Science.gov

Sample records for chemical structure information

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

    PubMed

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

    2014-08-01

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

  2. Recent Strategies for Retrieving Chemical Structure Information on the Web.

    ERIC Educational Resources Information Center

    Lo, Mei Ling

    1997-01-01

    Various methods for retrieving chemical structure information on the World Wide Web are discussed. Although graphical plug-in programs provide more search capabilities, users first have to obtain a copy of the programs. Tripos's WebSketch and ACD Interactive Lab adopt a different approach; using JAVA applets, users create and display a structure…

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

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

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

  4. Classification of Chemicals Based On Structured Toxicity Information

    EPA Science Inventory

    Thirty years and millions of dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data within the Toxicity Reference Database (ToxRefDB). Toxicity-bas...

  5. Use of selected toxicology information resources in assessing relationships between chemical structure and biological activity

    SciTech Connect

    Wassom, J.S.

    1985-09-01

    This paper addresses the subject of the use of the selected toxicology information resources in assessing relationships between chemical structure and specific end points. To assist the researcher in how to access the primary literature of genetic toxicology, teratogenesis, and carcinogenesis, three specific specialized information centers are discussed - Environmental Mutagen Information Center, Environmental Teratology Information Center, and Environmental Carcinogenesis Information Center. Also included are descriptions of information resources that contain evaluated (peer-reviewed) biological research results. The US Environmental Protection Agency Genetic Toxicology Program, the International Agency for Research on Cancer Monographs, and the Toxicology Data Bank are the best sources currently available to obtain peer-reviewed results for compounds tested for genotoxicity, carcinogenicity, and other toxicological end points. The value of published information lies in its use. It has become evident that most information cannot be accepted at face value for interpretation and analysis when subjected to stringent quality evaluation criteria. This deficit can be corrected by rigid editorship and the cognizance of authors. Increased interest in alternative methods to in vivo animal testing will be exemplified by use of short-term bioassays and in structure-activity relationship studies. With respect to this latter area, it must be remembered that mechanically (computer generated) derived data cannot substitute, at least at this stage, for data obtained from actual animal testing. The future of structure-activity relationship studies will rest only in their use as a predictive tool.

  6. Use of selected toxicology information resources in assessing relationships between chemical structure and biological activity.

    PubMed Central

    Wassom, J S

    1985-01-01

    This paper addresses the subject of the use of selected toxicology information resources in assessing relationships between chemical structure and specific biological end points. To assist the researcher in how to access the primary literature of genetic toxicology, teratogenesis, and carcinogenesis, three specific specialized information centers are discussed--Environmental Mutagen Information Center, Environmental Teratology Information Center, and Environmental Carcinogenesis Information Center. Also included are descriptions of information resources that contain evaluated (peer-reviewed) biological research results. The U.S. Environmental Protection Agency Genetic Toxicology Program, the International Agency for Research on Cancer Monographs, and the Toxicology Data Bank are the best sources currently available to obtain peer-reviewed results for compounds tested for genotoxicity, carcinogenicity, and other toxicological end points. The value of published information lies in its use. It has become evident that most information cannot be accepted at face value for interpretation and analysis when subjected to stringent quality evaluation criteria. This deficit can be corrected by rigid editorship and the cognizance of authors. Increased interest in alternative methods to in vivo animal testing will be exemplified by use of short-term bioassays and in structure-activity relationship studies. With respect to this latter area, it must be remembered that mechanically (computer generated) derived data cannot substitute, at least at this stage, for data obtained from actual animal testing. The future of structure-activity relationship studies will rest only in their use as a predictive tool. PMID:4065070

  7. Protein structural information derived from NMR chemical shift with the neural network program TALOS-N.

    PubMed

    Shen, Yang; Bax, Ad

    2015-01-01

    Chemical shifts are obtained at the first stage of any protein structural study by NMR spectroscopy. Chemical shifts are known to be impacted by a wide range of structural factors, and the artificial neural network based TALOS-N program has been trained to extract backbone and side-chain torsion angles from (1)H, (15)N, and (13)C shifts. The program is quite robust and typically yields backbone torsion angles for more than 90 % of the residues and side-chain χ 1 rotamer information for about half of these, in addition to reliably predicting secondary structure. The use of TALOS-N is illustrated for the protein DinI, and torsion angles obtained by TALOS-N analysis from the measured chemical shifts of its backbone and (13)C(β) nuclei are compared to those seen in a prior, experimentally determined structure. The program is also particularly useful for generating torsion angle restraints, which then can be used during standard NMR protein structure calculations.

  8. Chemical information science coverage in Chemical Abstracts.

    PubMed

    Wiggins, G

    1987-02-01

    For many years Chemical Abstracts has included in its coverage publications on chemical documentation or chemical information science. Although the bulk of those publications can be found in section 20 of Chemical Abstracts, many relevant articles were found scattered among 39 other sections of CA in 1984-1985. In addition to the scattering of references in CA, the comprehensiveness of Chemical Abstracts as a secondary source for chemical information science is called into question. Data are provided on the journals that contributed the most references on chemical information science and on the languages of publication of relevant articles.

  9. Chemical information systems

    SciTech Connect

    Zebora, M.

    1994-12-31

    The growing number of Federal and State regulations today from EPA to OSHA is putting a large burden on organizations to comply with regard to chemicals in the work place. The cornerstone of chemical information is the Material Safety Data Sheet (MSDS). The MSDS has been a requirement for chemical manufacturers for over fifteen years. Manufacturers of hazardous materials must provide MSDSs to purchasers. However, recent additional regulations from OSHA, in particular the Right To Know and the Hazard Communication Standard (Haz-Com) require that employers who use chemicals must be capable of providing an MSDS to every employee that requests one for a material that they work with. Paper filing systems to managing MSDSs are hard to maintain, costly, and inefficient. In multifacility organizations this can result in delays in distributions of those MSDSs to employees. At AT and T Bell Laboratories the Environmental Health and Safety Center has invested over a decade of development work into producing an integrated Chemical Inventory System/MSDS System. That system meets the requirements discussed in this paper and serves six major R and D laboratory facilities in three states. The system resides on a desktop personal computer. Operation of the system relies on teamwork between several diverse organizations which are involved in management of chemical safety at AT and T Bell Laboratories. The departments represented on that team are Industrial Hygiene and Safety, Environmental Management, Facilities Operations, Purchasing, Health Services, Research, and Environmental Data Management Services.

  10. Perspectives for the use of structural information and chemical genetics to develop inhibitors of Janus kinases

    PubMed Central

    Haan, Claude; Behrmann, Iris; Haan, Serge

    2010-01-01

    Abstract Gain-of-function mutations in the genes encoding Janus kinases have been discovered in various haematologic diseases. Jaks are composed of a FERM domain, an SH2 domain, a pseudokinase domain and a kinase domain, and a complex interplay of the Jak domains is involved in regulation of catalytic activity and association to cytokine receptors. Most activating mutations are found in the pseudokinase domain. Here we present recently discovered mutations in the context of our structural models of the respective domains. We describe two structural hotspots in the pseudokinase domain of Jak2 that seem to be associated either to myeloproliferation or to lymphoblastic leukaemia, pointing at the involvement of distinct signalling complexes in these disease settings. The different domains of Jaks are discussed as potential drug targets. We present currently available inhibitors targeting Jaks and indicate structural differences in the kinase domains of the different Jaks that may be exploited in the development of specific inhibitors. Moreover, we discuss recent chemical genetic approaches which can be applied to Jaks to better understand the role of these kinases in their biological settings and as drug targets. PMID:20132407

  11. Extraction of structural and chemical information from high angle annular dark-field image by an improved peaks finding method.

    PubMed

    Yin, Wenhao; Huang, Rong; Qi, Ruijuan; Duan, Chungang

    2016-09-01

    With the development of spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM), high angle annular dark filed (HAADF) imaging technique has been widely applied in the microstructure characterization of various advanced materials with atomic resolution. However, current qualitative interpretation of the HAADF image is not enough to extract all the useful information. Here a modified peaks finding method was proposed to quantify the HAADF-STEM image to extract structural and chemical information. Firstly, an automatic segmentation technique including numerical filters and watershed algorithm was used to define the sub-areas for each atomic column. Then a 2D Gaussian fitting was carried out to determine the atomic column positions precisely, which provides the geometric information at the unit-cell scale. Furthermore, a self-adaptive integration based on the column position and the covariance of statistical Gaussian distribution were performed. The integrated intensities show very high sensitivity on the mean atomic number with improved signal-to-noise (S/N) ratio. Consequently, the polarization map and strain distributions were rebuilt from a HAADF-STEM image of the rhombohedral and tetragonal BiFeO3 interface and a MnO2 monolayer in LaAlO3 /SrMnO3 /SrTiO3 heterostructure was discerned from its neighbor TiO2 layers. Microsc. Res. Tech. 79:820-826, 2016. © 2016 Wiley Periodicals, Inc. PMID:27324521

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

    PubMed

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

    2013-06-01

    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.

  13. Chemical structure of interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.

    1985-01-01

    The interfacial structure of silicon/dielectric and silicon/metal systems is particularly amenable to analysis using a combination of surface spectroscopies together with a variety of chemical structures of Si/SiO2, Si/SiO2Si3N4, Si/Si2N2O, Si/SiO2/Al, and Si/Native Oxide interfaces using high resolution (0.350 eV FWHM) X ray photoelectron spectroscopy. The general structure of these dielectric interfaces entails a monolayer chemical transition layer at the Si/dielectric boundary. Amorphous Si substrates show a wide variety of hydrogenated Si and Si(OH) sub x states that are not observed in thermal oxidation of single crystal material. Extended SiO2 layers greater than 8 A in thickness are shown to be stoichiometric SiO2, but to exhibit a wide variety of local network structures. In the nitrogen containing systems, an approach to stoichiometric oxynitride compounds with interesting impurity and electron trapping properties are seen. In native oxides, substantial topographical nonuniformity in oxide thickness and composition are found. Analysis of metal/oxide interfacial layers is accomplished by analytical removal of the Si substrate by UHV XeF2 dry etching methods.

  14. Chemical Information Literacy at a Liberal Arts College

    ERIC Educational Resources Information Center

    Greco, George E.

    2016-01-01

    Chemistry majors at Goucher College are now required to take a 1-credit course in their sophomore year entitled Chemical Information Literacy. Students in the course learn the structure and organization of the chemical literature, and how to carry out searches of various databases for topic, author, chemical compound, or structure. They learn…

  15. Chemical Bonding and Structural Information of Black CarbonReference Materials and Individual Carbonaceous AtmosphericAerosols

    SciTech Connect

    Hopkins, Rebecca J.; Tivanski, Alexei V.; Marten, Bryan D.; Gilles, Mary K.

    2007-04-25

    The carbon-to-oxygen ratios and graphitic nature of a rangeof black carbon standard reference materials (BC SRMs), high molecularmass humic-like substances (HULIS) and atmospheric particles are examinedusing scanning transmission X-ray microscopy (STXM) coupled with nearedge X-ray absorption fine structure (NEXAFS) spectroscopy. UsingSTXM/NEXAFS, individual particles with diameter>100 nm are studied,thus the diversity of atmospheric particles collected during a variety offield missions is assessed. Applying a semi-quantitative peak fittingmethod to the NEXAFS spectra enables a comparison of BC SRMs and HULIS toparticles originating from anthropogenic combustion and biomass burns,thus allowing determination of the suitability of these materials forrepresenting atmospheric particles. Anthropogenic combustion and biomassburn particles can be distinguished from one another using both chemicalbonding and structural ordering information. While anthropogeniccombustion particles are characterized by a high proportion ofaromatic-C, the presence of benzoquinone and are highly structurallyordered, biomass burn particles exhibit lower structural ordering, asmaller proportion of aromatic-C and contain a much higher proportion ofoxygenated functional groups.

  16. The utility of geometrical and chemical restraint information extracted from predicted ligand binding sites in protein structure refinement

    PubMed Central

    Brylinski, Michal; Lee, Seung Yup; Zhou, Hongyi

    2010-01-01

    Exhaustive exploration of molecular interactions at the level of complete proteomes requires efficient and reliable computational approaches to protein function inference. Ligand docking and ranking techniques show considerable promise in their ability to quantify the interactions between proteins and small molecules. Despite the advances in the development of docking approaches and scoring functions, the genome-wide application of many ligand docking/screening algorithms is limited by the quality of the binding sites in theoretical receptor models constructed by protein structure prediction. In this study, we describe a new template-based method for the local refinement of ligand-binding regions in protein models using remotely related templates identified by threading. We designed a Support Vector Regression (SVR) model that selects correct binding site geometries in a large ensemble of multiple receptor conformations. The SVR model employs several scoring functions that impose geometrical restraints on the Cα positions, account for the specific chemical environment within a binding site and optimize the interactions with putative ligands. The SVR score is well correlated with the RMSD from the native structure; in 47% (70%) of the cases, the Pearson’s correlation coefficient is >0.5 (>0.3). When applied to weakly homologous models, the average heavy atom, local RMSD from the native structure of the top-ranked (best of top five) binding site geometries is 3.1 Å (2.9 Å) for roughly half of the targets; this represents a 0.1 (0.3) Å average improvement over the original predicted structure. Focusing on the subset of strongly conserved residues, the average heavy atom RMSD is 2.6 Å (2.3 Å). Furthermore, we estimate the upper bound of template-based binding site refinement using only weakly related proteins to be ~2.6 Å RMSD. This value also corresponds to the plasticity of the ligand-binding regions in distant homologues. The Binding Site Refinement (BSR

  17. The Use of Chemical-Chemical Interaction and Chemical Structure to Identify New Candidate Chemicals Related to Lung Cancer.

    PubMed

    Chen, Lei; Yang, Jing; Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

    Lung cancer causes over one million deaths every year worldwide. However, prevention and treatment methods for this serious disease are limited. The identification of new chemicals related to lung cancer may aid in disease prevention and the design of more effective treatments. This study employed a weighted network, constructed using chemical-chemical interaction information, to identify new chemicals related to two types of lung cancer: non-small lung cancer and small-cell lung cancer. Then, a randomization test as well as chemical-chemical interaction and chemical structure information were utilized to make further selections. A final analysis of these new chemicals in the context of the current literature indicates that several chemicals are strongly linked to lung cancer. PMID:26047514

  18. The PubChem chemical structure sketcher.

    PubMed

    Ihlenfeldt, Wolf D; Bolton, Evan E; Bryant, Stephen H

    2009-12-17

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

  19. Classification and Dose-Response Characterization of Environmental Chemicals Based On Structured Toxicity Information From ToxRefDB

    EPA Science Inventory

    Thirty years and over a billion of today’s dollars worth of pesticide registration toxicity studies, historically stored as hardcopy and scanned documents, have been digitized into highly standardized and structured toxicity data, within the U.S. Environmental Protection Agency’s...

  20. A survey of chemical information systems

    NASA Technical Reports Server (NTRS)

    Dominick, Wayne D. (Editor); Shaikh, Aneesa Bashir

    1985-01-01

    A survey of the features, functions, and characteristics of a fairly wide variety of chemical information storage and retrieval systems currently in operation is given. The types of systems (together with an identification of the specific systems) addressed within this survey are as follows: patents and bibliographies (Derwent's Patent System; IFI Comprehensive Database; PULSAR); pharmacology and toxicology (Chemfile; PAGODE; CBF; HEEDA; NAPRALERT; MAACS); the chemical information system (CAS Chemical Registry System; SANSS; MSSS; CSEARCH; GINA; NMRLIT; CRYST; XTAL; PDSM; CAISF; RTECS Search System; AQUATOX; WDROP; OHMTADS; MLAB; Chemlab); spectra (OCETH; ASTM); crystals (CRYSRC); and physical properties (DETHERM). Summary characteristics and current trends in chemical information systems development are also examined.

  1. Identification of Chemical Toxicity Using Ontology Information of Chemicals.

    PubMed

    Jiang, Zhanpeng; Xu, Rui; Dong, Changchun

    2015-01-01

    With the advance of the combinatorial chemistry, a large number of synthetic compounds have surged. However, we have limited knowledge about them. On the other hand, the speed of designing new drugs is very slow. One of the key causes is the unacceptable toxicities of chemicals. If one can correctly identify the toxicity of chemicals, the unsuitable chemicals can be discarded in early stage, thereby accelerating the study of new drugs and reducing the R&D costs. In this study, a new prediction method was built for identification of chemical toxicities, which was based on ontology information of chemicals. By comparing to a previous method, our method is quite effective. We hope that the proposed method may give new insights to study chemical toxicity and other attributes of chemicals.

  2. Reverse engineering chemical structures from molecular descriptors : how many solutions?

    SciTech Connect

    Brown, William Michael; Martin, Shawn Bryan; Faulon, Jean-Loup Michel

    2005-06-01

    Physical, chemical and biological properties are the ultimate information of interest for chemical compounds. Molecular descriptors that map structural information to activities and properties are obvious candidates for information sharing. In this paper, we consider the feasibility of using molecular descriptors to safely exchange chemical information in such a way that the original chemical structures cannot be reverse engineered. To investigate the safety of sharing such descriptors, we compute the degeneracy (the number of structure matching a descriptor value) of several 2D descriptors, and use various methods to search for and reverse engineer structures. We examine degeneracy in the entire chemical space taking descriptors values from the alkane isomer series and the PubChem database. We further use a stochastic search to retrieve structures matching specific topological index values. Finally, we investigate the safety of exchanging of fragmental descriptors using deterministic enumeration.

  3. Mapping chemical structure-activity information of HAART-drug cocktails over complex networks of AIDS epidemiology and socioeconomic data of U.S. counties.

    PubMed

    Herrera-Ibatá, Diana María; Pazos, Alejandro; Orbegozo-Medina, Ricardo Alfredo; Romero-Durán, Francisco Javier; González-Díaz, Humberto

    2015-06-01

    Using computational algorithms to design tailored drug cocktails for highly active antiretroviral therapy (HAART) on specific populations is a goal of major importance for both pharmaceutical industry and public health policy institutions. New combinations of compounds need to be predicted in order to design HAART cocktails. On the one hand, there are the biomolecular factors related to the drugs in the cocktail (experimental measure, chemical structure, drug target, assay organisms, etc.); on the other hand, there are the socioeconomic factors of the specific population (income inequalities, employment levels, fiscal pressure, education, migration, population structure, etc.) to study the relationship between the socioeconomic status and the disease. In this context, machine learning algorithms, able to seek models for problems with multi-source data, have to be used. In this work, the first artificial neural network (ANN) model is proposed for the prediction of HAART cocktails, to halt AIDS on epidemic networks of U.S. counties using information indices that codify both biomolecular and several socioeconomic factors. The data was obtained from at least three major sources. The first dataset included assays of anti-HIV chemical compounds released to ChEMBL. The second dataset is the AIDSVu database of Emory University. AIDSVu compiled AIDS prevalence for >2300 U.S. counties. The third data set included socioeconomic data from the U.S. Census Bureau. Three scales or levels were employed to group the counties according to the location or population structure codes: state, rural urban continuum code (RUCC) and urban influence code (UIC). An analysis of >130,000 pairs (network links) was performed, corresponding to AIDS prevalence in 2310 counties in U.S. vs. drug cocktails made up of combinations of ChEMBL results for 21,582 unique drugs, 9 viral or human protein targets, 4856 protocols, and 10 possible experimental measures. The best model found with the original

  4. Mapping chemical structure-activity information of HAART-drug cocktails over complex networks of AIDS epidemiology and socioeconomic data of U.S. counties.

    PubMed

    Herrera-Ibatá, Diana María; Pazos, Alejandro; Orbegozo-Medina, Ricardo Alfredo; Romero-Durán, Francisco Javier; González-Díaz, Humberto

    2015-06-01

    Using computational algorithms to design tailored drug cocktails for highly active antiretroviral therapy (HAART) on specific populations is a goal of major importance for both pharmaceutical industry and public health policy institutions. New combinations of compounds need to be predicted in order to design HAART cocktails. On the one hand, there are the biomolecular factors related to the drugs in the cocktail (experimental measure, chemical structure, drug target, assay organisms, etc.); on the other hand, there are the socioeconomic factors of the specific population (income inequalities, employment levels, fiscal pressure, education, migration, population structure, etc.) to study the relationship between the socioeconomic status and the disease. In this context, machine learning algorithms, able to seek models for problems with multi-source data, have to be used. In this work, the first artificial neural network (ANN) model is proposed for the prediction of HAART cocktails, to halt AIDS on epidemic networks of U.S. counties using information indices that codify both biomolecular and several socioeconomic factors. The data was obtained from at least three major sources. The first dataset included assays of anti-HIV chemical compounds released to ChEMBL. The second dataset is the AIDSVu database of Emory University. AIDSVu compiled AIDS prevalence for >2300 U.S. counties. The third data set included socioeconomic data from the U.S. Census Bureau. Three scales or levels were employed to group the counties according to the location or population structure codes: state, rural urban continuum code (RUCC) and urban influence code (UIC). An analysis of >130,000 pairs (network links) was performed, corresponding to AIDS prevalence in 2310 counties in U.S. vs. drug cocktails made up of combinations of ChEMBL results for 21,582 unique drugs, 9 viral or human protein targets, 4856 protocols, and 10 possible experimental measures. The best model found with the original

  5. An Application of Interactive Computing - A Chemical Information System

    ERIC Educational Resources Information Center

    Feldmann, Richard J.; And Others

    1972-01-01

    A collection of computer programs to do chemical information retrieval are described in terms of the interactions between the computer and the chemist. In interacting with the computer, the chemist can graphically specify two-dimensional structures as queries and view structures as search results. (18 references) (Author/NH)

  6. Representation of chemical information in OASIS centralized 3D database for existing chemicals.

    PubMed

    Nikolov, Nikolai; Grancharov, Vanio; Stoyanova, Galya; Pavlov, Todor; Mekenyan, Ovanes

    2006-01-01

    The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of

  7. Representation of chemical information in OASIS centralized 3D database for existing chemicals.

    PubMed

    Nikolov, Nikolai; Grancharov, Vanio; Stoyanova, Galya; Pavlov, Todor; Mekenyan, Ovanes

    2006-01-01

    The present inventory of existing chemicals in regulatory agencies in North America and Europe, encompassing the chemicals of the European Chemicals Bureau (EINECS, with 61 573 discrete chemicals); the Danish EPA (159 448 chemicals); the U.S. EPA (TSCA, 56 882 chemicals; HPVC, 10 546 chemicals) and pesticides' active and inactive ingredients of the U.S. EPA (1379 chemicals); the Organization for Economic Cooperation and Development (HPVC, 4750 chemicals); Environment Canada (DSL, 10851 chemicals); and the Japanese Ministry of Economy, Trade, and Industry (16811), was combined in a centralized 3D database for existing chemicals. The total number of unique chemicals from all of these databases exceeded 185 500. Defined and undefined chemical mixtures and polymers are handled, along with discrete (hydrolyzing and nonhydrolyzing) chemicals. The database manager provides the storage and retrieval of chemical structures with 2D and 3D data, accounting for molecular flexibility by using representative sets of conformers for each chemical. The electronic and geometric structures of all conformers are quantum-chemically optimized and evaluated. Hence, the database contains over 3.7 million 3D records with hundreds of millions of descriptor data items at the levels of structures, conformers, or atoms. The platform contains a highly developed search subsystem--a search is possible on Chemical Abstracts Service numbers; names; 2D and 3D fragment searches; structural, conformational, or atomic properties; affiliation in other chemical databases; structure similarity; logical combinations; saved queries; and search result exports. Models (collections of logically related descriptors) are supported, including information on a model's author, date, bioassay, organs/tissues, conditions, administration, and so forth. Fragments can be interactively constructed using a visual structure editor. A configurable database browser is designed for the inspection and editing of all types of

  8. VITAL NMR: using chemical shift derived secondary structure information for a limited set of amino acids to assess homology model accuracy.

    PubMed

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa G; Tang, Ming; Harris, Jason; Baudry, Jerome; Schuler, Mary A; Rienstra, Chad M

    2012-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  9. VITAL NMR: Using Chemical Shift Derived Secondary Structure Information for a Limited Set of Amino Acids to Assess Homology Model Accuracy

    SciTech Connect

    Brothers, Michael C; Nesbitt, Anna E; Hallock, Michael J; Rupasinghe, Sanjeewa; Tang, Ming; Harris, Jason B; Baudry, Jerome Y; Schuler, Mary A; Rienstra, Chad M

    2011-01-01

    Homology modeling is a powerful tool for predicting protein structures, whose success depends on obtaining a reasonable alignment between a given structural template and the protein sequence being analyzed. In order to leverage greater predictive power for proteins with few structural templates, we have developed a method to rank homology models based upon their compliance to secondary structure derived from experimental solid-state NMR (SSNMR) data. Such data is obtainable in a rapid manner by simple SSNMR experiments (e.g., (13)C-(13)C 2D correlation spectra). To test our homology model scoring procedure for various amino acid labeling schemes, we generated a library of 7,474 homology models for 22 protein targets culled from the TALOS+/SPARTA+ training set of protein structures. Using subsets of amino acids that are plausibly assigned by SSNMR, we discovered that pairs of the residues Val, Ile, Thr, Ala and Leu (VITAL) emulate an ideal dataset where all residues are site specifically assigned. Scoring the models with a predicted VITAL site-specific dataset and calculating secondary structure with the Chemical Shift Index resulted in a Pearson correlation coefficient (-0.75) commensurate to the control (-0.77), where secondary structure was scored site specifically for all amino acids (ALL 20) using STRIDE. This method promises to accelerate structure procurement by SSNMR for proteins with unknown folds through guiding the selection of remotely homologous protein templates and assessing model quality.

  10. Information Structures and Undergraduate Students

    ERIC Educational Resources Information Center

    Lee, Hur-Li

    2008-01-01

    This study explores how undergraduates seek information across various information structures. Taking part in an interview, fifteen students of diverse backgrounds described their information seeking. The findings pointed to several issues relating to the underlying structures of information resources. Suggestions are made for structural…

  11. Chemical Biological Emergency Management Information System

    2004-06-15

    CB-EMIS is designed to provide information and analysis to transit system operators and emergency responders in the event of a chemical attack on a subway system. The software inforporates detector data, video images, train data, meteorological data, and above- and below-ground plume dispersion models, hight of the liquid level.

  12. Toxicological information series, IV. Information resources for chemical emergency response.

    PubMed

    Decker, W J

    1990-08-01

    The need for rapidly available information by community agencies responding to chemical emergencies (leaks, spills, releases, fires, explosions, etc.) can be met by a number of resources. These resources include local poison control centers, the Toxicology Data Network (National Library of Medicine), the Agency for Toxic Substances and Disease Registry, ATSDR/NLM's ANSWER, the National Chemical Response and Information Center, the National Pesticide Telecommunications Network, The National Response Center (U.S. Coast Guard), the Federal Emergency Management Agency, the U.S. Environmental Protection Agency, the National Safety Council, private-sector database vendors, and textbooks addressing hazardous substances.

  13. STRUCTURE-ACTIVITY RELATIONSHIP STUIDES AND THEIR ROLE IN PREDICTING AND INVESTIGATING CHEMICAL TOXICITY

    EPA Science Inventory

    Structure-Activity Relationship Studies and their Role in Predicting and Investigating Chemical Toxicity

    Structure-activity relationships (SAR) represent attempts to generalize chemical information relative to biological activity for the twin purposes of generating insigh...

  14. Information Content of Turbulent Chemical Plumes

    NASA Astrophysics Data System (ADS)

    Webster, D. R.; Roberts, P. J. W.; Rahman, S.; Dasi, L. P.

    1999-11-01

    The rapid decrease in concentration contaminants released into the natural environment due to turbulent diffusion has traditionally been modeled based on time-averaged quantities. In contrast to the time-averaged concentration characteristics, the instantaneous characteristics and information content are poorly understood. Instantaneous peak levels are important in many contexts, including the impact of contaminants on organisms and the local ecosystem. The current work is motivated by the need to understand how aquatic organisms, such as blue crabs, search for and locate turbulent chemical odor plume sources. A fundamental question is what information is available to an animal or observer indicating its relative position to the plume source. In this study, the chemical plume is released iso-kinetically into a fully-developed, uniform open channel flow at 50 mm/s. Instantaneous concentration and velocity fields are simultaneously measured using planar laser induced fluorescence (PLIF) and digital particle tracking velocimetry (DPTV), respectively. In addition to the mean and variance, quantities of interest include intermittency, the temporal rise slope of chemical concentration and spatial correlations.

  15. The past and future of chemical information - A report of the Chemical Information Division Session of the 200th Meeting of the American Chemical Society

    NASA Astrophysics Data System (ADS)

    Tokizane, Soichi

    At the historical meeting of the ACS CINF Division, the 1990 Herman Skolnik Award was presented to Dr. Ernst Meyer, who at BASF in Germany had developed a computer storage and retrieval system of chemical structures in 1960s. His and his colleagues' speeches in the award symposium were about the history of the development of chemical structure information in Germany. In the symposium of the Markush structure system, a hottest topic in this field, CAS's MARPAT and Markush-DARC co-developed by Questel, INPI, and Derwent were discussed by many papers. Other topics of this meeting were discussed, too.

  16. Valence-Bond Theory and Chemical Structure.

    ERIC Educational Resources Information Center

    Klein, Douglas J.; Trinajstic, Nenad

    1990-01-01

    Discussed is the importance of valence bond theory on the quantum-mechanical theory of chemical structure and the nature of the chemical bond. Described briefly are early VB theory, development of VB theory, modern versions, solid-state applications, models, treatment in textbooks, and flaws in criticisms of valence bond theory. (KR)

  17. Mining chemical information from open patents

    PubMed Central

    2011-01-01

    Linked Open Data presents an opportunity to vastly improve the quality of science in all fields by increasing the availability and usability of the data upon which it is based. In the chemical field, there is a huge amount of information available in the published literature, the vast majority of which is not available in machine-understandable formats. PatentEye, a prototype system for the extraction and semantification of chemical reactions from the patent literature has been implemented and is discussed. A total of 4444 reactions were extracted from 667 patent documents that comprised 10 weeks' worth of publications from the European Patent Office (EPO), with a precision of 78% and recall of 64% with regards to determining the identity and amount of reactants employed and an accuracy of 92% with regards to product identification. NMR spectra reported as product characterisation data are additionally captured. PMID:21999425

  18. Chemical oscillators in structured media.

    PubMed

    Epstein, Irving R; Vanag, Vladimir K; Balazs, Anna C; Kuksenok, Olga; Dayal, Pratyush; Bhattacharya, Amitabh

    2012-12-18

    Evolution is a characteristic feature of living systems, and many fundamental processes in life, including the cell cycle, take place in a periodic fashion. From a chemistry perspective, these repeating phenomena suggest the question of whether reactions in which concentrations oscillate could provide a basis and/or useful models for the behavior of organisms, and perhaps even their ability to evolve. In this Account, we examine several aspects of the behavior of the prototype oscillating chemical reaction, the Belousov-Zhabotinsky (BZ) system, carried out in microemulsions, arrays of micrometer-sized aqueous droplets suspended in oil, or hydrogels. Each of these environments contains elements of the compartmentalization that likely played a role in the development of the first living cells, and within them we observe behaviors not found in the BZ reaction in simple aqueous solution. Several of these phenomena resemble traits displayed by living organisms. For example, the nanodroplets in a BZ microemulsion "communicate" with each other through a phenomenon analogous to quorum sensing in bacteria to produce a remarkable variety of patterns and waves on length scales 10(5) times the size of a single droplet. A photosensitive version can "remember" an imposed image. Larger, micrometer-sized droplets exhibit similarly rich behavior and allow for the observation and control of individual droplets. These droplets offer promise for building arrays capable of computation by varying the strength and sign of the coupling between drops. Gels that incorporate a BZ catalyst and are immersed in a solution containing the BZ reactants change their shape and volume in oscillations that follow the variation in the redox state of the catalyst. Using this phenomenon, we can construct phototactic gel "worms" or segments of gel that attract one another. Whether such systems will provide more realistic caricatures of life, and whether they can serve as useful materials will largely

  19. The Indiana University Chemical Information Center Program of Chemical Literature Instruction.

    ERIC Educational Resources Information Center

    Wiggins, Gary

    1982-01-01

    Describes three chemical information science courses offered by Indiana University (IU) Department of Chemistry. Also describes goals and operation of IU's Chemical Information Center, created to implement online searching of chemical databases and to assume operation of the IU dissemination of information services based on Chemical Abstracts…

  20. Bayesian inference of protein structure from chemical shift data

    PubMed Central

    Bratholm, Lars A.; Christensen, Anders S.; Hamelryck, Thomas

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction. PMID:25825683

  1. Bayesian inference of protein structure from chemical shift data.

    PubMed

    Bratholm, Lars A; Christensen, Anders S; Hamelryck, Thomas; Jensen, Jan H

    2015-01-01

    Protein chemical shifts are routinely used to augment molecular mechanics force fields in protein structure simulations, with weights of the chemical shift restraints determined empirically. These weights, however, might not be an optimal descriptor of a given protein structure and predictive model, and a bias is introduced which might result in incorrect structures. In the inferential structure determination framework, both the unknown structure and the disagreement between experimental and back-calculated data are formulated as a joint probability distribution, thus utilizing the full information content of the data. Here, we present the formulation of such a probability distribution where the error in chemical shift prediction is described by either a Gaussian or Cauchy distribution. The methodology is demonstrated and compared to a set of empirically weighted potentials through Markov chain Monte Carlo simulations of three small proteins (ENHD, Protein G and the SMN Tudor Domain) using the PROFASI force field and the chemical shift predictor CamShift. Using a clustering-criterion for identifying the best structure, together with the addition of a solvent exposure scoring term, the simulations suggests that sampling both the structure and the uncertainties in chemical shift prediction leads more accurate structures compared to conventional methods using empirical determined weights. The Cauchy distribution, using either sampled uncertainties or predetermined weights, did, however, result in overall better convergence to the native fold, suggesting that both types of distribution might be useful in different aspects of the protein structure prediction.

  2. Current Research into Chemical and Textual Information Retrieval at the Department of Information Studies, University of Sheffield.

    ERIC Educational Resources Information Center

    Lynch, Michael F.; Willett, Peter

    1987-01-01

    Discusses research into chemical information and document retrieval systems at the University of Sheffield. Highlights include the use of cluster analysis methods for document retrieval and drug design, representation and searching of files of generic chemical structures, and the application of parallel computer hardware to information retrieval.…

  3. Challenges and Benefits of Chemical Information Service in Industry.

    ERIC Educational Resources Information Center

    Hansen, Mary E.; Curtis, Jan M.

    1997-01-01

    Discusses chemical information services offered in industrial chemical libraries, based on experiences at the 3M Library. Topics include qualifications of chemical information professionals; corporate culture; clients; services, including reference, current awareness, confidentiality, and end-user support; and information resources, including…

  4. Chemical structure and dynamics. Annual report 1995

    SciTech Connect

    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.

  5. Chemical structure and dynamics: Annual report 1996

    SciTech Connect

    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.

  6. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    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.

  7. Deducing chemical structure from crystallographically determined atomic coordinates

    PubMed Central

    Bruno, Ian J.; Shields, Gregory P.; Taylor, Robin

    2011-01-01

    An improved algorithm has been developed for assigning chemical structures to incoming entries to the Cambridge Structural Database, using only the information available in the deposited CIF. Steps in the algorithm include detection of bonds, selection of polymer unit, resolution of disorder, and assignment of bond types and formal charges. The chief difficulty is posed by the large number of metallo-organic crystal structures that must be processed, given our aspiration that assigned chemical structures should accurately reflect properties such as the oxidation states of metals and redox-active ligands, metal coordination numbers and hapticities, and the aromaticity or otherwise of metal ligands. Other complications arise from disorder, especially when it is symmetry imposed or modelled with the SQUEEZE algorithm. Each assigned structure is accompanied by an estimate of reliability and, where necessary, diagnostic information indicating probable points of error. Although the algorithm was written to aid building of the Cambridge Structural Database, it has the potential to develop into a general-purpose tool for adding chemical information to newly determined crystal structures. PMID:21775812

  8. Chemical Structure and Dynamics annual report 1997

    SciTech Connect

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

    1998-03-01

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

  9. Information System for Environmental Chemicals: Training for End Users.

    ERIC Educational Resources Information Center

    Voigt, Kristina; And Others

    1991-01-01

    Discusses factors to consider in identifying and accessing appropriate data sources for environmental chemical information and describes three training programs for end-users: (1) a course on retrieval of information on dangerous substances; (2) a seminar on German offline databases on chemicals; and (3) a workshop on the Information System for…

  10. Survey of Ongoing Federal Chemical Information and Data Systems.

    ERIC Educational Resources Information Center

    Thompson (John I.) and Co., Washington, DC.

    The purpose of the survey was to collect data relating to (1) present usage of chemical information and data in the Federal community; (2) techniques and equipment now used in the acquisition, processing, and transmission of information and data; and (3) direction of plans for future chemical information services at ongoing systems. The scope of…

  11. Chemical information from the source function.

    PubMed

    Gatti, Carlo; Cargnoni, Fausto; Bertini, Luca

    2003-03-01

    The source function, which enables one to equate the value of the electron density at any point within a molecule to a sum of atomic contributions, has been applied to a number of cases. The source function is a model-independent, quantitative measure of the relative importance of an atom's or group's contribution to the density at any point in a system, and it represents a potentially interesting tool to provide chemical information. It is shown that the source contribution from H to the electron density rho(b) at the bond critical point in HX diatomics decreases with increasing X's electronegativity, and that this decrease is a result of significant changes in the Laplacian distribution within the H-basin. It is also demonstrated that the source function from Li to rho(b) in LiX diatomics is a more sensitive index of atomic transferability than it is the lithium atomic energy or population. The observed changes are such as to ensure a constant percentage source contribution from Li to rho(b) throughout the LiX series, rather than a constant source as one would expect in the limit of perfect atomic transferability. Application of the source function to planar lithium clusters has revealed that the source function clearly discriminates between a nonnuclear electron density maximum and a maximum associated to a nucleus, on the basis of the relative weight of the source contributions from the basin associated to the maximum and from the remaining basins in the cluster. The source function has also allowed for a classification of hydrogen bonds in terms of characteristic source contributions to the density at the H-bond critical point from the H involved in the H-bond, the H-donor D, and the H-acceptor A. The source contribution from the H appears as the most distinctive marker of the H-bond strength, being highly negative for isolated H-bonds, slightly negative for polarized assisted H-bonds, close to zero for resonance-assisted H-bonds, and largely positive for

  12. Chemical structure and dynamics. Annual report 1994

    SciTech Connect

    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.

  13. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    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).

  14. Characteristics of comprehensive Chemical Industry Database CD-NET : Centered around chemical product information file

    NASA Astrophysics Data System (ADS)

    Takano, Hideo

    This paper describes Chemical Product Information File of Chemical Industry Database, CD-NET provided by Chemical Data Service Inc.. It defines "information" first, then explains file organization and presents how Chemical product Information File is located in CD-NET. Mentioning its complementary relation with JICST's JOIS-F the author defines the File as chemical product information for business purpose. All of the information items in the File emphasize that it is exactly a type of business and practical database. To distinguish general items from important items by product, all of the information is categorized into II classes by general chemical product and by area. The scope and emphasized items under each class are described in detail.

  15. Chemical information matters: an e-Research perspective on information and data sharing in the chemical sciences.

    PubMed

    Bird, Colin L; Frey, Jeremy G

    2013-08-21

    Recently, a number of organisations have called for open access to scientific information and especially to the data obtained from publicly funded research, among which the Royal Society report and the European Commission press release are particularly notable. It has long been accepted that building research on the foundations laid by other scientists is both effective and efficient. Regrettably, some disciplines, chemistry being one, have been slow to recognise the value of sharing and have thus been reluctant to curate their data and information in preparation for exchanging it. The very significant increases in both the volume and the complexity of the datasets produced has encouraged the expansion of e-Research, and stimulated the development of methodologies for managing, organising, and analysing "big data". We review the evolution of cheminformatics, the amalgam of chemistry, computer science, and information technology, and assess the wider e-Science and e-Research perspective. Chemical information does matter, as do matters of communicating data and collaborating with data. For chemistry, unique identifiers, structure representations, and property descriptors are essential to the activities of sharing and exchange. Open science entails the sharing of more than mere facts: for example, the publication of negative outcomes can facilitate better understanding of which synthetic routes to choose, an aspiration of the Dial-a-Molecule Grand Challenge. The protagonists of open notebook science go even further and exchange their thoughts and plans. We consider the concepts of preservation, curation, provenance, discovery, and access in the context of the research lifecycle, and then focus on the role of metadata, particularly the ontologies on which the emerging chemical Semantic Web will depend. Among our conclusions, we present our choice of the "grand challenges" for the preservation and sharing of chemical information.

  16. Structure activity relationships to assess new chemicals under TSCA

    SciTech Connect

    Auletta, A.E.

    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.

  17. THE IMPORTANCE OF SPATIAL ACCURACY FOR CHEMICAL INFORMATION MANAGEMENT

    EPA Science Inventory

    Information about chemicals can be critical to making timely decisions. The results of these decisions may not be realized for many years. In order to increase the value of chemical information and to create and utilize meaningful environmental models, the Environmental Prote...

  18. Chemical Information Instruction in Academe: Who Is Leading the Charge?

    ERIC Educational Resources Information Center

    Garritano, Jeremy R.; Culp, F. Bartow; Twiss-Brooks, Andrea

    2010-01-01

    Chemical information instruction (CII) has been recommended by the ACS Committee on Professional Training as a necessary component of the chemistry curriculum for both undergraduate and graduate students. Surveys conducted by the ACS Chemical Information Division (CINF) Education Committee in 1984 and 1993 showed the extent that CII had become…

  19. 78 FR 17656 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-22

    ... exemption (TME), and to publish in the Federal Register periodic status reports on the new chemicals under... Register periodic status reports on the new chemicals under review and the receipt of NOCs to manufacture... Table I. of this unit, EPA provides the following information (to the extent that such information...

  20. Informational laws of genome structures

    NASA Astrophysics Data System (ADS)

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-06-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined.

  1. Informational laws of genome structures

    PubMed Central

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-01-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

  2. Informational laws of genome structures.

    PubMed

    Bonnici, Vincenzo; Manca, Vincenzo

    2016-01-01

    In recent years, the analysis of genomes by means of strings of length k occurring in the genomes, called k-mers, has provided important insights into the basic mechanisms and design principles of genome structures. In the present study, we focus on the proper choice of the value of k for applying information theoretic concepts that express intrinsic aspects of genomes. The value k = lg2(n), where n is the genome length, is determined to be the best choice in the definition of some genomic informational indexes that are studied and computed for seventy genomes. These indexes, which are based on information entropies and on suitable comparisons with random genomes, suggest five informational laws, to which all of the considered genomes obey. Moreover, an informational genome complexity measure is proposed, which is a generalized logistic map that balances entropic and anti-entropic components of genomes and is related to their evolutionary dynamics. Finally, applications to computational synthetic biology are briefly outlined. PMID:27354155

  3. Annual Report 2002. Chemical Structure & Dynamics

    SciTech Connect

    Colson, Steven D.; Gephart, Roy E.

    2003-01-01

    This report describes the research and accomplishments of the Chemical Structure and Dynamics (CS&D) Group of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) from October 2000 through December 2001. Publications, presentations, and collaborations are listed from October 2000 to September 2002. The EMSL is a national user facility located at the Pacific Northwest National Laboratory, Richland, Washington. The CS&D program supports the Department of Energy?s mission of fostering fundamental research in the natural sciences to provide a basis for new and improved energy technologies and for understanding and mitigating the environmental impacts of energy use and contaminant releases.

  4. ASTM Data Banks and Chemical Information Sources

    ERIC Educational Resources Information Center

    Batik, Albert; Hale, Eleanor

    1972-01-01

    Among the data described are infrared indexes, mass spectral data, chromatographic data, X-ray emmission data, odor and taste threshold data, and thermodynamics data. This paper provides the chemical documentarian a complete reference source to a wide variety of analytical data. (Author/NH)

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

    DOEpatents

    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.

  6. Introducing Graduate Students to the Chemical Information Landscape: The Ongoing Evolution of a Graduate-Level Chemical Information Course

    ERIC Educational Resources Information Center

    Currano, Judith N.

    2016-01-01

    The University of Pennsylvania's doctoral chemistry curriculum has included a required course in chemical information since 1995. Twenty years later, the course has evolved from a loosely associated series of workshops on information resources to a holistic examination of the chemical literature and its place in the general research process. The…

  7. Computational analysis of RNA structures with chemical probing data.

    PubMed

    Ge, Ping; Zhang, Shaojie

    2015-06-01

    RNAs play various roles, not only as the genetic codes to synthesize proteins, but also as the direct participants of biological functions determined by their underlying high-order structures. Although many computational methods have been proposed for analyzing RNA structures, their accuracy and efficiency are limited, especially when applied to the large RNAs and the genome-wide data sets. Recently, advances in parallel sequencing and high-throughput chemical probing technologies have prompted the development of numerous new algorithms, which can incorporate the auxiliary structural information obtained from those experiments. Their potential has been revealed by the secondary structure prediction of ribosomal RNAs and the genome-wide ncRNA function annotation. In this review, the existing probing-directed computational methods for RNA secondary and tertiary structure analysis are discussed.

  8. Weighted voting-based consensus clustering for chemical structure databases.

    PubMed

    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. PMID:24830925

  9. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

    Emberson, R.; Hovius, N.; Hsieh, M.; Galy, A.

    2013-12-01

    Material eroded from active mountain belts can spend extended periods in depositional structures within the mountain catchments before reaching its final destination. This can be in the form of colluvial fills, debris fans, or alluvial valley fills and terraces. The existence of these landforms is testament to the catastrophic nature of the events that lead to their formation. Sourced by landslides or debris flows, the material that forms them is in many cases either unweathered or incompletely weathered (e.g. Hsieh and Chyi 2010). Due to their porosity and permeability, these deposits likely serve as locations for extensive chemical weathering within bedrock landscapes. Recent studies considering the weathering flux from active mountain belts (e.g. Calmels et al. 2011) have distinguished between shallow and deep groundwater in terms of the contribution to the solute budget from a catchment; in this study we have attempted to more tightly constrain the sources of these groundwater components in the context of the previously mentioned depositional structures. We have collected water samples from a large number of sites within the Chen-you-lan catchment (370 km2) in central west Taiwan to elucidate the location of chemical weathering as well as how the sourcing of weathering products varies depending on the meteorological conditions. Central Taiwan has good attributes for this work considering both the extremely active tectonics and tropical climate, (including extensive cyclonic activity) which stimulate both extensive physical erosion (Dadson et al. 2003) and chemical weathering (Calmels et al. 2011). The Chen-you-lan catchment in particular contains some of the largest alluvial deposits inside the Taiwan mountain belt (Hsieh and Chyi 2010). Our preliminary results suggest that weathering within intramontane deposits may be a significant source of solutes, with the hyporheic systems within mountain rivers of particular import. This input of solutes occurs over

  10. AN OVERVIEW OF WORLDWIDE CHEMICAL INFORMATION FACILITIES AND RESOURCES.

    ERIC Educational Resources Information Center

    National Science Foundation, Washington, DC.

    THIS DESCRIPTIVE OVERVIEW OF CHEMICAL INFORMATION TRANSFER ACTIVITIES AND SYSTEMS COVERS THE FULL RANGE OF INFORMATION SERVICES FROM TRADITIONAL PUBLICATION SERVICES THROUGH THE DEVELOPING COMPUTER-BASED SERVICES. THE REPORT IS CONCERNED WITH DOCUMENTATION RATHER THAN ORAL COMMUNICATION AND WITH RECOGNIZED INFORMATION SYSTEMS RATHER THAN INFORMAL…

  11. Chemical hazard information profile of triphenyl phosphite

    SciTech Connect

    Faust, R.A.; Wiedow, M.A.; Daugherty, M.W.; Ross, R.H.; Leitzke, J.S.

    1986-12-01

    The only human study located showed that triphenyl phosphite applied to the skin in a 1:3 dilution with cold cream for 48 h caused slight irritation, and challenge with the compound 14 days later produced a moderate sensitization reaction. The most significant health effects described in experimental animals are those affecting the nervous system. In adult rats, subacute exposure to the chemical produced gross ataxia and spinal cord neuropathy which predominantly affected the lateral and ventral columns of the lumber and sacral regions. Other symptoms included hyperexcitability and agitation after several days, muscle wasting, asymmetric gait, and hind-limb paralysis. All animals developed tail rigidity with a kinky appearance, and some animals displayed a circling behavior. The compound appeared to only weakly inhibit acetylcholinesterase activity. Single oral doses of triphenyl phosphite Gallus domesticus produced ataxia, and spinal cord and peripheral nerve histopathology. Neurotoxicity in rats, cats, and chickens indicated that triphenyl phosphite caused two distinct stages of action. Rats given s.c. injections of the chemical exhibit rapidly-developing stage or fine or coarse tremors which disappeared after a few hours. The later stage, occurring several days after treatment, caused hyperexcitability, spasticity and incoordination, followed by partial flaccid paralysis of the extremities. 135 refs., 2 tabs.

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

    PubMed

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

    2010-10-01

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

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

    PubMed

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

    2010-10-01

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

  14. Integrated chemical management system: A tool for managing chemical information at the Rocky Flats Environmental Technology Site

    SciTech Connect

    Costain, D.

    1995-07-01

    The Integrated Chemical Management System is a computer-based chemical information at the Rocky Flats Environmental Technology Site. Chemical containers are identified by bar code labels and information on the type, quantity and location of chemicals are tracked on individual data bases in separate buildings. Chemical inventories from multiple buildings are uploaded to a central sitewide chemical data base where reports are available from Product, Waste, and Chemical Use modules. Hazardous chemical information is provided by a separate Material Safety Data Sheet module and excess chemicals are traded between chemical owners and users with the aid of the Chemical Exchange Module.

  15. Functional cavitands: Chemical reactivity in structured environments

    PubMed Central

    Purse, Byron W.; Rebek, Julius

    2005-01-01

    Container-shaped molecules provide structured environments that impart geometric bounds on the motions and conformations of smaller molecular occupants. Moreover, they provide “solvation” that is constrained in time and space. When inwardly directed functional groups are present, they can interact chemically with the occupants. Additionally, the potential for reactivity and catalysis is greatly enhanced. Deep cavitands, derived from resorcinarenes, nearly surround smaller molecules and have been one of the most successful platforms for elaboration with functional groups. Derivatives bearing organic and metal-binding functional groups have been shown to affect recognition properties and selectively accelerate diverse reactions. In this review, we examine recent examples of these systems with an emphasis on how and why ordered nanoenvironments impart changes in the properties and reactivity of their occupants. PMID:16043720

  16. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 6 Domestic Security 1 2012-01-01 2012-01-01 false Chemical-terrorism vulnerability information. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL... Secretary shall administer this section consistent with section 550(c) of the Homeland...

  17. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 6 Domestic Security 1 2011-01-01 2011-01-01 false Chemical-terrorism vulnerability information. 27.400 Section 27.400 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL... Secretary shall administer this section consistent with section 550(c) of the Homeland...

  18. Encoding information into precipitation structures

    NASA Astrophysics Data System (ADS)

    Martens, Kirsten; Bena, Ioana; Droz, Michel; Rácz, Zoltan

    2008-12-01

    Material design at submicron scales would be profoundly affected if the formation of precipitation patterns could be easily controlled. It would allow the direct building of bulk structures, in contrast to traditional techniques which consist of removing material in order to create patterns. Here, we discuss an extension of our recent proposal of using electrical currents to control precipitation bands which emerge in the wake of reaction fronts in A+ + B- → C reaction-diffusion processes. Our main result, based on simulating the reaction-diffusion-precipitation equations, is that the dynamics of the charged agents can be guided by an appropriately designed time-dependent electric current so that, in addition to the control of the band spacing, the width of the precipitation bands can also be tuned. This makes straightforward the encoding of information into precipitation patterns and, as an amusing example, we demonstrate the feasibility by showing how to encode a musical rhythm.

  19. UNEP Chemicals' work: breaking the barriers to information access.

    PubMed

    Keita-Ouane, Fatoumata

    2003-08-21

    The global production and trade in chemicals was measured at 1.55 trillion US dollars in 1996, four times the amount of 1966. Chemicals represent 14% of imports and exports of OECD countries and the present decade has been characterised by the expansion of the production and use of chemicals in countries with economies in transition and developing countries. While some of these chemicals are benign at the levels we are usually exposed to them, others present risks to human health or the environment often across national boundaries. Failure to safely manage these risks could lead to serious and long-term consequences. The sound management of chemicals requires adequate information about their nature and use as well as their effects and control options. Much of this information can be culled from a variety of sources but that does not guarantee equal access to it by all those who are in need. To achieve equitable information distribution, the chemical unit of the United Nations Environment Programme (UNEP) operates many activities aimed at removing the geographical and technical barriers that prevent the free flow of chemical management information. These activities include the use of assorted media and activities to enhance countries' internal capacity to search and use the information available on the Internet. PMID:12909405

  20. Systems approach to chemical spill response information needs

    SciTech Connect

    Parnarouskis, M.C.; Flessner, M.F.; Potts, R.G.

    1980-01-01

    The Chemical Hazards Response Information System (CHRIS) has been specifically designed to meet the emergency needs of US Coast Guard field personnel, currently providing them with information on 900 hazardous chemicals, with methods of predicting hazards resulting from accidental discharges, and with procedures for selecting and implementing response to accident discharges. The major components of CHRIS and the computerized hazard assessment models within the Hazard Assessment Computer System are described in detail.

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

    EPA Science Inventory

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

  2. Construction of a Linux based chemical and biological information system.

    PubMed

    Molnár, László; Vágó, István; Fehér, András

    2003-01-01

    A chemical and biological information system with a Web-based easy-to-use interface and corresponding databases has been developed. The constructed system incorporates all chemical, numerical and textual data related to the chemical compounds, including numerical biological screen results. Users can search the database by traditional textual/numerical and/or substructure or similarity queries through the web interface. To build our chemical database management system, we utilized existing IT components such as ORACLE or Tripos SYBYL for database management and Zope application server for the web interface. We chose Linux as the main platform, however, almost every component can be used under various operating systems.

  3. Computerized management information systems and organizational structures

    NASA Technical Reports Server (NTRS)

    Zannetos, Z. S.; Sertel, M. R.

    1970-01-01

    The computerized management of information systems and organizational structures is discussed. The subjects presented are: (1) critical factors favoring centralization and decentralization of organizations, (2) classification of organizations by relative structure, (3) attempts to measure change in organization structure, and (4) impact of information technology developments on organizational structure changes.

  4. 78 FR 16698 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-03-18

    ... Information (CVI) for an additional 30 days for public comments. \\1\\ See 77 FR 74685. The 60-day Federal... statutory mandate at 72 FR 17688. Section 550 of the Homeland Security Appropriations Act of 2007 requires a... SECURITY Chemical Facility Anti-Terrorism Standards (CFATS) Chemical- Terrorism Vulnerability...

  5. Ice Cream Seminars for Graduate Students: Imparting Chemical Information Literacy

    ERIC Educational Resources Information Center

    Garritano, Jeremy R.

    2007-01-01

    This article provides information on a chemical information literacy program designed primarily for new graduate students. The full implementation of this program is discussed, including defining its purpose, topics covered, content presented, methods of marketing, and evaluation. The result is a series of voluntary seminars given biweekly…

  6. 77 FR 21769 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-11

    ... application for a test marketing exemption (TME), and to publish in the Federal Register periodic status... Federal Register periodic status reports on the new chemicals under review and the receipt of NOCs to... Table I. of this unit, EPA provides the following information (to the extent that such information...

  7. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

  8. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release may... shall be treated as classified information in accordance with 6 CFR 27.400(h) and (i). (4) Other...

  9. SYSTEM PERFORMANCE SPECIFICATION FOR A NATIONAL CHEMICAL INFORMATION SYSTEM.

    ERIC Educational Resources Information Center

    Information Management, Inc., Burlington, MA.

    THIS DOCUMENT CONTAINS A SET OF STATEMENTS ABOUT INFORMATION NEEDS, SYSTEM GOALS, SYSTEM REQUIREMENTS, AND SYSTEM SPECIFICATIONS FOR THE DEVELOPMENT OF A NATIONAL CHEMICAL INFORMATION SYSTEM. IN ITS PRESENT FORM, THE DOCUMENT CONSTITUTES A BASIS FOR FUTURE PLANNING. AS POLICY DECISIONS ARE MADE, TECHNICAL PROBLEMS SOLVED AND PLANS ARE ALTERED, THE…

  10. Conservation-dissipation structure of chemical reaction systems.

    PubMed

    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.

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

    PubMed

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

    2013-09-01

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

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

    PubMed

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

    2013-09-01

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

  13. Predictive Modeling of Chemical Hazard by Integrating Numerical Descriptors of Chemical Structures and Short-term Toxicity Assay Data

    PubMed Central

    Rusyn, Ivan; Sedykh, Alexander; Guyton, Kathryn Z.; Tropsha, Alexander

    2012-01-01

    Quantitative structure-activity relationship (QSAR) models are widely used for in silico prediction of in vivo toxicity of drug candidates or environmental chemicals, adding value to candidate selection in drug development or in a search for less hazardous and more sustainable alternatives for chemicals in commerce. The development of traditional QSAR models is enabled by numerical descriptors representing the inherent chemical properties that can be easily defined for any number of molecules; however, traditional QSAR models often have limited predictive power due to the lack of data and complexity of in vivo endpoints. Although it has been indeed difficult to obtain experimentally derived toxicity data on a large number of chemicals in the past, the results of quantitative in vitro screening of thousands of environmental chemicals in hundreds of experimental systems are now available and continue to accumulate. In addition, publicly accessible toxicogenomics data collected on hundreds of chemicals provide another dimension of molecular information that is potentially useful for predictive toxicity modeling. These new characteristics of molecular bioactivity arising from short-term biological assays, i.e., in vitro screening and/or in vivo toxicogenomics data can now be exploited in combination with chemical structural information to generate hybrid QSAR–like quantitative models to predict human toxicity and carcinogenicity. Using several case studies, we illustrate the benefits of a hybrid modeling approach, namely improvements in the accuracy of models, enhanced interpretation of the most predictive features, and expanded applicability domain for wider chemical space coverage. PMID:22387746

  14. 77 FR 74685 - Chemical Facility Anti-Terrorism Standards (CFATS) Chemical-Terrorism Vulnerability Information...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-12-17

    ... information provided. Special Instructions: Comments that include trade secrets, confidential commercial or.... Comments containing trade secrets, confidential commercial or financial information, CVI, SSI, or PCII... security of high-risk chemical facilities. On April 9, 2007, the Department issued an Interim Final...

  15. The origin and dynamic evolution of chemical information transfer.

    PubMed

    Steiger, Sandra; Schmitt, Thomas; Schaefer, H Martin

    2011-04-01

    Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general.

  16. Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

    PubMed Central

    Allali-Hassani, Abdellah; Pan, Patricia W; Dombrovski, Ludmila; Najmanovich, Rafael; Tempel, Wolfram; Dong, Aiping; Loppnau, Peter; Martin, Fernando; Thonton, Janet; Edwards, Aled M; Bochkarev, Alexey; Plotnikov, Alexander N; Vedadi, Masoud; Arrowsmith, Cheryl H

    2007-01-01

    The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique “chemical fingerprints” for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural “priming” of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone. PMID:17425406

  17. Enhanced Sensitivity of Micro Mechanical Chemical Sensors Through Structural Variation

    SciTech Connect

    Harris, J.C.

    2001-04-16

    Chemical detection devices are very effective; however, their bulkiness makes them undesirable for portable applications. The next generation of chemical detectors is microscopic mechanical devices capable of measuring trace amounts of chemical vapor within the environment. The chemicals do not react directly with the detector, instead intermolecular forces cause chemicals to adhere to the surface. This surface adhesion of the chemical creates surface stress on the detectors leading to measurable movement. Modifications to the structural design of these microstructures have resulted in signal enhancement to over seven hundred percent.

  18. Information Content of Molecular Structures

    PubMed Central

    Sullivan, David C.; Aynechi, Tiba; Voelz, Vincent A.; Kuntz, Irwin D.

    2003-01-01

    For a completely enumerated set of conformers of a macromolecule or for exhaustive lattice walks of model polymers it is straightforward to use Shannon information theory to deduce the information content of the ensemble. It is also practicable to develop numerical measures of the information content of sets of exact distance constraints applied to specific conformational ensembles. We examine the effects of experimental uncertainties by considering “noisy” constraints. The introduction of noise requires additional assumptions about noise distribution and conformational clustering protocols that make the problem of measuring information content more complex. We make use of a standard concept in communication theory, the “noise sphere,” to link uncertainty in measurements to information loss. Most of our numerical results are derived from two-dimensional lattice ensembles. Expressing results in terms of information per degree of freedom removes almost all of the chain length dependence. We also explore off-lattice polyalanine chains that yield surprisingly similar results. PMID:12829474

  19. Communication and re-use of chemical information in bioscience

    PubMed Central

    Murray-Rust, Peter; Mitchell, John BO; Rzepa, Henry S

    2005-01-01

    The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste are time-consuming and introduce errors. The meaning of chemical terms and the identity of compounds is often ambiguous. valuable experimental data such as spectra and computational results are almost always omitted. We describe an Open XML architecture at proof-of-concept which addresses these concerns. Compounds are identified through explicit connection tables or links to persistent Open resources such as PubChem. It is argued that if publishers adopt these tools and protocols, then the quality and quantity of chemical information available to bioscientists will increase and the authors, publishers and readers will find the process cost-effective. PMID:16026614

  20. Introducing Chemistry Undergraduate Students to Online Chemical Information Retrieval.

    ERIC Educational Resources Information Center

    Wolman, Yecheskel

    1985-01-01

    The results of manual and online searching are compared during a unit on online chemical information retrieval taught at Hebrew University. Strategies and results obtained are provided for student searches on the synthesis of vitamin K(3) from 2-methylnaphthalene and polywater. (JN)

  1. Chemical Information in Scirus and BASE (Bielefeld Academic Search Engine)

    ERIC Educational Resources Information Center

    Bendig, Regina B.

    2009-01-01

    The author sought to determine to what extent the two search engines, Scirus and BASE (Bielefeld Academic Search Engines), would be useful to first-year university students as the first point of searching for chemical information. Five topics were searched and the first ten records of each search result were evaluated with regard to the type of…

  2. Informing Workers of Chemical Hazards: The OSHA Hazard Communication Standard.

    ERIC Educational Resources Information Center

    American Chemical Society, Washington, DC.

    Practical information on how to implement a chemical-related safety program is outlined in this publication. Highlights of the federal Occupational Safety and Health Administrations (OSHA) Hazard Communication Standard are presented and explained. These include: (1) hazard communication requirements (consisting of warning labels, material safety…

  3. Support from Afar: Using Chemical Safety Information on the Internet.

    ERIC Educational Resources Information Center

    Stuart, Ralph

    One of the major challenges facing people committed to Teaching Safety in High Schools, Colleges, and Universities is keeping up with both the wide range of relevant technical information about potential hazards (ranging from fire protection to chemical hazards to biological issues) and the ever-changing world of safety regulations and standards.…

  4. 6 CFR 27.400 - Chemical-terrorism vulnerability information.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... inspection or audits under § 27.250; (6) Any records required to be created or retained under § 27.255; (7... record contains Chemical-terrorism Vulnerability Information controlled by 6 CFR 27.400. Do not disclose to persons without a “need to know” in accordance with 6 CFR 27.400(e). Unauthorized release...

  5. Information and computer-aided system for structural materials

    NASA Astrophysics Data System (ADS)

    Nekrashevitch, Ju. G.; Nizametdinov, Sh. U.; Polkovnikov, A. V.; Rumjantzev, V. P.; Surina, O. N.; Kalinin, G. M.; Sidorenkov, A. V.; Strebkov, Ju. S.

    1992-09-01

    An information and computer-aided system for structural materials data has been developed to provide data for the fusion and fission reactor system design. It is designed for designers, industrial engineers, and material science specialists and provides a friendly interface in an interactive mode. The database for structural materials contains the master files: chemical composition, physical, mechanical, corrosion, technological properties, regulatory and technical documentation. The system is implemented on a PC/AT running the PS/2 operating system.

  6. Field programmable chemistry: integrated chemical and electronic processing of informational molecules towards electronic chemical cells.

    PubMed

    Wagler, Patrick F; Tangen, Uwe; Maeke, Thomas; McCaskill, John S

    2012-07-01

    The topic addressed is that of combining self-constructing chemical systems with electronic computation to form unconventional embedded computation systems performing complex nano-scale chemical tasks autonomously. The hybrid route to complex programmable chemistry, and ultimately to artificial cells based on novel chemistry, requires a solution of the two-way massively parallel coupling problem between digital electronics and chemical systems. We present a chemical microprocessor technology and show how it can provide a generic programmable platform for complex molecular processing tasks in Field Programmable Chemistry, including steps towards the grand challenge of constructing the first electronic chemical cells. Field programmable chemistry employs a massively parallel field of electrodes, under the control of latched voltages, which are used to modulate chemical activity. We implement such a field programmable chemistry which links to chemistry in rather generic, two-phase microfluidic channel networks that are separated into weakly coupled domains. Electric fields, produced by the high-density array of electrodes embedded in the channel floors, are used to control the transport of chemicals across the hydrodynamic barriers separating domains. In the absence of electric fields, separate microfluidic domains are essentially independent with only slow diffusional interchange of chemicals. Electronic chemical cells, based on chemical microprocessors, exploit a spatially resolved sandwich structure in which the electronic and chemical systems are locally coupled through homogeneous fine-grained actuation and sensor networks and play symmetric and complementary roles. We describe how these systems are fabricated, experimentally test their basic functionality, simulate their potential (e.g. for feed forward digital electrophoretic (FFDE) separation) and outline the application to building electronic chemical cells. PMID:22309763

  7. Information Structure, Grammar and Strategy in Discourse

    ERIC Educational Resources Information Center

    Stevens, Jon

    2013-01-01

    This dissertation examines two information-structural phenomena, Givenness and Focus, from the perspective of both syntax and pragmatics. Evidence from English, German and other languages suggests a "split" analysis of information structure--the notions of Focus and Givenness, often thought to be closely related, exist independently at…

  8. Information Handling, Organizational Structure, and Power.

    ERIC Educational Resources Information Center

    Buckland, Michael K.

    1989-01-01

    Uses examples from military strategic communications to demonstrate that organizational structures and the distribution of power within organizational structures adapt to changes in information handling capability. It is concluded that delegation and decentralization can be viewed as indicative of inadequate information handling and that improved…

  9. Development of an Exchange Format for the European Environmental Chemical Data and Information Network (ECDIN).

    ERIC Educational Resources Information Center

    And Others; Proctor, David, J.

    1978-01-01

    Uses collection and storage of data in an environmental chemicals data bank to develop an exchange format of hierarchical tree structure between network partners. Rules identify and process the nodes in the tree in such a way that information is neither lost nor degraded upon transfer between network partners. (CWM)

  10. 77 FR 59891 - Proposed Information Collection; Comment Request; Chemical Weapons Convention Declaration and...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-10-01

    ... Bureau of Industry and Security Proposed Information Collection; Comment Request; Chemical Weapons...@bis.doc.gov . SUPPLEMENTARY INFORMATION: ] I. Abstract The Chemical Weapons Convention Implementation Act of 1998 and Commerce Chemical Weapons Convention Regulations (CWCR) specify the...

  11. Progressively Fostering Students' Chemical Information Skills in a Three-Year Chemical Engineering Program in France

    ERIC Educational Resources Information Center

    Gozzi, Christel; Arnoux, Marie-Jose´; Breuzard, Jere´my; Marchal, Claire; Nikitine, Clémence; Renaudat, Alice; Toulgoat, Fabien

    2016-01-01

    Literature searches are essential for scientists. Thus, courses on how to do a good literature search have been integrated in studies at CPE Lyon for many years. Recently, we modified our pedagogical approach in order to initiate students progressively in the search for chemical information. In addition, this new teaching organization is now based…

  12. Teaching Chemical Information in a Liberal Arts Curriculum

    NASA Astrophysics Data System (ADS)

    Ricker, Alison Scott; Thompson, Robert Q.

    1999-11-01

    We first offered Chemical Information as a one-credit, semester-long course in 1993 and have continued to team-teach it each fall. We offer this summary of our course as a model that might be adapted in other settings, acknowledging that no single course can adequately prepare chemists for the many challenges involved in finding, evaluating, and utilizing chemical information. The focus on information retrieval, evaluation, and presentation in a separate course has worked well for us, successfully integrating concepts of information literacy in a chemical context. We cover a wide array of topics, beginning with print and electronic resources on our campus and moving quickly to databases and other sources on the Internet. Searching CA Online via STN Express and STN Easy is emphasized more than any other single source. We have described the course in some detail elsewhere and give here a synopsis of our current approach and significant changes in the course over the last two years.

  13. Progress and challenges for chemical probing of RNA structure inside living cells

    PubMed Central

    Kubota, Miles; Tran, Catherine; Spitale, Robert C

    2016-01-01

    Proper gene expression is essential for the survival of every cell. Once thought to be a passive transporter of genetic information, RNA has recently emerged as a key player in nearly every pathway in the cell. A full description of its structure is critical to understanding RNA function. Decades of research have focused on utilizing chemical tools to interrogate the structures of RNAs, with recent focus shifting to performing experiments inside living cells. This Review will detail the design and utility of chemical reagents used in RNA structure probing. We also outline how these reagents have been used to gain a deeper understanding of RNA structure in vivo. We review the recent merger of chemical probing with deep sequencing. Finally, we outline some of the hurdles that remain in fully characterizing the structure of RNA inside living cells, and how chemical biology can uniquely tackle such challenges. PMID:26575240

  14. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    PubMed

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  15. Information of Structures in Galaxy Distribution

    NASA Astrophysics Data System (ADS)

    Fang, Fan

    2006-06-01

    We introduce an information-theoretic measure, the Rényi information, to describe the galaxy distribution in space. We discuss properties of the information measure and demonstrate its relationship with the probability distribution function and multifractal descriptions. Using the First Look Survey galaxy samples observed by the Infrared Array Camera on board the Spitzer Space Telescope, we present measurements of the Rényi information, as well as the counts-in-cells distribution and multifractal properties of galaxies in mid-infrared wavelengths. Guided by a multiplicative cascade simulation based on a binomial model, we verify our measurements and discuss the spatial selection effects on measuring information of the spatial structures. We derive structure scan functions at scales where selection effects are small for the Spitzer samples. We discuss the results and the potential of applying the Rényi information to the measurement of other spatial structures.

  16. Automated Physico-Chemical Cell Model Development through Information Theory

    SciTech Connect

    Peter J. Ortoleva

    2005-11-29

    The objective of this project was to develop predictive models of the chemical responses of microbial cells to variations in their surroundings. The application of these models is optimization of environmental remediation and energy-producing biotechnical processes.The principles on which our project is based are as follows: chemical thermodynamics and kinetics; automation of calibration through information theory; integration of multiplex data (e.g. cDNA microarrays, NMR, proteomics), cell modeling, and bifurcation theory to overcome cellular complexity; and the use of multiplex data and information theory to calibrate and run an incomplete model. In this report we review four papers summarizing key findings and a web-enabled, multiple module workflow we have implemented that consists of a set of interoperable systems biology computational modules.

  17. Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

    NASA Astrophysics Data System (ADS)

    Hay, Mark E.

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  18. Marine Chemical Ecology: Chemical Signals and Cues Structure Marine Populations, Communities, and Ecosystems

    PubMed Central

    Hay, Mark E.

    2012-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized. PMID:21141035

  19. Marine chemical ecology: chemical signals and cues structure marine populations, communities, and ecosystems.

    PubMed

    Hay, Mark E

    2009-01-01

    Chemical cues constitute much of the language of life in the sea. Our understanding of biotic interactions and their effects on marine ecosystems will advance more rapidly if this language is studied and understood. Here, I review how chemical cues regulate critical aspects of the behavior of marine organisms from bacteria to phytoplankton to benthic invertebrates and water column fishes. These chemically mediated interactions strongly affect population structure, community organization, and ecosystem function. Chemical cues determine foraging strategies, feeding choices, commensal associations, selection of mates and habitats, competitive interactions, and transfer of energy and nutrients within and among ecosystems. In numerous cases, the indirect effects of chemical signals on behavior have as much or more effect on community structure and function as the direct effects of consumers and pathogens. Chemical cues are critical for understanding marine systems, but their omnipresence and impact are inadequately recognized.

  20. Protein Structure Refinement Using 13Cα Chemical Shift Tensors

    PubMed Central

    Wylie, Benjamin J.; Schwieters, Charles D.; Oldfield, Eric; Rienstra, Chad M.

    2009-01-01

    We have obtained the 13Cα chemical shift tensors for each amino acid in the protein GB1. We then developed a CST force field and incorporated this into the Xplor-NIH structure determination program. GB1 structures obtained by using CST restraints had improved precision over those obtained in the absence of CST restraints, and were also more accurate. When combined with isotropic chemical shifts, distance and vector angle restraints, the root-mean squared error with respect to existing x-ray structures was better than ~1.0 Å. These results are of broad general interest since they show that chemical shift tensors can be used in protein structure refinement, improving both structural accuracy and precision, opening up the way to accurate de novo structure determination. PMID:19123862

  1. [Relationship between chemical structure and sweetness. XIV. Analogs of aspartame].

    PubMed

    De Nardo, M

    1977-07-01

    Several analogs structurally related to aspartame were prepared in order to establish if chemical modifications of the molecule might improve sweetness. None of these analogs exhibited any sweet taste; on the contrary in most cases they were bitter.

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

    PubMed

    Zarringhalam, Kourosh; Meyer, Michelle M; Dotu, Ivan; Chuang, Jeffrey H; Clote, Peter

    2012-01-01

    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.

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

    PubMed

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

    2015-11-01

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

  4. Information Access through Conceptual Structures and GIS.

    ERIC Educational Resources Information Center

    Priss, Uta; Old, John

    1998-01-01

    Presents a new technique for information access based on a combination of Geographic Information Systems (GIS) and conceptual structures as modeled in relational concept analysis. Describes a graphical interface that allows access of spatial, hierarchical, and linear data in a common manner; discusses its features and limits. (Author/AEF)

  5. Earth's interdependent thermal, structural, and chemical evolution

    NASA Astrophysics Data System (ADS)

    Hofmeister, A.; Criss, R. E.

    2012-12-01

    The popular view that 30-55% of Earth's global power is primordial, with deep layers emanating significant power, rests on misunderstandings and models that omit magmatism and outgassing. These processes link Earth's chemical and thermal evolution, while creating layers, mainly because magmas transport latent heat and radioactive isotopes rapidly upwards. We link chemistry to heat flow, measured and theoretical, to understand the interior layering and workings. Quasi-steady state conditions describe most of Earth's history: (1) Accretion was cold and was not a source of deep heat. (2) Friction during core formation cannot have greatly heated the interior (thermodynamics plus buoyancy). (3) Conduction is the governing microscopic mechanism in the deep Earth. (4) Using well-constrained values of thermal conductivity (k), we find that homogeneously distributed radionuclides provide extremely high internal temperature (T) under radial symmetry. Moreover, for any given global power, sequestering heat producing elements into the upper mantle reduces Earth's central temperature by a factor of 10 from a homogeneous distribution. Hence, (5) core formation was a major cooling event. From modern determinations of k(T) we provide a reference conductive geotherm. Present-day global power of 30 TW from heat flux measurements and sequestering of heat producing elements in the upper mantle and transition zone, produces nearly isothermal T = 5300 K below 670 km, which equals experimentally determined freezing of pure Fe0 at the inner core boundary. Core freezing buffers the interior temperatures, while the Sun constrains the surface temperature, providing steady state conditions: Earth's deep interior is isothermal due to these constraints, low flux and high k. Our geotherms point to a stagnant lower mantle and convection above 670 km. Rotational flattening cracks the brittle lithosphere, providing paths for buoyant magmas to ascend. Release of latent heat augments the conductive

  6. Structural Information Retention in Visual Art Processing.

    ERIC Educational Resources Information Center

    Koroscik, Judith Smith

    The accuracy of non-art college students' longterm retention of structural information presented in Leonardo da Vinci's "Mona Lisa" was tested. Seventeen female undergraduates viewed reproductions of the painting and copies that closely resembled structural attributes of the original. Only 3 of the 17 subjects reported having viewed a reproduction…

  7. Advanced Data Structure and Geographic Information Systems

    NASA Technical Reports Server (NTRS)

    Peuquet, D. (Principal Investigator)

    1984-01-01

    The current state of the art in specified areas of Geographic Information Systems GIS technology is examined. Study of the question of very large, efficient, heterogeneous spatial databases is required in order to explore the potential application of remotely sensed data for studying the long term habitability of the Earth. Research includes a review of spatial data structures and storage, development of operations required by GIS, and preparation of a testbed system to compare Vaster data structure with NASA's Topological Raster Structure.

  8. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

    Armbrust, T. S.; Odom, W. R.; Guikema, J. A.; Spooner, B. S. (Principal Investigator)

    1994-01-01

    Thylakoid membranes, obtained from leaves of 14 d soybean (Glycine max L. cv. Williams) plants, were treated with the chemical crosslinkers glutaraldehyde or 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC) to investigate the structural organization of photosystem I. Polypeptides were resolved using lithium dodecyl sulfate polyacrylamide gel electrophoresis, and were identified by western blot analysis using a library of polyclonal antibodies specific for photosystem I subunits. An electrophoretic examination of crosslinked thylakoids revealed numerous crosslinked products, using either glutaraldehyde or EDC. However, only a few of these could be identified by western blot analysis using subunit-specific polyclonal antibodies. Several glutaraldehyde dependent crosslinked species were identified. A single band was identified minimally composed of PsaC and PsaD, documenting the close interaction between these two subunits. The most interesting aspect of these studies was a crosslinked species composed of the PsaB subunit observed following EDC treatment of thylakoids. This is either an internally crosslinked species, which will provide structural information concerning the topology of the complex PsaB protein, a linkage with a polypeptide for which we do not yet have an immunological probe, or a masking of epitopes by the EDC linkage at critical locations in the peptide which is linked to PsaB.

  9. Forgotten topological index of chemical structure in drugs.

    PubMed

    Gao, Wei; Siddiqui, Muhammad Kamran; Imran, Muhammad; Jamil, Muhammad Kamran; Farahani, Mohammad Reza

    2016-05-01

    A massive of early drug tests implies that there exist strong inner relationships between the bio-medical and pharmacology characteristics of drugs and their molecular structures. The forgotten topological index was defined to be used in the analysis of drug molecular structures, which is quite helpful for pharmaceutical and medical scientists to grasp the biological and chemical characteristics of new drugs. Such tricks are popularly employed in developing countries where enough money is lacked to afford the relevant chemical reagents and equipment. In our article, by means of drug molecular structure analysis and edge dividing technology, we present the forgotten topological index of several widely used chemical structures which often appear in drug molecular graphs. PMID:27275112

  10. Chemical composition in relation with biomass ash structure

    NASA Astrophysics Data System (ADS)

    Holubcik, Michal; Jandacka, Jozef

    2014-08-01

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

  11. Entering new publication territory in chemoinformatics and chemical information science.

    PubMed

    Bajorath, Jürgen

    2015-01-01

    The F1000Research publishing platform offers the opportunity to launch themed article collections as a part of its dynamic publication environment. The idea of article collections is further expanded through the generation of publication channels that focus on specific scientific areas or disciplines. This editorial introduces the Chemical Information Science channel of F1000Research designed to collate high-quality publications and foster a culture of open peer review. Articles will be selected by guest editor(s) and a group of experts, the channel Editorial Board, and subjected to open peer review.

  12. Entering new publication territory in chemoinformatics and chemical information science

    PubMed Central

    Bajorath, Jürgen

    2015-01-01

    The F1000Research publishing platform offers the opportunity to launch themed article collections as a part of its dynamic publication environment. The idea of article collections is further expanded through the generation of publication channels that focus on specific scientific areas or disciplines. This editorial introduces the Chemical Information Science channel of F1000Research designed to collate high-quality publications and foster a culture of open peer review. Articles will be selected by guest editor(s) and a group of experts, the channel Editorial Board, and subjected to open peer review. PMID:26097687

  13. Information structure expectations in sentence comprehension

    PubMed Central

    Carlson, Katy; Dickey, Michael Walsh; Frazier, Lyn; Clifton, Charles

    2009-01-01

    In English, new information typically appears late in the sentence, as does primary accent. Because of this tendency, perceivers might expect the final constituent or constituents of a sentence to contain informational focus. This expectation should in turn affect how they comprehend focus-sensitive constructions such as ellipsis sentences. Results from four experiments on sluicing sentences (e.g., The mobster implicated the thug, but we can’t find out who else) suggest that perceivers do prefer to place focus late in the sentence, though that preference can be mitigated by prosodic information (pitch accents, Experiment 2) or syntactic information (clefted sentences, Experiment 3) indicating that focus is located elsewhere. Furthermore, it is not necessarily the direct object, but the informationally-focused constituent that is the preferred antecedent (Experiment 4). Expectations regarding the information structure of a sentence, which are only partly cancelable by means of overt focus markers, may explain persistent biases in ellipsis resolution. PMID:18609404

  14. Information Structure: Linguistic, Cognitive, and Processing Approaches

    PubMed Central

    Arnold, Jennifer E.; Kaiser, Elsi; Kahn, Jason M.; Kim, Lucy Kyoungsook

    2013-01-01

    Language form varies as a result of the information being communicated. Some of the ways in which it varies include word order, referential form, morphological marking, and prosody. The relevant categories of information include the way a word or its referent have been used in context, for example whether a particular referent has been previously mentioned or not, and whether it plays a topical role in the current utterance or discourse. We first provide a broad review of linguistic phenomena that are sensitive to information structure. We then discuss several theoretical approaches to explaining information structure: information status as a part of the grammar; information status as a representation of the speaker’s and listener’s knowledge of common ground and/or the knowledge state of other discourse participants; and the optimal systems approach. These disparate approaches reflect the fact that there is little consensus in the field about precisely which information status categories are relevant, or how they should be represented. We consider possibilities for future work to bring these lines of work together in explicit psycholinguistic models of how people encode information status and use it for language production and comprehension. PMID:26150905

  15. 77 FR 22559 - Proposed Information Collection; Comment Request; Chemical Weapons Convention Provisions of the...

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-04-16

    ... Bureau of Industry and Security Proposed Information Collection; Comment Request; Chemical Weapons...) 482-4895, Lawrence.Hall@bis.doc.gov . SUPPLEMENTARY INFORMATION: I. Abstract The Chemical Weapons... weapons (CW). The CWC prohibits the use, development, production, acquisition, stockpiling, retention,...

  16. Structuring medication related activities for information management.

    PubMed

    Luukkonen, Irmeli; Mykkänen, Juha; Kivekäs, Eija; Saranto, Kaija

    2014-01-01

    Medication treatment and the related information management are central parts of a patient's health care. As a cross-organizational and cooperative process, medication information management is a complex domain for development activities. We studied medication activities and related information management in a regional project in order to produce a shared broad picture of its processes and to understand the main issues and the needs for improvement. In this paper we provide a summary of the findings in a structured form, based on a six-dimensioned framework for design and analysis of activities and processes.

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

    PubMed

    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.

  18. The electronic structure and chemical bonding of vitamin B12

    NASA Astrophysics Data System (ADS)

    Kurmaev, E. Z.; Moewes, A.; Ouyang, L.; Randaccio, L.; Rulis, P.; Ching, W. Y.; Bach, M.; Neumann, M.

    2003-05-01

    The electronic structure and chemical bonding of vitamin B12 (cyanocobalamin) and B12-derivative (methylcobalamin) are studied by means of X-ray emission (XES) and photoelectron (XPS) spectroscopy. The obtained results are compared with ab initio electronic structure calculations using the orthogonalized linear combination of the atomic orbital method (OLCAO). We show that the chemical bonding in vitamin B12 is characterized by the strong Co-C bond and relatively weak axial Co-N bond. It is further confirmed that the Co-C bond in cyanocobalamin is stronger than that of methylcobalamin resulting in their different biological activity.

  19. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2012 CFR

    2012-01-01

    ... 6 Domestic Security 1 2012-01-01 2012-01-01 false Information regarding security risk for a... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information regarding security risk for a chemical facility. (a) Information to determine security risk. In order...

  20. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2013 CFR

    2013-01-01

    ... 6 Domestic Security 1 2013-01-01 2013-01-01 false Information regarding security risk for a... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information regarding security risk for a chemical facility. (a) Information to determine security risk. In order...

  1. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2014 CFR

    2014-01-01

    ... 6 Domestic Security 1 2014-01-01 2014-01-01 false Information regarding security risk for a... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information regarding security risk for a chemical facility. (a) Information to determine security risk. In order...

  2. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2011 CFR

    2011-01-01

    ... 6 Domestic Security 1 2011-01-01 2011-01-01 false Information regarding security risk for a... SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200 Information regarding security risk for a chemical facility. (a) Information to determine security risk. In order...

  3. The Cognitive Dimensions of Information Structures.

    ERIC Educational Resources Information Center

    Green, T. R. G.

    1994-01-01

    Describes a set of terms (viscosity, hidden dependencies, imposes guess-ahead, abstraction level, and secondary notation) intended as a set of discussion tools for nonspecialists to converse about the structural features of a range of information artifacts. Explains the terms using spreadsheets as an example. (SR)

  4. Prediction of Harmful Human Health Effects of Chemicals from Structure

    NASA Astrophysics Data System (ADS)

    Cronin, Mark T. D.

    There is a great need to assess the harmful effects of chemicals to which man is exposed. Various in silico techniques including chemical grouping and category formation, as well as the use of (Q)SARs can be applied to predict the toxicity of chemicals for a number of toxicological effects. This chapter provides an overview of the state of the art of the prediction of the harmful effects of chemicals to human health. A variety of existing data can be used to obtain information; many such data are formalized into freely available and commercial databases. (Q)SARs can be developed (as illustrated with reference to skin sensitization) for local and global data sets. In addition, chemical grouping techniques can be applied on "similar" chemicals to allow for read-across predictions. Many "expert systems" are now available that incorporate these approaches. With these in silico approaches available, the techniques to apply them successfully have become essential. Integration of different in silico approaches with each other, as well as with other alternative approaches, e.g., in vitro and -omics through the development of integrated testing strategies, will assist in the more efficient prediction of the harmful health effects of chemicals

  5. (77)Se chemical shift tensor of L-selenocystine: experimental NMR measurements and quantum chemical investigations of structural effects.

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

    The genetically encoded amino acid selenocysteine and its dimeric form, selenocystine, are both utilized by nature. They are found in active sites of selenoproteins, enzymes that facilitate a diverse range of reactions, including the detoxification of reactive oxygen species and regulation of redox pathways. Due to selenocysteine and selenocystine's specialized biological roles, it is of interest to examine their (77)Se NMR properties and how those can in turn be employed to study biological systems. We report the solid-state (77)Se NMR measurements of the L-selenocystine chemical shift tensor, which provides the first experimental chemical shift tensor information on selenocysteine-containing systems. Quantum chemical calculations of L-selenocystine models were performed to help understand various structural effects on (77)Se L-selenocystine's chemical shift tensor. The effects of protonation state, protein environment, and substituent of selenium-bonded carbon on the isotropic chemical shift were found to be in a range of ca. 10-20 ppm. However, the conformational effect was found to be much larger, spanning ca. 600 ppm for the C-Se-Se-C dihedral angle range of -180° to +180°. Our calculations show that around the minimum energy structure with a C-Se-Se-C dihedral angle of ca. -90°, the energy costs to alter the dihedral angle in the range from -120° to -60° are within only 2.5 kcal/mol. This makes it possible to realize these conformations in a protein or crystal environment. (77)Se NMR was found to be a sensitive probe to such changes and has an isotropic chemical shift range of 272 ± 30 ppm for this energetically favorable conformation range. The energy-minimized structures exhibited calculated isotropic shifts that lay within 3-9% of those reported in previous solution NMR studies. The experimental solid-state NMR isotropic chemical shift is near the lower bound of this calculated range for these readily accessible conformations. These results suggest

  6. Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance.

    PubMed

    Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

    2016-01-01

    Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields.

  7. Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

    PubMed Central

    Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

    2016-01-01

    Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields. PMID:27156575

  8. Sampling the structure and chemical order in assemblies of ferromagnetic nanoparticles by nuclear magnetic resonance

    NASA Astrophysics Data System (ADS)

    Liu, Yuefeng; Luo, Jingjie; Shin, Yooleemi; Moldovan, Simona; Ersen, Ovidiu; Hébraud, Anne; Schlatter, Guy; Pham-Huu, Cuong; Meny, Christian

    2016-05-01

    Assemblies of nanoparticles are studied in many research fields from physics to medicine. However, as it is often difficult to produce mono-dispersed particles, investigating the key parameters enhancing their efficiency is blurred by wide size distributions. Indeed, near-field methods analyse a part of the sample that might not be representative of the full size distribution and macroscopic methods give average information including all particle sizes. Here, we introduce temperature differential ferromagnetic nuclear resonance spectra that allow sampling the crystallographic structure, the chemical composition and the chemical order of non-interacting ferromagnetic nanoparticles for specific size ranges within their size distribution. The method is applied to cobalt nanoparticles for catalysis and allows extracting the size effect from the crystallographic structure effect on their catalytic activity. It also allows sampling of the chemical composition and chemical order within the size distribution of alloyed nanoparticles and can thus be useful in many research fields.

  9. The Chemical Structure and Acid Deterioration of Paper.

    ERIC Educational Resources Information Center

    Hollinger, William K., Jr.

    1984-01-01

    Describes the chemical structure of paper, including subatomic particles, atoms and molecules, and the forces that bond atoms into molecules, molecules into chains, chains into sheets, and sheets into layers. Acid is defined, and the deleterious role of acid in breaking the forces that bond atoms into molecules is detailed. (EJS)

  10. Tangent Sphere Model. An Analog to Chemical Structure.

    ERIC Educational Resources Information Center

    Schultz, Ethel L.

    1986-01-01

    Discusses the use of the Tangent Sphere Model (TSM) in introducing chemical structure to beginning chemistry students at both the secondary school and college levels. Describes various applications of the use of such models, including instruction of the atom's kernel and valence electrons. (TW)

  11. Information processing for aerospace structural health monitoring

    NASA Astrophysics Data System (ADS)

    Lichtenwalner, Peter F.; White, Edward V.; Baumann, Erwin W.

    1998-06-01

    Structural health monitoring (SHM) technology provides a means to significantly reduce life cycle of aerospace vehicles by eliminating unnecessary inspections, minimizing inspection complexity, and providing accurate diagnostics and prognostics to support vehicle life extension. In order to accomplish this, a comprehensive SHM system will need to acquire data from a wide variety of diverse sensors including strain gages, accelerometers, acoustic emission sensors, crack growth gages, corrosion sensors, and piezoelectric transducers. Significant amounts of computer processing will then be required to convert this raw sensor data into meaningful information which indicates both the diagnostics of the current structural integrity as well as the prognostics necessary for planning and managing the future health of the structure in a cost effective manner. This paper provides a description of the key types of information processing technologies required in an effective SHM system. These include artificial intelligence techniques such as neural networks, expert systems, and fuzzy logic for nonlinear modeling, pattern recognition, and complex decision making; signal processing techniques such as Fourier and wavelet transforms for spectral analysis and feature extraction; statistical algorithms for optimal detection, estimation, prediction, and fusion; and a wide variety of other algorithms for data analysis and visualization. The intent of this paper is to provide an overview of the role of information processing for SHM, discuss various technologies which can contribute to accomplishing this role, and present some example applications of information processing for SHM implemented at the Boeing Company.

  12. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets.

  13. Evaluation of the information content of RNA structure mapping data for secondary structure prediction.

    PubMed

    Quarrier, Scott; Martin, Joshua S; Davis-Neulander, Lauren; Beauregard, Arthur; Laederach, Alain

    2010-06-01

    Structure mapping experiments (using probes such as dimethyl sulfate [DMS], kethoxal, and T1 and V1 RNases) are used to determine the secondary structures of RNA molecules. The process is iterative, combining the results of several probes with constrained minimum free-energy calculations to produce a model of the structure. We aim to evaluate whether particular probes provide more structural information, and specifically, how noise in the data affects the predictions. Our approach involves generating "decoy" RNA structures (using the sFold Boltzmann sampling procedure) and evaluating whether we are able to identify the correct structure from this ensemble of structures. We show that with perfect information, we are always able to identify the optimal structure for five RNAs of known structure. We then collected orthogonal structure mapping data (DMS and RNase T1 digest) under several solution conditions using our high-throughput capillary automated footprinting analysis (CAFA) technique on two group I introns of known structure. Analysis of these data reveals the error rates in the data under optimal (low salt) and suboptimal solution conditions (high MgCl(2)). We show that despite these errors, our computational approach is less sensitive to experimental noise than traditional constraint-based structure prediction algorithms. Finally, we propose a novel approach for visualizing the interaction of chemical and enzymatic mapping data with RNA structure. We project the data onto the first two dimensions of a multidimensional scaling of the sFold-generated decoy structures. We are able to directly visualize the structural information content of structure mapping data and reconcile multiple data sets. PMID:20413617

  14. Information transfer in community structured multiplex networks

    NASA Astrophysics Data System (ADS)

    Solé Ribalta, Albert; Granell, Clara; Gómez, Sergio; Arenas, Alex

    2015-08-01

    The study of complex networks that account for different types of interactions has become a subject of interest in the last few years, specially because its representational power in the description of users interactions in diverse online social platforms (Facebook, Twitter, Instagram, etc.). The mathematical description of these interacting networks has been coined under the name of multilayer networks, where each layer accounts for a type of interaction. It has been shown that diffusive processes on top of these networks present a phenomenology that cannot be explained by the naive superposition of single layer diffusive phenomena but require the whole structure of interconnected layers. Nevertheless, the description of diffusive phenomena on multilayer networks has obviated the fact that social networks have strong mesoscopic structure represented by different communities of individuals driven by common interests, or any other social aspect. In this work, we study the transfer of information in multilayer networks with community structure. The final goal is to understand and quantify, if the existence of well-defined community structure at the level of individual layers, together with the multilayer structure of the whole network, enhances or deteriorates the diffusion of packets of information.

  15. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

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

    2015-12-01

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

  16. A bond-topological approach to theoretical mineralogy: crystal structure, chemical composition and chemical reactions

    NASA Astrophysics Data System (ADS)

    Hawthorne, Frank C.

    2012-11-01

    Here, I describe a theoretical approach to the structure and chemical composition of minerals based on their bond topology. This approach allows consideration of many aspects of minerals and mineral behaviour that cannot be addressed by current theoretical methods. It consists of combining the bond topology of the structure with aspects of graph theory and bond-valence theory (both long range and short range), and using the moments approach to the electronic energy density-of-states to interpret topological aspects of crystal structures. The structure hierarchy hypothesis states that higher bond-valence polyhedra polymerize to form the (usually anionic) structural unit, the excess charge of which is balanced by the interstitial complex (usually consisting of large low-valence cations and (H2O) groups). This hypothesis may be justified within the framework of bond topology and bond-valence theory, and may be used to hierarchically classify oxysalt minerals. It is the weak interaction between the structural unit and the interstitial complex that controls the stability of the structural arrangement. The principle of correspondence of Lewis acidity-basicity states that stable structures will form when the Lewis-acid strength of the interstitial complex closely matches the Lewis-base strength of the structural unit, and allows us to examine the factors that control the chemical composition and aspects of the structural arrangements of minerals. It also provides a connection between a structure, the speciation of its constituents in aqueous solution and its mechanism of crystallization. The moments approach to the electronic energy density-of-states provides a link between the bond topology of a structure and its thermodynamic properties, as indicated by correlations between average anion coordination number and reduced enthalpy of formation from the oxides for [6]Mg{/m [4]}Si n O( m+2 n) and MgSO4(H2O) n .

  17. Information and hierarchical structure in financial markets

    NASA Astrophysics Data System (ADS)

    Mantegna, R. N.

    1999-09-01

    I investigate the information content present in the time series of stock prices of a portfolio of stocks traded in a financial market. By investigating the correlation coefficient between pairs of stocks I provide a working definition of a generalized distance between the stocks of the portfolio. This generalized distance is used to obtain an ultrametric distance matrix between the stocks. The ultrametric structure of the portfolio investigated has associated a taxonomy which is meaningful from an economic point of view.

  18. Cuticle Structure in Relation to Chemical Composition: Re-assessing the Prevailing Model

    PubMed Central

    Fernández, Victoria; Guzmán-Delgado, Paula; Graça, José; Santos, Sara; Gil, Luis

    2016-01-01

    The surface of most aerial plant organs is covered with a cuticle that provides protection against multiple stress factors including dehydration. Interest on the nature of this external layer dates back to the beginning of the 19th century and since then, several studies facilitated a better understanding of cuticular chemical composition and structure. The prevailing undertanding of the cuticle as a lipidic, hydrophobic layer which is independent from the epidermal cell wall underneath stems from the concept developed by Brongniart and von Mohl during the first half of the 19th century. Such early investigations on plant cuticles attempted to link chemical composition and structure with the existing technologies, and have not been directly challenged for decades. Beginning with a historical overview about the development of cuticular studies, this review is aimed at critically assessing the information available on cuticle chemical composition and structure, considering studies performed with cuticles and isolated cuticular chemical components. The concept of the cuticle as a lipid layer independent from the cell wall is subsequently challenged, based on the existing literature, and on new findings pointing toward the cell wall nature of this layer, also providing examples of different leaf cuticle structures. Finally, the need for a re-assessment of the chemical and structural nature of the plant cuticle is highlighted, considering its cell wall nature and variability among organs, species, developmental stages, and biotic and abiotic factors during plant growth. PMID:27066059

  19. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

    nanomaterial with lateral dimensions in the hundreds of microns if not larger, with a corresponding atomic vertical thickness poses significant difficulties. Graphene's unique structure is dominated by surface area or potentially hybridized interfaces; consequently, the true realization of this remarkable nanomaterial in device constructs relies on engineering graphene interfaces at the surface in order to controllably mold the electronic structure. Near-edge X-ray absorption fine-structure (NEXAFS) spectroscopy and the transmission mode analogue scanning transmission X-ray microscopy (STXM) are particularly useful tools to study the unoccupied states of graphene and graphene interfaces. In addition, polarized NEXAFS and STXM studies provide information on surface orientation, bond sterics, and the extent of substrate alignment before and after interfacial hybridization. The work presented in this dissertation is fundamentally informed by NEXAFS and STXM measurements on graphene/metal, graphene/dielectric, and graphene/organic interfaces. We start with a general review of the electronic structure of freestanding graphene and graphene interfaces in Chapter 1. In Chapter 2, we investigate freestanding single-layer graphene via STXM and NEXAFS demonstrating that electronic structure heterogeneities from synthesis and processing are ubiquitous in 2-dimensional graphene. We show the mapping of discrete charge transfer regions as a result of doped impurities that decorate the surfaces of graphene and that transfer processing imparts local electronic corrugations or ripples. In corroboration with density functional theory, definitive assignments to the spectral features, global steric orientations of the localized domains, and quantitative charge transfer schemes are evidenced. In the following chapters, we deliberately (Chapter 3) incorporate substitutional nitrogen into reduced graphene oxide to induce C--N charge redistribution and improve global conductivity, (Chapter 4

  20. Ultrahigh resolution protein structures using NMR chemical shift tensors

    PubMed Central

    Wylie, Benjamin J.; Sperling, Lindsay J.; Nieuwkoop, Andrew J.; Franks, W. Trent; Oldfield, Eric; Rienstra, Chad M.

    2011-01-01

    NMR chemical shift tensors (CSTs) in proteins, as well as their orientations, represent an important new restraint class for protein structure refinement and determination. Here, we present the first determination of both CST magnitudes and orientations for 13Cα and 15N (peptide backbone) groups in a protein, the β1 IgG binding domain of protein G from Streptococcus spp., GB1. Site-specific 13Cα and 15N CSTs were measured using synchronously evolved recoupling experiments in which 13C and 15N tensors were projected onto the 1H-13C and 1H-15N vectors, respectively, and onto the 15N-13C vector in the case of 13Cα. The orientations of the 13Cα CSTs to the 1H-13C and 13C-15N vectors agreed well with the results of ab initio calculations, with an rmsd of approximately 8°. In addition, the measured 15N tensors exhibited larger reduced anisotropies in α-helical versus β-sheet regions, with very limited variation (18 ± 4°) in the orientation of the z-axis of the 15N CST with respect to the 1H-15N vector. Incorporation of the 13Cα CST restraints into structure calculations, in combination with isotropic chemical shifts, transferred echo double resonance 13C-15N distances and vector angle restraints, improved the backbone rmsd to 0.16 Å (PDB ID code 2LGI) and is consistent with existing X-ray structures (0.51 Å agreement with PDB ID code 2QMT). These results demonstrate that chemical shift tensors have considerable utility in protein structure refinement, with the best structures comparable to 1.0-Å crystal structures, based upon empirical metrics such as Ramachandran geometries and χ1/χ2 distributions, providing solid-state NMR with a powerful tool for de novo structure determination. PMID:21969532

  1. Predicting modes of toxic action from chemical structure: an overview.

    PubMed

    Bradbury, S P

    1994-01-01

    In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARs) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. A basic and fundamental understanding of toxicological principles has been considered crucial to the continued acceptance and application of these techniques as biologically relevant. As a consequence, there has been an evolution of QSAR development and application from that of a chemical-class perspective to one that is more consistent with assumptions regarding modes of toxic action. The assessment of a compound's likely mode of toxic action is critical for a correct QSAR selection; incorrect mode of action-based QSAR selections can result in 10- to 1000-fold errors in toxicity predictions. The establishment of toxicologically-credible techniques to assess mode of toxic action from chemical structure requires toxicodynamic knowledge bases that are clearly defined with regard to exposure regimes and biological models/endpoints and based on compounds that adequately span the diversity of chemicals anticipated for future applications. With such knowledge bases classification systems, including rule-based experts systems, have been established for use in predictive aquatic toxicology applications. PMID:8790641

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

    PubMed

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

    2012-02-28

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

  3. Chemical graphs, molecular matrices and topological indices in chemoinformatics and quantitative structure-activity relationships.

    PubMed

    Ivanciuc, Ovidiu

    2013-06-01

    Chemical and molecular graphs have fundamental applications in chemoinformatics, quantitative structureproperty relationships (QSPR), quantitative structure-activity relationships (QSAR), virtual screening of chemical libraries, and computational drug design. Chemoinformatics applications of graphs include chemical structure representation and coding, database search and retrieval, and physicochemical property prediction. QSPR, QSAR and virtual screening are based on the structure-property principle, which states that the physicochemical and biological properties of chemical compounds can be predicted from their chemical structure. Such structure-property correlations are usually developed from topological indices and fingerprints computed from the molecular graph and from molecular descriptors computed from the three-dimensional chemical structure. We present here a selection of the most important graph descriptors and topological indices, including molecular matrices, graph spectra, spectral moments, graph polynomials, and vertex topological indices. These graph descriptors are used to define several topological indices based on molecular connectivity, graph distance, reciprocal distance, distance-degree, distance-valency, spectra, polynomials, and information theory concepts. The molecular descriptors and topological indices can be developed with a more general approach, based on molecular graph operators, which define a family of graph indices related by a common formula. Graph descriptors and topological indices for molecules containing heteroatoms and multiple bonds are computed with weighting schemes based on atomic properties, such as the atomic number, covalent radius, or electronegativity. The correlation in QSPR and QSAR models can be improved by optimizing some parameters in the formula of topological indices, as demonstrated for structural descriptors based on atomic connectivity and graph distance. PMID:23701000

  4. Expert-system comparison of structural determinants of chemical toxicity to environmental bacteria

    SciTech Connect

    Pangrekar, J.; Rosenkranz, H.S. . Dept. of Environmental and Occupational Health); Klopman, G. . Dept. of Chemistry)

    1994-06-01

    The CASE (computer automated structure evaluation) structure-activity relational expert system was used to analyze the toxicity of a database of chemical sets to environmental bacteria (aerobic heterotrophs, nitrosomonas, methanogens, and photobacteria [Microtox [reg sign]test]). The analyses revealed that the data sets related to each of the antimicrobial activities, albeit containing a relatively small number of chemicals, are characterized by structural determinants significantly associated with the probability of antimicrobial activity, as well as with antibacterial potency. Although there were a number of similarities among the structural determinants associated with each of these antimicrobial activities, there were also features unique to each assay that presumably reflect species-specific targets of bactericidal activity. Overall the assay for antimethanogenic activity appears to be the most informative as well as the one most predictive of the activity in the other three assays.

  5. Electronic and chemical structure of metal-silicon interfaces

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  6. Chemical compatibility of structural materials in alkali metals

    SciTech Connect

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

    1995-04-01

    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.

  7. Structural cluster analysis of chemical reactions in solution

    NASA Astrophysics Data System (ADS)

    Gallet, Grégoire A.; Pietrucci, Fabio

    2013-08-01

    We introduce a simple and general approach to the problem of clustering structures from atomic trajectories of chemical reactions in solution. By considering distance metrics which are invariant under permutation of identical atoms or molecules, we demonstrate that it is possible to automatically resolve as distinct structural clusters the configurations corresponding to reactants, products, and transition states, even in presence of atom-exchanges and of hundreds of solvent molecules. Our approach strongly simplifies the analysis of large trajectories and it opens the way to the construction of kinetic network models of activated processes in solution employing the available efficient schemes developed for proteins conformational ensembles.

  8. Traditional Chemical Mapping of RNA Structure In Vitro and In Vivo.

    PubMed

    Fechter, Pierre; Parmentier, Delphine; Wu, ZongFu; Fuchsbauer, Olivier; Romby, Pascale; Marzi, Stefano

    2016-01-01

    Chemical probing is often used to gain knowledge on the secondary and tertiary structures of RNA molecules either free or engaged in complexes with ligands. The method monitors the reactivity of each nucleotide towards chemicals of various specificities reflecting the hydrogen bonding environment of each nucleotide within the RNA molecule. In addition, information can be obtained on the binding site of a ligand (noncoding RNAs, protein, metabolites), and on RNA conformational changes that accompanied ligand binding or perturbation of the environmental cues. The detection of the modifications can be obtained either by using end-labeled RNA molecules or by primer extension using reverse transcriptase. The goal of this chapter is to provide the reader with an experimental guide to probe the structure of RNA in vitro and in vivo with the most suitable chemical probes. PMID:27665595

  9. Structuring Broadcast Audio for Information Access

    NASA Astrophysics Data System (ADS)

    Gauvain, Jean-Luc; Lamel, Lori

    2003-12-01

    One rapidly expanding application area for state-of-the-art speech recognition technology is the automatic processing of broadcast audiovisual data for information access. Since much of the linguistic information is found in the audio channel, speech recognition is a key enabling technology which, when combined with information retrieval techniques, can be used for searching large audiovisual document collections. Audio indexing must take into account the specificities of audio data such as needing to deal with the continuous data stream and an imperfect word transcription. Other important considerations are dealing with language specificities and facilitating language portability. At Laboratoire d'Informatique pour la Mécanique et les Sciences de l'Ingénieur (LIMSI), broadcast news transcription systems have been developed for seven languages: English, French, German, Mandarin, Portuguese, Spanish, and Arabic. The transcription systems have been integrated into prototype demonstrators for several application areas such as audio data mining, structuring audiovisual archives, selective dissemination of information, and topic tracking for media monitoring. As examples, this paper addresses the spoken document retrieval and topic tracking tasks.

  10. An informationally structured room for robotic assistance.

    PubMed

    Tsuji, Tokuo; Mozos, Oscar Martinez; Chae, Hyunuk; Pyo, Yoonseok; Kusaka, Kazuya; Hasegawa, Tsutomu; Morooka, Ken'ichi; Kurazume, Ryo

    2015-01-01

    The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot. PMID:25912347

  11. Chemical Information Literacy: pK[subscript a] Values--Where Do Students Go Wrong?

    ERIC Educational Resources Information Center

    Flynn, Alison B.; Amellal, Delphine G.

    2016-01-01

    Chemical information literacy is an essential skillset for navigating, evaluating, and using the wealth of print and online information. Accordingly, efforts are underway to improve students' acquisition and mastery of this skillset. However, less is known about students' abilities related to finding and using chemical information to solve…

  12. Modeling mitochondrial protein evolution using structural information.

    PubMed

    Liò, Pietro; Goldman, Nick

    2002-04-01

    We present two new models of protein sequence evolution based on structural properties of mitochondrial proteins. We compare these models with others currently used in phylogenetic analyses, investigating their performance over both short and long evolutionary distances. We find that our models that incorporate secondary structure information from mitochondrial proteins are statistically comparable with existing models when studying 13 mitochondrial protein data sets from eutherian mammals. However, our models give a significantly improved description of the evolutionary process when used with 12 mitochondrial proteins from a broader range of organisms including fungi, plants, protists, and bacteria. Our models may thus be of use in estimating mitochondrial protein phylogenies and for the study of processes of mitochondrial protein evolution, in particular for distantly related organisms.

  13. Structural a priori information for reflection tomography

    SciTech Connect

    Jannaud, L.; Delprat-Jannaud, F.

    1994-12-31

    The model calculated by traveltime inversion is underdetermined. One solution to this problem is to introduce a priori information so as to reduce the set of possible solutions to those satisfactory from a geological point of view. In this paper, the authors impose geological constraints on the relative position of the reflectors and in particular on the location in depth of faults. To implement this method in the context of a Gauss-Newton algorithm for the inversion, the Jacobian of the impact points with respect to the model is computed. They thus compute, using the adjoint state technique, the exact jacobian at a low computational cost. To illustrate the efficiency of the method, field data acquired on fault structures are inversed. They obtain a structural model which is satisfactory from both a kinematic and a geological point of view.

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

    SciTech Connect

    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{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.

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

    NASA Astrophysics Data System (ADS)

    Mita, Hajime; Kuwahara, Yusuke; Nomoto, Shinya

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

  16. 78 FR 28586 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-05-15

    ...) Acid donor for (S) Ethanol, 2,2'- dyeing nylon and oxybis-,1,1'- nylon containing diformate. fabrics. P... C14 18, C16-C18 chemical. unsaturated, from fermentation. P-13-0319 3/1/2013 5/29/2013 CBI (G) Industrial (G) Glycerides, feedstock C14 18, C16-C18 chemical. unsaturated, from fermentation. P-13-0320...

  17. A Chemical Information Literacy Program for First-Year Students

    ERIC Educational Resources Information Center

    Gawalt, Ellen S.; Adams, Barbara

    2011-01-01

    The ability to navigate and understand the chemical literature is integral to the scientific research process. Learning these skills is therefore an important, though often overwhelming, part of an undergraduate chemical education. We describe an inquiry-based program designed to help chemistry students begin to learn to search and read the…

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

    PubMed

    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. PMID:27312313

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

    PubMed

    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.

  20. Exposure Levels for Chemical Threat Compounds; Information to Facilitate Chemical Incident Response

    SciTech Connect

    Hauschild, Veronique; Watson, Annetta Paule

    2013-01-01

    Exposure Standards, Limits and Guidelines for Chemical Threat Compunds ABSTRACT Exposure criteria for chemical warfare (CW) agents and certain toxic industrial chemicals (TICs) used as CW agents (such as chlorine fill in an improvised explosive device) have been developed for protection of the civilian general public, civilian employees in chemical agent processing facilities and deployed military populations. In addition, compound-specific concentrations have been developed to serve as how clean is clean enough clearance criteria guiding facility recovery following chemical terrorist or other hazardous release events. Such criteria are also useful to verify compound absence, identify containment boundaries and expedite facility recovery following chemical threat release. There is no single right value or concentration appropriate for all chemical hazard control applications. It is acknowledged that locating and comparing the many sources of CW agent and TIC exposure criteria has not been previously well-defined. This paper summarizes many of these estimates and assembles critical documentation regarding their derivation and use.

  1. Teaching Three-Dimensional Structural Chemistry Using Crystal Structure Databases. 3. The Cambridge Structural Database System: Information Content and Access Software in Educational Applications

    ERIC Educational Resources Information Center

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

    2011-01-01

    Parts 1 and 2 of this series described the educational value of experimental three-dimensional (3D) chemical structures determined by X-ray crystallography and retrieved from the crystallographic databases. In part 1, we described the information content of the Cambridge Structural Database (CSD) and discussed a representative teaching subset of…

  2. Domain theoretic structures in quantum information theory

    NASA Astrophysics Data System (ADS)

    Feng, Johnny

    2011-12-01

    In this thesis, we continue the study of domain theoretic structures in quantum information theory initiated by Keye Martin and Bob Coecke in 2002. The first part of the thesis is focused on exploring the domain theoretic properties of qubit channels. We discover that the Scott continuous qubit channels are exactly those that are unital or constant. We then prove that the unital qubit channels form a continuous dcpo, and identify various measurements on them. We show that Holevo capacity is a measurement on unital qubit channels, and discover the natural measurement in this setting. We find that qubit channels also form a continuous dcpo, but capacity fails to be a measurement. In the second part we focus on the study of exact dcpos, a domain theoretic structure, closely related to continuous dcpos, possessed by quantum states. Exact dcpos admit a topology, called the exact topology, and we show that the exact topology has an order theoretic characterization similar to the characterization of the Scott topology on continuous dcpos. We then explore the connection between exact and continuous dcpos; first, by identifying an important set of points, called the split points, that distinguishes between exact and continuous structures; second, by exploring a continuous completion of exact dcpos, and showing that we can recover the exact topology from the Scott topology of the completion.

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

    PubMed

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

    2016-08-01

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

  4. Privileged structures: efficient chemical "navigators" toward unexplored biologically relevant chemical spaces.

    PubMed

    Kim, Jonghoon; Kim, Heejun; Park, Seung Bum

    2014-10-22

    In the search for new therapeutic agents for currently incurable diseases, attention has turned to traditionally "undruggable" targets, and collections of drug-like small molecules with high diversity and quality have become a prerequisite for new breakthroughs. To generate such collections, the diversity-oriented synthesis (DOS) strategy was developed, which aims to populate new chemical space with drug-like compounds containing a high degree of molecular diversity. The resulting DOS-derived libraries have been of great value for the discovery of various bioactive small molecules and therapeutic agents, and thus DOS has emerged as an essential tool in chemical biology and drug discovery. However, the key challenge has become how to design and synthesize drug-like small-molecule libraries with improved biological relevancy as well as maximum molecular diversity. This Perspective presents the development of privileged substructure-based DOS (pDOS), an efficient strategy for the construction of polyheterocyclic compound libraries with high biological relevancy. We envisioned the specific interaction of drug-like small molecules with certain biopolymers via the incorporation of privileged substructures into polyheterocyclic core skeletons. The importance of privileged substructures such as benzopyran, pyrimidine, and oxopiperazine in rigid skeletons was clearly demonstrated through the discovery of bioactive small molecules and the subsequent identification of appropriate target biomolecule using a method called "fluorescence difference in two-dimensional gel electrophoresis". Focusing on examples of pDOS-derived bioactive compounds with exceptional specificity, we discuss the capability of privileged structures to serve as chemical "navigators" toward biologically relevant chemical spaces. We also provide an outlook on chemical biology research and drug discovery using biologically relevant compound libraries constructed by pDOS, biology-oriented synthesis, or

  5. Molecular information structures in the brain.

    PubMed

    Conrad, M

    1976-01-01

    This paper presents a theory of memory and memory mediated learning based on the manipulation of macromolecular conformations. The main features of the theory are: 1) the brain contains primary and reference neurons; 2) inputs from the external environment produce particular patterns of primary firing; 3) the firing of a primary neuron sensitizes certain of its dendrites; 4) the sensitized primaries are loaded by the reference neuron active at the time and in such a way that they fire when called by this reference neuron, thus reconstructing the original pattern of primary activity. The reference neurons may also be loaded by primaries, thus making it possible for the reconstruction process to be initiated by some feature of the initial input. Each reference neuron loads and calls at most one primary pattern of activity, thereby preventing superposition of memories. If the primaries are loadable by sequences of impulses, this makes it possible to increase the connectivity among the various types of neurons by using party-line organization. The loading and calling processes themselves are mediated by call molecules. These are allosteric enzymes, located in the dendrites of primary and reference neurons, whose states are set either by an impulse or sequence of impulses and which catalyze events leading to impulse formation whenever this input recurs. The call molecules are capable of duplicating their setting (or conformation) using either intra- or interneuronal potentials, thereby ensuring stability of the memory trace. The theory allows for general powers of memory manipulation (by rememorization), for the construction of time ordered, content ordered, and associative data structures, and for computation with global representations of the environment. It makes a large number of testable predictions, provides a natural interpretation for the structure of the cerebral cortex, and accounts for: resistance to cooling, differential effects of chemical agents on short

  6. 6 CFR 27.200 - Information regarding security risk for a chemical facility.

    Code of Federal Regulations, 2010 CFR

    2010-01-01

    ... 6 Domestic Security 1 2010-01-01 2010-01-01 false Information regarding security risk for a chemical facility. 27.200 Section 27.200 Domestic Security DEPARTMENT OF HOMELAND SECURITY, OFFICE OF THE SECRETARY CHEMICAL FACILITY ANTI-TERRORISM STANDARDS Chemical Facility Security Program § 27.200...

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

    PubMed

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

    2011-05-16

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

  8. PREDICTING TOXICOLOGICAL ENDPOINTS OF CHEMICALS USING QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIPS (QSARS)

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are being developed to predict the toxicological endpoints for untested chemicals similar in structure to chemicals that have known experimental toxicological data. Based on a very large number of predetermined descriptors, a...

  9. Using Patent Classification to Discover Chemical Information in a Free Patent Database: Challenges and Opportunities

    ERIC Educational Resources Information Center

    Ha¨rtinger, Stefan; Clarke, Nigel

    2016-01-01

    Developing skills for searching the patent literature is an essential element of chemical information literacy programs at the university level. The present article creates awareness of patents as a rich source of chemical information. Patent classification is introduced as a key-component in comprehensive search strategies. The free Espacenet…

  10. Multivariate chemical mapping of antibiotics and identification of structurally representative substances.

    PubMed

    Papa, Ester; Fick, Jerker; Lindberg, Richard; Johansson, Magnus; Gramatica, Paola; Andersson, Patrik L

    2007-03-01

    Antibiotics used in human and veterinary medicine have been found in samples from diverse environments in many parts of the world. To assess the environmental risks associated with them, data regarding their toxicity, occurrence, and fate are needed, but gathering such data is time-consuming and expensive. An efficient approach to address these difficulties would be to select a small subset of antibiotics with a wide variation in chemical characteristics, perform experimental tests on this subset, and then extrapolate the results to larger numbers of antibiotics, including the most potentially hazardous compounds. To assess the potential utility of such an approach, a set of 92 antibiotics for human use was studied and their structural properties were described with 24 chemical descriptors that included information on their steric, lipophilic, and electronic properties. Principal component analysis in combination with statistical experimental design was used to map the chemical diversity of the antibiotics and to select a small subset, a "training set", of 20 antibiotics. The chemical representativity of the training set was assessed in a quantitative structure-activity model established to predict ultimate biodegradation. The selected antibiotics showed to cover the chemical variation of the studied antibiotics and are suggested for use in future testing programs to assess antibiotics' fate and effects in the environment.

  11. Structure and chemical properties of molybdenum oxide thin films

    SciTech Connect

    Ramana, C. V.; Atuchin, V. V.; Pokrovsky, L. D.; Becker, U.; Julien, C. M.

    2007-07-15

    Molybdenum oxide (MoO{sub 3}) exhibits interesting structural, chemical, electrical, and optical properties, which are dependent on the growth conditions and the fabrication technique. In the present work, MoO{sub 3} films were produced by pulsed-laser deposition and dc magnetron sputtering under varying conditions of growth temperature (T{sub s}) and oxygen pressure (pO{sub 2}). The effect of growth conditions on the structure and chemical properties of MoO{sub 3} films was examined using x-ray diffraction, reflection high-energy electron diffraction, x-ray photoelectron spectroscopy, and infrared spectroscopic measurements. The analyses indicate that the microstructure of Mo oxide films is sensitive to T{sub s} and pO{sub 2}. The growth conditions were optimized to produce stoichiometric and highly textured polycrystalline MoO{sub 3} films. A comparison of the microstructure of MoO{sub 3} films grown using pulsed-laser deposition and sputtering methods is also presented.

  12. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

    Energetic structural materials (ESMs) constitute a new class of materials that provide dual functions of strength and energetic characteristics. ESMs are typically composed of micron-scale or nano-scale intermetallic mixtures or mixtures of metals and metal oxides, polymer binders, and structural reinforcements. Voids are included to produce a composite with favorable chemical reaction characteristics. In this thesis, a continuum approach is used to simulate gas-gun or explosive loading experiments where a strong shock is induced in the ESM by an impacting plate. Algorithms are developed to obtain equations of state of mixtures. It is usually assumed that the shock loading increases the energy of the ESM and causes the ESM to reach the transition state. It is also assumed that the activation energy needed to reach the transition state is a function of the temperature of the mixture. In this thesis, it is proposed that the activation energy is a function of temperature and the stress state of the mixture. The incorporation of such an activation energy is selected in this thesis. Then, a multi-scale chemical reaction model for a heterogeneous mixture is introduced. This model incorporates reaction initiation, propagation, and extent of completed reaction in spatially heterogeneous distributions of reactants. A new model is proposed for the pore collapse of mixtures. This model is formulated by modifying the Carol, Holt, and Nesterenko spherically symmetric model to include mixtures and compressibility effects. Uncertainties in the model result from assumptions in formulating the models for continuum relationships and chemical reactions in mixtures that are distributed heterogeneously in space and in numerical integration of the resulting equations. It is important to quantify these uncertainties. In this thesis, such an uncertainty quantification is investigated by systematically identifying the physical processes that occur during shock compression of ESMs which are

  13. Optical disk toxic information online system at Sumitomo Chemical Co. through telecommunication network in Japan

    NASA Astrophysics Data System (ADS)

    Kishida, Fumio; Omodaka, Hisakata; Ishihara, Koichiro; Yamada, Yoshinori; Kato, Hiromi

    Toxicity data about several hundred chemicals, handled and commercialized by Sumitomo Chemical Co., have been collected and estimated. These data are stored in an optical disk filing system "sanfile 8500D". Because the system is mounted with a keyword input panel "Word selecter", information retrieval system is simplified but precised. Online system through telecommunication network is extended between Sumitomo Chemical's works, laboratories, and others. Image informations are mailed from installed facsimili in sanfile 8500D directly.

  14. Sensitivity of chemical reaction networks: a structural approach. 1. Examples and the carbon metabolic network.

    PubMed

    Mochizuki, Atsushi; Fiedler, Bernold

    2015-02-21

    In biological cells, chemical reaction pathways lead to complex network systems like metabolic networks. One experimental approach to the dynamics of such systems examines their "sensitivity": each enzyme mediating a reaction in the system is increased/decreased or knocked out separately, and the responses in the concentrations of chemicals or their fluxes are observed. In this study, we present a mathematical method, named structural sensitivity analysis, to determine the sensitivity of reaction systems from information on the network alone. We investigate how the sensitivity responses of chemicals in a reaction network depend on the structure of the network, and on the position of the perturbed reaction in the network. We establish and prove some general rules which relate the sensitivity response to the structure of the underlying network. We describe a hierarchical pattern in the flux response which is governed by branchings in the network. We apply our method to several hypothetical and real life chemical reaction networks, including the metabolic network of the Escherichia coli TCA cycle.

  15. 76 FR 21339 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-04-15

    ... dispersions P-11-0052......... 11/01/10 01/29/11 Piedmont Chemical Industries (S) Uv curable (S) Fatty acids... Forbo Adhesives, LLC (G) Hot melt (G) Polyester polyurethane urethane polymer purge. P-11-0056......... 11/03/10 01/31/11 CBI (S) Acylic resin (G) Aliphatic used in uv urethane curable inks and...

  16. 75 FR 60444 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-09-30

    ... lithium component, contained iron phosphate. use P-10-0546 09/09/10 12/07/10 CBI (G) Battery electrode (G) Modified lithium component, contained iron phosphate. use P-10-0547 09/09/10 12/07/10 CBI (G) Chemical...

  17. 77 FR 5096 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-02-01

    .... producing packaging films. P-12-0089 12/06/2011 03/04/2012 Brueggemann (G) Zinc is a (S) Process Chemical U...) Isocyanate crosslinker P-11-0591 12/02/2011 11/23/2011 (G) Ipdi modified polyester resin P-11-0622...

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

    NASA Astrophysics Data System (ADS)

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

    2013-05-01

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

  19. The Stepping Stone Approach to Teaching Chemical Information Skills

    ERIC Educational Resources Information Center

    Yeagley, Andrew A.; Porter, Sarah E. G.; Rhoten, Melissa C.; Topham, Benjamin J.

    2016-01-01

    Information literacy is of paramount importance to any successful research program. Information techniques and skills should be infused throughout a student's undergraduate curriculum rather than being the focus of a single course. To this end, we have created several courses, beginning in the first year, where students review current scientific…

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

    PubMed Central

    Batke, Monika; Gütlein, Martin; Partosch, Falko; Gundert-Remy, Ursula; Helma, Christoph; Kramer, Stefan; Maunz, Andreas; Seeland, Madeleine; Bitsch, Annette

    2016-01-01

    Interest 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 the limitations of the

  1. CAS Online: A New Source of Substance Information from Chemical Abstracts Service.

    ERIC Educational Resources Information Center

    Farmer, Nick A.; O'Hara, Michael P.

    1980-01-01

    Describes features of a new type of chemical database which provides the ability to search for substances sharing particular structural characteristics. Search concepts are examined in detail, and menu selection of "screens," system commands, and interpretation of results (which appear in the form of chemical bond structures) are explained. (SW)

  2. CHEMICAL STRUCTURES IN COAL: GEOCHEMICAL EVIDENCE FOR THE PRESENCE OF MIXED STRUCTURAL COMPONENTS.

    USGS Publications Warehouse

    Hatcher, P.G.; Breger, I.A.; Maciel, G.E.; Szeverenyi, N.M.

    1983-01-01

    The purpose of this paper is to summarize work on the chemical structural components of coal, comparing them with their possible plant precursors in modern peat. Solid-state **1**3C nuclear magnetic resonance (NMR), infrared spectroscopy (IR), elemental analysis and, in some cases, individual compound analyses formed the bases for these comparisons.

  3. Information essence of chaotic surface structures

    NASA Astrophysics Data System (ADS)

    Solovieva, Anna B.; Timashev, Serge F.; Vstovsky, Grigory V.; Kotova, Svetlana L.; Belayev, Vladimir E.

    2003-05-01

    A general phenomenological approach - a Flicker Noise Spectroscopy (FNS)- to revelation of information valuable parameters characterizing the arbitrary chaotic surfaces was develop to distinguish their patterns and describe quantitatively their functional properties. The consideration was carried out in terms of correlation lengths and additional parameters characterizing the rate of correlation links lost in the sequences of surface irregularities. The parameters are obtained by fitting the Fourier spectra and structural functions (difference moments of different orders) calculated for the digitized surface profiles using the approximations derived on the base of model representation of the profiles as the sequences of irregularities of different types ("bursts", "jumps", etc.). The method developed was applied to revelation of effects of a shungit filling agent in polypropylen matrix on the composite properties, revelation of hydrogen treatment effects on the cleavage surfaces of LiF monocrystals after their dissolution in water with quantitative evaluations of their anisotropy, analysis of activity of vacuum deposited porphyrins layers in a photosensibilized gnenration of singlet oxygen into gaseous phase. The approach elaborated can be used for developing the new control tools in nano-technologies, microelectronics, production of polymeric material with the specific surface properties, and others.

  4. Information diffusion in structured online social networks

    NASA Astrophysics Data System (ADS)

    Li, Pei; Zhang, Yini; Qiao, Fengcai; Wang, Hui

    2015-05-01

    Nowadays, due to the word-of-mouth effect, online social networks have been considered to be efficient approaches to conduct viral marketing, which makes it of great importance to understand the diffusion dynamics in online social networks. However, most research on diffusion dynamics in epidemiology and existing social networks cannot be applied directly to characterize online social networks. In this paper, we propose models to characterize the information diffusion in structured online social networks with push-based forwarding mechanism. We introduce the term user influence to characterize the average number of times that messages are browsed which is incurred by a given type user generating a message, and study the diffusion threshold, above which the user influence of generating a message will approach infinity. We conduct simulations and provide the simulation results, which are consistent with the theoretical analysis results perfectly. These results are of use in understanding the diffusion dynamics in online social networks and also critical for advertisers in viral marketing who want to estimate the user influence before posting an advertisement.

  5. Chemical and structural investigations on (ferrocenylacyl)silanes

    SciTech Connect

    Sharma, H.K.; Vincenti, S.P.; Vicari, R.; Cervantes, F.; Pannell, K.H. )

    1990-07-01

    (Ferrocenylacyl)silanes, ({eta}{sup 5}-C{sub 5}H{sub 5})Fe({eta}{sup 5}-C{sub 5}H{sub 4})COSiR{sub 3} (R{sub 3} = Me{sub 3}, Me{sub 2}Ph, MePh{sub 2}, Ph{sub 3}), have been synthesized and their chemical, physical, and structural properties investigated. The compounds exhibit no photochemistry and are not subject to base-catalyzed rearrangements. Attempts to synthesize acyldisilanes FcCOSiR{prime}{sub 2}SiR{sub 3}, via hydrolysis of the corresponding ferrocenyldisilyldithianes, resulted in the formation of only FcCOSiR{sub 3}. Basicity measurements, via H-bonding to phenol, indicate the ferrocenyl group to be responsible for a major increase in the basicity of the acylsilanes. The structures of the four acyl complexes are reported and exhibit almost identical structural parameters about the carbonyl group, illustrating that the ferrocenyl group has a dominant steric effect upon the compounds.

  6. Evolution of polymer photovoltaic performances from subtle chemical structure variations.

    PubMed

    Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

    2012-11-21

    Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency. PMID:23042235

  7. Evolution of polymer photovoltaic performances from subtle chemical structure variations.

    PubMed

    Yan, Han; Li, Denghua; Lu, Kun; Zhu, Xiangwei; Zhang, Yajie; Yang, Yanlian; Wei, Zhixiang

    2012-11-21

    Conjugated polymers are promising replacements for their inorganic counterparts in photovoltaics due to their low cost, ease of processing, and straightforward thin film formation. New materials have been able to improve the power conversion efficiency of photovoltaic cells up to 8%. However, rules for rational material design are still lacking, and subtle chemical structure variations usually result in large performance discrepancies. The present paper reports a detailed study on the crystalline structure, morphology, and in situ optoelectronic properties of blend films of polythiophene derivatives and [6,6]-phenyl C61-butyric acid methyl ester by changing the alkyl side chain length and position of polythiophene. The correlation among the molecular structure, mesoscopic morphology, mesoscopic optoelectronic property and macroscopic device performance (highest efficiency above 4%) was directly established. Both solubility and intermolecular interactions should be considered in rational molecular design. Knowledge obtained from this study can aid the selection of appropriate processing conditions that improve blend film morphology, charge transport property, and overall solar cell efficiency.

  8. Structure of chemical vapor deposition titania/silica gel

    SciTech Connect

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

    1999-10-01

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

  9. Information performances and illative sequences: Sequential organization of explanations of chemical phase equilibrium

    NASA Astrophysics Data System (ADS)

    Brown, Nathaniel James Swanton

    While there is consensus that conceptual change is surprisingly difficult, many competing theories of conceptual change co-exist in the literature. This dissertation argues that this discord is partly the result of an inadequate account of the unwritten rules of human social interaction that underlie the field's preferred methodology---semi-structured interviewing. To better understand the contributions of interaction during explanations, I analyze eight undergraduate general chemistry students as they attempt to explain to various people, for various reasons, why phenomena involving chemical phase equilibrium occur. Using the methods of interaction analysis, I characterize the unwritten, but systematic, rules that these participants follow as they explain. The result is a description of the contributions of interaction to explaining. Each step in each explanation is a jointly performed expression of a subject-predicate relation, an interactive accomplishment I call an information performance (in-form, for short). Unlike clauses, in-forms need not have a coherent grammatical structure. Unlike speaker turns, in-forms have the clear function of expressing information. Unlike both clauses and speaker turns, in-forms are a co-construction, jointly performed by both the primary speaker and the other interlocutor. The other interlocutor strongly affects the form and content of each explanation by giving or withholding feedback at the end of each in-form, moments I call feedback-relevant places. While in-forms are the bricks out of which the explanation is constructed, they are secured by a series of inferential links I call an illative sequence. Illative sequences are forward-searching, starting with a remembered fact or observation and following a chain of inferences in the hope it leads to the target phenomenon. The participants treat an explanation as a success if the illative sequence generates an in-form that describes the phenomenon. If the illative sequence does

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

    PubMed Central

    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

  11. Chemical and structural analyses of titanium plates retrieved from patients.

    PubMed

    Pinto, C M S A; Asprino, L; de Moraes, M

    2015-08-01

    The aim of this study was to evaluate the microscopic structure and chemical composition of titanium bone plates and screws retrieved from patients with a clinical indication and to relate the results to the clinical conditions associated with the removal of these devices. Osteosynthesis plates and screws retrieved from 30 patients between January 2010 and September 2013 were studied by metallographic, gas, and energy dispersive X-ray (EDX) analyses and the medical records of these patients were reviewed. Forty-eight plates and 238 screws were retrieved. The time elapsed between plate and screw insertion and removal ranged between 11 days and 10 years. Metallographic analysis revealed that all the plates were manufactured from commercially pure titanium (CP-Ti). The screw samples analyzed consisted of Ti-6Al-4V alloy, except four samples, which consisted of CP-Ti. Titanium plates studied by EDX analysis presented greater than 99.7% titanium by mass. On gas analysis of Ti-6Al-4V screws, three samples were outside the standard values. One CP-Ti screw sample and one plate sample also presented an oxygen analysis value above the standard. The results indicated that the physical properties and chemical compositions of the plates and screws did not correspond with the need to remove these devices or the time of retention.

  12. Conversion of lignocellulosic biomass to nanocellulose: structure and chemical process.

    PubMed

    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

  13. Exposure levels for chemical threat compounds: information to facilitate chemical incident response.

    PubMed

    Hauschild, Veronique D; Watson, Annetta

    2013-01-01

    Although not widely known, a robust set of peer-reviewed public health and occupational exposure levels presently exist for key chemical warfare agents (CWAs) and certain acutely toxic industrial chemicals (TICs) identified as terrorist attack threats. Familiarity with these CWA and TIC exposure levels and their historic applications has facilitated emergency management decision-making by public and environmental health decision-makers. Specifically, multiple air, soil, and water exposure levels for CWAs and TICs summarized here have been extensively peer-reviewed and published; many have been recognized and are in use by federal and state health agencies as criteria for hazard zone prediction and assessment, occupational safety, and "how clean is clean enough" decisions. The key, however, is to know which criteria are most appropriate for specific decisions. While public safety is critical, high levels of concern often associated with perceived or actual proximity to extremely toxic chemical agents could result in overly cautious decisions that generate excessive delays, expenditure of scarce resources, and technological difficulties. Rapid selection of the most appropriate chemical exposure criteria is recommended to avoid such problems and expedite all phases of chemical incident response and recovery. PMID:24340456

  14. SOD: Chemical composition, Flexibility and apertures, Other information

    NASA Astrophysics Data System (ADS)

    Fischer, R. X.; Baur, W. H.

    This document is part of Subvolume E `Zeolite-Type Crystal Structures and their Chemistry. Framework Type Codes RON to STI' of Volume 14 `Microporous and other Framework Materials with Zeolite-Type Structures' of Landolt-Börnstein Group IV `Physical Chemistry'.

  15. 3rd annual symposium of chemical and pharmaceutical structure analysis.

    PubMed

    Weng, Naidong; Zheng, Jenny; Lee, Mike

    2012-08-01

    The 3rd Annual Symposium on Chemical and Pharmaceutical Structure Analysis was once again held in Shanghai, where a rich history of 'East meets West' continued. This meeting is dedicated to bringing together scientists from pharmaceutical companies, academic institutes, CROs and instrument vendors to discuss current challenges and opportunities on the forefront of pharmaceutical research and development. The diversified symposia and roundtables are highly interactive events where scientists share their experiences and visions in a collegial setting. The symposium highlighted speakers and sessions that provided first-hand experiences as well as the latest guidance and industrial/regulatory thinking, which was reflected by the theme of this year's meeting 'From Bench to Decision Making - from Basics to Application.' In addition to the highly successful Young Scientist Excellence Award, new events were featured at this year's meeting, such as the Executive Roundtable and the inaugural Innovator Award.

  16. Lipids: From Chemical Structures, Biosynthesis, and Analyses to Industrial Applications.

    PubMed

    Li-Beisson, Yonghua; Nakamura, Yuki; Harwood, John

    2016-01-01

    Lipids are one of the major subcellular components, and play numerous essential functions. As well as their physiological roles, oils stored in biomass are useful commodities for a variety of biotechnological applications including food, chemical feedstocks, and fuel. Due to their agronomic as well as economic and societal importance, lipids have historically been subjected to intensive studies. Major current efforts are to increase the energy density of cell biomass, and/or create designer oils suitable for specific applications. This chapter covers some basic aspects of what one needs to know about lipids: definition, structure, function, metabolism and focus is also given on the development of modern lipid analytical tools and major current engineering approaches for biotechnological applications. This introductory chapter is intended to serve as a primer for all subsequent chapters in this book outlining current development in specific areas of lipids and their metabolism. PMID:27023229

  17. Haz-Map: Information on Hazardous Chemicals and Occupational Diseases

    MedlinePlus

    ... Occupational Diseases High Risk Jobs Non-Occupational Activities Industries Job Tasks Processes Symptoms/Findings Customer Service: tehip@teh.nlm.nih.gov Specialized Information Services U.S.National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894 ...

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

    NASA Astrophysics Data System (ADS)

    Elsner, Martin; Schreglmann, Kathrin

    2015-04-01

    Few technologies are being discussed in such controversial terms as hydraulic fracturing ("fracking") in the recovery of unconventional gas. Particular concern regards the chemicals that may return to the surface as a result of hydraulic fracturing. These are either "fracking chemicals" - chemicals that are injected together with the fracking fluid to optimize the fracturing performance or geogenic substances which may turn up during gas production, in the so-called produced water originating from the target formation. Knowledge about them is warranted for several reasons. (1) Monitoring. Air emissions are reported to arise from well drilling, the gas itself or condensate tanks. In addition, potential spills and accidents bear the danger of surface and shallow groundwater contaminations. Monitoring strategies are therefore warranted to screen for "indicator" substances of potential impacts. (2) Chemical Analysis. To meet these analytical demands, target substances must be defined so that adequate sampling approaches and analytical methods can be developed. (3) Transformation in the Subsurface. Identification and classification of fracking chemicals (aromatics vs. alcohols vs. acids, esters, etc.) is further important to assess the possibility of subsurface reactions which may potentially generate new, as yet unidentified transformation products. (4) Wastewater Treatment. For the same reason chemical knowledge is important for optimized wastewater treatment strategies. (5) Human and Ecosystem Health. Knowledge of the most frequent fracking chemicals is further essential for risk assessment (environmental behavior, toxicity) (6) Public Discussions. Finally, an overview of reported fracking chemicals can provide unbiased scientific into current public debates and enable critical reviews of Green Chemistry approaches. Presently, however, such information is not readily available. We aim to close this knowledge gap by providing a quantitative overview of chemical

  19. RASP: rapid and robust backbone chemical shift assignments from protein structure.

    PubMed

    MacRaild, Christopher A; Norton, Raymond S

    2014-03-01

    Chemical shift prediction has an unappreciated power to guide backbone resonance assignment in cases where protein structure is known. Here we describe Resonance Assignment by chemical Shift Prediction (RASP), a method that exploits this power to derive protein backbone resonance assignments from chemical shift predictions. Robust assignments can be obtained from a minimal set of only the most sensitive triple-resonance experiments, even for spectroscopically challenging proteins. Over a test set of 154 proteins RASP assigns 88 % of residues with an accuracy of 99.7 %, using only information available from HNCO and HNCA spectra. Applied to experimental data from a challenging 34 kDa protein, RASP assigns 90 % of manually assigned residues using only 40 % of the experimental data required for the manual assignment. RASP has the potential to significantly accelerate the backbone assignment process for a wide range of proteins for which structural information is available, including those for which conventional assignment strategies are not feasible. PMID:24445369

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

    SciTech Connect

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

    2012-08-07

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

  1. Bioturbo similarity searching: combining chemical and biological similarity to discover structurally diverse bioactive molecules.

    PubMed

    Wassermann, Anne Mai; Lounkine, Eugen; Glick, Meir

    2013-03-25

    Virtual screening using bioactivity profiles has become an integral part of currently applied hit finding methods in pharmaceutical industry. However, a significant drawback of this approach is that it is only applicable to compounds that have been biologically tested in the past and have sufficient activity annotations for meaningful profile comparisons. Although bioactivity data generated in pharmaceutical institutions are growing on an unprecedented scale, the number of biologically annotated compounds still covers only a minuscule fraction of chemical space. For a newly synthesized compound or an isolated natural product to be biologically characterized across multiple assays, it may take a considerable amount of time. Consequently, this chemical matter will not be included in virtual screening campaigns based on bioactivity profiles. To overcome this problem, we herein introduce bioturbo similarity searching that uses chemical similarity to map molecules without biological annotations into bioactivity space and then searches for biologically similar compounds in this reference system. In benchmark calculations on primary screening data, we demonstrate that our approach generally achieves higher hit rates and identifies structurally more diverse compounds than approaches using chemical information only. Furthermore, our method is able to discover hits with novel modes of inhibition that traditional 2D and 3D similarity approaches are unlikely to discover. Test calculations on a set of natural products reveal the practical utility of the approach for identifying novel and synthetically more accessible chemical matter.

  2. THE USE OF STRUCTURE-ACTIVITY RELATIONSHIPS IN INTEGRATING THE CHEMISTRY AND TOXICOLOGY OF ENDOCRINE DISRUPTING CHEMICALS

    EPA Science Inventory

    Structure activity relationships (SARs) are based on the principle that structurally similar chemicals should have similar biological activity. SARs relate specifically-defined toxicological activity of chemicals to their molecular structure and physico-chemical properties. To de...

  3. Temporal and Statistical Information in Causal Structure Learning

    ERIC Educational Resources Information Center

    McCormack, Teresa; Frosch, Caren; Patrick, Fiona; Lagnado, David

    2015-01-01

    Three experiments examined children's and adults' abilities to use statistical and temporal information to distinguish between common cause and causal chain structures. In Experiment 1, participants were provided with conditional probability information and/or temporal information and asked to infer the causal structure of a 3-variable mechanical…

  4. Sources of toxicity and exposure information for identifying chemicals of high concern to children

    SciTech Connect

    Stone, Alex; Delistraty, Damon

    2010-11-15

    Due to the large number of chemicals in commerce without adequate toxicity characterization data, coupled with an ineffective federal policy for chemical management in the United States, many states are grappling with the challenge to identify toxic chemicals that may pose a risk to human health and the environment. Specific populations (e.g., children, elderly) are particularly sensitive to these toxic chemicals. In 2008, the Children's Safe Product Act (CSPA) was passed in Washington State. The CSPA included specific requirements to identify High Priority Chemicals (HPCs) and Chemicals of High Concern to Children (CHCCs). To implement this legislation, a methodology was developed to identify HPCs from authoritative scientific and regulatory sources on the basis of toxicity criteria. Another set of chemicals of concern was then identified from authoritative sources, based on their potential exposure to children. Exposure potential was evaluated by identifying chemicals detected in biomonitoring studies (i.e., human tissues), as well as those present in residential exposure media (e.g., indoor air, house dust, drinking water, consumer products). Accordingly, CHCCs were defined as HPCs that also appear in biomonitoring studies or relevant exposure media. For chemicals with unique Chemical Abstracts Service (CAS) numbers, we identified 2044 HPCs and 2219 chemicals with potential exposure to children, resulting in 476 CHCCs. The process of chemical identification is dynamic, so that chemicals may be added or subtracted as new information becomes available. Although beyond the scope of this paper, the 476 CHCCs will be prioritized in a more detailed assessment, based on the strength and weight of evidence of toxicity and exposure data. Our approach was developed to be flexible which allows the addition or removal of specific sources of toxicity or exposure information, as well as transparent to allow clear identification of inputs. Although the methodology was

  5. Quantitative structure-property relationships for chemical functional use and weight fractions in consumer articles

    EPA Science Inventory

    Chemical functional use -- the functional role a chemical plays in processes or products -- may be a useful heuristic for predicting human exposure potential in that it comprises information about the compound's likely physical properties and the product formulations or articles ...

  6. 75 FR 39520 - Certain New Chemicals; Receipt and Status Information

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-07-09

    ... manufacturing copper indium metal selenide solar panel. The finished solar panel with copper indium metal selenide deposited on the substrate is encapsulated with the complete solar panel unit. The solar panel is... provide any technical information and/or data that you used. v. If you estimate potential costs or...

  7. Investigating the correlations among the chemical structures, bioactivity profiles and molecular targets of small molecules

    PubMed Central

    Cheng, Tiejun; Wang, Yanli; Bryant, Stephen H.

    2010-01-01

    Motivation: Most of the previous data mining studies based on the NCI-60 dataset, due to its intrinsic cell-based nature, can hardly provide insights into the molecular targets for screened compounds. On the other hand, the abundant information of the compound–target associations in PubChem can offer extensive experimental evidence of molecular targets for tested compounds. Therefore, by taking advantages of the data from both public repositories, one may investigate the correlations between the bioactivity profiles of small molecules from the NCI-60 dataset (cellular level) and their patterns of interactions with relevant protein targets from PubChem (molecular level) simultaneously. Results: We investigated a set of 37 small molecules by providing links among their bioactivity profiles, protein targets and chemical structures. Hierarchical clustering of compounds was carried out based on their bioactivity profiles. We found that compounds were clustered into groups with similar mode of actions, which strongly correlated with chemical structures. Furthermore, we observed that compounds similar in bioactivity profiles also shared similar patterns of interactions with relevant protein targets, especially when chemical structures were related. The current work presents a new strategy for combining and data mining the NCI-60 dataset and PubChem. This analysis shows that bioactivity profile comparison can provide insights into the mode of actions at the molecular level, thus will facilitate the knowledge-based discovery of novel compounds with desired pharmacological properties. Availability: The bioactivity profiling data and the target annotation information are publicly available in the PubChem BioAssay database (ftp://ftp.ncbi.nlm.nih.gov/pubchem/Bioassay/). Contact: ywang@ncbi.nlm.nih.gov; bryant@ncbi.nlm.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online. PMID:20947527

  8. Structuring Information to Enhance Human Information Processing and Decision Style

    ERIC Educational Resources Information Center

    Harries-Belck, Nancy

    1978-01-01

    A pretest-posttest research design was used to measure changes in three criterion variables of 150 students enrolled in an undergraduate textile class using programmed instructional materials. Findings have implications for the design of organized learning sequences to help individuals process information more efficiently for complex…

  9. Electrochemical Probing through a Redox Capacitor To Acquire Chemical Information on Biothiols.

    PubMed

    Liu, Zhengchun; Liu, Yi; Kim, Eunkyoung; Bentley, William E; Payne, Gregory F

    2016-07-19

    The acquisition of chemical information is a critical need for medical diagnostics, food/environmental monitoring, and national security. Here, we report an electrochemical information processing approach that integrates (i) complex electrical inputs/outputs, (ii) mediators to transduce the electrical I/O into redox signals that can actively probe the chemical environment, and (iii) a redox capacitor that manipulates signals for information extraction. We demonstrate the capabilities of this chemical information processing strategy using biothiols because of the emerging importance of these molecules in medicine and because their distinct chemical properties allow evaluation of hypothesis-driven information probing. We show that input sequences can be tailored to probe for chemical information both qualitatively (step inputs probe for thiol-specific signatures) and quantitatively. Specifically, we observed picomolar limits of detection and linear responses to concentrations over 5 orders of magnitude (1 pM-0.1 μM). This approach allows the capabilities of signal processing to be extended for rapid, robust, and on-site analysis of chemical information.

  10. Ideologically Structured Information Exchange among Environmental Groups

    ERIC Educational Resources Information Center

    Lhotka, Laura; Bailey, Conner; Dubois, Mark

    2008-01-01

    We use social network analysis to test the hypothesis that group ideology affects information exchange among environmental groups. The analysis is based on interviews with leaders of 136 environmental groups in Alabama. This paper adds to the literature on resource mobilization among social movement organizations by exploring information exchange…

  11. IMPROVING THE ENVIRONMENTAL PERFORMANCE OF CHEMICAL PROCESSES THROUGH THE USE OF INFORMATION TECHNOLOGY

    EPA Science Inventory

    Efforts are currently underway at the USEPA to develop information technology applications to improve the environmental performance of the chemical process industry. These efforts include the use of genetic algorithms to optimize different process options for minimal environmenta...

  12. 40 CFR 711.5 - Chemical substances for which information must be reported.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 40 Protection of Environment 32 2012-07-01 2012-07-01 false Chemical substances for which information must be reported. 711.5 Section 711.5 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) TOXIC SUBSTANCES CONTROL ACT TSCA CHEMICAL DATA REPORTING REQUIREMENTS § 711.5...

  13. Information resources for assessing health effects from chemical exposure: Office of pesticides programs

    SciTech Connect

    Fenner-Crisp, P.

    1990-12-31

    The US Environmental Protection Agency (EPA) Office of Pesticide Programs is trying to develop a complete picture of a chemical`s toxicity and exposure profile. It is also important to share information in the office`s files because of pesticides, particularly as a consequence of agricultural use, find their way into places not necessarily intended.

  14. Transfer of the EPA/NIH Chemical Information System (CIS) to Private Management.

    ERIC Educational Resources Information Center

    Kadec, Sarah T.; Jover, Antonio

    This paper discusses the programmatic concerns, the evaluation, and the ultimate decisions which led to the transfer of CIS (Chemical Information System) to the private sector. CIS is a complex, integrated system of some 20 chemical databases and data analysis programs which provide access to physical, toxicological, environmental effects, and…

  15. Structural and chemical derivatization of graphene for electronics and sensing

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    Graphene - a single atom thick two dimensional sheet of sp 2 bonded carbon atoms arranged in a honeycomb lattice - has shown great promise for both fundamental research & applications because of its unique electrical, optical, thermal, mechanical and chemical properties. Derivatization of graphene unlocks a plethora of novel properties unavailable to their pristine parent "graphene". In this dissertation we have synthesized various structural and chemical derivatives of graphene; characterized them in detail; and leveraged their exotic properties for diverse applications. We have synthesized protein/DNA/ethylenediamine functionalized derivatives of graphene via a HATU catalyzed amide reaction of primary-amine-containing moieties with graphene oxide (GO) -- an oxyfunctional graphene derivative. In contrast to non-specificity of graphene, this functionalization of GO has enabled highly specific interactions with analytes. Devices fabricated from the protein (concanavalin -- A) and DNA functionalized graphene derivatives were demonstrated to enable label-free, specific detection of bacteria and DNA molecules, respectively, with single quanta sensitivity. Room temperature electrical characterization of the sensors showed a generation of ˜ 1400 charge carriers for single bacterium attachment and an increase of 5.6 X 1012 charge carriers / cm2 for attachment of a single complementary strand of DNA. This work has shown for the first time the viability of graphene for bio-electronics and sensing at single quanta level. Taking the bio-interfacing of graphene to the next level, we demonstrate the instantaneous swaddling of a single live bacterium (Bacillus subtilis ) with several hundred sq. micron (˜ 600 mum2) areal protein-functionalized graphene sheets. The atomic impermeability and high yield strength of graphene resulted in hermetic compartmentalization of bacteria. This enabled preservation of the dimensional and topological characteristics of the bacterium against

  16. A SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  17. SURVEY OF CHEMICAL AND BIOLOGICAL STRUCTURE IN THREE FLORIDA BAYOU-ESTUARIES.

    EPA Science Inventory

    Structural and functional characteristics of the benthic biota were determined and compared for three urbanized bayous, in conjuction with sediment chemical quality and acute toxicity. Sediment chemical contamination in the bayous was common. Numerical sediment quality assessmen...

  18. Endocrine disrupting chemicals (EDCs) and female cancer: Informing the patients.

    PubMed

    Rachoń, Dominik

    2015-12-01

    Breast and uterine cancer are the most frequent female gender related neoplasms whose growth is mostly estrogen dependent. Therefore, any EDC exhibiting estrogenic effects may increase the risk of these two malignancies. This review focuses on the potential role of EDCs with estrogenic potential on the risk of breast and uterine neoplasms but also points to the possible role of the exposure to EDCs in the pathogenesis of ovarian and cervical cancer. It also underlines the necessity of informing the public about the presence of EDCs in common consumer products, their detrimental health effects and methods of reducing the exposure risk.

  19. DSSTox and Chemical Information Technologies in Support of PredictiveToxicology

    EPA Science Inventory

    The EPA NCCT Distributed Structure-Searchable Toxicity (DSSTox) Database project initially focused on the curation and publication of high-quality, standardized, chemical structure-annotated toxicity databases for use in structure-activity relationship (SAR) modeling. In recent y...

  20. Infochemistry and infofuses for the chemical storage and transmission of coded information

    PubMed Central

    Thomas, Samuel W.; Chiechi, Ryan C.; LaFratta, Christopher N.; Webb, Michael R.; Lee, Andrew; Wiley, Benjamin J.; Zakin, Mitchell R.; Walt, David R.; Whitesides, George M.

    2009-01-01

    This article describes a self-powered system that uses chemical reactions—the thermal excitation of alkali metals—to transmit coded alphanumeric information. The transmitter (an “infofuse”) is a strip of the flammable polymer nitrocellulose patterned with alkali metal ions; this pattern encodes the information. The wavelengths of 2 consecutive pulses of light represent each alphanumeric character. While burning, infofuses transmit a sequence of pulses (at 5–20 Hz) of atomic emission that correspond to the sequence of metallic salts (and therefore to the encoded information). This system combines information technology and chemical reactions into a new area—“infochemistry”—that is the first step toward systems that combine sensing and transduction of chemical signals with multicolor transmission of alphanumeric information. PMID:19470465

  1. Chemical etching of deformation sub-structures in quartz

    NASA Astrophysics Data System (ADS)

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

    1983-02-01

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

  2. Equity and Information: Information Regulation, Environmental Justice, and Risks from Toxic Chemicals

    ERIC Educational Resources Information Center

    Shapiro, Marc D.

    2005-01-01

    Decreases over time in pounds of industrial chemical emissions have led to concerns that nonminority, higher-income communities have benefited disproportionately in reductions in risk. Toxic chemical release data, modeled for toxicity and dispersion in square kilometer units across 45 states, are used to test six sets of hypotheses of potential…

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

    PubMed

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

    2011-02-01

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

  4. Utilizing the charge field effect on amide (15)N chemical shifts for protein structure validation.

    PubMed

    Bader, Reto

    2009-01-01

    Of all the nuclei in proteins, the nuclear magnetic resonance (NMR) chemical shifts of nitrogen are the theoretically least well understood. In this study, quantum chemical methods are used in combination with polarizable-continuum models in order to show that consideration of the effective electric field, including charge screening due to solvation, improves considerably the consistencies of statistical relationships between experimental and computed amide (15)N shifts between various sets of charged and uncharged oligopeptides and small organic molecules. A single conversion scheme between shielding parameters from first principles using density functional theory (DFT) and experimental shifts is derived that holds for all classes of compounds examined here. This relationship is then used to test the accuracy of such (15)N chemical shift predictions in the cyclic decapeptide antibiotic gramicidin S (GS). GS has previously been studied in great detail, both by NMR and X-ray crystallography. It adopts a well-defined backbone conformation, and hence, only a few discrete side chain conformational states need to be considered. Moreover, a charge-relay effect of the two cationic ornithine side chains to the protein backbone has been described earlier by NMR spectroscopy. Here, DFT-derived backbone amide nitrogen chemical shifts were calculated for multiple conformations of GS. Overall, the structural dynamics of GS is revisited in view of chemical shift behavior along with energetic considerations. Together, the study demonstrates proof of concept that (15)N chemical shift information is particularly useful in the analysis and validation of protein conformational states in a charged environment.

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

    PubMed

    Elsner, Martin; Hoelzer, Kathrin

    2016-04-01

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

  6. Quantitative structure-activity relationship models of chemical transformations from matched pairs analyses.

    PubMed

    Beck, Jeremy M; Springer, Clayton

    2014-04-28

    The concepts of activity cliffs and matched molecular pairs (MMP) are recent paradigms for analysis of data sets to identify structural changes that may be used to modify the potency of lead molecules in drug discovery projects. Analysis of MMPs was recently demonstrated as a feasible technique for quantitative structure-activity relationship (QSAR) modeling of prospective compounds. Although within a small data set, the lack of matched pairs, and the lack of knowledge about specific chemical transformations limit prospective applications. Here we present an alternative technique that determines pairwise descriptors for each matched pair and then uses a QSAR model to estimate the activity change associated with a chemical transformation. The descriptors effectively group similar transformations and incorporate information about the transformation and its local environment. Use of a transformation QSAR model allows one to estimate the activity change for novel transformations and therefore returns predictions for a larger fraction of test set compounds. Application of the proposed methodology to four public data sets results in increased model performance over a benchmark random forest and direct application of chemical transformations using QSAR-by-matched molecular pairs analysis (QSAR-by-MMPA).

  7. Building Structural Complexity in Semiconductor Nanocrystals through Chemical Transformations

    SciTech Connect

    Sadtler, Bryce F

    2009-05-01

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

  8. Informational biopolymer structure in early living forms.

    NASA Technical Reports Server (NTRS)

    Dayhoff, M. O.; Mclaughlin, P. J.; Barker, W. C.; Hunt, L. T.

    1972-01-01

    Some studies devoted to the search in various organisms for 'relics' of the biochemical nature of ancient organisms, preserved by the conservative nature of the evolutionary process in all living species, are reviewed. Investigations of five families of informational molecules constituting such 'relics' in very diverse organisms are reported. They include: cytochrome c, ferredoxin, trypsin, transfer ribonucleic acid (RNA), and 5S ribosomal RNA. It is shown that, even from these few informational molecules, some interesting inferences about early living organisms can be drawn.

  9. Pattern information extraction from crystal structures

    NASA Astrophysics Data System (ADS)

    Okuyan, Erhan; Güdükbay, Uğur; Gülseren, Oğuz

    2007-04-01

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

  10. Teaching Text Structure: Examining the Affordances of Children's Informational Texts

    ERIC Educational Resources Information Center

    Jones, Cindy D.; Clark, Sarah K.; Reutzel, D. Ray

    2016-01-01

    This study investigated the affordances of informational texts to serve as model texts for teaching text structure to elementary school children. Content analysis of a random sampling of children's informational texts from top publishers was conducted on text structure organization and on the inclusion of text features as signals of text…

  11. The Interaction of Information Structure and Syntactic Representation in Chinese

    ERIC Educational Resources Information Center

    Hsu, Yu-Yin

    2013-01-01

    This dissertation concerns the interaction of syntax and information structure in Mandarin Chinese and puts the theoretical assumption of parallelism between clauses and noun phrases to the test. It examines and validates the information structural status of the object phrases preposed to clause-internal positions. I argue that Rizzi's (1997)…

  12. Informal Reading Inventories & Text Type/Structure.

    ERIC Educational Resources Information Center

    Gillis, M. K.; Olson, Mary W.

    Experienced teachers enrolled in two graduate reading classes examined seven informal reading inventories (IRIs)--three at the elementary level and four at the secondary level--to (1) discover what text types (narrative or expository) they used at each level to measure student comprehension skills and determine instructional levels and (2)…

  13. Students' Chemical Information Project, October 1967 - September 1968. Final Report: Part II.

    ERIC Educational Resources Information Center

    Callaghan, A.; And Others

    Part II of the Students' Chemical Information Project (SCIP), designed to spread the use of computer-based information services among research scientists and technologists, contains details of the project operations, statistics, results of questionnaires and research reports from liaison scientists (See LI 002 562 for Part I). Chapter I: Operation…

  14. QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP MODELS FOR PREDICTION OF ESTROGEN RECEPTOR BINDING AFFINITY OF STRUCTURALLY DIVERSE CHEMICALS

    EPA Science Inventory

    The demonstrated ability of a variety of structurally diverse chemicals to bind to the estrogen receptor has raised the concern that chemicals in the environment may be causing adverse effects through interference with nuclear receptor pathways. Many structure-activity relationsh...

  15. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem.

    PubMed

    Kim, Sunghwan; Thiessen, Paul A; Bolton, Evan E; Bryant, Stephen H

    2015-07-01

    PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)-a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system.

  16. PUG-SOAP and PUG-REST: web services for programmatic access to chemical information in PubChem.

    PubMed

    Kim, Sunghwan; Thiessen, Paul A; Bolton, Evan E; Bryant, Stephen H

    2015-07-01

    PubChem (http://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, developed and maintained by the US National Institutes of Health (NIH). PubChem contains more than 180 million depositor-provided chemical substance descriptions, 60 million unique chemical structures and 225 million bioactivity assay results, covering more than 9000 unique protein target sequences. As an information resource for the chemical biology research community, it routinely receives more than 1 million requests per day from an estimated more than 1 million unique users per month. Programmatic access to this vast amount of data is provided by several different systems, including the US National Center for Biotechnology Information (NCBI)'s Entrez Utilities (E-Utilities or E-Utils) and the PubChem Power User Gateway (PUG)-a common gateway interface (CGI) that exchanges data through eXtended Markup Language (XML). Further simplifying programmatic access, PubChem provides two additional general purpose web services: PUG-SOAP, which uses the simple object access protocol (SOAP) and PUG-REST, which is a Representational State Transfer (REST)-style interface. These interfaces can be harnessed in combination to access the data contained in PubChem, which is integrated with the more than thirty databases available within the NCBI Entrez system. PMID:25934803

  17. Community structure detection based on the neighbor node degree information

    NASA Astrophysics Data System (ADS)

    Tang, Li-Ying; Li, Sheng-Nan; Lin, Jian-Hong; Guo, Qiang; Liu, Jian-Guo

    2016-11-01

    Community structure detection is of great significance for better understanding the network topology property. By taking into account the neighbor degree information of the topological network as the link weight, we present an improved Nonnegative Matrix Factorization (NMF) method for detecting community structure. The results for empirical networks show that the largest improved ratio of the Normalized Mutual Information value could reach 63.21%. Meanwhile, for synthetic networks, the highest Normalized Mutual Information value could closely reach 1, which suggests that the improved method with the optimal λ can detect the community structure more accurately. This work is helpful for understanding the interplay between the link weight and the community structure detection.

  18. Axiomatic Evaluation Method and Content Structure for Information Appliances

    ERIC Educational Resources Information Center

    Guo, Yinni

    2010-01-01

    Extensive studies have been conducted to determine how best to present information in order to enhance usability, but not what information is needed to be presented for effective decision making. Hence, this dissertation addresses the factor structure of the nature of information needed for presentation and proposes a more effective method than…

  19. Nuclear spins and moments: Fundamental structural information

    SciTech Connect

    Semmes, P.B.

    1991-01-01

    Predictions for the low energy structure of well deformed odd-A Pm and Sm nuclei in the A {approx} 130 region are given, based on the particle-rotor model. Distinctive magnetic dipole properties (static moments and transition rates) are expected for certain Nilsson configurations, and comparisons to recent data are made for {sup 133}Pm, {sup 135}Sm and {sup 133}Sm.

  20. Nuclear spins and moments: Fundamental structural information

    SciTech Connect

    Semmes, P.B.

    1991-12-31

    Predictions for the low energy structure of well deformed odd-A Pm and Sm nuclei in the A {approx} 130 region are given, based on the particle-rotor model. Distinctive magnetic dipole properties (static moments and transition rates) are expected for certain Nilsson configurations, and comparisons to recent data are made for {sup 133}Pm, {sup 135}Sm and {sup 133}Sm.

  1. Phase structure rewrite systems in information retrieval

    NASA Technical Reports Server (NTRS)

    Klingbiel, P. H.

    1985-01-01

    Operational level automatic indexing requires an efficient means of normalizing natural language phrases. Subject switching requires an efficient means of translating one set of authorized terms to another. A phrase structure rewrite system called a Lexical Dictionary is explained that performs these functions. Background, operational use, other applications and ongoing research are explained.

  2. Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

    PubMed

    Astakhov, Vadim

    2009-01-01

    Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

  3. Structures and chemical properties of silicene: unlike graphene.

    PubMed

    Jose, Deepthi; Datta, Ayan

    2014-02-18

    The discovery of graphene and its remarkable and exotic properties have aroused interest in other elements and molecules that form 2D atomic layers, such as metal chalcogenides, transition metal oxides, boron nitride, silicon, and germanium. Silicene and germanene, the Si and Ge counterparts of graphene, have interesting fundamental physical properties with potential applications in technology. For example, researchers expect that silicene will be relatively easy to incorporate within existing silicon-based electronics. In this Account, we summarize the challenges and progress in the field of silicene research. Theoretical calculations have predicted that silicene possesses graphene-like properties such as massless Dirac fermions that carry charge and the quantum spin Hall effect. Researchers are actively exploring the physical and chemical properties of silicene and tailoring it for wide variety of applications. The symmetric buckling in each of the six-membered rings of silicene differentiates it from graphene and imparts a variety of interesting properties with potential technological applications. The pseudo-Jahn-Teller (PJT) distortion breaks the symmetry and leads to the buckling in silicenes. In graphene, the two sublattice structures are equivalent, which does not allow for the opening of the band gap by an external electric field. However, in silicene where the neighboring Si atoms are displaced alternatively perpendicular to the plane, the intrinsic buckling permits a band gap opening in silicene in the presence of external electric field. Silicene's stronger spin orbit coupling than graphene has far reaching applications in spintronic devices. Because silicon prefers sp(3) hybridization over sp(2), hydrogenation is much easier in silicene. The hydrogenation of silicene to form silicane opens the band gap and increases the puckering angle. Lithiation can suppress the pseudo-Jahn-Teller distortion in silicene and hence can flatten silicene's structure

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

    PubMed

    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

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

    PubMed Central

    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

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

    PubMed

    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

    2016-05-27

    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.

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

    NASA Astrophysics Data System (ADS)

    Kaya, Ebru; Erduran, Sibel

    2013-07-01

    In this paper, we trace the work of some philosophers of chemistry to draw some implications for the improvement of chemical education. We examine some key features of chemical knowledge, and how these features are relevant for school chemistry teaching and learning. In particular, we examine Laszlo's ( Foundations of Chemistry 1:225-238, 1999) notion of concept duality, Jacob's ( HYLE-International Journal for Philosophy of Chemistry 7:31-50, 2001) descriptions of chemical language and Goodwin's ( Foundations of Chemistry 10:117-127, 2008) explication of structural explanations in organic chemistry to highlight the particular ways in which chemical knowledge is structured. We use examples of textbooks and curricula to illustrate that even though the mentioned aspects of are relevant to and are covered in educational contexts, the philosophical dimensions of this coverage is absent in textbooks and curricula. The emphasis in the use of these features of chemical knowledge seems to be more on the conceptual definitions rather than on their "epistemological nature". We argue that chemical education will be improved through the inclusion of the philosophical perspectives in chemistry teaching and learning by highlighting the specific ways in which chemical knowledge functions.

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

    PubMed

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

    2016-08-22

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

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

    SciTech Connect

    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.

  10. Predicting hepatotoxicity using ToxCast in vitro bioactivity and chemical structure

    EPA Science Inventory

    Background: The U.S. EPA ToxCastTM program is screening thousands of environmental chemicals for bioactivity using hundreds of high-throughput in vitro assays to build predictive models of toxicity. We represented chemicals based on bioactivity and chemical structure descriptors ...

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

    PubMed

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

    2016-09-01

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

  12. Visual Chemistry: Three-Dimensional Perception of Chemical Structures.

    ERIC Educational Resources Information Center

    Balaban, Alexandru T.

    1999-01-01

    Discusses in great detail aspects connected with the visual and mental processing of chemical images. Presents various types of conventions for translating three-dimensional objects into two-dimensional representations. (Author/CCM)

  13. Information-preserving structures: A general framework for quantum zero-error information

    SciTech Connect

    Blume-Kohout, Robin; Ng, Hui Khoon; Poulin, David; Viola, Lorenza

    2010-12-15

    Quantum systems carry information. Quantum theory supports at least two distinct kinds of information (classical and quantum), and a variety of different ways to encode and preserve information in physical systems. A system's ability to carry information is constrained and defined by the noise in its dynamics. This paper introduces an operational framework, using information-preserving structures, to classify all the kinds of information that can be perfectly (i.e., with zero error) preserved by quantum dynamics. We prove that every perfectly preserved code has the same structure as a matrix algebra, and that preserved information can always be corrected. We also classify distinct operational criteria for preservation (e.g., 'noiseless','unitarily correctible', etc.) and introduce two natural criteria for measurement-stabilized and unconditionally preserved codes. Finally, for several of these operational criteria, we present efficient (polynomial in the state-space dimension) algorithms to find all of a channel's information-preserving structures.

  14. Review of the Literature on Determinants of Chemical Hazard Information Recall among Workers and Consumers.

    PubMed

    Sathar, Farzana; Dalvie, Mohamed Aqiel; Rother, Hanna-Andrea

    2016-01-01

    In many low and middle income countries (LMIC), workers' and consumers' only access to risk and hazard information in relation to the chemicals they use or work with is on the chemical label and safety data sheet. Recall of chemical hazard information is vital in order for label warnings and precautionary information to promote effective safety behaviors. A literature review, therefore, was conducted on determinants of chemical hazard information recall among workers and consumers globally. Since comprehension and recall are closely linked, the determinants of both were reviewed. Literature was reviewed from both online and print peer reviewed journals for all study designs and countries. This review indicated that the level of education, previous training and the inclusion of pictograms on the hazard communication material are all factors that contribute to the recall of hazard information. The influence of gender and age on recall is incongruent and remains to be explored. More research is required on the demographic predictors of the recall of hazard information, the effect of design and non-design factors on recall, the effect of training on the recall among low literate populations and the examining of different regions or contexts. PMID:27258291

  15. Review of the Literature on Determinants of Chemical Hazard Information Recall among Workers and Consumers

    PubMed Central

    Sathar, Farzana; Dalvie, Mohamed Aqiel; Rother, Hanna-Andrea

    2016-01-01

    In many low and middle income countries (LMIC), workers’ and consumers’ only access to risk and hazard information in relation to the chemicals they use or work with is on the chemical label and safety data sheet. Recall of chemical hazard information is vital in order for label warnings and precautionary information to promote effective safety behaviors. A literature review, therefore, was conducted on determinants of chemical hazard information recall among workers and consumers globally. Since comprehension and recall are closely linked, the determinants of both were reviewed. Literature was reviewed from both online and print peer reviewed journals for all study designs and countries. This review indicated that the level of education, previous training and the inclusion of pictograms on the hazard communication material are all factors that contribute to the recall of hazard information. The influence of gender and age on recall is incongruent and remains to be explored. More research is required on the demographic predictors of the recall of hazard information, the effect of design and non-design factors on recall, the effect of training on the recall among low literate populations and the examining of different regions or contexts. PMID:27258291

  16. Extracting Structural information from Galaxy Images

    NASA Astrophysics Data System (ADS)

    Hayes, Wayne B.; Davis, D.

    2010-05-01

    The amount of data from sky images is large and growing. About 1 million galaxies can be discerned in the Sloan Digital Sky Survey (SDSS). The Large Synoptic Survey Telescope (LSST) is being built and will scan the entire sky repeatedly, providing images of millions of galaxies and petabytes of data every night. The Joint Dark Energy Mission (JDEM) is a proposed orbiting satellite that will repeatedly map the entire sky from orbit, providing images of perhaps billions of galaxies. Unfortunately, given an image of a spiral galaxy, there does not exist an automated vision algorithm that can even tell us which direction the spiral arms wind, much less count them or provide any other quantitative information about them. To wit, the largest galaxy classification project is the Galaxy Zoo, in which thousands of human volunteers classify images by eye over the web. Although valuable, such human classifications will provide only limited objective quantitative measurements, and will soon be overwhelmed with more data than humans can handle. However, such information would prove an invaluable source for astronomers and cosmologists to test current theories of galaxy formation and cosmic evolution (which can now be simulated with high accuracy on large computers, producing copious predictions that cannot be tested due to a lack of objective, quantitative observational data). In this talk, I will report on preliminary results from dynamical grammars and other machine learning and vision techniques to "parse" images of galaxies, starting us on the road towards producing quantitative data that will be useful for astronomers to test theories.

  17. Prediction of the rodent carcinogenicity of organic compounds from their chemical structures using the FALS method.

    PubMed Central

    Moriguchi, I; Hirano, H; Hirono, S

    1996-01-01

    Fuzzy adaptive least-squares (FALS), a pattern recognition method recently developed in our laboratory for correlating structure with activity rating, was used to generate quantitative structure-activity relationship (QSAR) models on the carcinogenicity of organic compounds of several chemical classes. Using the predictive models obtained from the chemical class-based FALS QSAR approach, the rodent carcinogenicity or noncarcinogenicity of a group of organic chemicals currently being tested by the U.S. National Toxicology Program was estimated from their chemical structures. PMID:8933054

  18. Prediction of the rodent carcinogenicity of organic compounds from their chemical structures using the FALS method

    SciTech Connect

    Moriguchi, Ikuo; Hirono, Shuichi; Hirano, Hiroyuki

    1996-10-01

    Fuzzy adaptive least-squares (FALS), a pattern recognition method recently developed in our laboratory for correlating structure with activity rating, was used to generate quantitative structure-activity relationship (QSAR) models on the carcinogenicity of organic compounds of several chemical classes. Using the predictive models obtained from the chemical class-based FALS QSAR approach, the rodent carcinogenicity or noncarcinogenicity of a group of organic chemicals currently being tested by the U.S. National Toxicology Program was estimated from their chemical structures. 12 refs., 4 tabs.

  19. An Event-Related Potentials Study of Mental Rotation in Identifying Chemical Structural Formulas

    ERIC Educational Resources Information Center

    Huang, Chin-Fei; Liu, Chia-Ju

    2012-01-01

    The purpose of this study was to investigate how mental rotation strategies affect the identification of chemical structural formulas. This study conducted event-related potentials (ERPs) experiments. In addition to the data collected in the ERPs, a Chemical Structure Conceptual Questionnaire and interviews were also admin-istered for data…

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

    PubMed

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

    2014-06-01

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

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

    PubMed

    Montes-Grajales, Diana; Olivero-Verbel, Jesus

    2015-01-01

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

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

    PubMed

    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.

  3. Lunar clinopyroxenes: Chemical composition, structural state, and texture

    USGS Publications Warehouse

    Ross, M.; Bence, A.E.; Dwornik, E.J.; Clark, J.R.; Papike, J.J.

    1970-01-01

    Single-crystal x-ray diffraction, microprobe, optical and electron optical examinations of clinopyroxenes from Apollo 11 lunar samples 10003, 10047, 10050, and 10084 show that generally the crystals are composed of (001) augite-pigeonite intergrowths in varying ratios. Transmission electron micrographs reveal abundant exsolution lamellae, many only 60 A?? thick. In addition to the phase inhomogeneities, primary chemical inhomogeneities are clearly demonstrated. There are reciprocal relationships between calcium and iron and between Ti4+ + 2Al and R2+ + 2Si. Our evidence suggests that a chemically inhomogeneous subcalcic C2/c augite was the only primary pyroxene from which pigeonite later exsolved.

  4. Crystal Structure and Chemical Composition of a Presolar Silicate from the Queen Elizabeth Range 99177 Meteorite

    NASA Technical Reports Server (NTRS)

    Nguyen, A. N.; Keller, L. P.; Rahman, Z.; Messenger, S.

    2013-01-01

    Mineral characterization of presolar silicate grains, the most abundant stardust phase, has provided valuable information about the formation conditions in circumstellar environments and in super-nova (SN) outflows. Spectroscopic observations of dust around evolved stars suggest a majority of amor-phous, Mg-rich olivine grains, but crystalline silicates, most of which are pyroxene, have also been observed [1]. The chemical compositions of hundreds of presolar silicates have been determined by Auger spectroscopy and reveal high Fe contents and nonstoichiometric compositions intermediate to olivine and pyroxene [2-6]. The unexpectedly high Fe contents can partly be attributed to secondary alteration on the meteorite parent bodies, as some grains have Fe isotopic anomalies from their parent stellar source [7]. Only about 35 presolar silicates have been studied for their mineral structures and chemical compositions by transmission electron microscopy (TEM). These grains display a wide range of compositions and structures, including crystalline forsterite, crystalline pyroxene, nanocrystalline grains, and a majority of amorphous nonstoichiometric grains. Most of these grains were identified in the primitive Acfer 094 meteorite. Presolar silicates from this meteorite show a wide range of Fe-contents, suggestive of secondary processing on the meteorite parent body. The CR chondrite QUE 99177 has not suffered as much alteration [8] and displays the highest presolar silicate abundance to date among carbonaceous chondrites [3, 6]. However, no mineralogical studies of presolar silicates from this meteorite have been performed. Here we examine the mineralogy of a presolar silicate from QUE 99177.

  5. The chemical, physical and structural properties of estuarine ice in Great Bay, New Hampshire

    USGS Publications Warehouse

    Meese, D.A.; Gow, A.J.; Mayewski, P.A.; Ficklin, W.; Loder, T.C.

    1987-01-01

    The purpose of this study was to provide general information on the chemical, physical and structural properties of estuarine ice and show how it compares with sea ice found at higher latitudes in order to determine whether the ice in Great Bay can be used as an analog in the study of arctic sea ice. Ice cores and water samples were collected during the 1983-1984 winter season at Adams Point in Great Bay, New Hampshire. Concentrations of chloride, nitrogen (as nitrate and nitrite), bromide, phosphate, sulfate and silicate were determined for samples chosen on the basis of identifiable stratigraphic layers (i.e. bubble size and shape, sediment layers, etc.). Similarities between ice formation in Great Bay and those in the arctic regions include the nature of the freezing process and the ice types produced. In addition, the distribution and concentration of chemical constituents were found to be similar to those observed in arctic sea ice. Factors affecting the chemistry of the ice in Great Bay include rainfall during the freezing season, the presence of sediment layers in the ice cores, the nature of incorporation of brine into the crystal structure of the ice and the drainage of brine. ?? 1987.

  6. Toxicological information on chemicals published in the Russian language: Contribution to REACH and 3Rs.

    PubMed

    Sihtmäe, Mariliis; Dubourguier, Henri-Charles; Kahru, Anne

    2009-07-28

    This review is reporting on the current situation of publicly available toxicological and ecotoxicological information on chemicals published in Russian language in various libraries, databases as well as in the Internet. This information can be beneficial for the new EU chemical policy REACH and for the development of intelligent testing strategies (involving also QSAR and QAAR) that enable a significant increase in the use of non-testing information for regulatory decision making, thus minimizing the need for animal testing according to the 3R's strategy. Currently, the access to this information is limited due to the language barrier and low level of digitalization of respective journals and books. Fortunately, on-line translation services are overcoming language barriers already now. PMID:19433131

  7. Toxicological information on chemicals published in the Russian language: Contribution to REACH and 3Rs.

    PubMed

    Sihtmäe, Mariliis; Dubourguier, Henri-Charles; Kahru, Anne

    2009-07-28

    This review is reporting on the current situation of publicly available toxicological and ecotoxicological information on chemicals published in Russian language in various libraries, databases as well as in the Internet. This information can be beneficial for the new EU chemical policy REACH and for the development of intelligent testing strategies (involving also QSAR and QAAR) that enable a significant increase in the use of non-testing information for regulatory decision making, thus minimizing the need for animal testing according to the 3R's strategy. Currently, the access to this information is limited due to the language barrier and low level of digitalization of respective journals and books. Fortunately, on-line translation services are overcoming language barriers already now.

  8. Predicting modes of toxic action from chemical structure

    EPA Science Inventory

    Like many of the papers in the ET&C top 100 list, the development of the fathead minnow database and the assignment of modes of action to the 617 chemicals therein was the result of a comprehensive research effort by a multidisciplinary team of researchers with expertise in quant...

  9. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

    PubMed Central

    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

  10. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action.

    PubMed

    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

  11. Combining QSAR Modeling and Text-Mining Techniques to Link Chemical Structures and Carcinogenic Modes of Action

    PubMed Central

    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.

  12. Structured Information Management Using New Techniques for Processing Text.

    ERIC Educational Resources Information Center

    Gibb, Forbes; Smart, Godfrey

    1990-01-01

    Describes the development of a software system, SIMPR (Structured Information Management: Processing and Retrieval), that will process documents by indexing them and classifying their subjects. Topics discussed include information storage and retrieval, file inversion techniques, modelling the user, natural language searching, automatic indexing,…

  13. Information on Quantifiers and Argument Structure in English Learner's Dictionaries.

    ERIC Educational Resources Information Center

    Lee, Thomas Hun-tak

    1993-01-01

    Lexicographers have been arguing for the inclusion of abstract and complex grammatical information in dictionaries. This paper examines the extent to which information about quantifiers and the argument structure of verbs is encoded in English learner's dictionaries. The Oxford Advanced Learner's Dictionary (1989), the Longman Dictionary of…

  14. Creating Information Structures That Work for the New Millennium.

    ERIC Educational Resources Information Center

    Gordon, Heather

    This paper discusses the impact of globalization and new information and communication technologies on the structures and practices of higher education. The first section addresses the integration of library and information technology services, focusing on experiences at the University of the Sunshine Coast (Queensland, Australia). The second…

  15. One drop chemical derivatization--DESI-MS analysis for metabolite structure identification.

    PubMed

    Lubin, Arnaud; Cabooter, Deirdre; Augustijns, Patrick; Cuyckens, Filip

    2015-07-01

    Structural elucidation of metabolites is an important part during the discovery and development process of new pharmaceutical drugs. Liquid Chromatography (LC) in combination with Mass Spectrometry (MS) is usually the technique of choice for structural identification but cannot always provide precise structural identification of the studied metabolite (e.g. site of hydroxylation and site of glucuronidation). In order to identify those metabolites, different approaches are used combined with MS data including nuclear magnetic resonance, hydrogen/deuterium exchange and chemical derivatization followed by LC-MS. Those techniques are often time-consuming and/or require extra sample pre-treatment. In this paper, a fast and easy to set up tool using desorption electrospray ionization-MS for metabolite identification is presented. In the developed method, analytes in solution are simply dried on a glass plate with printed Teflon spots and then a single drop of derivatization mixture is added. Once the spot is dried, the derivatized compound is analyzed. Six classic chemical derivatizations were adjusted to work as a one drop reaction and applied on a list of compounds with relevant functional groups. Subsequently, two successive reactions on a single spot of amoxicillin were tested and the methodology described was successfully applied on an in vitro incubated alprazolam metabolite. All reactions and analyses were performed within an hour and gave useful structural information by derivatizing functional groups, making the method a time-saving and efficient tool for metabolite identification if used in addition or in some cases as an alternative to common methods.

  16. 75 FR 68809 - Agency Information Collection Activities: Importation Bond Structure

    Federal Register 2010, 2011, 2012, 2013, 2014

    2010-11-09

    ... information collection was previously published in the Federal Register (75 FR 50772) on August 17, 2010... Structure AGENCY: U.S. Customs and Border Protection, Department of Homeland Security. ACTION: 30-day notice... review and approval in accordance with the Paperwork Reduction Act: Importation Bond Structure. This is...

  17. Information Structure and the Licensing of English Subjects

    ERIC Educational Resources Information Center

    Mack, Jennifer Elaine

    2010-01-01

    Most approaches to argument realization in English are grounded in lexical semantic structure. While it is widely acknowledged that there is an intimate relationship between information structure and grammatical relations such as "subject," there have been few attempts to formalize this observation. This dissertation proposes an "interface model…

  18. Chemical mixtures from a public health perspective: the importance of research for informed decision making.

    PubMed

    Sexton, K; Beck, B D; Bingham, E; Brain, J D; DeMarini, D M; Hertzberg, R C; O'Flaherty, E J; Pounds, J G

    1995-12-28

    When considered from a public health perspective, the central question regarding chemical mixtures is deceptively simple: Are current approaches to risk assessment for chemical mixtures affording effective (adequate) and efficient (cost-effective) protection for members of our society? Answering this question realistically depends on an understanding of the hierarchical goals of public health (i.e. prevention, intervention, treatment) and an accurate evaluation of the extent to which these goals are being achieved. To allow decision makers to make informed judgments about the health risks of chemical mixtures, adequate scientific knowledge and understanding must be available to support risk assessment activities, which are an integral part of the regulatory decision making process. Designing and implementing relevant research depends on the existence of a feedback loop between researchers and regulators, where the information needs of regulators influence the nature and direction of research and the information and understanding generated by researchers improves the scientific basis for public health decisions. A clear, consistent, commonly accepted taxonomy for describing important mixture-related phenomena is a key factor in creating and maintaining the necessary feedback loop. Ultimately, both researchers and regulators share a common goal with regard to chemical mixtures; improving the state-of-the-science so that we can make informed decisions about protecting public health. A survey of research issues and needs that are crucial to attaining this goal is presented. PMID:8571378

  19. Compilation of Physicochemical and Toxicological Information About Hydraulic Fracturing-Related Chemicals (Draft Database)

    EPA Science Inventory

    The purpose of this product is to make accessible the information about the 1,173 hydraulic fracturing-related chemicals that were listed in the external review draft of the Hydraulic Fracturing Drinking Water Assessment that was released recently. The product consists of a serie...

  20. On the evolving open peer review culture for chemical information science.

    PubMed

    Walters, W Patrick; Bajorath, Jürgen

    2015-01-01

    Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science channel of F1000Research.

  1. Incorporating Chemical Information Instruction and Environmental Science into the First-Year Organic Chemistry Laboratory

    ERIC Educational Resources Information Center

    Landolt, R. G.

    2006-01-01

    The chemical information instruction and environmental science which is incorporated into a first-year organic chemistry laboratory is presented. The students are charged with devised search strategies, conducting online searches and limiting the project scope to ocean systems. The laboratory serves to provide for search strategy development…

  2. The Effect of Peer Review on Information Literacy Outcomes in a Chemical Literature Course

    ERIC Educational Resources Information Center

    Zwicky, David A.; Hands, Michael D.

    2016-01-01

    This article describes the use of peer review in a writing project involving upper-level chemistry students in a chemical literature course, with the goal of improving student performance in meeting information literacy outcomes. Students were asked to find articles on a topic of their choice over the course of a semester and assemble the results…

  3. On the evolving open peer review culture for chemical information science

    PubMed Central

    Walters, W. Patrick; Bajorath, Jürgen

    2015-01-01

    Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science channel of F1000Research. PMID:26913193

  4. On the evolving open peer review culture for chemical information science.

    PubMed

    Walters, W Patrick; Bajorath, Jürgen

    2015-01-01

    Compared to the traditional anonymous peer review process, open post-publication peer review provides additional opportunities -and challenges- for reviewers to judge scientific studies. In this editorial, we comment on the open peer review culture and provide some guidance for reviewers of manuscripts submitted to the Chemical Information Science channel of F1000Research. PMID:26913193

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

    PubMed

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

    2016-06-20

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

  6. Structural information content of networks: graph entropy based on local vertex functionals.

    PubMed

    Dehmer, Matthias; Emmert-Streib, Frank

    2008-04-01

    In this paper we define the structural information content of graphs as their corresponding graph entropy. This definition is based on local vertex functionals obtained by calculating j-spheres via the algorithm of Dijkstra. We prove that the graph entropy and, hence, the local vertex functionals can be computed with polynomial time complexity enabling the application of our measure for large graphs. In this paper we present numerical results for the graph entropy of chemical graphs and discuss resulting properties. PMID:18243802

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

    SciTech Connect

    Nagaoka, Masataka

    2015-12-31

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

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

    NASA Technical Reports Server (NTRS)

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

    2003-01-01

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

  9. Effects of chemical treatments on hemp fibre structure

    NASA Astrophysics Data System (ADS)

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

    2013-07-01

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

  10. Chemical Industry Corrosion Management: A Comprehensive Information System (ASSET 2). Final Report

    SciTech Connect

    John, Randy C.; Young, Arthur L.; Pelton, Arthur D.; Thompson, William T.; Wright, Ian G.

    2008-10-10

    The research sponsored by this project has greatly expanded the ASSET corrosion prediction software system to produce a world-class technology to assess and predict engineering corrosion of metals and alloys corroding by exposure to hot gases. The effort included corrosion data compilation from numerous industrial sources and data generation at Shell Oak Ridge National Laboratory and several other companies for selected conditions. These data were organized into groupings representing various combinations of commercially available alloys and corrosion by various mechanisms after acceptance via a critical screening process to ensure the data were for alloys and conditions, which were adequately well defined, and of sufficient repeatability. ASSET is the largest and most capable, publicly-available technology in the field of corrosion assessment and prediction for alloys corroding by high temperature processes in chemical plants, hydrogen production, energy conversion processes, petroleum refining, power generation, fuels production and pulp/paper processes. The problems addressed by ASSET are: determination of the likely dominant corrosion mechanism based upon information available to the chemical engineers designing and/or operating various processes and prediction of engineering metal losses and lifetimes of commercial alloys used to build structural components. These assessments consider exposure conditions (metal temperatures, gas compositions and pressures), alloy compositions and exposure times. Results of the assessments are determination of the likely dominant corrosion mechanism and prediction of the loss of metal/alloy thickness as a function of time, temperature, gas composition and gas pressure. The uses of these corrosion mechanism assessments and metal loss predictions are that the degradation of processing equipment can be managed for the first time in a way which supports efforts to reduce energy consumption, ensure structural integrity of equipment

  11. Stochastic Generator of Chemical Structure. 3. Reaction Network Generation

    SciTech Connect

    FAULON,JEAN-LOUP; SAULT,ALLEN G.

    2000-07-15

    A new method to generate chemical reaction network is proposed. The particularity of the method is that network generation and mechanism reduction are performed simultaneously using sampling techniques. Our method is tested for hydrocarbon thermal cracking. Results and theoretical arguments demonstrate that our method scales in polynomial time while other deterministic network generator scale in exponential time. This finding offers the possibility to investigate complex reacting systems such as those studied in petroleum refining and combustion.

  12. Topological Index as a Sorting Device for Coding Chemical Structures

    ERIC Educational Resources Information Center

    Hosoya, Haruo

    1972-01-01

    Although the topological index does not uniquely correspond to the individual structure of a graph, it roughly represents the topological nature of the graph. Examples are given for using the topological index as a first sorting device for coding and retrieving structures, especially of fused polycyclic systems. (14 references) (Author/NH)

  13. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids. PMID:27172125

  14. Estimating the Potential Toxicity of Chemicals Associated with Hydraulic Fracturing Operations Using Quantitative Structure-Activity Relationship Modeling.

    PubMed

    Yost, Erin E; Stanek, John; DeWoskin, Robert S; Burgoon, Lyle D

    2016-07-19

    The United States Environmental Protection Agency (EPA) identified 1173 chemicals associated with hydraulic fracturing fluids, flowback, or produced water, of which 1026 (87%) lack chronic oral toxicity values for human health assessments. To facilitate the ranking and prioritization of chemicals that lack toxicity values, it may be useful to employ toxicity estimates from quantitative structure-activity relationship (QSAR) models. Here we describe an approach for applying the results of a QSAR model from the TOPKAT program suite, which provides estimates of the rat chronic oral lowest-observed-adverse-effect level (LOAEL). Of the 1173 chemicals, TOPKAT was able to generate LOAEL estimates for 515 (44%). To address the uncertainty associated with these estimates, we assigned qualitative confidence scores (high, medium, or low) to each TOPKAT LOAEL estimate, and found 481 to be high-confidence. For 48 chemicals that had both a high-confidence TOPKAT LOAEL estimate and a chronic oral reference dose from EPA's Integrated Risk Information System (IRIS) database, Spearman rank correlation identified 68% agreement between the two values (permutation p-value =1 × 10(-11)). These results provide support for the use of TOPKAT LOAEL estimates in identifying and prioritizing potentially hazardous chemicals. High-confidence TOPKAT LOAEL estimates were available for 389 of 1026 hydraulic fracturing-related chemicals that lack chronic oral RfVs and OSFs from EPA-identified sources, including a subset of chemicals that are frequently used in hydraulic fracturing fluids.

  15. Access and use of information resources in assessing health risks from chemical exposure: Proceedings

    SciTech Connect

    Not Available

    1990-12-31

    Health risk assessment is based on access to comprehensive information about potentially hazardous agents in question. Relevant information is scattered throughout the literature, and often is not readily accessible. To be useful in assessment efforts, emerging scientific findings, risk assess parameters, and associated data must be compiled and evaluated systemically. The US Environmental Protection Agency (EPA) and Oak Ridge National Laboratory (ORNL) are among the federal agencies heavily involved in this effort. This symposium was a direct response by EPA and ORNL to the expressed needs of individuals involved in assessing risks from chemical exposure. In an effort to examine the state of the risk assessment process, the availability of toxicological information, and the future development and transfer of this information, the symposium provided an excellent cadre of speakers and participants from state and federal agencies, academia and research laboratories to address these topics. This stimulating and productive gathering discussed concerns associated with (1) environmental contamination by chemicals; (2) laws regulating chemicals; (3) information needs and resources; (4) applications; (5) challenges and priorities; and (6)future issues. Individual reports are processed separately for the data bases.

  16. Using the Viking biology experimental results to obtain chemical information about Martian regolith

    NASA Technical Reports Server (NTRS)

    Plumb, Robert C.

    1992-01-01

    Although initially formulated as biology experiments, most of the results produced by the Viking Labeled Release (LR), Gas Exchange (GEX), and Pyrolytic Release (PR) experiments have been reproduced by chemical means. The experiments do not need more study as 'biological' phenomena, but they do deserve much more careful consideration from a chemical viewpoint. They are the only 'wet-chemical' experiments that scientists have performed on another planet, but they have not found very general use as sources of scientific information. There is a large set of potentially useful chemical observations, e.g., the three resolvable and precisely measured kinetic components of the release of C-14-labeled gases, the thermal sensitivity and magnitudes of the oxidation reaction(s) of the LR experiments, the kinetics and magnitude of the O2 and CO2 release of the GEX experiments, the thermal sensitivity of the GEX results, the differences between the thermal sensitivity of the GEX and the thermal sensitivity of the LR responses, and the kinetics and magnitudes of the LR successive injection reabsorption effect. It should be possible to test many chemical aspects of hypothetical martian phenomena in experiments using the biology experimental configurations and derive much valuable information by comparisons with the Viking observations.

  17. Use of near infrared spectra to probe the chemical structure of type Ia supernovae

    NASA Astrophysics Data System (ADS)

    Marion, George Howard

    2006-08-01

    Type Ia Supernovae (SNe Ia) are intrinsically interesting as very large explosions involving extreme and exotic physics. SNe Ia have become important cosmologically because their relative uniformity and high luminosity make them effective "standard candles" for distance estimates at large redshifts. We identified the near infrared (NIR; 0.8--2.5 mum) as a nearly unexplored and potentially very productive region for SNe Ia research. The NIR is a rich source of information about many explosion products that are obscured or blended at other wavelengths. We designed and implemented a systematic program to obtain NIR spectra from SNe Ia. We developed new tools and techniques to acquire, process, and interpret the data. We used synthetic models of SNe Ia explosions to aid the interpretation of results, and we used the observations to constrain the models. We obtained a large data set of NIR spectra that permits us to make important deductions about the chemical structure of SNe Ia. We show that NIR spectra have a uniform spectral evolution for normal SNe Ia. Thus our sample of forty-one spectra can be arranged in a time series to probe the chemical structure from the outer layers to deep inside the SN. We show that the burning products reside in distinct layers with no large scale mixing. We use multiple methods to demonstrate that burning consumes nearly the entire progenitor, making the amount of fuel the same for all SNe Ia explosions. That helps explain the homogeneity of SNe Ia. The two most popular explosion models produce different results that are detectable in the NIR. Our discoveries about the physical structure of SNe Ia agree well with the predictions of delayed detonation (DD) explosion models. Pure deflagration models are directly contradicted by our results and merger models are disfavored. Our results open the NIR window for SNe Ia research and we propose future directions for this field.

  18. Chemical feasibility of lithium as a matrix for structural composites

    NASA Technical Reports Server (NTRS)

    Swann, R. T.; Esterling, D. M.

    1984-01-01

    The chemical compatibility of lithium with tows of carbon and aramid fibers and silicon carbide and boron monofilaments was investigated by encapsulating the fibers in liquid lithium and also by sintering. The lithium did not readily wet the various fibers. In particular, very little lithium infiltration into the carbon and aramid tows was achieved and the strength of the tows was seriously degraded. The strength of the boron and silicon carbide monofilaments, however, was not affected by the liquid lithium. Therefore lithium is not feasible as a matrix for carbon and aramid fibers, but a composite containing boron or silicon carbide fibers in a lithium matrix may be feasible for specialized applications.

  19. Chemical structure and properties of midazolam compared with other benzodiazepines

    PubMed Central

    Gerecke, M.

    1983-01-01

    1 A short review is given of the basic chemical development in the field of `classical' and `annelated' benzodiazepines, distinguishing between pro-drugs and directly acting compounds. 2 Some properties of midazolam that are of special interest for its practical use are discussed, such as: the basicity of its imidazole ring nitrogen, which allows water-soluble salts and well-tolerated aqueous injectable solutions to be prepared; its stability to hydrolytic degradation; its rapid metabolic inactivation, which is mainly determined by the methyl group on the imidazole ring, and which is much faster than that of classical benzodiazepines. PMID:6138062

  20. Molecular structure, spectroscopic assignments and other quantum chemical calculations of anticancer drugs - A review.

    PubMed

    Ghasemi, A S; Deilam, M; Sharifi-Rad, J; Ashrafi, F; Hoseini-Alfatemi, S M

    2015-01-01

    In many texts, both theoretical and experimental studies on molecular structure and spectroscopic assignments of anticancer medicines have been reported. Molecular geometry parameters have been experimentally obtained by x-ray structure determination method and optimized using computational chemistry method like density functional theory. In this review, we consider calculations based on density function theory at B3LYP/6-31G (d,p) and B3LYP/6-311++G (d,p) levels of theory. Based on optimized geometric parameters of the molecules, molecular structures (length of bonds, bond angles and torsion angles) and vibrational assignments have been obtained. Molecular stability and bond strength have been investigated by applying natural bond orbital (NBO) analysis. Other molecular properties such as mulliken population analysis, thermodynamic properties and polarizabitities of these drugs have been reported. Calculated energies of HOMO and LUMO show that charge transfer occurs in the molecular. Information about the size, shape, charge density distribution and site of molecular chemical reactivity has been obtained by mapping electron density isosurface of electrostatic and compared with experiment data. PMID:26638891

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

    PubMed

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

    2013-02-01

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

  2. Information resources for assessing health effects from chemical exposure: Challenges, priorities, and future issues

    SciTech Connect

    Seigel, S.

    1990-12-31

    Issues related to developing information resources for assessing the health effects from chemical exposure include the question of how to address the individual political issues relevant to identifying and determining the timeliness, scientific credibility, and completeness of such kinds of information resources. One of the important ways for agencies to share information is through connection tables. This type of software is presently being used to build information products for some DHHS agencies. One of the challenges will be to convince vendors of data of the importance of trying to make data files available to communities that need them. In the future, information processing will be conducted with neural networks, object-oriented database management systems, and fuzzy-set technologies, and meta analysis techniques.

  3. Proposal for a new tomographic device providing information on the chemical properties of a body section

    SciTech Connect

    Gatti, E.; Rehak, P.; Kemmer, J.

    1986-02-27

    A system to analyze the chemical properties of a region of tissue located deep inside the human body without having to access it is proposed. The method is based on a high precision detection of x-rays or ..gamma..-rays (photons) from an external source Compton scattered from the tissue under inspection. The method provides chemical information of plane regions lying not too deep inside the body (<6 cm). The amount of radiation absorbed by the body is about the same as needed for a standard x-ray tomography. The exposure time is estimated to be shorter than 10 minutes. 37 refs., 13 figs.

  4. Allocation of chemical and structural defenses in the sponge Melophlus sarasinorum

    PubMed Central

    Rohde, Sven; Schupp, Peter J.

    2011-01-01

    Sponges have evolved a variety of chemical and structural defense mechanisms to avoid predation. While chemical defense is well established in sponges, studies on structural defense are rare and with ambiguous results. We used field and laboratory experiments to investigate predation patterns and the anti-predatory defense mechanisms of the sponge Melophlus sarasinorum, a common inhabitant of Indo-pacific coral reefs. Specifically, we aimed to investigate whether M. sarasinorum is chemically or structurally defended against predation and if the defenses are expressed differently in the ectosomal and choanosomal tissue of the sponge. Chemical defense was measured as feeding deterrence, structural defense as feeding deterrence and toughness. Our results demonstrated that chemical defense is evenly distributed throughout the sponge and works in conjunction with a structurally defended ectosome to further reduce predation levels. The choanosome of the sponge contained higher protein levels, but revealed no structural defense. We conclude that the equal distribution of chemical defenses throughout M. sarasinorum is in accordance with Optimal Defense Theory (ODT) in regards to fish predation, while structural defense supports ODT by being restricted to the surface layer which experiences the highest predation risks from mesograzers. PMID:21461028

  5. Allocation of chemical and structural defenses in the sponge Melophlus sarasinorum.

    PubMed

    Rohde, Sven; Schupp, Peter J

    2011-03-15

    Sponges have evolved a variety of chemical and structural defense mechanisms to avoid predation. While chemical defense is well established in sponges, studies on structural defense are rare and with ambiguous results. We used field and laboratory experiments to investigate predation patterns and the anti-predatory defense mechanisms of the sponge Melophlus sarasinorum, a common inhabitant of Indo-pacific coral reefs. Specifically, we aimed to investigate whether M. sarasinorum is chemically or structurally defended against predation and if the defenses are expressed differently in the ectosomal and choanosomal tissue of the sponge. Chemical defense was measured as feeding deterrence, structural defense as feeding deterrence and toughness. Our results demonstrated that chemical defense is evenly distributed throughout the sponge and works in conjunction with a structurally defended ectosome to further reduce predation levels. The choanosome of the sponge contained higher protein levels, but revealed no structural defense. We conclude that the equal distribution of chemical defenses throughout M. sarasinorum is in accordance with Optimal Defense Theory (ODT) in regards to fish predation, while structural defense supports ODT by being restricted to the surface layer which experiences the highest predation risks from mesograzers.

  6. PREDICTION OF CHEMICAL REACTIVITY PARAMETERS AND PHYSICAL PROPERTIES OF ORGANIC COMPOUNDS FROM MOLECULAR STRUCTURE USING SPARC

    EPA Science Inventory

    The computer program SPARC (SPARC Performs Automated Reasoning in Chemistry) has been under development for several years to estimate physical properties and chemical reactivity parameters of organic compounds strictly from molecular structure. SPARC uses computational algorithms...

  7. National measures under the chemical weapons convention to protect confidential business information and compensate for its loss

    SciTech Connect

    Tanzman, E.A.; Kellman, B.

    1995-07-01

    This report contains a discussion presented at the Regional Seminar on the National Authority and the Chemical Weapons Convention. Measures to protect confidential business information and compensation for information which has not been sufficiently protected is discussed.

  8. Chemical, electrochemical, and structural properties of endohedral metallofullerenes.

    PubMed

    Chaur, Manuel N; Melin, Frederic; Ortiz, Angy L; Echegoyen, Luis

    2009-01-01

    Ever since the first experimental evidence of the existence of endohedral metallofullerenes (EMFs) was obtained, the search for carbon cages with encapsulated metals and small molecules has become a very active field of research. EMFs exhibit unique electronic and structural features, with potential applications in many fields. Furthermore, functionalized EMFs offer additional potential applications because of their higher solubility and their ease of characterization by X-ray crystallography and other techniques. Herein we review the general field of EMFs, particularly of functionalized EMFs. We also address their structures and their (electrochemical) properties, as well as applications of these fascinating compounds.

  9. Chemical Structures and Bioactivities of Sulfated Polysaccharides from Marine Algae

    PubMed Central

    Jiao, Guangling; Yu, Guangli; Zhang, Junzeng; Ewart, H. Stephen

    2011-01-01

    Sulfated polysaccharides and their lower molecular weight oligosaccharide derivatives from marine macroalgae have been shown to possess a variety of biological activities. The present paper will review the recent progress in research on the structural chemistry and the bioactivities of these marine algal biomaterials. In particular, it will provide an update on the structural chemistry of the major sulfated polysaccharides synthesized by seaweeds including the galactans (e.g., agarans and carrageenans), ulvans, and fucans. It will then review the recent findings on the anticoagulant/antithrombotic, antiviral, immuno-inflammatory, antilipidemic and antioxidant activities of sulfated polysaccharides and their potential for therapeutic application. PMID:21566795

  10. [Global trends of food safety information associated with chemicals in food].

    PubMed

    Yamamoto, Miyako; Uneyama, Chikako; Toda, Miou; Morikawa, Kaoru

    2005-01-01

    Recently, a number of food safety problems have frequently arisen and consumer concerns have drastically increased. In order to meet these concerns, we have been publishing a biweekly bulletin called "Food Safety Information" since April 2003, monitoring the latest information from overseas on food safety. In this paper, we analyze the recent trends of information on food chemicals in the bulletin published between April 2003 and March 2005 in order to clarify the problems that need to be followed up. Among the 1,199 entries on food chemicals included in the bulletin, about 50% were from the EU and European organizations such as the FSA (UK). Approximately 20% of the total information focused on food contaminants such as heavy metals, dioxins, PCBs and mycotoxins. Scientific evidence-based information on dietary supplements and herb products was also suggested to be important to protect public health as well as food contaminants. We monitor the latest information on food safety constantly and continuously, which is important for long-term follow up of food safety issues of concern. We also provide the bulletin to the general public through the website as well as to researchers and risk managers. PMID:16541754

  11. Reinforcing Visual Grouping Cues to Communicate Complex Informational Structure.

    PubMed

    Bae, Juhee; Watson, Benjamin

    2014-12-01

    In his book Multimedia Learning [7], Richard Mayer asserts that viewers learn best from imagery that provides them with cues to help them organize new information into the correct knowledge structures. Designers have long been exploiting the Gestalt laws of visual grouping to deliver viewers those cues using visual hierarchy, often communicating structures much more complex than the simple organizations studied in psychological research. Unfortunately, designers are largely practical in their work, and have not paused to build a complex theory of structural communication. If we are to build a tool to help novices create effective and well structured visuals, we need a better understanding of how to create them. Our work takes a first step toward addressing this lack, studying how five of the many grouping cues (proximity, color similarity, common region, connectivity, and alignment) can be effectively combined to communicate structured text and imagery from real world examples. To measure the effectiveness of this structural communication, we applied a digital version of card sorting, a method widely used in anthropology and cognitive science to extract cognitive structures. We then used tree edit distance to measure the difference between perceived and communicated structures. Our most significant findings are: 1) with careful design, complex structure can be communicated clearly; 2) communicating complex structure is best done with multiple reinforcing grouping cues; 3) common region (use of containers such as boxes) is particularly effective at communicating structure; and 4) alignment is a weak structural communicator. PMID:26356911

  12. The chemical and hydrologic structure of Poas volcano, Costa Rica

    USGS Publications Warehouse

    Rowe, G.L.; Brantley, S.L.; Fernandez, J.F.; Borgia, A.

    1995-01-01

    Comparison of the chemical characteristics of spring and river water draining the flanks of Poas Volcano, Costa Rica indicates that acid chloride sulfate springs of the northwestern flank of the volcano are derived by leakage and mixing of acid brines formed in the summit hydrothermal system with dilute flank groundwater. Acid chloride sulfate waters of the Rio Agrio drainage basin on the northwestern flank are the only waters on Poas that are affected by leakage of acid brines from the summit hydrothermal system. Acid sulfate waters found on the northwestern flank are produced by the interaction of surface and shallow groundwater with dry and wet acid deposition of SO2 and H2SO4 aerosols, respectively. The acid deposition is caused by a plume of acid gases that is released by a shallow magma body located beneath the active crater of Poas. -from Authors

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

    PubMed Central

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

    2014-01-01

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

  14. Chemical Structure and Accidental Explosion Risk in the Research Laboratory

    ERIC Educational Resources Information Center

    Churchill, David G.

    2006-01-01

    Tips that laboratory researchers and beginning graduate students can use to safeguard against explosion hazard with emphasis on clear illustrations of molecular structure are discussed. Those working with hazardous materials must proceed cautiously and may want to consider alternative and synthetic routes.

  15. Are the Chemical Structures in your QSAR Correct?

    EPA Science Inventory

    Quantitative structure-activity relationships (QSARs) are used to predict many different endpoints, utilize hundreds and even thousands of different parameters (or descriptors), and are created using a variety of approaches. The one thing they all have in common is the assumptio...

  16. Informational Complexity and Functional Activity of RNA Structures

    PubMed Central

    Carothers, James M.; Oestreich, Stephanie C.; Davis, Jonathan H.

    2004-01-01

    Very little is known about the distribution of functional DNA, RNA, and protein molecules in sequence space. The question of how the number and complexity of distinct solutions to a particular biochemical problem varies with activity is an important aspect of this general problem. Here we present a comparison of the structures and activities of eleven distinct GTP-binding RNAs (aptamers). By experimentally measuring the amount of information required to specify each optimal binding structure, we show that defining a structure capable of 10-fold tighter binding requires approximately 10 additional bits of information. This increase in information content is equivalent to specifying the identity of five additional nucleotide positions and corresponds to an ∼1000-fold decrease in abundance in a sample of random sequences. We observe a similar relationship between structural complexity and activity in a comparison of two catalytic RNAs (ribozyme ligases), raising the possibility of a general relationship between the complexity of RNA structures and their functional activity. Describing how information varies with activity in other heteropolymers, both biological and synthetic, may lead to an objective means of comparing their functional properties. This approach could be useful in predicting the functional utility of novel heteropolymers. PMID:15099096

  17. Unraveling the 13C NMR Chemical Shifts in Single-Walled Carbon Nanotubes: Dependence on Diameter and Electronic Structure

    SciTech Connect

    Engtrakul, C.; Irurzun, V. M.; Gjersing, E. L.; Holt, J. M.; Larsen, B. A.; Resasco, D. E.; Blackburn, J. L.

    2012-03-14

    The atomic specificity afforded by nuclear magnetic resonance (NMR) spectroscopy could enable detailed mechanistic information about single-walled carbon nanotube (SWCNT) functionalization as well as the noncovalent molecular interactions that dictate ground-state charge transfer and separation by electronic structure and diameter. However, to date, the polydispersity present in as-synthesized SWCNT populations has obscured the dependence of the SWCNT {sup 13}C chemical shift on intrinsic parameters such as diameter and electronic structure, meaning that no information is gleaned for specific SWCNTs with unique chiral indices. In this article, we utilize a combination of {sup 13}C labeling and density gradient ultracentrifugation (DGU) to produce an array of {sup 13}C-labeled SWCNT populations with varying diameter, electronic structure, and chiral angle. We find that the SWCNT isotropic {sup 13}C chemical shift decreases systematically with increasing diameter for semiconducting SWCNTs, in agreement with recent theoretical predictions that have heretofore gone unaddressed. Furthermore, we find that the {sup 13}C chemical shifts for small diameter metallic and semiconducting SWCNTs differ significantly, and that the full-width of the isotropic peak for metallic SWCNTs is much larger than that of semiconducting nanotubes, irrespective of diameter.

  18. Atmospheric chemical and thermal structure evolution after one Titan year

    NASA Astrophysics Data System (ADS)

    Coustenis, Athena; Bampasidis, Georgios; Achterberg, Richard; Lavvas, Panayiotis; Vinatier, Sandrine; Nixon, Conor; Jennings, Donald; Teanby, Nicolas; Flasar, F. Michael; Carlson, Ronald; Orton, Glenn; Romani, Paul; Guandique, Ever

    2013-04-01

    Our radiative transfer code (ARTT) was applied to Cassini Composite Infrared Spectrometer (CIRS) data taken during Titan flybys from 2004-2010 and to the 1980 Voyager 1 flyby values inferred from the re-analysis of the Infrared Radiometer Spectrometer (IRIS) spectra [1], as well as to the intervening ground- and space- based observations (such as with ISO, [2]), providing us with a new view of the stratospheric evolution over a Titanian year (V1 encounter Ls=9° was reached in mid-2010). CIRS nadir and limb spectral [3,4] show variations in temperature and chemical composition in the stratosphere during the Cassini mission, before and after the Northern Spring Equinox (NSE). We find indication for a weakening of the temperature gradient with warming of the stratosphere and cooling of the lower mesosphere. In addition, we infer precise concentrations for the trace gases and their main isotopologues and find that the chemical composition in Titan's stratosphere varied significantly with latitude during the 6 terrestrial years investigated here, with increased mixing ratios towards the northern latitudes. In particular, we find a maximum enhancement of several gases observed at northern latitudes up to 50°N around mid-2009, at the time of the NSE. We find that this raise is followed by a rapid decrease in chemical inventory in 2010 probably due to changes in the cross vortex mixing or northward migration of the vortex boundary [5,6,7] consistent with the weakening thermal gradient. The finding also ties into the location of the maximum temperature gradient, which appears to be moving northward over the winter/spring season. The return of today's abundances close to the Voyager values (at the same season) is an indication that, as for the Earth, the solar radiation dominates over the other energy sources even at 10AU [8]. Nevertheless, the differences observed for some complex hydrocarbons in the North pole indicate that the other processes could be at play as well

  19. Electronic structure evaluation through quantum chemical descriptors of 17β-aminoestrogens with an anticoagulant effect.

    PubMed

    Raya, Angélica; Barrientos-Salcedo, Carolina; Rubio-Póo, Consuelo; Soriano-Correa, Catalina

    2011-06-01

    17β-aminoestrogens have been experimentally studied due to their anticoagulant effect, shown both in in vitro and in vivo assays; this is a non-typical behavior for steroids. The anticoagulant effect of these aminoestrogens has been related to the aromaticity of the A-ring of the steroid molecule; as well as to the length of the amino-alcohol side-chain at C17, which might have an influence on the biological activity of these compounds. The study of the electronic structure of 17β-aminoestrogens using quantum chemical descriptors could provide significant information and may contribute to a better understanding of structure-activity relationships in these molecules. In this work, we present a density functional theory (DFT) study at the B3LYP level of theory for selected 17β-aminoestrogens compounds, with the main purpose of characterizing their electronic and physicochemical properties and relating them to their anticoagulant effect, using quantum chemical descriptors such as: atomic charges, bond order, electrostatic potential isosurface analysis, hardness, electrophilicity and aromaticity indexes. The results obtained from these quantum chemical descriptors, led us to characterize the physicochemical properties, reactive sites and substituent influence on electronic structure, as well as to identify additional quantum chemical descriptors that could be associated with the anticoagulant effect of 17β-aminoestrogens.

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

    NASA Astrophysics Data System (ADS)

    Werheit, Helmut

    2016-10-01

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

  1. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+). PMID:26852210

  2. Quantum-chemical calculations of the structure of trioxyl radicals

    NASA Astrophysics Data System (ADS)

    Semes'ko, D. G.; Khursan, S. L.

    2008-08-01

    Density functional theory and ab initio methods were used to consider the structure and main channels of consumption of HOOO and CH3OOO. A correct description of these systems required the simultaneous inclusion of the dynamic and static components of electron correlation energy. The MRMP2( 19 × 11)/aug-cc-pVTZ approximation was used to find that both cis and trans structures of trioxyl radicals were stable (the cis isomer was more favorable energetically), whereas the gauche structure corresponded to the top of a potential barrier. The energy barrier to rotations about the RO-OO bond was found to be 10.9 19.7 kJ/mol for HOOO and 18.7 39.1 kJ/mol for CH3OOO. The main channels of the consumption of ROOO radicals were decomposition to the RO radical and molecular oxygen or to the hydroperoxyl radical and a carbonyl compound (the latter reaction occurred if there were α-C-H bonds). The MRMP2(19 × 11)/aug-cc-pVTZ//PBE0/aug-cc-pVTZ method was used to estimate the total energy of dissociation of the O-O bond in HOOO and CH3OOO (20 kJ/mol) and the height of the energy barrier to the isomerization of CH3OOO (8.0 kJ/mol).

  3. Chemical and structural characterization of copper adsorbed on mosses (Bryophyta).

    PubMed

    González, Aridane G; Jimenez-Villacorta, Felix; Beike, Anna K; Reski, Ralf; Adamo, Paola; Pokrovsky, Oleg S

    2016-05-01

    The adsorption of copper on passive biomonitors (devitalized mosses Hypnum sp., Sphagnum denticulatum, Pseudoscleropodium purum and Brachythecium rutabulum) was studied under different experimental conditions such as a function of pH and Cu concentration in solution. Cu assimilation by living Physcomitrella patents was also investigated. Molecular structure of surface adsorbed and incorporated Cu was studied by X-ray Absorption Spectroscopy (XAS). Devitalized mosses exhibited the universal adsorption pattern of Cu as a function of pH, with a total binding sites number 0.05-0.06 mmolg(dry)(-1) and a maximal adsorption capacity of 0.93-1.25 mmolg(dry)(-1) for these devitalized species. The Extended X-ray Absorption Fine Structure (EXAFS) fit of the first neighbor demonstrated that for all studied mosses there are ∼4.5 O/N atoms around Cu at ∼1.95 Å likely in a pseudo-square geometry. The X-ray Absorption Near Edge Structure (XANES) analysis demonstrated that Cu(II)-cellulose (representing carboxylate groups) and Cu(II)-phosphate are the main moss surface binding moieties, and the percentage of these sites varies as a function of solution pH. P. patens exposed during one month to Cu(2+) yielded ∼20% of Cu(I) in the form of Cu-S(CN) complexes, suggesting metabolically-controlled reduction of adsorbed and assimilated Cu(2+).

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

    NASA Astrophysics Data System (ADS)

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

    2016-09-01

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

  5. Neural network recognition of chemical class information in mobility spectra obtained at high temperatures

    NASA Technical Reports Server (NTRS)

    Bell, S.; Nazarov, E.; Wang, Y. F.; Rodriguez, J. E.; Eiceman, G. A.

    2000-01-01

    A minimal neural network was applied to a large library of high-temperature mobility spectra drawn from 16 chemical classes including 154 substances with 2000 spectra at various concentrations. A genetic algorithm was used to create a representative subset of points from the mobility spectrum as input to a cascade-type back-propagation network. This network demonstrated that significant information specific to chemical class was located in the spectral region near the reactant ions. This network failed to generalize the solution to unfamiliar compounds necessitating the use of complete spectra in network processing. An extended back-propagation network classified unfamiliar chemicals by functional group with a mean for average values of 0.83 without sulfides and 0.79 with sulfides. Further experiments confirmed that chemical class information was resident in the spectral region near the reactant ions. Deconvolution of spectra demonstrated the presence of ions, merged with the reactant ion peaks that originated from introduced samples. The ability of the neural network to generalize the solution to unfamiliar compounds suggests that these ions are distinct and class specific.

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

    SciTech Connect

    Maciel, G.E.

    1996-09-30

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

  7. Combining Chemical Information Literacy, Communication Skills, Career Preparation, Ethics, and Peer Review in a Team-Taught Chemistry Course

    ERIC Educational Resources Information Center

    Jones, Mary Lou Baker; Seybold, Paul G.

    2016-01-01

    The widely acknowledged need to include chemical information competencies and communication skills in the undergraduate chemistry curriculum can be accommodated in a variety of ways. We describe a team-taught, semester-length course at Wright State University which combines chemical information literacy, written and oral communication skills,…

  8. Magnetic and Structural Properties of Chemically Synthesized Ni and

    NASA Astrophysics Data System (ADS)

    Bonder, Michael; Leslie-Pelecky, Diandra L.; Zhang, X. Q.; Rieke, R. D.

    1996-03-01

    The reduction of nickel salts using a technique developed by Rieke and co-workers produces highly chemically reactive particles with enhanced magnetic properties due to their nanoscale size. As-synthesized particles are 2-5 nm in diameter and range from superparamagnetic to ferromagnetic, depending on synthesis details. Grain sizes from 5 nm to 1000 nm have been produced by subsequent vacuum annealing. The maximum coercivities and remanence ratios are obtained during the first half-hour to hour of annealing. Coercivities in these systems may be up to ten times the value of bulk nickel, with remanence ratios approaching 0.5. Transmission electron microscopy shows that the nickel grains are square and sometimes embedded in a lithium halide matrix. Under appropriate synthesis and annealing conditions, the as-synthesized particles can be transformed into the metastable Ni_3C phase, which has important implications in catalysis. Comparison with Stoner-Wohlfarth and Holz-Scherrer predictions of the magnetic properties will be made.

  9. Nano structured carbon nitrides prepared by chemical vapour deposition

    NASA Astrophysics Data System (ADS)

    Karuppannan, Ramesh; Prashantha, M.

    2010-08-01

    Nanostructured carbon nitride films were prepared by pyrolysis assisted chemical vapour deposition(CVD). A two zone furnace with a temperature profile having a uniform temperature over a length of 20 cm length has been designed and developed. The precursor Azabenzimidazole was taken in a quartz tube and evaporated at 400 0C. The dense vapours enter the pyrolysis zone kept at a desired temperature and deposit on the quartz substrates. The FTIR spectrum of the prepared samples shows peaks at 1272 cm-1 (C.N stretching) and 1600 cm-1 (C=N) confirms the bonding of nitrogen with carbon. Raman D and G peaks, are observed at 1360 cm-1 and 1576 cm-1 respectively. XPS core level spectra of C 1s and N 1s show the formation of π bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is ~100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

  10. Regioselective sulfation of Artemisia sphaerocephala polysaccharide: Characterization of chemical structure.

    PubMed

    Wang, Junlong; Yang, Wen; Wang, Jiancheng; Wang, Xia; Wu, Fang; Yao, Jian; Zhang, Ji; Lei, Ziqiang

    2015-11-20

    The biological activities of sulfated polysaccharides are related to the substitution positions of functional groups. In this study, regioselective sulfation of Artemisia sphaerocephala polysaccharides (SRSASP) was prepared by using triphenylchloromethane (TrCl) as protecting precursor. FT-IR spectra and X-ray photoelectron spectroscopy (XPS) showed that SO(3-) group (S(6+), high binding energy of 168.7eV) was widely present in sulfated polysaccharides. (13)C NMR spectroscopy showed that C-2 and C-3 substitution was occurred but not fully sulfation. Meanwhile, C-6 substituted signals near 65ppm were not observed. The degree of substitution varied from 0.44 to 0.63 in SRSASP which could be attributed to the low reactivity at secondary hydroxyl. Monosaccharide composition result showed a decrease in the ratio of mannose/glucose, indicating the change of chemical composition in sulfated polysaccharides. In size-exclusion chromatograph analysis, a decrease in molecular weight and broadening of molecular weight distribution of sulfated polysaccharides was also observed. It could be attributed to the hydrolysis of polysaccharide in the sulfated reaction.

  11. Structural features of endocrine active chemicals--A comparison of in vivo and in vitro data.

    PubMed

    Lewin, Geertje; Escher, Sylvia E; van der Burg, Bart; Simetska, Nelly; Mangelsdorf, Inge

    2015-08-01

    Studies on reproductive toxicity need high numbers of test animals. Therefore, we investigated whether chemical structural features (SF) in combination with in vitro data on specific adverse outcome pathways (AOPs) may be used for predicting reproductive toxicity of untested chemicals. Using the OECD Toolbox and expert judgment, we identified 89 structure groups for 275 chemicals for which the results of prenatal developmental toxicity or multigeneration studies were present in the Fraunhofer database on Fertility and Developmental Toxicity in experimental animals (FeDTex) database. Likewise, we evaluated 220 chemicals which had been tested in reporter gene assays on endocrine ((anti)estrogenic and (anti)androgenic) properties in the CALUX(®) test battery. There was a large spread of effect levels for substances within the chemical structure groups for both, in vivo and in vitro results. The groups of highest concern (diphenyl derivatives, planar conjugated systems with fused rings, phenols and organophosphates) correlated quite well, however, between the in vivo and in vitro data on estrogenic activity. For the 56 chemicals represented in both databases, lowest effect doses in vivo correlated well with the estrogenic activity in vitro. These results suggest that a panel of assays covering relevant AOPs and data on metabolism and toxicokinetics may allow prediction of relative reproductive or development toxicity potency within the identified chemical structure groups.

  12. Impact of uncertainty in soil, climatic, and chemical information in a pesticide leaching assessment

    NASA Astrophysics Data System (ADS)

    Loague, Keith; Green, Richard E.; Giambelluca, Thomas W.; Liang, Tony C.; Yost, Russell S.

    1990-01-01

    A simple mobility index, when combined with a geographic information system, can be used to generate rating maps which indicate qualitatively the potential for various organic chemicals to leach to groundwater. In this paper we investigate the magnitude of uncertainty associated with pesticide mobility estimates as a result of data uncertainties. Our example is for the Pearl Harbor Basin, Oahu, Hawaii. The two pesticides included in our analysis are atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) and diuron [3-(3,4-dichlorophenyul)-1,1-dimethylarea]. The mobility index used here is known as the Attenuation Factor ( AF); it requires soil, hydrogeologic, climatic and chemical information as input data. We employ first-order uncertainty analysis to characterize the uncertainty in estimates of AF resulting from uncertainties in the various input data. Soils in the Pearl Harbor Basin are delineated at the order taxonomic category for this study. Our results show that there can be a significant amount of uncertainty in estimates of pesticide mobility for the Pearl Harbor Basin. This information needs to be considered if future decisions concerning chemical regulation are to be based on estimates of pesticide mobility determined from simple indices.

  13. Structural defects and chemical interaction of implanted ions with substrate structure in amorphous SiO2

    NASA Astrophysics Data System (ADS)

    Hosono, Hideo; Matsunami, Noriaki

    1993-11-01

    Structural defects in SiO2 glasses implanted with Li+, N+, O+, F+, Si+, and P+ ions were examined by vacuum-ultraviolet-absorption and electron-paramagnetic-resonance spectroscopies as well as thermal-gas-release analysis. The chemical interaction of implanted ions with substrate structure was considered on the basis of the obtained results. It is found that the type of predominant defects is controlled by the electronegative nature of implants. Silicon-silicon homobonds, which are oxygen-vacancy-type defects, are produced by electropositive implants (i.e., Li, P, and Si) at concentrations comparable to those of the implants. On the other hand, in the case of electronegative implants (F and O) O2 molecules and peroxy radicals (POR), both of which may be regarded as oxygen-interstitial-type defects, are the major defects and the total concentrations of these two defects are comparable to implant concentrations. These results indicate that chemical interaction of implanted ions with SiO2 is primarily controlled by the electronegative nature of implants. Electropositive implants (M) react chemically with oxygen atoms in the substrate structure to form M-O bonds, leaving Si-Si bonds. Electronegative implants (A) react chemically with silicon atoms to form Si-A bonds and oxygen atoms recoiled with implants combine with each other to form O2 molecules or react with the silica-network structure to form POR's. Concentrations of these predominant defects relative to implants can be used quantitatively to describe the strength of chemical interactions. When the chemical interaction is strong, both concentrations are comparable. On the other hand, when the chemical interaction is weak, concentrations of these defects are much smaller than those of implants because the major fraction of implants occur in a neutral state without forming chemical bonds with constituents of the substrate. Nitrogen is an example of this category and the major fraction of implanted nitrogen atoms

  14. Thesaurus of terms for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A Thesaurus of approximately 700 subject terms used to describe the six problem areas in the mechanics of structural failure is presented. The initial criteria for the selection of terms are their significance and frequency of use in the literature describing the mechanics of structural failure. The purpose of the Thesaurus is to provide the Aerospace Safety Research and Data Institute a list of key works and identifiers that afford effective retrieval of information regarding failure modes and mechanisms for aerospace structures. The Thesaurus includes both a conventional listing of subject terms and a Key Words In Context (KWIC) listing.

  15. Structural and fluid-chemical properties of fault zones

    SciTech Connect

    Bruhn, R.L. . Dept. of Geology and Geophysics)

    1992-01-01

    Fault fluids are mostly NaCl-CO[sub 2]-H[sub 2]O mixtures that originate by metamorphism, escape of connate water from wall rock, circulation of meteoric water, and perhaps contain components derived form igneous and subcrustal sources. Rupturing extends downward into metamorphic terrains undergoing greenschist and amphibolite facies metamorphism, where mineral alteration triggered by fluid pressure transients may extend several hundred meters to perhaps several kilometers into the wall rock. Fluid flowing into regions of lower temperature and/or pressure causes retrograde metamorphic alteration of fault and wall rock, and cementation of fractures. Fault permeability is heterogeneous because irregular, discontinuous lenses of cataclastic and gouge are encased in a heterogeneous damage layer characterized by intense fracturing and hydrothermal alteration. Permeability is also controlled by the geometry of corrugated slip surfaces which create anisotropic flow channels with greatest permeability parallel to long-axes of corrugations. Mineral assemblages and fluid inclusions provide evidence for fluid pressure cycling. Fluid pressure drops when permeability is enhanced by rupturing and subsequently increases as fractures deform, heal and become cemented with alteration minerals. Rates of hydrothermal alteration are comparable to, and sometimes faster, than those of mechanically induced permeability reduction. Effects of fluid chemistry on fault mechanics are not as well understood as fluid pressure effects. Frictional properties of fault surfaces are changed by chemical corrosion, cementation, and pressure solution. Strengthening by fluid pressure drop during dilatant fracturing may be partially offset by a decrease in fluid bulk modulus triggered by effervescence of CO[sub 2].

  16. Silicon Oxysulfide, OSiS: Rotational Spectrum, Quantum-Chemical Calculations, and Equilibrium Structure.

    PubMed

    Thorwirth, Sven; Mück, Leonie Anna; Gauss, Jürgen; Tamassia, Filippo; Lattanzi, Valerio; McCarthy, Michael C

    2011-06-01

    Silicon oxysulfide, OSiS, and seven of its minor isotopic species have been characterized for the first time in the gas phase at high spectral resolution by means of Fourier transform microwave spectroscopy. The equilibrium structure of OSiS has been determined from the experimental data using calculated vibration-rotation interaction constants. The structural parameters (rO-Si = 1.5064 Å and rSi-S = 1.9133 Å) are in very good agreement with values from high-level quantum chemical calculations using coupled-cluster techniques together with sophisticated additivity and extrapolation schemes. The bond distances in OSiS are very short in comparison with those in SiO and SiS. This unexpected finding is explained by the partial charges calculated for OSiS via a natural population analysis. The results suggest that electrostatic effects rather than multiple bonding are the key factors in determining bonding in this triatomic molecule. The data presented provide the spectroscopic information needed for radio astronomical searches for OSiS.

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

    NASA Astrophysics Data System (ADS)

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

    2014-01-01

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

  18. Structure, Kinetic, and Chemical Mechanism of Isocitrate Dehydrogenase-1 from Mycobacterium tuberculosis

    PubMed Central

    Quartararo, Christine E.; Hazra, Saugata; Hadi, Timin; Blanchard, John S.

    2013-01-01

    Mycobacterium tuberculosis (Mtb) is the leading cause of death due to a bacterial infection. The success of the Mtb pathogen has largely been attributed to the nonreplicating, persistence phase of the life cycle, for which the glyoxylate shunt is required. In Escherichia coli flux through the shunt is controlled by regulation of isocitrate dehydrogenase (ICDH). In Mtb, the mechanism of regulation is unknown, and currently there is no mechanistic or structural information on ICDH. We optimized expression and purification to a yield high enough to perform the first detailed kinetic and structural studies for Mtb ICDH-1. A large solvent kinetic isotope effect (D2OV = 3.0 ± 0.2, D2O[V/Kisocitrate] = 1.5 ± 0.3) and a smaller primary kinetic isotope effect (DV = 1.3 ± 0.1, D[V/K[2R-2H]isocitrate] = 1.5 ± 0.2) allowed us to perform the first multiple kinetic isotope effect studies on any ICDH and suggest a chemical mechanism. In this mechanism, protonation of the enolate to form product α-ketoglutarate is the rate-limiting step. We report the first structure of Mtb ICDH-1 to 2.18 Å by X-ray crystallography with NADPH and Mn2+ bound. It is a homodimer in which each subunit has a Rossmann fold, and a common top domain of interlocking beta sheets. Mtb ICDH-1 is most structurally similar to the R132H mutant human ICDH found in glioblastomas. Similar to human R132H ICDH, Mtb ICDH-1 also catalyses the formation of α-hydroxyglutarate. Our data suggest that regulation of Mtb ICDH-1 is novel. PMID:23409873

  19. Prenuclear Accentuation in English: Phonetics, Phonology, Information Structure

    ERIC Educational Resources Information Center

    Bishop, Jason Brandon

    2013-01-01

    A primary function of prosody in many languages is to convey information structure--the "packaging" of a sentence's content into categories such as "focus", "given" and "topic". In English and other West Germanic languages it is widely assumed that focus is signaled prosodically by the location of a…

  20. From Informal Strategies to Structured Procedures: Mind the Gap!

    ERIC Educational Resources Information Center

    Anghileri, Julia; Beishuizen, Meindert

    This paper explores written calculation methods for solving division problems used by students in England and the Netherlands at two points in the same school year. It analyzes informal strategies and identifies progression toward more structured procedures that result from different teaching approaches. Comparison of the methods used by fifth…

  1. From Informal Strategies to Structured Procedures: Mind the Gap!

    ERIC Educational Resources Information Center

    Anghileri, Julia; Beishuizen, Meindert; Van Putten, Kees

    2002-01-01

    Explores written calculation methods for division used by pupils in England (n=276) and the Netherlands (n=259). Analyses informal strategies and identifies progression towards more structured procedures that result from different teaching approaches. Comparison of methods used shows greater success in the Dutch approach which is based on…

  2. Impact of Information Technology Governance Structures on Strategic Alignment

    ERIC Educational Resources Information Center

    Gordon, Fitzroy R.

    2013-01-01

    This dissertation is a study of the relationship between Information Technology (IT) strategic alignment and IT governance structure within the organization. This dissertation replicates Asante (2010) among a different population where the prior results continue to hold, the non-experimental approach explored two research questions but include two…

  3. Prosodic Marking of Information Structure by Malaysian Speakers of English

    ERIC Educational Resources Information Center

    Gut, Ulrike; Pillai, Stefanie

    2014-01-01

    Various researchers have shown that second language (L2) speakers have difficulties with marking information structure in English prosodically: They deviate from native speakers not only in terms of pitch accent placement (Grosser, 1997; Gut, 2009; Ramírez Verdugo, 2002) and the type of pitch accent they produce (Wennerstrom, 1994, 1998) but also…

  4. Review of "Conceptual Structures: Information Processing in Mind and Machine."

    ERIC Educational Resources Information Center

    Smoliar, Stephen W.

    This review of the book, "Conceptual Structures: Information Processing in Mind and Machine," by John F. Sowa, argues that anyone who plans to get involved with issues of knowledge representation should have at least a passing acquaintance with Sowa's conceptual graphs for a database interface. (Used to model the underlying semantics of a…

  5. A hierarachical data structure representation for fusing multisensor information

    SciTech Connect

    Maren, A.J. . Space Inst.); Pap, R.M.; Harston, C.T. )

    1989-01-01

    A major problem with MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the data element, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Data-element fusion has problems with coregistration. Attempts to fuse information using the features of segmented data relies on a Presumed similarity between the segmentation characteristics of each data stream. Symbolic-level fusion requires too much advance processing (including object identification) to be useful. MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Data Structure (HDS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The HDS is an intermediate representation between the raw or smoothed data stream and symbolic interpretation of the data. it represents the structural organization of the data. Fused HDSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based region interpretation.

  6. A hierarachical data structure representation for fusing multisensor information

    SciTech Connect

    Maren, A.J.; Pap, R.M.; Harston, C.T.

    1989-12-31

    A major problem with MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the data element, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Data-element fusion has problems with coregistration. Attempts to fuse information using the features of segmented data relies on a Presumed similarity between the segmentation characteristics of each data stream. Symbolic-level fusion requires too much advance processing (including object identification) to be useful. MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Data Structure (HDS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The HDS is an intermediate representation between the raw or smoothed data stream and symbolic interpretation of the data. it represents the structural organization of the data. Fused HDSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based region interpretation.

  7. Information diversity in structure and dynamics of simulated neuronal networks.

    PubMed

    Mäki-Marttunen, Tuomo; Aćimović, Jugoslava; Nykter, Matti; Kesseli, Juha; Ruohonen, Keijo; Yli-Harja, Olli; Linne, Marja-Leena

    2011-01-01

    Neuronal networks exhibit a wide diversity of structures, which contributes to the diversity of the dynamics therein. The presented work applies an information theoretic framework to simultaneously analyze structure and dynamics in neuronal networks. Information diversity within the structure and dynamics of a neuronal network is studied using the normalized compression distance. To describe the structure, a scheme for generating distance-dependent networks with identical in-degree distribution but variable strength of dependence on distance is presented. The resulting network structure classes possess differing path length and clustering coefficient distributions. In parallel, comparable realistic neuronal networks are generated with NETMORPH simulator and similar analysis is done on them. To describe the dynamics, network spike trains are simulated using different network structures and their bursting behaviors are analyzed. For the simulation of the network activity the Izhikevich model of spiking neurons is used together with the Tsodyks model of dynamical synapses. We show that the structure of the simulated neuronal networks affects the spontaneous bursting activity when measured with bursting frequency and a set of intraburst measures: the more locally connected networks produce more and longer bursts than the more random networks. The information diversity of the structure of a network is greatest in the most locally connected networks, smallest in random networks, and somewhere in between in the networks between order and disorder. As for the dynamics, the most locally connected networks and some of the in-between networks produce the most complex intraburst spike trains. The same result also holds for sparser of the two considered network densities in the case of full spike trains.

  8. Organohelium compounds: structures, stabilities and chemical bonding analyses.

    PubMed

    Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

    2014-02-24

    This paper deals with the possibility of forming short and relatively strong carbon-helium bonds in small typical organic molecules through substitution of one or several H atoms by He(+). A structural and energetics study (based on high-level calculations) of this unusual bonding, as well as a topological characterization of the resulting cations, is undertaken. Stable species generally requires substitution of about half of the hydrogen atoms for formation. Under these conditions, the number of such species appears to be potentially unlimited. "True" C-He bonds exhibit equilibrium distances ranging from 1.327 (C2H2He2(2+)) to 1.129 Å (He2CO(2+)). The energies of neutral He releasing range from approximately 5 kcal mol(-1) [He2CO(2+), (Z)-C2H2He2(2+)] to 25 kcal mol(-1) (C2HHe3(3+)), but remain most frequently around 10 kcal mol(-1). However, most of He(+)-substituted hydrocarbons are metastable with respect to C-C cleavage, except derivatives of ethene. Atoms in molecules (AIM) and electron localization function (ELF) topological descriptors classify the C-He bond as a weak charge-shift interaction [S. Shaik, D. Danovich, B. Silvi, D. L. Lauvergnat, P. C. Hiberty, Chem. Eur. J. 2005, 11, 6358-6371] in agreement with a recent publication by Rzepa [S. H. Rzepa, Nat. Chem. 2010, 2, 390-393]. He2CO(2+) is the only investigated compound that presents a C-He bonding ELF basin, which indicates a non-negligible covalent contribution to the bond. Other modifications in the electronic structure, such as the breaking of the triple bond in ethyne derivatives or the loss of aromaticity in C6H3He3(3+), are also nicely revealed by the ELF topology. PMID:24488791

  9. Three-dimensional microwave imaging with incorporated prior structural information

    NASA Astrophysics Data System (ADS)

    Golnabi, Amir H.; Meaney, Paul M.; Epstein, Neil R.; Paulsen, Keith D.

    2012-03-01

    Microwave imaging for biomedical applications, especially for early detection of breast cancer and effective treatment monitoring, has attracted increasing interest in last several decades. This fact is due to the high contrast between the dielectric properties of the normal and malignant breast tissues at microwave frequencies. The available range of dielectric properties for different soft tissue can provide important functional information about tissue health. Nonetheless, one of the limiting weaknesses of microwave imaging is that unlike conventional modalities, such as X-ray CT or MRI, it inherently cannot provide high-resolution images. The conventional modalities can produce highly resolved anatomical information but often cannot provide the functional information required for diagnoses. Previously, we have developed a regularization strategy that can incorporate prior anatomical information from MR or other sources and use it in a way to refine the resolution of the microwave images, while also retaining the functional nature of the reconstructed property values. In the present work, we extend the use of prior structural information in microwave imaging from 2D to 3D. This extra dimension adds a significant layer of complexity to the entire image reconstruction procedure. In this paper, several challenges with respect to the 3D microwave imaging will be discussed and the results of a series of 3D simulation and phantom experiments with prior structural information will be studied.

  10. ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions.

    PubMed

    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

  11. ToxAlerts: A Web Server of Structural Alerts for Toxic Chemicals and Compounds with Potential Adverse Reactions

    PubMed Central

    2012-01-01

    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

  12. Structural Simulations and Conservation Analysis -Historic Building Information Model (HBIM)

    NASA Astrophysics Data System (ADS)

    Dore, C.; Murphy, M.; McCarthy, S.; Brechin, F.; Casidy, C.; Dirix, E.

    2015-02-01

    In this paper the current findings to date of the Historic Building Information Model (HBIM) of the Four Courts in Dublin are presented. The Historic Building Information Model (HBIM) forms the basis for both structural and conservation analysis to measure the impact of war damage which still impacts on the building. The laser scan survey was carried out in the summer of 2014 of the internal and external structure. After registration and processing of the laser scan survey, the HBIM was created of the damaged section of the building and is presented as two separate workflows in this paper. The first is the model created from historic data, the second a procedural and segmented model developed from laser scan survey of the war damaged drum and dome. From both models structural damage and decay simulations will be developed for documentation and conservation analysis.

  13. Structural, chemical, and isotopic microanalytical investigations of graphite from supernovae

    NASA Astrophysics Data System (ADS)

    Croat, T. Kevin; Bernatowicz, Thomas; Amari, Sachiko; Messenger, Scott; Stadermann, Frank J.

    2003-12-01

    value of 0.122. Significant variations about the mean V/Ti ratio were also seen among TiCs in the same graphite, likely indicating chemical equilibration with the surrounding gas over a range of temperatures. In general, the diversity in internal TiC properties suggests that TiCs formed first and had substantially diverse histories before incorporation into the graphite, implying some degree of turbulent mixing in the SN outflows. In most graphites, there is a decrease in the number density of TiCs as a function of increasing radial dis- tance, caused by either preferential depletion of TiCs from the gas or an acceleration of graphite growth with decreasing ambient temperature. In several graphites, TiCs showed a trend of larger V/Ti ratios with increasing distance from the graphite center, an indication of progressive equilibration with the surrounding gas before they were sequestered in the graphites. In all but one graphite, no trend was seen in the TiC size vs. distance from the graphite center, implying that appreciable TiC growth had effectively stopped before the graphites formed, or else that graphite growth was rapid compared to TiC growth. Taken together, the chemical variations among internal grains as well as the presence of partially amorphous rims and epitaxial Fe phases on some TiCs clearly indicate that the phase condensation sequence was TiC, followed by the iron phases (only found in some graphites) and finally graphite. Since graphite typically condenses at a higher temperature than iron at low pressures (<10 -3 bars) in a gas with C > O and otherwise solar composition, the observed condensation sequence implies a relative iron enrichment in the gas or greater supersaturation of graphite relative to iron. The TEM observations allow inferences to be made about the physical conditions in the gas from which the grains condensed. Given the TiC sizes and abundances, the gas was evidently quite dusty. From the observed TiC size range of ˜20 nm to ˜500 nm

  14. Structural, chemical, and isotopic microanalytical investigations of graphite from supernovae

    NASA Astrophysics Data System (ADS)

    Croat, T. Kevin; Bernatowicz, Thomas; Amari, Sachiko; Messenger, Scott; Stadermann, Frank J.

    2003-12-01

    value of 0.122. Significant variations about the mean V/Ti ratio were also seen among TiCs in the same graphite, likely indicating chemical equilibration with the surrounding gas over a range of temperatures. In general, the diversity in internal TiC properties suggests that TiCs formed first and had substantially diverse histories before incorporation into the graphite, implying some degree of turbulent mixing in the SN outflows. In most graphites, there is a decrease in the number density of TiCs as a function of increasing radial dis- tance, caused by either preferential depletion of TiCs from the gas or an acceleration of graphite growth with decreasing ambient temperature. In several graphites, TiCs showed a trend of larger V/Ti ratios with increasing distance from the graphite center, an indication of progressive equilibration with the surrounding gas before they were sequestered in the graphites. In all but one graphite, no trend was seen in the TiC size vs. distance from the graphite center, implying that appreciable TiC growth had effectively stopped before the graphites formed, or else that graphite growth was rapid compared to TiC growth. Taken together, the chemical variations among internal grains as well as the presence of partially amorphous rims and epitaxial Fe phases on some TiCs clearly indicate that the phase condensation sequence was TiC, followed by the iron phases (only found in some graphites) and finally graphite. Since graphite typically condenses at a higher temperature than iron at low pressures (<10 -3 bars) in a gas with C > O and otherwise solar composition, the observed condensation sequence implies a relative iron enrichment in the gas or greater supersaturation of graphite relative to iron. The TEM observations allow inferences to be made about the physical conditions in the gas from which the grains condensed. Given the TiC sizes and abundances, the gas was evidently quite dusty. From the observed TiC size range of ˜20 nm to ˜500 nm

  15. Alternatives Assessment Frameworks: Research Needs for the Informed Substitution of Hazardous Chemicals

    PubMed Central

    Jacobs, Molly M.; Malloy, Timothy F.; Tickner, Joel A.; Edwards, Sally

    2015-01-01

    Background Given increasing pressures for hazardous chemical replacement, there is growing interest in alternatives assessment to avoid substituting a toxic chemical with another of equal or greater concern. Alternatives assessment is a process for identifying, comparing, and selecting safer alternatives to chemicals of concern (including those used in materials, processes, or technologies) on the basis of their hazards, performance, and economic viability. Objectives The purposes of this substantive review of alternatives assessment frameworks are to identify consistencies and differences in methods and to outline needs for research and collaboration to advance science policy practice. Methods This review compares methods used in six core components of these frameworks: hazard assessment, exposure characterization, life-cycle impacts, technical feasibility evaluation, economic feasibility assessment, and decision making. Alternatives assessment frameworks published from 1990 to 2014 were included. Results Twenty frameworks were reviewed. The frameworks were consistent in terms of general process steps, but some differences were identified in the end points addressed. Methodological gaps were identified in the exposure characterization, life-cycle assessment, and decision–analysis components. Methods for addressing data gaps remain an issue. Discussion Greater consistency in methods and evaluation metrics is needed but with sufficient flexibility to allow the process to be adapted to different decision contexts. Conclusion Although alternatives assessment is becoming an important science policy field, there is a need for increased cross-disciplinary collaboration to refine methodologies in support of the informed substitution and design of safer chemicals, materials, and products. Case studies can provide concrete lessons to improve alternatives assessment. Citation Jacobs MM, Malloy TF, Tickner JA, Edwards S. 2016. Alternatives assessment frameworks: research

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

    NASA Astrophysics Data System (ADS)

    Sandhage, Kenneth H.

    2010-06-01

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

  17. Automatic chemical structure annotation of an LC-MS(n) based metabolic profile from green tea.

    PubMed

    Ridder, Lars; van der Hooft, Justin J J; Verhoeven, Stefan; de Vos, Ric C H; Bino, Raoul J; Vervoort, Jacques

    2013-06-18

    Liquid chromatography coupled with multistage accurate mass spectrometry (LC-MS(n)) can generate comprehensive spectral information of metabolites in crude extracts. To support structural characterization of the many metabolites present in such complex samples, we present a novel method ( http://www.emetabolomics.org/magma ) to automatically process and annotate the LC-MS(n) data sets on the basis of candidate molecules from chemical databases, such as PubChem or the Human Metabolite Database. Multistage MS(n) spectral data is automatically annotated with hierarchical trees of in silico generated substructures of candidate molecules to explain the observed fragment ions and alternative candidates are ranked on the basis of the calculated matching score. We tested this method on an untargeted LC-MS(n) (n ≤ 3) data set of a green tea extract, generated on an LC-LTQ/Orbitrap hybrid MS system. For the 623 spectral trees obtained in a single LC-MS(n) run, a total of 116,240 candidate molecules with monoisotopic masses matching within 5 ppm mass accuracy were retrieved from the PubChem database, ranging from 4 to 1327 candidates per molecular ion. The matching scores were used to rank the candidate molecules for each LC-MS(n) component. The median and third quartile fractional ranks for 85 previously identified tea compounds were 3.5 and 7.5, respectively. The substructure annotations and rankings provided detailed structural information of the detected components, beyond annotation with elemental formula only. Twenty-four additional components were putatively identified by expert interpretation of the automatically annotated data set, illustrating the potential to support systematic and untargeted metabolite identification. PMID:23662787

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

    PubMed

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

    2016-10-01

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

  19. Trypanocidal nitroimidazole derivatives: relationships among chemical structure and genotoxic activity.

    PubMed

    Buschini, Annamaria; Giordani, Federica; de Albuquerque, Cristina Northfleet; Pellacani, Claudia; Pelosi, Giorgio; Rossi, Carlo; Zucchi, Tânia Maria Araújo Domingues; Poli, Paola

    2007-05-15

    Human American trypanosomiasis is resurgent in Latin Americans, and new drugs are urgently required as current medications suffer from a number of drawbacks. Some nitroheterocycles have been demonstrated to exert a potent activity against trypanosomes. However, host toxicity issues halted their development as trypanocides. As part of the efforts to develop new compounds in order to treat parasitic infections, it is important to define their structure-activity relationship. In this study, 5-nitromegazol and two of its analogues, 4-nitromegazol, and 1-methyl-5-nitro-2-imidazolecarboxaldehyde 5-nitroimidazole-thiosemicarbazone, were tested and compared for in vitro induction of DNA damage in human leukocytes by the comet assay, performed at different pHs to better identify the types of damage. Specific oxidatively generated damage to DNA was also measured by using the comet assay with endonucleases. DNA damage was found in 5-nitromegazol-treated cells: oxidative stress appeared as the main source of DNA damage. 4-Nitromegazol did not produce any significant effect, thus confirming that 4-nitroimidazoles isomers have no important biological activity. The 5-nitroimidazole-thiosemicarbazone induced DNA damage with a higher efficiency than 5-nitromegazol. The central role in the reduction process played by the acidic hydrazine proton present in the thiosemicarbazone group but not in the cyclic (thiadiazole) form can contribute to rationalise our results. Given its versatility, thiosemicarbazone moiety could be involved in different reactions with nitrogenous bases (nucleophilic and/or electrophilic attacks).

  20. Chemical Emissions of Residential Materials and Products: Review of Available Information

    SciTech Connect

    Willem, Henry; Singer, Brett

    2010-09-15

    This report is prepared in the context of a larger program whose mission is to advance understanding of ventilation and indoor air quality in U.S. homes. A specific objective of this program is to develop the scientific basis ? through controlled experiments, monitoring and analysis ? for health risk-based ventilation standards. Appropriate and adequate ventilation is a basic element of a healthy home. Ventilation provides outdoor air and in the process removes indoor odors and contaminants including potentially unhealthful chemicals emitted by indoor materials, products and activities. Ventilation traditionally was assured to occur via infiltration of outdoor air through cracks and other leakage pathways in the residential building envelope. As building air tightness is improved for energy efficiency, infiltration can be reduced to inadequate levels. This has lead to the development of standards requiring mechanical ventilation. Though nominally intended to ensure acceptable indoor air quality, the standards are not explicitly tied to health risk or pollutant exposure targets. LBNL is currently designing analyses to assess the impact of varying ventilation standards on pollutant concentrations, health risks and energy use. These analyses require information on sources of chemical pollutant emissions, ideally including emission rates and the impact of ventilation on emissions. Some information can be obtained from recent studies that report measurements of various air contaminants and their concentrations in U.S. residences. Another way to obtain this information is the bottom-up approach of collecting and evaluating emissions data from construction and interior materials and common household products. This review contributes to the latter approach by summarizing available information on chemical emissions from new residential products and materials. We review information from the scientific literature and public sources to identify and discuss the databases that

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

    PubMed

    Salmina, Elena S; Haider, Norbert; Tetko, Igor V

    2015-01-01

    The article describes a classification system termed "extended functional groups" (EFG), which are an extension of a set previously used by the CheckMol software, that covers in addition heterocyclic compound classes and periodic table groups. The functional groups are defined as SMARTS patterns and are available as part of the ToxAlerts tool (http://ochem.eu/alerts) of the On-line CHEmical database and Modeling (OCHEM) environment platform. The article describes the motivation and the main ideas behind this extension and demonstrates that EFG can be efficiently used to develop and interpret structure-activity relationship models. PMID:26703557

  2. Using quantitative structural property relationships, chemical fate models, and the chemical partitioning space to investigate the potential for long range transport and bioaccumulation of complex halogenated chemical mixtures.

    PubMed

    Gawor, Anya; Wania, Frank

    2013-09-01

    Some substances are mixtures of very large number of constituents which vary widely in their properties, and thus also in terms of their environmental fate and the hazard that they may pose to humans and the environment. Examples of such substances include industrial chemicals such as the chlorinated paraffins, technical pesticides such as toxaphene, and unintended combustion side products, such as mixed halogenated dibenzo-p-dioxins and dibenzofurans. Here we describe a simple graphical superposition method that could precede a more detailed hazard assessment for such substances. First, partitioning and degradation properties for each individual constituent of a mixture are estimated with high-throughput quantitative structure-property relationships. Placed in a chemical partitioning space, i.e. a coordinate system defined by two partitioning coefficients, the mixtures appear as 'clouds'. When model-derived hazard assessment metrics, such as the potential for bioaccumulation and long range transport, are superimposed on these clouds, the resulting maps identify the constituents with the highest value for a particular parameter and thus potentially the greatest hazard. The maps also indicate transparently how the potential for long range transport and bioaccumulation is dependent on structural attributes, such as chain length, and the degree and type of halogenation. In contrast to previous approaches, in which the mixture is represented by a single set of properties or those of a few selected constituents, the whole range of environmental fate behaviors displayed by the constituents of a mixture are being considered. The approach is illustrated with three sets of chemical substances.

  3. Ensuring Adequate Health and Safety Information for Decision Makers during Large-Scale Chemical Releases

    NASA Astrophysics Data System (ADS)

    Petropoulos, Z.; Clavin, C.; Zuckerman, B.

    2015-12-01

    The 2014 4-Methylcyclohexanemethanol (MCHM) spill in the Elk River of West Virginia highlighted existing gaps in emergency planning for, and response to, large-scale chemical releases in the United States. The Emergency Planning and Community Right-to-Know Act requires that facilities with hazardous substances provide Material Safety Data Sheets (MSDSs), which contain health and safety information on the hazardous substances. The MSDS produced by Eastman Chemical Company, the manufacturer of MCHM, listed "no data available" for various human toxicity subcategories, such as reproductive toxicity and carcinogenicity. As a result of incomplete toxicity data, the public and media received conflicting messages on the safety of the contaminated water from government officials, industry, and the public health community. Two days after the governor lifted the ban on water use, the health department partially retracted the ban by warning pregnant women to continue avoiding the contaminated water, which the Centers for Disease Control and Prevention deemed safe three weeks later. The response in West Virginia represents a failure in risk communication and calls to question if government officials have sufficient information to support evidence-based decisions during future incidents. Research capabilities, like the National Science Foundation RAPID funding, can provide a solution to some of the data gaps, such as information on environmental fate in the case of the MCHM spill. In order to inform policy discussions on this issue, a methodology for assessing the outcomes of RAPID and similar National Institutes of Health grants in the context of emergency response is employed to examine the efficacy of research-based capabilities in enhancing public health decision making capacity. The results of this assessment highlight potential roles rapid scientific research can fill in ensuring adequate health and safety data is readily available for decision makers during large

  4. Raman investigation of magma mingling experiments as a tool for tracking the chemical and structural evolution of melt.

    NASA Astrophysics Data System (ADS)

    Di Genova, D.; Morgavi, D.; Hess, K. U.; Pritchard, C. J.; Borovkov, N.; Perugini, D.; Larson, P. B.; Dingwell, D. B.

    2014-12-01

    Magma mixing is a petrologic phenomenon, for which extensive evidence has been documented in rocks young and old, from intrusive and effusive igneous environments. Although magma mixing between mafic and silicic magmas is regarded as a major differentiation process, documentation of the mechanisms acting in melt interaction, both in its physical and chemical aspects, is still incomplete. We present the first Raman spectroscopic investigation of the products of magma-mixing experiments performed using natural basaltic and rhyolitic melts from the Yellowstone Norris-Mammoth Corridor. The mixing process is driven by a recently-developed apparatus that generates chaotic streamlines in the melts, mimicking the development of magma mixing in nature. The chemical variation of major elements is studied in detail by electron microprobe (EMPA) on mixed filaments of 1000 μm diameter. Raman and microprobe measurements have been performed every 10 μm this allow us to investigate the evolution of silicate structure, from the rhyolitic to the basaltic composition. Deconvoluted Raman spectra collected from the mixed experiment yield information about network-forming structural units (Qn species, where n indicates the number of bridging oxygen). By combining Raman spectra and chemical analyses we show, for the first time, how the percent of Qn species evolve with chemical composition in these natural silicate melts. Moreover, our results show how the ratio of network modifiers respect to network former cations, dramatically affects the Raman spectra of the rhyolitic end-member.

  5. Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control.

    PubMed

    Frank, Philipp; Schreiter, Joerg; Haefner, Sebastian; Paschew, Georgi; Voigt, Andreas; Richter, Andreas

    2016-01-01

    Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature.

  6. Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control

    PubMed Central

    Frank, Philipp; Schreiter, Joerg; Haefner, Sebastian; Paschew, Georgi; Voigt, Andreas; Richter, Andreas

    2016-01-01

    Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature. PMID:27571209

  7. Integrated Microfluidic Membrane Transistor Utilizing Chemical Information for On-Chip Flow Control.

    PubMed

    Frank, Philipp; Schreiter, Joerg; Haefner, Sebastian; Paschew, Georgi; Voigt, Andreas; Richter, Andreas

    2016-01-01

    Microfluidics is a great enabling technology for biology, biotechnology, chemistry and general life sciences. Despite many promising predictions of its progress, microfluidics has not reached its full potential yet. To unleash this potential, we propose the use of intrinsically active hydrogels, which work as sensors and actuators at the same time, in microfluidic channel networks. These materials transfer a chemical input signal such as a substance concentration into a mechanical output. This way chemical information is processed and analyzed on the spot without the need for an external control unit. Inspired by the development electronics, our approach focuses on the development of single transistor-like components, which have the potential to be used in an integrated circuit technology. Here, we present membrane isolated chemical volume phase transition transistor (MIS-CVPT). The device is characterized in terms of the flow rate from source to drain, depending on the chemical concentration in the control channel, the source-drain pressure drop and the operating temperature. PMID:27571209

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

    PubMed

    Cortes-Ciriano, Isidro; Bender, Andreas

    2015-12-28

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

  9. A hierarchical structure approach to MultiSensor Information Fusion

    SciTech Connect

    Maren, A.J.; Pap, R.M.; Harston, C.T.

    1989-12-31

    A major problem with image-based MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the pixel, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Pixel-level fusion has problems with coregistration of the images or data. Attempts to fuse information using the features of segmented images or data relies an a presumed similarity between the segmentation characteristics of each image or data stream. Symbolic-level fusion requires too much advance processing to be useful, as we have seen in automatic target recognition tasks. Image-based MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Scene Structure (HSS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The MSS is intermediate between a pixel-based representation and a scene interpretation representation, and represents the perceptual organization of an image. Fused HSSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based,region interpretation.

  10. A hierarchical structure approach to MultiSensor Information Fusion

    SciTech Connect

    Maren, A.J. . Space Inst.); Pap, R.M.; Harston, C.T. )

    1989-01-01

    A major problem with image-based MultiSensor Information Fusion (MSIF) is establishing the level of processing at which information should be fused. Current methodologies, whether based on fusion at the pixel, segment/feature, or symbolic levels, are each inadequate for robust MSIF. Pixel-level fusion has problems with coregistration of the images or data. Attempts to fuse information using the features of segmented images or data relies an a presumed similarity between the segmentation characteristics of each image or data stream. Symbolic-level fusion requires too much advance processing to be useful, as we have seen in automatic target recognition tasks. Image-based MSIF systems need to operate in real-time, must perform fusion using a variety of sensor types, and should be effective across a wide range of operating conditions or deployment environments. We address this problem through developing a new representation level which facilitates matching and information fusion. The Hierarchical Scene Structure (HSS) representation, created using a multilayer, cooperative/competitive neural network, meets this need. The MSS is intermediate between a pixel-based representation and a scene interpretation representation, and represents the perceptual organization of an image. Fused HSSs will incorporate information from multiple sensors. Their knowledge-rich structure aids top-down scene interpretation via both model matching and knowledge-based,region interpretation.

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

    PubMed Central

    Haniam, P.; Kunsombat, C.; Chiangga, S.; Songsasen, A.

    2014-01-01

    Thin films of cobalt oxides (CoO and Co3O4) fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures. PMID:24672354

  12. Synthesis of cobalt oxides thin films fractal structures by laser chemical vapor deposition.

    PubMed

    Haniam, P; Kunsombat, C; Chiangga, S; Songsasen, A

    2014-01-01

    Thin films of cobalt oxides (CoO and Co3O4) fractal structures have been synthesized by using laser chemical vapor deposition at room temperature and atmospheric pressure. Various factors which affect the density and crystallization of cobalt oxides fractal shapes have been examined. We show that the fractal structures can be described by diffusion-limited aggregation model and discuss a new possibility to control the fractal structures. PMID:24672354

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

    PubMed Central

    2013-01-01

    Background 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. Results 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. Conclusions By using a simple web application it was

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

    PubMed

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

    2013-10-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-10-01

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

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

    PubMed Central

    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

    2016-01-01

    The absence of effective therapeutics against Alzheimer's disease (AD) is a result of the limited understanding of its multifaceted aetiology. Because of the lack of chemical tools to identify pathological factors, investigations into AD pathogenesis have also been insubstantial. Here we report chemical regulators that demonstrate distinct specificity towards targets linked to AD pathology, including metals, amyloid-β (Aβ), metal–Aβ, reactive oxygen species, and free organic radicals. We obtained these chemical regulators through a rational structure-mechanism-based design strategy. We performed structural variations of small molecules for fine-tuning their electronic properties, such as ionization potentials and mechanistic pathways for reactivity towards different targets. We established in vitro and/or in vivo efficacies of the regulators for modulating their targets' reactivities, ameliorating toxicity, reducing amyloid pathology, and improving cognitive deficits. Our chemical tools show promise for deciphering AD pathogenesis and discovering effective drugs. PMID:27734843

  17. Analysis of weblike network structures of directed graphs for chemical reactions in methane plasmas

    SciTech Connect

    Sakai, Osamu Nobuto, Kyosuke; Miyagi, Shigeyuki; Tachibana, Kunihide

    2015-10-15

    Chemical reactions of molecular gases like methane are so complicated that a chart of decomposed and/or synthesized species originating from molecules in plasma resembles a weblike network in which we write down species and reactions among them. Here we consider properties of the network structures of chemical reactions in methane plasmas. In the network, atoms/molecules/radical species are assumed to form nodes and chemical reactions correspond to directed edges in the terminology of graph theory. Investigation of the centrality index reveals importance of CH{sub 3} in the global chemical reaction, and difference of an index for each radical species between cases with and without electrons clarifies that the electrons are at an influential position to tighten the network structure.

  18. Chemical functionalization of silicene: spontaneous structural transition and exotic electronic properties.

    PubMed

    Huang, Bing; Xiang, H J; Wei, Su-Huai

    2013-10-01

    The use of newly discovered silicene for various optoelectronic applications depends largely on the possibility of controlling its electronic properties by chemical functionalization. To investigate this possibility, we systemically study the structural and electronic properties of chemically functionalized silicene by employing first-principles calculations combined with the cluster expansion approach. Interestingly, we find that chemically functionalized epitaxial silicene is generally accompanied by a spontaneous structural transition, which originates from the preference of sp(3) hybridization of silicon. To realized continuously tunable band gaps, chemical functionalization of freestanding silicene at ~900 K is proposed. Finally, we predict that metastable silicene can also be used as an important host material to produce novel functional materials via substitutional doping. For example, the discovered ordered Si(8)P(4) could be a strong candidate for thin-film solar cell absorbers beyond bulk Si.

  19. Chromogenic chemical probe for protein structural characterization via ultraviolet photodissociation mass spectrometry.

    PubMed

    O'Brien, John P; Pruet, Jeff M; Brodbelt, Jennifer S

    2013-08-01

    A chemical probe/ultraviolet photodissociation (UVPD) mass spectrometry strategy for evaluating structures of proteins and protein complexes is reported, as demonstrated for lysozyme and beta-lactoglobulin with and without bound ligands. The chemical probe, NN, incorporates a UV chromophore that endows peptides with high cross sections at 351 nm, a wavelength not absorbed by unmodified peptides. Thus, NN-modified peptides can readily be differentiated from nonmodified peptides in complex tryptic digests created upon proteolysis of proteins after their exposure to the NN chemical probe. The NN chemical probe also affords two diagnostic reporter ions detected upon UVPD of the NN-modified peptide that provides a facile method for the identification of NN peptides within complex mixtures. Quantitation of the modified and unmodified peptides allows estimation of the surface accessibilities of lysine residues based on their relative reactivities with the NN chemical probe.

  20. A novel approach to structural alignment using realistic structural and environmental information.

    PubMed

    Chen, Yu; Crippen, Gordon M

    2005-12-01

    In the era of structural genomics, it is necessary to generate accurate structural alignments in order to build good templates for homology modeling. Although a great number of structural alignment algorithms have been developed, most of them ignore intermolecular interactions during the alignment procedure. Therefore, structures in different oligomeric states are barely distinguishable, and it is very challenging to find correct alignment in coil regions. Here we present a novel approach to structural alignment using a clique finding algorithm and environmental information (SAUCE). In this approach, we build the alignment based on not only structural coordinate information but also realistic environmental information extracted from biological unit files provided by the Protein Data Bank (PDB). At first, we eliminate all environmentally unfavorable pairings of residues. Then we identify alignments in core regions via a maximal clique finding algorithm. Two extreme value distribution (EVD) form statistics have been developed to evaluate core region alignments. With an optional extension step, global alignment can be derived based on environment-based dynamic programming linking. We show that our method is able to differentiate three-dimensional structures in different oligomeric states, and is able to find flexible alignments between multidomain structures without predetermined hinge regions. The overall performance is also evaluated on a large scale by comparisons to current structural classification databases as well as to other alignment methods. PMID:16260755

  1. Structure-activity relationships: quantitative techniques for predicting the behavior of chemicals in the ecosystem

    SciTech Connect

    Nirmalakhandan, N.; Speece, R.E.

    1988-06-01

    Quantitative Structure-Activity Relationships (QSARs) are used increasingly to screen and predict the toxicity and the fate of chemicals released into the environment. The impetus to use QSAR methods in this area has been the large number of synthetic chemicals introduced into the ecosystem via intensive agriculture and industrialization. Because of the costly and time-consuming nature of environmental fate testing, QSARs have been effectively used to screen large classes of chemical compounds and flag those that appear to warrant more thorough testing.

  2. Quantitative structure-activity relationships for chemical toxicity to environmental bacteria

    SciTech Connect

    Blum, D.J.; Speece, R.E. )

    1991-10-01

    Quantitative structure-activity relationships (QSARs) were developed for nonreactive chemical toxicity to each of four groups of bacteria of importance in environmental engineering: aerobic heterotrophs, methanogens, Nitrosomonas, and Microtox. The QSARs were based on chemicals covering a range of structures and including important environmental pollutants (i.e., chlorinated and other substituted benzenes, phenols, and aliphatic hydrocarbons). QSARs were developed for each chemical class and for combinations of chemical classes. Three QSAR methods (groups of chemical describing parameters) were evaluated for their accuracy and ease of use: log P, linear solvation energy relationships (LSER), and molecular connectivity. Successful QSARs were found for each group of bacteria and by each method, with correlation coefficients (adjusted r2) between 0.79 and 0.95. LSER QSARs incorporated the widest range of chemicals with the greatest accuracy. Log P and molecular connectivity QSARs are easier to use because their parameters are readily available. Outliers from the QSARs likely due to reactive toxicity included acryls, low pKa compounds, and aldehydes. Nitro compounds and chlorinated aliphatic hydrocarbons and alcohols showed enhanced toxicity to the methanogens only. Chemicals with low IC50 concentrations (log IC50 mumol/liter less than 1.5) were often outliers for Nitrosomonas. QSARs were validated statistically and with literature data. A suggested method is provided for use of the QSARs.

  3. Chemical structure imaging of a single molecule by atomic force microscopy at room temperature

    PubMed Central

    Iwata, Kota; Yamazaki, Shiro; Mutombo, Pingo; Hapala, Prokop; Ondráček, Martin; Jelínek, Pavel; Sugimoto, Yoshiaki

    2015-01-01

    Atomic force microscopy is capable of resolving the chemical structure of a single molecule on a surface. In previous research, such high resolution has only been obtained at low temperatures. Here we demonstrate that the chemical structure of a single molecule can be clearly revealed even at room temperature. 3,4,9,10-perylene tetracarboxylic dianhydride, which is strongly adsorbed onto a corner-hole site of a Si(111)–(7 × 7) surface in a bridge-like configuration is used for demonstration. Force spectroscopy combined with first-principle calculations clarifies that chemical structures can be resolved independent of tip reactivity. We show that the submolecular contrast over a central part of the molecule is achieved in the repulsive regime due to differences in the attractive van der Waals interaction and the Pauli repulsive interaction between different sites of the molecule. PMID:26178193

  4. Terrestrial chemical spill information system through remote sensing, GIS, and V.B. 6.0

    NASA Astrophysics Data System (ADS)

    Dwarakish, G. S.; Jeba S., Angel; Srinikethan, G.; Natesan, Usha

    2009-01-01

    India has made remarkable progress in creating a modern and diversified industrial base, since its independence. Most of the refineries, petrochemical and fertilizer industries are located in the coastal zone and catered by 12 major ports along the 7500 km length of Indian coastline. Since, transportation of crude oil and POL products from ports to refineries are mostly by pipelines, rail/ road, besides some quantity by barge/ ships along the coast, there will be chances of oil spill/leakage. Managing these events before and during their occurrence is imperative to the protection of people and natural resources. The present study was carried out with a view to develop Terrestrial Chemical Spill Information System [TCSIS], using Remote Sensing [RS], GIS and VB 6.0., for the Mangalore coastal zone industrial area of Dakshina Kannada district, Karnataka state, along West Coast of India. The study area lies between 74°45'00'' to 74°52'30''E longitude and 12°52'30'' to 13°00'00''N latitude. The database of TCSIS consists of both conventional data and RS data, and analysed using ERDAS Imagine 9.0 and ArcGIS 8.3 software. Different thematic maps prepared include LU/LC map, drainage map, road and pipeline network map, slope map, Digital Elevation Model, relative risk maps and pipeline route for the transportation of hazardous chemicals from port to refinery. The TCSIS module developed using RS, GIS and V.B.6.0, characterizes the ability of a spilled chemical to immediately impact human health, natural resources, and incorporates these into an overall measure of terrestrial chemical risk and aids in planning, preventing and responding to a terrestrial chemical spill.

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

    PubMed

    Hartman, Joshua D; Beran, Gregory J O

    2014-11-11

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

  6. Structural, optical and charge generation properties of chalcostibite and tetrahedrite copper antimony sulfide thin films prepared from metal xanthates† †Electronic supplementary information (ESI) available: Chemical structures of the used metal xanthates, additional XRD, SEM-EDX and UV-vis data. See DOI: 10.1039/c5ta05777a Click here for additional data file.

    PubMed Central

    MacLachlan, Andrew J.; Brown, Michael D.

    2015-01-01

    Herein, we report on a solution based approach for the preparation of thin films of copper antimony sulfide, an emerging absorber material for third generation solar cells. In this work, copper and antimony xanthates are used as precursor materials for the formation of two different copper antimony sulfide phases: chalcostibite (CuSbS2) and tetrahedrite (Cu12Sb4S13). Both phases were thoroughly investigated regarding their structural and optical properties. Moreover, thin films of chalcostibite and tetrahedrite were prepared on mesoporous TiO2 layers and photoinduced charge transfer in these metal sulfide/TiO2 heterojunctions was studied via transient absorption spectroscopy. Photoinduced charge transfer was detected in both the chalcostibite as well as the tetrahedrite sample, which is an essential property in view of applying these materials as light-harvesting agents in semiconductor sensitized solar cells. PMID:27019713

  7. A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

    PubMed

    Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

    2016-01-01

    When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity.

  8. A Systems Biology Approach for Identifying Hepatotoxicant Groups Based on Similarity in Mechanisms of Action and Chemical Structure.

    PubMed

    Hebels, Dennie G A J; Rasche, Axel; Herwig, Ralf; van Westen, Gerard J P; Jennen, Danyel G J; Kleinjans, Jos C S

    2016-01-01

    When evaluating compound similarity, addressing multiple sources of information to reach conclusions about common pharmaceutical and/or toxicological mechanisms of action is a crucial strategy. In this chapter, we describe a systems biology approach that incorporates analyses of hepatotoxicant data for 33 compounds from three different sources: a chemical structure similarity analysis based on the 3D Tanimoto coefficient, a chemical structure-based protein target prediction analysis, and a cross-study/cross-platform meta-analysis of in vitro and in vivo human and rat transcriptomics data derived from public resources (i.e., the diXa data warehouse). Hierarchical clustering of the outcome scores of the separate analyses did not result in a satisfactory grouping of compounds considering their known toxic mechanism as described in literature. However, a combined analysis of multiple data types may hypothetically compensate for missing or unreliable information in any of the single data types. We therefore performed an integrated clustering analysis of all three data sets using the R-based tool iClusterPlus. This indeed improved the grouping results. The compound clusters that were formed by means of iClusterPlus represent groups that show similar gene expression while simultaneously integrating a similarity in structure and protein targets, which corresponds much better with the known mechanism of action of these toxicants. Using an integrative systems biology approach may thus overcome the limitations of the separate analyses when grouping liver toxicants sharing a similar mechanism of toxicity. PMID:27311473

  9. Information-driven structural modelling of protein-protein interactions.

    PubMed

    Rodrigues, João P G L M; Karaca, Ezgi; Bonvin, Alexandre M J J

    2015-01-01

    Protein-protein docking aims at predicting the three-dimensional structure of a protein complex starting from the free forms of the individual partners. As assessed in the CAPRI community-wide experiment, the most successful docking algorithms combine pure laws of physics with information derived from various experimental or bioinformatics sources. Of these so-called "information-driven" approaches, HADDOCK stands out as one of the most successful representatives. In this chapter, we briefly summarize which experimental information can be used to drive the docking prediction in HADDOCK, and then focus on the docking protocol itself. We discuss and illustrate with a tutorial example a "classical" protein-protein docking prediction, as well as more recent developments for modelling multi-body systems and large conformational changes. PMID:25330973

  10. Instruction in information structuring improves Bayesian judgment in intelligence analysts.

    PubMed

    Mandel, David R

    2015-01-01

    An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information) for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts' probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem). Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target's membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments.

  11. Encoding techniques for complex information structures in connectionist systems

    NASA Technical Reports Server (NTRS)

    Barnden, John; Srinivas, Kankanahalli

    1990-01-01

    Two general information encoding techniques called relative position encoding and pattern similarity association are presented. They are claimed to be a convenient basis for the connectionist implementation of complex, short term information processing of the sort needed in common sense reasoning, semantic/pragmatic interpretation of natural language utterances, and other types of high level cognitive processing. The relationships of the techniques to other connectionist information-structuring methods, and also to methods used in computers, are discussed in detail. The rich inter-relationships of these other connectionist and computer methods are also clarified. The particular, simple forms are discussed that the relative position encoding and pattern similarity association techniques take in the author's own connectionist system, called Conposit, in order to clarify some issues and to provide evidence that the techniques are indeed useful in practice.

  12. Instruction in information structuring improves Bayesian judgment in intelligence analysts

    PubMed Central

    Mandel, David R.

    2015-01-01

    An experiment was conducted to test the effectiveness of brief instruction in information structuring (i.e., representing and integrating information) for improving the coherence of probability judgments and binary choices among intelligence analysts. Forty-three analysts were presented with comparable sets of Bayesian judgment problems before and immediately after instruction. After instruction, analysts' probability judgments were more coherent (i.e., more additive and compliant with Bayes theorem). Instruction also improved the coherence of binary choices regarding category membership: after instruction, subjects were more likely to invariably choose the category to which they assigned the higher probability of a target's membership. The research provides a rare example of evidence-based validation of effectiveness in instruction to improve the statistical assessment skills of intelligence analysts. Such instruction could also be used to improve the assessment quality of other types of experts who are required to integrate statistical information or make probabilistic assessments. PMID:25904882

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

    PubMed

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

    2015-02-20

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

  14. Structural-chemical modeling of transition of coals to the plastic state

    SciTech Connect

    A.M. Gyul'maliev; S.G. Gagarin

    2007-02-15

    The structural-chemical simulation of the formation of plastic state during the thermal treatment (pyrolysis, coking) of coals is based on allowance for intermolecular interactions in the organic matter. The feasibility of transition of coals to the plastic state is determined by the ratio between the onset plastic state (softening) and runaway degradation temperatures, values that depend on the petrographic composition and the degree of metamorphism of coals and the distribution of structural and chemical characteristics of organic matter. 33 refs., 8 figs., 2 tabs.

  15. Relationship between chemical structure and the occupational asthma hazard of low molecular weight organic compounds

    PubMed Central

    Jarvis, J; Seed, M; Elton, R; Sawyer, L; Agius, R

    2005-01-01

    Aims: To investigate quantitatively, relationships between chemical structure and reported occupational asthma hazard for low molecular weight (LMW) organic compounds; to develop and validate a model linking asthma hazard with chemical substructure; and to generate mechanistic hypotheses that might explain the relationships. Methods: A learning dataset used 78 LMW chemical asthmagens reported in the literature before 1995, and 301 control compounds with recognised occupational exposures and hazards other than respiratory sensitisation. The chemical structures of the asthmagens and control compounds were characterised by the presence of chemical substructure fragments. Odds ratios were calculated for these fragments to determine which were associated with a likelihood of being reported as an occupational asthmagen. Logistic regression modelling was used to identify the independent contribution of these substructures. A post-1995 set of 21 asthmagens and 77 controls were selected to externally validate the model. Results: Nitrogen or oxygen containing functional groups such as isocyanate, amine, acid anhydride, and carbonyl were associated with an occupational asthma hazard, particularly when the functional group was present twice or more in the same molecule. A logistic regression model using only statistically significant independent variables for occupational asthma hazard correctly assigned 90% of the model development set. The external validation showed a sensitivity of 86% and specificity of 99%. Conclusions: Although a wide variety of chemical structures are associated with occupational asthma, bifunctional reactivity is strongly associated with occupational asthma hazard across a range of chemical substructures. This suggests that chemical cross-linking is an important molecular mechanism leading to the development of occupational asthma. The logistic regression model is freely available on the internet and may offer a useful but inexpensive adjunct to the

  16. Enhancing community detection by using local structural information

    NASA Astrophysics Data System (ADS)

    Xiang, Ju; Hu, Ke; Zhang, Yan; Bao, Mei-Hua; Tang, Liang; Tang, Yan-Ni; Gao, Yuan-Yuan; Li, Jian-Ming; Chen, Benyan; Hu, Jing-Bo

    2016-03-01

    Many real-world networks, such as gene networks, protein-protein interaction networks and metabolic networks, exhibit community structures, meaning the existence of groups of densely connected vertices in the networks. Many local similarity measures in the networks are closely related to the concept of the community structures, and may have a positive effect on community detection in the networks. Here, various local similarity measures are used to extract local structural information, which is then applied to community detection in the networks by using the edge-reweighting strategy. The effect of the local similarity measures on community detection is carefully investigated and compared in various networks. The experimental results show that the local similarity measures are crucial for the improvement of community detection methods, while the positive effect of the local similarity measures is closely related to the networks under study and applied community detection methods.

  17. Register of experts for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Stuhrke, W. F.

    1975-01-01

    This register is comprised of a list of approximately 300 experts from approximately 90 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure: (1) life prediction for structural materials, (2) fracture toughness testing, (3) fracture mechanics analysis; (4) hydrogen embrittlement; (5) protective coatings; and (6) composite materials. The criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. Each author included is listed by organizational affiliation, address, and principal field of expertise. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The register includes two indexes; an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  18. Nanoscale chemical and structural study of Co-based FEBID structures by STEM-EELS and HRTEM

    PubMed Central

    2011-01-01

    Nanolithography techniques in a scanning electron microscope/focused ion beam are very attractive tools for a number of synthetic processes, including the fabrication of ferromagnetic nano-objects, with potential applications in magnetic storage or magnetic sensing. One of the most versatile techniques is the focused electron beam induced deposition, an efficient method for the production of magnetic structures highly resolved at the nanometric scale. In this work, this method has been applied to the controlled growth of magnetic nanostructures using Co2(CO)8. The chemical and structural properties of these deposits have been studied by electron energy loss spectroscopy and high-resolution transmission electron microscopy at the nanometric scale. The obtained results allow us to correlate the chemical and structural properties with the functionality of these magnetic nanostructures. PMID:22085532

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

    PubMed

    Altheimer, Benjamin D; Mehta, Manish A

    2014-04-10

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

  20. Mode of action and the assessment of chemical hazards in the presence of limited data: use of structure-activity relationships (SAR) under TSCA, Section 5.

    PubMed Central

    Auer, C M; Nabholz, J V; Baetcke, K P

    1990-01-01

    Section 5 of the Toxic Substances Control Act (TSCA) requires that manufacturers and importers of new chemicals must submit a Premanufacture Notification (PMN) to the U.S. Environmental Protection Agency 90 days before they intend to commence manufacture or import. Certain information such as chemical identity, uses, etc., must be included in the notification. The submission of test data on the new substance, however, is not required, although any available health and environmental information must be provided. Nonetheless, over half of all PMNs submitted to the agency do not contain any test data; because PMN chemicals are new, no test data is generally available in the scientific literature. Given this situation, EPA has had to develop techniques for hazard assessment that can be used in the presence of limited test data. EPA's approach has been termed "structure-activity relationships" (SAR) and involves three major components: the first is critical evaluation and interpretation of available toxicity data on the chemical; the second component involves evaluation of test data available on analogous substances and/or potential metabolites; and the third component involves the use of mathematical expressions for biological activity known as "quantitative structure-activity relationships" (QSARs). At present, the use of QSARs is limited to estimating physical chemical properties, environmental toxicity, and bioconcentration factors. An important overarching element in EPA's approach is the experience and judgment of scientific assessors in interpreting and integrating the available data and information. Examples are provided that illustrate EPA's approach to hazard assessment for PMN chemicals. PMID:2269224

  1. Predicting metabolic pathways of small molecules and enzymes based on interaction information of chemicals and proteins.

    PubMed

    Gao, Yu-Fei; Chen, Lei; Cai, Yu-Dong; Feng, Kai-Yan; Huang, Tao; Jiang, Yang

    2012-01-01

    Metabolic pathway analysis, one of the most important fields in biochemistry, is pivotal to understanding the maintenance and modulation of the functions of an organism. Good comprehension of metabolic pathways is critical to understanding the mechanisms of some fundamental biological processes. Given a small molecule or an enzyme, how may one identify the metabolic pathways in which it may participate? Answering such a question is a first important step in understanding a metabolic pathway system. By utilizing the information provided by chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions, a novel method was proposed by which to allocate small molecules and enzymes to 11 major classes of metabolic pathways. A benchmark dataset consisting of 3,348 small molecules and 654 enzymes of yeast was constructed to test the method. It was observed that the first order prediction accuracy evaluated by the jackknife test was 79.56% in identifying the small molecules and enzymes in a benchmark dataset. Our method may become a useful vehicle in predicting the metabolic pathways of small molecules and enzymes, providing a basis for some further analysis of the pathway systems.

  2. Enhancement of infrared spectral images for maximizing chemical information by minimizing baseline interferences.

    PubMed

    Bu, Dongsheng; Huffman, Scott W; Seelenbinder, John A; Brown, Chris W

    2005-05-01

    The popularity of spectral images in many areas of analysis has greatly increased during the last decade due to the development of charge-coupled device (CCD) and infrared sensitive cameras. Large amounts of spatial information can be obtained in short periods of time. The general goal in analytical chemistry is to convert spectral images into chemical images, which show the spatial locations of various chemical components. Self-modeling multivariate curve resolution methods can be used to extract pure component spectra from the mixture spectra in images and produce chemical images. However, there is a difficulty in processing infrared spectral images due to large pixel-to-pixel baseline variations. Herein, a method for minimizing baseline interferences using fast Fourier transform (FFT) filtering in both the spectral and spatial domains is discussed. The methodology is demonstrated on a microscopic sample of butter contaminated with non-pathogenic E. coli and on a cross-sectional sample of rabbit aorta containing plaque. The processing to reduce baseline effects improved the spatial resolution without compromising the spectral resolution.

  3. The smell of change: warming affects species interactions mediated by chemical information.

    PubMed

    Sentis, Arnaud; Ramon-Portugal, Felipe; Brodeur, Jacques; Hemptinne, Jean-Louis

    2015-10-01

    Knowledge of how temperature influences an organism's physiology and behaviour is of paramount importance for understanding and predicting the impacts of climate change on species' interactions. While the behaviour of many organisms is driven by chemical information on which they rely on to detect resources, conspecifics, natural enemies and competitors, the effects of temperature on infochemical-mediated interactions remain largely unexplored. Here, we experimentally show that temperature strongly influences the emission of infochemicals by ladybeetle larvae, which, in turn, modifies the oviposition behaviour of conspecific females. Temperature also directly affects female perception of infochemicals and their oviposition behaviour. Our results suggest that temperature-mediated effects on chemical communication can influence flows across system boundaries (e.g. immigration and emigration) and thus alter the dynamics and stability of ecological networks. We therefore argue that investigating the effects of temperature on chemical communication is a crucial step towards a better understanding of the functioning of ecological communities facing rapid environmental changes. PMID:25820469

  4. Qualitative and quantitative structure-activity relationship modelling for predicting blood-brain barrier permeability of structurally diverse chemicals.

    PubMed

    Gupta, S; Basant, N; Singh, K P

    2015-01-01

    In this study, structure-activity relationship (SAR) models have been established for qualitative and quantitative prediction of the blood-brain barrier (BBB) permeability of chemicals. The structural diversity of the chemicals and nonlinear structure in the data were tested. The predictive and generalization ability of the developed SAR models were tested through internal and external validation procedures. In complete data, the QSAR models rendered ternary classification accuracy of >98.15%, while the quantitative SAR models yielded correlation (r(2)) of >0.926 between the measured and the predicted BBB permeability values with the mean squared error (MSE) <0.045. The proposed models were also applied to an external new in vitro data and yielded classification accuracy of >82.7% and r(2) > 0.905 (MSE < 0.019). The sensitivity analysis revealed that topological polar surface area (TPSA) has the highest effect in qualitative and quantitative models for predicting the BBB permeability of chemicals. Moreover, these models showed predictive performance superior to those reported earlier in the literature. This demonstrates the appropriateness of the developed SAR models to reliably predict the BBB permeability of new chemicals, which can be used for initial screening of the molecules in the drug development process.

  5. Formation of copper porous structures under near-equilibrium chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Kornyushchenko, A. S.; Natalich, V. V.; Perekrestov, V. I.

    2016-05-01

    The mechanism of copper structure formation under near-equilibrium conditions in a chemically-active medium-condensate system has been investigated. The desired conditions have been implemented using CVD system. Copper chloride CuCl2 was used as a source material, and mixture of hydrogen with nitrogen served as a working gas. The influence of the evaporation temperature, condensation temperature and state of the growth surface on the porous structures formation has been investigated. It has been established, that the structure formation mechanism is determined by layer-by-layer or normal crystal growth, nucleation and growth of whiskers, and also by partial intergrowth of structural elements.

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

    NASA Astrophysics Data System (ADS)

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

    2001-07-01

    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.

  7. 3D Chemical Similarity Networks for Structure-Based Target Prediction and Scaffold Hopping.

    PubMed

    Lo, Yu-Chen; Senese, Silvia; Damoiseaux, Robert; Torres, Jorge Z

    2016-08-19

    Target identification remains a major challenge for modern drug discovery programs aimed at understanding the molecular mechanisms of drugs. Computational target prediction approaches like 2D chemical similarity searches have been widely used but are limited to structures sharing high chemical similarity. Here, we present a new computational approach called chemical similarity network analysis pull-down 3D (CSNAP3D) that combines 3D chemical similarity metrics and network algorithms for structure-based drug target profiling, ligand deorphanization, and automated identification of scaffold hopping compounds. In conjunction with 2D chemical similarity fingerprints, CSNAP3D achieved a >95% success rate in correctly predicting the drug targets of 206 known drugs. Significant improvement in target prediction was observed for HIV reverse transcriptase (HIVRT) compounds, which consist of diverse scaffold hopping compounds targeting the nucleotidyltransferase binding site. CSNAP3D was further applied to a set of antimitotic compounds identified in a cell-based chemical screen and identified novel small molecules that share a pharmacophore with Taxol and display a Taxol-like mechanism of action, which were validated experimentally using in vitro microtubule polymerization assays and cell-based assays.

  8. Reconstructing Information in Large-Scale Structure via Logarithmic Mapping

    NASA Astrophysics Data System (ADS)

    Szapudi, Istvan

    We propose to develop a new method to extract information from large-scale structure data combining two-point statistics and non-linear transformations; before, this information was available only with substantially more complex higher-order statistical methods. Initially, most of the cosmological information in large-scale structure lies in two-point statistics. With non- linear evolution, some of that useful information leaks into higher-order statistics. The PI and group has shown in a series of theoretical investigations how that leakage occurs, and explained the Fisher information plateau at smaller scales. This plateau means that even as more modes are added to the measurement of the power spectrum, the total cumulative information (loosely speaking the inverse errorbar) is not increasing. Recently we have shown in Neyrinck et al. (2009, 2010) that a logarithmic (and a related Gaussianization or Box-Cox) transformation on the non-linear Dark Matter or galaxy field reconstructs a surprisingly large fraction of this missing Fisher information of the initial conditions. This was predicted by the earlier wave mechanical formulation of gravitational dynamics by Szapudi & Kaiser (2003). The present proposal is focused on working out the theoretical underpinning of the method to a point that it can be used in practice to analyze data. In particular, one needs to deal with the usual real-life issues of galaxy surveys, such as complex geometry, discrete sam- pling (Poisson or sub-Poisson noise), bias (linear, or non-linear, deterministic, or stochastic), redshift distortions, pro jection effects for 2D samples, and the effects of photometric redshift errors. We will develop methods for weak lensing and Sunyaev-Zeldovich power spectra as well, the latter specifically targetting Planck. In addition, we plan to investigate the question of residual higher- order information after the non-linear mapping, and possible applications for cosmology. Our aim will be to work out

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

    PubMed

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

    2014-07-01

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

  10. Bacterial community structure is indicative of chemical inputs in the Upper Mississippi River

    PubMed Central

    Staley, Christopher; Gould, Trevor J.; Wang, Ping; Phillips, Jane; Cotner, James B.; Sadowsky, Michael J.

    2014-01-01

    Local and regional associations between bacterial communities and nutrient and chemical concentrations were assessed in the Upper Mississippi River in Minnesota to determine if community structure was associated with discrete types of chemical inputs associated with different land cover. Bacterial communities were characterized by Illumina sequencing of the V6 region of 16S rDNA and compared to >40 chemical and nutrient concentrations. Local bacterial community structure was shaped primarily by associations among bacterial orders. However, order abundances were correlated regionally with nutrient and chemical concentrations, and were also related to major land coverage types. Total organic carbon and total dissolved solids were among the primary abiotic factors associated with local community composition and co-varied with land cover. Escherichia coli concentration was poorly related to community composition or nutrient concentrations. Abundances of 14 bacterial orders were related to land coverage type, and seven showed significant differences in abundance (P ≤ 0.046) between forested or anthropogenically-impacted sites. This study identifies specific bacterial orders that were associated with chemicals and nutrients derived from specific land cover types and may be useful in assessing water quality. Results of this study reveal the need to investigate community dynamics at both the local and regional scales and to identify shifts in taxonomic community structure that may be useful in determining sources of pollution in the Upper Mississippi River. PMID:25339945

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

    PubMed

    Labudde, D; Leitner, D; Krüger, M; Oschkinat, H

    2003-01-01

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

  12. Bioluminescence tomography with structural and functional a priori information

    NASA Astrophysics Data System (ADS)

    Yan, Han; Unlu, Mehmet B.; Nalcioglu, Orhan; Gulsen, Gultekin

    2010-02-01

    Multispectral bioluminescence tomography (BLT) is one of the seemingly promising approaches to recover 3D tomographic images of bioluminescence source distribution in vivo. In bioluminescence tomography, internal light source, such as luciferase is activated within a volume and multiple wavelength emission data from the internal bioluminescence sources is acquired for reconstruction. The underline non-uniqueness problem associated with non-spectrally resolved intensity-based bioluminescence tomography was demonstrated by Dehghani et al. and it also shown that using a spectrally resolved technique, an accurate solution for the source distribution can be calculated from the measured data if both functional and anatomical a priori information are at hand. Thus it is of great desire to develop an imaging system that is capable of simultaneously acquiring both the optical and structural a priori information as well as acquiring the bioluminescence data. In this paper we present our first combined optical tomography and CT system which constitutes with a cool CCD camera ( perkin elmer "cold blue"), laser launching units and Xray CT( Dxray proto-type). It is capable of acquiring non contact diffuse optical tomography (DOT) data which is used for functional a priori; X-ray CT images which yields the structure information; and BLT images. Physical phantom experiments are designed to verify the system accuracy, repeatability and resolution. These studies shows the feasibility of such imaging system and its potential.

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

    PubMed

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

    2007-01-01

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

  14. Graphene oxide thin films: influence of chemical structure and deposition methodology.

    PubMed

    Hidalgo, R S; López-Díaz, D; Velázquez, M Mercedes

    2015-03-10

    We synthesized graphene oxide sheets of different functionalization by oxidation of two different starting materials, graphite and GANF nanofibers, followed by purification based on alkaline washing. The chemical structure of graphene oxide materials was determined by X-ray photoelectron spectroscopy (XPS), and the nanoplatelets were characterized by ζ potential and dynamic light scattering (DLS) measurements. The XPS results indicated that the chemical structure depends on the starting material. Two different deposition methodologies, Langmuir-Blodgett (LB) and Langmuir-Schaefer (LS), were employed to build the graphene oxide thin films. The film morphology was analyzed by scanning electron microscopy (SEM). The SEM images allow us to conclude that the LB methodology provides the highest coverage. This coverage is almost independent of the chemical composition of sheets. Conversely, the coverage obtained by the LS methodology increases with the percentage of C-O groups attached to sheets. Surface-pressure isotherms of these materials were interpreted according to the Volmer model.

  15. Chemical and structural analysis of the bone-implant interface by TOF-SIMS, SEM, FIB and TEM: Experimental study in animal

    NASA Astrophysics Data System (ADS)

    Palmquist, Anders; Emanuelsson, Lena; Sjövall, Peter

    2012-06-01

    Although bone-anchored implants are widely used in reconstructive medicine, the mechanism of osseointegration is still not fully understood. Novel analytical tools are needed to further understand this process, where both the chemical and structural aspects of the bone-implant interface are important. The aim of this study was to evaluate the advantages of combining time-of-flight secondary ion mass spectroscopy (TOF-SIMS) with optical (LM), scanning (SEM) and transmission electron microscopy (TEM) techniques for studying the bone-implant interface of bone-anchored implants. Laser-modified titanium implants with surrounded bone retrieved after 8 weeks healing in rabbit were dehydrated and resin embedded. Three types of sample preparation were studied to evaluate the information gained by combining TOF-SIMS, SEM, FIB and TEM. The results show that imaging TOF-SIMS can provide detailed chemical information, which in combination with structural information from microscopy methods provide a more complete characterization of anatomical structures at the bone-implant interface. By investigating various sample preparation techniques, it is shown that grinded cross section samples can be used for chemical imaging using TOF-SIMS, if careful consideration of potential preparation artifacts is taken into account. TOF-SIMS analysis of FIB-prepared bone/implant cross section samples show distinct areas corresponding to bone tissue and implant with a sharp interface, although without chemical information about the organic components.

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

    NASA Astrophysics Data System (ADS)

    Deschamps, Frédéric; Khan, Amir

    2016-09-01

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

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

    PubMed

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

    2005-06-01

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

  18. Effect of chemical structure on film-forming properties of seed oils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The film thickness of seven seed oils and two petroleum-based oils of varying chemical structures, was investigated by the method of optical interferometry under pure rolling conditions, and various combinations of entrainment speed (u), load, and temperature. The measured film thickness (h measured...

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

    PubMed Central

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

    2004-01-01

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

  20. The Effect of Three-Dimensional Simulations on the Understanding of Chemical Structures and Their Properties

    ERIC Educational Resources Information Center

    Urhahne, Detlef; Nick, Sabine; Schanze, Sascha

    2009-01-01

    In a series of three experimental studies, the effectiveness of three-dimensional computer simulations to aid the understanding of chemical structures and their properties was investigated. Arguments for the usefulness of three-dimensional simulations were derived from Mayer's generative theory of multimedia learning. Simulations might lead to a…

  1. Electronic Structure of Pi Systems: Part III--Applications in Spectroscopy and Chemical Reactivity.

    ERIC Educational Resources Information Center

    Fox, Marye Anne; Matsen, F. A.

    1985-01-01

    Shows that electronic structure diagrams make more accurate predictions of spectral properties and chemical reactivity for simple pi systems than do either Huckel molecular orbital or valence bond theory alone. Topics addressed include absorption and photoelectron spectra, spin density distribution in radicals, and several problems regarding…

  2. Using Concept Mapping to Uncover Students' Knowledge Structures of Chemical Bonding Concepts

    ERIC Educational Resources Information Center

    Burrows, Nikita L.; Mooring, Suazette Reid

    2015-01-01

    General chemistry is the first undergraduate course in which students further develop their understanding of fundamental chemical concepts. Many of these fundamental topics highlight the numerous conceptual interconnections present in chemistry. However, many students possess incoherent knowledge structures regarding these topics. Therefore,…

  3. Effect of chemically active media on the structure and properties of cubic boron nitride

    SciTech Connect

    Bogatyreva, G.P.; Maevsky, V.M.; Zusmanov, E.R.; Roitsin, A.V.

    1997-10-01

    Properties of cubic boron nitride (cBN) powders from 2 to 200 mm particle size have been studied before and after chemical treatment. Impurity compositions of the bulk and surface, density, magnetic, electrophysical, physicochemical, and radio-spectroscopic characteristics are considered. Structural changes in samples and the origin of the observed effects are discussed.

  4. Correlation between chemical structure and rodent repellency of benzoic acid derivatives

    USGS Publications Warehouse

    Fearn, J.E.; DeWitt, J.B.

    1965-01-01

    Sixty-five benzoic acid derivatives were either prepared or obtained from commercial concerns, tested for rat repellency, and their indices of repellency computed. The data from these tests were considered analytically for any correlation between chemical structure and rat repellency. The results suggest a qualitative relationship which is useful in deciding probability of repellency in other compounds.

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

    SciTech Connect

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

    2010-11-05

    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 groupP that diffracted to atomic-resolution (0.95 {angstrom}), enabling the X-ray structure of kaliotoxin to be determined by direct methods.

  6. Microwave imaging of the breast with incorporated structural information

    NASA Astrophysics Data System (ADS)

    Golnabi, Amir H.; Meaney, Paul M.; Geimer, Shireen D.; Paulsen, Keith D.

    2010-03-01

    Microwave imaging for biomedical applications, especially for early detection of breast cancer and effective treatment monitoring, has attracted increasing interest in last several decades. This fact is due to the high contrast between the dielectric properties of the normal and malignant breast tissues at microwave frequencies ranging from high megahertz to low gigahertz. The available range of dielectric properties for different soft tissue can provide considerable functional information about tissue health. Nonetheless, one of the limiting weaknesses of microwave imaging is, unlike that for conventional modalities such as X-ray CT or MRI, it cannot inherently provide high-resolution images. The conventional modalities can produce highly resolved anatomical information but often cannot provide the functional information required for diagnoses. We have developed a soft prior regularization strategy that can incorporate the prior anatomical information from X-ray CT, MR or other sources, and use it in a way to exploit the resolution of these images while also retaining the functional nature of the microwave images. The anatomical information is first used to create an imaging zone mesh, which segments separate internal substructures, and an associated weighting matrix that numerically groups the values of closely related nodes within the mesh. This information is subsequently used as a regularizing term for the Gauss-Newton reconstruction algorithm. This approach exploits existing technology in a systematic way without making potentially biased assumptions about the properties of visible structures. In this paper we continue our initial investigation on this matter with a series of breast-shaped simulation and phantom experiments.

  7. An Informationally Structured Room for Robotic Assistance †

    PubMed Central

    Tsuji, Tokuo; Mozos, Oscar Martinez; Chae, Hyunuk; Pyo, Yoonseok; Kusaka, Kazuya; Hasegawa, Tsutomu; Morooka, Ken'ichi; Kurazume, Ryo

    2015-01-01

    The application of assistive technologies for elderly people is one of the most promising and interesting scenarios for intelligent technologies in the present and near future. Moreover, the improvement of the quality of life for the elderly is one of the first priorities in modern countries and societies. In this work, we present an informationally structured room that is aimed at supporting the daily life activities of elderly people. This room integrates different sensor modalities in a natural and non-invasive way inside the environment. The information gathered by the sensors is processed and sent to a centralized management system, which makes it available to a service robot assisting the people. One important restriction of our intelligent room is reducing as much as possible any interference with daily activities. Finally, this paper presents several experiments and situations using our intelligent environment in cooperation with our service robot. PMID:25912347

  8. Predicate argument structure frames for modeling information in operative notes.

    PubMed

    Wang, Yan; Pakhomov, Serguei; Melton, Genevieve B

    2013-01-01

    The rich information about surgical procedures contained in operative notes is a valuable data source for improving the clinical evidence base and clinical research. In this study, we propose a set of Predicate Argument Structure (PAS) frames for surgical action verbs to assist in the creation of an information extraction (IE) system to automatically extract details about the techniques, equipment, and operative steps from operative notes. We created PropBank style PAS frames for the 30 top surgical action verbs based on examination of randomly selected sample sentences from 3,000 Laparoscopic Cholecystectomy notes. To assess completeness of the PAS frames to represent usage of same action verbs, we evaluated the PAS frames created on sample sentences from operative notes of 6 other gastrointestinal surgical procedures. Our results showed that the PAS frames created with one type of surgery can successfully denote the usage of the same verbs in operative notes of broader surgical categories. PMID:23920664

  9. Assessment of quantitative structure-activity relationship of toxicity prediction models for Korean chemical substance control legislation

    PubMed Central

    Kim, Kwang-Yon; Shin, Seong Eun; No, Kyoung Tai

    2015-01-01

    Objectives For successful adoption of legislation controlling registration and assessment of chemical substances, it is important to obtain sufficient toxicological experimental evidence and other related information. It is also essential to obtain a sufficient number of predicted risk and toxicity results. Particularly, methods used in predicting toxicities of chemical substances during acquisition of required data, ultimately become an economic method for future dealings with new substances. Although the need for such methods is gradually increasing, the-required information about reliability and applicability range has not been systematically provided. Methods There are various representative environmental and human toxicity models based on quantitative structure-activity relationships (QSAR). Here, we secured the 10 representative QSAR-based prediction models and its information that can make predictions about substances that are expected to be regulated. We used models that predict and confirm usability of the information expected to be collected and submitted according to the legislation. After collecting and evaluating each predictive model and relevant data, we prepared methods quantifying the scientific validity and reliability, which are essential conditions for using predictive models. Results We calculated predicted values for the models. Furthermore, we deduced and compared adequacies of the models using the Alternative non-testing method assessed for Registration, Evaluation, Authorization, and Restriction of Chemicals Substances scoring system, and deduced the applicability domains for each model. Additionally, we calculated and compared inclusion rates of substances expected to be regulated, to confirm the applicability. Conclusions We evaluated and compared the data, adequacy, and applicability of our selected QSAR-based toxicity prediction models, and included them in a database. Based on this data, we aimed to construct a system that can be used

  10. Development of a Fundamental Understanding of Chemical Bonding and Electronic Structure in Spinel Compounds

    SciTech Connect

    Sickafus, K.E.; Wills, J.M.; Chen, S.-P.; Terry, J.H., Jr.; Hartmann, T.; Sheldon, R.I.

    1999-05-14

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos national Laboratory (LANL). Hundreds of ceramic compounds possess the spinel crystal structure and exhibit a remarkable variety of properties, ranging from compounds that are electrical insulators to compounds that are superconducting, or from compounds with ferri- and antiferromagnetic behavior to materials with colossal magnetoresistive characteristics. The unique crystal structure of spinel compounds is in many ways responsible for the widely varying physical properties of spinels. The objective of this project is to investigate the nature of chemical bonding, point defects, and electronic structure in compounds with the spinel crystal structure. Our goal is to understand and predict the stability of the spinel structure as a function of chemical composition, stoichiometry, and cation disorder. The consequences of cation disorder in spinel materials can be profound . The ferromagnetic characteristics of magnesioferrite, for instance, are entirely attributable to disorder on the cation sublattices. Our studies provide insight into the mechanisms of point defect formation and cation disorder and their effects on the electronic band structure and crystal structure of spinel-structure materials. our ultimate objective is to develop a more substantive knowledge of the spinel crystal structure and to promote new and novel uses for spinel compounds. The technical approach to achieve our goals is to combine first-principles calculations with experimental measurements. The structural and electronic properties of spinel samples were experimentally determined primarily with X-ray and neutron scattering, optical and X-ray absorption, and electron energy-loss spectroscopy. Total energy electronic structure calculations were performed to determine structural stability, band structure, density of states, and electron distribution. We also used shell

  11. Development of a Fundamental Understanding of Chemical Bonding and Electronic Structure in Spinel Compounds

    SciTech Connect

    Sickafus, K.E.; Wills, J.M.; Chen, S.-P.; Terry, J.H., Jr.; Hartmann, T.; Sheldon, R.I.

    1999-06-03

    This is the final report of a three-year, Laboratory-Directed Research and Development (LDRD) project at the Los Alamos National Laboratory (LANL). Hundreds of ceramic compounds possess the spinel crystal structure and exhibit a remarkable variety of properties, ranging from compounds that are electrical insulators to compounds that are superconducting, or from compounds with ferri- and antiferromagnetic behavior to materials with colossal magnetoresistive characteristics. The unique crystal structure of spinel compounds is in many ways responsible for the widely varying physical properties of spinels. The objective of this project is to investigate the nature of chemical bonding, point defects, and electronic structure in compounds with the spinel crystal structure. Our goal is to understand and predict the stability of the spinel structure as a function of chemical composition, stoichiometry, and cation disorder. The consequences of cation disorder in spinel materials can be profound . The ferromagnetic characteristics of magnesioferrite, for instance, are entirely attributable to disorder on the cation sublattices. Our studies provide insight into the mechanisms of point defect formation and cation disorder and their effects on the electronic band structure and crystal structure of spinel-structure materials. Our ultimate objective is to develop a more substantive knowledge of the spinel crystal structure and to promote new and novel uses for spinel compounds. The technical approach to achieve our goals is to combine first-principles calculations with experimental measurements. The structural and electronic properties of spinel samples were experimentally determined primarily with X-ray and neutron scattering, optical and X-ray absorption, and electron energy-loss spectroscopy. Total energy electronic structure calculations were performed to determine structural stability, band structure, density of states, and electron distribution. We also used shell

  12. Register of experts for information on mechanics of structural failure

    NASA Technical Reports Server (NTRS)

    Carpenter, J. L., Jr.; Moya, N.

    1973-01-01

    A list of approximately 150 experts from approximately 60 organizations who have published results of theoretical and/or experimental research related to six problem areas in the mechanics of structural failure is presented. Each author included is listed by organizational affiliation, address and principal field of expertise. The initial criteria for the selection of names for the register are recent contributions to the literature, participation in or support of relevant research programs, and referral by peers. The purpose of the register is to present, in easy reference form, sources for dependable information regarding failure modes and mechanisms of aerospace structures. The Register includes two indexes: an alphabetical listing of the experts and an alphabetical listing of the organizations with whom they are affiliated.

  13. Chemical synthesis and structure elucidation of bovine {kappa}-casein (1-44)

    SciTech Connect

    Bansal, Paramjit S.; Grieve, Paul A.; Marschke, Ronald J.; Daly, Norelle L.; McGhie, Emily; Craik, David J.; Alewood, Paul F. . E-mail: p.alewood@imb.uq.edu.au

    2006-02-24

    The caseins ({alpha}{sub s1}, {alpha}{sub s2}, {beta}, and {kappa}) 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 {kappa}-casein, the protein which maintains the micellar structure of the caseins. {kappa}-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{sup 8} to Arg{sup 34}. This is First report which demonstrates extensive secondary structure within the casein class of proteins.

  14. Exploring 3D structural influences of aliphatic and aromatic chemicals on α-cyclodextrin binding.

    PubMed

    Linden, Lukas; Goss, Kai-Uwe; Endo, Satoshi

    2016-04-15

    Binding of solutes to macromolecules is often influenced by steric effects caused by the 3D structures of both binding partners. In this study, the 1:1 α-cyclodextrin (αCD) binding constants (Ka1) for 70 organic chemicals were determined to explore the solute-structural effects on the αCD binding. Ka1 was measured using a three-part partitioning system with either a headspace or a passive sampler serving as the reference phase. The Ka1 values ranged from 1.08 to 4.97 log units. The results show that longer linear aliphatic chemicals form more stable complexes than shorter ones, and that the position of the functional group has a strong influence on Ka1, even stronger than the type of the functional group. Comparison of linear and variously branched aliphatic chemicals indicates that having a sterically unhindered alkyl chain is favorable for binding. These results suggest that only one alkyl chain can enter the binding cavity. Relatively small aromatic chemicals such as 1,3-dichlorobenzene bind to αCD well, while larger ones like tetrachlorobenzene and 3-ring aromatic chemicals show only a weak interaction with αCD, which can be explained by cavity exclusion. The findings of this study help interpret cyclodextrin binding data and facilitate the understanding of binding processes to macromolecules.

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

    NASA Astrophysics Data System (ADS)

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

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

  16. Bridging the pressure gap: Can we get local quantitative structural information at 'near-ambient' pressures?

    NASA Astrophysics Data System (ADS)

    Woodruff, D. P.

    2016-10-01

    In recent years there have been an increasing number of investigations aimed at 'bridging the pressure gap' between UHV surface science experiments on well-characterised single crystal surfaces and the much higher (ambient and above) pressures relevant to practical catalyst applications. By applying existing photon-in/photon-out methods and developing instrumentation to allow photoelectron emission to be measured in higher-pressure sample environments, it has proved possible to obtain surface compositions and spectroscopic fingerprinting of chemical and molecular states of adsorbed species at pressures up to a few millibars. None of these methods, however, provide quantitative structural information on the local adsorption sites of isolated atomic and molecular adsorbate species under these higher-pressure reaction conditions. Methods for gaining this information are reviewed and evaluated.

  17. Chemical and structural stability of lithium-ion battery electrode materials under electron beam.

    PubMed

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

    2014-01-01

    The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi(0.4)Mn(0.4)Co(0.18)Ti(0.02)O2 particles, repeated electron beam irradiation induced a phase transition from an layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.

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

    PubMed Central

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

    2014-01-01

    The investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. However, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi0.4Mn0.4Co0.18Ti0.02O2 particles, repeated electron beam irradiation induced a phase transition from an layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results. PMID:25027190

  19. Tensegrity II. How structural networks influence cellular information processing networks

    NASA Technical Reports Server (NTRS)

    Ingber, Donald E.

    2003-01-01

    The major challenge in biology today is biocomplexity: the need to explain how cell and tissue behaviors emerge from collective interactions within complex molecular networks. Part I of this two-part article, described a mechanical model of cell structure based on tensegrity architecture that explains how the mechanical behavior of the cell emerges from physical interactions among the different molecular filament systems that form the cytoskeleton. Recent work shows that the cytoskeleton also orients much of the cell's metabolic and signal transduction machinery and that mechanical distortion of cells and the cytoskeleton through cell surface integrin receptors can profoundly affect cell behavior. In particular, gradual variations in this single physical control parameter (cell shape distortion) can switch cells between distinct gene programs (e.g. growth, differentiation and apoptosis), and this process can be viewed as a biological phase transition. Part II of this article covers how combined use of tensegrity and solid-state mechanochemistry by cells may mediate mechanotransduction and facilitate integration of chemical and physical signals that are responsible for control of cell behavior. In addition, it examines how cell structural networks affect gene and protein signaling networks to produce characteristic phenotypes and cell fate transitions during tissue development.

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

    DOE PAGES

    Yu, Peiqiang

    2007-01-01

    Synchrotron-based Fourier transform infrared microspectroscopy (S-FTIR) has been developed as a rapid, direct, non-destructive, bioanalytical technique. This technique takes advantage of synchrotron light brightness and small effective source size and is capable of exploring the molecular chemical features and make-up within microstructures of a biological tissue without destruction of inherent structures at ultra-spatial resolutions within cellular dimension. To date there has been very little application of this advanced synchrotron technique to the study of plant and animal tissues' inherent structure at a cellular or subcellular level. In this article, a novel approach was introduced to show the potential of themore » newly developed, advanced synchrotron-based analytical technology, which can be used to reveal molecular structural-chemical features of various plant and animal tissues.« less

  1. Chemical Probes Allow Structural Insight into the Condensation Reaction of Nonribosomal Peptide Synthetases.

    PubMed

    Bloudoff, Kristjan; Alonzo, Diego A; Schmeing, T Martin

    2016-03-17

    Nonribosomal peptide synthetases (NRPSs) synthesize a vast variety of small molecules, including antibiotics, antitumors, and immunosuppressants. The NRPS condensation (C) domain catalyzes amide bond formation, the central chemical step in nonribosomal peptide synthesis. The catalytic mechanism and substrate determinants of the reaction are under debate. We developed chemical probes to structurally study the NRPS condensation reaction. These substrate analogs become covalently tethered to a cysteine introduced near the active site, to mimic covalent substrate delivery by carrier domains. They are competent substrates in the condensation reaction and behave similarly to native substrates. Co-crystal structures show C domain-substrate interactions, and suggest that the catalytic histidine's principle role is to position the α-amino group for nucleophilic attack. Structural insight provided by these co-complexes also allowed us to alter the substrate specificity profile of the reaction with a single point mutation.

  2. Chemical activity induces dynamical force with global structure in a reaction-diffusion-convection system.

    PubMed

    Mahara, Hitoshi; Okada, Koichi; Nomura, Atsushi; Miike, Hidetoshi; Sakurai, Tatsunari

    2009-07-01

    We found a rotating global structure induced by the dynamical force of local chemical activity in a thin solution layer of excitable Belousov-Zhabotinsky reaction coupled with diffusion. The surface flow and deformation associated with chemical spiral waves (wavelength about 1 mm) represents a global unidirectional structure and a global tilt in the entire Petri dish (100 mm in diameter), respectively. For these observations, we scanned the condition of hierarchal pattern selection. From this result, the bromomalonic acid has an important role to induce the rotating global structure. An interaction between a reaction-diffusion process and a surface-tension-driven effect leads to such hierarchal pattern with different scales. PMID:19658764

  3. Electronic structure and chemical bonding of amorphous chromium carbide thin films

    NASA Astrophysics Data System (ADS)

    Magnuson, Martin; Andersson, Matilda; Lu, Jun; Hultman, Lars; Jansson, Ulf

    2012-06-01

    The microstructure, electronic structure and chemical bonding of chromium carbide thin films with different carbon contents have been investigated with high-resolution transmission electron microscopy, electron energy loss spectroscopy and soft x-ray absorption-emission spectroscopies. Most of the films can be described as amorphous nanocomposites with non-crystalline CrCx in an amorphous carbon matrix. At high carbon contents, graphene-like structures are formed in the amorphous carbon matrix. At 47 at.% carbon content, randomly oriented nanocrystallites are formed creating a complex microstructure of three components. The soft x-ray absorption-emission study shows additional peak structures exhibiting non-octahedral coordination and bonding.

  4. Wet-chemical synthesis and applications of non-layer structured two-dimensional nanomaterials

    PubMed Central

    Tan, Chaoliang; Zhang, Hua

    2015-01-01

    Non-layer structured nanomaterials with single- or few-layer thickness have two-dimensional sheet-like structures and possess intriguing properties. Recent years have seen major advances in development of a host of non-layer structured ultrathin two-dimensional nanomaterials such as noble metals, metal oxides and metal chalcogenides. The wet-chemical synthesis has emerged as the most promising route towards high-yield and mass production of such nanomaterials. These nanomaterials are now finding increasing applications in a wide range of areas including catalysis, energy production and storage, sensor and nanotherapy, to name but a few. PMID:26303763

  5. Structure and chemical composition of the dentin-enamel junction analyzed by Confocal Raman Microscopy

    NASA Astrophysics Data System (ADS)

    Desoutter, A.; Salehi, H.; Slimani, A.; Marquet, P.; Jacquot, B.; Tassery, H.; Cuisinier, F. J. G.

    2014-02-01

    The structure and chemical composition of the human dentin-enamel junction (DEJ) was studied using confocal Raman microscopy - a chemical imaging technique. Slices of non-fixed, sound teeth were prepared with an Isomet diamond saw and scanned with Witec Alpha300R system. The combination of different characteristics peaks of phosphate, carbonate and organic matrix (respectively 960, 1072 and 1545 cm-1), generates images representing the chemical composition of the DEJ area. Images are also calculated using peak ratios enabling precise determination of the chemical composition across the DEJ. Then, with two characterized peaks, different pictures are calculated to show the ratio of two components. The images of the spatial distribution of mineral phosphate (960cm-1) to organic matrix (1545 cm-1) ratios, mineral carbonates (1072cm-1) to mineral phosphate ratios; and mineral carbonates to organic matrix ratios were reconstructed. Cross sectional and calculated graphic profile show the variations of the different chemical component ratios through the enamel and the dentin. Phosphate to organic ratio shows an accumulation of organic material under the enamel surface. The cross sectional profile of these pictures shows a high phosphate content compared to enamel in the vicinity of the DEJ. The Confocal Raman imaging technique can be used to further provide full chemical imaging of tooth, particularly of the whole DEJ and to study enamel and dentin decay.

  6. Setting the most robust effluent level under severe uncertainty: application of information-gap decision theory to chemical management.

    PubMed

    Yokomizo, Hiroyuki; Naito, Wataru; Tanaka, Yoshinari; Kamo, Masashi

    2013-11-01

    Decisions in ecological risk management for chemical substances must be made based on incomplete information due to uncertainties. To protect the ecosystems from the adverse effect of chemicals, a precautionary approach is often taken. The precautionary approach, which is based on conservative assumptions about the risks of chemical substances, can be applied selecting management models and data. This approach can lead to an adequate margin of safety for ecosystems by reducing exposure to harmful substances, either by reducing the use of target chemicals or putting in place strict water quality criteria. However, the reduction of chemical use or effluent concentrations typically entails a financial burden. The cost effectiveness of the precautionary approach may be small. Hence, we need to develop a formulaic methodology in chemical risk management that can sufficiently protect ecosystems in a cost-effective way, even when we do not have sufficient information for chemical management. Information-gap decision theory can provide the formulaic methodology. Information-gap decision theory determines which action is the most robust to uncertainty by guaranteeing an acceptable outcome under the largest degree of uncertainty without requiring information about the extent of parameter uncertainty at the outset. In this paper, we illustrate the application of information-gap decision theory to derive a framework for setting effluent limits of pollutants for point sources under uncertainty. Our application incorporates a cost for reduction in pollutant emission and a cost to wildlife species affected by the pollutant. Our framework enables us to settle upon actions to deal with severe uncertainty in ecological risk management of chemicals.

  7. Educational and Commercial Utilization of a Chemical Information Center. Biannual Summary, June 25, 1968 to June 25, 1970.

    ERIC Educational Resources Information Center

    Schwartz, Eugene S.; And Others

    The design, implementation and operation of the Computer Search Center of IIT Research Institute, an information center to educate and link industry and academic institutions to chemical and other scientific information systems, is described. Format conversion, profile input, search and output programs developed over a two-year period are detailed…

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

    PubMed

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

    2016-07-01

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

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

    SciTech Connect

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

    2010-05-17

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

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

    NASA Astrophysics Data System (ADS)

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

    2009-08-01

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

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

    PubMed

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

    2015-11-01

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

  12. Using phylogenetic information and chemical properties to predict species tolerances to pesticides.

    PubMed

    Guénard, Guillaume; Carsten von der Ohe, Peter; Carlisle Walker, Steven; Lek, Sovan; Legendre, Pierre

    2014-08-22

    Direct estimation of species' tolerance to pesticides and other toxic organic substances is a combinatorial problem, because of the large number of species-substance pairs. We propose a statistical modelling approach to predict tolerances associated with untested species-substance pairs, by using models fitted to tested pairs. This approach is based on the phylogeny of species and physico-chemical descriptors of pesticides, with both kinds of information combined in a bilinear model. This bilinear modelling approach predicts tolerance in untested species-compound pairs based on the facts that closely related species often respond similarly to toxic compounds and that chemically similar compounds often have similar toxic effects. The three tolerance models (median lethal concentration after 96 h) used up to 25 aquatic animal species and up to nine pesticides (organochlorines, organophosphates and carbamates). Phylogeny was estimated using DNA sequences, while the pesticides were described by their mode of toxic action and their octanol-water partition coefficients. The models explained 77-84% of the among-species variation in tolerance (log10 LC50). In cross-validation, 84-87% of the predicted tolerances for individual species were within a factor of 10 of the observed values. The approach can also be used to model other species response to multivariate stress factors.

  13. Social learning of predators in the dark: understanding the role of visual, chemical and mechanical information

    PubMed Central

    Manassa, R. P.; McCormick, M. I.; Chivers, D. P.; Ferrari, M. C. O.

    2013-01-01

    The ability of prey to observe and learn to recognize potential predators from the behaviour of nearby individuals can dramatically increase survival and, not surprisingly, is widespread across animal taxa. A range of sensory modalities are available for this learning, with visual and chemical cues being well-established modes of transmission in aquatic systems. The use of other sensory cues in mediating social learning in fishes, including mechano-sensory cues, remains unexplored. Here, we examine the role of different sensory cues in social learning of predator recognition, using juvenile damselfish (Amphiprion percula). Specifically, we show that a predator-naive observer can socially learn to recognize a novel predator when paired with a predator-experienced conspecific in total darkness. Furthermore, this study demonstrates that when threatened, individuals release chemical cues (known as disturbance cues) into the water. These cues induce an anti-predator response in nearby individuals; however, they do not facilitate learnt recognition of the predator. As such, another sensory modality, probably mechano-sensory in origin, is responsible for information transfer in the dark. This study highlights the diversity of sensory cues used by coral reef fishes in a social learning context. PMID:23804616

  14. Use of chemical-mechanical polishing for fabricating photonic bandgap structures

    DOEpatents

    Fleming, James G.; Lin, Shawn-Yu; Hetherington, Dale L.; Smith, Bradley K.

    1999-01-01

    A method is disclosed for fabricating a two- or three-dimensional photonic bandgap structure (also termed a photonic crystal, photonic lattice, or photonic dielectric structure). The method uses microelectronic integrated circuit (IC) processes to fabricate the photonic bandgap structure directly upon a silicon substrate. One or more layers of arrayed elements used to form the structure are deposited and patterned, with chemical-mechanical polishing being used to planarize each layer for uniformity and a precise vertical tolerancing of the layer. The use of chemical-mechanical planarization allows the photonic bandgap structure to be formed over a large area with a layer uniformity of about two-percent. Air-gap photonic bandgap structures can also be formed by removing a spacer material separating the arrayed elements by selective etching. The method is useful for fabricating photonic bandgap structures including Fabry-Perot resonators and optical filters for use at wavelengths in the range of about 0.2-20 .mu.m.

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

    PubMed

    Koch, M A; Waldmann, H

    2006-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Zaharieva, Roussislava

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

  17. Chemical and structural characterisation of DGEBA-based epoxies by time of flight secondary ion mass spectrometry (ToF-SIMS) as a preliminary to polymer interphase characterisation.

    PubMed

    Passlack, Sven; Brodyanski, Alexander; Bock, Wolfgang; Kopnarski, Michael; Presser, Melanie; Geiss, Paul Ludwig; Possart, Gunnar; Steinmann, Paul

    2009-04-01

    Time-of-flight secondary ion mass spectrometry (ToF-SIMS) has become a powerful tool in the field of surface analysis since it provides information about the top few monolayers of a sample, i.e. on the chemical composition of the sample surface. Thus, the general question arises whether a surface-sensitive technique like ToF-SIMS would be appropriate to detect systematic chemical and/or structural changes in organic bulk polymers caused by varying a chemical content of the initial components or by tracking, e.g. curing processes in such materials. It is shown that careful sample preparation and the use of multivariate methods permit the quantitative acquisition of chemical and structural information about bulk polymers from the secondary ion signals. The hardener concentration and a cross-linking coefficient in diglycidyl ether of bisphenol A based epoxies were determined by ToF-SIMS measurements on samples with different resin to hardener ratio and varying curing time. In future work, we will use the developed method to investigate the local composition of adhesively bonded joints. In particular, the mapping of the chemical and structural properties in the so-called interphase will then be of interest.

  18. Spatial data in geographic information system format on agricultural chemical use, land use, cropping practices in the United States

    USGS Publications Warehouse

    Battaglin, W.A.; Goolsby, D.A.

    1995-01-01

    The spatial data in geographic information system format described in this report consist of estimates for all counties in the conterminous United States of the annual use of 96 herbicides in 1989; annual sales of nitrogen fertilizer, in tons, for 1985-91; and agricultural expenses, land use, chemical use, livestock holdings, and cropping practices in 1987. The source information, originally in tabular form, is summarized as digital polygon attribute data in the 18 geographic information system spatial data layers (coverages) provided. The information in these coverages can be used in estimating regional agricultural-chemical use or agricultural practices and in producing visual displays and mapping relative rates of agricultural-chemical use or agricultural practices across broad regions of the United States.

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

    PubMed

    Mueller, Leonard J; Dunn, Michael F

    2013-09-17

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

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

    PubMed

    Sulatha, M S; Natarajan, Upendra

    2011-02-24

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

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

    NASA Astrophysics Data System (ADS)

    Urakov, A. L.

    2016-04-01

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

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

    PubMed

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

    2006-05-17

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

  3. Automated detection of structural alerts (chemical fragments) in (eco)toxicology

    PubMed Central

    Lepailleur, Alban; Poezevara, Guillaume; Bureau, Ronan

    2013-01-01

    This mini-review describes the evolution of different algorithms dedicated to the automated discovery of chemical fragments associated to (eco)toxicological 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. PMID:24688706

  4. Incorporating High-Throughput Exposure Predictions With Dosimetry-Adjusted In Vitro Bioactivity to Inform Chemical Toxicity Testing.

    PubMed

    Wetmore, Barbara A; Wambaugh, John F; Allen, Brittany; Ferguson, Stephen S; Sochaski, Mark A; Setzer, R Woodrow; Houck, Keith A; Strope, Cory L; Cantwell, Katherine; Judson, Richard S; LeCluyse, Edward; Clewell, Harvey J; Thomas, Russell S; Andersen, Melvin E

    2015-11-01

    We previously integrated dosimetry and exposure with high-throughput screening (HTS) to enhance the utility of ToxCast HTS data by translating in vitro bioactivity concentrations to oral equivalent doses (OEDs) required to achieve these levels internally. These OEDs were compared against regulatory exposure estimates, providing an activity-to-exposure ratio (AER) useful for a risk-based ranking strategy. As ToxCast efforts expand (ie, Phase II) beyond food-use pesticides toward a wider chemical domain that lacks exposure and toxicity information, prediction tools become increasingly important. In this study, in vitro hepatic clearance and plasma protein binding were measured to estimate OEDs for a subset of Phase II chemicals. OEDs were compared against high-throughput (HT) exposure predictions generated using probabilistic modeling and Bayesian approaches generated by the U.S. Environmental Protection Agency (EPA) ExpoCast program. This approach incorporated chemical-specific use and national production volume data with biomonitoring data to inform the exposure predictions. This HT exposure modeling approach provided predictions for all Phase II chemicals assessed in this study whereas estimates from regulatory sources were available for only 7% of chemicals. Of the 163 chemicals assessed in this study, 3 or 13 chemicals possessed AERs < 1 or < 100, respectively. Diverse bioactivities across a range of assays and concentrations were also noted across the wider chemical space surveyed. The availability of HT exposure estimation and bioactivity screening tools provides an opportunity to incorporate a risk-based strategy for use in testing prioritization.

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

    NASA Astrophysics Data System (ADS)

    Sun, Jinmei; Guo, Wanlin

    2010-02-01

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

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

    PubMed Central

    Williams, Jane; Walter, Darren; Challen, Kirsty

    2007-01-01

    Background A number of significant chemical incidents occur in the UK each year and may require Emergency Departments (EDs) to receive and manage contaminated casualties. Previously UK EDs have been found to be under-prepared for this, but since October 2005 acute hospital Trusts have had a statutory responsibility to maintain decontamination capacity. We aimed to evaluate the level of preparedness of Emergency Departments in North West England for managing chemical incidents. Methods A face-to-face semi-structured interview was carried out with the Nurse Manager or a nominated deputy in all 18 Emergency Departments in the Region. Results 16/18 departments had a written chemical incident plan but only 7 had the plan available at interview. All had a designated decontamination area but only 11 felt that they were adequately equipped. 12/18 had a current training programme for chemical incident management and 3 had no staff trained in decontamination. 13/18 could contain contaminated water from casualty decontamination and 6 could provide shelter for casualties before decontamination. Conclusion We have identified major inconsistencies in the preparedness of North West Emergency Departments for managing chemical incidents. Nationally recognized standards on incident planning, facilities, equipment and procedures need to be agreed and implemented with adequate resources. Issues of environmental safety and patient dignity and comfort should also be addressed. PMID:18096030

  7. The Generalization of Mutual Information as the Information between a Set of Variables: The Information Correlation Function Hierarchy and the Information Structure of Multi-Agent Systems

    NASA Technical Reports Server (NTRS)

    Wolf, David R.

    2004-01-01

    The topic of this paper is a hierarchy of information-like functions, here named the information correlation functions, where each function of the hierarchy may be thought of as the information between the variables it depends upon. The information correlation functions are particularly suited to the description of the emergence of complex behaviors due to many- body or many-agent processes. They are particularly well suited to the quantification of the decomposition of the information carried among a set of variables or agents, and its subsets. In more graphical language, they provide the information theoretic basis for understanding the synergistic and non-synergistic components of a system, and as such should serve as a forceful toolkit for the analysis of the complexity structure of complex many agent systems. The information correlation functions are the natural generalization to an arbitrary number of sets of variables of the sequence starting with the entropy function (one set of variables) and the mutual information function (two sets). We start by describing the traditional measures of information (entropy) and mutual information.

  8. Determination of the oxidative stability of perfluoropolyalkyl ethers and correlation with chemical structure

    NASA Technical Reports Server (NTRS)

    Helmick, Larry S.; Jones, William R., Jr.

    1992-01-01

    The oxidative stabilities of several perfluoropolyalkyl ethers (PFPAE) with related chemical structures were determined by thermal gravimetric analysis and correlated with their chemical structures. These results show that oxidative stability increases as the number of difluoroformal groups decreases and as trifluoromethyl substituents are added. They are also consistent with a recently proposed intramolecular disproportionation reaction mechanism involving coordination of successive ether oxygens to a Lewis acid. Since polytetrafluoroethylene contains no oxygen, it provides an indication of the upper limit to oxidative stability of PFPAE fluids. These results also show that oxidative decomposition of PFPAE fluids requires the presence of an active metal as well as air. Consequently, it may be possible to minimize decomposition and thus improve oxidative stability by passivating reactive metal surfaces.

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

    SciTech Connect

    Veremeichik, T. F.

    2006-07-15

    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.

  10. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study

    NASA Astrophysics Data System (ADS)

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules.

  11. Molecular structure and vibrational bands and 13C chemical shift assignments of both enmein-type diterpenoids by DFT study.

    PubMed

    Wang, Tao; Wu, Yi fang; Wang, Xue liang

    2014-01-01

    We report here theoretical and experimental studies on the molecular structure and vibrational and NMR spectra of both natural enmein type diterpenoids molecule (6, 7-seco-ent-kaurenes enmein type), isolated from the leaves of Isodon japonica (Burm.f.) Hara var. galaucocalyx (maxin) Hara. The optimized geometry, total energy, NMR chemical shifts and vibrational wavenumbers of epinodosinol and epinodosin have been determined using B3LYP method with 6-311G (d,p) basis set. A complete vibrational assignment is provided for the observed IR spectra of studied compounds. The calculated wavenumbers and 13C c.s. are in an excellent agreement with the experimental values. Quantum chemical calculations at the B3LYP/6-311G (d,p) level of theory have been carried out on studied compounds to obtain a set of molecular electronic properties (MEP,HOMO, LUMO and gap energies ΔEg). Electrostatic potential surfaces have been mapped over the electron density isosurfaces to obtain information about the size, shape, charge density distribution and chemical reactivity of the molecules. PMID:24013676

  12. Electronic Structure Theory and Multi-Structural Statistical Thermodynamics for Computational Chemical Kinetics

    NASA Astrophysics Data System (ADS)

    Papajak, Ewa

    This thesis involves the development and application of methods for accurate computational thermochemistry. It consists of two parts. The first part focuses on the accuracy of the electronic structure methods. In particular, various augmentation schemes for one-electron basis sets are presented and tested for density functional theory (DFT) calculations and for wave function theory (WFT) calculations. The relationship between diffuse basis functions and basis set superposition error is discussed. For WFT, we also compare the efficiency of conventional one-electron basis-sets to that of newly developed explicitly correlated methods. Various ways of approaching the complete basis set limit of WFT calculations are explained, and recommendations are made for the best ways of achieving balance between the basis set size, higher-order correlation, and relativistic corrections. Applications of this work include computation of barrier heights, reaction and bond energies, electron affinities, ionization potentials, and noncovalent interactions. The second part of this thesis focuses on the problem of incorporating multi-structural effects and anharmonicity effects in the torsional modes into partition function calculations, especially by using a new multi-structural torsion (MS-T) method. Applications of the MS-T method include partition functions of molecules and radicals important for combustion research. These partition functions are used to obtain thermodynamic functions that are the most reliable results available to date for these molecules. The multi-structural approach is also applied to two kinetics problems: The hydrogen abstraction from carbon-3 of 1-butanol by hydroperoxyl radical; The 1,5-hydrogen shift isomerization of the 1-butoxyl radical. In both cases multi-structural effects play an important role in the final results.

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

    PubMed

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

    2011-11-15

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

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

    PubMed

    Debska, Barbara; Guzowska-Swider, Barbara

    2003-04-01

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

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

    PubMed

    Spaldonová, R; Corba, J

    1979-01-01

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

  16. Prediction of biodegradability from chemical structure: Modeling or ready biodegradation test data

    SciTech Connect

    Loonen, H.; Lindgren, F.; Hansen, B.

    1999-08-01

    Biodegradation data were collected and evaluated for 894 substances with widely varying chemical structures. All data were determined according to the Japanese Ministry of International Trade and Industry (MITI) I test protocol. The MITI I test is a screening test for ready biodegradability and has been described by Organization for Economic Cooperation and Development (OECD) test guideline 301 C and European Union (EU) test guideline C4F. The chemicals were characterized by a set of 127 predefined structural fragments. This data set was used to develop a model for the prediction of the biodegradability of chemicals under standardized OECD and EU ready biodegradation test conditions. Partial least squares (PLS) discriminant analysis was used for the model development. The model was evaluated by means of internal cross-validation and repeated external validation. The importance of various structural fragments and fragment interactions was investigated. The most important fragments include the presence of a long alkyl chain; hydroxy, ester, and acid groups (enhancing biodegradation); and the presence of one or more aromatic rings and halogen substituents (regarding biodegradation). More than 85% of the model predictions were correct for using the complete data set. The not readily biodegradable predictions were slightly better than the readily biodegradable predictions (86 vs 84%). The average percentage of correct predictions from four external validation studies was 83%. Model optimization by including fragment interactions improve the model predicting capabilities to 89%. It can be concluded that the PLS model provides predictions of high reliability for a diverse range of chemical structures. The predictions conform to the concept of readily biodegradable (or not readily biodegradable) as defined by OECD and EU test guidelines.

  17. Structure activity relationship studies on chemically non-reactive glycine sulfonamide inhibitors of diacylglycerol lipase.

    PubMed

    Chupak, Louis S; Zheng, Xiaofan; Hu, Shuanghua; Huang, Yazhong; Ding, Min; Lewis, Martin A; Westphal, Ryan S; Blat, Yuval; McClure, Andrea; Gentles, Robert G

    2016-04-01

    N-Benzylic-substituted glycine sulfonamides that reversibly inhibit diacylglycerol (DAG) lipases are reported. Detailed herein are the structure activity relationships, profiling characteristics and physico-chemical properties for the first reported series of DAG lipase (DAGL) inhibitors that function without covalent attachment to the enzyme. Highly potent examples are presented that represent valuable tool compounds for studying DAGL inhibition and constitute important leads for future medicinal chemistry efforts.

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

    PubMed

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

    2016-09-01

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

  19. On Added Information for ML Factor Analysis with Mean and Covariance Structures.

    ERIC Educational Resources Information Center

    Yung, Yiu-Fai; Bentler, Peter M.

    1999-01-01

    Using explicit formulas for the information matrix of maximum likelihood factor analysis under multivariate normal theory, gross and net information for estimating the parameters in a covariance structure gained by adding the associated mean structure are defined. (Author/SLD)

  20. Electronic structure and nuclear magnetic resonance chemical shift of solids and surfaces

    NASA Astrophysics Data System (ADS)

    Pfrommer, Bernd Georg

    Several different topics related to the electronic structure of solids and surfaces are discussed in this thesis. With the quasi-Newton algorithm for relaxing crystal structures and a new ab initio method to compute nuclear magnetic resonance (NMR) chemical shifts, numerical methods are developed and implemented to efficiently compute properties related to the electronic structure. These techniques are then applied to a range of different materials. The quasi-Newton method is used to study the recently discovered high-pressure R8 phase of silicon, and the fcc-hcp high-pressure structural phase transition of xenon. Using the pressure-induced magnetic phase transition of a model atomic hydrogen crystal as a test system, the accuracy of density functional theory in both the generalized gradient approximation (GGA) and the local spin density approximation (LSDA) is compared to variational quantum Monte Carlo (VQMC) calculations (1). Finally, for the first time, the NMR chemical shift of extended systems such as amorphous carbon and the hydrogenated diamond (111) surface are calculated from first principles. 1. In the first chapter, a model body-centered cubic (bcc) atomic hydrogen solid is studied using density functional theory in LSDA and GGA. 2. How a quasi-Newton method can be used to simultaneously relax the internal coordinates and lattice parameters of crystals under pressure is the subject of the second chapter. 3. Chapter three presents a detailed ab initio study of the electronic and structural properties of the recently discovered R8 phase of silicon. 4. In chapter four, the fcc-hcp high pressure structural phase transition of xenon is calculated. 5. Chapter five describes a theory for the ab initio computation of the NMR chemical shift in extended systems, using periodic boundary conditions. 6. In chapter six, the NMR chemical shift spectra of diamond, CVD diamond, and diamond-like amorphous carbon are computed from first principles. 7. Unexpected features