] than those for MW stars, but similar to those of stars in the Sagittarius stream, other dwarf spheroidal galaxies, and the Large Magellanic Cloud. This demonstrates that GASS stars have a chemical enrichment history typical of dwarf galaxies-and unlike those of typical MW stars (at least MW stars near the Sun). Nevertheless, these abundance results cannot definitively rule out the possibility that GASS was dynamically created out of a previously formed, outer MW disk because ΛCDM-based structure formation models show that galactic disks grow outward by accretion of dwarf galaxies. On the other hand, the chemical patterns seen in GASS stars do provide striking verification that accretion of dwarf galaxies has indeed happened at the edge of the MW disk.

Combustion flame-plasma hybrid reactor systems, and chemical reactant sources

Science.gov (United States)

Kong, Peter C

2013-11-26

Combustion flame-plasma hybrid reactor systems, chemical reactant sources, and related methods are disclosed. In one embodiment, a combustion flame-plasma hybrid reactor system comprising a reaction chamber, a combustion torch positioned to direct a flame into the reaction chamber, and one or more reactant feed assemblies configured to electrically energize at least one electrically conductive solid reactant structure to form a plasma and feed each electrically conductive solid reactant structure into the plasma to form at least one product is disclosed. In an additional embodiment, a chemical reactant source for a combustion flame-plasma hybrid reactor comprising an elongated electrically conductive reactant structure consisting essentially of at least one chemical reactant is disclosed. In further embodiments, methods of forming a chemical reactant source and methods of chemically converting at least one reactant into at least one product are disclosed.

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

International Nuclear Information System (INIS)

Vetere, V.

2002-09-01

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 X 3 M-L species (X=F, Cl; M=La, Nd, U; L = NH 3 , 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)

Investigation of electronic structure and chemical bonding of intermetallic Pd2HfIn: An ab-initio study

Science.gov (United States)

Bano, Amreen; Gaur, N. K.

2018-05-01

Ab-initio calculations are carried out to study the electronic and chemical bonding properties of Intermetallic full Heusler compound Pd2HfIn which crystallizes in F-43m structure. All calculations are performed by using density functional theory (DFT) based code Quantum Espresso. Generalized gradient approximations (GGA) of Perdew- Burke- Ernzerhof (PBE) have been adopted for exchange-correlation potential. Calculated electronic band structure reveals the metallic character of the compound. From partial density of states (PDoS), we found the presence of relatively high intensity electronic states of 4d-Pd atom at Fermi level. We have found a pseudo-gap just abouve the Fermi level and N(E) at Fermi level is observed to be 0.8 states/eV, these finding indicates the existence of superconducting character in Pd2HfIn.

Three-dimensionality of space in the structure of the periodic table of chemical elements

International Nuclear Information System (INIS)

Veremeichik, T. F.

2006-01-01

The effect of the dimension of the 3D homogeneous and isotropic Euclidean space, and the electron spin on the self-organization of the electron systems of atoms of chemical elements is considered. It is shown that the finite dimension of space creates the possibility of periodicity in the structure of an electron cloud, while the value of the dimension determines the number of stable systems of electrons at different levels of the periodic table of chemical elements and some characteristics of the systems. The conditions for the stability of systems of electrons and the electron system of an atom as a whole are considered. On the basis of the results obtained, comparison with other hierarchical systems (nanostructures and biological structures) is performed

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 spec......, indicate apparent variation of the ceria valence state across and along the film. No element segregation to the grain boundaries is detected. These results are discussed in the context of solid oxide fuel cell applications.......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...

Chemical structure and properties of low-molecular furin inhibitors

Directory of Open Access Journals (Sweden)

T. V. Osadchuk

2016-12-01

Full Text Available The review is devoted to the analysis of the relationship between a chemical structure and properties of low-molecular weight inhibitors of furin, the most studied proprotein convertase, which is involved in the development of some pathologies, such as oncologic diseases, viral and bacterial infections, etc. The latest data concerning the influence of peptides, pseudo-peptides, aromatic and heterocyclic compounds, some natural ones such as flavonoids, coumarins, and others on enzyme inactivation are considered. The power of furin inhibition is shown to rise with the increasing number of positively charged groups in the structure of these compounds. Peptidomimetics (Ki = 5-8 pM are shown to be the most effective furin inhibitors. The synthesized substances, however, have not been used in practical application yet. Nowadays it is very important to find more selective inhibitors, improve their stability, bioavailability and safety for the human organism.

A phenomenological model for the structure-composition relationship of the high Tc cuprates based on simple chemical principles

International Nuclear Information System (INIS)

Alarco, J.A.; Talbot, P.C.

2012-01-01

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 d 8 and d 9 ) 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.

On the thermal phase structure of QCD at vanishing chemical potentials

CERN Document Server

Kabana, S

2011-01-01

The hypothesis is investigated, that the thermal structure of QCD phases at and near zero chemical potentials is determined by long range coherence, inducing the gauge boson pair condensate. The latter reflects the dynamical nature of gauge boson Bogoliubov transformations at the origin of localization of all color fields inside hadrons at low temperature in contrast to loss of such localization above a unique critical temperature.

A Comprehensive Approach for Pectin Chemical and Functional Characterization

DEFF Research Database (Denmark)

de Sousa, António Felipe Gomes Teixeira

In this work, a comprehensive approach for the chemical and functional analysis of pectin was used in order to relate the different extraction conditions used to the polymer structure and the final functional (mainly gelling) properties. A wide range of methods were utilized including chemical an...

Uranium complexes with macrosyclic polyethers. Synthesis and structural chemical analysis

International Nuclear Information System (INIS)

Elbasyouny, A.

1983-01-01

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 1 H-NMR and 13 C-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 H 2 O molecules per formula unit. (orig./EF) [de

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

Energy Technology Data Exchange (ETDEWEB)

Gosavi, S.R., E-mail: srgosavi.taloda@gmail.com [C. H. C. Arts, S. G. P. Commerce, and B. B. J. P. Science College, Taloda, Dist., Nandurbar 425413, M. S. (India); Nikam, C.P. [B.S.S.P.M.S. Arts, Commerce and Science College, Songir, Dist., Dhule 424309, M. S. (India); Shelke, A.R.; Patil, A.M. [Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India); Ryu, S.-W. [Department of Physics, Chonnam National University, Gwangju 500-757 (Korea, Republic of); Bhat, J.S. [Department of Physics, Karnatak University, Dharwad 580003 (India); Deshpande, N.G., E-mail: nicedeshpande@yahoo.co.in [Department of Physics, Shivaji University, Kolhapur 416004, M.S. (India)

2015-06-15

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.

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

International Nuclear Information System (INIS)

Gosavi, S.R.; Nikam, C.P.; Shelke, A.R.; Patil, A.M.; Ryu, S.-W.; Bhat, J.S.; Deshpande, N.G.

2015-01-01

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

MIMO Self-Tuning Control of Chemical Process Operation

DEFF Research Database (Denmark)

Hallager, L.; Jørgensen, S. B.; Goldschmidt, L.

1984-01-01

The problem of selecting a feasible model structure for a MIMO self-tuning controller (MIMOSC) is addressed. The dependency of the necessary structure complexity in relation to the specific process operating point is investigated. Experimental results from a fixed-bed chemical reactor are used...

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...

Innovative Strategies to Develop Chemical Categories Using a Combination of Structural and Toxicological Properties

Directory of Open Access Journals (Sweden)

Monika Batke

2016-09-01

Full Text Available 1.AbstractInterest is increasing in the development of non-animal methods for toxicological evaluations. These methods are however, particularly challenging for complex toxicological endpoints such as repeated dose toxicity. European Legislation, e.g. the European Union´s Cosmetic Directive and REACH, demands the use of alternative methods. Frameworks, such as the Read-across Assessment Framework or the Adverse Outcome Pathway Knowledge Base, support the development of these methods. The aim of the project presented in this publication was to develop substance categories for a read-across with complex endpoints of toxicity based on existing databases. The basic conceptual approach was to combine structural similarity with shared mechanisms of action. Substances with similar chemical structure and toxicological profile form candidate categories suitable for read-across. We combined two databases on repeated dose toxicity, RepDose database and ELINCS database to form a common database for the identification of categories. The resulting database contained physicochemical, structural and toxicological data, which were refined and curated for cluster analyses. We applied the Predictive Clustering Tree (PCT approach for clustering chemicals based on structural and on toxicological information to detect groups of chemicals with similar toxic profiles and pathways/mechanisms of toxicity. As many of the experimental toxicity values were not available, this data was imputed by predicting them with a multi-label classification method, prior to clustering. The clustering results were evaluated by assessing chemical and toxicological similarities with the aim of identifying clusters with a concordance between structural information and toxicity profiles/mechanisms. From these chosen clusters, seven were selected for a quantitative read-across, based on a small ratio of NOAEL of the members with the highest and the lowest NOAEL in the cluster (<5. We discuss

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

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

International Nuclear Information System (INIS)

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

2010-01-01

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 ( 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 1 H-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 1 H-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

Replication of noise-sustained autocatalytic chemical structures.

Science.gov (United States)

Izús, Gonzalo G; Deza, Roberto R; Sánchez, Alejandro D

2010-06-21

Autocatalytic systems in a differential-flow reactor may undergo a differential-flow-induced chemical instability toward a convectively unstable regime, in which noise-sustained structures may appear. This is the case of a system with Gray-Scott kinetics in a packed-bed reactor, as reported in [B. von Haeften and G. Izus, Phys. Rev. E 67, 056207 (2003)]. In this work, two identical copies of such a system are coupled in master-slave configuration and submitted to independent spatiotemporal Gaussian white noise sources. Numerical simulation of two-dimensional reactors with uniform and Poiseuille flows reveals that the slave system replicates to a very high degree of precision and the convective patterns arising in the master one due to the presence of noise. The quality of this synchronization is assessed through several measures. A convective instability in the synchronization manifold is theoretically predicted and numerically confirmed.

Hybrid carrageenans: isolation, chemical structure, and gel properties.

Science.gov (United States)

Hilliou, Loic

2014-01-01

Hybrid carrageenan is a special class of carrageenan with niche application in food industry. This polysaccharide is extracted from specific species of seaweeds belonging to the Gigartinales order. This chapter focuses on hybrid carrageenan showing the ability to form gels in water, which is known in the food industry as weak kappa or kappa-2 carrageenan. After introducing the general chemical structure defining hybrid carrageenan, the isolation of the polysaccharide will be discussed focusing on the interplay between seaweed species, extraction parameters, and the hybrid carrageenan chemistry. Then, the rheological experiments used to determine the small and large deformation behavior of gels will be detailed before reviewing the relationships between gel properties and hybrid carrageenan chemistry. © 2014 Elsevier Inc. All rights reserved.

Cross-cultural structures of concentric and diametric dualism in Lévi-Strauss' structural anthropology: structures of relation underlying the self and ego relation?

Science.gov (United States)

Downes, Paul

2003-02-01

The parallels between Jung's and Lévi-Strauss' concentric cross-cultural structures of the unconscious are highlighted. Lévi-Strauss' basic contrasts between concentric and diametric dualisms are developed into psychologically relevant differences regarding symmetry, connection and separation, and interaction between foreground and background structures respectively. These contrasts between concentric and diametric structures are applied as a common structural framework for understanding Jungian conceptions of the self, the ego and their relations, Freudian views of compensation and repetition in obsessional neurosis, and Winnicott's conception of a child's transitional object. Developing the contrasts between concentric and diametric structures reveals a compensatory relation between both structures. This supports an argument that concentric structures express the self and diametric structures express the ego in their mutual compensatory interrelation. Contrasting concentric with diametric structures challenges traditional Western logic, including Fordham's view that it is contradictory to treat the self as both centre and totality. It also develops an understanding of Jung's transcendent function which seeks to go beyond the ego-shadow opposition.

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.

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

Chemical reactivity of cation-exchanged zeolites

OpenAIRE

Pidko, E.A.

2008-01-01

Zeolites modified with metal cations have been extensively studied during the last two decades because of their wide application in different technologically important fields such as catalysis, adsorption and gas separation. Contrary to the well-understood mechanisms of chemical reactions catalyzed by Brønsted acid sites in the hydrogen forms of zeolites, the nature of chemical reactivity, and related, the structure of the metal-containing ions in cation-exchanged zeolites remains the subject...

Role of graphene on the surface chemical reactions of BiPO4-rGO with low OH-related defects.

Science.gov (United States)

Gao, Erping; Wang, Wenzhong

2013-11-21

Graphene has been widely introduced into photocatalysis to enhance photocatalytic performance due to its unique physical and chemical properties. However, the effect of graphene on the surface chemical reactions of photocatalysis has not been clearly researched, which is important for photocatalysis because photocatalytic reactions ultimately occur on the catalyst surface. Herein, a two-step solution-phase reaction has been designed to synthesize quasi-core-shell structured BiPO4-rGO cuboids and the role of graphene on the surface chemical reactions was investigated in detail. It was found that the introduced graphene modified the process and the mechanism of the surface chemical reactions. The change mainly originates from the interaction between graphene and the adsorbed O2 molecule. Due to the electron transfer from graphene to adsorbed O2, graphene could tune the interfacial charge transport and efficiently activate molecular oxygen to form O2˙(-) anions as the major oxidation species instead of ˙OH. In addition, the two-step synthesis approach could efficiently suppress the formation of OH-related defects in the lattice. As a result, the BiPO4-rGO composite exhibited superior photocatalytic activity to BiPO4 and P25, about 4.3 times that of BiPO4 and 6.9 times that of P25.

Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm.

Science.gov (United States)

Skinnider, Michael A; Dejong, Chris A; Franczak, Brian C; McNicholas, Paul D; Magarvey, Nathan A

2017-08-16

Natural products represent a prominent source of pharmaceutically and industrially important agents. Calculating the chemical similarity of two molecules is a central task in cheminformatics, with applications at multiple stages of the drug discovery pipeline. Quantifying the similarity of natural products is a particularly important problem, as the biological activities of these molecules have been extensively optimized by natural selection. The large and structurally complex scaffolds of natural products distinguish their physical and chemical properties from those of synthetic compounds. However, no analysis of the performance of existing methods for molecular similarity calculation specific to natural products has been reported to date. Here, we present LEMONS, an algorithm for the enumeration of hypothetical modular natural product structures. We leverage this algorithm to conduct a comparative analysis of molecular similarity methods within the unique chemical space occupied by modular natural products using controlled synthetic data, and comprehensively investigate the impact of diverse biosynthetic parameters on similarity search. We additionally investigate a recently described algorithm for natural product retrobiosynthesis and alignment, and find that when rule-based retrobiosynthesis can be applied, this approach outperforms conventional two-dimensional fingerprints, suggesting it may represent a valuable approach for the targeted exploration of natural product chemical space and microbial genome mining. Our open-source algorithm is an extensible method of enumerating hypothetical natural product structures with diverse potential applications in bioinformatics.

Multivariate analysis of chromatographic retention data as a supplementary means for grouping structurally related compounds.

Science.gov (United States)

Fasoula, S; Zisi, Ch; Sampsonidis, I; Virgiliou, Ch; Theodoridis, G; Gika, H; Nikitas, P; Pappa-Louisi, A

2015-03-27

In the present study a series of 45 metabolite standards belonging to four chemically similar metabolite classes (sugars, amino acids, nucleosides and nucleobases, and amines) was subjected to LC analysis on three HILIC columns under 21 different gradient conditions with the aim to explore whether the retention properties of these analytes are determined from the chemical group they belong. Two multivariate techniques, principal component analysis (PCA) and discriminant analysis (DA), were used for statistical evaluation of the chromatographic data and extraction similarities between chemically related compounds. The total variance explained by the first two principal components of PCA was found to be about 98%, whereas both statistical analyses indicated that all analytes are successfully grouped in four clusters of chemical structure based on the retention obtained in four or at least three chromatographic runs, which, however should be performed on two different HILIC columns. Moreover, leave-one-out cross-validation of the above retention data set showed that the chemical group in which an analyte belongs can be 95.6% correctly predicted when the analyte is subjected to LC analysis under the same four or three experimental conditions as the all set of analytes was run beforehand. That, in turn, may assist with disambiguation of analyte identification in complex biological extracts. Copyright © 2015 Elsevier B.V. All rights reserved.

Heating induced structural and chemical behavior of KD2PO4 in the 25 °C–215 °C temperature range

International Nuclear Information System (INIS)

Botez, Cristian E.; Morris, Joshua L.; Encerrado Manriquez, Andres J.; Anchondo, Adan

2013-01-01

We have used powder x-ray diffraction (XRD) to investigate the structural and chemical modifications undergone by KD 2 PO 4 (DKDP) upon heating from room temperature to 215 °C. Full-profile (Le Bail) analysis of our temperature-resolved data shows no evidence of polymorphic structural transitions or deuterium–hydrogen isotope exchange occurring below T s = 185 °C. The lattice parameters of DKDP vary smoothly upon heating to T s and are 0.2% to 0.6% greater than those of its isostructural hydrogenated counterpart KH 2 PO 4 (KDP). In addition, XRD isotherms collected at T s demonstrate the structural and chemical stability of the title compound at this temperature over a 10.5 h time period. Upon further heating, however, the tetragonal DKDP phase becomes unstable, as evidenced by its transition to a monoclinic DKDP modification and eventual chemical decomposition via dehydration. - Highlights: • Structural and chemical behavior of KD 2 PO 4 is investigated upon heating to 215 °C • No polymorphic transitions or deuterium-hydrogen isotope exchange below T s = 185 °C • KD 2 PO 4 is structurally and chemically stable at T s over a 10.5 h time period • KD 2 PO 4 chemically decomposes via dehydration upon heating above T d = 195 °C

Magnitude differences in agronomic, chemical, nutritional, and structural features among different varieties of forage corn grown on dry land and irrigated land.

Science.gov (United States)

Xin, Hangshu; Abeysekara, Samen; Zhang, Xuewei; Yu, Peiqiang

2015-03-11

In this study, eight varieties of corn forage grown in semiarid western Canada (including Pioneer P2501, Pioneer P39m26, Pioneer P7443, Hyland HL3085, Hyland HLBaxxos, Hyland HLR219, Hyland HLSR22, and Pickseed Silex BT) were selected to explore the effect of irrigation implementation in comparison with nonirrigation on (1) agronomic characteristics, (2) basic chemical profiles explored by using a near-infrared reflectance (NIR) system, and (3) protein and carbohydrate internal structural parameters revealed by using an attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FTIR) system. Also, principal component analysis (PCA) was performed on spectroscopic data for clarification of differences in molecular structural makeup among the varieties. The results showed that irrigation treatment significantly increased (P forages. Significant interactions of irrigation treatment and corn variety were observed on most agronomic characteristics (DM yield, T/ha, days to tasseling, days to silking) and crude fiber (CF) and ether extract (EE) contents as well as some spectral data such as cellulosic compounds (CELC) peak intensity, peak ratios of CHO third peak to CELC, α-helix to β-sheet, and CHO third peak to amide I. Additionally, the spectral ratios of chemical functional groups that related to structural and nonstructural carbohydrates and protein polymers in forages did not remain constant over corn varieties cultivated with and without water treatment. Moreover, different cultivars had different growth, structure, and nutrition performances in this study. Although significant differences could be found in peak intensities, PCA results indicated some structural similarities existed between two treated corn forages with the exception of HL3085 and HLBaxxos. In conclusion, irrigation and corn variety had interaction effects on agronomic, chemical, nutritional, and structural features. Further study on the optimum level of irrigation for corn forage

Chemical states and electronic structure of a HfO(-2)/Ge(001) interface

International Nuclear Information System (INIS)

Seo, Kang-ill; McIntyre, Paul C.; Stanford U., Materials Sci. Dept.; Sun, Shiyu; Lee, Dong-Ick; Pianetta, Piero; SLAC, SSRL; Saraswat, Krishna C.; Stanford U., Elect. Eng. Dept.

2005-01-01

We report the chemical bonding structure and valence band alignment at the HfO 2 /Ge (001) interface by systematically probing various core level spectra as well as valence band spectra using soft x-rays at the Stanford Synchrotron Radiation Laboratory. We investigated the chemical bonding changes as a function of depth through the dielectric stack by taking a series of synchrotron photoemission spectra as we etched through the HfO 2 film using a dilute HF-solution. We found that a very non-stoichiometric GeO x layer exists at the HfO 2 /Ge interface. The valence band spectra near the Fermi level in each different film structure were carefully analyzed, and as a result, the valence band offset between Ge and GeO x was determined to be ΔE v (Ge-GeO x ) = 2.2 ± 0.15 eV, and that between Ge and HfO 2 , ΔE v (Ge-HfO 2 ) = 2.7 ± 0.15 eV

Sticking non-stick: Surface and Structure control of Diamond-like Carbon in Plasma Enhanced Chemical Vapour Deposition

Science.gov (United States)

Jones, B. J.; Nelson, N.

2016-10-01

This short review article explores the practical use of diamond-like carbon (DLC) produced by plasma enhanced chemical vapour deposition (PECVD). Using as an example issues relating to the DLC coating of a hand-held surgical device, we draw on previous works using atomic force microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, scanning electron microscopy, tensiometry and electron paramagnetic resonance. Utilising data from these techniques, we examine the surface structure, substrate-film interface and thin film microstructure, such as sp2/sp3 ratio (graphitic/diamond-like bonding ratio) and sp2 clustering. We explore the variations in parameters describing these characteristics, and relate these to the final device properties such as friction, wear resistance, and diffusion barrier integrity. The material and device characteristics are linked to the initial plasma and substrate conditions.

Sticking non-stick: Surface and Structure control of Diamond-like Carbon in Plasma Enhanced Chemical Vapour Deposition

International Nuclear Information System (INIS)

Jones, B J; Nelson, N

2016-01-01

This short review article explores the practical use of diamond-like carbon (DLC) produced by plasma enhanced chemical vapour deposition (PECVD). Using as an example issues relating to the DLC coating of a hand-held surgical device, we draw on previous works using atomic force microscopy, X-ray photoelectron spectroscopy, Raman spectroscopy, scanning electron microscopy, tensiometry and electron paramagnetic resonance. Utilising data from these techniques, we examine the surface structure, substrate-film interface and thin film microstructure, such as sp 2 /sp 3 ratio (graphitic/diamond-like bonding ratio) and sp 2 clustering. We explore the variations in parameters describing these characteristics, and relate these to the final device properties such as friction, wear resistance, and diffusion barrier integrity. The material and device characteristics are linked to the initial plasma and substrate conditions. (paper)

Heteromolecular metal–organic interfaces: Electronic and structural fingerprints of chemical bonding

International Nuclear Information System (INIS)

Stadtmüller, Benjamin; Schröder, Sonja; Kumpf, Christian

2015-01-01

Highlights: • We present a study of molecular donor–acceptor blends adsorbed on Ag(1 1 1). • Geometric and electronic structure of blends and pristine phases are compared. • The surface bonding of the acceptor is strengthened, that of the donor weakened. • But counter intuitively, the acceptor (donor) bond length becomes larger (smaller). • This contradiction is resolved by a model based on charge transfer via the surface. - Abstract: Beside the fact that they attract highest interest in the field of organic electronics, heteromolecular structures adsorbed on metal surfaces, in particular donor–acceptor blends, became a popular field in fundamental science, possibly since some surprising and unexpected behaviors were found for such systems. One is the apparent breaking of a rather fundamental rule in chemistry, namely that stronger chemical bonds go along with shorter bond lengths, as it is, e.g., well-known for the sequence from single to triple bonds. In this review we summarize the results of heteromolecular monolayer structures adsorbed on Ag(1 1 1), which – regarding this rule – behave in a counterintuitive way. The charge acceptor moves away from the substrate while its electronic structure indicates a stronger chemical interaction, indicated by a shift of the formerly lowest unoccupied molecular orbital toward higher binding energies. The donor behaves in the opposite way, it gives away charge, hence, electronically the bonding to the surface becomes weaker, but at the same time it also approaches the surface. It looks as if the concordant link between electronic and geometric structure was broken. But both effects can be explained by a substrate-mediated charge transfer from the donor to the acceptor. The charge reorganization going along with this transfer is responsible for both, the lifting-up of the acceptor molecule and the filling of its LUMO, and also for the reversed effects at the donor molecules. In the end, both molecules

Accessing and using chemical databases

DEFF Research Database (Denmark)

Nikolov, Nikolai Georgiev; Pavlov, Todor; Niemelä, Jay Russell

2013-01-01

Computer-based representation of chemicals makes it possible to organize data in chemical databases-collections of chemical structures and associated properties. Databases are widely used wherever efficient processing of chemical information is needed, including search, storage, retrieval......, and dissemination. Structure and functionality of chemical databases are considered. The typical kinds of information found in a chemical database are considered-identification, structural, and associated data. Functionality of chemical databases is presented, with examples of search and access types. More details...... are included about the OASIS database and platform and the Danish (Q)SAR Database online. Various types of chemical database resources are discussed, together with a list of examples....

Influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with carcinogenic and anticoagulant effect of 17β-aminoestrogens

Energy Technology Data Exchange (ETDEWEB)

Soriano-Correa, Catalina, E-mail: socc@puma2.zaragoza.unam.mx [Química Computacional, FES-Zaragoza, Universidad Nacional Autónoma de México (UNAM), Iztapalapa, Mexico City (Mexico); Raya, Angélica [Unidad Profesional Interdisciplinaria de Ingeniería Campus Guanajuato, Instituto Politécnico Nacional (IPN), Silao de la Victoria, Guanajuato (Mexico); Barrientos-Salcedo, Carolina [Laboratorio de Química Médica y Quimiogenómica, Facultad de Bioanálisis Campus Veracruz - Boca del Río, Universidad Veracruzana, Veracruz (Mexico); Esquivel, Rodolfo O. [Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa (UAM-Iztapalapa), Mexico City (Mexico)

2014-06-25

Highlights: • The aromatic A-ring of 17β-aminoestrogens contribute to its anticoagulant effect. • The electron-donor substituent groups favored the basicity of 17β-aminoestrogens. • The physicochemical properties are important in the carcinogenic effect of anticoagulant molecules. - Abstract: Activity of steroid hormones is dependent upon a number of factors, as solubility, transport and metabolism. The functional differences caused by structural modifications could exert an influence on the chemical reactivity and biological effect. The goal of this work is to study the influence of the physicochemical and aromatic properties on the chemical reactivity and its relation with the carcinogenic risk that can associate with the anticoagulant effect of 17β-aminoestrogens using quantum-chemical descriptors at the DFT-B3LYP, BH and HLYP and M06-2X levels. The relative acidity of (H1) of the hydroxyl group increases with electron-withdrawing groups. Electron-donor groups favor the basicity. The steric hindrance of the substituents decreases the aromatic character and consequently diminution the carcinogenic effect. Density descriptors: hardness, electrophilic index, atomic charges, molecular orbitals, electrostatic potential and their geometric parameters permit analyses of the chemical reactivity and physicochemical features and to identify some reactive sites of 17β-aminoestrogens.

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.

Impact of oil and related chemicals on the marine environment

International Nuclear Information System (INIS)

1993-01-01

This review updates a previous review entitled ''Impact of Oil on the Marine Environment''. It covers oil and individual hydrocarbons, used lubricating oils, chemical control agents for oil spills, and wastes from offshore petroleum operations. It considers all major knowledge generated since the mid-1970s. The review covers its topics comprehensively, from a consideration of the composition, sources and inputs of oil to its ecological and human health effects and its effects on man's use of the sea. The review addresses several key questions on the present levels of contamination, the impact of hydrocarbons and related chemicals on marine biota, the recovery potential of marine ecosystems exposed to these contaminants, the degree of protection required for marine ecosystems known to be vulnerable and sensitive, and recommended research and other actions to fill gaps in knowledge. The review describes the hazards of marine oil pollution and associated chemicals and wastes as they are understood currently, and clarifies the importance of reducing oil inputs in coastal and offshore waters. It assists in considering fundamental questions, asked by the public and decision-makers alike, such as: how much oil is entering our oceans, and how much harm is it doing? (author)

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations

Science.gov (United States)

Arjunan, V.; Kalaivani, M.; Marchewka, M. K.; Mohan, S.

2013-04-01

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G**, cc-pVDZ and 6-311++G** basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak Osbnd H⋯O and Nsbnd H⋯O hydrogen bonds shows notable vibrational effects.

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…

Chemical vapour deposition of carbon nanotubes

CSIR Research Space (South Africa)

Arendse, CJ

2006-02-01

Full Text Available , effective, more versatile and easily scalable to large substrate sizes. In this paper, we present a design of the hot-wire CVD system constructed at the CSIR for the deposition of CNTs. Additionally, we will report on the structure of CNTs deposited... exhibit exceptional chemical and physical properties related to toughness, chemical inertness, magnetism, and electrical and thermal conductivity. A variety of preparation methods to synthesise CNTs are known, e.g. carbon-arc discharge, laser ablation...

Structure of Colloidal Flocs in relation to the Dynamic Properties of Unstable Suspension

Directory of Open Access Journals (Sweden)

Yasuhisa Adachi

2012-01-01

Full Text Available Dynamic behaviors of unstable colloidal dispersions are reviewed in terms of floc formation. Geometrical structure of flocs in terms of chemical conditions and formation mechanics is a key to predict macroscopic transportation properties. The rate of sedimentation and rheological properties can be described with the help of fractal dimension (D that is the function of the number of contacts between clusters (Nc. It is also well known that the application of water soluble polymers and polyelectrolytes, which are usually used as a conditioner or flocculants in colloidal dispersions, critically affects the process of flocculation. The resulted floc structure is also influenced by the application of polymer. In order to reveal the roles of the polymers, the elementary rate process of polymer reaching to colloidal interface and subsequent reconformation process into more stable adsorption state are needed to be analyzed. The properties of permeable flocs and adsorbed polymer (polyelectrolyte layers formed on the colloidal surfaces remain to be worked out in relation to inhomogeneous porous structure and electrokinetics in the future.

Donated chemical probes for open science.

Science.gov (United States)

Müller, Susanne; Ackloo, Suzanne; Arrowsmith, Cheryl H; Bauser, Marcus; Baryza, Jeremy L; Blagg, Julian; Böttcher, Jark; Bountra, Chas; Brown, Peter J; Bunnage, Mark E; Carter, Adrian J; Damerell, David; Dötsch, Volker; Drewry, David H; Edwards, Aled M; Edwards, James; Elkins, Jon M; Fischer, Christian; Frye, Stephen V; Gollner, Andreas; Grimshaw, Charles E; IJzerman, Adriaan; Hanke, Thomas; Hartung, Ingo V; Hitchcock, Steve; Howe, Trevor; Hughes, Terry V; Laufer, Stefan; Li, Volkhart Mj; Liras, Spiros; Marsden, Brian D; Matsui, Hisanori; Mathias, John; O'Hagan, Ronan C; Owen, Dafydd R; Pande, Vineet; Rauh, Daniel; Rosenberg, Saul H; Roth, Bryan L; Schneider, Natalie S; Scholten, Cora; Singh Saikatendu, Kumar; Simeonov, Anton; Takizawa, Masayuki; Tse, Chris; Thompson, Paul R; Treiber, Daniel K; Viana, Amélia Yi; Wells, Carrow I; Willson, Timothy M; Zuercher, William J; Knapp, Stefan; Mueller-Fahrnow, Anke

2018-04-20

Potent, selective and broadly characterized small molecule modulators of protein function (chemical probes) are powerful research reagents. The pharmaceutical industry has generated many high-quality chemical probes and several of these have been made available to academia. However, probe-associated data and control compounds, such as inactive structurally related molecules and their associated data, are generally not accessible. The lack of data and guidance makes it difficult for researchers to decide which chemical tools to choose. Several pharmaceutical companies (AbbVie, Bayer, Boehringer Ingelheim, Janssen, MSD, Pfizer, and Takeda) have therefore entered into a pre-competitive collaboration to make available a large number of innovative high-quality probes, including all probe-associated data, control compounds and recommendations on use (https://openscienceprobes.sgc-frankfurt.de">https://openscienceprobes.sgc-frankfurt.dehttps://openscienceprobes.sgc-frankfurt.de/">/). Here we describe the chemical tools and target-related knowledge that have been made available, and encourage others to join the project. © 2018, Müller et al.

Sensing signatures mediated by chemical structure of molecular solids in laser-induced plasmas.

Science.gov (United States)

Serrano, Jorge; Moros, Javier; Laserna, J Javier

2015-03-03

Laser ablation of organic compounds has been investigated for almost 30 years now, either in the framework of pulse laser deposition for the assembling of new materials or in the context of chemical sensing. Various monitoring techniques such as atomic and molecular fluorescence, time-of-flight mass spectrometry, and optical emission spectroscopy have been used for plasma diagnostics in an attempt to understand the spectral signature and potential origin of gas-phase ions and fragments from organic plasmas. Photochemical and photophysical processes occurring within these systems are generally much more complex than those suggested by observation of optical emission features. Together with laser ablation parameters, the structural and chemical-physical properties of molecules seem to be closely tied to the observed phenomena. The present manuscript, for the first time, discusses the role of molecular structure in the optical emission of organic plasmas. Factors altering the electronic distribution within the organic molecule have been found to have a direct impact on its ensuing optical emissions. The electron structure of an organic molecule, resulting from the presence, nature, and position of its atoms, governs the breakage of the molecule and, as a result, determines the extent of atomization and fragmentation that has proved to directly impact the emissions of CN radicals and C2 dimers. Particular properties of the molecule respond more positively depending on the laser irradiation wavelength, thereby redirecting the ablation process through photochemical or photothermal decomposition pathways. It is of paramount significance for chemical identification purposes how, despite the large energy stored and dissipated by the plasma and the considerable number of transient species formed, the emissions observed never lose sight of the original molecule.

Electronic structure and chemical properties of superheavy elements

Energy Technology Data Exchange (ETDEWEB)

Pershina, V [Gesellschaft fuer Schwerionenforschung (GSI), Helmholtzzentrum fuer Schwerionenforschung Gmbh (Germany)

2009-12-31

Relativistic electronic structure calculations of superheavy elements (Z>=104) are analyzed. Preference is given to those related to experimental research. The role of relativistic effects is discussed.

Relation between chemical shift artifact and infiltration on MR imaging of renal cell carcinoma

International Nuclear Information System (INIS)

Yoshigoe, Fukuo; Makino, Hideki; Yanada, Syuichi; Ohishi, Yukihiko; Mashima, Yasuoki; Yamada, Hideo.

1994-01-01

Retrospective study on the relation between existence of the interruption and disturbance of chemical shift artifact and tumor infiltration at the periphery of the kidney on MR imaging was evaluated in 28 cases with renal cell carcinoma. Judgement was possible in 9 out of the 11 cases with pathological stage below pT2 and 14 cases out of 17 pT3 cases. Judgement was impracticable in 5 cases because the peripheral fat tissue of the kidney was too less to observe chemical shift artifact and the tumor was spreading at the side opposite to the chemical shift artifact. Chemical shift artifact on MRI in this study correlated well with renal tumor infiltration. (author)

[Relativity of commercial specification of Menthae Herba based on chemical analysis].

Science.gov (United States)

Ye, Dan; Zhao, Ming; Shao, Yang; Ouyang, Zhen; Peng, Hua-sheng; Han Bang-xing; Zhang, Wei-wan-qi; Gu, Xue-mei

2015-01-01

In order to compare the differences of 35 Menthae Herba samples collected on the market and at producing areas, the contents of six total terpenoids, the essential oil and chromatographic fingerprints were analyzed, which provided evidences for drawing up the commodity specifications and grading criteria of Menthae Herba. GC-MS method was used to analyze the chemical constituents of 35 different samples. The chromatographic fingerprints obtained by using GC were then evaluated by similarity analysis, hierarchical clustering analysis and principal component analysis. The relativity between the content of six terpenoids and the essential oil were studied. In this study, the chemical profiles of 35 samples from different producing areas had significant disparity. All samples collected in the report could be categorized into four chemical types, L-menthol, pulegone, carvone and L-menthone, but the chemical profiles had no relationship with the areas. The chromatographic fingerprints of the samples from different types were dissimilar, while the different producing areas were difficult to be separated. It was indicated that the content of volatile oil was positively correlated with the content of L-menthol and the sum of six total terpenoids. The content of the essential oil, L-menthol and the sum of six total terpenoids of Menthae Herba were considered as one of the commercial specifications and grading criteria. These results in the research could be helpful to draw up the commercial specification and grading criteria of Menthae Herba from a view of chemical information.

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

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)

Lu, Xincheng; Jiang, Jianchun; Sun, Kang; Wang, Jinbiao; Zhang, Yanping

2014-01-01

Highlights: • Activated carbons with different pore structure and surface chemical properties were prepared by modification process. • HgCl 2 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 Hg 2+ adsorption ability of samples was investigated. The results show that the Hg 2+ 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

Intelligent structures and design of energy related facilities

International Nuclear Information System (INIS)

Namba, Haruyuki

1994-01-01

Possibility of applying intelligent structural concepts to civil design of energy plants is discussed. Intelligent structures, which are now common in aerospace engineering field, are also referred to as adaptive structures or smart structures depending on cases. Among various existing concepts, reconfigurable structures, precise shape control, structural monitoring using smart materials of optical fiber sensors, and relation with recent innovative communication technologies are focused from civil engineering point of view. Application of such new technologies will help to enhance design of energy related plants, which include multiplex functions which need to be very reliable and safe. (author)

Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML.

Science.gov (United States)

Durairaj, Vijayasarathi; Punnaivanam, Sankar

2015-09-01

Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named "ChemEnt" for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined. Copyright © 2015 Elsevier Inc. All rights reserved.

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

Structure and vibrational spectra of melaminium bis(trifluoroacetate) trihydrate: FT-IR, FT-Raman and quantum chemical calculations

Science.gov (United States)

Sangeetha, V.; Govindarajan, M.; Kanagathara, N.; Marchewka, M. K.; Gunasekaran, S.; Anbalagan, G.

Melaminium bis(trifluoroacetate) trihydrate (MTFA), an organic material has been synthesized and single crystals of MTFA have been grown by the slow solvent evaporation method at room temperature. X-ray powder diffraction analysis confirms that MTFA crystal belongs to the monoclinic system with space group P2/c. The molecular geometry, vibrational frequencies and intensity of the vibrational bands have been interpreted with the aid of structure optimization based on density functional theory (DFT) B3LYP method with 6-311G(d,p) and 6-311++G(d,p) basis sets. The X-ray diffraction data have been compared with the data of optimized molecular structure. The theoretical results show that the crystal structure can be reproduced by optimized geometry and the vibrational frequencies show good agreement with the experimental values. The nuclear magnetic resonance (NMR) chemical shift of the molecule has been calculated by the gauge independent atomic orbital (GIAO) method and compared with experimental results. HOMO-LUMO, and other related molecular and electronic properties are calculated. The Mulliken and NBO charges have also been calculated and interpreted.

Structural and vibrational spectral investigations of melaminium maleate monohydrate by FTIR, FT-Raman and quantum chemical calculations.

Science.gov (United States)

Arjunan, V; Kalaivani, M; Marchewka, M K; Mohan, S

2013-04-15

The structural investigations of the molecular complex of melamine with maleic acid, namely melaminium maleate monohydrate have been carried out by quantum chemical methods in addition to FTIR, FT-Raman and far-infrared spectral studies. The quantum chemical studies were performed with DFT (B3LYP) method using 6-31G(**), cc-pVDZ and 6-311++G(**) basis sets to determine the energy, structural and thermodynamic parameters of melaminium maleate monohydrate. The hydrogen atom from maleic acid was transferred to the melamine molecule giving the singly protonated melaminium cation. The ability of ions to form spontaneous three-dimensional structure through weak OH···O and NH···O hydrogen bonds shows notable vibrational effects. Copyright © 2013 Elsevier B.V. All rights reserved.

DFT/GIAO calculations of the relative contributions of hyperconjugation to the chemical shifts of ethanol

International Nuclear Information System (INIS)

Carneiro, J. Walkimar de M.; Dias, Jacques F.; Seidl, Peter R.; Tostes, J. Glauco R.

2002-01-01

Our previous DFT/GIAO calculations on different types of alcohols reveal that the rotation of the hydroxyl group can affect the chemical shift of carbons and hydrogens close to the substituent in different ways. Besides the steric and electrostatic effects that have been widely studied, hyperconjugation with the lone pairs on oxygen of the hydroxyl group leads to changes in bond lengths and angles as well as to different charge distributions. As all three of these factors also affect chemical shifts, we undertook a systematic investigation of their relative contributions to the chemical shifts of ethanol, a molecule in which there is minimum interference among these factors. Calculations by the B3LYP method at the 6-31G(d) level for ethanol conformers corresponding to a rotation around the carbon-oxygen bond at 30 dec increments are used to show how relative contributions vary with the dihedral angle formed between the carbon-carbon and oxygen-hydrogen bonds (C-C-O-H). Largest contributions to carbon chemical shifts can be attributed to changes in bond lengths while for hydrogen chemical shifts also contribute significantly differences in charge distribution. (author)

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

A new class of HIV-1 protease inhibitor: the crystallographic structure, inhibition and chemical synthesis of an aminimide peptide isostere.

Science.gov (United States)

Rutenber, E E; McPhee, F; Kaplan, A P; Gallion, S L; Hogan, J C; Craik, C S; Stroud, R M

1996-09-01

The essential role of HIV-1 protease (HIV-1 PR) in the viral life cycle makes it an attractive target for the development of substrate-based inhibitors that may find efficacy as anti-AIDS drugs. However, resistance has arisen to potent peptidomimetic drugs necessitating the further development of novel chemical backbones for diversity based chemistry focused on probing the active site for inhibitor interactions and binding modes that evade protease resistance. AQ148 is a potent inhibitor of HIV-1 PR and represents a new class of transition state analogues incorporating an aminimide peptide isostere. A 3-D crystallographic structure of AQ148, a tetrapeptide isostere, has been determined in complex with its target HIV-1 PR to a resolution of 2.5 A and used to evaluate the specific structural determinants of AQ148 potency and to correlate structure-activity relationships within the class of related compounds. AQ148 is a competitive inhibitor of HIV-1 PR with a Ki value of 137 nM. Twenty-nine derivatives have been synthesized and chemical modifications have been made at the P1, P2, P1', and P2' sites. The atomic resolution structure of AQ148 bound to HIV-1 PR reveals both an inhibitor binding mode that closely resembles that of other peptidomimetic inhibitors and specific protein/inhibitor interactions that correlate with structure-activity relationships. The structure provides the basis for the design, synthesis and evaluation of the next generation of hydroxyethyl aminimide inhibitors. The aminimide peptide isostere is a scaffold with favorable biological properties well suited to both the combinatorial methods of peptidomimesis and the rational design of potent and specific substrate-based analogues.

Interactions between structural and chemical biomimetism in synthetic stem cell niches

International Nuclear Information System (INIS)

Nava, Michele M; Raimondi, Manuela T; Credi, Caterina; De Marco, Carmela; Turri, Stefano; Cerullo, Giulio; Osellame, Roberto

2015-01-01

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)

Structural damage and chemical contaminants on reprocessed arthroscopic shaver blades.

Science.gov (United States)

Kobayashi, Masahiko; Nakagawa, Yasuaki; Okamoto, Yukihiro; Nakamura, Shinichiro; Nakamura, Takashi

2009-02-01

In response to socioeconomic pressure to cut budgets in medicine, single-use surgical instruments are often reprocessed despite potential biological hazard. To evaluate the quality and contaminants of reprocessed shaver blades. Reprocessed shaver blades have mechanical damage and chemical contamination. Controlled laboratory study. Seven blades and 3 abraders were reprocessed 1 time or 3 times and then were assessed. In the first part of the study, structural damage on the blades after 3 reprocessings was compared to that after 1 reprocessing using optical microscopy. In the second part, surface damage was observed using optical microscopy and scanning electron microscopy; elemental and chemical analyses of contaminants found by the microscopy were performed using scanning electron microscopy/energy dispersive x-ray spectroscopy, scanning Auger microscopy, and Fourier transform infrared spectroscopy. Optical microscopic examination revealed abrasion on the surface of the inner blade and cracks on the inner tube after 1 reprocessing. These changes were more evident after 3 reprocessings. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the blade reprocessed once showed contaminants containing calcium, carbon, oxygen, and silicon, and Fourier transform infrared spectroscopy demonstrated biological protein consisting mainly of collagen, some type of salts, and polycarbonate used in plastic molding. Scanning electron microscopy/energy dispersive x-ray spectroscopy of the inner cutter of the reprocessed abrader revealed contaminants containing carbon, calcium, phosphorous, and oxygen, and Fourier transform infrared spectroscopy showed H2O, hydroxyapatite, and hydroxyl proteins. Scanning Auger microscopy showed that the tin-nickel plating on the moving blade and abrader was missing in some locations. This is the first study to evaluate both mechanical damage and chemical contaminants containing collagen, hydroxyapatite, and salts

Preparation of TiC/W core–shell structured powders by one-step activation and chemical reduction process

International Nuclear Information System (INIS)

Ding, Xiao-Yu; Luo, Lai-Ma; Huang, Li-Mei; Luo, Guang-Nan; Zhu, Xiao-Yong; Cheng, Ji-Gui; Wu, Yu-Cheng

2015-01-01

Highlights: • A novel wet chemical method was used to prepare TiC/W core–shell structure powders. • TiC nanoparticles were well-encapsulated by W shells. • TiC phase was present in the interior of tungsten grains. - Abstract: In the present study, one-step activation and chemical reduction process as a novel wet-chemical route was performed for the preparation of TiC/W core–shell structured ultra-fine powders. The XRD, FE-SEM, TEM and EDS results demonstrated that the as-synthesized powders are of high purity and uniform with a diameter of approximately 500 nm. It is also found that the TiC nanoparticles were well-encapsulated by W shells. Such a unique process suggests a new method for preparing X/W (X refers the water-insoluble nanoparticles) core–shell nanoparticles with different cores

Sea Cucumber Glycosides: Chemical Structures, Producing Species and Important Biological Properties.

Science.gov (United States)

Mondol, Muhammad Abdul Mojid; Shin, Hee Jae; Rahman, M Aminur; Islam, Mohamad Tofazzal

2017-10-17

Sea cucumbers belonging to echinoderm are traditionally used as tonic food in China and other Asian countries. They produce abundant biologically active triterpene glycosides. More than 300 triterpene glycosides have been isolated and characterized from various species of sea cucumbers, which are classified as holostane and nonholostane depending on the presence or absence of a specific structural unit γ(18,20)-lactone in the aglycone. Triterpene glycosides contain a carbohydrate chain up to six monosaccharide units mainly consisting of d-xylose, 3-O-methy-d-xylose, d-glucose, 3-O-methyl-d-glucose, and d-quinovose. Cytotoxicity is the common biological property of triterpene glycosides isolated from sea cucumbers. Besides cytotoxicity, triterpene glycosides also exhibit antifungal, antiviral and hemolytic activities. This review updates and summarizes our understanding on diverse chemical structures of triterpene glycosides from various species of sea cucumbers and their important biological activities. Mechanisms of action and structural-activity relationships (SARs) of sea cucumber glycosides are also discussed briefly.

A multimedia exposure assessment methodology for evaluating the performance of the design of structures containing chemical and radioactive wastes

International Nuclear Information System (INIS)

Stephanatos, B.N.; Molholt, B.; Walter, K.P.; MacGregor, A.

1991-01-01

The objectives of this work are to develop a multimedia exposure assessment methodology for the evaluation of existing and future design of structures containing chemical and radioactive wastes and to identify critical parameters for design optimization. The designs are evaluated in terms of their compliance with various federal and state regulatory requirements. Evaluation of the performance of a particular design is presented within the scope of a given exposure pathway. An exposure pathway has four key components: (1) a source and mechanism of chemical release, (2) a transport medium; (3) a point of exposure; and (4) a route of exposure. The first step in the analysis is the characterization of the waste source behavior. The rate and concentration of releases from the source are evaluated using appropriate mathematical models. The migration of radionuclides and chemicals is simulated through each environmental medium to the exposure point. The total exposure to the potential receptor is calculated, and an estimate of the health effects of the exposure is made. Simulation of the movement of radionuclides and chemical wastes from the source to the receptor point includes several processes. If the predicted human exposure to contaminants meets the performance criteria, the design has been validated. Otherwise the structure design is improved to meet the performance criteria. A phased modeling approach is recommended at a particular mixed waste site. A relatively simple model is initially used to pinpoint critical fate and transport processes and design parameters. The second phase of the modeling effort involves the use of more complex and resource intensive fate and transport models. This final step in the modeling process provides more accurate estimates of contaminant concentrations at the point of exposure. Thus the human dose is more accurately predicted, providing better design validation

Structural and optical characterization of self-assembled Ge nanocrystal layers grown by plasma-enhanced chemical vapor deposition

NARCIS (Netherlands)

Saeed, S.; Buters, F.; Dohnalova, K.; Wosinski, L.; Gregorkiewicz, T.

2014-01-01

We present a structural and optical study of solid-state dispersions of Ge nanocrystals prepared by plasma-enhanced chemical vapor deposition. Structural analysis shows the presence of nanocrystalline germanium inclusions embedded in an amorphous matrix of Si-rich SiO2. Optical characterization

Predicting work-related flow in the chemical industry / Erika Maree

OpenAIRE

Maree, Erika

2008-01-01

In a new world of work characterised by competitiveness, benchmarking, technological innovation and efficiency, the South African chemical industry needs to function at an optimal level to meet the demands of its stakeholders and employees. The industry needs leadership of the highest standard and an efficient, productive workforce. The objective of this study was to determine the relationship between leader empowering behaviour, self-efficacy, job resources and work-related flow for empl...

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole

Science.gov (United States)

Arjunan, V.; Raj, Arushma; Santhanam, R.; Marchewka, M. K.; Mohan, S.

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. 1H and 13C NMR chemical shifts and the electronic transitions of the molecule are also discussed.

Structural, vibrational, electronic investigations and quantum chemical studies of 2-amino-4-methoxybenzothiazole.

Science.gov (United States)

Arjunan, V; Raj, Arushma; Santhanam, R; Marchewka, M K; Mohan, S

2013-02-01

Extensive vibrational investigations of 2-amino-4-methoxybenzothiazole have been carried out with FTIR and FT-Raman spectral techniques. The electronic structure of the molecule has been analysed by UV-Visible and NMR spectroscopies. The DFT studies were carried out with B3LYP and HF methods utilising 6-31G(d,p), 6-311++G(d,p) and cc-pVDZ basis sets to determine the structural, thermodynamical, vibrational, electronic characteristics of the compound and also to understand the electronic and steric influence of the methoxy amino groups on the skeletal frequencies. The mixing of the fundamental modes was determined with the help of total energy distribution (TED). The energies of the frontier molecular orbitals have also been determined. The kinetic and thermodynamic stability and chemical hardness of the molecule have been determined. Complete NBO analysis was also carried out to find out the intramolecular electronic interactions and their stabilisation energy. (1)H and (13)C NMR chemical shifts and the electronic transitions of the molecule are also discussed. Copyright © 2012 Elsevier B.V. All rights reserved.

Polar and chemical domain structures of lead scandium tantalate (PST)

International Nuclear Information System (INIS)

Peng, J.L.; Bursill, L.A.

1993-01-01

The local structure of chemical and polar domains and domain walls is determined directly by atomic resolution high-resolution electron microscopy. Thus the Pb, Ta and Sc atomic positions may be located in the images of very thin crystals. Furthermore the Pb cation displacements away from the ideal perovskite A-site have been measured directly for the first time. Local variations in polarization direction may be mapped directly off the images, provided certain electron optical conditions are met. The results are relevant to recent theories of polar-glass behaviour in relaxor-type complex oxide functional ceramics. 17 refs., 9 figs

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...

A probabilistic approach for validating protein NMR chemical shift assignments

International Nuclear Information System (INIS)

Wang Bowei; Wang, Yunjun; Wishart, David S.

2010-01-01

It has been estimated that more than 20% of the proteins in the BMRB are improperly referenced and that about 1% of all chemical shift assignments are mis-assigned. These statistics also reflect the likelihood that any newly assigned protein will have shift assignment or shift referencing errors. The relatively high frequency of these errors continues to be a concern for the biomolecular NMR community. While several programs do exist to detect and/or correct chemical shift mis-referencing or chemical shift mis-assignments, most can only do one, or the other. The one program (SHIFTCOR) that is capable of handling both chemical shift mis-referencing and mis-assignments, requires the 3D structure coordinates of the target protein. Given that chemical shift mis-assignments and chemical shift re-referencing issues should ideally be addressed prior to 3D structure determination, there is a clear need to develop a structure-independent approach. Here, we present a new structure-independent protocol, which is based on using residue-specific and secondary structure-specific chemical shift distributions calculated over small (3-6 residue) fragments to identify mis-assigned resonances. The method is also able to identify and re-reference mis-referenced chemical shift assignments. Comparisons against existing re-referencing or mis-assignment detection programs show that the method is as good or superior to existing approaches. The protocol described here has been implemented into a freely available Java program called 'Probabilistic Approach for protein Nmr Assignment Validation (PANAV)' and as a web server (http://redpoll.pharmacy.ualberta.ca/PANAVhttp://redpoll.pharmacy.ualberta.ca/PANAV) which can be used to validate and/or correct as well as re-reference assigned protein chemical shifts.

Coulombic Interaction in Finnish Middle School Chemistry: A Systemic Perspective on Students' Conceptual Structure of Chemical Bonding

Science.gov (United States)

Joki, Jarkko; Lavonen, Jari; Juuti, Kalle; Aksela, Maija

2015-01-01

The aim of this study was to design a novel and holistic way to teach chemical bonding at the middle school level according to research on the teaching and learning of bonding. A further aim was to investigate high achieving middle school students' conceptual structures concerning chemical bonding by using a systemic perspective. Students in one…

Structure and chemical characteristics of natural mineral deposit Terbunskaya (Lipetsk region, Russia)

Energy Technology Data Exchange (ETDEWEB)

Motyleva, S., E-mail: motyleva-svetlana@mail.ru; Mertvishcheva, M. [All-Russian Horticular Institute for Breeding, Agrotechnology and Nursery Russian Academy of Agricultural Sciences, Moskow (Russian Federation); Shchuchka, R.; Gulidova, V. [Yelets state university named after I. A. Bunin, Yelets (Russian Federation)

2015-07-22

New knowledge about the mineralogical features Terbunsky mineral. Investigated 5 fractions isolated from the incision (2-2,5 m). Terbunskaya deposit belongs to minerals Santonian age. Scanning electron microscopy and energy dispersive analysis of fractions isolated studied in detail. In the coarse fractions found ancient organic remains of algae and micro-organisms that have been sedimented together with the mineral component during geological periods. The share of organic inclusions does not exceed 1.5%. Chemical composition confirms the presence of silicon and carbonate organisms. Advantageously proportion of minerals having a layered structure with a plurality of micro and nano pore size 600 - 80-nm and an average chemical composition (wt%): Na (0,64), Mg (0,54), Al (13.48), Si (27 57), K (2.39) Ca (0.75)

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)

1998-12-31

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.

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.

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.C.

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

Total chemical synthesis and X-ray structure of kaliotoxin by racemic protein crystallography.

Science.gov (United States)

Pentelute, Brad L; Mandal, Kalyaneswar; Gates, Zachary P; Sawaya, Michael R; Yeates, Todd O; Kent, Stephen B H

2010-11-21

Here we report the total synthesis of kaliotoxin by 'one pot' native chemical ligation of three synthetic peptides. A racemic mixture of D- and L-kaliotoxin synthetic protein molecules gave crystals in the centrosymmetric space group P1 that diffracted to atomic-resolution (0.95 Å), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships

DEFF Research Database (Denmark)

Arnau, E G; Andersen, Klaus Ejner; Bruze, M

2000-01-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships...... (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application......" in their chemical structure, indicating an ability to modify skin proteins and thus behave as a skin sensitizer, were tested on the patient. The patient reacted positively to the synthetic fragrance p-t-butyl-alpha-methylhydrocinnamic aldehyde (Lilial), a widely used fragrance compound not present in the fragrance...

The impact of chemical structure and molecular packing on the electronic polarisation of fullerene arrays.

Science.gov (United States)

Few, Sheridan; Chia, Cleaven; Teo, Daniel; Kirkpatrick, James; Nelson, Jenny

2017-07-19

Electronic polarisation contributes to the electronic landscape as seen by separating charges in organic materials. The nature of electronic polarisation depends on the polarisability, density, and arrangement of polarisable molecules. In this paper, we introduce a microscopic, coarse-grained model in which we treat each molecule as a polarisable site, and use an array of such polarisable dipoles to calculate the electric field and associated energy of any arrangement of charges in the medium. The model incorporates chemical structure via the molecular polarisability and molecular packing patterns via the structure of the array. We use this model to calculate energies of charge pairs undergoing separation in finite fullerene lattices of different chemical and crystal structures. The effective dielectric constants that we estimate from this approach are in good quantitative agreement with those measured experimentally in C 60 and phenyl-C 61 -butyric acid methyl ester (PCBM) films, but we find significant differences in dielectric constant depending on packing and on direction of separation, which we rationalise in terms of density of polarisable fullerene cages in regions of high field. In general, we find lattices containing molecules of more isotropic polarisability tensors exhibit higher dielectric constants. By exploring several model systems we conclude that differences in molecular polarisability (and therefore, chemical structure) appear to be less important than differences in molecular packing and separation direction in determining the energetic landscape for charge separation. We note that the results are relevant for finite lattices, but not necessarily for infinite systems. We propose that the model could be used to design molecular systems for effective electronic screening.

A Parallel Multiblock Structured Grid Method with Automated Interblocked Unstructured Grids for Chemically Reacting Flows

Science.gov (United States)

Spiegel, Seth Christian

An automated method for using unstructured grids to patch non- C0 interfaces between structured blocks has been developed in conjunction with a finite-volume method for solving chemically reacting flows on unstructured grids. Although the standalone unstructured solver, FVFLO-NCSU, is capable of resolving flows for high-speed aeropropulsion devices with complex geometries, unstructured-mesh algorithms are inherently inefficient when compared to their structured counterparts. However, the advantages of structured algorithms in developing a flow solution in a timely manner can be negated by the amount of time required to develop a mesh for complex geometries. The global domain can be split up into numerous smaller blocks during the grid-generation process to alleviate some of the difficulties in creating these complex meshes. An even greater abatement can be found by allowing the nodes on abutting block interfaces to be nonmatching or non-C 0 continuous. One code capable of solving chemically reacting flows on these multiblock grids is VULCAN, which uses a nonconservative approach for patching non-C0 block interfaces. The developed automated unstructured-grid patching algorithm has been installed within VULCAN to provide it the capability of a fully conservative approach for patching non-C0 block interfaces. Additionally, the FVFLO-NCSU solver algorithms have been deeply intertwined with the VULCAN source code to solve chemically reacting flows on these unstructured patches. Finally, the CGNS software library was added to the VULCAN postprocessor so structured and unstructured data can be stored in a single compact file. This final upgrade to VULCAN has been successfully installed and verified using test cases with particular interest towards those involving grids with non- C0 block interfaces.

Nanotechnology for chemical engineers

CERN Document Server

Salaheldeen Elnashaie, Said; Hashemipour Rafsanjani, Hassan

2015-01-01

The book describes the basic principles of transforming nano-technology into nano-engineering with a particular focus on chemical engineering fundamentals. This book provides vital information about differences between descriptive technology and quantitative engineering for students as well as working professionals in various fields of nanotechnology. Besides chemical engineering principles, the fundamentals of nanotechnology are also covered along with detailed explanation of several specific nanoscale processes from chemical engineering point of view. This information is presented in form of practical examples and case studies that help the engineers and researchers to integrate the processes which can meet the commercial production. It is worth mentioning here that, the main challenge in nanostructure and nanodevices production is nowadays related to the economic point of view. The uniqueness of this book is a balance between important insights into the synthetic methods of nano-structures and nanomaterial...

Chemical Ecology of Stingless Bees.

Science.gov (United States)

Leonhardt, Sara Diana

2017-04-01

Stingless bees (Hymenoptera, Apidae: Meliponini) represent a highly diverse group of social bees confined to the world's tropics and subtropics. They show a striking diversity of structural and behavioral adaptations and are important pollinators of tropical plants. Despite their diversity and functional importance, their ecology, and especially chemical ecology, has received relatively little attention, particularly compared to their relative the honeybee, Apis mellifera. Here, I review various aspects of the chemical ecology of stingless bees, from communication over resource allocation to defense. I list examples in which functions of specific compounds (or compound groups) have been demonstrated by behavioral experiments, and show that many aspects (e.g., queen-worker interactions, host-parasite interactions, neuronal processing etc.) remain little studied. This review further reveals that the vast majority of studies on the chemical ecology of stingless bees have been conducted in the New World, whereas studies on Old World stingless bees are still comparatively rare. Given the diversity of species, behaviors and, apparently, chemical compounds used, I suggest that stingless bees provide an ideal subject for studying how functional context and the need for species specificity may interact to shape pheromone diversification in social insects.

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.

Protein backbone angle restraints from searching a database for chemical shift and sequence homology

Energy Technology Data Exchange (ETDEWEB)

Cornilescu, Gabriel; Delaglio, Frank; Bax, Ad [National Institutes of Health, Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases (United States)

1999-03-15

Chemical shifts of backbone atoms in proteins are exquisitely sensitive to local conformation, and homologous proteins show quite similar patterns of secondary chemical shifts. The inverse of this relation is used to search a database for triplets of adjacent residues with secondary chemical shifts and sequence similarity which provide the best match to the query triplet of interest. The database contains 13C{alpha}, 13C{beta}, 13C', 1H{alpha} and 15N chemical shifts for 20 proteins for which a high resolution X-ray structure is available. The computer program TALOS was developed to search this database for strings of residues with chemical shift and residue type homology. The relative importance of the weighting factors attached to the secondary chemical shifts of the five types of resonances relative to that of sequence similarity was optimized empirically. TALOS yields the 10 triplets which have the closest similarity in secondary chemical shift and amino acid sequence to those of the query sequence. If the central residues in these 10 triplets exhibit similar {phi} and {psi} backbone angles, their averages can reliably be used as angular restraints for the protein whose structure is being studied. Tests carried out for proteins of known structure indicate that the root-mean-square difference (rmsd) between the output of TALOS and the X-ray derived backbone angles is about 15 deg. Approximately 3% of the predictions made by TALOS are found to be in error.

Structure and chemical bond characteristics of LaB6

International Nuclear Information System (INIS)

Bai Lina; Ma Ning; Liu Fengli

2009-01-01

The structure and chemical bond characteristics of LaB 6 have been achieved by means of the density functional theory using the state-of-the-art full-potential linearized augmented plane wave (FPLAPW) method, which are implemented within the EXCITING code. The results show our optimized lattice constant a (4.158 A), parameter z (0.1981) and bulk modulus B (170.4 GPa) are in good agreement with the corresponding experimental data. Electron localization function (ELF) shows the La-La bond mainly is ionic bond, La-B bond is between ionic and covalent bond while the covalent bond between the nearest neighbor B atoms (B2 and B3) is a little stronger than that between the nearer neighbor B atoms (B1 and B4).

Chemical cosmology

CERN Document Server

Boeyens, Jan CA

2010-01-01

The composition of the most remote objects brought into view by the Hubble telescope can no longer be reconciled with the nucleogenesis of standard cosmology and the alternative explanation, in terms of the LAMBDA-Cold-Dark-Matter model, has no recognizable chemical basis. A more rational scheme, based on the chemistry and periodicity of atomic matter, opens up an exciting new interpretation of the cosmos in terms of projective geometry and general relativity. The response of atomic structure to environmental pressure predicts non-Doppler cosmical redshifts and equilibrium nucleogenesis by alp

CSI 3.0: a web server for identifying secondary and super-secondary structure in proteins using NMR chemical shifts.

Science.gov (United States)

Hafsa, Noor E; Arndt, David; Wishart, David S

2015-07-01

The Chemical Shift Index or CSI 3.0 (http://csi3.wishartlab.com) is a web server designed to accurately identify the location of secondary and super-secondary structures in protein chains using only nuclear magnetic resonance (NMR) backbone chemical shifts and their corresponding protein sequence data. Unlike earlier versions of CSI, which only identified three types of secondary structure (helix, β-strand and coil), CSI 3.0 now identifies total of 11 types of secondary and super-secondary structures, including helices, β-strands, coil regions, five common β-turns (type I, II, I', II' and VIII), β hairpins as well as interior and edge β-strands. CSI 3.0 accepts experimental NMR chemical shift data in multiple formats (NMR Star 2.1, NMR Star 3.1 and SHIFTY) and generates colorful CSI plots (bar graphs) and secondary/super-secondary structure assignments. The output can be readily used as constraints for structure determination and refinement or the images may be used for presentations and publications. CSI 3.0 uses a pipeline of several well-tested, previously published programs to identify the secondary and super-secondary structures in protein chains. Comparisons with secondary and super-secondary structure assignments made via standard coordinate analysis programs such as DSSP, STRIDE and VADAR on high-resolution protein structures solved by X-ray and NMR show >90% agreement between those made with CSI 3.0. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

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.

Core-shell SrTiO3/graphene structure by chemical vapor deposition for enhanced photocatalytic performance

Science.gov (United States)

He, Chenye; Bu, Xiuming; Yang, Siwei; He, Peng; Ding, Guqiao; Xie, Xiaoming

2018-04-01

Direct growth of high quality graphene on the surface of SrTiO3 (STO) was realized through chemical vapor deposition (CVD), to construct few-layer 'graphene shell' on every STO nanoparticle. The STO/graphene composite shows significantly enhanced UV light photocatalytic activity compared with the STO/rGO reference. Mechanism analysis confirms the role of special core-shell structure and chemical bond (Tisbnd C) for rapid interfacial electron transfer and effective electron-hole separation.

Stability of biogenic metal(loid) nanomaterials related to the colloidal stabilization theory of chemical nanostructures.

Science.gov (United States)

Piacenza, Elena; Presentato, Alessandro; Turner, Raymond J

2018-02-25

In the last 15 years, the exploitation of biological systems (i.e. plants, bacteria, mycelial fungi, yeasts, and algae) to produce metal(loid) (Me)-based nanomaterials has been evaluated as eco-friendly and a cost-effective alternative to the chemical synthesis processes. Although the biological mechanisms of biogenic Me-nanomaterial (Bio-Me-nanomaterials) production are not yet completely elucidated, a key advantage of such bio-nanostructures over those chemically synthesized is related to their natural thermodynamic stability, with several studies ascribed to the presence of an organic layer surrounding these Bio-Me-nanostructures. Different macromolecules (e.g. proteins, peptides, lipids, DNA, and polysaccharides) or secondary metabolites (e.g. flavonoids, terpenoids, glycosides, organic acids, and alkaloids) naturally produced by organisms have been indicated as main contributors to the stabilization of Bio-Me-nanostructures. Nevertheless, the chemical-physical mechanisms behind the ability of these molecules in providing stability to Bio-Me-nanomaterials are unknown. In this context, transposing the stabilization theory of chemically synthesized Me-nanomaterials (Ch-Me-nanomaterials) to biogenic materials can be used towards a better comprehension of macromolecules and secondary metabolites role as stabilizing agents of Bio-Me-nanomaterials. According to this theory, nanomaterials are generally featured by high thermodynamic instability in suspension, due to their high surface area and surface energy. This feature leads to the necessity to stabilize chemical nanostructures, even during or directly after their synthesis, through the development of (i) electrostatic, (ii) steric, or (iii) electrosteric interactions occurring between molecules and nanomaterials in suspension. Based on these three mechanisms, this review is focused on parallels between the stabilization of biogenic or chemical nanomaterials, suggesting which chemical-physical mechanisms may be

Student Misconceptions in Chemical Equilibrium as Related to Cognitive Level and Achievement.

Science.gov (United States)

Wheeler, Alan E.; Kass, Heidi

Reported is an investigation to determine the nature and extent of student misconceptions in chemical equilibrium and to ascertain the degree to which certain misconceptions are related to chemistry achievement and to performance on specific tasks involving cognitive transformations characteristic of the concrete and formal operational stages of…

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.

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.

Electronic structure, chemical bonding, phase stability, and ground-state properties of YNi2-x(Co/Cu)xB2C

International Nuclear Information System (INIS)

Ravindran, P.; Johansson, B.; Eriksson, O.

1998-01-01

In order to understand the role of Ni site substitution on the electronic structure and chemical bonding in YNi 2 B 2 C, we have made systematic electronic-structure studies on YNi 2 B 2 C as a function of Co and Cu substitution using the supercell approach within the local density approximation. The equilibrium volume, bulk modulus (B 0 ) and its pressure derivative (B 0 ' ), Grueneisen constant (γ G ), Debye temperature (Θ D ), cohesive energy (E c ), and heat of formation (ΔH) are calculated for YNi 2-x (Co/Cu) x B 2 C (x=0,0.5,1.0,1.5,2). From the total energy, electron-energy band structure, site decomposed density of states, and charge-density contour we have analyzed the structural stability and chemical bonding behavior of YNi 2 B 2 C as a function of Co/Cu substitution. We find that the simple rigid band model successfully explains the electronic structure and structural stability of Co/Cu substitution for Ni. In addition to studying the chemical bonding and electronic structure we present a somewhat speculative analysis of the general trends in the behavior of critical temperature for superconductivity as a function of alloying. copyright 1998 The American Physical Society

Rheological, structural and chemical evolution of bitumen under gamma irradiation

International Nuclear Information System (INIS)

Mouazen, M.; Poulesquen, A.; Bart, F.; Masson, J.; Charlot, M.; Vergnes, B.

2013-01-01

Bitumen derived from crude oil by fractional distillation has been used in the nuclear industry as a radioactive waste encapsulation matrix. When subjected to α, β and γ self-irradiation, this organic matrix undergoes radiolysis, generating hydrogen bubbles and modifying the physical and chemical properties of the material. In this paper, the effects of irradiation on bitumen materials, especially in terms of its physical, chemical, structural and rheological properties, were characterized at radiation doses ranging from 1 to 7 MGy. An increase in the shear viscosity and melt yield stress was observed with increasing doses. Similarly, the elastic and viscous moduli (G' and G'') increase with the dose, with a more pronounced increase for G' that reflects enhanced elasticity arising from radiation-induced cross-linking. In addition, a low-frequency plateau is observed for G', reflecting pseudo-solid behavior and leading to an increase of the complex viscosity. This behavior is due to increased interactions between asphaltene particles, and to aromatization of the bitumen by γ-radiations. Cross-linking of bitumen enhances its strength, as confirmed by various techniques (modulated DSC, DTA/TGA, SEC, FTIR and XRD). (authors)

Combined use of computational chemistry and chemoinformatics methods for chemical discovery

Energy Technology Data Exchange (ETDEWEB)

Sugimoto, Manabu, E-mail: sugimoto@kumamoto-u.ac.jp [Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555 (Japan); Institute for Molecular Science, 38 Nishigo-Naka, Myodaiji, Okazaki 444-8585 (Japan); CREST, Japan Science and Technology Agency, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012 (Japan); Ideo, Toshihiro; Iwane, Ryo [Graduate School of Science and Technology, Kumamoto University, 2-39-1, Kurokami, Chuo-ku, Kumamoto 860-8555 (Japan)

2015-12-31

Data analysis on numerical data by the computational chemistry calculations is carried out to obtain knowledge information of molecules. A molecular database is developed to systematically store chemical, electronic-structure, and knowledge-based information. The database is used to find molecules related to a keyword of “cancer”. Then the electronic-structure calculations are performed to quantitatively evaluate quantum chemical similarity of the molecules. Among the 377 compounds registered in the database, 24 molecules are found to be “cancer”-related. This set of molecules includes both carcinogens and anticancer drugs. The quantum chemical similarity analysis, which is carried out by using numerical results of the density-functional theory calculations, shows that, when some energy spectra are referred to, carcinogens are reasonably distinguished from the anticancer drugs. Therefore these spectral properties are considered of as important measures for classification.

Chemical effects in the mine structure

International Nuclear Information System (INIS)

1992-02-01

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) [de

Comprehensive DFT study on molecular structures of Lewisites in support of the Chemical Weapons Convention

Science.gov (United States)

Saeidian, Hamid; Sahandi, Morteza

2015-11-01

The structure of all of Lewisite's stereoisomers has been examined by B3LYP/6-311++G(3df,3pd) calculations. The geometry analysis for trans Lewisite L1-1 shows that the calculated bond angles, bond distances and dipole moment have a satisfactory relation compared with experimental values. HOMO-LUMO analysis of Lewisites reveals that L1-2 and L3-7 have the maximum and minimum electrophilicity index, respectively. The calculated chemical shifts were compared with experimental data, showing a very good agreement both for 1H and 13C. The vibrational and Raman frequencies of Lewisites have been precisely assigned and theoretical data were compared with the experimental vibrations. The bonding trends and Mulliken and atomic polar tensor charge distribution in Lewisites can be explained by the Bent's rule and the donor-acceptor interaction, respectively.

Structural, mechanical and chemical evaluation of molar-incisor hypomineralization-affected enamel: A systematic review.

Science.gov (United States)

Elhennawy, Karim; Manton, David John; Crombie, Felicity; Zaslansky, Paul; Radlanski, Ralf J; Jost-Brinkmann, Paul-Georg; Schwendicke, Falk

2017-11-01

To systematically assess and contrast reported differences in microstructure, mineral density, mechanical and chemical properties between molar-incisor-hypomineralization-affected (MIH) enamel and unaffected enamel. Studies on extracted human teeth, clinically diagnosed with MIH, reporting on the microstructure, mechanical properties or the chemical composition and comparing them to unaffected enamel were reviewed. Electronic databases (PubMed, Embase and Google Scholar) were screened; hand searches and cross-referencing were also performed. Twenty-two studies were included. Fifteen studies on a total of 201 teeth investigated the structural properties, including ten (141 teeth) on microstructure and seven (60 teeth) on mineral density; six (29 teeth) investigated the mechanical properties and eleven (87 teeth) investigated the chemical properties of MIH-affected enamel and compared them to unaffected enamel. Studies unambiguously found a reduction in mineral quantity and quality (reduced Ca and P content), reduction of hardness and modulus of elasticity (also in the clinically sound-appearing enamel bordering the MIH-lesion), an increase in porosity, carbon/carbonate concentrations and protein content compared to unaffected enamel. were ambiguous with regard to the extent of the lesion through the enamel to the enamel-dentin junction, the Ca/P ratio and the association between clinical appearance and defect severity. There is an understanding of the changes related to MIH-affected enamel. The association of these changes with the clinical appearance and resulting implications for clinical management are unclear. MIH-affected enamel is greatly different from unaffected enamel. This has implications for management strategies. The possibility of correlating the clinical appearance of MIH-affected enamel with the severity of enamel changes and deducing clinical concepts (risk stratification etc.) is limited. Crown Copyright © 2017. Published by Elsevier Ltd. All

Structure and Properties of Hydrophobic Aggregation Hydrogel with Chemical Sensitive Switch

Directory of Open Access Journals (Sweden)

Jiufang Duan

2017-01-01

Full Text Available Hydrogels with chemical sensitive switch have control release properties in special environments. A series of polyacrylamide-octadecyl methacrylate hydrogels crosslinked by N,N′-bis (acryloyl cystamine were synthesized as potential chemical sensitive system. When this hydrogel encounters dithiothreitol it can change its quality. The properties of the hydrogels were characterized by infrared spectroscopy, contact angle, and scanning electron microscopy. The water absorption of the hydrogel has the maximum value of 475%, when the content of octadecyl methacrylate is 5 wt%. The amount of weight loss was changed from 34.6% to 17.2%, as the content of octadecyl methacrylate increased from 3 wt% to 9.4 wt%. At the same time, the stress of the hydrogel decreased from 67.01% to 47.61%; the strength of the hydrogel reaches to the maximum 0.367 Mpa at 7 wt% octadecyl methacrylate. The increasing content of octadecyl methacrylate from 3 wt% to 9.4 wt% can enhance the hydrophobicity of the hydrogel; the contact angle of water to hydrogel changed from 14.10° to 19.62°. This hydrogel has the porous structure which permits loading of oils into the gel matrix. The functionalities of the hydrogel make it have more widely potential applications in chemical sensitive response materials.

CyBy(2): a structure-based data management tool for chemical and biological data.

Science.gov (United States)

Höck, Stefan; Riedl, Rainer

2012-01-01

We report the development of a powerful data management tool for chemical and biological data: CyBy(2). CyBy(2) is a structure-based information management tool used to store and visualize structural data alongside additional information such as project assignment, physical information, spectroscopic data, biological activity, functional data and synthetic procedures. The application consists of a database, an application server, used to query and update the database, and a client application with a rich graphical user interface (GUI) used to interact with the server.

Relating structure and dynamics in organisation models

NARCIS (Netherlands)

Jonkers, C.M.; Treur, J.

2002-01-01

To understand how an organisational structure relates to dynamics is an interesting fundamental challenge in the area of social modelling. Specifications of organisational structure usually have a diagrammatic form that abstracts from more detailed dynamics. Dynamic properties of agent systems,

Relating structure and dynamics in organisation models

NARCIS (Netherlands)

Jonker, C.M.; Treur, J.

2003-01-01

To understand how an organisational structure relates to dynamics is an interesting fundamental challenge in the area of social modelling. Specifications of organisational structure usually have a diagrammatic form that abstracts from more detailed dynamics. Dynamic properties of agent systems, on

ANALYSIS AND IDENTIFICATION SPIKING CHEMICAL COMPOUNDS RELATED TO CHEMICAL WEAPON CONVENTION IN UNKNOWN WATER SAMPLES USING GAS CHROMATOGRAPHY AND GAS CHROMATOGRAPHY ELECTRON IONIZATION MASS SPECTROMETRY

Directory of Open Access Journals (Sweden)

Harry Budiman

2010-06-01

Full Text Available The identification and analysis of chemical warfare agents and their degradation products is one of important component for the implementation of the convention. Nowadays, the analytical method for determination chemical warfare agent and their degradation products has been developing and improving. In order to get the sufficient analytical data as recommended by OPCW especially in Proficiency Testing, the spiking chemical compounds related to Chemical Weapon Convention in unknown water sample were determined using two different techniques such as gas chromatography and gas chromatography electron-impact ionization mass spectrometry. Neutral organic extraction, pH 11 organic extraction, cation exchanged-methylation, triethylamine/methanol-silylation were performed to extract the chemical warfare agents from the sample, before analyzing with gas chromatography. The identification of chemical warfare agents was carried out by comparing the mass spectrum of chemicals with mass spectrum reference from the OPCW Central Analytical Database (OCAD library while the retention indices calculation obtained from gas chromatography analysis was used to get the confirmation and supported data of  the chemical warfare agents. Diisopropyl methylphosphonate, 2,2-diphenyl-2-hydroacetic acid and 3-quinuclidinol were found in unknown water sample. Those chemicals were classified in schedule 2 as precursor or reactant of chemical weapons compound in schedule list of Chemical Weapon Convention.   Keywords: gas chromatography, mass spectrometry, retention indices, OCAD library, chemical warfare agents

The role of chemical admixtures in the formation of the structure of cement stone

Directory of Open Access Journals (Sweden)

Sopov Viktor

2017-01-01

Full Text Available The influence of sulfates and carbonates of potassium and sodium on the character of the formation of the microstructure of cement stone was studied. The role of cations in the structure formation of cement stone is shown. The efficiency of chemical additives, hardening accelerators, was estimated from the ratio of the volumes of gel and capillary micropores. The ratio of gel and capillary pores allows to determine the efficiency coefficient of the action of chemical additives. It is shown that the potassium carbonate for Portland cement is the most effective additive for hardening in terms of microstructure modification, and potassium sulfate for slag Portland cement.

Structure Analysis of Effective Chemical Compounds against Dengue Viruses Isolated from Isatis tinctoria.

Science.gov (United States)

Gao, Bo; Zhang, Jianming; Xie, Lianhui

2018-01-01

The history of Chinese herb research can be traced back to thousands of years ago, and the abundant knowledge accumulated for these herbs makes them good candidates for developing new natural drugs. Isatis tinctoria is probably the most well-studied Chinese herb, which has been identified to be effective against dengue fever. However, the underlying biological mechanisms are still unclear. In this study, we adopt combined methods of bioactive trace technology and phytochemical extraction and separation, to guide the isolation and purification of the effective chemical constituents on the water-soluble components of aerial parts of Isatis tinctoria . In addition, we apply polarimetry and 1D or 2D nuclear magnetic resonance (NMR) spectroscopy to identify their structures, which lay a foundation for further study on the biological mechanisms underlying medicinal effects of Isatis tinctoria using in vitro and in vivo experiments. Specifically, we identify and infer the structures of 27 types of chemical compounds named GB-1, GB-2, …, GB-27, respectively, among which GB-7 is a novel compound. Further study of these compounds is critical to reveal the secrets behind the medicinal effects of Isatis tinctoria .

Structure Analysis of Effective Chemical Compounds against Dengue Viruses Isolated from Isatis tinctoria

Directory of Open Access Journals (Sweden)

Bo Gao

2018-01-01

Full Text Available The history of Chinese herb research can be traced back to thousands of years ago, and the abundant knowledge accumulated for these herbs makes them good candidates for developing new natural drugs. Isatis tinctoria is probably the most well-studied Chinese herb, which has been identified to be effective against dengue fever. However, the underlying biological mechanisms are still unclear. In this study, we adopt combined methods of bioactive trace technology and phytochemical extraction and separation, to guide the isolation and purification of the effective chemical constituents on the water-soluble components of aerial parts of Isatis tinctoria. In addition, we apply polarimetry and 1D or 2D nuclear magnetic resonance (NMR spectroscopy to identify their structures, which lay a foundation for further study on the biological mechanisms underlying medicinal effects of Isatis tinctoria using in vitro and in vivo experiments. Specifically, we identify and infer the structures of 27 types of chemical compounds named GB-1, GB-2, …, GB-27, respectively, among which GB-7 is a novel compound. Further study of these compounds is critical to reveal the secrets behind the medicinal effects of Isatis tinctoria.

Impact of crystallization on the structure and chemical durability of borosilicate glass

International Nuclear Information System (INIS)

Nicoleau, Elodie

2016-01-01

This work describes a new approach to help understand the chemical durability of partially crystallized nuclear waste conditioning matrices. Among the studies carried out on nuclear waste deep geological disposal, long term behavior studies have so far been conducted on homogeneous glassy matrices. However, as the crystalline phases may generate modifications in the chemical composition and properties of such matrices, the description and a better understanding of their effects on the chemical durability of waste packages are of primary importance. A protocol to study the durability of heterogeneous model matrices of nuclear interest containing different types of crystalline phases was developed. It is based on a detailed description of the morphology, microstructure and structure of the glassy matrix and crystalline phases, and on the study of various alteration regimes. Three crystal phases that may form when higher concentrations of waste are immobilized in Uranium Oxide type conditioning glasses were studied: alkali and alkaline earth molybdates, rare earth silicates and ruthenium oxide. The results highlight the roles of the composition and the structure of the surrounding glassy matrix as the parameters piloting the alteration kinetics of the partially crystallized glassy matrices. This behavior is identical whatever the nature of the crystalline phases, as long as these phases do not lead to a composition gradient and do not percolate within the glassy matrix. Given these results, a methodology to study partially crystallized matrices with no composition gradient is then suggested. Its key development lies firstly in the evaluation of the behavior of partially crystallized matrices through the experimental study of the residual glassy matrix in various alteration regimes. This methodology may be adapted to the case of new glass formulations with more complex compositions (e.g. highly waste-loaded glass), which may contain crystals formed during cooling

Electronic structure of magnesium diboride and related compounds

International Nuclear Information System (INIS)

Paduani, C.

2003-01-01

The electronic structure of AlB 2 -type diborides and related compounds has been investigated in first-principles calculations with the molecular cluster discrete variational method. For MgB 2 was studied the effect of the lattice relaxation on the total density of states at the Fermi energy (N(ε F )). The results indicated that a contraction of about 2% in the lattice spacings a and c can lead to a slight increase of N(ε F ) for boron. In the MB 2 diborides, M=Al, Ti, V, Cr, Zr, Nb, Mo and Ta, the largest contributions to N(ε F ) is observed for Cr, Mo and Nb. TiB 2 possess the highest chemical stability in the series. The electronic specific heat coefficient γ also is calculated for the diborides. The method is employed to obtain the partial B2p contribution to the total DOS at the Fermi level with the introduction of a monolayer of solute atoms as a substitution for Mg atoms of Na, Al, Ca, Ti, V, Cr, Zr, Nb, Mo and Ta in layered superstructures.. /M/B 2 /Mg/B 2 /.. A stronger covalent bonding between boron atoms is identified in these cases. (copyright 2003 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

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...

Effect of chemical peeling on the skin in relation to UV irradiation.

Science.gov (United States)

Funasaka, Yoko; Abdel-Daim, Mohamed; Kawana, Seiji; Nishigori, Chikako

2012-07-01

Chemical peeling is one of the dermatological treatments available for certain cutaneous diseases and conditions or improvement of cosmetic appearance of photoaged skin. However, it needs to be clarified whether the repetitive procedure of chemical peeling on photodamaged skin is safe and whether the different chemicals used for peeling results in similar outcomes or not. In this article, we reviewed the effect of peeling or peeling agents on the skin in relation to ultraviolet (UV) radiation. The pretreatment of peeling agents usually enhance UV sensitivity by inducing increased sunburn cell formation, lowering minimum erythematous dose and increasing cyclobutane pyrimidine dimers. However, this sensitivity is reversible and recovers to normal after 1-week discontinuation. Using animals, the chronic effect of peeling and peeling agents was shown to prevent photocarcinogenesis. There is also an in vitro study using culture cells to know the detailed mechanisms of peeling agents, especially on cell proliferation and apoptotic changes via activating signalling cascades and oxidative stress. It is important to understand the effect of peeling agents on photoaged skin and to know how to deal with UV irradiation during the application of peeling agents and treatment of chemical peeling in daily life. © 2012 John Wiley & Sons A/S.

Recurrence Relations for the Equilibrium Means of Distributions Arising in Chemical Reactions

Directory of Open Access Journals (Sweden)

E.K. Elsheikh

1997-12-01

Full Text Available In this paper we derive recurrence relations that describe how the equilibrium mean of the number molecules of a reactant varies with each of the parameters defining the initial state for four basic reversible chemical reactions. In essence, the relations provide a rationale for updating the equilibrium mean following the addition (or removal of a molecule of one of the types involved in the reaction, there being a relation for each type. With a new parameterization introduced for each reaction, the relations provide a convenient means of evaluating the means, variances and other important moments without any need to work out the underlying distributions. As an application, the relations are used to numerically assess-approximate expressions for the means and variances.

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.

Relations between structural and superconducting properties of bulk and thin film high-Tc materials

International Nuclear Information System (INIS)

Hessel Andersen, N.

1994-06-01

The structural ordering of oxygen deficient and Co-doped YBCO (YBa 2 Cu 3-y Co y O 6+x ) have been studied experimentally, and by computer simulations of the oxygen ordering in the basal plane of the structure. The calculations are based on the two-dimensional ASYNNNI model and its modifications. Good agreement is established between the ASYNNNI calculations and the experimentally observed structural properties of the double cell ortho-II structure and the oxygen disordering process from Co-doping into the basal plane. A model that relates the superconducting transition temperature T c (x) of undoped YBCO and T c (y) of Co-doped YBCO to the formation of specific domains of the two orthorhombic ordered oxygen phases, ortho-I and ortho-II, shows a close agreement with experimental T c (x) and T c (y) data of samples prepared under equilibrium conditions. The structural changes as a result of metal ion substitutions and oxidation/reduction processes have been studied by neutron powder diffraction in Pb 2 Sr 2 Ln 1-x Ca x Cu 3 O 8+y (Ln = Y and Ho), Nd 1.85 Ce 0.15 CuO 4+y , and chemically oxidized La 2-x Sr x CuO 4+y 2 Cu 3-y Al y O 6+x (y 2 Cu 3 O 6+x and Bi 2 Sr 2 CaCu 2 O 8+x thin films deposited on SrTiO 3 (001), MgO (001), LaAlO 3 (001), and NdGaO 3 (001) substrates has been studied by x-ray diffraction, TEM and RBS, and the structural ordering has been analysed in relation to their superconducting properties. (au) (30 ills., 29 refs.)

Chemical structures of an n-butanol counterflow flame

Energy Technology Data Exchange (ETDEWEB)

Sarathy, S.M.; Thomson, M.J. [Toronto Univ., ON (Canada). Dept. of Mechanical and Industrial Engineering

2007-07-01

N-butanol, also known as biobutanol, is an attractive alternative biofuel that can replace gasoline in transportation applications. Biobutanol can be produced via the fermentation of sugars, starches, and lignocellulose obtained from agricultural feedstocks. Although biobutanol offers several advantages over ethanol, its detailed combustion characteristics are not well known. In order to determine the effect of fuel structure on combustion products, this paper presented the results of a study that examined the emission and temperature profiles of an n-butanol counterflow flame. The paper presented the experimental data and discussed the potential reaction mechanisms that rationalized the observed species profiles. It was found that significant quantities of acetylene, acetaldehyde, ethane, and propene were measured in the n-butanol flame and that the reaction pathways leading to the formation of these compounds were yet to be identified. In addition, significant concentrations of formaldehyde and acetaldehyde were found. Results will be utilized to validate a detailed chemical kinetic model for n-butanol combustion. 13 refs., 3 figs.

Electronic, structural and chemical effects of charge-transfer at organic/inorganic interfaces

Science.gov (United States)

Otero, R.; Vázquez de Parga, A. L.; Gallego, J. M.

2017-07-01

During the last decade, interest on the growth and self-assembly of organic molecular species on solid surfaces spread over the scientific community, largely motivated by the promise of cheap, flexible and tunable organic electronic and optoelectronic devices. These efforts lead to important advances in our understanding of the nature and strength of the non-bonding intermolecular interactions that control the assembly of the organic building blocks on solid surfaces, which have been recently reviewed in a number of excellent papers. To a large extent, such studies were possible because of a smart choice of model substrate-adsorbate systems where the molecule-substrate interactions were purposefully kept low, so that most of the observed supramolecular structures could be understood simply by considering intermolecular interactions, keeping the role of the surface always relatively small (although not completely negligible). On the other hand, the systems which are more relevant for the development of organic electronic devices include molecular species which are electron donors, acceptors or blends of donors and acceptors. Adsorption of such organic species on solid surfaces is bound to be accompanied by charge-transfer processes between the substrate and the adsorbates, and the physical and chemical properties of the molecules cannot be expected any longer to be the same as in solution phase. In recent years, a number of groups around the world have started tackling the problem of the adsorption, self- assembly and electronic and chemical properties of organic species which interact rather strongly with the surface, and for which charge-transfer must be considered. The picture that is emerging shows that charge transfer can lead to a plethora of new phenomena, from the development of delocalized band-like electron states at molecular overlayers, to the existence of new substrate-mediated intermolecular interactions or the strong modification of the chemical

Phenomenological structure functions and Gribov-Lipatov relation

International Nuclear Information System (INIS)

Choudhary, D.K.; Misra, A.K.

1987-01-01

An analysis of the Giribov-Lipatov relation using the phenomenological forms of the structure function F 2 ep is made. The analysis indicate breakdown of the relation at PETRA energies. Plausible reasons of the breakdown of Gribov-Lipatov relation are discussed together with its phenomenological form. 33 refs., 6 figures. (author)

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

International Nuclear Information System (INIS)

Belio R, I.A.; Reyes G, J.

1998-01-01

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 (PO 4 ) 6 (OH 4 ) 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)

Chemical and structural analysis of Eucalyptus globulus and E. camaldulensis leaf cuticles: a lipidized cell wall region

Directory of Open Access Journals (Sweden)

Paula eGuzmán

2014-09-01

Full Text Available The plant cuticle has traditionally been conceived as an independent hydrophobic layer that covers the external epidermal cell wall. Due to its complexity, the existing relationship between cuticle chemical composition and ultra-structure remains unclear to date. This study aimed to examine the link between chemical composition and structure of isolated, adaxial leaf cuticles of Eucalyptus camaldulensis and E. globulus by the gradual extraction and identification of lipid constituents (cutin and soluble lipids, coupled to spectroscopic and microscopic analyses. The soluble compounds and cutin monomers identified could not be assigned to a concrete internal cuticle ultra-structure. After cutin depolymerization, a cellulose network resembling the cell wall was observed, with different structural patterns in the regions ascribed to the cuticle proper and cuticular layer, respectively. Our results suggest that the current cuticle model should be revised, stressing the presence and major role of cell wall polysaccharides. It is concluded that the cuticle may be interpreted as a modified cell wall region which contains additional lipids. The major heterogeneity of the plant cuticle makes it difficult to establish a direct link between cuticle chemistry and structure with the existing methodologies.

Effort problem of chemical pipelines

Energy Technology Data Exchange (ETDEWEB)

Okrajni, J.; Ciesla, M.; Mutwil, K. [Silesian Technical University, Katowice (Poland)

1998-12-31

The problem of the technical state assessment of the chemical pipelines working under mechanical and thermal loading has been shown in the paper. The pipelines effort after the long time operating period has been analysed. Material geometrical and loading conditions of the crack initiation and crack growth process in the chosen object has been discussed. Areas of the maximal effort have been determined. The material structure charges after the long time operating period have been described. Mechanisms of the crack initiation and crack growth in the pipeline elements have been analysed and mutual relations between the chemical and mechanical influences have been shown. (orig.) 16 refs.

Chemical warfare agents.

Science.gov (United States)

Kuca, Kamil; Pohanka, Miroslav

2010-01-01

Chemical warfare agents are compounds of different chemical structures. Simple molecules such as chlorine as well as complex structures such as ricin belong to this group. Nerve agents, vesicants, incapacitating agents, blood agents, lung-damaging agents, riot-control agents and several toxins are among chemical warfare agents. Although the use of these compounds is strictly prohibited, the possible misuse by terrorist groups is a reality nowadays. Owing to this fact, knowledge of the basic properties of these substances is of a high importance. This chapter briefly introduces the separate groups of chemical warfare agents together with their members and the potential therapy that should be applied in case someone is intoxicated by these agents.

Thai students' mental model of chemical bonding

Science.gov (United States)

Sarawan, Supawadee; Yuenyong, Chokchai

2018-01-01

This Research was finding the viewing about concept of chemical bonding is fundamental to subsequent learning of various other topics related to this concept in chemistry. Any conceptions about atomic structures that students have will be shown their further learning. The purpose of this study is to interviews conceptions held by high school chemistry students about metallic bonding and to reveal mental model of atomic structures show according to the educational level. With this aim, the questionnaire prepared making use of the literature and administered for analysis about mental model of chemical bonding. It was determined from the analysis of answers of questionnaire the 10th grade, 11th grade and 12th grade students. Finally, each was shown prompts in the form of focus cards derived from curriculum material that showed ways in which the bonding in specific metallic substances had been depicted. Students' responses revealed that learners across all three levels prefer simple, realistic mental models for metallic bonding and reveal to chemical bonding.

Chemical structure and radiation stability of solid crystalline antibiotics: thiamphenicol and chloramphenicol

International Nuclear Information System (INIS)

Varshney, Lalit; Soe Nwe

1997-01-01

Antibiotics in solid state show significant radiation resistance and some of them are exposed to gamma or electron beam irradiation for sterilization. Even small radiation degradation in solid state antibiotics is not desirable. Two antibiotics namely thiamphenicol (TPL) and chloramphenicol (CPL) having similar chemical and solid state structure were irradiated at different graded radiation doses to study their stability. Differential scanning calorimetry (DSC) was used to evaluate purity, entropy of radiation processing, heat of fusion and melting point. (author). 3 refs., 1 tab

An orthologous transcriptional signature differentiates responses towards closely related chemicals in Arabidopsis thaliana and brassica napus

Science.gov (United States)

Herbicides are structurally diverse chemicals that inhibit plant-specific targets, however their off-target and potentially differentiating side-effects are less well defined. In this study, genome-wide expression profiling based on Affymetrix AtH1 arrays was used to identify dis...

Identification of new candidate drugs for lung cancer using chemical-chemical interactions, chemical-protein interactions and a K-means clustering algorithm.

Science.gov (United States)

Lu, Jing; Chen, Lei; Yin, Jun; Huang, Tao; Bi, Yi; Kong, Xiangyin; Zheng, Mingyue; Cai, Yu-Dong

2016-01-01

Lung cancer, characterized by uncontrolled cell growth in the lung tissue, is the leading cause of global cancer deaths. Until now, effective treatment of this disease is limited. Many synthetic compounds have emerged with the advancement of combinatorial chemistry. Identification of effective lung cancer candidate drug compounds among them is a great challenge. Thus, it is necessary to build effective computational methods that can assist us in selecting for potential lung cancer drug compounds. In this study, a computational method was proposed to tackle this problem. The chemical-chemical interactions and chemical-protein interactions were utilized to select candidate drug compounds that have close associations with approved lung cancer drugs and lung cancer-related genes. A permutation test and K-means clustering algorithm were employed to exclude candidate drugs with low possibilities to treat lung cancer. The final analysis suggests that the remaining drug compounds have potential anti-lung cancer activities and most of them have structural dissimilarity with approved drugs for lung cancer.

On the structural factors of soil humic matter related to soil water repellence in fire-affected soils

Science.gov (United States)

Almendros, G.; González-Vila, F. J.; González-Pérez, J. A.; Knicker, H.; De la Rosa, J. M.; Dettweiler, C.; Hernández, Z.

2012-04-01

In order to elucidate the impact of forest fires on physical and chemical properties of the soils as well as on the chemical composition of the soil organic matter, samples from two Mediterranean soils with contrasted characteristics and vegetation (O horizon, Lithic Leptosols under Quercus ilex and Pinus pinaster) and one agricultural soil (Ap horizon, Luvisol) were heated at 350 °C in laboratory conditions for three successive steps up to 600 s. The C- and N-depletion in the course of the heating showed small changes up to an oxidation time of 300 s. On the other side, and after 600 s, considerable C-losses (between 21% in the Luvisol and 50% in the Leptosols) were observed. The relatively low N-depletion ca. 4% (Luvisol) and 21% (Leptosol under pine) suggested preferential loss of C and the subsequent relative enrichment of nitrogen. Paralleling the progressive depletion of organic matter, the Leptosols showed a significant increase of both pH and electrical conductivity. The former change paralleled the rapid loss of carboxyl groups, whereas the latter point to the relative enrichment of ash with a bearing on the concentration of inorganic ions, which could be considered a positive effect for the post-fire vegetation. The quantitative and qualitative analyses by solid-state 13C NMR spectra of the humic fractions in the samples subjected to successive heating times indicate significant concentration of aromatic structures newly-formed in the course of the dehydration and cyclization of carbohydrates (accumulation of black carbon-type polycyclic aromatic structures), and probably lipids and peptides. The early decarboxylation, in addition to the depletion of O-alkyl hydrophilic constituents and further accumulation of secondary aromatic structures resulted in the dramatic increase in the soil water drop penetration time. It was confirmed that this enhancement of the soil hydrophobicity is not related to an increased concentration of soil free lipid, but is

Chemical durability of silicoborate glasses

International Nuclear Information System (INIS)

Nieto, M.I.; Rodriguez, M.A.; Rubio, J.; Fernandez, A.; Oteo, J.L.

1987-01-01

A general view of the durability in silicoborate glasses is presented with more emphasis on the etching factors (chemical composition, lattice structure, pH...) the techniques used for this study and the experimental results. Likewise, the research presently developed in this area at the Instituto de Ceramica y Vidrio, CSIC, is related to the applications. Future research in this field is also mentioned. (author) 15 figs

A 3D visualization of spatial relationship between geological structure and groundwater chemical profile around Iwate volcano, Japan: based on the ARCGIS 3D Analyst

Science.gov (United States)

Shibahara, A.; Ohwada, M.; Itoh, J.; Kazahaya, K.; Tsukamoto, H.; Takahashi, M.; Morikawa, N.; Takahashi, H.; Yasuhara, M.; Inamura, A.; Oyama, Y.

2009-12-01

We established 3D geological and hydrological model around Iwate volcano to visualize 3D relationships between subsurface structure and groundwater profile. Iwate volcano is a typical polygenetic volcano located in NE Japan, and its body is composed of two stratovolcanoes which have experienced sector collapses several times. Because of this complex structure, groundwater flow around Iwate volcano is strongly restricted by subsurface construction. For example, Kazahaya and Yasuhara (1999) clarified that shallow groundwater in north and east flanks of Iwate volcano are recharged at the mountaintop, and these flow systems are restricted in north and east area because of the structure of younger volcanic body collapse. In addition, Ohwada et al. (2006) found that these shallow groundwater in north and east flanks have relatively high concentration of major chemical components and high 3He/4He ratios. In this study, we succeeded to visualize the spatial relationship between subsurface structure and chemical profile of shallow and deep groundwater system using 3D model on the GIS. In the study region, a number of geological and hydrological datasets, such as boring log data and groundwater chemical profile, were reported. All these paper data are digitized and converted to meshed data on the GIS, and plotted in the three dimensional space to visualize spatial distribution. We also inputted digital elevation model (DEM) around Iwate volcano issued by the Geographical Survey Institute of Japan, and digital geological maps issued by Geological Survey of Japan, AIST. All 3D models are converted into VRML format, and can be used as a versatile dataset on personal computer.

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.

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

International Nuclear Information System (INIS)

Al Alam, A.F.

2009-06-01

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. ScFe 2 ) and Haucke (e.g. LaNi 5 ) phases on one hand, and ternary cerium based (e.g. CeRhSn) and uranium based (e.g. U 2 Ni 2 Sn) alloys on the other hand. (author)

Meteorite impact craters and possibly impact-related structures in Estonia

Science.gov (United States)

Plado, Jüri

2012-10-01

Three structures (Neugrund, Kärdla, and Kaali) of proven impact origin make Estonia the most cratered country in the world by area. In addition, several candidate impact structures exist, waiting for future studies to determine their origin. This article is an overview of these proven and possible impact structures, including some breccia layers. It summarizes the information and descriptions of the morphology; geological characteristics; and mineralogical, chemical, and geophysical data available in the literature. The overview was prepared to make information in many earlier publications in local journals (many of which had been published in Estonian or Russian) accessible to the international community. This review summarizes the facts and observations in a historical fashion, summarizing the current state of knowledge with some additional comments, and providing the references.

Chemical constituents of Salacia elliptica (Celastraceae)

International Nuclear Information System (INIS)

Duarte, Lucienir Pains; Figueiredo, Rute Cunha; Sousa, Grasiely Faria de; Soares, Debora Barbosa da Silva; Rodrigues, Salomao Bento Vasconcelos; Silva, Fernando Cesar; Silva, Gracia Divina de Fatima; Vieira Filho, Sidney Augusto

2010-01-01

The chemical investigation of Salacia elliptica allowed to the isolation of 20 constituents: two polyols, one xanthone, a mixture of long chain hydrocarbons, one carboxylic acid, one polymer, two steroidal compounds, one aromatic ester and eleven pentacyclic triterpenes. These triterpenes include 3β-stearyloxy-oleanane, 3β-stearyloxy-ursane, one seco-friedelane, and eight compounds of the friedelane series. The chemical structure and the relative configuration of a new triterpene 1,3-dioxo-16α-hydroxyfriedelane (15) were established through 1 H and 13 C NMR including 2D experiments (HMBC, HMQC, COSY and NOESY) and herein reported for the first time (author)

Reaction kinetics and transformation of carbadox and structurally related compounds with aqueous chlorine.

Science.gov (United States)

Shah, Amisha D; Kim, Jae-Hong; Huang, Ching-Hua

2006-12-01

The potential release of carbadox (CDX), a commonly used antibacterial agent in swine husbandry, into water systems is of a concern due to its carcinogenic and genotoxic effects. Until this study, the reactivity of carbadox (possessing quinoxaline N,N'-dioxide and hydrazone moieties) toward aqueous chlorine has yetto be investigated in depth. Chemical reactivity, reaction kinetics, and transformation pathways of carbadox and structurally related compounds with free chlorine under typical water treatment conditions were determined. This study found that only CDX and desoxycarbadox (DCDX), a main metabolite of CDX with no ring N-oxide groups, react rapidly with free chlorine while other structurally related compounds including olaquindox, quindoxin, quinoxaline N-oxide, quinoxaline, and quinoline N-oxide do not. The reaction kinetics of CDX and DCDX with chlorine are highly pH dependent (e.g., the apparent second-order rate constant, kapp, for CDX ranges from 51.8 to 3.15 x 10(4) M(-1)s(-1) at pH 4-11). The high reactivity of CDX and DCDX to chlorine involves deprotonation of their hydrazone N-H moieties where initial chlorine attack results in a reactive intermediate that is further attacked by nucleophiles in the matrix to yield non-chlorinated, hydroxylated, and larger molecular weight byproducts. All of the CDX's byproducts retain their biologically active N-oxide groups, suggesting that they may remain as active antibacterial agents.

Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.

Science.gov (United States)

Koch, Mathilde; Duigou, Thomas; Carbonell, Pablo; Faulon, Jean-Loup

2017-12-19

Network generation tools coupled with chemical reaction rules have been mainly developed for synthesis planning and more recently for metabolic engineering. Using the same core algorithm, these tools apply a set of rules to a source set of compounds, stopping when a sink set of compounds has been produced. When using the appropriate sink, source and rules, this core algorithm can be used for a variety of applications beyond those it has been developed for. Here, we showcase the use of the open source workflow RetroPath2.0. First, we mathematically prove that we can generate all structural isomers of a molecule using a reduced set of reaction rules. We then use this enumeration strategy to screen the chemical space around a set of monomers and predict their glass transition temperatures, as well as around aminoglycosides to search structures maximizing antibacterial activity. We also perform a screening around aminoglycosides with enzymatic reaction rules to ensure biosynthetic accessibility. We finally use our workflow on an E. coli model to complete E. coli metabolome, with novel molecules generated using promiscuous enzymatic reaction rules. These novel molecules are searched on the MS spectra of an E. coli cell lysate interfacing our workflow with OpenMS through the KNIME Analytics Platform. We provide an easy to use and modify, modular, and open-source workflow. We demonstrate its versatility through a variety of use cases including molecular structure enumeration, virtual screening in the chemical space, and metabolome completion. Because it is open source and freely available on MyExperiment.org, workflow community contributions should likely expand further the features of the tool, even beyond the use cases presented in the paper.

Direction dependent structures in general relativity

International Nuclear Information System (INIS)

Herberthson, M.

1993-01-01

This thesis deals with, within the theory of general relativity, asymptotic properties of certain types of space-times. Using conformal transformations, it is possible to describe asymptotic properties of a physical space-time in terms of the local behaviour of the new, rescaled space-time. One then uses so called direction dependent structures. We present two such structures and applications to them. One structure is used in the study of spacelike (or spatial) infinity. We discuss the asymptotic conditions on the gravitational and the electromagnetic field, especially the conditions put on directions corresponding to future and past null infinity. It is shown that these fields have desired physical properties. The other structure is used in connection with timelike infinity. Using this structure, we suggest a new definition of timelike infinity. This definition differs significantly from earlier definitions, and leads to the concept of asymptotically stationary space-times. We also suggest a definition of asymptotic flatness at future null infinity, and a definition of a black hole which is, in a sense, local. Both of these definitions fit nicely into the structure. (24 refs.)

Structural plasticity: how intermetallics deform themselves in response to chemical pressure, and the complex structures that result.

Science.gov (United States)

Berns, Veronica M; Fredrickson, Daniel C

2014-10-06

Interfaces between periodic domains play a crucial role in the properties of metallic materials, as is vividly illustrated by the way in which the familiar malleability of many metals arises from the formation and migration of dislocations. In complex intermetallics, such interfaces can occur as an integral part of the ground-state crystal structure, rather than as defects, resulting in such marvels as the NaCd2 structure (whose giant cubic unit cell contains more than 1000 atoms). However, the sources of the periodic interfaces in intermetallics remain mysterious, unlike the dislocations in simple metals, which can be associated with the exertion of physical stresses. In this Article, we propose and explore the concept of structural plasticity, the hypothesis that interfaces in complex intermetallic structures similarly result from stresses, but ones that are inherent in a defect-free parent structure, rather than being externally applied. Using DFT-chemical pressure analysis, we show how the complex structures of Ca2Ag7 (Yb2Ag7 type), Ca14Cd51 (Gd14Ag51 type), and the 1/1 Tsai-type quasicrystal approximant CaCd6 (YCd6 type) can all be traced to large negative pressures around the Ca atoms of a common progenitor structure, the CaCu5 type with its simple hexagonal 6-atom unit cell. Two structural paths are found by which the compounds provide relief to the Ca atoms' negative pressures: a Ca-rich pathway, where lower coordination numbers are achieved through defects eliminating transition metal (TM) atoms from the structure; and a TM-rich path, along which the addition of spacer Cd atoms provides the Ca coordination environments greater independence from each other as they contract. The common origins of these structures in the presence of stresses within a single parent structure highlights the diverse paths by which intermetallics can cope with competing interactions, and the role that structural plasticity may play in navigating this diversity.

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.

Relativity, symmetry and the structure of quantum theory

CERN Document Server

Klink, William H; Schweiger, Wolfgang

Quantum theory is one of the most successful of all physical theories. Our everyday world is dominated by devices that function because of knowledge of the quantum world. Yet many, physicists and non-physicists alike, find the theory which explains the behavior of the quantum world baffling and strange. This book is the first in a series of three that argues that relativity and symmetry determine the structure of quantum theory. That is to say, the structure of quantum theory is what it is because of relativity and symmetry. There are different types of relativity, each leading to a particular type of quantum theory. This book deals specifically with what we call Newton relativity, the form of relativity built into Newtonian mechanics, and the quantum theory to which it gives rise, which we call Galilean (often misleadingly called non-relativistic) quantum theory. Key Features: • Meaning and significance of the term of relativity; discussion of the principle of relativity. • Relation of symmetry to relati...

Electronic structure of magnesium diboride and related compounds

Energy Technology Data Exchange (ETDEWEB)

Paduani, C. [Departamento de Fisica, Universidade Federal de Santa Catarina, UFSC, Florianopolis, CEP 88040-900, SC (Brazil)

2003-11-01

The electronic structure of AlB{sub 2}-type diborides and related compounds has been investigated in first-principles calculations with the molecular cluster discrete variational method. For MgB{sub 2} was studied the effect of the lattice relaxation on the total density of states at the Fermi energy (N({epsilon}{sub F})). The results indicated that a contraction of about 2% in the lattice spacings a and c can lead to a slight increase of N({epsilon}{sub F}) for boron. In the MB{sub 2} diborides, M=Al, Ti, V, Cr, Zr, Nb, Mo and Ta, the largest contributions to N({epsilon}{sub F}) is observed for Cr, Mo and Nb. TiB{sub 2} possess the highest chemical stability in the series. The electronic specific heat coefficient {gamma} also is calculated for the diborides. The method is employed to obtain the partial B2p contribution to the total DOS at the Fermi level with the introduction of a monolayer of solute atoms as a substitution for Mg atoms of Na, Al, Ca, Ti, V, Cr, Zr, Nb, Mo and Ta in layered superstructures.. /M/B{sub 2}/Mg/B{sub 2}/.. A stronger covalent bonding between boron atoms is identified in these cases. (copyright 2003 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

Accurate protein structure modeling using sparse NMR data and homologous structure information.

Science.gov (United States)

Thompson, James M; Sgourakis, Nikolaos G; Liu, Gaohua; Rossi, Paolo; Tang, Yuefeng; Mills, Jeffrey L; Szyperski, Thomas; Montelione, Gaetano T; Baker, David

2012-06-19

While information from homologous structures plays a central role in X-ray structure determination by molecular replacement, such information is rarely used in NMR structure determination because it can be incorrect, both locally and globally, when evolutionary relationships are inferred incorrectly or there has been considerable evolutionary structural divergence. Here we describe a method that allows robust modeling of protein structures of up to 225 residues by combining (1)H(N), (13)C, and (15)N backbone and (13)Cβ chemical shift data, distance restraints derived from homologous structures, and a physically realistic all-atom energy function. Accurate models are distinguished from inaccurate models generated using incorrect sequence alignments by requiring that (i) the all-atom energies of models generated using the restraints are lower than models generated in unrestrained calculations and (ii) the low-energy structures converge to within 2.0 Å backbone rmsd over 75% of the protein. Benchmark calculations on known structures and blind targets show that the method can accurately model protein structures, even with very remote homology information, to a backbone rmsd of 1.2-1.9 Å relative to the conventional determined NMR ensembles and of 0.9-1.6 Å relative to X-ray structures for well-defined regions of the protein structures. This approach facilitates the accurate modeling of protein structures using backbone chemical shift data without need for side-chain resonance assignments and extensive analysis of NOESY cross-peak assignments.

VPPD Lab - The Chemical Product Simulator

DEFF Research Database (Denmark)

Kalakul, Sawitree; Hussain, Rehan; Elbashir, Nimir

2015-01-01

, detergent, etc.). It has interface to identify workflow/data-flow for the inter-related activities between knowledge-based system and model-based calculation procedures to systematically, efficiently and robustly solve various types of product design-analysis problems. The application of the software......In this paper, the development of a systematic model-based framework for product design, implemented in the new product design software called VPPD-Lab is presented. This framework employs its in-house knowledge-based system to design and evaluate chemical products. The built-in libraries...... of product performance models and product-chemical property models are used to evaluate different classes of product. The product classes are single molecular structure chemicals (lipids, solvents, aroma, etc.), blended products (gasoline, jet-fuels, lubricants, etc.), and emulsified product (hand wash...

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.

[Neutron scatter studies of chromatin structure related to function

International Nuclear Information System (INIS)

Bradbury, E.M.

1990-01-01

This study is concerned with the application of neutron scatter techniques to the different structural states of nucleosomes and chromatin with the long term objective of understanding how the enormous lengths of DNA are folded into chromosomes. Micrococcal nuclease digestion kinetics have defined two subnucleosome particles; the chromatosome with 168 bp DNA, the histone octamer and one H1 and the nucleosome core particle with 146 bp DNA and the histone octamer. As will be discussed, the structure of the 146 bp DNA core particle is known in solution at low resolution from neutron scatter studies and in crystals. Based on this structure, the authors have a working model for the chromatosome and the mode of binding of H1. In order to define the structure of the nucleosome and also the different orders of chromatin structures they need to know the paths of DNA that link nucleosomes and the factors associated with chromosome functions that act on those DNA paths. The major region for this situation is the inherent variabilities in nucleosome DNA sequences, in the histone subtypes and their states of chemical modification and in the precise locations of nucleosomes. Such variabilities obscure the underlying principles that govern the packaging of DNA into the different structural states of nucleosomes and chromatin. The only way to elucidate these principles is to study the structures of nucleosomes and oligonucleosomes that are fully defined. They have largely achieved these objectives

Structure soil structure interaction effects: Seismic analysis of safety related collocated concrete structures

International Nuclear Information System (INIS)

Joshi, J.R.

2000-01-01

The Process, Purification and Stack Buildings are collocated safety related concrete shear wall structures with plan dimensions in excess of 100 feet. An important aspect of their seismic analysis was the determination of structure soil structure interaction (SSSI) effects, if any. The SSSI analysis of the Process Building, with one other building at a time, was performed with the SASSI computer code for up to 50 frequencies. Each combined model had about 1500 interaction nodes. Results of the SSSI analysis were compared with those from soil structure interaction (SSI) analysis of the individual buildings, done with ABAQUS and SASSI codes, for three parameters: peak accelerations, seismic forces and the in-structure floor response spectra (FRS). The results may be of wider interest due to the model size and the potential applicability to other deep soil layered sites. Results obtained from the ABAQUS analysis were consistently higher, as expected, than those from the SSI and SSSI analyses using the SASSI. The SSSI effect between the Process and Purification Buildings was not significant. The Process and Stack Building results demonstrated that under certain conditions a massive structure can have an observable effect on the seismic response of a smaller and less stiff structure

Chemical composition, crystal size and lattice structural changes after incorporation of strontium into biomimetic apatite.

Science.gov (United States)

Li, Z Y; Lam, W M; Yang, C; Xu, B; Ni, G X; Abbah, S A; Cheung, K M C; Luk, K D K; Lu, W W

2007-03-01

Recently, strontium (Sr) as ranelate compound has become increasingly popular in the treatment of osteoporosis. However, the lattice structure of bone crystal after Sr incorporation is yet to be extensively reported. In this study, we synthesized strontium-substituted hydroxyapatite (Sr-HA) with different Sr content (0.3%, 1.5% and 15% Sr-HA in mole ratio) to simulate bone crystals incorporated with Sr. The changes in chemical composition and lattice structure of apetite after synthetic incorporation of Sr were evaluated to gain insight into bone crystal changes after incorporation of Sr. X-ray diffraction (XRD) patterns revealed that 0.3% and 1.5% Sr-HA exhibited single phase spectrum, which was similar to that of HA. However, 15% Sr-HA induced the incorporation of HPO4(2-) and more CO3(2-), the crystallinity reduced dramatically. Transmission electron microscopy (TEM) images showed that the crystal length and width of 0.3% and 1.5% Sr-HA increased slightly. Meanwhile, the length and width distribution were broadened and the aspect ratio decreased from 10.68+/-4.00 to 7.28+/-2.80. The crystal size and crystallinity of 15% Sr-HA dropped rapidly, which may suggest that the fundamental crystal structure is changed. The findings from this work indicate that current clinical dosage which usually results in Sr incorporation of below 1.5% may not change chemical composition and lattice structure of bone, while it will broaden the bone crystal size distribution and strengthen the bone.

Integrity of Safety-Related Fast Reactor Structures

International Nuclear Information System (INIS)

Rose, R.T.; Tomkins, B.

1981-01-01

The LMFBR contains several structural items whose integrity must be safeguarded during the life of the plant. These items include the main core support structures (strongback, diagrid) and the primary tank to which these structures are attached. In order to demonstrate an acceptable level of structural integrity, the chosen design philosophy must be supported by both analytical and experimental evidence. This paper describes the current approaches in the UK to these requirements. Section 2 describes the materials mechanical properties tests performed to date on both fracture toughness and fatigue crack growth in Type 316 austenitic stainless steel plate and weldments. This data illustrates the problems in identifying the relevant materials fracture parameters for use in assessments. Section 3 shows the test programmes in hand to extend the materials programmes to tests on structural features (mainly welded wide plate tests) which incorporate the complexity of weldments in a structural context. This includes experimental evidence on the effects of local weld residual stresses on structural failure. Various routes are open for the integrity assessment of FR structures. These are discussed in Section 4 but in effect they reduce to a fracture mechanics approach using some technique to cope with elastic-plastic fracture. The main problems at present relate to our ability in analysis to cope with residual stresses and the post-initiation region of the fracture resistance curve. Also, there is the problem of initial defect sizing by current NDE techniques. Current conservative analytical assessments give acceptable defect sizes of order a few millimetres in irradiated weldments. Finally, Section 5 discusses the options open in design to cope with safety related structures under normal and abnormal loading conditions. It is clear that several options exist in design to satisfy the demand for high integrity

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

Reliability of containment and safety-related structures

International Nuclear Information System (INIS)

Nessim, M.A.

1995-09-01

A research program on Reliability of Containment and Safety-related Structures has been developed and is described in this document. This program is designed to support AECB's regulatory activities aimed at ensuring the safety of these structures. These activities include evaluating submissions by operators and requesting special assessments when necessary. The results of the proposed research will also be useful in revising and enhancing the CSA design standards for containment and safety-related structures. The process of developing the research program started with an information collection and review phase. The sources of information included C-FER's previous work in the area, various recent research publications, regulatory documents and relevant design standards, and a detailed discussion with AECB staff. The second step was to outline the process of reliability evaluation, and identify the required models and parameters. Comparison between the required and available information was used to identify gaps in the state-of-the-art, and the research program was designed to fill these gaps. The program is organized in four major topics, namely: development of an approach for reliability analysis; compilation and development of the required analysis tools; application to specific problems related to design, assessment, maintenance and testing of structures; and testing and validation. It is suggested that the program should be supported by an on-going process of communication and consultation between AECB staff and industry experts. This will lend credibility to the results and facilitate their future application. (author). 1 fig

Chemical and structural properties of Pd nanoparticle-decorated graphene-Electron spectroscopic methods and QUASES

Czech Academy of Sciences Publication Activity Database

Lesiak, B.; Jiříček, Petr; Bieloshapka, Igor

2017-01-01

Roč. 404, May (2017), s. 300-309 ISSN 0169-4332 R&D Projects: GA MŠk LM2015088 Institutional support: RVO:68378271 Keywords : graphite (Gr) * graphene oxide (GO) * reduced graphene oxide (RGO) * Pd nanoparticles * XPS * QUASES * REELS * chemical and structural properties Subject RIV: BM - Solid Matter Physics ; Magnetism OBOR OECD: Condensed matter physics (including formerly solid state physics, supercond.) Impact factor: 3.387, year: 2016

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

Study of post annealing influence on structural, chemical and electrical properties of ZTO thin films

International Nuclear Information System (INIS)

Jain, Vipin Kumar; Kumar, Praveen; Kumar, Mahesh; Jain, Praveen; Bhandari, Deepika; Vijay, Y.K.

2011-01-01

Research highlights: → Structural, chemical and electrical properties of cost effective ZTO thin films with varying concentrations. → Effect of annealing of ZTO films. - Abstract: Zinc-Tin-Oxide (ZTO) thin films were deposited on glass substrate with varying concentrations (ZnO:SnO 2 ; 100:0, 90:10, 70:30 and 50:50 wt.%) at room temperature by flash evaporation technique. These deposited ZTO films were annealed at 450 deg. C in vacuum. These films were characterized to study the effect of annealing and addition of SnO 2 concentration on the structural, chemical and electrical properties. The XRD analysis indicates that crystallization of the ZTO films strongly depends on the concentration of SnO 2 and post annealing where annealed films showed polycrystalline nature. Atomic force microscopy (AFM) images manifest the surface morphology of these ZTO thin films. The XPS core level spectra of Zn(2p), O(1s) and Sn(3d) have been deconvoluted into their Gaussian component to evaluate the chemical changes, while valence band spectra reveal the electronic structures of these films. A small shift in Zn(2p) and Sn(3d) core level towards higher binding energy and O(1s) core level towards lower binding energy have been observed. The minimum electrical resistivity (ρ ∼ 3.69 x 10 -2 Ω-cm), maximum carrier concentration (n ∼ 3.26 x 10 19 cm -3 ) and Hall mobility (μ ∼ 5.2 cm 2 v -1 s -1 ) were obtained for as-prepared ZTO (50:50) film thereafter move towards lowest resistivity (ρ ∼ 1.12 x 10 -3 Ω-cm), highest carrier concentration (n ∼ 2.96 x 10 20 cm -3 ) and mobility (μ ∼ 18.8 cm 2 v -1 s -1 ) for annealed ZTO (50:50) thin film.

LCA of Chemicals and Chemical Products

DEFF Research Database (Denmark)

Fantke, Peter; Ernstoff, Alexi

2018-01-01

This chapter focuses on the application of Life Cycle Assessment (LCA) to evaluate the environmental performance of chemicals as well as of products and processes where chemicals play a key role. The life cycle stages of chemical products, such as pharmaceuticals drugs or plant protection products......, are discussed and differentiated into extraction of abiotic and biotic raw materials, chemical synthesis and processing, material processing, product manufacturing, professional or consumer product use, and finally end-of-life . LCA is discussed in relation to other chemicals management frameworks and concepts...... including risk assessment , green and sustainable chemistry , and chemical alternatives assessment. A large number of LCA studies focus on contrasting different feedstocks or chemical synthesis processes, thereby often conducting a cradle to (factory) gate assessment. While typically a large share...

Changes in soil bacterial community structure as a result of incorporation of Brassica plants compared with continuous planting eggplant and chemical disinfection in greenhouses.

Science.gov (United States)

Li, Tianzhu; Liu, Tongtong; Zheng, Chengyu; Kang, Chunsheng; Yang, Zichao; Yao, Xiaotong; Song, Fengbin; Zhang, Runzhi; Wang, Xuerong; Xu, Ning; Zhang, Chunyi; Li, Wei; Li, Shumin

2017-01-01

Greenhouse eggplant monocropping in China has contributed to the aggravation of soil-borne diseases, reductions in crop quality and yield, and the degradation of physical and chemical soil properties. Crop rotation is one effective way of alleviating the problems of continuous cropping worldwide; however, few studies have reported changes in soil bacterial community structures and physical and chemical soil properties after Brassica vegetables had been rotated with eggplant in greenhouses. In this experiment, mustard-eggplant (BFN) and oilseed rape-eggplant (BFC) rotations were studied to identify changes in the physicochemical properties and bacterial community structure in soil that was previously subject to monocropping. Samples were taken after two types of Brassica plants incorporated into soil for 15 days to compare with continually planted eggplant (control, CN) and chemical disinfection of soil (CF) in greenhouses. MiSeq pyrosequencing was used to analyze soil bacterial diversity and structure in the four different treatments. A total of 55,129 reads were identified, and rarefaction analysis showed that the soil treatments were equally sampled. The bacterial richness of the BFC treatment and the diversity of the BFN treatment were significantly higher than those of the other treatments. Further comparison showed that the bacterial community structures of BFC and BFN treatments were also different from CN and CF treatments. The relative abundance of several dominant bacterial genera in the BFC and BFN treatments (such as Flavobacteria, Stenotrophomonas, Massilia and Cellvibrio, which played different roles in improving soil fertility and advancing plant growth) was distinctly higher than the CN or CF treatments. Additionally, the total organic matter and Olsen-P content of the BFC and BFN treatments were significantly greater than the CN treatment. We conclude that Brassica vegetables-eggplant crop rotations could provide a more effective means of solving

Speciation of trace elements in biological samples by nuclear analytical and related techniques coupled with chemical and biochemical separation

International Nuclear Information System (INIS)

Chen, C.Y.; Gao, Y.X.; Li, B.; Yu, H.W.; Li, Y.F.; Sun, J.; Chai, Z.F.

2005-01-01

In the past, most analytical problems relating to biological systems were addressed by measuring the total concentrations of elements. Now there is increasing interest of the importance of their chemical forms, in which an element is present in biological systems, e.g., the oxidation state, the binding state with macromolecules, or even the molecular structure. The biological effects of chromium, which is classified as an essential nutrient, are dependent upon its oxidation. state. In general, trivalent chromium is biochemically active, whereas hexavalent chromium is considered to be toxic. Mercury is one of serious environmental persistent pollutants. However, organic forms of mercury are known to possess much higher toxicity than inorganic mercury. Therefore, information on speciation is critically required in order to better understanding of their bioavailability, metabolism, transformation, and toxicity in vivo. Recently, chemical speciation of selenium, mercury, copper, zinc, iron, and so on, has been investigated by INAA, ICP-MS, XRF, EXAFS and related techniques combined with chemical and biochemical separation (extraction, chromatography, gel electrophoresis, etc.). INAA, XRF, and ICP-MS have superior advantages in aspect of multielemental analysis with high accuracy and sensitivity, which render the possibility of analyzing various elements of interest simultaneously. These offline or online techniques have been flexibly applied to different biological matrixes, such as human hair, serum, urine, various tissues and organs in our researches. In addition, EXAFS provides structural information about the moiety of metal centers up to a distance of approximately 4-5 Anstrom. For instance, hepatocellular carcinoma (HCC) is one of the most common cancers worldwide. Imbalance of elements, such as Se, Zn, Fe, Cu, Cd, Ca, etc., has been found in the whole blood or serum of patients with HCC. We found that the profiles of Se, Cd, Fe, Zn and Cu-containing proteins

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.

Chemical constituents of Salacia elliptica (Celastraceae)

Energy Technology Data Exchange (ETDEWEB)

Duarte, Lucienir Pains; Figueiredo, Rute Cunha; Sousa, Grasiely Faria de; Soares, Debora Barbosa da Silva; Rodrigues, Salomao Bento Vasconcelos; Silva, Fernando Cesar; Silva, Gracia Divina de Fatima, E-mail: lucienir@ufmg.b [Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, MG (Brazil). Dept. de Quimica; Vieira Filho, Sidney Augusto [Universidade Federal de Ouro Preto, MG (Brazil). Escola de Farmacia. Dept. de Farmacia

2010-07-01

The chemical investigation of Salacia elliptica allowed to the isolation of 20 constituents: two polyols, one xanthone, a mixture of long chain hydrocarbons, one carboxylic acid, one polymer, two steroidal compounds, one aromatic ester and eleven pentacyclic triterpenes. These triterpenes include 3{beta}-stearyloxy-oleanane, 3{beta}-stearyloxy-ursane, one seco-friedelane, and eight compounds of the friedelane series. The chemical structure and the relative configuration of a new triterpene 1,3-dioxo-16alpha-hydroxyfriedelane (15) were established through {sup 1}H and {sup 13}C NMR including 2D experiments (HMBC, HMQC, COSY and NOESY) and herein reported for the first time (author)

Chemical constituents of Salacia elliptica (Celastraceae

Directory of Open Access Journals (Sweden)

Lucienir Pains Duarte

2010-01-01

Full Text Available The chemical investigation of Salacia elliptica allowed to the isolation of 20 constituents: two polyols, one xanthone, a mixture of long chain hydrocarbons, one carboxylic acid, one polymer, two steroidal compounds, one aromatic ester and eleven pentacyclic triterpenes. These triterpenes include 3β-stearyloxy-oleanane, 3β-stearyloxy-ursane, one seco-friedelane, and eight compounds of the friedelane serie. The chemical structure and the relative configuration of a new triterpene 1,3-dioxo-16α-hydroxyfriedelane (15 were established through ¹H and 13C NMR including 2D experiments (HMBC, HMQC, COSY and NOESY and herein reported for the first time.

Ab initio study of electron-ion structure factors in binary liquids with different types of chemical bonding

International Nuclear Information System (INIS)

Klevets, Ivan; Bryk, Taras

2014-01-01

Electron-ion structure factors, calculated in ab initio molecular dynamics simulations, are reported for several binary liquids with different kinds of chemical bonding: metallic liquid alloy Bi–Pb, molten salt RbF, and liquid water. We derive analytical expressions for the long-wavelength asymptotes of the partial electron-ion structure factors of binary systems and show that the analytical results are in good agreement with the ab initio simulation data. The long-wavelength behaviour of the total charge structure factors for the three binary liquids is discussed

Composition-structure-property relation of oxide glasses

DEFF Research Database (Denmark)

Hermansen, Christian

also increases such properties. Yet, these rules are not strictly followed even for the simplest binary oxide glasses, such as alkali silicates, borates and phosphates. In this thesis it is argued that the missing link between composition and properties is the glass structure. Structural models...... are proposed based on topological selection rules and experimentally verified. The relation between structure and properties is evaluated using topological constraint theory, which in its essence is a theory that quantifies the two intuitions of the glass scientist. The end result is a quantitative model...

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.

Identification of Lilial as a fragrance sensitizer in a perfume by bioassay-guided chemical fractionation and structure-activity relationships

DEFF Research Database (Denmark)

Gimenéz-Arnau, Elena; Andersen, K E; Bruze, M

2000-01-01

Fragrance materials are among the most common causes of allergic contact dermatitis. The aim of this study was to identify in a perfume fragrance allergens not included in the fragrance mix, by use of bioassay-guided chemical fractionation and chemical analysis/structure-activity relationships...... (SARs). The basis for the investigation was a 45-year-old woman allergic to her own perfume. She had a negative patch test to the fragrance mix and agreed to participate in the study. Chemical fractionation of the perfume concentrate was used for repeated patch testing and/or repeated open application...

Chemical modifications and reactions in DNA nanostructures

DEFF Research Database (Denmark)

Gothelf, Kurt Vesterager

2017-01-01

such as hydrocarbons or steroids have been introduced to change the surface properties of DNA origami structures, either to protect the DNA nanostructure or to dock it into membranes and other hydrophobic surfaces. DNA nanostructures have also been used to control covalent chemical reactions. This article provides......DNA nanotechnology has the power to form self-assembled and well-defined nanostructures, such as DNA origami, where the relative positions of each atom are known with subnanometer precision. Our ability to synthesize oligonucleotides with chemical modifications in almost any desired position...... provides rich opportunity to incorporate molecules, biomolecules, and a variety of nanomaterials in specific positions on DNA nanostructures. Several standard modifications for oligonucleotides are available commercially, such as dyes, biotin, and chemical handles, and such modified oligonucleotides can...

Pulse NMR-spectroscopy of structural changes of chemically modified polypropylene

International Nuclear Information System (INIS)

Gafarov, A.M.; Galibeev, S.S.; Kochnev, A.M.; Sukhanov, P.P.; Arkhireev, V.P.

2004-01-01

The structure of polypropylene compositions is studied by the method of pulse NMR-spectroscopy. The polypropylene compositions are derived by means of the modification by multicomponent systems. The analysis of relaxation times in a wide temperature range is carried out. Character of changes going on at a level of supermolecular structures is described. It is shown that the amplifications that manifest themselves under the polypropylene modification by the mixtures based on 2,4-tolyilendiisocyanate and e-caprolactam, are related to the change in the intermolecular interaction and formation of a more ordered polymer structure. (authors)

Long-term degradation of chemical structures and mechanical properties in polyethylene induced by ion-beam irradiation

International Nuclear Information System (INIS)

Oka, T.; Hama, Y.

2004-01-01

The long-term degradation in polyethylene irradiated with ion beams was studied. We found the changes of the chemical structures and the mechanical properties with time storage. S-PE has a good resistance to ion-beam irradiation because the crystallinity and density were very low. (author)

Ab initio investigations of the electronic structure and chemical bonding of Li2ZrN2

International Nuclear Information System (INIS)

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

2012-01-01

The electronic structure of the ternary nitride Li 2 ZrN 2 is examined from ab initio with DFT computations for an assessment of the properties of chemical bonding. The compound is found insulating with 1.8 eV band gap; it becomes metallic and less ionic upon removal of one equivalent of Li. The chemical interaction is found mainly between Zr and N on one hand and Li and N on the other hand. While all pair interactions are bonding, antibonding N–N interactions are found dominant at the top of the valence band of Li 2 ZrN 2 and they become less intense upon removal of Li. From energy differences the partial delithiation leading to Li 2−x ZrN 2 (x=∼1) is favored. - Graphical abstract: Trigonal structure of Li 2 ZrN 2 showing the Zr–N–Li layers along the c-axis. Highlights: ► Li 2 ZrN 2 calculated insulating with a 1.8 eV gap in agreement with its light green color. ► Lithium de-intercalation is energetically favored for one out of two Li equivalents. ► Li plays little role in the change of the structure, ensured by Zr and N binding. ► Similar changes in the electronic structure as for various intercalated phases of ZrN.

The influence of condensed tannin structure on rate of microbial mineralization and reactivity to chemical assays.

Science.gov (United States)

Norris, Charlotte E; Preston, Caroline M; Hogg, Karen E; Titus, Brian D

2011-03-01

We examined how tannin structure influences reactivity in tannin assays and carbon and nitrogen mineralization. Condensed tannins from the foliage of ten tree and shrub species and from pecan shells (Carya illinoensis) had different proportions of: (a) epicatechin (cis) and catechin (trans) isomers, (b) procyanidin (PC) and prodelphinidin (PD) monomers, and (c) different chain lengths. The response of each tannin to several widely used tannin assays was determined. Although there was some variation in response to proanthocyanidin (butanol/HCl) and Folin Ciocalteu assays, we did not deduce any predictable relationship between tannin structure and response to either assay. There was little variation in protein precipitation among the different tannins. To assess biological activity, six of the tannins were incubated with forest humus for 22 days. We determined that, while PC-based tannins remained at least partly extractable for the duration of the incubation, tannins with a high proportion of PD subunits rapidly became unextractable from soil. There was a positive correlation between net nitrogen mineralization and cis chemical structure. Carbon mineralization was enhanced initially by the addition of tannins to humus, but after 22 days, a negative correlation between the proportion of cis subunits and respiration was determined. Overall, we were not able to demonstrate consistent effects of structure on either microbial mineralization or reactivity to chemical assays; such relationships remain elusive.

Structural studies of crystals of organic and organoelement compounds using modern quantum chemical calculations within the framework of the density functional theory

International Nuclear Information System (INIS)

Korlyukov, Alexander A; Antipin, Mikhail Yu

2012-01-01

The review generalizes the results of structural studies of crystals of organic and organometallic compounds by modern quantum chemical calculations within the framework of the density functional theory reported in the last decade. Features of the software for such calculations are discussed. Examples of the use of quantum chemical calculations for the studies of the electronic structure, spectroscopic and other physicochemical properties of molecular crystals are presented. The bibliography includes 223 references.

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.

Molecular Structure of Phenytoin: NMR, UV-Vis and Quantum Chemical Calculations

Directory of Open Access Journals (Sweden)

Raluca Luchian

2015-12-01

Full Text Available Due to the presence of the carbonyl and imide groups in the structure of 5,5-diphenylhydantoin (DPH, the possibility for this compound to be involved in hydrogen bonding intermolecular interactions is obvious. Even though such interactions are presumably responsible for the mechanism of action of this drug, however, to the best of our knowledge, the self-hydrogen bonding interactions between the DPH monomers have not been addressed till now. Furthermore, studies reporting on the spectroscopic characteristics of this molecule are scarcely reported in the literature. Here we report on the possible dimers of DPH, investigated by quantum chemical calculations at B3LYP/6-31+G(2d,2p level of theory. Twelve unique DPH dimers were structurally optimized in gas-phase, as well as in ethanol and DMSO and then were used to compute the population-averaged UV-Vis and NMR spectra using Boltzmann statistics. UV-Vis and NMR techniques were employed to assess experimentally the spectroscopical response of this compound. DFT calculations are also used to investigate the structural transformations between the solid and liquid phase, as well as for describing the electronic transitions and for the assignment of NMR spectra of DPH.

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

Science.gov (United States)

Montes-Grajales, Diana; Olivero-Verbel, Jesus

2015-01-02

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. Copyright © 2014. Published by Elsevier Ireland Ltd.

Chemical shift homology in proteins

International Nuclear Information System (INIS)

Potts, Barbara C.M.; Chazin, Walter J.

1998-01-01

The degree of chemical shift similarity for homologous proteins has been determined from a chemical shift database of over 50 proteins representing a variety of families and folds, and spanning a wide range of sequence homologies. After sequence alignment, the similarity of the secondary chemical shifts of C α protons was examined as a function of amino acid sequence identity for 37 pairs of structurally homologous proteins. A correlation between sequence identity and secondary chemical shift rmsd was observed. Important insights are provided by examining the sequence identity of homologous proteins versus percentage of secondary chemical shifts that fall within 0.1 and 0.3 ppm thresholds. These results begin to establish practical guidelines for the extent of chemical shift similarity to expect among structurally homologous proteins

Local atomic structure and chemical order in amorphous SiGe:H and SiC:H alloys

International Nuclear Information System (INIS)

Pisarkiewicz, T.; Stapinski, T.

1994-01-01

The local structure and chemical ordering in amorphous hydrogenated silicon-germanium and silicon-carbon alloys were analyzed mainly with the help of extended x-ray absorption fine structure (EXAFS) spectroscopy, Raman scattering and electron diffraction. Ge-Ge and Ge-Si distances were found to be independent of concentration and the composition of the first coordination shell around Ge is consistent with a random mixing of the two species in a-Si 1-x Ge:H alloy. The first-coordination-shell average bond lengths for Si-Si and SiC in a-Si 1-x C x :H are also constant with concentration x and the comparison of the first coordination shell composition around Si with average concentration indicates that the alloys tends to be chemically ordered. The degree of crystallinity in microcrystalline Si films determined by EXAFS is in agreement with that obtained in Raman scattering analysis. (author). 16 refs, 5 figs

Identification of chemical warfare agent with radiological measurements

International Nuclear Information System (INIS)

Liu Boxue; Li Yun; Ai Xianyun

2000-01-01

There are three non-destructive radiological methods for identification of warfare agents and TNT. Their principles and problems related were discussed. Portable isotopic neutron spectroscopy is based on the assay of key elemental composition (such as Cl, P, H, As, S, N) in chemical agents by neutron induced prompt gamma ray analysis. Hydrogen concentration measurement by means of using thermal neutron can be employed to identify chemical warfare agents and TNT that contains different hydrogen fraction. The calibration curves of thermal neutron count rate against hydrogen concentration were measured. X ray imagination system can be used to determine the internal structure of chemical bombs, there by to identify them. The radiological methods are very useful for identification of old chemical weapons abandoned by Japan Army during World War 2