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Sample records for chemicals structurally related

  1. 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.

  2. 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).

  3. 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…

  4. Structural Modification of Metal Oxide Nanoparticles in Chemical Vapor Synthesis and Related Properties

    NASA Astrophysics Data System (ADS)

    Lee, Jai-Sung; Lee, Chang-Woo; Lee, Kyoung-No

    2011-10-01

    This paper overviews recent studies on structural modification of metal oxide nanoparticles occurring in the process of chemical vapour condensation (CVC) and related peculiar properties. Hollow nanostructure is controlled at specific process conditions where the pressure in the reactor and the evaporation temperature play an important role in terms of kinematical equilibrium during particle formation and decomposition of precursors in the CVC reactor. As a natural consequence, particle properties also rely on a large surface area from the hollow nanostructure. In this review paper, phase transformation, chemical reactivity and microstructural evolution of nanoparticles are discussed based on hollow nanostructure.

  5. PACSY, a relational database management system for protein structure and chemical shift analysis.

    PubMed

    Lee, Woonghee; Yu, Wookyung; Kim, Suhkmann; Chang, Iksoo; Lee, Weontae; Markley, John L

    2012-10-01

    PACSY (Protein structure And Chemical Shift NMR spectroscopY) is a relational database management system that integrates information from the Protein Data Bank, the Biological Magnetic Resonance Data Bank, and the Structural Classification of Proteins database. PACSY provides three-dimensional coordinates and chemical shifts of atoms along with derived information such as torsion angles, solvent accessible surface areas, and hydrophobicity scales. PACSY consists of six relational table types linked to one another for coherence by key identification numbers. Database queries are enabled by advanced search functions supported by an RDBMS server such as MySQL or PostgreSQL. PACSY enables users to search for combinations of information from different database sources in support of their research. Two software packages, PACSY Maker for database creation and PACSY Analyzer for database analysis, are available from http://pacsy.nmrfam.wisc.edu.

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

    PubMed

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

    2016-01-12

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

  7. 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

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

    PubMed

    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.

  9. Structure-activity relations between alkyl nucleophilic chemicals causing duodenal ulcer and adrenocortical necrosis

    SciTech Connect

    Szabo, S.; Reynolds, E.S.; Unger, S.H.

    1982-10-01

    Structure-activity relationships were qualitatively and quantitatively examined for 56 chemicals (e.g., derivatives of propionitrile, acrylonitrile and cysteamine) which caused duodenal ulcer and/or adrenocortical necrosis in rats. For the first time the duodenal ulcerogenic property of numerous chemicals has been studied in a rational and predictive manner. Ulcerogenic activity was most intense in the carbonitriles attached to two or three carbon backbones and diminished by shortening, lengthening, branching, unsaturating, halogenating or hydroxylating the carbon chains. Different modes of action are implied. Adrenocorticolytic potency was associated with unsaturation of the carbon chain and substitution of the nitrile by thiol or amine radicals. An action of these chemicals on the central nervous system has been suggested.

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

    PubMed Central

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

    2016-01-01

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

  11. Relations between the structure of storage and the transport of chemical compounds in karstic aquifers

    NASA Astrophysics Data System (ADS)

    Vaute, L.; Drogue, C.; Garrelly, L.; Ghelfenstein, M.

    1997-12-01

    Study of the movement of chemical compounds naturally present in the water, or which result from pollution, are examined according to the reservoir structure in karstic aquifers. Structure is represented by a simple geometrical model; slow flow takes place in blocks with a network of low-permeability cracks. The blocks are separated by highly permeable karstic conduits that allow rapid flow, and these form the aquifer drainage system. The karst studied covers 110 km 2. It is fed by an interrupted stream draining a 35 km 2 non-karstic basin, contaminated at the entry to the karst by effluents from a sewage treatment station. The underground water reappears as a resurgence with an annual average flow of approximately 1 m 3 s -1, after an apparent underground course of 8 km in the karst. Several local sources of pollution (effluent from septic tanks) contaminate the underground water during its course. Sixteen measurement operations were performed at 12 water points, between the interrupted stream and the spring. Some sampling points were at drains, and others were in the low-permeability fissured blocks. Comparison at each point of the concentrations of 14 chemical compounds gave the following results: when pollutant discharge occurs in a permeable zone, movement is rapid in the drainage network formed by the karstic conduits, and does not reach the less permeable fissured blocks which are thus protected; however, if discharge is in a low-permeability zone, the flow does not allow rapid movement of the polluted water, and this increases the pollutant concentration at the discharge. This simple pattern can be upset by a reversal of the apparent piezometric gradient between a block and a conduit during floods or pumping; this may reverse flow directions and hence modify the movement of contaminants. The study made it possible to site five boreholes whose positions in the karstic structure were unknown, showing the interest of such an approach for the forecasting of the

  12. Structural and chemical properties of grass lignocelluloses related to conversion for biofuels.

    PubMed

    Anderson, William F; Akin, Danny E

    2008-05-01

    Grass lignocelluloses, such as those in corn and switchgrass, are a major resource in the emerging cellulose-to-ethanol strategy for biofuels. The potential bioconversion of carbohydrates in this potential resource, however, is limited by the associated aromatic constituents within the grass fiber. These aromatics include both lignins, which are phenylpropanoid units of various types, and low-molecular weight phenolic acids. Structural and chemical studies over the years have identified the location and limitation to fiber degradation imposed by a variety of these aromatic barriers. For example, coniferyl lignin appears to be the most effective limitation to biodegradation, existing in xylem cells of vascular tissues. On the other hand, cell walls with syringyl lignin, e.g., leaf sclerenchyma, are often less recalcitrant. Ferulic and p-coumaric acids that are esterified to hemicellulosic sugars constitute a major limitation to biodegradation in non-lignified cell walls in grass fibers, especially warm season species. Non-chemical methods to improve bioconversion of the lignocelluloses through modification of aromatics include: (1) use of lignin-degrading white rot fungi, (2) pretreatment with phenolic acid esterases, and (3) plant breeding to modify cell wall aromatics. In addition to increased availability of carbohydrates for fermentation, separation and collection of aromatics could provide value-added co-products to improve the economics of bioconversion.

  13. The influence of relative humidity on structural and chemical changes during carbonation of hydraulic lime

    SciTech Connect

    El-Turki, A. E-mail: A.El-Turki@bristol.ac.uk; Ball, R.J.; Allen, G.C

    2007-08-15

    Studies monitoring the carbonation of NHL3.5 hydraulic lime are described. Weight-gain measurements, focused ion beam imaging, X-ray diffraction, X-ray photoelectron spectroscopy and Raman spectroscopy were used to monitor changes in structure and composition occurring in lime pastes after exposure to 100% carbon dioxide at relative humidities of 65 and 97%. Lime paste exposed to a relative humidity (R.H.) of 97% indicated a higher carbonation rate compared to paste exposed to 65% R.H. Surface analysis showed that the sample exposed to a relative humidity of 97% was completely carbonated. No calcium hydroxide was detected. A small amount of calcium hydroxide was, however, present at the surface of the sample exposed to 65% R.H. These observations suggest that high humidity results in the formation of a thin layer of crystalline calcium carbonate covering silicate and hydroxide phases. The actual mass increase of the sample also indicated that uncarbonated calcium hydroxide remained beneath the surface.

  14. Computerized crystal-chemical classification of silicates and related materials with CRYSTANA and formula notation for classified structures

    NASA Astrophysics Data System (ADS)

    Klein, Hans-Joachim; Liebau, Friedrich

    2008-09-01

    The computer program CRYSTANA is described which implements a method for the crystal-chemical classification of silicates and related materials. This method is mainly based upon the topological structure of the connected units of a compound and can be applied when the units are built from tetrahedra as coordination polyhedra. The classification parameters and the rules which have to be applied for their determination are summarized and a formalization of the method is provided based upon a finite graph representation of the units. A description of how CRYSTANA can be used and which kind of output it produces is included. From this output crystal-chemical formulas can be derived, which differ slightly from an existing notation in order to meet recommendations of the International Union of Crystallography.

  15. Studies on Brassica carinata seed. 2. Carbohydrate molecular structure in relation to carbohydrate chemical profile, energy values, and biodegradation characteristics.

    PubMed

    Xin, Hangshu; Falk, Kevin C; Yu, Peiqiang

    2013-10-23

    The objectives of this study were to investigate (1) the carbohydrate chemical profile, (2) the energy values, (3) the rumen neutral detergent fiber (NDF) degradation kinetics, (4) the carbohydrate-related functional group structural features using a Fourier transform infrared (FTIR) spectroscopic technique with attenuated total reflectance (ATR), and (5) the correlations between carbohydrate intrinsic structural features and nutritional profiles in three strains of Brassica carinata in yellow and brown seed coats, with comparison to canola seed as a reference. The results showed that yellow B. carinata strains 111000EM and AAC A100 were lower for contents of neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and carbohydrate (CHO) and higher for contents of total digestible nutrients (TDN), energy values, and effective degradable NDF (EDNDF) than brown-seeded 110915EM. In comparison, brown canola seed (Brassica napus L.) had more fiber content and less EDNDF. Also, carinata strains showed significantly different IR intensities in structural carbohydrate (SCHO), cellulosic compounds (CELC), and total CHO profiles. These structural variations might be one of the possible reasons for various fiber profile and biodegradation characteristics for ruminants in oilseeds. However, multivariate analyses within carbohydrate regions indicated there were still some structural relationships among the four oilseed samples. Moreover, the correlation study showed that the changes of CELC and CHO peak intensities were highly related with some changes in CHO chemical profile, energy values, and in situ NDF degradation kinetics in B. carinata and canola seeds. Further study with a large sample size is still necessary to figure out whether CHO molecular spectral information could be used to predict nutrient values and biological behavior in oilseeds.

  16. Comparative studies on the spermatotoxic effects of dinoseb and its structurally related chemicals.

    PubMed

    Takahashi, Ken L; Hojo, Hitoshi; Aoyama, Hiroaki; Teramoto, Shoji

    2004-06-01

    Three dinitrophenolic compounds, dinoseb (DNBP; 7.5 mg/kg b.w.), 4,6-dinitro-o-cresol (DNOC; 4, 7.5, 15 mg/kg b.w.), and 2,4-dinitrophenol (DNP; 7.5, 15, 30 mg/kg b.w.) were administered orally to sexually matured Jcl:SD male rats for 5 consecutive days. Half of the males in each group were necropsied at 3 (D3) and 14 (D14) days after the last dosing, respectively, and examined for the effects of dinitrophenols on spermato-/spermiogenesis. DNBP (7.5 mg/kg), DNOC (15 mg/kg), and DNP (30 mg/kg) caused 1, 5, and 0 deaths, respectively, as well as a decreased body weights during the treatment. Although examinations on D3 revealed no treatment-related alterations, DNBP and DNOC resulted in reduced sperm motility and increased incidence of tailless sperm in the cauda epididymis on D14. DNP also caused slightly increased incidence of tailless sperm on D14. These results demonstrate that DNBP, DNOC, and DNP manifest similar spermatotoxic effects at or around a lethal dose in rats.

  17. Determination of process-related impurities in N-acetylglucosamine prepared by chemical and enzymatic methods: structural elucidation and quantification.

    PubMed

    Kim, Yi Soo; Lee, Sung Joong; Choi, Jin Young; Kim, Yun-Hi; Desta, Kebede Taye; Piao, Zhe; Choi, Su-Lim; Nam, Sang-Jip; Kang, Kyung-Yun; Abd El-Aty, A M; Shin, Yong Chul; Shin, Sung Chul

    2016-07-01

    β-N-acetylglucosamine (β-AG) is a monosaccharide distributed widely in living organisms with various pivotal roles. The presence of particulates and impurities can affect the safety and efficacy of a product for its intended duration of use. Thus, the current study was carried out to identify and quantify the potentially-harmful process related impurities; namely α-N,6-diacetylglucosamine (α-DAG) and α-N-acetylglucosamine (α-AG), derived from the chemical and enzymatic synthesis of β-AG. The impurities were characterized using a high resolution mass spectrometry, a nuclear magnetic resonance spectroscopy, and liquid chromatography-tandem mass spectrometry (LC/MS/MS). The developed method showed a good linearity (R (2) ≥ 0.998), satisfactory precision (≤6.1 % relative standard deviation), intra- and inter-day accuracy (88.20-97.50 %), extraction recovery (89.30-110.50 %), matrix effect (89.70-105.20 %), and stability (92.70-101.60 %). The method was successfully applied to determine the level of α-DAG that was 3.04 and 0.07 % of the total β-AG, following chemical and enzymatic methods, respectively. It can be concluded that the enzymatic rather than the chemical method is more efficient for the synthesis of β-AG. Characterization of impurities heeds the signal for acquiring and evaluating data that establishes biological safety.

  18. Structure and flow properties of syn-rift border faults: The interplay between fault damage and fault-related chemical alteration (Dombjerg Fault, Wollaston Forland, NE Greenland)

    NASA Astrophysics Data System (ADS)

    Kristensen, Thomas B.; Rotevatn, Atle; Peacock, David C. P.; Henstra, Gijs A.; Midtkandal, Ivar; Grundvåg, Sten-Andreas

    2016-11-01

    Structurally controlled, syn-rift, clastic depocentres are of economic interest as hydrocarbon reservoirs; understanding the structure of their bounding faults is of great relevance, e.g. in the assessment of fault-controlled hydrocarbon retention potential. Here we investigate the structure of the Dombjerg Fault Zone (Wollaston Forland, NE Greenland), a syn-rift border fault that juxtaposes syn-rift deep-water hanging-wall clastics against a footwall of crystalline basement. A series of discrete fault strands characterize the central fault zone, where discrete slip surfaces, fault rock assemblages and extreme fracturing are common. A chemical alteration zone (CAZ) of fault-related calcite cementation envelops the fault and places strong controls on the style of deformation, particularly in the hanging-wall. The hanging-wall damage zone includes faults, joints, veins and, outside the CAZ, disaggregation deformation bands. Footwall deformation includes faults, joints and veins. Our observations suggest that the CAZ formed during early-stage fault slip and imparted a mechanical control on later fault-related deformation. This study thus gives new insights to the structure of an exposed basin-bounding fault and highlights a spatiotemporal interplay between fault damage and chemical alteration, the latter of which is often underreported in fault studies. To better elucidate the structure, evolution and flow properties of faults (outcrop or subsurface), both fault damage and fault-related chemical alteration must be considered.

  19. Relation between growth rate and structure of graphene grown in a 4″ showerhead chemical vapor deposition reactor.

    PubMed

    Bekdüz, B; Beckmann, Y; Meier, J; Rest, J; Mertin, W; Bacher, G

    2017-04-07

    The chemical vapor deposition (CVD) growth of graphene on copper is controlled by a complex interplay of substrate preparation, substrate temperature, pressure and flow of reactive gases. A large variety of recipes have been suggested in literature, often quite specific to the reactor, which is being used. Here, we report on a relation between growth rate and quality of graphene grown in a scalable 4″ CVD reactor. The growth rate is varied by substrate pre-treatment, chamber pressure, and methane to hydrogen (CH4:H2) ratio, respectively. We found that at lower growth rates graphene grains become hexagonal rather than randomly shaped, which leads to a reduced defect density and a sheet resistance down to 268 Ω/sq.

  20. Relating Chemical Structure to Cellular Response: An Integrative Analysis of Gene Expression, Bioactivity, and Structural Data Across 11,000 Compounds.

    PubMed

    Chen, B; Greenside, P; Paik, H; Sirota, M; Hadley, D; Butte, A J

    2015-10-01

    A central premise in systems pharmacology is that structurally similar compounds have similar cellular responses; however, this principle often does not hold. One of the most widely used measures of cellular response is gene expression. By integrating gene expression data from Library of Integrated Network-based Cellular Signatures (LINCS) with chemical structure and bioactivity data from PubChem, we performed a large-scale correlation analysis of chemical structures and gene expression profiles of over 11,000 compounds taking into account confounding factors such as biological conditions (e.g., cell line, dose) and bioactivities. We found that structurally similar compounds do indeed yield similar gene expression profiles. There is an ∼20% chance that two structurally similar compounds (Tanimoto Coefficient ≥ 0.85) share significantly similar gene expression profiles. Regardless of structural similarity, two compounds tend to share similar gene expression profiles in a cell line when they are administrated at a higher dose or when the cell line is sensitive to both compounds.

  1. CHEMICAL STRUCTURE INDEXING OF TOXICITY DATA ON ...

    EPA Pesticide Factsheets

    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 that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database. Standardizing chemical structure annotation of public toxicity databases

  2. Structural and Mechanistic Insights into Development of Chemical Tools to Control Individual and Inter-Related Pathological Features in Alzheimer's Disease.

    PubMed

    Lee, Hyuck Jin; Korshavn, Kyle J; Nam, Younwoo; Kang, Juhye; Paul, Thomas J; Kerr, Richard A; Youn, Il Seung; Ozbil, Mehmet; Kim, Kwang S; Ruotolo, Brandon T; Prabhakar, Rajeev; Ramamoorthy, Ayyalusamy; Lim, Mi Hee

    2017-02-21

    To elucidate the involvement of individual and inter-related pathological factors [i.e., amyloid-β (Aβ), metals, and oxidative stress] in the pathogenesis of Alzheimer's disease (AD), chemical tools have been developed. Characteristics required for such tool construction, however, have not been clearly identified; thus, the optimization of available tools or new design has been limited. Here, key structural properties and mechanisms that can determine tools' regulatory reactivities with multiple pathogenic features found in AD are reported. A series of small molecules was built up through rational structural selection and variations onto the framework of a tool useful for in vitro and in vivo metal-Aβ investigation. Variations include: (i) location and number of an Aβ interacting moiety; (ii) metal binding site; and (iii) denticity and structural flexibility. Detailed biochemical, biophysical, and computational studies were able to provide a foundation of how to originate molecular formulas to devise chemical tools capable of controlling the reactivities of various pathological components through distinct mechanisms. Overall, this multidisciplinary investigation illustrates a structure-mechanism-based strategy of tool invention for such a complicated brain disease.

  3. Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

    PubMed Central

    Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

    2016-01-01

    In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable. PMID:27597259

  4. Fungicidal activities of soil humic/fulvic acids as related to their chemical structures in greenhouse vegetable fields with cultivation chronosequence

    NASA Astrophysics Data System (ADS)

    Wu, Meng; Song, Mengya; Liu, Ming; Jiang, Chunyu; Li, Zhongpei

    2016-09-01

    In the background of rapid expansion of plastic greenhouse vegetable production in China, many environmental risks have emerged in recent years. In this study, the soils with a chronosequence in greenhouse vegetable fields were collected and the soil humic acids (HAs) and fluvic acids (FAs) were extracted and purified. The soil HAs and FAs were found to show inhibition activities against phytopathogenic fungi for the first time. Fourier transform infrared spectroscopy was performed to investigate the chemical structures of HAs and FAs. The variation of relative peak areas indicated the chemical structure of HAs become more complex and stable under continuous cultivation. The PCA analysis showed HAs and FAs could be distinctly separated from each other and cultivation years mainly determined the variation. Mantel test and RDA analysis indicated the active components (aliphatic peaks for HAs and COOH, OH peaks for FAs) had positive correlation with the inhibition rates of HAs and FAs against phytopathogenic fungi. According to our research, the active fungicidal components in soil HAs and FAs decreased along with the extension of cultivation years, which made the soil suffer more risk to phytopathogenic fugi. So we believe continuous cultivation too many years in PGVP systems is inadvisable.

  5. Structural and functional effects of selective chemical modifications of Scapharca inaequivalvis haemoglobins in relation to their unique assembly.

    PubMed Central

    Boffi, A; Gattoni, M; Santucci, R; Vecchini, P; Ascoli, F; Chiancone, E

    1987-01-01

    The structural and functional roles of lysyl and thiol groups in the dimeric (HbI) and tetrameric (HbII) haemoglobins from the mollusc Scapharca inaequivalvis have been assessed. In these haemoglobins a unique mode of assembly (the haem-carrying E and F helices form the intersubunit contact of the dimeric unit) is associated with co-operative oxygen binding. Extensive acylation is accompanied by significant haem oxidation. Modification of one or two lysyl residues per chain (corresponding to approximately 20% of the total residues) does not affect the structural and functional properties of both haemoglobins, in line with the proposal that the intersubunit contacts are rich in hydrophobic residues. The modification of the thiol groups does not influence the state of association in both HbI and HbII, despite the location of the cysteine residue common to all polypeptide chains in the vicinity of the major intersubunit contact. The effect on the functional properties depends on the size of the thiol reagent: p-chloromercuribenzoate and phenylmercuric acetate increase the oxygen affinity about 20-fold, but iodoacetamide and mercuric chloride have no effect. Moreover, electrophoresis experiments indicate that p-chloromercuribenzoate is bound in a co-operative fashion, the degree of co-operativity being much higher in the dimeric HbI. Thus, only in HbII are intermediates containing substoichiometric amounts of p-chloromercuribenzoate formed in significant amounts. Their oxygen binding properties show that reaction of only one thiol group/tetramer suffices to alter the oxygen affinity of the molecule. Images Fig. 1. Fig. 3. Fig. 4. PMID:3593205

  6. DSSTox chemical-index files for exposure-related ...

    EPA Pesticide Factsheets

    The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on September 20, 2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare and search the chemical content in each resource, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resources such as PubChem (http://pubchem.ncbi.nlm.nih.gov). The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus (GEO) Series (based on data extracted on September 20, 2008). ARYEXP and GEOGSE contain 887 and 1064 unique chemical substances mapped to 1835 and 2381 chemical exposure-related experiment accession IDs, respectively. The standardized files allow one to assess, compare and search the chemical content in each resource, in the context of the larger DSSTox toxicology data network, as well as across large public cheminformatics resourc

  7. Structure factor in chemical sensorics

    SciTech Connect

    Gutman, E.E.; Belysheva, T.V.; Ryabtsev, S.V.; Chibirova, F.H.

    1996-12-31

    Additions of metals and metal oxides to semiconductor metal oxide films improve usually their gas sensitive sensor properties namely for detection of toxic and flammable gases. The aim of this work is the obtaining of new data and the elucidation of the role of the structure and the chemical nature of promoters in semiconductor gas sensorics. As examples, the authors consider the systems CO-SnO{sub 2} and O{sub 3}-In{sub 2}O{sub 3} sensors. The elaboration of mentioned sensors is aimed at the measurement of small gas constituent in Earth`s and Marth`s atmospheres.

  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. 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).

  10. 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.

  11. Histochemical analysis of the chemical structure of blood group-related carbohydrate chains in serous cells of human submandibular glands using lectin staining and glycosidase digestion.

    PubMed

    Ito, N; Nishi, K; Nakajima, M; Okamura, Y; Hirota, T

    1989-07-01

    Using lectin staining methods in combination with exo- and endo-glycosidase digestion procedures, we analyzed the chemical structure of different types of blood group-related substances in serous cells of formalin-fixed, paraffin-embedded human submandibular glands. Serous cells produced only H antigen; A and B antigens were not present, and the expression of H antigen is dependent on the secretor status of the tissue donor. Although reactivity with Ulex europaeus agglutinin I (UEA-I) was not markedly reduced by alpha-L-fucosidase digestion, an affinity for peanut agglutinin (PNA) was seen after fucosidase digestion in the cells from secretors. In those from nonsecretors, no PNA reactivity appeared after enzyme digestion. On the other hand, sialidase digestion elicited PNA reactivity in serous cells irrespective of the donor's secretor status. PNA reactivity observed after fucosidase or sialidase digestion was susceptible to endo-alpha-N-acetylgalactosaminidase (endo-GalNAc-dase) digestion. SBA reactivity in UEA-I-negative cells from secretors, or in cells from fetuses and newborn infants, was markedly reduced by beta-galactosidase digestion. After galactosidase digestion, reactivity with Griffonia simplicifolia agglutinin II (GSA-II) appeared in the corresponding cells. This GSA-II reactivity was almost completely eliminated by subsequent beta-N-acetylhexosaminidase digestion. Whereas PNA reactivity in these cells was not reduced by beta-galactosidase treatment, it was significantly diminished by endo-GalNAc-dase digestion. These results suggest that at least two kinds of precursor disaccharides are produced in submandibular serous cells, i.e., SBA-reactive D-galactose-(beta 1-3,4)-N-acetyl-D-glucosamine and PNA-reactive D-galactose-(beta 1-3)-N-acetyl-D-galactosamine alpha 1-serine or threonine (O-glycosidically linked Type 3 chain or T antigen). Final fucosylation and synthesis of these two types of precursor chain appear to be under the control of the secretor

  12. Detect changes in lipid-related structure of brown- and yellow-seeded Brassica Carinata seed during rumen fermentation in relation to basic chemical profile using ATR-FT/IR molecular spectroscopy with chemometrics.

    PubMed

    Xin, Hangshu; Yu, Peiqiang

    2014-12-10

    In this experiment, brown- and yellow-seeded Brassica carinata were selected to use as a model to investigate whether there were any changes in lipid-related structure make-up (including CH3 and CH2 asymmetric and symmetric stretching bands ca. 3010-2765cm(-1), unsaturated lipid band ca. 3043-2987cm(-1) and carbonyl CO ester band ca. 1789-1701cm(-1)) of oilseed tissue during rumen in situ incubation using attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FT/IR). Correlations of lipid spectral characteristics with basic chemical profile and multivariate analyses for clarifying structural differences within lipid regions between two carinata seeds were also measured. The results showed that most spectral parameters in both carinata seeds were reduced as incubation time increased. However, the extent of changes in peak intensity of carbonyl CO ester group of brown-seeded carinata was not in fully accordance with that of yellow-seeded carinata. Additionally, these lipid structure features were highly correlated with the concentrations of OM (positively), CP (positively), NDF (negatively) and EE (positively) in carinata seeds after 0, 12, 24 and 48h of incubation. Based on the results from multivariate analyses, neither AHCA nor PCA could produce any distinctions in rumen residues between brown- and yellow-seeded carinata in spectra at lipid regions. It was concluded that besides for original feed samples, spectroscopic technique of ATR-FT/IR could also be used for rumen degradation residues in detecting changes in lipid-related molecular structure make-up. Further studies are needed to explore more details in lipid metabolism during ruminal fermentation with the combined consideration on both metabolic basis and molecular structural basis.

  13. Insight into Amyloid Structure Using Chemical Probes

    PubMed Central

    Reinke, Ashley A.; Gestwicki, Jason E.

    2011-01-01

    Alzheimer’s disease (AD) is a common neurodegenerative disorder characterized by the deposition of amyloids in the brain. One prominent form of amyloid is composed of repeating units of the amyloid-β (Aβ) peptide. Over the past decade, it has become clear that these Aβ amyloids are not homogeneous; rather, they are composed of a series of structures varying in their overall size and shape and the number of Aβ peptides they contain. Recent theories suggest that these different amyloid conformations may play distinct roles in disease, although their relative contributions are still being discovered. Here, we review how chemical probes, such as congo red, thioflavin T and their derivatives, have been powerful tools for better understanding amyloid structure and function. Moreover, we discuss how design and deployment of conformationally selective probes might be used to test emerging models of AD. PMID:21457473

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

    PubMed

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

    2014-07-07

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

  15. 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)

  16. The influence of the substitution pattern on the molecular conformation of ureido-1,2,5-oxadiazoles, related to STAT3 inhibitors: chemical behavior and structural investigation.

    PubMed

    Villa, Stefania; Masciocchi, Daniela; Gelain, Arianna; Meneghetti, Fiorella

    2012-07-01

    Signal transducer and activator of transcription 3 (STAT3) is a protein constitutively activated by aberrant upstream tyrosine kinase activities in a broad spectrum of human solid and blood tumors. Therefore, the availability of drugs affecting STAT3 may have important therapeutic potential for the treatment of cancer. Pursuing our efforts in exploring the influence of the substitution pattern of the ureido 1,2,5-oxadiazole moiety on the molecular conformation, new compounds substituted at positions 3 and 4 on the furazane ring were synthesized. The inhibition properties vs. STAT3 of the novel compounds were evaluated in a dual-luciferase assay, using HCT-116 cells, and the results evidenced a moderate activity only for the compounds endowed with a planar arrangement. Crystallographic studies of the new derivatives were performed in order to evidence the peculiar chemical behavior and to evaluate how structural modulations affected the biological properties.

  17. 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...

  18. Probing structural patterns of ion association and solvation in mixtures of imidazolium ionic liquids with acetonitrile by means of relative (1)H and (13)C NMR chemical shifts.

    PubMed

    Marekha, Bogdan A; Kalugin, Oleg N; Bria, Marc; Idrissi, Abdenacer

    2015-09-21

    Mixtures of ionic liquids (ILs) with polar aprotic solvents in different combinations and under different conditions (concentration, temperature etc.) are used widely in electrochemistry. However, little is known about the key intermolecular interactions in such mixtures depending on the nature of the constituents and mixture composition. In order to systematically address the intermolecular interactions, the chemical shift variation of (1)H and (13)C nuclei has been followed in mixtures of imidazolium ILs 1-n-butyl-3-methylimidazolium tetrafluoroborate (BmimBF4), 1-n-butyl-3-methylimidazolium hexafluorophosphate (BmimPF6), 1-n-butyl-3-methylimidazolium trifluoromethanesulfonate (BmimTfO) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide (BmimTFSI) with molecular solvent acetonitrile (AN) over the entire composition range at 300 K. The concept of relative chemical shift variation is proposed to assess the observed effects on a unified and unbiased scale. We have found that hydrogen bonds between the imidazolium ring hydrogen atoms and electronegative atoms of anions are stronger in BmimBF4 and BmimTfO ILs than those in BmimTFSI and BmimPF6. Hydrogen atom at position 2 of the imidazolium ring is substantially more sensitive to interionic hydrogen bonding than those at positions 4-5 in the case of BmimTfO and BmimTFSI ILs. These hydrogen bonds are disrupted upon dilution in AN due to ion dissociation which is more pronounced at high dilutions. Specific solvation interactions between AN molecules and IL cations are poorly manifested.

  19. Quantum-chemical study of relation of spectral and luminescent properties of positively solvatochromic malononitrile-based merocyanine dyes with their structure

    NASA Astrophysics Data System (ADS)

    Kashapova, E. R.; Bazyl', O. K.; Svetlichnyi, V. A.; Ishchenko, A. A.; Kulinich, A. V.

    2011-01-01

    The electronic structure, the spectra, and the efficiency of photophysical processes of energy deactivation are calculated by a semiempirical method for three positively solvatochromic merocyanine dyes with different polymethine chain lengths. The electronic structure and spectra calculated by different modifications of the INDO method at different molecular geometries are compared, and the optimum geometry of the isolated molecule is chosen. The absorption spectra of dyes are interpreted, including the short-wave-length bands related to transitions to highest excited states. The possibility of a specific electrophilic solvation of these compounds in the ground and fluorescent states, as well as the contribution of specific intermolecular interactions to the total interaction with the medium, is estimated. The role played by the trans-cis isomerization of isolated merocyanine molecules in the deactivation of their excited states is considered.

  20. 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...

  1. Chemical structure and dynamics: Annual report 1993

    SciTech Connect

    Colson, S.D.

    1994-07-01

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

  2. 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.

  3. 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.

  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. Slow processes in viscous liquids: Stress and structural relaxation, chemical reaction freezing, crystal nucleation and microemulsion arrest, in relation to liquid fragility

    NASA Astrophysics Data System (ADS)

    Angell, C. A.; Alba, C.; Arzimanoglou, A.; Fan, J.; Böhmer, R.; Lu, Q.; Sanchez, E.; Senapati, H.; Tatsumisago, M.

    1992-05-01

    We review a variety of measurements on model systems in the medium viscosity range which seem consistent with both thermodynamical (entropy vanishing) and dynamical (mode coupling) origins of glassy behavior and then examine behavior near and below Tg to seek relations between liquid fragility and the non-exponential and non-linear aspects of liquid relaxation processes. We include the model ionic system Ca(NO3)2-KNO3 and analogs, van der Waals systems, and the covalently-bonded system Ge-As-Se in which the relation of liquid properties to the vector percolation concepts of Phillips and Thorpe can be conveniently studied. With some basic phenomenology in the liquid state itself thereby established, we turn attention to longer length-scale processes occurring in viscous liquid media. Among these will be the kinetics of nucleation of crystals, the freezing of microemulsion droplet sizes during continuous cooling of temperature sensitive microemulsions, and the freezing of chemical reactions during continuous cooling or continuous evaporation of solvent. The latter freezings can occur at temperatures which are far above the solvent glass transition temperature depending on solvent fragility, which may be a consideration in the strategies adopted by nature in preservation of plant and insect integrity in cold and arid climates. Finally we consider the slowing down which occurs in liquids with density maxima like water and SiO2 which appear to have, as their low temperature metastable limits, spinodal instabilities (with associated divergences in physical properties) in place of the usual ideal glass transitions. So far little studied for lack of tractable slow systems, these offer a new and challenging arena for relaxation studies.

  6. Protein structure determination from NMR chemical shifts.

    PubMed

    Cavalli, Andrea; Salvatella, Xavier; Dobson, Christopher M; Vendruscolo, Michele

    2007-06-05

    NMR spectroscopy plays a major role in the determination of the structures and dynamics of proteins and other biological macromolecules. Chemical shifts are the most readily and accurately measurable NMR parameters, and they reflect with great specificity the conformations of native and nonnative states of proteins. We show, using 11 examples of proteins representative of the major structural classes and containing up to 123 residues, that it is possible to use chemical shifts as structural restraints in combination with a conventional molecular mechanics force field to determine the conformations of proteins at a resolution of 2 angstroms or better. This strategy should be widely applicable and, subject to further development, will enable quantitative structural analysis to be carried out to address a range of complex biological problems not accessible to current structural techniques.

  7. 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.

  8. Relating hygroscopicity and optical properties to chemical composition and structure of secondary organic aerosol particles generated from the ozonolysis of α-pinene

    NASA Astrophysics Data System (ADS)

    Denjean, C.; Formenti, P.; Picquet-Varrault, B.; Pangui, E.; Zapf, P.; Katrib, Y.; Giorio, C.; Tapparo, A.; Monod, A.; Temime-Roussel, B.; Decorse, P.; Mangeney, C.; Doussin, J. F.

    2015-03-01

    Secondary organic aerosol (SOA) were generated from the ozonolysis of α-pinene in the CESAM (French acronym for Experimental Multiphasic Atmospheric Simulation Chamber) simulation chamber. The SOA formation and aging were studied by following their optical, hygroscopic and chemical properties. The optical properties were investigated by determining the particle complex refractive index (CRI). The hygroscopicity was quantified by measuring the effect of relative humidity (RH) on the particle size (size growth factor, GF) and on the scattering coefficient (scattering growth factor, f(RH)). The oxygen to carbon atomic ratios (O : C) of the particle surface and bulk were used as a sensitive parameter to correlate the changes in hygroscopic and optical properties of the SOA composition during their formation and aging in CESAM. The real CRI at 525 nm wavelength decreased from 1.43-1.60 (±0.02) to 1.32-1.38 (±0.02) during the SOA formation. The decrease in the real CRI correlated to the O : C decrease from 0.68 (±0.20) to 0.55 (±0.16). In contrast, the GF remained roughly constant over the reaction time, with values of 1.02-1.07 (±0.02) at 90% (±4.2%) RH. Simultaneous measurements of O : C of the particle surface revealed that the SOA was not composed of a homogeneous mixture, but contained less oxidised species at the surface which may limit water absorption. In addition, an apparent change in both mobility diameter and scattering coefficient with increasing RH from 0 to 30% was observed for SOA after 14 h of reaction. We postulate that this change could be due to a change in the viscosity of the SOA from a predominantly glassy state to a predominantly liquid state.

  9. Valid Structure Diagrams and Chemical Gibberish

    ERIC Educational Resources Information Center

    Tauber, Stephen J.; Rankin, Kirk

    1972-01-01

    Chemical structure diagrams are considered as utterances in a written language. Two types of grammars are considered for this language: topological grammars and geometric grammars. The hypothesis is presented that compact computer storage may become accessible via grammars. (15 references) (Author/NH)

  10. Chemical Composition of Impact Glass and Suevite-Type Partial Melts of the Rab and Krk Islands and Their Relation with the Proposed Krk Impact Structure in Northern Adriatic, Croatia

    NASA Astrophysics Data System (ADS)

    Čalogović, M.; Marjanac, T.; Fazinić, S.; Strmić-Palinkaš, S.; Tomša, A. M.; Marjanac, L.

    2015-09-01

    Chemical composition of Krk impact structure ejecta represented by incomplete melts and glasses indicate affinity with Pleistocene loess as target lithology, and suggests Pleistocene age of the impact.

  11. Chemical profiling of silicon nitride structures

    NASA Technical Reports Server (NTRS)

    Vasquez, R. P.

    1989-01-01

    X ray photoelectron spectroscopy (XPS), spectroscopic ellipsometry (SE), and scanning electron microscopy (SEM) were used to study structural and chemical inhomogeneities in several electronic materials and device structures of relevance to radiation hard electronics. The systems studied include metal nitride oxide semiconductor (MNOS) structures, silicon oxynitride (SiO(x)N(y)) formed by the thermal nitridation of SiO2, and semiconductor on insulator (SOI) structures. Studies of MNOS structures suggest that the effect of H2 annealing is to make the Si3N4/SiO2 interface less abrupt by causing interdiffusion of silanol and silamine groups with subsequent oxynitride formation. Another effect of the annealing appears to be to relieve the strain at the SiO2/Si interface.

  12. 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.

  13. Rapid High Spatial Resolution Chemical Characterization of Soil Structure to Illuminate Nutrient Distribution Mechanisms Related to Carbon Cycling Using Laser Ablation Aerosol Mass Spectrometry

    NASA Astrophysics Data System (ADS)

    Hicks, R. K.; Alexander, M. L. L.; Newburn, M. K.

    2015-12-01

    Soils contain approximately half of Earth's terrestrial carbon. As such, it is important to understand the factors that control the cycling of this soil organic carbon between the land and the atmosphere. Models that attribute the persistence of soil organic carbon to the intrinsic properties of the molecules themselves are inconsistent with recent observations— for example, materials that are more thermodynamically stable have been found to have a shorter lifetime in soils than ones that are less stable, and vice versa. A new explanation has therefore been posited that invokes ecosystem properties as a whole, and not just intrinsic molecular properties, as the kinetic factor controlling soil carbon dynamics. Because soil dynamics occur on a small scale, techniques with high spatial resolution are required for their study. Existing techniques such as TOF-SIMS require preparation of the sample and introduction into a high vacuum system, and do not address the need to examine large numbers of sample systems without perturbation of chemical and physical properties. To address this analytical challenge, we have coupled a laser ablation (LA) module to an Aerodyne aerosol mass spectrometer (AMS), thereby enabling sample introduction and subsequent measurement of small amounts of soil organic matter by the laser ablation aerosol mass spectrometer (LA-AMS). Due to the adjustable laser beam width, the LA-AMS can probe spot sizes ranging from 1-150 μm in diameter, liberating from 10-100 ng/pulse. With a detection limit of 1 pM, the AMS allows for chemical characterization of the ablated material in terms of elemental ratios, compound classes, and TOC/TOM ratios. Furthermore, the LA-AMS is capable of rapid, in-situ sampling under ambient conditions, thereby eliminating the need for sample processing or transport before analysis. Here, we will present the first results from systematic studies aimed at validating the LA-AMS method as well as results from initial measurements

  14. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... 21 Food and Drugs 9 2014-04-01 2014-04-01 false Definitions relating to listed chemicals. 1300.02....02 Definitions relating to listed chemicals. (a) Any term not defined in this part shall have the... respect to the sale or purchase of a scheduled listed chemical product, means a sale or purchase...

  15. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... 21 Food and Drugs 9 2011-04-01 2011-04-01 false Definitions relating to listed chemicals. 1300.02....02 Definitions relating to listed chemicals. (a) Any term not defined in this part shall have the... international transaction in a listed chemical by— (i) Negotiating contracts; (ii) Serving as an agent...

  16. Chemical Structures at the Desktop: Integrating Drawing Tools with On-Line Registry Files.

    ERIC Educational Resources Information Center

    Baumgras, Jan L.; Rogers, Anne E.

    1995-01-01

    Examines and reviews the ability of various software packages and database systems to recognize and process chemical structures generated by chemical drawing packages, especially the ability of relational database management systems to recognize and process chemical structures from a variety of sources. The need for better standard representations…

  17. Chemical hazards related to clandestine drug laboratories.

    PubMed

    Hughart, J L

    2000-09-01

    The number of clandestine drug laboratories in the United States and Europe has increased as a result of the rising popularity of methamphetamine, Ecstasy, and gamma-hydroxybutyrate among young people and drug abusers, and a shift from complex production procedures for these drugs to simpler "cold cook" methods involving household chemicals. Fires, explosions, corrosive chemicals, and toxic substances at clandestine drug laboratories have caused injuries and deaths among police officers, firefighters, and the public. Impurities in clandestine synthetic drugs have also caused injuries among people consuming the drugs. Information about these hazards should be communicated to public safety professionals and young people to reduce the number of injuries and deaths.

  18. 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.

  19. Chemical structures of 4-oxo-flavonoids in relation to inhibition of oxidized low-density lipoprotein (LDL)-induced vascular endothelial dysfunction.

    PubMed

    Yi, Long; Jin, Xin; Chen, Chun-Ye; Fu, Yu-Jie; Zhang, Ting; Chang, Hui; Zhou, Yong; Zhu, Jun-Dong; Zhang, Qian-Yong; Mi, Man-Tian

    2011-01-01

    Vascular endothelial dysfunction induced by oxidative stress has been demonstrated to be the initiation step of atherosclerosis (AS), and flavonoids may play an important role in AS prevention and therapy. Twenty-three flavonoids categorized into flavones, flavonols, isoflavones, and flavanones, all with 4-oxo-pyronenucleus, were examined for what structural characteristics are required for the inhibitory effects on endothelial dysfunction induced by oxidized low-density lipoprotein (oxLDL). Human vascular endothelial cells EA.hy926 were pretreated with different 4-oxo-flavonoids for 2 hs, and then exposed to oxLDL for another 24 hs. Cell viability and the level of malondialdehyde (MDA), nitric oxide (NO) and soluble intercellular adhesion molecule-1 (sICAM-1) were measured, respectively. Then, correlation analysis and paired comparison were used to analyze the structure-activity relationships. Significant correlations were observed between the number of -OH moieties in total or in B-ring and the inhibitory effectson endothelial dysfunction. Furthermore, 3',4'-ortho-dihydroxyl on B-ring, 3-hydroxyl on C-ring and 2,3-double bondwere correlated closely to the inhibitory effects of flavonolson cell viability decrease and lipid peroxidation. 5,7-meta-dihydroxyl group on A-ring was crucial for the anti-inflammatory effects of flavones and isoflavones in endothelial cells. Moreover, the substituted position of B-ring on C3 rather than C2 was important for NO release. Additionally, hydroxylation at C6 position significantly attenuated the inhibitory effects of 4-oxo-flavonoids on endothelial dysfunction. Our findings indicated that the effective agents in inhibiting endothelial dysfunction include myricetin, quercetin, luteolin, apigenin, genistein and daidzein. Our work might provide some evidence for AS prevention and a strategy for the design of novel AS preventive agents.

  20. Understanding chemical expansion in perovskite-structured oxides.

    PubMed

    Marrocchelli, Dario; Perry, Nicola H; Bishop, Sean R

    2015-04-21

    In this work, chemical expansion in perovskite oxides was characterized in detail, motivated, inter alia, by a desire to understand the lower chemical expansion coefficients observed for perovskites in comparison to fluorite-structured oxides. Changes in lattice parameter and in local atomic arrangements taking place during compositional changes of perovskites, i.e., stoichiometric expansion, were investigated by developing an empirical model and through molecular dynamics and density functional theory atomistic simulations. An accurate empirical expression for predicting lattice constants of perovskites was developed, using a similar approach to previous reports. From this equation, analytical expressions relating chemical expansion coefficients to separate contributions from the cation and anion sublattices, assuming Shannon ionic radii, were developed and used to isolate the effective radius of an oxygen vacancy, rV. Using both experimental and simulated chemical expansion coefficient data, rV for a variety of perovskite compositions was estimated, and trends in rV were studied. In most cases, rV was slightly smaller than or similar to the radius of an oxide ion, but larger than in the fluorite structured materials. This result was in good agreement with the atomistic simulations, showing contractive relaxations of the closest oxide ions towards the oxygen vacancy. The results indicate that the smaller chemical expansion coefficients of perovskites vs. fluorites are largely due to the smaller change in cation radii in perovskites, given that the contraction around the oxygen vacancy appears to be less in this structure. Limitations of applicability for the model are discussed.

  1. Chemical Structures of 4-Oxo-Flavonoids in Relation to Inhibition of Oxidized Low-Density Lipoprotein (LDL)-Induced Vascular Endothelial Dysfunction

    PubMed Central

    Yi, Long; Jin, Xin; Chen, Chun-Ye; Fu, Yu-Jie; Zhang, Ting; Chang, Hui; Zhou, Yong; Zhu, Jun-Dong; Zhang, Qian-Yong; Mi, Man-Tian

    2011-01-01

    Vascular endothelial dysfunction induced by oxidative stress has been demonstrated to be the initiation step of atherosclerosis (AS), and flavonoids may play an important role in AS prevention and therapy. Twenty-three flavonoids categorized into flavones, flavonols, isoflavones, and flavanones, all with 4-oxo-pyronenucleus, were examined for what structural characteristics are required for the inhibitory effects on endothelial dysfunction induced by oxidized low-density lipoprotein (oxLDL). Human vascular endothelial cells EA.hy926 were pretreated with different 4-oxo-flavonoids for 2 hs, and then exposed to oxLDL for another 24 hs. Cell viability and the level of malondialdehyde (MDA), nitric oxide (NO) and soluble intercellular adhesion molecule-1 (sICAM-1) were measured, respectively. Then, correlation analysis and paired comparison were used to analyze the structure–activity relationships. Significant correlations were observed between the number of −OH moieties in total or in B-ring and the inhibitory effectson endothelial dysfunction. Furthermore, 3′,4′-ortho-dihydroxyl on B-ring, 3-hydroxyl on C-ring and 2,3-double bondwere correlated closely to the inhibitory effects of flavonolson cell viability decrease and lipid peroxidation. 5,7-meta-dihydroxyl group on A-ring was crucial for the anti-inflammatory effects of flavones and isoflavones in endothelial cells. Moreover, the substituted position of B-ring on C3 rather than C2 was important for NO release. Additionally, hydroxylation at C6 position significantly attenuated the inhibitory effects of 4-oxo-flavonoids on endothelial dysfunction. Our findings indicated that the effective agents in inhibiting endothelial dysfunction include myricetin, quercetin, luteolin, apigenin, genistein and daidzein. Our work might provide some evidence for AS prevention and a strategy for the design of novel AS preventive agents. PMID:22016603

  2. Relative influence of chemical and non-chemical stressors on invertebrate communities: a case study in the Danube River.

    PubMed

    Rico, Andreu; Van den Brink, Paul J; Leitner, Patrick; Graf, Wolfram; Focks, Andreas

    2016-11-15

    A key challenge for the ecological risk assessment of chemicals has been to evaluate the relative contribution of chemical pollution to the variability observed in biological communities, as well as to identify multiple stressor groups. In this study we evaluated the toxic pressure exerted by >200 contaminants to benthic macroinvertebrates in the Danube River using the Toxic Unit approach. Furthermore, we evaluated correlations between several stressors (chemical and non-chemical) and biological indices commonly used for the ecological status assessment of aquatic ecosystems. We also performed several variation partitioning analyses to evaluate the relative contribution of contaminants and other abiotic parameters (i.e. habitat characteristics, hydromorphological alterations, water quality parameters) to the structural and biological trait variation of the invertebrate community. The results of this study show that most biological indices significantly correlate to parameters related to habitat and physico-chemical conditions, but showed limited correlation with the calculated toxic pressure. The calculated toxic pressure, however, showed little variation between sampling sites, which complicates the identification of pollution-induced effects. The results of this study show that the variation in the structure and trait composition of the invertebrate community are mainly explained by habitat and water quality parameters, whereas hydromorphological alterations play a less important role. Among the water quality parameters, physico-chemical parameters such as suspended solids, nutrients or dissolved oxygen explained a larger part of the variation in the invertebrate community as compared to metals or organic contaminants. Significant correlations exist between some physico-chemical measurements (e.g. nutrients) and some chemical classes (i.e. pharmaceuticals, chemicals related to human presence) which constitute important multiple stressor groups. This study

  3. Chemical biology at the crossroads of molecular structure and mechanism.

    PubMed

    Doudna, Jennifer A

    2005-11-01

    Chemical insight into biological function is the holy grail of structural biology. Small molecules are central players as building blocks, effectors and probes of macromolecular structure and function.

  4. Rule-Based Classification of Chemical Structures by Scaffold.

    PubMed

    Schuffenhauer, Ansgar; Varin, Thibault

    2011-08-01

    Databases for small organic chemical molecules usually contain millions of structures. The screening decks of pharmaceutical companies contain more than a million of structures. Nevertheless chemical substructure searching in these databases can be performed interactively in seconds. Because of this nobody has really missed structural classification of these databases for the purpose of finding data for individual chemical substructures. However, a full deck high-throughput screen produces also activity data for more than a million of substances. How can this amount of data be analyzed? Which are the active scaffolds identified by an assays? To answer such questions systematic classifications of molecules by scaffolds are needed. In this review it is described how molecules can be hierarchically classified by their scaffolds. It is explained how such classifications can be used to identify active scaffolds in an HTS data set. Once active classes are identified, they need to be visualized in the context of related scaffolds in order to understand SAR. Consequently such visualizations are another topic of this review. In addition scaffold based diversity measures are discussed and an outlook is given about the potential impact of structural classifications on a chemically aware semantic web.

  5. Chemical and structural effects of base modifications in messenger RNA

    NASA Astrophysics Data System (ADS)

    Harcourt, Emily M.; Kietrys, Anna M.; Kool, Eric T.

    2017-01-01

    A growing number of nucleobase modifications in messenger RNA have been revealed through advances in detection and RNA sequencing. Although some of the biochemical pathways that involve modified bases have been identified, research into the world of RNA modification -- the epitranscriptome -- is still in an early phase. A variety of chemical tools are being used to characterize base modifications, and the structural effects of known base modifications on RNA pairing, thermodynamics and folding are being determined in relation to their putative biological roles.

  6. 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.

  7. Device for collecting chemical compounds and related methods

    DOEpatents

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

    2013-01-01

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

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

    EPA Pesticide Factsheets

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

  9. Mapping of protein structural ensembles by chemical shifts.

    PubMed

    Baskaran, Kumaran; Brunner, Konrad; Munte, Claudia E; Kalbitzer, Hans Robert

    2010-10-01

    Applying the chemical shift prediction programs SHIFTX and SHIFTS to a data base of protein structures with known chemical shifts we show that the averaged chemical shifts predicted from the structural ensembles explain better the experimental data than the lowest energy structures. This is in agreement with the fact that proteins in solution occur in multiple conformational states in fast exchange on the chemical shift time scale. However, in contrast to the real conditions in solution at ambient temperatures, the standard NMR structural calculation methods as well chemical shift prediction methods are optimized to predict the lowest energy ground state structure that is only weakly populated at physiological temperatures. An analysis of the data shows that a chemical shift prediction can be used as measure to define the minimum size of the structural bundle required for a faithful description of the structural ensemble.

  10. Closing in on Chemical Bonds by Opening up Relativity Theory

    PubMed Central

    Whitney, Cynthia Kolb

    2008-01-01

    This paper develops a connection between the phenomenology of chemical bonding and the theory of relativity. Empirical correlations between electron numbers in atoms and chemical bond stabilities in molecules are first reviewed and extended. Quantitative chemical bond strengths are then related to ionization potentials in elements. Striking patterns in ionization potentials are revealed when the data are viewed in an element-independent way, where element-specific details are removed via an appropriate scaling law. The scale factor involved is not explained by quantum mechanics; it is revealed only when one goes back further, to the development of Einstein’s special relativity theory. PMID:19325749

  11. Closing in on chemical bonds by opening up relativity theory.

    PubMed

    Whitney, Cynthia K

    2008-03-01

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

  12. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  13. Structures and Stabilization Mechanisms in Chemically Stabilized Ceramics

    NASA Astrophysics Data System (ADS)

    Gai-Boyes, Pratibha L.; Saltzberg, Michael A.; Vega, Alexander

    1993-09-01

    Structural complexities and disorder in chemically stabilized cristobalites (CSC), which are room temperature silica-based ceramics, prepared by a wet chemical route, are described. CSC displays many of the structural characteristics of the high temperature cristobalite, elucidated by HREM and X-ray diffraction. In-situ electron diffraction and NMR results suggest that the disorder is structural and is static.

  14. A Java chemical structure editor supporting the Modular Chemical Descriptor Language (MCDL).

    PubMed

    Trepalin, Sergei V; Yarkov, Alexander V; Pletnev, Igor V; Gakh, Andrei A

    2006-03-29

    A compact Modular Chemical Descriptor Language (MCDL) chemical structure editor (Java applet) is described. The small size (approximately 200 KB) of the applet allows its use to display and edit chemical structures in various Internet applications. The editor supports the MCDL format, in which structures are presented in compact canonical form and is capable of restoring bond orders as well as of managing atom and bond drawing overlap. A small database of cage and large cyclic fragment is used for optimal representation of difficult-to-draw molecules. The improved algorithm of the structure diagram generation can be used for other chemical notations that lack atomic coordinates (SMILES, InChI).

  15. Chemical Structural Novelty: On-Targets and Off-Targets

    PubMed Central

    Yera, Emmanuel R.; Cleves, Ann. E.; Jain, Ajay N.

    2011-01-01

    Drug structures may be quantitatively compared based on 2D topological structural considerations and based on 3D characteristics directly related to binding. A framework for combining multiple similarity computations is presented along with its systematic application to 358 drugs with overlapping pharmacology. Given a new molecule along with a set of molecules sharing some biological effect, a single score based on comparison to the known set is produced, reflecting either 2D similarity, 3D similarity, or their combination. For prediction of primary targets, the benefit of 3D over 2D was relatively small, but for prediction of off-targets, the added benefit was large. In addition to assessing prediction, the relationship between chemical similarity and pharmacological novelty was studied. Drug pairs that shared high 3D similarity but low 2D similarity (i.e. a novel scaffold) were shown to be much more likely to exhibit pharmacologically relevant differences in terms of specific protein target modulation. PMID:21916467

  16. Chemical biology of homocysteine thiolactone and related metabolites.

    PubMed

    Jakubowski, Hieronim; Głowacki, Rafał

    2011-01-01

    Protein-related homocysteine (Hcy) metabolism produces Hcy-thiolactone, N-Hcy-protein, and N epsilon-homocysteinyl-lysine (N epsilon-Hcy-Lys). Hcy-thiolactone is generated in an error-editing reaction in protein biosynthesis when Hcy is erroneously selected in place of methionine by methionyl-tRNA synthetase. Hcy-thiolactone, an intramolecular thioester, is chemically reactive and forms isopeptide bonds with protein lysine residues in a process called N-homocysteinylation, which impairs or alters the protein's biological function. The resulting protein damage is exacerbated by a thiyl radical-mediated oxidation. N-Hcy-proteins undergo structural changes leading to aggregation and amyloid formation. These structural changes generate proteins, which are toxic and which induce an autoimmune response. Proteolytic degradation of N-Hcy-proteins generates N epsilon-Hcy-Lys. Levels of Hcy-thiolactone, N-Hcy-protein, and N epsilon-Hcy-Lys increase under pathological conditions in humans and mice and have been linked to cardiovascular and brain disorders. This chapter reviews fundamental biological chemistry of Hcy-thiolactone, N-Hcy-protein, and N epsilon-Hcy-Lys and discusses their clinical significance.

  17. Chemical structure analysis of starch and cellulose derivatives.

    PubMed

    Mischnick, Petra; Momcilovic, Dane

    2010-01-01

    Starch and cellulose are the most abundant and important representatives of renewable biomass. Since the mid-19th century their properties have been changed by chemical modification for commercial and scientific purposes, and there substituted polymers have found a wide range of applications. However, the inherent polydispersity and supramolecular organization of starch and cellulose cause the products resulting from their modification to display high complexity. Chemical composition analysis of these mixtures is therefore a challenging task. Detailed knowledge on substitution patterns is fundamental for understanding structure-property relationships in modified cellulose and starch, and thus also for the improvement of reproducibility and rational design of properties. Substitution patterns resulting from kinetically or thermodynamically controlled reactions show certain preferences for the three available hydroxyl functions in (1→4)-linked glucans. Spurlin, seventy years ago, was the first to describe this in an idealized model, and nowadays this model has been extended and related to the next hierarchical levels, namely, the substituent distribution in and over the polymer chains. This structural complexity, with its implications for data interpretation, and the analytical approaches developed for its investigation are outlined in this article. Strategies and methods for the determination of the average degree of substitution (DS), monomer composition, and substitution patterns at the polymer level are presented and discussed with respect to their limitations and interpretability. Nuclear magnetic resonance spectroscopy, chromatography, capillary electrophoresis, and modern mass spectrometry (MS), including tandem MS, are the main instrumental techniques employed, in combination with appropriate sample preparation by chemical and enzymatic methods.

  18. ACToR Chemical Structure processing using Open Source ...

    EPA Pesticide Factsheets

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

  19. Dissipative structures and related methods

    DOEpatents

    Langhorst, Benjamin R; Chu, Henry S

    2013-11-05

    Dissipative structures include at least one panel and a cell structure disposed adjacent to the at least one panel having interconnected cells. A deformable material, which may comprise at least one hydrogel, is disposed within at least one interconnected cell proximate to the at least one panel. Dissipative structures may also include a cell structure having interconnected cells formed by wall elements. The wall elements may include a mesh formed by overlapping fibers having apertures formed therebetween. The apertures may form passageways between the interconnected cells. Methods of dissipating a force include disposing at least one hydrogel in a cell structure proximate to at least one panel, applying a force to the at least one panel, and forcing at least a portion of the at least one hydrogel through apertures formed in the cell structure.

  20. 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.

  1. Preliminary Problem Definition Study of 48 Munitions-Related Chemicals. Volume II. Propellant-Related Chemicals

    DTIC Science & Technology

    1978-04-01

    million lb/year. This production rate will increase as the dye and rubber market grows and as planned new diphenyl- a;nine production facilities become...this chemical are estimated at Ř million lb/year. In the civilian market , lead salicylate is used as a stabilizer in flooring and other vinyl compounds...these four reports. In addition a general methodology report was also prepared. This report describes the search strategy and evaluation methodology

  2. Detect changes in protein structure of carinata meal during rumen fermentation in relation to basic chemical profile and comparison with canola meal using ATR-FT/IR molecular spectroscopy with chemometrics

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Yu, Peiqiang

    2013-08-01

    As far as we know, no study has been carried out on whether protein structure changes in the feed during rumen fermentation from other research team. This study was conducted to characterize protein structure spectral changes in carinata meal during ruminal fermentation using Fourier transform infrared spectroscopy (FT/IR) technique with ATR. The objectives were to find out whether (1) protein internal structure (in terms of protein amide profile and protein secondary structure profile) changed after in situ ruminal fermentation at 0, 12, 24 and 48 h in carinata meal and conventional canola meal was used as a reference; (2) there was any correlation between protein spectral parameters and basic chemical profile in in situ rumen residue samples; and (3) the protein structural chemical make-up of carinata meal differed from canola meal during 48 h rumen incubation. The results showed that protein structure features in both carinata meal and canola meal were altered as incubation time increased (P < 0.0001) and linear and curvilinear relationships (P < 0.05) on amide II height and area, height and area ratio of amide I and II as well as height ratio of α-helix and β-sheet were observed within 48 h ruminal fermentation. And the amide I height and area as well as α-helix height and β-sheet height were in the highest level of IR absorbance at 0 h and then gradually declined linearly (P < 0.0001) by 30-38% after 48 h incubation. These results indicated that not only quantities decreased but also inherent structure changed in protein chemical make-up during ruminal fermentation. Meanwhile, strong correlations were found between protein spectral parameters and some basic nutrients profile such as CP (positively) and NDF (negatively). And both AHCA and PCA results showed that in situ rumen residues from carinata meal was not distinguished from those from canola meal, suggesting some relationship in structural make-up exhibited between them within protein region during 48

  3. Detect changes in protein structure of carinata meal during rumen fermentation in relation to basic chemical profile and comparison with canola meal using ATR-FT/IR molecular spectroscopy with chemometrics.

    PubMed

    Xin, Hangshu; Yu, Peiqiang

    2013-08-01

    As far as we know, no study has been carried out on whether protein structure changes in the feed during rumen fermentation from other research team. This study was conducted to characterize protein structure spectral changes in carinata meal during ruminal fermentation using Fourier transform infrared spectroscopy (FT/IR) technique with ATR. The objectives were to find out whether (1) protein internal structure (in terms of protein amide profile and protein secondary structure profile) changed after in situ ruminal fermentation at 0, 12, 24 and 48 h in carinata meal and conventional canola meal was used as a reference; (2) there was any correlation between protein spectral parameters and basic chemical profile in in situ rumen residue samples; and (3) the protein structural chemical make-up of carinata meal differed from canola meal during 48 h rumen incubation. The results showed that protein structure features in both carinata meal and canola meal were altered as incubation time increased (P<0.0001) and linear and curvilinear relationships (P<0.05) on amide II height and area, height and area ratio of amide I and II as well as height ratio of α-helix and β-sheet were observed within 48 h ruminal fermentation. And the amide I height and area as well as α-helix height and β-sheet height were in the highest level of IR absorbance at 0 h and then gradually declined linearly (P<0.0001) by 30-38% after 48 h incubation. These results indicated that not only quantities decreased but also inherent structure changed in protein chemical make-up during ruminal fermentation. Meanwhile, strong correlations were found between protein spectral parameters and some basic nutrients profile such as CP (positively) and NDF (negatively). And both AHCA and PCA results showed that in situ rumen residues from carinata meal was not distinguished from those from canola meal, suggesting some relationship in structural make-up exhibited between them within protein region during 48 h

  4. The Effects of CW (Chemical Warfare)-Related Chemicals on Social Behavior and Performance

    DTIC Science & Technology

    1985-10-01

    g-o3oi 9\\a AD- The Effects of CW-Related Che~icala onne k So1ial Behavior and Performancec 0) 0o Annual Report Bradford N. Punnell W. Ben Iturrian...11. TITLE (include Security Classification) The Effects of CW-Related Chemicals on Social Behavior and Performance 12. PERSONAL AUTHOR(S) Bradford N...performance that will be sensitive to the effects Ofb/C•4 -related chemicals considered Tor use as l antidotes or prophyractics against-a agents

  5. Chemical-induced disease relation extraction with various linguistic features

    PubMed Central

    Gu, Jinghang; Qian, Longhua; Zhou, Guodong

    2016-01-01

    Understanding the relations between chemicals and diseases is crucial in various biomedical tasks such as new drug discoveries and new therapy developments. While manually mining these relations from the biomedical literature is costly and time-consuming, such a procedure is often difficult to keep up-to-date. To address these issues, the BioCreative-V community proposed a challenging task of automatic extraction of chemical-induced disease (CID) relations in order to benefit biocuration. This article describes our work on the CID relation extraction task on the BioCreative-V tasks. We built a machine learning based system that utilized simple yet effective linguistic features to extract relations with maximum entropy models. In addition to leveraging various features, the hypernym relations between entity concepts derived from the Medical Subject Headings (MeSH)-controlled vocabulary were also employed during both training and testing stages to obtain more accurate classification models and better extraction performance, respectively. We demoted relation extraction between entities in documents to relation extraction between entity mentions. In our system, pairs of chemical and disease mentions at both intra- and inter-sentence levels were first constructed as relation instances for training and testing, then two classification models at both levels were trained from the training examples and applied to the testing examples. Finally, we merged the classification results from mention level to document level to acquire final relations between chemicals and diseases. Our system achieved promising F-scores of 60.4% on the development dataset and 58.3% on the test dataset using gold-standard entity annotations, respectively. Database URL: https://github.com/JHnlp/BC5CIDTask PMID:27052618

  6. Chemical-induced disease relation extraction with various linguistic features.

    PubMed

    Gu, Jinghang; Qian, Longhua; Zhou, Guodong

    2016-01-01

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

  7. 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

  8. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... not a customer for purposes of this definition. (13) The term established record as an importer means... 21 Food and Drugs 9 2010-04-01 2010-04-01 false Definitions relating to listed chemicals. 1300.02 Section 1300.02 Food and Drugs DRUG ENFORCEMENT ADMINISTRATION, DEPARTMENT OF JUSTICE DEFINITIONS §...

  9. Why relevant chemical information cannot be exchanged without disclosing structures

    NASA Astrophysics Data System (ADS)

    Filimonov, Dmitry; Poroikov, Vladimir

    2005-09-01

    Both society and industry are interested in increasing the safety of pharmaceuticals. Potentially dangerous compounds could be filtered out at early stages of R&D by computer prediction of biological activity and ADMET characteristics. Accuracy of such predictions strongly depends on the quality & quantity of information contained in a training set. Suggestion that some relevant chemical information can be added to such training sets without disclosing chemical structures was generated at the recent ACS Symposium. We presented arguments that such safety exchange of relevant chemical information is impossible. Any relevant information about chemical structures can be used for search of either a particular compound itself or its close analogues. Risk of identifying such structures is enough to prevent pharma industry from relevant chemical information exchange.

  10. Profiling differences in chemical composition of brain structures using Raman spectroscopy.

    PubMed

    Daković, Marko; Stojiljković, Aleksandra S; Bajuk-Bogdanović, Danica; Starčević, Ana; Puškaš, Laslo; Filipović, Branislav; Uskoković-Marković, Snežana; Holclajtner-Antunović, Ivanka

    2013-12-15

    Raman spectroscopy enables non-invasive investigation of chemical composition of biological tissues. Due to similar chemical composition, the analysis of Raman spectra of brain structures and assignment of their spectral features to chemical constituents presents a particular challenge. In this study we demonstrate that standard and independent component analysis of Raman spectra is capable of assessment of differences in chemical composition between functionally related gray and white matter structures. Our results show the ability of Raman spectroscopy to successfully depict variation in chemical composition between structurally similar and/or functionally connected brain structures. The observed differences were attributed to variations in content of proteins and lipids in these structures. Independent component analysis enabled separation of contributions of major constituents in spectra and revealed spectral signatures of low-concentration metabolites. This provided finding of discrepancies between structures of striatum as well as between white matter structures. Raman spectroscopy can provide information about variations in contents of major chemical constituents in brain structures, while the application of independent component analysis performed on obtained spectra can help in revealing minute differences between closely related brain structures.

  11. 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.

  12. 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

  13. Symmetry relations in chemical kinetics arising from microscopic reversibility.

    PubMed

    Adib, Artur B

    2006-01-20

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

  14. Nematic films at chemically structured surfaces

    NASA Astrophysics Data System (ADS)

    Silvestre, N. M.; Telo da Gama, M. M.; Tasinkevych, M.

    2017-02-01

    We investigate theoretically the morphology of a thin nematic film adsorbed at flat substrate patterned by stripes with alternating aligning properties, normal and tangential respectively. We construct a simple ‘exactly-solvable’ effective interfacial model where the liquid crystal distortions are accounted for via an effective interface potential. We find that chemically patterned substrates can strongly deform the nematic-air interface. The amplitude of this substrate-induced undulations increases with decreasing average film thickness and with increasing surface pattern pitch. We find a regime where the interfacial deformation may be described in terms of a material-independent universal scaling function. Surprisingly, the predictions of the effective interfacial model agree semi-quantitatively with the results of the numerical solution of a full model based on the Landau-de Gennes theory coupled to a square-gradient phase field free energy functional for a two phase system.

  15. Chemical Profiling of Silicon Nitride Structures

    DTIC Science & Technology

    1989-06-01

    Zip Can*) 7b ADORESSC, State. anid 71PCoaej 4.800 Oak Grove Drive ?asadena CA 91103 Hanscom AFB MA 01721-S-COC 3a NAM );: ION SPCNSOR!NG 130 OFItSYMBOL...I Chapter 2: Studies of Metal -Nitride-Oxide-Semiconductor (MNOS) Structures ................................ 12 Chapter 3...3 88 II. SO Formed by Ion Implantation .......................................................... 8 89 Ill. SO

  16. New Chemicals Program Review of Alternatives for PFOA and Related Chemicals

    EPA Pesticide Factsheets

    In 2006, EPA and the eight major companies in the industry launched the 2010/15 PFOA Stewardship Program, in which companies committed to reduce global facility emissions and product content of PFOA and related chemicals by 95 percent by 2010, and to work

  17. 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

  18. THE INVESTIGATION OF STRUCTURAL PROPERTIES AND CHEMICAL TRANSFORMATIONS OF CARBAZOLE AND SOME OF ITS DERIVATIVES

    DTIC Science & Technology

    AZOLES, ALKYL RADICALS, AMIDES, CHEMICAL RADICALS, CHEMICAL REACTIONS , GLYCINE, HETEROCYCLIC COMPOUNDS, METHYL RADICALS, MOLECULAR STRUCTURE, ULTRAVIOLET SPECTROPHOTOMETERS, ULTRAVIOLET SPECTROSCOPY.

  19. 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.

  20. 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.

  1. Mining chemical structural information from the drug literature.

    PubMed

    Banville, Debra L

    2006-01-01

    It is easier to find too many documents on a life science topic than to find the right information inside these documents. With the application of text data mining to biological documents, it is no surprise that researchers are starting to look at applications that mine out chemical information. The mining of chemical entities--names and structures--brings with it some unique challenges, which commercial and academic efforts are beginning to address. Ultimately, life science text data mining applications need to focus on the marriage of biological and chemical information.

  2. Environmental chemicals and breast cancer risk--a structural chemistry perspective.

    PubMed

    Weyandt, Jamie; Ellsworth, Rachel E; Hooke, Jeffrey A; Shriver, Craig D; Ellsworth, Darrell L

    2008-01-01

    In modern industrialized societies, people are exposed to thousands of naturally occurring and synthetic chemicals throughout their lifetime. Although certain occupational chemicals are known to be carcinogenic in humans, it has been difficult to definitively determine the adverse health effects of many environmental pollutants due to their tremendous chemical diversity and absence of a consistent structural motif. Many environmental chemicals are metabolized in the body to reactive intermediates that readily react with DNA to form modified bases known as adducts, while other compounds mimic the biological function of estrogen. Because environmental chemicals tend to accumulate in human tissues and have carcinogenic and/or estrogenic properties, there is heightened interest in determining whether environmental chemicals increase risk for endocrine-related cancers, including breast cancer. Breast cancer is the most common cancer in women worldwide, but established risk factors account for a relatively small proportion of cases and causative factors remain ambiguous and poorly defined. In this review, we outline the structural chemistry of environmental contaminants, describe mechanisms of carcinogenesis and molecular pathways through which these chemicals may exert detrimental health effects, review current knowledge of relationships between chemicals and breast cancer risk, and highlight future directions for research on environmental contributions to breast cancer. Improved understanding of the relationship between environmental chemicals and breast cancer will help to educate the general public about real and perceived dangers of these pollutants in our environment and has the potential to reduce individual risk by changing corporate practices and improving public health policies.

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

    NASA Astrophysics Data System (ADS)

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

    2014-07-01

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

  4. 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.

  5. 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

  6. Property distribution of drug-related chemical databases*

    NASA Astrophysics Data System (ADS)

    Oprea, Tudor I.

    2000-04-01

    The process of compound selection and prioritization is crucial for both combinatorial chemistry (CBC) and high throughput screening (HTS). Compound libraries have to be screened for unwanted chemical structures, as well as for unwanted chemical properties. Property extrema can be eliminated by using property filters, in accordance with their actual distribution. Property distribution was examined in the following compound databases: MACCS-II Drug Data Report (MDDR), Current Patents Fast-alert, Comprehensive Medicinal Chemistry, Physician Desk Reference, New Chemical Entities, and the Available Chemical Directory (ACD). The ACDF and MDDRF subsets were created by removing reactive functionalities from the ACD and MDDR databases, respectively. The ACDF subset was further filtered by keeping only molecules with a `drug-like' score [Ajay et al., J. Med. Chem., 41 (1998) 3314; Sadowski and Kubinyi, J. Med. Chem., 41 (1998) 3325] below 0.8. The following properties were examined: molecular weight (MW), the calculated octanol/water partition coefficient (CLOGP), the number of rotatable (RTB) and rigid bonds (RGB), the number of rings (RNG), and the number of hydrogen bond donors (HDO) and acceptors (HAC). Of these, MW and CLOGP follow a Gaussian distribution, whereas all other descriptors have an asymmetric (truncated Gaussian) distribution. Four out of five compounds in ACDF and MDDRF pass the `rule of 5' test, a probability scheme that estimates oral absorption proposed by Lipinski et al. [Adv. Drug Deliv. Rev., 23 (1997) 3]. Because property distributions of HDO, HAC, MW and CLOGP (used in the `rule of 5' test) do not differ significantly between these datasets, the `rule of 5' does not distinguish `drugs' from `nondrugs'. Therefore, Pareto analyses were performed to examine skewed distributions in all compound collections. Seventy percent of the `drug-like' compounds were found between the following limits: 0 ≤ HDO ≤ 2, 2 ≤ HAC ≤ 9, 2 ≤ RTB ≤ 8, and 1

  7. 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.

  8. 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)

  9. 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)

  10. 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…

  11. Chemical Vapor Deposition Growth of Graphene and Related Materials

    NASA Astrophysics Data System (ADS)

    Kitaura, Ryo; Miyata, Yasumitsu; Xiang, Rong; Hone, James; Kong, Jing; Ruoff, Rodney S.; Maruyama, Shigeo

    2015-12-01

    Research on atomic layers including graphene, hexagonal boron nitride (hBN), transition metal dichalcogenides (TMDCs) and their heterostructures has attracted a great deal of attention. Chemical vapor deposition (CVD) can provide large-area structure-defined high-quality atomic layer samples, which have considerably contributed to the recent advancement of atomic-layer research. In this article, we focus on the CVD growth of various atomic layers and review recent progresses including (1) the CVD growth of graphene using methane and ethanol as carbon sources, (2) the CVD growth of hBN using borazine and ammonia borane, (3) the CVD growth of various TMDCs using single and multi-furnace methods, and (4) CVD growth of vertical and lateral heterostructures such as graphene/hBN, MoS2/graphite, WS2/hBN and MoS2/WS2.

  12. 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.

  13. Chemical structure indexing of toxicity data on the internet: moving toward a flat world.

    PubMed

    Richard, Ann M; Gold, Lois Swirsky; Nicklaus, Marc C

    2006-05-01

    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 that are accelerating the pace of this transformation, with particular reference to toxicology-related chemical information. Chemical content annotators, structure locator services, large structure/data aggregator web sites, structure browsers, International Union of Pure and Applied Chemistry (IUPAC) International Chemical Identifier (InChI) codes, toxicity data models and public chemical/biological activity profiling initiatives are all playing a role in overcoming barriers to the integration of toxicity data, and are bringing researchers closer to the reality of a mineable chemical Semantic Web. An example of this integration of data is provided by the collaboration among researchers involved with the Distributed Structure-Searchable Toxicity (DSSTox) project, the Carcinogenic Potency Project, projects at the National Cancer Institute and the PubChem database.

  14. Computer prediction of possible toxic action from chemical structure; the DEREK system.

    PubMed

    Sanderson, D M; Earnshaw, C G

    1991-07-01

    1. The development of DEREK, a computer-based expert system (derived from the LHASA chemical synthesis design program) for the qualitative prediction of possible toxic action of compounds on the basis of their chemical structure is described. 2. The system is able to perceive chemical sub-structures within molecules and relate these to a rulebase linking the sub-structures with likely types of toxicity. 3. Structures can be drawn in directly at a computer graphics terminal or retrieved automatically from a suitable in-house database. 4. The system is intended to aid the selection of compounds based on toxicological considerations, or separately to indicate specific toxicological properties to be tested for early in the evaluation of a compound, so saving time, money and some laboratory animals and resources.

  15. 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.

  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. Modeling proteins using a super-secondary structure library and NMR chemical shift information.

    PubMed

    Menon, Vilas; Vallat, Brinda K; Dybas, Joseph M; Fiser, Andras

    2013-06-04

    A remaining challenge in protein modeling is to predict structures for sequences with no sequence similarity to any experimentally solved structure. Based on earlier observations, the library of protein backbone supersecondary structure motifs (Smotifs) saturated about a decade ago. Therefore, it should be possible to build any structure from a combination of existing Smotifs with the help of limited experimental data that are sufficient to relate the backbone conformations of Smotifs between target proteins and known structures. Here, we present a hybrid modeling algorithm that relies on an exhaustive Smotif library and on nuclear magnetic resonance chemical shift patterns without any input of primary sequence information. In a test of 102 proteins, the algorithm delivered 90 homology-model-quality models, among them 24 high-quality ones, and a topologically correct solution for almost all cases. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available.

  18. 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.

  19. Applications of the Cambridge Structural Database in chemical education1

    PubMed Central

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

    2010-01-01

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

  20. Computational analysis of RNA structures with chemical probing data

    PubMed Central

    Ge, Ping; Zhang, Shaojie

    2015-01-01

    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. PMID:25687190

  1. (Sub)structure Searches in Databases Containing Generic Chemical Structure Representations.

    ERIC Educational Resources Information Center

    Schoch-Grubler, Ursula

    1990-01-01

    Reviews three database systems available for searching generic chemical structure representations: (1) Derwent's Chemical Code System; (2) IDC's Gremas System; and (3) Derwent's Markush DARC System. Various types of searches are described, features desirable to users are discussed, and comparison searches are described that measured recall and…

  2. 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

  3. Epidemiological assessment of occupationally related, chemically induced sperm count suppression

    SciTech Connect

    Milby, T.H.; Whorton, D.

    1980-02-01

    Occupationally related, chemically induced sperm count suppression is a recently recognized problem, first brought to light in connection with the manufacture and formulation of dibromochloropropane (DBCP). The authors studied sperm count data from four occupational cohorts - two exposed to DBCP and two exposed to epichlorohydrin (ECH). In both DBCP cohorts there was a significant difference (alpha = 0.05) between sperm count distribution functions of the exposed group and of the non-exposed group. A much higher percentage of exposed men was oligospermic and the median sperm count for each exposed group was substantially lower than that for the respective non-exposed group. In the ECH cohorts there was no significant difference between sperm count data for the exposed group and for the non-exposed group. The authors concluded that exposure to DBCP, but not to ECH, was positively associated with detectable sperm count suppression. It is suggested that the key to identifying and assessing occupationally related sperm count suppression lies in the proper classification and interpretation of group sperm count data.

  4. 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.

  5. 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

  6. 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.

  7. 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

  8. 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.

  9. Determination of amyloid core structure using chemical shifts.

    PubMed

    Skora, Lukasz; Zweckstetter, Markus

    2012-12-01

    Amyloid fibrils are the pathological hallmark of a large variety of neurodegenerative disorders. The structural characterization of amyloid fibrils, however, is challenging due to their non-crystalline, heterogeneous, and often dynamic nature. Thus, the structure of amyloid fibrils of many proteins is still unknown. We here show that the structure calculation program CS-Rosetta can be used to obtain insight into the core structure of amyloid fibrils. Driven by experimental solid-state NMR chemical shifts and taking into account the polymeric nature of fibrils CS-Rosetta allows modeling of the core of amyloid fibrils. Application to the Y145X stop mutant of the human prion protein reveals a left-handed β-helix.

  10. A Novel Approach: Chemical Relational Databases, and the ...

    EPA Pesticide Factsheets

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as

  11. Teaching Structural Formulas in Chemistry: How Students Relate Structural Formulas to the Solubility of Substances.

    ERIC Educational Resources Information Center

    Goedhart, Martin; van Duin, Yvonne

    Structural formulas give professional chemists information about physical and chemical properties of corresponding compounds. In chemistry education at secondary schools, structural formulas are introduced in the context of chemical bonding. Structural formulas are not introduced as representations of the properties of chemical compounds. This…

  12. 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.

  13. Electronic structure imperfections and chemical bonding at graphene interfaces

    NASA Astrophysics Data System (ADS)

    Schultz, Brian Joseph

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

  14. 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.

  15. The chemical structure and the crystalline structures of Bombyx mori silk fibroin.

    PubMed

    Lotz, B; Colonna Cesari, F

    1979-01-01

    Some recent data (i.e. published in the last ten years) on the chemical and crystalline structures of B. mori silk are reviewed. The main emphasis is put on the crystallizable portion of silk fibroin, including its chemical constitution and its molecular conformation (at the crystallographic unit-cell level) in the two crystalline modifications : the beta pleated sheet and the silk I structures. The structural aspects are based on a discussion of X-ray and electron diffraction data, and on conformational energy analyses of a model (Ala-Gly)n polypeptide of silk fibroin.

  16. Linear complexions: Confined chemical and structural states at dislocations.

    PubMed

    Kuzmina, M; Herbig, M; Ponge, D; Sandlöbes, S; Raabe, D

    2015-09-04

    For 5000 years, metals have been mankind's most essential materials owing to their ductility and strength. Linear defects called dislocations carry atomic shear steps, enabling their formability. We report chemical and structural states confined at dislocations. In a body-centered cubic Fe-9 atomic percent Mn alloy, we found Mn segregation at dislocation cores during heating, followed by formation of face-centered cubic regions but no further growth. The regions are in equilibrium with the matrix and remain confined to the dislocation cores with coherent interfaces. The phenomenon resembles interface-stabilized structural states called complexions. A cubic meter of strained alloy contains up to a light year of dislocation length, suggesting that linear complexions could provide opportunities to nanostructure alloys via segregation and confined structural states.

  17. Chemically Resolved Structure of the Sn/Ge(111) Surface

    NASA Astrophysics Data System (ADS)

    Lee, Tien-Lin; Warren, Samantha; Cowie, Bruce C. C.; Zegenhagen, Jörg

    2006-02-01

    The structure and chemical states of the Sn/Ge(111) surface are characterized by x-ray standing waves combined with photoemission. For the room temperature 3×3 phase two chemical components, approximately 0.4 eV apart, are observed for both Sn 3d and 4d core levels. Our model-independent, x-ray standing wave analysis shows unambiguously that the two components originate from Sn adatoms located at two different heights separated vertically by 0.23 Å, in favor of a model composed of a fluctuating Sn layer. Contrary to the most accepted scenario, the stronger Sn 3d and 4d components, which appear at the lower binding-energy sides and account for 2/3 of the Sn adatoms, are identified to be associated with the higher Sn position, manifesting their filled valence state character.

  18. Atomically Resolved Structural and Chemical Investigation of Single MXene Sheets.

    PubMed

    Karlsson, Linda H; Birch, Jens; Halim, Joseph; Barsoum, Michel W; Persson, Per O Å

    2015-08-12

    The properties of two-dimensional (2D) materials depend strongly on the chemical and electrochemical activity of their surfaces. MXene, one of the most recent additions to 2D materials, shows great promise as an energy storage material. In the present investigation, the chemical and structural properties of individual Ti3C2 MXene sheets with associated surface groups are investigated at the atomic level by aberration corrected STEM-EELS. The MXene sheets are shown to exhibit a nonuniform coverage of O-based surface groups which locally affect the chemistry. Additionally, native point defects which are proposed to affect the local surface chemistry, such as oxidized titanium adatoms (TiOx), are identified and found to be mobile.

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

    NASA Astrophysics Data System (ADS)

    Mohanty, Nihar Ranjan

    the degrading effects of harsh environments such as the ultrahigh vacuum (˜ 10-5 Torr) and high intensity electron beam (˜ 150 A/cm2) in a transmission electron microscope (TEM) column. While an unwrapped bacterium shrank by ˜ 76% and displayed significant charge buildup in the TEM column; a wrapped bacterium remained uncontracted and undamaged owing to the graphenic wraps. This work has shown for the first time an impermeable graphenic encasement of bacteria and its application in high vacuum TEM imaging without using any lengthy traditional biological TEM sample preparation techniques. In an inch-scale, we fabricated robust free-standing paper composed of TWEEN/Graphene composite which exhibited excellent chemical stability and mechanical strength. This paper displayed excellent biocompatibility towards three mammalian cell lines while inhibiting the non-specific binding of bacteria (Bacillus cereus). We predict this composite and its derivatives to have excellent applications in biomedical engineering for transplant devices, invasive instrument coatings and implants. We also demonstrate a novel, ultra-fast and high yield process for reducing GO to reduced graphene oxide (RGO) using a facile hydride-based chemistry. The RGO sheets thus-produced exhibited high carrier mobilities (˜ 100-600 cm2/V·s) and reinstatement of the ambipolar characteristic of graphene. Raman spectra and UV-Vis spectroscopy on the RGO sheets displayed a high degree of restoration of the crystalline sp2 lattice with relatively low defects. We fabricated graphene nanoribbons (GNRs) -- 1D structural derivatives of graphene -- using a nano-scale cutting process from highly oriented pyrolytic graphite (HOPG) blocks, with widths pre-determinable between 5 nm to 600 nm. The as-produced GNRs had very high aspect ratio in the longitudinal direction (˜ 0.01); exhibited predominantly mono-layered structure (< 10% bilayer); and smooth edges (Raman ID/G ˜ 0.25 -0.28). Low temperature electrical

  20. TSCA Work Plan Chemical Problem Formulation and Initial Assessment Tetrabromobisphenol A and Related Chemicals Cluster Flame Retardants

    EPA Pesticide Factsheets

    EPA released a problem formulation for TBBPA and related chemicals used as a flame retardants in plastics/printed circuit boards for electronics. The goal of this problem formulation was to identify scenarios where further risk analysis may be necessary.

  1. Environmental Fate of Organophosphorus Compounds Related to Chemical Weapons

    SciTech Connect

    Davisson, M L; Love, A H; Vance, A; Reynolds, J G

    2005-02-08

    chloride and hydroxyl (strong nucleophile) dominated experimental solutions. Because of its overwhelming abundance in solution relative to hydroxyl ion, bicarbonate likely effectively competes in nucleophilic attack on phosphorus. The addition of natural dissolved organic matter at 100 mg/L in pH 7 bicarbonate buffered solution slowed VX hydrolysis rates {approx}2 times relative to controls, suggesting hydrophobic interaction. Adsorption experiments derived isotherms from batch aqueous experiments on montmorillonite clay, iron-oxyhydroxide goethite, and on amorphous silica. VX had moderate affinity for montmorillonite and amorphous silica, and very low affinity toward goethite. The addition of dissolved organic matter into solution enhanced VX adsorption to goethite, consistent with its high affinity for hydrophobic organic matter (log K{sub oc} = 2.52). Diisopropylaminoethylthiol (DESH), a hydrolysis product of VX showed equivalent adsorption to montmorillonite, and poor affinity to goethite and silica. However, hydrolysis products O-Ethylmethylphosphonic acid (EMPA) and methylphosphonic acid (MPA) strongly adsorbed on goethite, but not on montmorillonite or silica, suggesting a ligand-exchange mechanism. VX degraded rapidly when completely dried onto goethite followed by rehydration, consistent with an irreversible chemical adsorption mechanism.

  2. Canopy Structure in Relation to Rainfall Interception

    NASA Astrophysics Data System (ADS)

    Fathizadeh, Omid; Mohsen Hosseini, Seyed; Keim, Richard

    2016-04-01

    Spatial variation of throughfall (TF) is linked to canopy structure. The effects of canopy structure on the spatial redistribution of rainfall in deciduous stands remains poorly documented. Therefore, the objective of this study is to evaluate the influence of canopy structure such as stand density on the partitioning of incident rainfall when passing through the canopy of Brant's oak (Quercus branti) forest stands. The study site is the Zagros forests in the western Iranian state of Ilam, protected forests of Dalab region. Twelve TF plots (50 m × 50 m) with 30 gauges randomly placed within each plot were established. Interception loss was computed as the difference between rain and TF. Canopy cover (%) and leaf area index (LAI, m2 m-2) were estimated from the analysis of hemispherical photographs obtained during the fully leafed period. Relative interception varied from ˜4% at 0.1 LAI and canopy cover of 10% to ˜25% at 1.5 LAI and canopy cover of 65%. Interception represents a significant component of the seasonal water balance of oak forests, particularly in the case of intensive plantings. Keywords: Canopy Structure, Rainfall redistribution, Zagros forests, Quercus branti

  3. 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...

  4. Chemical and structural diversity of siRNA molecules.

    PubMed

    Nawrot, Barbara; Sipa, Katarzyna

    2006-01-01

    Short interfering RNAs (siRNAs) are 21-23 nt long double-stranded oligoribonucleotides which in mammalian cells exhibit a potency for sequence-specific gene silencing via an RNA interference (RNAi) pathway. It has been already proven that exogenous, chemically synthesized siRNA molecules are effective inhibitors of gene expression and are widely applied for analysis of protein function and proteomics-based target identification. Moreover, since their discovery siRNA molecules have been implemented as potential candidates for therapeutic applications. Variously modified siRNA molecules containing sugar modifications (2'-OMe, -F, -O-allyl, -amino, orthoesters and LNA analogues), internucleotide phospodiester bond modifications (phosphorothioates, boranophosphates), base modifications (s(2)U) as well as 3'-terminal cholesterol-conjugated constructs were investigated as potential candidates for effective inhibition of gene expression. This chapter reviews an impact of chemical and structural modifications of siRNA molecules on their serum and thermal stability, cellular and in vivo activity, cellular uptake, biodistribution and cytotoxicity. Functional analysis of chemically modified siRNA molecules allows for better understanding of the mechanism of the RNA interference process as well as demonstrates immense efforts in optimizing in vivo potency of siRNA molecules for RNAi-based drug design.

  5. Computer-assisted mechanistic structure-activity studies: application to diverse classes of chemical carcinogens.

    PubMed Central

    Loew, G H; Poulsen, M; Kirkjian, E; Ferrell, J; Sudhindra, B S; Rebagliati, M

    1985-01-01

    In the first part of this paper we have indicated how the techniques and capabilities of theoretical chemistry, together with experimental results, can be used in a mechanistic approach to structure-activity studies of toxicity. In the second part, we have illustrated how this computer-assisted approach has been used to identify and calculate causally related molecular indicators of relative carcinogenic activity in five classes of chemical carcinogens: polycyclic aromatic hydrocarbons and their methyl derivatives, aromatic amines, chloroethanes, chloroalkenes and dialkyl nitrosamines. In each class of chemicals studied, candidate molecular indicators have been identified that could be useful in predictive screening of unknown compounds. In addition, further insights into some mechanistic aspects of chemical carcinogenesis have been obtained. Finally, experiments have been suggested to both verify the usefulness of the indicators and test their mechanistic implications. PMID:3905382

  6. Chemical probes for higher-order structure in RNA.

    PubMed Central

    Peattie, D A; Gilbert, W

    1980-01-01

    Three chemical reactions can probe the secondary and tertiary interactions of RNA molecules in solution. Dimethyl sulfate monitors the N-7 of guanosines and senses tertiary interactions there, diethyl pyrocarbonate detects stacking of adenosines, and an alternate dimethyl sulfate reaction examines the N-3 of cytidines and thus probes base pairing. The reactions work between 0 degrees C and 90 degrees C and at pH 4.5--8.5 in a variety of buffers. As an example we follow the progressive denaturation of yeast tRNAPhe terminally labeled with 32P as the tertiary and secondary structures sequentially melt out. A single autoradiograph of a terminally labeled molecule locates regions of higher-order structure and identifies the bases involved. Images PMID:6159633

  7. A quantum chemical method for rapid optimization of protein structures.

    PubMed

    Wada, Mitsuhito; Sakurai, Minoru

    2005-01-30

    A quantum chemical method for rapid optimization of protein structures is proposed. In this method, a protein structure is treated as an assembly of amino acid units, and the geometry optimization of each unit is performed with taking the effect of its surrounding environment into account. The optimized geometry of a whole protein is obtained by repeated application of such a local optimization procedure over the entire part of the protein. Here, we implemented this method in the MOPAC program and performed geometry optimization for three different sizes of proteins. Consequently, these results demonstrate that the total energies of the proteins are much efficiently minimized compared with the use of conventional optimization methods, including the MOZYME algorithm (a representative linear-scaling method) with the BFGS routine. The proposed method is superior to the conventional methods in both CPU time and memory requirements.

  8. Sample preparation of organic liquid for off-site analysis of chemical weapons convention related compounds.

    PubMed

    Pardasani, Deepak; Palit, Meehir; Gupta, A K; Shakya, Purushottam; Sekhar, K; Dubey, D K

    2005-02-15

    Off-site analysis of chemical warfare agents (CWAs) and related compounds plays a key role in the verification program of the Chemical Weapons Convention (CWC). The analysis results, aiming toward unambiguous identication of compounds, depend on the type of sample preparation method. Development of milder sample preparation methods, which offer good recoveries and do not alter the structure of analytes, is highly desirable. Organic liquid with high hydrocarbon background is a frequently encountered challenge in off-site analysis and in official proficiency tests conducted by OPCW. Sample cleanup procedures, namely, solvent exchange followed by cooling and liquid-liquid extraction were studied to eliminate the hydrocarbons from organic liquid. Acetonitrile, a polar aprotic solvent, was effectively used to remove the background in both methods, and recoveries of spiked CWAs by the two techniques were between 69 and 99%.

  9. Exploiting syntactic and semantics information for chemical-disease relation extraction.

    PubMed

    Zhou, Huiwei; Deng, Huijie; Chen, Long; Yang, Yunlong; Jia, Chen; Huang, Degen

    2016-01-01

    Identifying chemical-disease relations (CDR) from biomedical literature could improve chemical safety and toxicity studies. This article proposes a novel syntactic and semantic information exploitation method for CDR extraction. The proposed method consists of a feature-based model, a tree kernel-based model and a neural network model. The feature-based model exploits lexical features, the tree kernel-based model captures syntactic structure features, and the neural network model generates semantic representations. The motivation of our method is to fully utilize the nice properties of the three models to explore diverse information for CDR extraction. Experiments on the BioCreative V CDR dataset show that the three models are all effective for CDR extraction, and their combination could further improve extraction performance.Database URL:http://www.biocreative.org/resources/corpora/biocreative-v-cdr-corpus/.

  10. DSSTox chemical-index files for exposure-related experiments in ArrayExpress and Gene Expression Omnibus: enabling toxico-chemogenomics data linkages

    EPA Science Inventory

    The Distributed Structure-Searchable Toxicity (DSSTox) ARYEXP and GEOGSE files are newly published, structure-annotated files of the chemical-associated and chemical exposure-related summary experimental content contained in the ArrayExpress Repository and Gene Expression Omnibus...

  11. The chemical structure of the Hawaiian mantle plume.

    PubMed

    Ren, Zhong-Yuan; Ingle, Stephanie; Takahashi, Eiichi; Hirano, Naoto; Hirata, Takafumi

    2005-08-11

    The Hawaiian-Emperor volcanic island and seamount chain is usually attributed to a hot mantle plume, located beneath the Pacific lithosphere, that delivers material sourced from deep in the mantle to the surface. The shield volcanoes of the Hawaiian islands are distributed in two curvilinear, parallel trends (termed 'Kea' and 'Loa'), whose rocks are characterized by general geochemical differences. This has led to the proposition that Hawaiian volcanoes sample compositionally distinct, concentrically zoned, regions of the underlying mantle plume. Melt inclusions, or samples of local magma 'frozen' in olivine phenocrysts during crystallization, may record complexities of mantle sources, thereby providing better insight into the chemical structure of plumes. Here we report the discovery of both Kea- and Loa-like major and trace element compositions in olivine-hosted melt inclusions in individual, shield-stage Hawaiian volcanoes--even within single rock samples. We infer from these data that one mantle source component may dominate a single lava flow, but that the two mantle source components are consistently represented to some extent in all lavas, regardless of the specific geographic location of the volcano. We therefore suggest that the Hawaiian mantle plume is unlikely to be compositionally concentrically zoned. Instead, the observed chemical variation is probably controlled by the thermal structure of the plume.

  12. Comparison of the 'chemical' and 'structural' approaches to the optimization of the thrombin-binding aptamer.

    PubMed

    Tatarinova, Olga; Tsvetkov, Vladimir; Basmanov, Dmitry; Barinov, Nikolay; Smirnov, Igor; Timofeev, Edward; Kaluzhny, Dmitry; Chuvilin, Andrey; Klinov, Dmitry; Varizhuk, Anna; Pozmogova, Galina

    2014-01-01

    Noncanonically structured DNA aptamers to thrombin were examined. Two different approaches were used to improve stability, binding affinity and biological activity of a known thrombin-binding aptamer. These approaches are chemical modification and the addition of a duplex module to the aptamer core structure. Several chemically modified aptamers and the duplex-bearing ones were all studied under the same conditions by a set of widely known and some relatively new methods. A number of the thrombin-binding aptamer analogs have demonstrated improved characteristics. Most importantly, the study allowed us to compare directly the two approaches to aptamer optimization and to analyze their relative advantages and disadvantages as well as their potential in drug design and fundamental studies.

  13. A system structure for predictive relations in penetration mechanics

    NASA Astrophysics Data System (ADS)

    Korjack, Thomas A.

    1992-02-01

    The availability of a software system yielding quick numerical models to predict ballistic behavior is a requisite for any research laboratory engaged in material behavior. What is especially true about accessibility of rapid prototyping for terminal impaction is the enhancement of a system structure which will direct the specific material and impact situation towards a specific predictive model. This is of particular importance when the ranges of validity are at stake and the pertinent constraints associated with the impact are unknown. Hence, a compilation of semiempirical predictive penetration relations for various physical phenomena has been organized into a data structure for the purpose of developing a knowledge-based decision aided expert system to predict the terminal ballistic behavior of projectiles and targets. The ranges of validity and constraints of operation of each model were examined and cast into a decision tree structure to include target type, target material, projectile types, projectile materials, attack configuration, and performance or damage measures. This decision system implements many penetration relations, identifies formulas that match user-given conditions, and displays the predictive relation coincident with the match in addition to a numerical solution. The physical regimes under consideration encompass the hydrodynamic, transitional, and solid; the targets are either semi-infinite or plate, and the projectiles include kinetic and chemical energy. A preliminary databases has been constructed to allow further development of inductive and deductive reasoning techniques applied to ballistic situations involving terminal mechanics.

  14. 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.

  15. 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

  16. BioSM: metabolomics tool for identifying endogenous mammalian biochemical structures in chemical structure space.

    PubMed

    Hamdalla, Mai A; Mandoiu, Ion I; Hill, Dennis W; Rajasekaran, Sanguthevar; Grant, David F

    2013-03-25

    The structural identification of unknown biochemical compounds in complex biofluids continues to be a major challenge in metabolomics research. Using LC/MS, there are currently two major options for solving this problem: searching small biochemical databases, which often do not contain the unknown of interest or searching large chemical databases which include large numbers of nonbiochemical compounds. Searching larger chemical databases (larger chemical space) increases the odds of identifying an unknown biochemical compound, but only if nonbiochemical structures can be eliminated from consideration. In this paper we present BioSM; a cheminformatics tool that uses known endogenous mammalian biochemical compounds (as scaffolds) and graph matching methods to identify endogenous mammalian biochemical structures in chemical structure space. The results of a comprehensive set of empirical experiments suggest that BioSM identifies endogenous mammalian biochemical structures with high accuracy. In a leave-one-out cross validation experiment, BioSM correctly predicted 95% of 1388 Kyoto Encyclopedia of Genes and Genomes (KEGG) compounds as endogenous mammalian biochemicals using 1565 scaffolds. Analysis of two additional biological data sets containing 2330 human metabolites (HMDB) and 2416 plant secondary metabolites (KEGG) resulted in biochemical annotations of 89% and 72% of the compounds, respectively. When a data set of 3895 drugs (DrugBank and USAN) was tested, 48% of these structures were predicted to be biochemical. However, when a set of synthetic chemical compounds (Chembridge and Chemsynthesis databases) were examined, only 29% of the 458,207 structures were predicted to be biochemical. Moreover, BioSM predicted that 34% of 883,199 randomly selected compounds from PubChem were biochemical. We then expanded the scaffold list to 3927 biochemical compounds and reevaluated the above data sets to determine whether scaffold number influenced model performance

  17. Salt, Chlor-Alkali, and Related Heavy Chemicals

    NASA Astrophysics Data System (ADS)

    Bommaraju, Tilak V.

    The chemical category of inorganic salts encompasses many substances that dissociate completely in water, but only one salt, sodium chloride, is referred to by the common name, salt. Sodium chloride is ubiquitous in both its occurrence and its many uses. To date, there are over 14,000 uses for salt.1 Salt is used as a feedstock for many chemicals including chlorine, caustic soda (sodium hydroxide), synthetic soda ash (sodium carbonate), sodium chlorate, sodium sulfate, and metallic sodium. By indirect methods, sodium chloride is also used to produce hydrochloric acid and many other sodium salts. In its natural mineral form, salt may take on some color from some of the trace elements and other salts present, however, pure sodium chloride is a white to colorless crystalline substance, fairly soluble in water.2 Also known as halite, the substance is an essential nutrient to humans and animals for proper bodily functions.

  18. Relation of sensory perception with chemical composition of bioprocessed lingonberry.

    PubMed

    Viljanen, Kaarina; Heiniö, Raija-Liisa; Juvonen, Riikka; Kössö, Tuija; Puupponen-Pimiä, Riitta

    2014-08-15

    The impact of bioprocessing on lingonberry flavour was studied by sensory evaluation and chemical analysis (organic acids, mannitol, phenolic compounds, sugars and volatile compounds). Bioprocessing of lingonberries with enzymes, lactic acid bacteria (LAB) or yeast, or their combination (excluding pure LAB fermentation) affected their perceived flavour and chemical composition. Sweetness was associated especially with enzyme treatment but also with enzyme+LAB treatment. Yeast fermentation caused significant changes in volatile aroma compounds and perceived flavour, whereas minor changes were detected in LAB or enzyme-treated berries. Increased concentration of organic acids, ethanol and some phenolic acids correlated with perceived fermented odour/flavour in yeast fermentations, in which increase in benzoic acid level was significant. In enzymatic treatment decreasing anthocyanins correlated well with decreased perceived colour intensity. Enzyme treatment is a potential tool to decrease naturally acidic flavour of lingonberry. Fermentation, especially with yeast, could be an interesting new approach to increase the content of natural preservatives, such as antimicrobial benzoic acid.

  19. Effects of lignin structure on hydrodeoxygenation reactivity of pine wood lignin to valuable chemicals

    DOE PAGES

    Wang, Hongliang; Ben, Haoxi; Southeast Univ., Nanjing; ...

    2017-01-05

    Hydrodeoxygenation (HDO) of two dilute acid flow through pretreated softwood lignin samples, including residual lignin in pretreated solid residues (ReL) and recovered insoluble lignin in pretreated liquid (RISL), with apparent different physical and chemical structures, was comprehensively studied. A combination of catalysts (HY zeolite and Ru/Al2O3) was employed to investigate the effects of lignin structures, especially condensed structures, on the HDO upgrading process. Results indicated that the condensed structure and short side chains in lignin hindered its HDO conversion under different reaction conditions, including catalyst loading and composition, hydrogen pressure, and reaction time. In addition to lignin structure, HY zeolitemore » was found crucial for lignin depolymerization, while Ru/Al2O3 and relatively high hydrogen pressure (4 MPa) were necessary for upgrading unstable oxy-compounds to cyclohexanes at high selectivity (>95 wt %). Since the lignin structure essentially affects its reactivity during HDO conversion, the yield and selectivity of HDO products can be predicted by detailed characterization of the lignin structure. Furthermore, the insights gained from this study in the fundamental reaction mechanisms based on the lignin structure will facilitate upgrading of lignin to high-value products for applications in the production of both fuels and chemicals.« less

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. Structural simplification of chemical reaction networks in partial steady states.

    PubMed

    Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa

    2016-11-01

    We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology.

  5. Tailoring Surface Chemical Properties Using Electronic Structure Theory

    NASA Astrophysics Data System (ADS)

    Norskov, Jens

    2012-02-01

    Electronic structure methods based on density functional theory have reached a level of sophistication where they can be used to describe complete catalytic reactions on transition metal surfaces. This opens the possibility that computational methods can be used to tailor surfaces with desired chemical properties. Recent progress in this direction for transition metal catalysts will be discussed. A series of concepts will be introduced to describe and understand trends in reactivity from one metal surface to the next. It is shown how these concepts can be used to identify the factors determining the catalytic activity of a given transition metal surface, and how this can form the basis for screening of a large number of metals and alloys for catalytic properties.

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

    PubMed

    Hilliou, Loic

    2014-01-01

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

  7. Bio-related noble metal nanoparticle structure property relationships

    NASA Astrophysics Data System (ADS)

    Leonard, Donovan Nicholas

    Structure property relationships of noble metal nanoparticles (NPs) can be drastically different than bulk properties of the same metals. This research study used state-of-the-art analytical electron microscopy and scanned probe microscopy to determine material properties on the nanoscale of bio-related Au and Pd NPs. Recently, it has been demonstrated the self-assembly of Au NPs on functionalized silica surfaces creates a conductive surface. Determination of the aggregate morphology responsible for electron conduction was studied by atomic force microscopy (AFM) and scanning electron microscopy (SEM). In addition, changes in the electrical properties of the substrates after low temperature (<350°C) annealing was also studied. It was found that coalescence and densification of the Au NP aggregates disrupted the interconnected network which subsequently created a loss of conductivity. Investigation of bio-related Au/SiO2 core-shell NPs determined why published experimental results showed the sol-gel silica shell improved, by almost an order of magnitude, the detection efficiency of a DNA detection assay. Novel 360° rotation scanning TEM (STEM) imaging allowed study of individual NP surface morphology and internal structure. Electron energy loss spectroscopy (EELS) spectrum imaging determined optoelectronic properties and chemical composition of the silica shell used to encapsulate Au NPs. Results indicated the sol-gel deposited SiO2 had a band gap energy of ˜8.9eV, bulk plasmon-peak energy of ˜25.5eV and chemical composition of stoichiometric SiO2. Lastly, an attempt to elicit structure property relationships of novel RNA mediated Pd hexagon NPs was performed. Selected area electron diffraction (SAD), low voltage scanning transmission electron microscopy (LV-STEM), electron energy loss spectroscopy (EELS) and energy dispersive spectroscopy (EDS) were chosen for characterization of atomic ordering, chemical composition and optoelectronic properties of the novel

  8. Interplay between chemical reactions and transport in structured spaces

    NASA Astrophysics Data System (ADS)

    Konkoli, Zoran

    2005-07-01

    The main motivation behind this study is to understand the interplay between the reactions and transport in a geometries that are not compact. Typical examples of compact geometries are a box or a sphere. A network made of containers C1,C2,…,CN and tubes is an example of the space that is structured and noncompact. In containers, particles react with the rate λ . Tubes connecting containers allow for the exchange of chemicals with the transport rate D . A situation is considered where a number of reactants is small and kinetics is noise dominated. A method is presented that can be used to calculate the average and higher moments of the reaction time. A number of different chemical reactions are studied and their performance compared in various ways. Two schemes are discussed in general, the reaction on a fixed geometry ensemble (ROGE) and the geometry on a fixed reaction ensemble, examples are given in the ROGE case. The most important findings are as follows. (i) There is a large number of reactions that run faster in a networklike geometry. Such reactions contain antagonistic catalytic influences in the intermediate stages of a reaction scheme that are best dealt with in a networklike structure. (ii) Antagonistic catalytic influences are hard to identify since they are strongly connected to the pattern of injected molecules (inject pattern) and depend on the choice of molecules that have to be synthesized at the end (task pattern). (iii) The reaction time depends strongly on the details of the inject and task patterns.

  9. Thiaminylated adenine nucleotides. Chemical synthesis, structural characterization and natural occurrence.

    PubMed

    Frédérich, Michel; Delvaux, David; Gigliobianco, Tiziana; Gangolf, Marjorie; Dive, Georges; Mazzucchelli, Gabriel; Elias, Benjamin; De Pauw, Edwin; Angenot, Luc; Wins, Pierre; Bettendorff, Lucien

    2009-06-01

    Thiamine and its three phosphorylated derivatives (mono-, di- and triphosphate) occur naturally in most cells. Recently, we reported the presence of a fourth thiamine derivative, adenosine thiamine triphosphate, produced in Escherichia coli in response to carbon starvation. Here, we show that the chemical synthesis of adenosine thiamine triphosphate leads to another new compound, adenosine thiamine diphosphate, as a side product. The structure of both compounds was confirmed by MS analysis and 1H-, 13C- and 31P-NMR, and some of their chemical properties were determined. Our results show an upfield shifting of the C-2 proton of the thiazolium ring in adenosine thiamine derivatives compared with conventional thiamine phosphate derivatives. This modification of the electronic environment of the C-2 proton might be explained by a through-space interaction with the adenosine moiety, suggesting U-shaped folding of adenosine thiamine derivatives. Such a structure in which the C-2 proton is embedded in a closed conformation can be located using molecular modeling as an energy minimum. In E. coli, adenosine thiamine triphosphate may account for 15% of the total thiamine under energy stress. It is less abundant in eukaryotic organisms, but is consistently found in mammalian tissues and some cell lines. Using HPLC, we show for the first time that adenosine thiamine diphosphate may also occur in small amounts in E. coli and in vertebrate liver. The discovery of two natural thiamine adenine compounds further highlights the complexity and diversity of thiamine biochemistry, which is not restricted to the cofactor role of thiamine diphosphate.

  10. 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.

  11. Structural and Optical Study of Chemical Bath Deposited Nano-Structured CdS Thin Films

    NASA Astrophysics Data System (ADS)

    Kumar, Suresh; Sharma, Dheeraj; Sharma, Pankaj; Sharma, Vineet; Barman, P. B.; Katyal, S. C.

    2011-12-01

    CdS is commonly used as window layer in polycrystalline solar cells. The paper presents a structural and optical study of CdS nano-structured thin films. High quality CdS thin films are grown on commercial glass by means of chemical bath deposition. It involves an alkaline solution of cadmium salt, a complexant, a chalcogen source and a non-ionic surfactant. The films have been prepared under various process parameters. The chemically deposited films are annealed to estimate its effect on the structural and optical properties of films. These films (as -deposited and annealed) have been characterized by means of XRD, SEM and UV-Visible spectrophotometer. XRD of films show the nano-crystalline nature. The energy gap of films is found to be of direct in nature.

  12. Identification of structure-activity relationships from screening a structurally compact DNA-encoded chemical library.

    PubMed

    Franzini, Raphael M; Ekblad, Torun; Zhong, Nan; Wichert, Moreno; Decurtins, Willy; Nauer, Angela; Zimmermann, Mauro; Samain, Florent; Scheuermann, Jörg; Brown, Peter J; Hall, Jonathan; Gräslund, Susanne; Schüler, Herwig; Neri, Dario

    2015-03-23

    Methods for the rapid and inexpensive discovery of hit compounds are essential for pharmaceutical research and DNA-encoded chemical libraries represent promising tools for this purpose. We here report on the design and synthesis of DAL-100K, a DNA-encoded chemical library containing 103 200 structurally compact compounds. Affinity screening experiments and DNA-sequencing analysis provided ligands with nanomolar affinities to several proteins, including prostate-specific membrane antigen and tankyrase 1. Correlations of sequence counts with binding affinities and potencies of enzyme inhibition were observed and enabled the identification of structural features critical for activity. These results indicate that libraries of this type represent a useful source of small-molecule binders for target proteins of pharmaceutical interest and information on structural features important for binding.

  13. MOZART, a global chemical transport model for ozone and related chemical tracers: 1. Model description

    NASA Astrophysics Data System (ADS)

    Brasseur, G. P.; Hauglustaine, D. A.; Walters, S.; Rasch, P. J.; Müller, J.-F.; Granier, C.; Tie, X. X.

    1998-11-01

    We present a new global three-dimensional chemical-transport model (called MOZART) developed in the framework of the NCAR Community Climate Model (CCM) and aimed at studying the distribution and budget of tropospheric ozone and its precursors. The model, developed with a horizontal resolution of 2.8° in longitude and latitude, includes 25 levels in the vertical between the Earth's surface and an upper boundary located at approximately 35 km altitude. In its present configuration the model calculates the global distribution of 56 chemical constituents with a timestep of 20 min, and accounts for surface emission and deposition, large-scale advective transport, subscale convective and boundary layer exchanges, chemical and photochemical transformations, as well as wet scavenging. Transport is simulated "off line" from CCM with dynamical variables provided every 3 hours from preestablished history tapes. Advection is calculated using the semi-Lagrangian transport scheme [Rasch and Williamson, 1990] developed for the MATCH model of Rasch et al. [1997]. Convective and boundary layer transports are expressed according to Hack [1994] and Holtslag and Boville [1993], respectively. A detailed evaluation of the model results is provided in a companion paper [Hauglustaine et al., this issue]. An analysis of the spatial and temporal variability in the chemical fields predicted by the model suggests that regional events such as summertime ozone episodes in polluted areas can be simulated by MOZART.

  14. 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.

  15. 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

  16. DOCKING OF STRUCTURALLY RELATED DIOLEPOXIDES OF BENZO(GHI)FLUORANTHENE WITH DNA

    EPA Science Inventory

    Docking of structurally-related diolepoxides of benzo{ghi}fluoranthene and benzo{c}phenanthrene with DNA
    Polycyclic aromatic hydrocarbons are a class of chemicals found in the environment. Some class members are potent carcinogens while others with similar structures show litt...

  17. Numerical and chemical classification of Streptosporangium and some related actinomycetes.

    PubMed

    Whitham, T S; Athalye, M; Minnikin, D E; Goodfellow, M

    One hundred and seventeen streptosporangia from soil were compared with marker strains of the family Streptosporangiaceae for many phenotypic properties. The data were examined using the Jaccard, pattern and simple matching coefficients with clustering achieved using average, complete and single linkage algorithms. Particular confidence was placed in the product of the pattern, average linkage analysis given the sharp definition of aggregate groups and clusters and a combination of low test error and high cophenetic correlation values. The test strains were assigned to five aggregate groups that were equated with the genera Streptosporangium (group A), Microbispora (group B), Planobispora and Planomonospora (Group C), Kutzneria (neé Streptosporangium viridogriseum (group D), and Microtetraspora (group E). The streptosporangia, both isolates and marker strains, were assigned to 5 major, 7 minor and 18 single membered clusters. Representative streptosporangia examined for chemical markers were characterised by the presence of meso-diaminopimelic acid in whole-organism hydrolysates, complex mixtures of straight- and branched chain fatty acids, di- and tetrahydrogenated menaquinones as predominant isoprenologues, and complex polar lipid patterns containing diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol, phosphatidylinositol mannosides and uncharacterised components. The chemical and numerical data support the taxonomic integrity of the validly described species of Streptosporangium and suggest that the genus is markedly underspeciated.

  18. Quantum chemical and spectroscopic analysis of calcium hydroxyapatite and related materials

    SciTech Connect

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

    2007-02-15

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

  19. 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.

  20. Structural analysis of photosystem I polypeptides using chemical crosslinking.

    PubMed

    Armbrust, T S; Odom, W R; Guikema, J A

    1994-07-01

    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.

  1. Heparins: process-related physico-chemical and compositional characteristics, fingerprints and impurities.

    PubMed

    Liverani, Lino; Mascellani, Giuseppe; Spelta, Franco

    2009-11-01

    During the past 25 years, heparin extraction and purification processes have changed. The results of these changes are reflected by the continuous increase in potency of the International Standard for heparin. This increase is due not only to a higher purity, but also to a number of changes in the physico-chemical characteristics of heparin. For long time, all these changes have been disregarded as non-critical by regulatory authorities. Heparin marketing authorisation was reviewed only two years ago and Pharmacopoeia monographs were reviewed just for the addition of new tests, mainly aimed at tackling the oversulfated chondroitin sulfate (OSCS) crisis. Currently, heparin monographs are again under revision. Such changes, different for each manufacturer, have caused a further increase in the heterogeneity of individual batches of heparin. This review aims at showing that chemical, physical and biological characteristics of heparin (such as disaccharide composition, amount of low sulfated and high sulfated sequences, molecular weight profiles [MW], activities, structural artifacts, fingerprints and glycosaminoglycans impurities) are all process-dependent and may significantly vary when different processes are used to minimise the content of dermatan sulfate. The wide heterogeneity of the physico-chemical characteristics of currently marketed heparin and the lack of suitable and shareable reference standards for the identification/quantification of process-related impurities caused, and are still causing, heated debates among scientific institutions, companies and authorities.

  2. 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.

  3. Metal accumulation by stream bryophytes, related to chemical speciation.

    PubMed

    Tipping, E; Vincent, C D; Lawlor, A J; Lofts, S

    2008-12-01

    Metal accumulation by aquatic bryophytes was investigated using data for headwater streams of differing chemistry. The Windermere Humic Aqueous Model (WHAM) was applied to calculate chemical speciation, including competitive proton and metal interactions with external binding sites on the plants. The speciation modelling approach gives smaller deviations between observed and predicted bryophyte contents of Cu, Zn, Cd and Pb than regressions based on total filtered metal concentrations. If all four metals, and Ni, are considered together, the WHAM predictions are superior at the 1% level. Optimised constants for bryophyte binding by the trace metals are similar to those for humic substances and simple carboxylate ligands. Bryophyte contents of Na, Mg and Ca are approximately explained by binding at external sites, while most of the K is intracellular. Oxide phases account for some of the Al, and most of the Mn, Fe and Co.

  4. Relative cancer risks of chemical contaminants in the great lakes

    NASA Astrophysics Data System (ADS)

    Bro, Kenneth M.; Sonzogni, William C.; Hanson, Mark E.

    1987-08-01

    Anyone who drinks water or eats fish from the Great Lakes consumes potentially carcinogenic chemicals. In choosing how to respond to such pollution, it is important to put the risks these contaminants pose in perspective. Based on recent measurements of carcinogens in Great Lakes fish and water, calculations of lifetime risks of cancer indicate that consumers of sport fish face cancer risks from Great Lakes contaminants that are several orders of magnitude higher than the risks posed by drinking Great Lakes water. But drinking urban groundwater and breathing urban air may be as hazardous as frequent consumption of sport fish from the Great Lakes. Making such comparisons is difficult because of variation in types and quality of information available and in the methods for estimating risk. Much uncertainty pervades the risk assessment process in such areas as estimating carcinogenic potency and human exposure to contaminants. If risk assessment is to be made more useful, it is important to quantify this uncertainty.

  5. CD-REST: a system for extracting chemical-induced disease relation in literature.

    PubMed

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug-disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed fromhttp://clinicalnlptool.com/cdr The online CD-REST demonstration system is available athttp://clinicalnlptool.com/cdr/cdr.html. Database URL:http://clinicalnlptool.com/cdr;http://clinicalnlptool.com/cdr/cdr.html.

  6. 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...

  7. 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...

  8. Deformability Calculation for Estimation of the Relative Stability of Chemically Modified RNA Duplexes.

    PubMed

    Masaki, Yoshiaki; Sekine, Mitsuo; Seio, Kohji

    2017-03-02

    Chemical modification of RNA duplexes alters their stability. We have attempted to develop a computational approach to estimate the thermal stability of chemically modified duplexes. These studies revealed that the deformability of chemically modified RNA duplexes, calculated from molecular dynamics simulations, could be used as a good indicator for estimating the effect of chemical modification on duplex thermal stability. This unit describes how deformability calculation can be applied to estimate the relative stability of chemically modified RNA duplexes. © 2017 by John Wiley & Sons, Inc.

  9. [60]Fullerene-peptides: bio-nano conjugates with structural and chemical diversity.

    PubMed

    Barron, Andrew R

    2016-01-01

    [60]Fullerene-peptides represent a simple yet chemically diverse example of a bio-nano conjugate. The C60 moiety provides the following attributes to the conjugate: (a) precise three-dimensional architecture, (b) a large hydrophobic mass and (c) unique electronic properties. Conversely, the peptide component provides: (a) structural diversity depending on the overall length and amino acids composition, (b) charge flexibility and (c) secondary structure and recognition. Recent advances in the synthetic strategy for [60]fullerene-peptide synthesis from both pre-formed peptides and using solid phase peptide synthesis (SPPS) are described. The effects of the hydrophobic C60 on the secondary structure of the peptide depend on the sequence of the latter, but in general the relative stability of particular structures is greatly enhanced. The ability of the [60]fullerene substituent to dramatically modify both cellular uptake and transdermal transport is discussed as is the effects on cell viability and antimicrobial activity.

  10. Identification of New Candidate Genes and Chemicals Related to Esophageal Cancer Using a Hybrid Interaction Network of Chemicals and Proteins.

    PubMed

    Gao, Yu-Fei; Yuan, Fei; Liu, Junbao; Li, Li-Peng; He, Yi-Chun; Gao, Ru-Jian; Cai, Yu-Dong; Jiang, Yang

    2015-01-01

    Cancer is a serious disease responsible for many deaths every year in both developed and developing countries. One reason is that the mechanisms underlying most types of cancer are still mysterious, creating a great block for the design of effective treatments. In this study, we attempted to clarify the mechanism underlying esophageal cancer by searching for novel genes and chemicals. To this end, we constructed a hybrid network containing both proteins and chemicals, and generalized an existing computational method previously used to identify disease genes to identify new candidate genes and chemicals simultaneously. Based on jackknife test, our generalized method outperforms or at least performs at the same level as those obtained by a widely used method--the Random Walk with Restart (RWR). The analysis results of the final obtained genes and chemicals demonstrated that they highly shared gene ontology (GO) terms and KEGG pathways with direct and indirect associations with esophageal cancer. In addition, we also discussed the likelihood of selected candidate genes and chemicals being novel genes and chemicals related to esophageal cancer.

  11. 40 CFR 180.3 - Tolerances for related pesticide chemicals.

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ...-diethylphosphorodithioate)) containing approximately 70 percent cis and trans isomers and approximately 30 percent related... its beta isomer. m-(1-Methylbutyl)phenyl methylcarbamate. Methyl parathion. Naled (1,2-dibromo-2,2... and its isomer 2,3,5-trimethylphenyl methylcarbamate. (6) The following pesticides are members of...

  12. 40 CFR 180.3 - Tolerances for related pesticide chemicals.

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ...-diethylphosphorodithioate)) containing approximately 70 percent cis and trans isomers and approximately 30 percent related... its beta isomer. m-(1-Methylbutyl)phenyl methylcarbamate. Methyl parathion. Naled (1,2-dibromo-2,2... and its isomer 2,3,5-trimethylphenyl methylcarbamate. (6) The following pesticides are members of...

  13. Discourse structure and relative clause processing.

    PubMed

    Mak, Willem M; Vonk, Wietski; Schriefers, Herbert

    2008-01-01

    Studies in several languages have shown that subject-relative clauses are easier to process than object-relative clauses. Mak, Vonk, and Schriefers (2006) have proposed the topichood hypothesis to account for the preference for subject-relative clauses. This hypothesis claims that the entity in the relative clause that is most topicworthy will be chosen as the subject. By default, the antecedent of the relative clause will be chosen as the subject of the relative clause, because it is the topic of the relative clause. However, when the noun phrase (NP) in the relative clause is also topicworthy, the preference for the antecedent to be the subject will disappear. This was confirmed in two experiments. In Experiment 1, we tested relative clauses with a personal pronoun in the relative clause. We obtained a preference for object-relative clauses, in line with the assumption that personal pronouns refer to a discourse topic and are thus topicworthy. In Experiment 2, the discourse status of the NP in the relative clause was manipulated; either it was not present in the preceding context, or it was the discourse topic. The experiment showed that when the NP in the relative clause refers to the discourse topic, the difficulty of object-relative clauses is reduced, in comparison with relative clauses with an NP that is new in the discourse, even in the absence of any explicit cue in the relative clause itself. The experiments show that discourse factors guide processing at the sentence level.

  14. Review of chemical vapor deposition of graphene and related applications.

    PubMed

    Zhang, Yi; Zhang, Luyao; Zhou, Chongwu

    2013-10-15

    Since its debut in 2004, graphene has attracted enormous interest because of its unique properties. Chemical vapor deposition (CVD) has emerged as an important method for the preparation and production of graphene for various applications since the method was first reported in 2008/2009. In this Account, we review graphene CVD on various metal substrates with an emphasis on Ni and Cu. In addition, we discuss important and representative applications of graphene formed by CVD, including as flexible transparent conductors for organic photovoltaic cells and in field effect transistors. Growth on polycrystalline Ni films leads to both monolayer and few-layer graphene with multiple layers because of the grain boundaries on Ni films. We can greatly increase the percentage of monolayer graphene by using single-crystalline Ni(111) substrates, which have smooth surface and no grain boundaries. Due to the extremely low solubility of carbon in Cu, Cu has emerged as an even better catalyst for the growth of monolayer graphene with a high percentage of single layers. The growth of graphene on Cu is a surface reaction. As a result, only one layer of graphene can form on a Cu surface, in contrast with Ni, where more than one layer can form through carbon segregation and precipitation. We also describe a method for transferring graphene sheets from the metal using polymethyl methacrylate (PMMA). CVD graphene has electronic properties that are potentially valuable in a number of applications. For example, few-layer graphene grown on Ni can function as flexible transparent conductive electrodes for organic photovoltaic cells. In addition, because we can synthesize large-grain graphene on Cu foil, such large-grain graphene has electronic properties suitable for use in field effect transistors.

  15. Using chemical shifts to determine structural changes in proteins upon complex formation.

    PubMed

    Cavalli, Andrea; Montalvao, Rinaldo W; Vendruscolo, Michele

    2011-08-04

    Methods for determining protein structures using only chemical shift information are progressively becoming more accurate and reliable. A major problem, however, in the use of chemical shifts for the determination of the structures of protein complexes is that the changes in the chemical shifts upon binding tend to be rather limited and indeed often smaller than the standard errors made in the predictions of chemical shifts corresponding to given structures. We present a procedure that, despite this problem, enables one to use of chemical shifts to determine accurately the conformational changes that take place upon complex formation.

  16. 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

  17. Nepheline structural and chemical dependence on melt composition

    SciTech Connect

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

    2016-02-01

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

  18. Strategic Considerations in the Design of a Screening System for Substructure Searches of Chemical Structure Files

    ERIC Educational Resources Information Center

    Adamson, George W.; And Others

    1973-01-01

    A major problem in the design of screening systems for substructure searches of chemical structure files is the development of a methodology for selection of an optimal set of structural characteristics to act as screens. Distributions of several structural characteristics of the Chemical Abstracts Service Registry System are summarized. (13…

  19. The relationship between the toxicity and structure of nitroaromatic chemicals

    SciTech Connect

    Bailey, M.C.; Spanggord, R.J.

    1981-10-01

    The acute toxicities of nitrotoluene, dinitrotoluene, trinitrotoluene, aminonitrotoluene, aminodinitrotoluene, and dinitrobenzene isomers were evaluated in fathead minnows. For the nitroaromatics, toxicity appeared to be related to the number and orientation of nitro groups; compounds with nitro groups positioned ortho or para to each other were appreciably more toxic than isomers having the nitro groups in the meta orientation. In contrast, the toxicities of the aminonitrotoluenes and aminodinitrotoluenes were not related in any obvious way to their structures. Two mechanisms may account for the differences in toxicity between the nitroaromatic isomers: nucleophilic displacement of a nitro group and reduction of a nitro group. The available data indicate that reduction of a nitro group is the more likely pathway.

  20. Structure, Thermodynamics and Kinetics of Chemically Heterogeneous Interfaces

    NASA Astrophysics Data System (ADS)

    Palafox Hernandez, Jesus Pablo

    2011-12-01

    In this work we have used atomistic computer simulations to examine the structure, thermodynamics and transport properties, for two models of chemically heterogeneous interfaces: an ideal model (repulsive soft spheres against a potential wall), and a metal alloy interface (Cu-Pb). In both systems, interfacial prefreezing (crystal formation above the melting point of the fluid) was observed and this prefreezing was seen to promote heterogeneous nucleation, when the systems were cooled below the melting temperature. In our study of inverse-power repulsive soft spheres, we found that the soft-sphere fluid exhibited prefreezing at the wall surface. Similar behavior was previously observed in hard-sphere fluids at hard wall [17, 18, 20], however, to our knowledge, this the first time that prefreezing is reported for soft spheres. The prediction of prefreezing is based on the calculation of interfacial free energies wall-crystal (gammawc) and wall-fluid (gammawf) using a variant of the cleaving wall method. With the calculated, gammawc and gamma wf together with gammacf, previously computed [79], the tendency to prefreeze was quantified by the wetting angle formed between the metastable crystal phase on the wall and the soft-sphere fluid. We found that all the closest packing orientations [(111) FCC and (110) BCC] developed prefreezing (complete wetting). A detailed atomic-level characterization of the structure, energetics and transport properties of the planar Cu/Pb solid-liquid interface in equilibrium was performed at a several temperatures (625K and 750K) above the melting point of Pb and for two Cu crystal orientations [(111) and (100)]. Among the most relevant findings are that the Cu(100)/Pb interfaces presents surfaces alloying and the Cu(111)/Pb exhibits a prefreezing layer of Pb crystal. It was also observed that both interfaces have a nucleation barrier that prevents heterogeneous nucleation and that the mechanisms by which each structure promotes

  1. 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

  2. Nanolithography and nanochemistry: probe-related patterning techniques and chemical modification for nanometer-sized devices.

    PubMed

    Wouters, Daan; Schubert, Ulrich S

    2004-05-03

    The size regime for devices produced by photolithographic techniques is limited. Therefore, other patterning techniques have been intensively studied to create smaller structures. Scanning-probe-based patterning techniques, such as dip-pen lithography, local force-induced patterning, and local-probe oxidation-based techniques are highly promising because of their relative ease and widespread availability. The latter of these is especially interesting because of the possibility of producing nanopatterns for a broad range of chemical and physical modification and functionalization processes; both the production of nanometer-sized electronic devices and the formation of devices involving (bio)molecular recognition and sensor applications is possible. This Review highlights the development of various scanning probe systems and the possibilities of local oxidation methods, as well as giving an overview of state-of-the-art nanometer-sized devices, and a view of future development.

  3. Controllable Synthesis of Graphene by Plasma‐Enhanced Chemical Vapor Deposition and Its Related Applications

    PubMed Central

    Li, Menglin; Liu, Donghua; Song, Xuefen; Wei, Dapeng; Wee, Andrew Thye Shen

    2016-01-01

    Graphene and its derivatives hold a great promise for widespread applications such as field‐effect transistors, photovoltaic devices, supercapacitors, and sensors due to excellent properties as well as its atomically thin, transparent, and flexible structure. In order to realize the practical applications, graphene needs to be synthesized in a low‐cost, scalable, and controllable manner. Plasma‐enhanced chemical vapor deposition (PECVD) is a low‐temperature, controllable, and catalyst‐free synthesis method suitable for graphene growth and has recently received more attentions. This review summarizes recent advances in the PECVD growth of graphene on different substrates, discusses the growth mechanism and its related applications. Furthermore, the challenges and future development in this field are also discussed. PMID:27980983

  4. 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.

  5. 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...

  6. Immunoanalysis Methods for the Detection of Dioxins and Related Chemicals

    PubMed Central

    Tian, Wenjing; Xie, Heidi Qunhui; Fu, Hualing; Pei, Xinhui; Zhao, Bin

    2012-01-01

    With the development of biotechnology, approaches based on antibodies, such as enzyme-linked immunosorbent assay (ELISA), active aryl hydrocarbon immunoassay (Ah-I) and other multi-analyte immunoassays, have been utilized as alternatives to the conventional techniques based on gas chromatography and mass spectroscopy for the analysis of dioxin and dioxin-like compounds in environmental and biological samples. These screening methods have been verified as rapid, simple and cost-effective. This paper provides an overview on the development and application of antibody-based approaches, such as ELISA, Ah-I, and multi-analyte immunoassays, covering the sample extraction and cleanup, antigen design, antibody preparation and immunoanalysis. However, in order to meet the requirements for on-site fast detection and relative quantification of dioxins in the environment, further optimization is needed to make these immuno-analytical methods more sensitive and easy to use. PMID:23443395

  7. Chemical Carcinogenesis Testing and Related Issues - Subchronic Studies and Related Issues

    DTIC Science & Technology

    1985-05-01

    animals. "The dictum that ’inbred mice are as essential to the biologist as pure chemicals are for the chemist’ needs re- examination. The fact is that...been made that evidence for malignancy is essential before designating a 97 chemical as a carcinogen (Newberne, 1982; Newberne et al., 1982...administration in corn oil has come under considerable criti- cism. Although the fundamental reasor3 for this criticism are not easy to discern, those

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

    NASA Astrophysics Data System (ADS)

    Kumari, Amrita; Dorai, Kavita

    2013-06-01

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

  9. 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.

  10. Chemical Structure of Lipid A Isolated from Flavobacterium meningosepticum Lipopolysaccharide

    PubMed Central

    Kato, Hitomi; Haishima, Yuji; Iida, Takatoshi; Tanaka, Akira; Tanamoto, Ken-ichi

    1998-01-01

    The chemical structure of the lipid A of the lipopolysaccharide component isolated from Flavobacterium meningosepticum IFO 12535 was elucidated. Methylation and nuclear magnetic resonance analyses showed that two kinds of hydrophilic backbone exist in the free lipid A: a β (1→6)-linked 2-amino-2-deoxy-d-glucose, which is usually present in enterobacterial lipid A’s, and a 2-amino-6-O-(2,3-diamino-2,3-dideoxy-β-d-glucopyranosyl)-2-deoxy-d-glucose, in a molar ratio of 1.00:0.35. Both backbones were α-glycosidically phosphorylated in position 1, and the hydroxyl groups at positions 4, 4′, and 6′ were unsubstituted. Liquid secondary ion-mass spectrometry revealed a pseudomolecular ion at m/z 1673 [M-H]− as a major monophosphoryl lipid A component carrying five acyl groups. Fatty acid analysis showed that the lipid A contained 1 mol each of amide-linked (R)-3-OH iC17:0, ester-linked (R)-3-OH iC15:0, amide-linked (R)-3-O-(iC15:0)-iC17:0, and both amide- and ester-linked (R)-3-OH C16:0. Fatty acid distribution analyses using several mass spectrometry determinations demonstrated that the former two constituents were distributed on positions 2 and 3 of the reducing terminal unit of the backbones and that the latter two were attached to the 2′ and 3′ positions in the nonreducing terminal residue. PMID:9683486

  11. 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 ...

  12. A computer-Based System for Handling Chemical Nomenclature and Structural Representations

    ERIC Educational Resources Information Center

    Rowlett, Russell J.; Tate, Fred A.

    1972-01-01

    Among other improvements in chemical nomenclature used in the Chemical Registry System, Chemical Abstracts Service intends to standardize the fundamental principles for naming cyclic structures so that procedures for the derivation of ring names can become more amenable to computer generation and translation. (Author/NH)

  13. Two functions of the density matrix and their relation to the chemical bond

    NASA Astrophysics Data System (ADS)

    Schmider, Hartmut L.; Becke, Axel D.

    2002-02-01

    We examine and compare two previously introduced functions of the one-particle density matrix that are suitable to represent its off-diagonal structure in a condensed form and that have illustrative connections to the nature of the chemical bond. One of them, the Localized-Orbital Locator (LOL) [J. Molec. Struct. (THEOCHEM) 527, 51 (2000)], is based only on the noninteracting kinetic-energy density τ and the charge density ρ at a point, and gives an intuitive measure of the relative speed of electrons in its vicinity. Alternatively, LOL focuses on regions that are dominated by single localized orbitals. The other one, the Parity Function P [J. Chem. Phys. 105, 11134 (1996)], is a section through the Wigner phase-space function at zero momentum, and contains information about the phase of the interference of atomiclike orbital contributions from bound centers. In this paper, we discuss the way in which these functions condense information in the density matrix, and illustrate on a variety of examples of unusual chemical bonds how they can help to understand the nature of "covalence."

  14. Use of trophic magnification factors and related measures to characterize bioaccumulation potential of chemicals.

    PubMed

    Conder, Jason M; Gobas, Frank A P C; Borgå, Katrine; Muir, Derek C G; Powell, David E

    2012-01-01

    Recent technical workgroups have concluded that trophic magnification factors (TMFs) are useful in characterizing the bioaccumulation potential of a chemical, because TMFs provide a holistic measure of biomagnification in food webs. The objectives of this article are to provide a critical analysis of the application of TMFs for regulatory screening for bioaccumulation potential, and to discuss alternative methods for supplementing TMFs and assessing biomagnification in cases where insufficient data are available to determine TMFs. The general scientific consensus is that chemicals are considered bioaccumulative if they exhibit a TMF > 1. However, comparison of study-derived TMF estimates to this threshold value should be based on statistical analyses such that variability is quantified and false positive and false negative errors in classification of bioaccumulation potential are minimized. An example regulatory decision-making framework is presented to illustrate the use of statistical power analyses to minimize assessment errors. Suggestions for considering TMF study designs and TMFs obtained from multiple studies are also provided. Alternative bioaccumulation metrics are reviewed for augmenting TMFs and for substituting in situations in which field data for deriving TMFs are unavailable. Field-derived, trophic level-normalized biomagnification factors (BMF(TL) s), biota-sediment accumulation factors (BSAF(TL) s), and bioaccumulation factors (BAF(TL) s) are recommended if data are available, because these measures are most closely related to the biomagnification processes characterized by TMFs. Field- and laboratory-derived BAFs and bioconcentration factors are generally less accurate in predicting biomagnification. However, bioconcentration factors and BAFs remain useful for characterizing bioaccumulation as a result of the transfer of chemicals from abiotic environmental compartments to lower trophic levels. Modeling that incorporates available laboratory

  15. Synchronization of chemical noise-sustained structures in asymmetrically coupled differential-flow reactors.

    PubMed

    Izús, Gonzalo G; Sánchez, Alejandro D

    2013-12-01

    The differential-flow-induced chemical instability is investigated in the context of two coupled reactors with cubic autocatalytic kinetics (the Gray-Scott model). Previous results for master-slave arrangement [Izús, Deza, and Sánchez, J. Chem. Phys. 132, 234112 (2010)] are extended in this study to include bidirectional coupling between reactions. Numerical simulations in the convectively unstable regime show that synchronized noise-sustained structures are developed in both reactors due to the selective amplification of noise. A theoretical analysis shows that the nature of the synchronization and the stability of the synchronized manifold are related with the properties of the critical modes.

  16. 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

  17. Relating Students' Reasoning To the History of Science: The Case of Chemical Equilibrium.

    ERIC Educational Resources Information Center

    Van Driel, Jan H.; De Vos, Wobbe; Verloop, Nico

    1998-01-01

    Relates the reasoning of students introduced to the concept of chemical equilibrium to the historical development of the concept. Concludes that the study of authentic historical sources may inspire the design of effective teaching activities. Contains 33 references. (DDR)

  18. Exploring biological, chemical and geomorphological patterns in fluvial ecosystems with Structural Equation Modelling

    NASA Astrophysics Data System (ADS)

    Bizzi, S.; Surridge, B.; Lerner, D. N.:

    2009-04-01

    River ecosystems represent complex networks of interacting biological, chemical and geomorphological processes. These processes generate spatial and temporal patterns in biological, chemical and geomorphological variables, and a growing number of these variables are now being used to characterise the status of rivers. However, integrated analyses of these biological-chemical-geomorphological networks have rarely been undertaken, and as a result our knowledge of the underlying processes and how they generate the resulting patterns remains weak. The apparent complexity of the networks involved, and the lack of coherent datasets, represent two key challenges to such analyses. In this paper we describe the application of a novel technique, Structural Equation Modelling (SEM), to the investigation of biological, chemical and geomorphological data collected from rivers across England and Wales. The SEM approach is a multivariate statistical technique enabling simultaneous examination of direct and indirect relationships across a network of variables. Further, SEM allows a-priori conceptual or theoretical models to be tested against available data. This is a significant departure from the solely exploratory analyses which characterise other multivariate techniques. We took biological, chemical and river habitat survey data collected by the Environment Agency for 400 sites in rivers spread across England and Wales, and created a single, coherent dataset suitable for SEM analyses. Biological data cover benthic macroinvertebrates, chemical data relate to a range of standard parameters (e.g. BOD, dissolved oxygen and phosphate concentration), and geomorphological data cover factors such as river typology, substrate material and degree of physical modification. We developed a number of a-priori conceptual models, reflecting current research questions or existing knowledge, and tested the ability of these conceptual models to explain the variance and covariance within the

  19. Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network

    PubMed Central

    Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

    2016-01-01

    Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer. PMID:27149165

  20. Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network.

    PubMed

    Li, Zhandong; An, Lifeng; Li, Hao; Wang, ShaoPeng; Zhou, You; Yuan, Fei; Li, Lin

    2016-05-05

    Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.

  1. Evolution of salt-related structures

    SciTech Connect

    Bishop, R.S.

    1988-01-01

    Several types of structures (piercements, turtles, and nonpiercements) are caused by salt movement. Reconstructions show that the emplacement process is basically the same for many geometrically dissimilar structures, but that the great differences of shape originated from different patterns of sediment loading, salt thickness, and basin evolution. The reconstructions are generalizations derived from numerous real examples to show timing, evolution of dip, origin of thickness changes and overchanges, how the salt-sediment volume exchange occurs, and diagnostic criteria to interpret these events. Such reconstructions help to discriminate between turtles and nonpiercements, to interpret lithofacies, and to unravel the role of sedimentary events on the structural evolution. In addition, they illustrate the mechanism of diapirism, using criteria to help distinguish diapirism in an overburden having strength (the mechanism assumed here) from diapirism in a viscous overburden (the classical buoyancy theory). In general, many piercements may start quite early (even before a density inversion exists) and move primarily by extrusion or may alternate between extrusion and intrusion beneath a thin overburden. The pattern of sedimentation largely determines the pattern of diapirism. In contrast, nonpiercements and turtle structures are passive features and may form whenever salt migrates away from them to an adjacent ''escape hatch.'' For example, nonpiercements may not form by salt rising vertically, but rather by salt moving away horizontally to some point of escape. In other words, the dome remains static while the overburden collapses into the rim syncline.

  2. CD-REST: a system for extracting chemical-induced disease relation in literature

    PubMed Central

    Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

    2016-01-01

    Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug–disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed from http://clinicalnlptool.com/cdr. The online CD-REST demonstration system is available at http://clinicalnlptool.com/cdr/cdr.html. Database URL: http://clinicalnlptool.com/cdr; http://clinicalnlptool.com/cdr/cdr.html PMID:27016700

  3. Network structural analysis using directed graph for chemical reaction analysis in weakly-ionized plasmas

    NASA Astrophysics Data System (ADS)

    Nobuto, Kyosuke; Mizui, Yasutaka; Miyagi, Shigeyuki; Sakai, Osamu; Murakami, Tomoyuki

    2016-09-01

    We visualize complicated chemical reaction systems in weakly-ionized plasmas by analysing network structure for chemical processes, and calculate some indexes by assuming interspecies relationships to be a network to clarify them. With the current social evolution, the mean size of general data which we can use in computers grows huge, and significance of the data analysis increases. The methods of the network analysis which we focus on in this study do not depend on a specific analysis target, but the field where it has been already applied is still limited. In this study, we analyse chemical reaction systems in plasmas for configuring the network structure. We visualize them by expressing a reaction system in a specific plasma by a directed graph and examine the indexes and the relations with the characteristic of the species in the reaction system. For example, in the methane plasma network, the centrality index reveals importance of CH3 in an influential position of species in the reaction. In addition, silane and atmospheric pressure plasmas can be also visualized in reaction networks, suggesting other characteristics in the centrality indexes.

  4. 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

  5. Some critical issues and concerns related to research advances on toxicology of chemical mixtures.

    PubMed Central

    Yang, R S

    1998-01-01

    This paper addresses some of the issues and concerns on research advances on the toxicology of chemical mixtures. Emphases will be selectively given to the following questions and answers: Can mechanistic studies be conducted on chemical mixtures? The fact that any studies, including mechanistic studies, of single chemicals are really the study of the parent chemical plus its metabolites underscores the relevance of mechanistic studies on chemical mixtures. Can predictions be made on the health effects of chemical mixtures? Some successes are already evident in the literature on simpler chemical mixtures. For more complex mixtures, it is possible and we propose an approach here. What can we learn from other disciplines (the importance of interdisciplinary collaboration)? Two aspects, the knowledge and methodologies available in clinical pharmacology and the latest advances in structure-oriented lumping in chemical engineering, are discussed in detail. Unrepeatable results: The possibility of magnification of biologic variability because of low-level exposures to chemical mixtures is suggested with special reference to some known examples, including the controversial study on synergistic interactions of endocrine disruptors. Is the driving force for scientific investigations on chemical mixtures the legislative and regulatory atmosphere? Two laws with chemical mixtures specifically in the language are quoted and discussed. Their implications regarding research funding and activities are described. What are the pitfalls of applying for research funding on investigating chemical mixtures? The dilemma at least one investigator faces in pursuing research funding is elaborated. The questions and issues listed above are not all inclusive, but they represent some of the aspects that need to be brought into the open in the scientific community for discussion and/or debate. Thus, the primary objective of this paper is to provide some momentum for the beginning of a fruitful

  6. Probabilistic Relational Structures and Their Applications

    ERIC Educational Resources Information Center

    Domotor, Zoltan

    The principal objects of the investigation reported were, first, to study qualitative probability relations on Boolean algebras, and secondly, to describe applications in the theories of probability logic, information, automata, and probabilistic measurement. The main contribution of this work is stated in 10 definitions and 20 theorems. The basic…

  7. 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.

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

    PubMed Central

    Galdeano, Carles; Ciulli, Alessio

    2017-01-01

    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. PMID:27193077

  9. Application of a microcoil probe head in NMR analysis of chemicals related to the chemical weapons convention.

    PubMed

    Koskela, Harri; Vanninen, Paula

    2008-07-15

    A 1.7-mm microcoil probe head was tested in the analysis of organophosphorus compounds related to the Chemical Weapons Convention. The microcoil probe head demonstrated a high mass sensitivity in the detection of traces of organophosphorus compounds in samples. Methylphosphonic acid, the common secondary degradation product of sarin, soman, and VX, was detected at level 50 ng (0.52 nmol) from a 30-microL water sample using proton-observed experiments. Direct phosphorus observation of methylphosphonic acid with (31)P{(1)H} NMR experiment was feasible at the 400-ng (4.17 nmol) level. Application of the microcoil probe head in the spiked sample analysis was studied with a test water sample containing 2-10 microg/mL of three organophosphorus compounds. High-quality (1)H NMR, (31)P{(1)H} NMR, 2D (1)H-(31)P fast-HMQC, and 2D TOCSY spectra were obtained in 3 h from the concentrated 1.7-mm NMR sample prepared from 1 mL of the water solution. Furthermore, a 2D (1)H-(13)C fast-HMQC spectrum with sufficient quality was possible to measure in 5 h. The microcoil probe head demonstrated a considerable sensitivity improvement and reduction of measurement times for the NMR spectroscopy in identification of chemicals related to the Chemical Weapons Convention.

  10. 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.

  11. 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

  12. 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.

  13. 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.

  14. Supersaturated lysozyme solution structure studied by chemical cross-linking.

    PubMed

    Hall, Clayton L; Clemens, John R; Brown, Amanda M; Wilson, Lori J

    2005-06-01

    Glutaraldehyde cross-linking followed by separation has been used to detect aggregates of chicken egg-white lysozyme (CEWL) in supersaturated solutions. In solutions of varying NaCl content, the number of aggregates was found to be related to the ionic strength of the solution. Separation by SDS-PAGE showed that percentage of dimer in solution ranged from 25.3% for no NaCl to 27.1% at 15% NaCl, and the aggregates larger than dimer increased from 1.9% for no NaCl to 36.8% at 15% NaCl. Conversely, the percentage of monomers decreased from 72.8% without NaCl to 36.1% at 15% NaCl. Molecular weights by capillary electrophoresis (SDS-CE) were found to be multiples of the monomer molecular weights, with the exception of trimer, which indicates a very compact structure. Native separation was accomplished using size-exclusion chromatography (SEC) and gave a lower monomer concentration and higher aggregate concentration than SDS-CE, which is a denaturing separation method. Most noticeably, trimers were absent in the SEC separation. The number of aggregates did not change with increased time between addition of NaCl and addition of cross-linking agent when separated by gel electrophoresis (SDS-PAGE). The results suggest that high ionic strength CEWL solutions are highly aggregated and that denaturing separation methods disrupt cross-linked products.

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

    PubMed

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

    2013-09-01

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

  16. 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

  17. 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...

  18. Chemical Structure Search on the World Wide Web.

    ERIC Educational Resources Information Center

    Inlenfeldt, Wolf-D.

    Chemists have been very active in utilizing the World Wide Web as an information distribution medium and much interesting scientific chemical information is already offered on it. Various classical text-based search engines have made locating information on the Web easier. However, keyword-based searches are often insufficient for chemists…

  19. Interspecies quantitative structure-activity relationships (QSARs) for eco-toxicity screening of chemicals: the role of physicochemical properties.

    PubMed

    Furuhama, A; Hasunuma, K; Aoki, Y

    2015-01-01

    In addition to molecular structure profiles, descriptors based on physicochemical properties are useful for explaining the eco-toxicities of chemicals. In a previous study we reported that a criterion based on the difference between the partition coefficient (log POW) and distribution coefficient (log D) values of chemicals enabled us to identify aromatic amines and phenols for which interspecies relationships with strong correlations could be developed for fish-daphnid and algal-daphnid toxicities. The chemicals that met the log D-based criterion were expected to have similar toxicity mechanisms (related to membrane penetration). Here, we investigated the applicability of log D-based criteria to the eco-toxicity of other kinds of chemicals, including aliphatic compounds. At pH 10, use of a log POW - log D > 0 criterion and omission of outliers resulted in the selection of more than 100 chemicals whose acute fish toxicities or algal growth inhibition toxicities were almost equal to their acute daphnid toxicities. The advantage of log D-based criteria is that they allow for simple, rapid screening and prioritizing of chemicals. However, inorganic molecules and chemicals containing certain structural elements cannot be evaluated, because calculated log D values are unavailable.

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

    PubMed

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

    2015-09-01

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

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

    NASA Technical Reports Server (NTRS)

    1976-01-01

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

  2. 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.

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

    NASA Astrophysics Data System (ADS)

    Nagaoka, Masataka

    2015-12-01

    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.

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

    NASA Astrophysics Data System (ADS)

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

    2008-06-01

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

  5. IMPACT OF GRAIN EVOLUTION ON THE CHEMICAL STRUCTURE OF PROTOPLANETARY DISKS

    SciTech Connect

    Vasyunin, A. I.; Birnstiel, T.; Zhukovska, S.; Henning, T.; Dullemond, C. P.; Wiebe, D. S. E-mail: zhukovska@mpia.de E-mail: dullemon@mpia.de E-mail: dwiebe@inasan.ru

    2011-02-01

    We study the impact of dust evolution in a protoplanetary disk (PPD) around a T Tauri star on the disk's chemical composition. For the first time, we utilize a comprehensive model of dust evolution, which includes growth, fragmentation, and sedimentation. Specific attention is paid to the influence of grain evolution on the penetration of the UV field in the disk. A chemical model that includes a comprehensive set of gas-phase and grain-surface chemical reactions is used to simulate the chemical structure of the disk. The main effect of grain evolution on the disk's chemical composition comes from sedimentation and, to a lesser degree, from reduction of the total grain-surface area. The net effect of grain growth is suppressed by the fragmentation process which maintains a population of small grains, dominating the total grain surface area. We consider three models of dust properties. In model GS, both growth and sedimentation are taken into account. In models A5 and A4, all grains are assumed to be the same size (10{sup -5} cm and 10{sup -4} cm, respectively) with a constant gas-to-dust mass ratio of 100. As in previous studies, the 'three-layer' pattern (cold midplane, warm molecular layer, and hot atmosphere) in the disk-chemical structure is preserved in all models, but shifted closer to the midplane in models with increased grain size (GS and A4). Unlike other similar studies, we find that in models GS and A4, the column densities of most gas-phase species are enhanced by 1-3 orders of magnitude relative to those in a model with pristine dust (A5), while column densities of their surface counterparts are decreased. We show that column densities of certain species, such as C{sub 2}H, HC{sub 2n+1}N (n = 0-3), H{sub 2}O, and some other molecules, as well as the C{sub 2}H{sub 2}/HCN abundance ratio, all of which are accessible with Herschel and ALMA, can be used as observational tracers of early stages of the grain evolution process in PPDs.

  6. Battery structures, self-organizing structures and related methods

    SciTech Connect

    Chiang, Yet-Ming; Moorehead, William D; Gozdz, Antoni S; Holman, Richard K; Loxley, Andrew L; Riley, Jr., Gilbert N.; Viola, Michael S

    2012-06-26

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling force on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionically conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  7. Battery structures, self-organizing structures and related methods

    SciTech Connect

    Chiang, Yet-Ming; Moorehead, William D.; Gozdz, Antoni S.; Holman, Richard K.; Loxley, Andrew L.; Riley, Jr., Gilbert N.; Viola, Michael S.

    2011-08-02

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling force on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionically conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  8. Battery structures, self-organizing structures and related methods

    SciTech Connect

    Chiang, Yet Ming; Moorehead, William Douglas; Gozdz, Antoni S.; Holman, Richard K.; Loxley, Andrew; Riley, Jr., Gilbert N.; Viola, Michael S.

    2009-08-25

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling force on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionically conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  9. Battery structures, self-organizing structures and related methods

    SciTech Connect

    Chiang, Yet-Ming; Moorehead, William D; Gozdz, Antoni S; Holman, Richard K; Loxley, Andrew L; Riley, Jr., Gilbert N.; Viola, Michael S

    2012-05-01

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling force on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionically conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  10. Battery structures, self-organizing structures, and related methods

    SciTech Connect

    Chiang, Yet-Ming; Moorehead, William Douglas

    2013-11-19

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling forve on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionicaily conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  11. Battery Structures, self-organizing structures, and related methods

    SciTech Connect

    Chiang, Yet-Ming; Moorehead, William Douglas

    2013-11-12

    An energy storage device includes a first electrode comprising a first material and a second electrode comprising a second material, at least a portion of the first and second materials forming an interpenetrating network when dispersed in an electrolyte, the electrolyte, the first material and the second material are selected so that the first and second materials exert a repelling force on each other when combined. An electrochemical device, includes a first electrode in electrical communication with a first current collector; a second electrode in electrical communication with a second current collector; and an ionically conductive medium in ionic contact with said first and second electrodes, wherein at least a portion of the first and second electrodes form an interpenetrating network and wherein at least one of the first and second electrodes comprises an electrode structure providing two or more pathways to its current collector.

  12. Toward Relatively General and Accurate Quantum Chemical Predictions of Solid-State (17)O NMR Chemical Shifts in Various Biologically Relevant Oxygen-Containing Compounds.

    PubMed

    Rorick, Amber; Michael, Matthew A; Yang, Liu; Zhang, Yong

    2015-09-03

    Oxygen is an important element in most biologically significant molecules, and experimental solid-state (17)O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state (17)O NMR chemical shift tensor properties are still challenging in many cases, and in particular, each of the prior computational works is basically limited to one type of oxygen-containing system. This work provides the first systematic study of the effects of geometry refinement, method, and basis sets for metal and nonmetal elements in both geometry optimization and NMR property calculations of some biologically relevant oxygen-containing compounds with a good variety of XO bonding groups (X = H, C, N, P, and metal). The experimental range studied is of 1455 ppm, a major part of the reported (17)O NMR chemical shifts in organic and organometallic compounds. A number of computational factors toward relatively general and accurate predictions of (17)O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient (R(2)) value of 0.9880 and a mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and an R(2) value of 0.9926 for all shift-tensor properties. These results shall facilitate future computational studies of (17)O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help the refinement and determination of active-site structures of some oxygen-containing substrate-bound proteins.

  13. 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.

  14. 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.

  15. 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.

  16. Investigation of Chemical Durability Mechanisms and Structure of Fluoride Glasses.

    DTIC Science & Technology

    1988-03-01

    coatings on fluoride glasses , it is possible to state the following conclusions: ()Coatings are necessary for both bulk and fiber optics to avoid major...interest for fiber optics applications.’ The chemicalSp . b g rdurability behavior of fluoride glasses not containing zirconium will be reported in later... fiber optics glass containing the base ZBL composition with where X = ppm in solution. V = solution volume (mL), S = additives of Al, Li, and Pb (Fig. 2

  17. Kinetics with chemical reactions and nonequilibrium structures in open systems

    NASA Astrophysics Data System (ADS)

    Aristov, Vladimir; Frolova, Anna; Zabelok, Sergei

    2013-10-01

    Simulations of flows on the basis of kinetic equations for mixtures with chemical reactions are performed. The Nonuniform Relaxation Problems (NRP) are formulated and solved. The Unified Flow Solver (UFS) is used for 1D and 2D NRP. The nonequilibrium kinetics can provide results outside the traditional theory of macroscopic phenomena based on the Navier-Stokes equations. Nonequilibrium flows with different properties in relaxation zones are described.

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

    PubMed

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

    2016-01-01

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

  19. Application of data mining tools for classification of protein structural class from residue based averaged NMR chemical shifts.

    PubMed

    Kumar, Arun V; Ali, Rehana F M; Cao, Yu; Krishnan, V V

    2015-10-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue's averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80% accuracy measured by Matthew correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with >90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments.

  20. Application of Data Mining Tools for Classification of Protein Structural Class from Residue Based Averaged NMR Chemical Shifts

    PubMed Central

    Kumar, Arun. V.; Ali, Rehana F.M.; Cao, Yu; Krishnan, V.V.

    2015-01-01

    The number of protein sequences deriving from genome sequencing projects is outpacing our knowledge about the function of these proteins. With the gap between experimentally characterized and uncharacterized proteins continuing to widen, it is necessary to develop new computational methods and tools for protein structural information that is directly related to function. Nuclear magnetic resonance (NMR) provides powerful means to determine three-dimensional structures of proteins in the solution state. However, translation of the NMR spectral parameters to even low-resolution structural information such as protein class requires multiple time consuming steps. In this paper, we present an unorthodox method to predict the protein structural class directly by using the residue’s averaged chemical shifts (ACS) based on machine learning algorithms. Experimental chemical shift information from 1491 proteins obtained from Biological Magnetic Resonance Bank (BMRB) and their respective protein structural classes derived from structural classification of proteins (SCOP) were used to construct a data set with 119 attributes and 5 different classes. Twenty four different classification schemes were evaluated using several performance measures. Overall the residue based ACS values can predict the protein structural classes with 80 % accuracy measured by Matthew Correlation coefficient. Specifically protein classes defined by mixed αβ or small proteins are classified with > 90% correlation. Our results indicate that this NMR-based method can be utilized as a low-resolution tool for protein structural class identification without any prior chemical shift assignments. PMID:25758094

  1. 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

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

    EPA Science Inventory

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

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

    PubMed Central

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

    2009-01-01

    Background and Aims Previous studies have reported effects of pollen source on the oil concentration of maize (Zea mays) kernels through modifications to both the embryo/kernel ratio and embryo oil concentration. The present study expands upon previous analyses by addressing pollen source effects on the growth of kernel structures (i.e. pericarp, endosperm and embryo), allocation of embryo chemical constituents (i.e. oil, protein, starch and soluble sugars), and the anatomy and histology of the embryos. Methods Maize kernels with different oil concentration were obtained from pollinations with two parental genotypes of contrasting oil concentration. The dynamics of the growth of kernel structures and allocation of embryo chemical constituents were analysed during the post-flowering period. Mature kernels were dissected to study the anatomy (embryonic axis and scutellum) and histology [cell number and cell size of the scutellums, presence of sub-cellular structures in scutellum tissue (starch granules, oil and protein bodies)] of the embryos. Key Results Plants of all crosses exhibited a similar kernel number and kernel weight. Pollen source modified neither the growth period of kernel structures, nor pericarp growth rate. By contrast, pollen source determined a trade-off between embryo and endosperm growth rates, which impacted on the embryo/kernel ratio of mature kernels. Modifications to the embryo size were mediated by scutellum cell number. Pollen source also affected (P < 0·01) allocation of embryo chemical compounds. Negative correlations among embryo oil concentration and those of starch (r = 0·98, P < 0·01) and soluble sugars (r = 0·95, P < 0·05) were found. Coincidently, embryos with low oil concentration had an increased (P < 0·05–0·10) scutellum cell area occupied by starch granules and fewer oil bodies. Conclusions The effects of pollen source on both embryo/kernel ratio and allocation of embryo chemicals seems to be related to the early

  4. The universal relation of galactic chemical evolution: the origin of the mass-metallicity relation

    SciTech Connect

    Zahid, H. Jabran; Dima, Gabriel I.; Kudritzki, Rolf-Peter; Kewley, Lisa J.; Geller, Margaret J.; Hwang, Ho Seong; Silverman, John D.; Kashino, Daichi

    2014-08-20

    We examine the mass-metallicity relation for z ≲ 1.6. The mass-metallicity relation follows a steep slope with a turnover, or 'knee', at stellar masses around 10{sup 10} M {sub ☉}. At stellar masses higher than the characteristic turnover mass, the mass-metallicity relation flattens as metallicities begin to saturate. We show that the redshift evolution of the mass-metallicity relation depends only on the evolution of the characteristic turnover mass. The relationship between metallicity and the stellar mass normalized to the characteristic turnover mass is independent of redshift. We find that the redshift-independent slope of the mass-metallicity relation is set by the slope of the relationship between gas mass and stellar mass. The turnover in the mass-metallicity relation occurs when the gas-phase oxygen abundance is high enough that the amount of oxygen locked up in low-mass stars is an appreciable fraction of the amount of oxygen produced by massive stars. The characteristic turnover mass is the stellar mass, where the stellar-to-gas mass ratio is unity. Numerical modeling suggests that the relationship between metallicity and the stellar-to-gas mass ratio is a redshift-independent, universal relationship followed by all galaxies as they evolve. The mass-metallicity relation originates from this more fundamental universal relationship between metallicity and the stellar-to-gas mass ratio. We test the validity of this universal metallicity relation in local galaxies where stellar mass, metallicity, and gas mass measurements are available. The data are consistent with a universal metallicity relation. We derive an equation for estimating the hydrogen gas mass from measurements of stellar mass and metallicity valid for z ≲ 1.6 and predict the cosmological evolution of galactic gas masses.

  5. Chemical Tagging Can Work: Identification of Stellar Phase-space Structures Purely by Chemical-abundance Similarity

    NASA Astrophysics Data System (ADS)

    Hogg, David W.; Casey, Andrew R.; Ness, Melissa; Rix, Hans-Walter; Foreman-Mackey, Daniel; Hasselquist, Sten; Ho, Anna Y. Q.; Holtzman, Jon A.; Majewski, Steven R.; Martell, Sarah L.; Mészáros, Szabolcs; Nidever, David L.; Shetrone, Matthew

    2016-12-01

    Chemical tagging promises to use detailed abundance measurements to identify spatially separated stars that were, in fact, born together (in the same molecular cloud) long ago. This idea has not yielded much practical success, presumably because of the noise and incompleteness in chemical-abundance measurements. We have succeeded in substantially improving spectroscopic measurements with The Cannon, which has now delivered 15 individual abundances for ∼ {10}5 stars observed as part of the APOGEE spectroscopic survey, with precisions around 0.04 dex. We test the chemical-tagging hypothesis by looking at clusters in abundance space and confirming that they are clustered in phase space. We identify (by the k-means algorithm) overdensities of stars in the 15-dimensional chemical-abundance space delivered by The Cannon, and plot the associated stars in phase space. We use only abundance-space information (no positional information) to identify stellar groups. We find that clusters in abundance space are indeed clusters in phase space, and we recover some known phase-space clusters and find other interesting structures. This is the first-ever project to identify phase-space structures at the survey-scale by blind search purely in abundance space; it verifies the precision of the abundance measurements delivered by The Cannon the prospects for future data sets appear very good.

  6. Effects of chemical contaminants on growth, age-structure, and reproduction of Mytilus edulis complex from Puget sound, Washington.

    PubMed

    Kagley, Anna N; Kardong, Kyle E; Snider, Robert G; Casillas, Edmundo

    2014-07-01

    Bivalves are used as sentinel species to detect chemical contaminants in the marine environment, but biological effects on indigenous populations that result from chemical exposure are largely unknown. We assessed age-weight, length-weight relationships, age structure, and reproductive status (i.e. fecundity, egg size) of the blue mussel Mytilus edulis complex from six sites in central Puget Sound, Washington, and one site in the relatively pristine area of northern Puget Sound. Results of this study suggest that mussels from urban areas of Puget Sound exhibit a lower growth rate, altered population age-structure, and potential reproductive impairment as a result of exposure to chemical contaminants. These findings support the use of mussels as sentinel species to assess the biological effects of contaminants on invertebrate populations.

  7. The screening of chemicals for juvenoid-related endocrine activity using the water flea Daphnia magna.

    PubMed

    Wang, Helen Ying; Olmstead, Allen W; Li, Hong; Leblanc, Gerald A

    2005-09-10

    U.S. Environmental Protection Agency is charged with developing a screening and testing paradigm for detecting endocrine toxicity of chemicals that are subject to regulation under the Food Quality Protection and the Safe Drinking Water Acts. In this study, we developed and evaluated a screening assay that could be employed to detect juvenoid-related endocrine-modulating activity in an invertebrate species. Juvenoid activity, anti-juvenoid activity, and juvenoid potentiator activity of chemicals was assessed using the water flea Daphnia magna. Male sex determination is under the regulatory control of juvenoid hormone, presumably methyl farnesoate, and this endpoint was used to detect juvenoid modulating activity of chemicals. Eighteen chemicals were evaluated for juvenoid agonist activity. Positive responses were detected with the juvenoid hormones methyl farnesoate and juvenile hormone III along with the insect growth regulating insecticides pyriproxyfen, fenoxycarb, and methoprene. Weak juvenoid activity also was detected with the cyclodiene insecticide dieldrin. Assays performed repetitively with compounds that gave either strong positive, weak positive, or negative response were 100% consistent indicating that the assay is not prone to false positive or negative responses. Five candidate chemicals were evaluated for anti-juvenoid activity and none registered positive. Four chemicals (all trans-retinoic acid, methoprene, kinoprene, bisphenol A) also were evaluated for their ability to potentiate the activity of methyl farnesoate. All registered positive. Results demonstrate that an in vivo assay with a crustacean species customarily employed in toxicity testing can be used to effectively screen chemicals for juvenoid-modulating activity.

  8. Chemically related 4,5-linked aminoglycoside antibiotics drive subunit rotation in opposite directions

    PubMed Central

    Wasserman, Michael R.; Pulk, Arto; Zhou, Zhou; Altman, Roger B.; Zinder, John C.; Green, Keith D.; Garneau-Tsodikova, Sylvie; Doudna Cate, Jamie H.; Blanchard, Scott C.

    2015-01-01

    Dynamic remodelling of intersubunit bridge B2, a conserved RNA domain of the bacterial ribosome connecting helices 44 (h44) and 69 (H69) of the small and large subunit, respectively, impacts translation by controlling intersubunit rotation. Here we show that aminoglycosides chemically related to neomycin—paromomycin, ribostamycin and neamine—each bind to sites within h44 and H69 to perturb bridge B2 and affect subunit rotation. Neomycin and paromomycin, which only differ by their ring-I 6′-polar group, drive subunit rotation in opposite directions. This suggests that their distinct actions hinge on the 6′-substituent and the drug's net positive charge. By solving the crystal structure of the paromomycin–ribosome complex, we observe specific contacts between the apical tip of H69 and the 6′-hydroxyl on paromomycin from within the drug's canonical h44-binding site. These results indicate that aminoglycoside actions must be framed in the context of bridge B2 and their regulation of subunit rotation. PMID:26224058

  9. 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

  10. STRUCTURE AND FEEDBACK IN 30 DORADUS. II. STRUCTURE AND CHEMICAL ABUNDANCES

    SciTech Connect

    Pellegrini, E. W.; Baldwin, J. A.; Ferland, G. J.

    2011-09-01

    We use our new optical-imaging and spectrophotometric survey of key diagnostic emission lines in 30 Doradus, together with CLOUDY photoionization models, to study the physical conditions and ionization mechanisms along over 4000 individual lines of sight at points spread across the face of the extended nebula, out to a projected radius 75 pc from R136 at the center of the ionizing cluster NGC 2070. We focus on the physical conditions, geometry, and importance of radiation pressure on a point-by-point basis, with the aim of setting observational constraints on important feedback processes. We find that the dynamics and large-scale structure of 30 Dor are set by a confined system of X-ray bubbles in rough pressure equilibrium with each other and with the confining molecular gas. Although the warm (10,000 K) gas is photoionized by the massive young stars in NGC 2070, the radiation pressure does not currently play a major role in shaping the overall structure. The completeness of our survey also allows us to create a composite spectrum of 30 Doradus, simulating the observable spectrum of a spatially unresolved, distant giant extragalactic H II region. We find that the highly simplified models used in the 'strong line' abundance technique do in fact reproduce our observed line strengths and deduced chemical abundances, in spite of the more than one order of magnitude range in the ionization parameter and density of the actual gas in 30 Dor.

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

    NASA Astrophysics Data System (ADS)

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

    2013-09-01

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

  12. Computer Translation of Systematic Chemical Nomenclature to Structural Formulas--Steroids

    ERIC Educational Resources Information Center

    Stillwell, R. N.

    1973-01-01

    A program (FORMULA) is described which translates the systematic chemical names of steroids to structural formulas which, with a suitable graphic output device could be used for direct typesetting. (10 references) (Author)

  13. 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...

  14. 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...

  15. A review of the natural occurrence, synthetic production and use of carcinogenic hydrazines and related chemicals.

    PubMed

    Toth, B

    2000-01-01

    This writing details the natural occurrence, synthetic production and use of the carcinogenic hydrazines and related chemicals. Twenty-three such chemicals were found in nature in mushrooms, tobacco, bay leaves, antibiotics, soil and other sources. The synthetically-produced hydrazines and related chemicals include 61 compounds which were or are in use as pharmaceutical drugs, agricultural substances, industrial chemicals and fuels for military and space vehicles and rockets. Because there is an overlap between the naturally-occurring and synthetically-produced compounds, their total number is 76. Altogether, 98 hydrazines and related chemicals were studied for carcinogenic action thus far, of which 84 were found to be carcinogenic and the remaining 14 were inactive. This means that the human population is exposed in various degrees to a substantial number of these agents. Therefore, the hydrazine class, unlike the polycyclic aromatic hydrocarbons, N-nitroso compounds, and aromatic amines, poses a greater environmental risk to the human population. In view of these considerations, it appears reasonable to proceed with additional experimentation in this field of interest.

  16. Structure of porcine heart cytoplasmic malate dehydrogenase: combining x-ray diffraction and chemical sequence data in structural studies

    SciTech Connect

    Birktoft, J.J.; Bradshaw, R.A.; Banaszak, L.J.

    1987-05-19

    The amino acid sequence of cytoplasmic malate dehydrogenase (sMDH) has been determined by a combination of X-ray crystallographic and chemical sequencing methods. The initial molecular model incorporated an X-ray amino acid sequence that derived primarily from an evaluation of a multiple isomorphous replacement phased electron density map calculated at 2.5-A resolution. Following restrained least-squares crystallographic refinement, difference electron density maps were calculated from model phases, and attempts were made to upgrade the X-ray amino acid sequence. The method used to find the positions of peptides in the X-ray structure was similar to those used for studying protein homology and was shown to be successful for large fragments. For sMDH, X-ray methods by themselves were insufficient to derive a complete amino acid sequence, even with partial chemical sequence data. However, for this relatively large molecule at medium resolution, the electron density maps were of considerable help in determining the linear position of peptide fragments. The N-acetylated polypeptide chain of sMDH has 331 amino acids and has been crystallographically refined to an R factor of 19% for 2.5-A resolution diffraction data.

  17. A relation between sphere size and chemical composition of Australian opal

    NASA Astrophysics Data System (ADS)

    Milke, R.; Liesegang, M.

    2012-12-01

    Opal forms in dissolution-reprecipitation processes in an interplay of factors such as pH, solution chemistry, host rock composition, temperature, pressure and time. The key to their understanding is on the chemical and structural micro- and nanoscale. Opal-A has a very low degree of order on the atomic scale. In contrast, on microscale precious opal is characterized by highly ordered stacking of monodisperse spheres. Despite progress in the synthesis of opaline structures, there is no satisfactory answer to the ordering process leading to natural photonic crystals due to the multiple influences in geological systems. Also, the processes leading to the preservation of microscopic structures through opal pseudomorphs are widely unknown. We investigated silicified materials and their host rocks from the opal fields of Andamooka (South Australia) and Yowah (Queensland) by petrographic microscopy, XRD, SEM, Raman spectroscopy and EMPA. The opaline silica filled voids and replaced several substances such as fossil shells, trigonal crystals, clasts in a silicified breccia, wood, ooids and rhombic, elongated minerals of uncertain origin. SEM investigations reveal the abundant presence of opal-A, commonly consisting of spheres 150-260 nm in diameter. Monodisperse spheres with a relative standard deviation in sphere diameter of less than 9% are composed of up to three shells. XRD and Raman spectroscopic investigations show that opal-A initially possesses varying degrees of crystallinity. The main broad Si-O-Si band in Raman scattering spectra at 412±6 cm-1 and the main peak in X-ray diffractograms at 4,004pm0,011 A (FWHM of 7,1pm0,4 2theta) are negatively correlated. The mean water content of opal-A is in the range of 4 - 8 wt%. Impurities of all opal-A samples are Al, Fe, Ca, Na and K, all but Al appearing only in traces. Polydisperse spheres have more uniform element concentrations than monodisperse ones. Recrystallized fossil shells with perfectly replicated

  18. Fiber ring laser interrogated zeolite-coated singlemode-multimode-singlemode structure for trace chemical detection.

    PubMed

    Lan, X; Huang, J; Han, Q; Wei, T; Gao, Z; Jiang, H; Dong, J; Xiao, H

    2012-06-01

    Zeolite thin films were synthesized on the claddingless multimode portion of a singlemode-multimode-singlemode (SMS) fiber structure to construct a chemical vapor sensor. The zeolite-coated SMS structure was inserted into a fiber ring amplifier to produce a laser line. Combining the strong molecular adsorption capability of the nanoporous zeolite and the high signal-to-noise ratio of the fiber laser, the device was demonstrated for chemical vapor sensing with a low detection limit.

  19. Chemical bonding and electronic-structure in MAX phases as viewed by X-ray spectroscopy and density functional theory

    NASA Astrophysics Data System (ADS)

    Magnuson, Martin; Mattesini, Maurizio

    2017-01-01

    This is a critical review of MAX-phase carbides and nitrides from an electronic-structure and chemical bonding perspective. This large group of nanolaminated materials is of great scientific and technological interest and exhibit a combination of metallic and ceramic features. These properties are related to the special crystal structure and bonding characteristics with alternating strong M-C bonds in high-density MC slabs, and relatively weak M-A bonds between the slabs. Here, we review the trend and relationship between the chemical bonding, conductivity, elastic and magnetic properties of the MAX phases in comparison to the parent binary MX compounds with the underlying electronic structure probed by polarized X-ray spectroscopy. Spectroscopic studies constitute important tests of the results of state-of-the-art electronic structure density functional theory that is extensively discussed and are generally consistent. By replacing the elements on the M, A, or X-sites in the crystal structure, the corresponding changes in the conductivity, elasticity, magnetism and other materials properties makes it possible to tailor the characteristics of this class of materials by controlling the strengths of their chemical bonds.

  20. Some basic data structures and algorithms for chemical generic programming.

    PubMed

    Zhang, Wei; Hou, Tingjun; Qiao, Xuebin; Xu, Xiaojie

    2004-01-01

    Here, we report a template library used for molecular operation, the Molecular Handling Template Library (MHTL). The library includes some generic data structures and generic algorithms, and the two parts are associated with each other by two concepts: Properties and Molecule. The concept Properties describes the interface to access objects' properties, and the concept Molecule describes the minimum requirement for a molecular class. Data structures include seven models of Properties, each using a different method to access properties, and two models of molecular classes. Algorithms include molecular file manipulation subroutines, SMARTS language interpreter and matcher functions, and molecular OpenGL rendering functions.

  1. 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

  2. Analogies (Adages) as Aids for Comprehending Structural Relations in Text.

    ERIC Educational Resources Information Center

    Moreno, Virginia; Di Vesta, Francis J.

    1994-01-01

    In 2 experiments involving a total of 43 college students, adages (relational metaphors) were found to facilitate processing of general ideas and higher-order principles. The higher the degree of structural relations embedded in the titles of passages, the greater the recall and accessibility of system-related ideas. (SLD)

  3. 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

  4. Chemical structure of the deep atmosphere of Jupiter

    NASA Technical Reports Server (NTRS)

    Barshay, S. S.; Lewis, J. S.

    1978-01-01

    Equilibrium abundances calculated for a system of over 500 compounds of 27 selected elements along a nominal Jupiter adiabat are reported. Several species predicted to be of negligible abundance in the visible upper troposphere if chemical equilibrium is exactly attained are found to be potential tracers of rapid vertical motions. Vertical mixing of certain species, especially CO, PH3, AsH3, GeS, and GeH4, may provide detectable quantities of these species near the visible cloudtops due to quenching and incomplete equilibration of the rapidly rising, rapidly cooling gas. Observational prospects for detecting such tracers of deep circulation are discussed in the light of the spectroscopic detection of CO in the 5-micron window on Jupiter and the confirmation of PH3 on both Jupiter and Saturn.

  5. Chemical ordering in Cr3Al and relation to semiconducting behavior

    NASA Astrophysics Data System (ADS)

    Boekelheide, Z.; Stewart, D. A.; Hellman, F.

    2012-08-01

    Cr3Al shows semiconductor-like behavior which has been attributed to a combination of antiferromagnetism and chemical ordering of the Cr and Al atoms on the bcc sublattice. This article presents a detailed theoretical and experimental study of the chemical ordering in Cr3Al. Using density functional theory within the Korringa-Kohn-Rostoker (KKR) formalism, we consider five possible structures with the Cr3Al stoichiometry: a bcc solid solution, two-phase C11b Cr2Al+Cr, off-stoichiometric C11b Cr3Al, D03 Cr3Al, and X-phase Cr3Al. The calculations show that the chemically ordered, rhombohedrally distorted X-phase structure has the lowest energy of those considered and should, therefore, be the ground state found in nature, while the D03 structure has the highest energy and should not occur. While KKR calculations of the X phase indicate a pseudogap in the density of states, additional calculations using a full potential linear muffin-tin orbital approach and a plane-wave technique show a narrow band gap. Experimentally, thin films of Cr1-xAlx were grown and the concentration, growth temperature, and substrate were varied systematically. The peak resistivity (2400 μΩ-cm) is found for films with x=0.25, grown epitaxially on a 300 ∘C MgO substrate. At this x, a transition between nonmetallic and metallic behavior occurs at a growth temperature of about 400 ∘C, which is accompanied by a change in chemical ordering from X phase to C11b Cr3Al. These results clarify the range of possible structures for Cr3Al and the relationship between chemical ordering and electronic transport behavior.

  6. 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.

  7. Structure determination of noncanonical RNA motifs guided by 1H NMR chemical shifts

    PubMed Central

    Sripakdeevong, Parin; Cevec, Mirko; Chang, Andrew T.; Erat, Michèle C.; Ziegeler, Melanie; Zhao, Qin; Fox, George E.; Gao, Xiaolian; Kennedy, Scott D.; Kierzek, Ryszard; Nikonowicz, Edward P.; Schwalbe, Harald; Sigel, Roland K. O.; Turner, Douglas H.; Das, Rhiju

    2014-01-01

    Structured non-coding RNAs underline fundamental cellular processes, but determining their 3D structures remains challenging. We demonstrate herein that integrating NMR 1H chemical shift data with Rosetta de novo modeling can consistently return high-resolution RNA structures. On a benchmark set of 23 noncanonical RNA motifs, including 11 blind targets, Chemical-Shift-ROSETTA for RNA (CS-ROSETTA-RNA) recovered the experimental structures with high accuracy (0.6 to 2.0 Å all-heavy-atom rmsd) in 18 cases. PMID:24584194

  8. 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...

  9. Chemical structure and biological activity of the diazepines

    PubMed Central

    Danneberg, P.; Weber, K. H.

    1983-01-01

    1 Since the introduction of chlordiazepoxide and diazepam many diazepines have been developed. Use of these drugs is increasing and considerable knowledge has accumulated about their mechanisms of action. 2 The structural and pharmacological properties of these drugs are surveyed briefly. PMID:6140944

  10. 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.

  11. Assessing the Chemical Accuracy of Protein Structures via Peptide Acidity

    PubMed Central

    Anderson, Janet S.; Hernández, Griselda; LeMaster, David M.

    2012-01-01

    Although the protein native state is a Boltzmann conformational ensemble, practical applications often require a representative model from the most populated region of that distribution. The acidity of the backbone amides, as reflected in hydrogen exchange rates, is exquisitely sensitive to the surrounding charge and dielectric volume distribution. For each of four proteins, three independently determined X-ray structures of differing crystallographic resolution were used to predict exchange for the static solvent-exposed amide hydrogens. The average correlation coefficients range from 0.74 for ubiquitin to 0.93 for Pyrococcus furiosus rubredoxin, reflecting the larger range of experimental exchange rates exhibited by the latter protein. The exchange prediction errors modestly correlate with the crystallographic resolution. MODELLER 9v6-derived homology models at ~60% sequence identity (36% identity for chymotrypsin inhibitor CI2) yielded correlation coefficients that are ~0.1 smaller than for the cognate X-ray structures. The most recently deposited NOE-based ubiquitin structure and the original NMR structure of CI2 fail to provide statistically significant predictions of hydrogen exchange. However, the more recent RECOORD refinement study of CI2 yielded predictions comparable to the X-ray and homology model-based analyses. PMID:23182463

  12. 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...

  13. 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...

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

    ERIC Educational Resources Information Center

    Wheeler, Alan E.; Kass, Heidi

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

  15. Structural, chemical and biological aspects of antioxidants for strategies against metal and metalloid exposure

    PubMed Central

    2009-01-01

    Oxidative stress contributes to the pathophysiology of exposure to heavy metals/metalloid. Beneficial renal effects of some medications, such as chelation therapy depend at least partially on the ability to alleviate oxidative stress. The administration of various natural or synthetic antioxidants has been shown to be of benefit in the prevention and attenuation of metal induced biochemical alterations. These include vitamins, N-acetylcysteine, α-lipoic acid, melatonin, dietary flavonoids and many others. Human studies are limited in this regard. Under certain conditions, surprisingly, the antioxidant supplements may exhibit pro-oxidant properties and even worsen metal induced toxic damage. To date, the evidence is insufficient to recommend antioxidant supplements in subject with exposure to metals. Prospective, controlled clinical trials on safety and effectiveness of different therapeutic antioxidant strategies either individually or in combination with chelating agent are indispensable. The present review focuses on structural, chemical and biological aspects of antioxidants particularly related to their chelating properties. PMID:20716905

  16. Structure and magnetic properties of iron nanoparticles synthesized by chemical vapor condensation

    NASA Astrophysics Data System (ADS)

    Lee, D. H.; Jang, T. S.; Lee, D. W.; Kim, B. K.

    2004-06-01

    Iron nanoparticles were synthesized by chemical vapor condensation (CVC) without the aid of LN2 chiller. The powder synthesized at 400 °C was a mixture of amorphous and crystalline -Fe. Fully crystallized iron particles were then obtained at and above 600 °C. When the reactor temperature was 1000 °C, however, nonmagnetic -Fe was stabilized together with -Fe. The synthesized particles, mostly possessing the core-shell type structure, were all nearly spherical, but the average particle size rapidly increased as the temperature increased. The surface layer that enclosed the iron core and became thicker in smaller particles was Fe3O4 or Fe3O4-related amorphous. Except for the one synthesized at 1000 °C, the iron nanoparticles were not fully saturated. The iron nanoparticles (20 nm) synthesized at 600 °C exhibited iHc 1.0 kOe and Ms 170 emu/g.

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

    NASA Astrophysics Data System (ADS)

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

    2015-10-01

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

  18. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2001-11-01

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

  20. 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

  1. LigandBox: A database for 3D structures of chemical compounds.

    PubMed

    Kawabata, Takeshi; Sugihara, Yusuke; Fukunishi, Yoshifumi; Nakamura, Haruki

    2013-01-01

    A database for the 3D structures of available compounds is essential for the virtual screening by molecular docking. We have developed the LigandBox database (http://ligandbox.protein.osaka-u.ac.jp/ligandbox/) containing four million available compounds, collected from the catalogues of 37 commercial suppliers, and approved drugs and biochemical compounds taken from KEGG_DRUG, KEGG_COMPOUND and PDB databases. Each chemical compound in the database has several 3D conformers with hydrogen atoms and atomic charges, which are ready to be docked into receptors using docking programs. The 3D conformations were generated using our molecular simulation program package, myPresto. Various physical properties, such as aqueous solubility (LogS) and carcinogenicity have also been calculated to characterize the ADME-Tox properties of the compounds. The Web database provides two services for compound searches: a property/chemical ID search and a chemical structure search. The chemical structure search is performed by a descriptor search and a maximum common substructure (MCS) search combination, using our program kcombu. By specifying a query chemical structure, users can find similar compounds among the millions of compounds in the database within a few minutes. Our database is expected to assist a wide range of researchers, in the fields of medical science, chemical biology, and biochemistry, who are seeking to discover active chemical compounds by the virtual screening.

  2. [Relationship between chemical constituents and herbs properties of relative plant herbs].

    PubMed

    Cao, Jia; Wang, Yun

    2013-02-01

    The material fundament of Chinese herbs is chemical constituents which represented the properties of herbs, including five fundamental natures (cold, cool, neutral, warm and hot), seven flavors (sour, bitter, sweet, salty, acerbity, mild and pungent) and twelve meridians (liver, heart, spleen, lung, kidney, Xin Bao, Gall bladder, small intestine, stomach, large intestine, bladder and San Jiao). In this article, authors study the relationship between chemical constituents of plant herbs and their properties. First, authors build a relationship network where the herbs with similar chemical compositions are connected each other. The particular difference of our work is to filter the common chemical constituents that many plants from different families contained. As a result, considering relative plants have similar chemical constituents, the relative plant herbs are clustering closely and the herbs of different family are connected loosely in our network. The results indicates that the method of building the herbs network is correct. The characteristics of herbs' properties in the network are that the same properties are usually connected regardless the plant families. There is "properties hole" phenomenon, that is, the majority of adjacent drugs of a herb have a certain properties, while the drug does not have the properties.

  3. Chemical composition of groundwater and relative mortality for cardiovascular diseases in the Slovak Republic.

    PubMed

    Rapant, S; Fajčíková, K; Cvečková, V; Ďurža, A; Stehlíková, B; Sedláková, D; Ženišová, Z

    2015-08-01

    The study deals with the analysis of relationship between chemical composition of the groundwater/drinking water and the data on relative mortality for cardiovascular diseases (ReI) in the Slovak Republic. Primary data consist of the Slovak national database of groundwater analyses (20,339 chemical analyses, 34 chemical elements/compounds) and data on ReI collected for the 10-year period (1994-2003). The chemical and health data were unified in the same form and expressed as the mean values for each of 2883 municipalities within the Slovak Republic for further analysis. Artificial neural network was used as mathematic method for model data analysis. The most significant chemical elements having influence on ReI were identified together with their limit values (maximal acceptable, minimal necessary and optimal). Based on the results of calculations, made through the neural networks, the following ten chemical elements/parameters in the groundwater were defined as the most significant for ReI: Ca + Mg (mmol l(-1)), Ca, Mg, TDS, Cl, HCO3, SO4, NO3, SiO2 and PO4. The obtained results document the highest relationship between ReI and the groundwater contents of Ca + Mg (mmol l(-1)), Ca and Mg. Following limit values were set for the most significant groundwater chemicals/parameters: Ca + Mg 4.4-7.6 mmol l(-1), Ca > 89.4 mg l(-1) and Mg 42-78.1 mg l(-1). At these concentration ranges, the relative mortality for cardiovascular diseases in the Slovak Republic reaches the lowest levels. These limit values are about twice higher in comparison with the current Slovak valid guideline values for the drinking water.

  4. Structural elucidation of organic contaminants by chemical ionisation mass spectrometry

    NASA Astrophysics Data System (ADS)

    Moldovan, Zaharie

    2009-08-01

    The PI-CI mass spectra formation for a new family of aromatic amines, with general formula: R1-Ph-NH-Ph-R2 is discussed in correlation with the R1 and R2 structure. The compounds where isolated from some environmental samples by GC/MS technique. The characteristic ions are produced by rearrangement processes involving olefin and alkane neutral molecule elimination from [M+H]+ and sole olefin molecule elimination from [M+ C2H5]+.

  5. 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

    2016-05-05

    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+).

  6. Relations between structural and dynamic thermal characteristics of building walls

    SciTech Connect

    Kossecka, E.; Kosny, J.

    1996-10-01

    The effect of internal thermal structure on dynamic characteristics of walls is analyzed. The concept of structure factors is introduced and the conditions they impose on response factors are given. Simple examples of multilayer walls, representing different types of thermal resistance and capacity distribution, are analyzed to illustrate general relations between structure factors and response factors. The idea of the ``thermally equivalent wall``, a plane multilayer structure, with dynamic characteristics similar to those of a complex structure, in which three-dimensional heat flow occurs, is presented.

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

    PubMed Central

    Maeda, Miki H.

    2015-01-01

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

  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. Some Physical and Chemical Aspects of Striation Structure.

    DTIC Science & Technology

    1980-08-15

    represents a convective loss: 4 V0 a k Vn/8 (5) where vn is the fast neutral speed and the relation Ax Ak = (6) for a Gaussian profile has been used. In...and I. M. Pikus, "Kinetics of High-Energy Heavy-Particle Collisional Processes," in DNA 1948H. 4. F. W. Sears, An Introduction to Themodynamics , the...ane/ax)l (A-15a) LB = IB0 2/(aB0 2/x)l (A-15b) Equation (A-3) permits the scale lengths to be related : Ln= aL8 (A-16) with 0 8n (Pe + Pi)/Bo2 (A-17

  11. BioCreative V CDR task corpus: a resource for chemical disease relation extraction.

    PubMed

    Li, Jiao; Sun, Yueping; Johnson, Robin J; Sciaky, Daniela; Wei, Chih-Hsuan; Leaman, Robert; Davis, Allan Peter; Mattingly, Carolyn J; Wiegers, Thomas C; Lu, Zhiyong

    2016-01-01

    Community-run, formal evaluations and manually annotated text corpora are critically important for advancing biomedical text-mining research. Recently in BioCreative V, a new challenge was organized for the tasks of disease named entity recognition (DNER) and chemical-induced disease (CID) relation extraction. Given the nature of both tasks, a test collection is required to contain both disease/chemical annotations and relation annotations in the same set of articles. Despite previous efforts in biomedical corpus construction, none was found to be sufficient for the task. Thus, we developed our own corpus called BC5CDR during the challenge by inviting a team of Medical Subject Headings (MeSH) indexers for disease/chemical entity annotation and Comparative Toxicogenomics Database (CTD) curators for CID relation annotation. To ensure high annotation quality and productivity, detailed annotation guidelines and automatic annotation tools were provided. The resulting BC5CDR corpus consists of 1500 PubMed articles with 4409 annotated chemicals, 5818 diseases and 3116 chemical-disease interactions. Each entity annotation includes both the mention text spans and normalized concept identifiers, using MeSH as the controlled vocabulary. To ensure accuracy, the entities were first captured independently by two annotators followed by a consensus annotation: The average inter-annotator agreement (IAA) scores were 87.49% and 96.05% for the disease and chemicals, respectively, in the test set according to the Jaccard similarity coefficient. Our corpus was successfully used for the BioCreative V challenge tasks and should serve as a valuable resource for the text-mining research community.Database URL: http://www.biocreative.org/tasks/biocreative-v/track-3-cdr/.

  12. 9. UNIDENTIFIED STRUCTURE FOUNDATIONS IN RELATION TO THE NORTH TRAINING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. UNIDENTIFIED STRUCTURE FOUNDATIONS IN RELATION TO THE NORTH TRAINING WALL, LOOKING TO THE EAST. - Oakland Harbor Training Walls, Mouth of Federal Channel to Inner Harbor, Oakland, Alameda County, CA

  13. Clinical and forensic signs related to chemical burns: a mechanistic approach.

    PubMed

    Dinis-Oliveira, Ricardo Jorge; Carvalho, Félix; Moreira, Roxana; Proença, Jorge Brandão; Santos, Agostinho; Duarte, José Alberto; Bastos, Maria de Lourdes; Magalhães, Teresa

    2015-06-01

    This manuscript highlights and critically analyses clinical and forensic signs related to chemical burns. Signs that may lead to suspicion of a particular chemical are thoroughly discussed regarding its underlying mechanisms. Burns due to sulfuric, hydrofluoric, nitric, hydrochloric (muriatic) and acetic (including derivatives) acids, hydrogen sulphide, sodium (caustic soda) and calcium (cement) hydroxides, paraquat, burns after inflation and rupture of airbags, povidone-iodine, chlorhexidine/alcohol (in preterm infants), laxatives, and vesicants (warfare agents), will be reviewed since these are the most common agents found in daily practice, for which relevant and timed information may be helpful in formulating an emergency treatment protocols and toxicological analysis.

  14. Iron Oxide Surface Chemistry: Effect of Chemical Structure on Binding in Benzoic Acid and Catechol Derivatives.

    PubMed

    Korpany, Katalin V; Majewski, Dorothy D; Chiu, Cindy T; Cross, Shoronia N; Blum, Amy Szuchmacher

    2017-03-13

    The excellent performance of functionalized iron oxide nanoparticles (IONPs) in nanomaterial and biomedical applications often relies on achieving the attachment of ligands to the iron oxide surface both in sufficient number and with proper orientation. Toward this end, we determine relationships between the ligand chemical structure and surface binding on magnetic IONPs for a series of related benzoic acid and catechol derivatives. Ligand exchange was used to introduce the model ligands, and the resultant nanoparticles were characterized using Fourier transform infrared-attenuated internal reflectance spectroscopy, transmission electron microscopy, and nanoparticle solubility behavior. An in-depth analysis of ligand electronic effects and reaction conditions reveals that the nature of ligand binding does not solely depend on the presence of functional groups known to bind to IONPs. The structure of the resultant ligand-surface complex was primarily influenced by the relative positioning of hydroxyl and carboxylic acid groups within the ligand and whether or not HCl(aq) was added to the ligand-exchange reaction. Overall, this study will help guide future ligand-design and ligand-exchange strategies toward realizing truly custom-built IONPs.

  15. Structure and Chemical Durability of Lead Crystal Glass.

    PubMed

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

    2016-11-01

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

  16. Electronic structure modulation of graphene edges by chemical functionalization

    NASA Astrophysics Data System (ADS)

    Taira, Remi; Yamanaka, Ayaka; Okada, Susumu

    2016-11-01

    Using the density functional theory with the effective screening medium method, we study the electronic properties of graphene nanoribbons with zigzag edges that are terminated by hydrogen and ketone, hydroxyl, carbonyl, and carboxyl functional groups. Our calculations showed that the work function and electronic structures of the edges of the nanoribbons are sensitive to the functional groups attached to the edges. The nearly free electron state emerges in the vacuum region outside the hydroxylated edges and crosses the Fermi level, indicating the possibility of negative electron affinity at the edges.

  17. Titan's winter polar vortex structure revealed by chemical tracers

    NASA Astrophysics Data System (ADS)

    Teanby, N. A.; de Kok, R.; Irwin, P. G. J.; Osprey, S.; Vinatier, S.; Gierasch, P. J.; Read, P. L.; Flasar, F. M.; Conrath, B. J.; Achterberg, R. K.; Bézard, B.; Nixon, C. A.; Calcutt, S. B.

    2008-12-01

    The winter polar vortex on Saturn's largest moon Titan has profound effects on atmospheric circulation and chemistry and for the current northern midwinter season is the major dynamical feature of Titan's stratosphere and mesosphere. We use 2 years of observations from Cassini's composite infrared spectrometer to determine cross sections of five independent chemical tracers (HCN, HC3N, C2H2, C3H4, and C4H2), which are then used to probe dynamical processes occurring within the vortex. Our results provide compelling evidence that the vortex acts as a strong mixing barrier in the stratosphere and mesosphere, effectively separating a tracer-enriched air mass in the north from air at lower latitudes. In the mesosphere, above the level of the vortex jet, a tracer-depleted zone extends away from the north pole toward the equator and enrichment is confined to high northern latitudes. However, below this level, mixing processes cause tongues of gas to extend away from the polar region toward the equator. These features are not reproduced by current general circulation models and suggest that a residual polar circulation is present and that waves and instabilities form a more important part of Titan's atmospheric dynamics than previously thought. We also observe an unexpected enrichment of C4H2 in the northern stratosphere, which suggests photochemical polymerization of C2H2. Our observations provide stringent new constraints for dynamical and photochemical models and identify key polar processes for the first time. Some of the processes we see have analogues in Earth's polar vortex, while others are unique to Titan.

  18. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures.

    PubMed

    Tsuruoka, Shuji; Matsumoto, Hidetoshi; Castranova, Vincent; Porter, Dale W; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2015-12-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential.

  19. Differentiation of chemical reaction activity of various carbon nanotubes using redox potential: Classification by physical and chemical structures

    PubMed Central

    Castranova, Vincent; Porter, Dale W.; Yanagisawa, Takashi; Saito, Naoto; Kobayashi, Shinsuke; Endo, Morinobu

    2016-01-01

    The present study systematically examined the kinetics of a hydroxyl radical scavenging reaction of various carbon nanotubes (CNTs) including double-walled and multi-walled carbon nanotubes (DWCNTs and MWCNTs), and carbon nano peapods (AuCl3@DWCNT). The theoretical model that we recently proposed based on the redox potential of CNTs was used to analyze the experimental results. The reaction kinetics for DWCNTs and thin MWCNTs agreed well with the theoretical model and was consistent with each other. On the other hand, thin and thick MWCNTs behaved differently, which was consistent with the theory. Additionally, surface morphology of CNTs substantially influenced the reaction kinetics, while the doped particles in the center hollow parts of CNTs (AuCl3@DWCNT) shifted the redox potential in a different direction. These findings make it possible to predict the chemical and biological reactivity of CNTs based on the structural and chemical nature and their influence on the redox potential. PMID:26783369

  20. Review of Recent Researches Related to Lightning to Tall Structures

    NASA Astrophysics Data System (ADS)

    Baba, Yoshihiro

    In this technical note, fundamental characteristics of lightning to tall structures are described, and recent researches related to lightning to tall structures are reviewed. In Section 2, the relationship between the incidence of lightning to a tall structure and the structure height, and that between the incidence of upward lightning initiated from a tall structure and the structure height, both of which were obtained by Eriksson empirically, are shown. Also, winter lightning strikes to tall structures and to wind-turbine-generator towers located on the coastal area of the Sea of Japan are described. In Section 3, characteristics of a current wave propagating along a tall structure hit by lightning are discussed. Also, simplified transmission-line representations for lightning strikes to a tall structure and to flat ground are shown, and dependences of the peak current on the observation height (top or bottom of the structure) and on the current risetime, obtained from the analysis using the simplified representations, are shown. In Section 4, median values of lightning currents measured on tall structures are shown. In Section 5, the electromagnetic field environment in the vicinity of a tall structure hit by lightning is discussed. Also, the far-field enhancement factor and the far-field-to-current conversion factor for lightning strikes to tall structures are shown.

  1. Structural features of the pore formed by Staphylococcus aureus alpha-toxin inferred from chemical modification and primary structure analysis.

    PubMed

    Menestrina, G; Belmonte, G; Parisi, V; Morante, S

    1992-09-01

    Staphylococcus aureus alpha-toxin makes cells and model membranes permeable to ions and uncharged molecules by opening oligomeric pores of uniform size. Its primary sequence reveals peculiar features which give some hints on the structure of the pore. A flexible region separating the toxin into two halves, several amphiphilic beta-strands and two amphiphilic alpha-helices long enough to span the hydrophobic core of the lipid bilayer are predicted. In analogy to bacterial porins, we propose that the inner walls of the pore are, at least in part, built by an amphiphilic beta-barrel. The model is consistent with circular dichroism data and with the electrophysiological properties of the pore. Functional information on this toxin were obtained by chemical modification of its four histidine residues. Specific carbethoxylation suggested they have different roles: one is required for specific receptor binding, one for oligomerisation and two for unspecific lipid binding. A tentative assignment of each histidine to its specific role is done on the basis of the structural predictions. A functionally related hemolysin, Aeromonas hydrophyla aerolysin, reveals remarkably similar features including the presence and location of histidines involved in receptor binding and oligomerisation.

  2. Rabbit Tamm–Horsfall urinary glycoprotein. Chemical composition and subunit structure

    PubMed Central

    Marr, Anne M. S.; Neuberger, A.; Ratcliffe, Wendy A.

    1971-01-01

    1. Tamm–Horsfall glycoprotein from rabbit urine has been isolated and characterized. The homogeneity of the preparation has been established by a variety of procedures including disc gel electrophoresis and ultracentrifugation in aqueous solution, sodium dodecyl sulphate and formic acid. 2. The chemical composition has been determined and a carbohydrate content of approx. 31% was obtained. The relative contents of the amino acids were shown to be very similar to those in human Tamm–Horsfall glycoprotein. A trace of lipid was also detected. 3. Leucine was identified as the only N-terminal amino acid. 4. The subunit structure was investigated in the presence of sodium dodecyl sulphate by gel filtration and disc gel electrophoresis. These studies indicated that the subunit possessed a molecular weight of approx. 84000±6000. A similar value was obtained after reduction and S-alkylation of the glycoprotein indicating that the disulphide bonds were all intrachain. 5. A minimum value for the chemical molecular weight of 85000±6000 was obtained from the number of N-terminal amino acids released by cyanogen bromide cleavage of the glycoprotein. 6. The immunological properties of the glycoprotein were studied. Cross reactivity was demonstrated between human Tamm–Horsfall glycoprotein and a guinea-pig anti-rabbit Tamm–Horsfall antiserum. ImagesFig. 2.Fig. 4.Fig. 5. PMID:5129252

  3. MOZART, a global chemical transport model for ozone and related chemical tracers: 2. Model results and evaluation

    NASA Astrophysics Data System (ADS)

    Hauglustaine, D. A.; Brasseur, G. P.; Walters, S.; Rasch, P. J.; Müller, J.-F.; Emmons, L. K.; Carroll, M. A.

    1998-11-01

    In this second of two companion papers, we present results from a new global three-dimensional chemical transport model, called MOZART (model for ozone and related chemical tracers). MOZART is developed in the framework of the National Center for Atmospheric Research (NCAR) Community Climate Model (CCM) and includes a detailed representation of tropospheric chemistry. The model provides the distribution of 56 chemical species at a spatial resolution of 2.8° in both latitude and longitude, with 25 levels in the vertical (from the surface to level of 3 mbar) and a time step of 20 min. The meteorological information is supplied from a 2-year run of the NCAR Community Climate Model. The simulated distributions of ozone (O3) and its precursors are evaluated by comparison with observational data. The distribution of methane, nonmethane hydrocarbons (NMHCs), and CO are generally well simulated by the model. The model evaluation in the tropics stresses the need for a better representation of biomass burning emissions in order to evaluate the budget of carbon monoxide, nitrogen species, and ozone with more accuracy in these regions, MOZART reproduces the NO observations in most parts of the troposphere. Nitric acid, however, is overestimated over the Pacific by up to a factor of 10 and over continental regions by a factor of 2-3. Discrepancies are also found in the simulation of PAN in the upper troposphere and in biomass burning regions. These results highlight shortcomings in our understanding of the nitrogen budget in the troposphere. The seasonal cycle of ozone in the troposphere is generally well reproduced by the model in comparison with ozone soundings. MOZART tends, however, to underestimate O3 at higher latitudes, and specifically above 300 mbar. The global photochemical production and destruction of ozone in the troposphere are 3018 Tg/yr and 2511 Tg/yr, respectively (net ozone production of 507 Tg/yr). The stratospheric influx of O3 is estimated to be 391 Tg

  4. (Neutron scatter studies of chromatin structure related to function)

    SciTech Connect

    Bradbury, E.M.

    1990-01-01

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

  5. Assessing relative bioactivity of chemical substances using quantitative molecular network topology analysis.

    PubMed

    Edberg, Anna; Soeria-Atmadja, Daniel; Bergman Laurila, Jonas; Johansson, Fredrik; Gustafsson, Mats G; Hammerling, Ulf

    2012-05-25

    Structurally different chemical substances may cause similar systemic effects in mammalian cells. It is therefore necessary to go beyond structural comparisons to quantify similarity in terms of their bioactivities. In this work, we introduce a generic methodology to achieve this on the basis of Network Biology principles and using publicly available molecular network topology information. An implementation of this method, denoted QuantMap, is outlined and applied to antidiabetic drugs, NSAIDs, 17β-estradiol, and 12 substances known to disrupt estrogenic pathways. The similarity of any pair of compounds is derived from topological comparison of intracellular protein networks, directly and indirectly associated with the respective query chemicals, via a straightforward pairwise comparison of ranked proteins. Although output derived from straightforward chemical/structural similarity analysis provided some guidance on bioactivity, QuantMap produced substance interrelationships that align well with reports on their respective perturbation properties. We believe that QuantMap has potential to provide substantial assistance to drug repositioning, pharmacology evaluation, and toxicology risk assessment.

  6. Chemical shift prediction for protein structure calculation and quality assessment using an optimally parameterized force field.

    PubMed

    Nielsen, Jakob T; Eghbalnia, Hamid R; Nielsen, Niels Chr

    2012-01-01

    The exquisite sensitivity of chemical shifts as reporters of structural information, and the ability to measure them routinely and accurately, gives great import to formulations that elucidate the structure-chemical-shift relationship. Here we present a new and highly accurate, precise, and robust formulation for the prediction of NMR chemical shifts from protein structures. Our approach, shAIC (shift prediction guided by Akaikes Information Criterion), capitalizes on mathematical ideas and an information-theoretic principle, to represent the functional form of the relationship between structure and chemical shift as a parsimonious sum of smooth analytical potentials which optimally takes into account short-, medium-, and long-range parameters in a nuclei-specific manner to capture potential chemical shift perturbations caused by distant nuclei. shAIC outperforms the state-of-the-art methods that use analytical formulations. Moreover, for structures derived by NMR or structures with novel folds, shAIC delivers better overall results; even when it is compared to sophisticated machine learning approaches. shAIC provides for a computationally lightweight implementation that is unimpeded by molecular size, making it an ideal for use as a force field.

  7. Cutaneous signs of systemic toxicity due to dioxins and related chemicals

    SciTech Connect

    Dunagin, W.G.

    1984-04-01

    The controversy about dioxin effects on human health received a great deal of attention recently when the State of Missouri was declared to have a dioxin crisis. However, dioxin and several related chemicals are widespread throughout the world. Cutaneous signs play an important part in evaluating toxicity of dioxin and similar chemicals. Chloracne is the most sensitive indicator of significant dioxin exposure. Porphyria cutanea tarda and hyperpigmentation are other known cutaneous effects, and malignant fibrous histiocytomas of the skin may possibly be associated, although data are inconclusive on this point. The AMC Council on Scientific Affairs recommended that all physicians become familiar with chloracne and other toxic effects of dioxin. Dermatologists, especially, should be aware of the problem and may discover early cases of previously unsuspected exposure to this group of chemicals.

  8. 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.”

  9. Gender and sexual orientation in relation to hypothalamic structures.

    PubMed

    Swaab, D F; Gooren, L J; Hofman, M A

    1992-01-01

    Animal experiments have provided evidence for the presence of sex differences from the synaptic level up to behaviour. Although sex differences in the human brain may have been presumed implicitly since the days of Aristotle, research on the presence of functional and structural sex differences of the human brain started only relatively recently. The most conspicuous sex difference in the mammalian brain was described by Gorski et al. [1978] in the preoptic area (POA) of the rat hypothalamus. We found that the volume of a putative homologue of this sexually dimorphic nucleus (SDN) in the adult human hypothalamus was more than twice as large in men as in women and contained about twice as many cells. Recently a similar sex difference and volume has been described for the human bed nucleus of the stria terminalis and 'interstitial nuclei of the hypothalamus' (INAH). Sexual differentiation of the hypothalamus was generally believed to take place between 4 and 7 months of gestation. A life span study on the SDN of more than 100 subjects revealed, however, that only after the age of 2-4 years postnatally sexual differentiation becomes manifest by a decrease in volume and cell number in the female SDN. If sexual differentiation of the brain indeed takes place postnatally, not only chemical and hormonal factors may influence this process but also social factors. A prominent theory on the development of sexual orientation is that it develops as a result of an interaction between the developing brain and sex hormones. According to Dörner's hypothesis, male homosexuals have a female differentiation of the hypothalamus. This hypothesis was not supported by our observations on the SDN. Neither the SDN volume nor the cell number in the hypothalamus of homosexual men differed from that of heterosexual men. However, a difference in SCN cell number was observed in relation to sexual orientation. The volume and cell number of the SCN of homosexual men was twice as large as that of

  10. 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.

  11. Chemical structures of hydrazine-treated graphene oxide and generation of aromatic nitrogen doping.

    PubMed

    Park, Sungjin; Hu, Yichen; Hwang, Jin Ok; Lee, Eui-Sup; Casabianca, Leah B; Cai, Weiwei; Potts, Jeffrey R; Ha, Hyung-Wook; Chen, Shanshan; Oh, Junghoon; Kim, Sang Ouk; Kim, Yong-Hyun; Ishii, Yoshitaka; Ruoff, Rodney S

    2012-01-24

    Chemically modified graphene platelets, produced via graphene oxide, show great promise in a variety of applications due to their electrical, thermal, barrier and mechanical properties. Understanding the chemical structures of chemically modified graphene platelets will aid in the understanding of their physical properties and facilitate development of chemically modified graphene platelet chemistry. Here we use (13)C and (15)N solid-state nuclear magnetic resonance spectroscopy and X-ray photoelectron spectroscopy to study the chemical structure of (15)N-labelled hydrazine-treated (13)C-labelled graphite oxide and unlabelled hydrazine-treated graphene oxide, respectively. These experiments suggest that hydrazine treatment of graphene oxide causes insertion of an aromatic N(2) moiety in a five-membered ring at the platelet edges and also restores graphitic networks on the basal planes. Furthermore, density-functional theory calculations support the formation of such N(2) structures at the edges and help to elucidate the influence of the aromatic N(2) moieties on the electronic structure of chemically modified graphene platelets.

  12. Physical and chemical characterization of tire-related particles: comparison of particles generated using different methodologies.

    PubMed

    Kreider, Marisa L; Panko, Julie M; McAtee, Britt L; Sweet, Leonard I; Finley, Brent L

    2010-01-01

    The purpose of this study was to characterize the physical and chemical properties of particles generated from the interaction of tires and road surfaces. Morphology, size distribution, and chemical composition were compared between particles generated using different methods, including on-road collection, laboratory generation under simulated driving conditions, and cryogenic breaking of tread rubber. Both on-road collected and laboratory generated particles exhibited the elongated shape typical of tire wear particles, whereas tread particles were more angular. Despite similar morphology for the on-road collected and the laboratory generated particles, the former were smaller on average. It is not clear at this stage if the difference is significant to the physical and chemical behavior of the particles. The chemical composition of the particles differed, with on-road generated particles containing chemical contributions from sources other than tires, such as pavement or particulates generated from other traffic-related sources. Understanding the differences between these particles is essential in apportioning contaminant contributions to the environment between tires, roadways, and other sources, and evaluating the representativeness of toxicity studies using different types of particulate generated.

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

    PubMed

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

    2015-01-01

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

  14. Social Structure in Relatively Closed and Open Schools

    ERIC Educational Resources Information Center

    Coughlan, Robert J.

    1970-01-01

    This study examined the ways in which teacher work values affect group development within relatively closed and open school organizational systems. The overall findings suggest that these different types of formal organization generate dissimilar social structures in their work groups which are related to the disparate work values of group…

  15. 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

    2015-12-23

    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.

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

    PubMed

    Chao, J H; Chuang, C Y

    2011-01-01

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

  17. Federal agencies active in chemical industry-related research and development

    SciTech Connect

    1995-09-29

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

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

    PubMed

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

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts--sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond ((h3)J(NC')) spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding.

  19. Protein Structure Validation and Refinement Using Amide Proton Chemical Shifts Derived from Quantum Mechanics

    PubMed Central

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

    2013-01-01

    We present the ProCS method for the rapid and accurate prediction of protein backbone amide proton chemical shifts - sensitive probes of the geometry of key hydrogen bonds that determine protein structure. ProCS is parameterized against quantum mechanical (QM) calculations and reproduces high level QM results obtained for a small protein with an RMSD of 0.25 ppm (r = 0.94). ProCS is interfaced with the PHAISTOS protein simulation program and is used to infer statistical protein ensembles that reflect experimentally measured amide proton chemical shift values. Such chemical shift-based structural refinements, starting from high-resolution X-ray structures of Protein G, ubiquitin, and SMN Tudor Domain, result in average chemical shifts, hydrogen bond geometries, and trans-hydrogen bond (h3JNC') spin-spin coupling constants that are in excellent agreement with experiment. We show that the structural sensitivity of the QM-based amide proton chemical shift predictions is needed to obtain this agreement. The ProCS method thus offers a powerful new tool for refining the structures of hydrogen bonding networks to high accuracy with many potential applications such as protein flexibility in ligand binding. PMID:24391900

  20. 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.

  1. 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

  2. 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.

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

    PubMed

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

    2016-10-13

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

  4. 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.

  5. 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

  6. 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

  7. Structure-activity comparison of hydrazine to other Nasotoxic chemicals. Final report, August-October 1991

    SciTech Connect

    Godin, C.S.; Wall, H.G.

    1992-08-01

    The biotransformation of 19 chemicals that have caused nasal epithelial toxicity in-long-term carcinogenesis experiments in laboratory rodents was compared with the biotransformation of hydrazine, in order to determine if these chemicals share common metabolic pathways. Ten of the 19 chemicals were tumorigenic; four were epoxides or epoxide-formers; three were metabolized to reactive aldehydes; and one was metabolized to a lactone ring. The two remaining chemicals, p-cresidene and 2,6-xylidene, possess an amino group that can undergo biotransformation to reactive metabolites in a way similar to hydrazine, but there is no evidence to support this hypothesis. Therefore, none of the 19 chemicals are metabolized in a way similar to hydrazine.... Structure-activity, Hydrazine, Nasotoxicity, Carcinogenicity.

  8. Electrical, structural and chemical characterization of Si sheet material

    NASA Technical Reports Server (NTRS)

    Ast, D. G.

    1985-01-01

    Web Dendritic Si ribbons are deformed under a well-defined four point bending stress. Since the mechanical properties of Si are known to depend on the 0 content of the material, 0 measurements using Fourier Transform Infrared Spectroscopy were done to determine a proper control sample of non-defected single crystal Si. Four point bending revealed a unique two step bending behavior for the Web Si ribbons. An initial theory for this behavior involves the interaction of the dislocations generated by the deformation with the central twin planes of the ribbons. Measurements showed a uniformly high 0 content for the Web Si ribbons, approximately 10 to the 18th power atoms/cu.cm. The Web samples had a much broader absorption peak at 9 microns than is usually seen for well-annealed single crystal Si. This broadening is thought to be related to stress in the Web Si ribbons. Two samples containing a known amount of residual stress support this hypothesis. Also, a shoulder on the infrared absorption peak associated with interstitial 0 in Si appears in the transmission vs. wavenumber plots for some of the Web samples. This shoulder has been associated with 0-vacancy complexes or with 0 at dislocations. The O content and configuration do not seem to correlate with the growth configuration of the Web Si ribbon.

  9. Transcriptome Sequencing of Chemically Induced Aquilaria sinensis to Identify Genes Related to Agarwood Formation

    PubMed Central

    Ye, Wei; Wu, Hongqing; He, Xin; Wang, Lei; Zhang, Weimin; Li, Haohua; Fan, Yunfei; Tan, Guohui; Liu, Taomei; Gao, Xiaoxia

    2016-01-01

    Background Agarwood is a traditional Chinese medicine used as a clinical sedative, carminative, and antiemetic drug. Agarwood is formed in Aquilaria sinensis when A. sinensis trees are threatened by external physical, chemical injury or endophytic fungal irritation. However, the mechanism of agarwood formation via chemical induction remains unclear. In this study, we characterized the transcriptome of different parts of a chemically induced A. sinensis trunk sample with agarwood. The Illumina sequencing platform was used to identify the genes involved in agarwood formation. Methodology/Principal Findings A five-year-old Aquilaria sinensis treated by formic acid was selected. The white wood part (B1 sample), the transition part between agarwood and white wood (W2 sample), the agarwood part (J3 sample), and the rotten wood part (F5 sample) were collected for transcriptome sequencing. Accordingly, 54,685,634 clean reads, which were assembled into 83,467 unigenes, were obtained with a Q20 value of 97.5%. A total of 50,565 unigenes were annotated using the Nr, Nt, SWISS-PROT, KEGG, COG, and GO databases. In particular, 171,331,352 unigenes were annotated by various pathways, including the sesquiterpenoid (ko00909) and plant–pathogen interaction (ko03040) pathways. These pathways were related to sesquiterpenoid biosynthesis and defensive responses to chemical stimulation. Conclusions/Significance The transcriptome data of the different parts of the chemically induced A. sinensis trunk provide a rich source of materials for discovering and identifying the genes involved in sesquiterpenoid production and in defensive responses to chemical stimulation. This study is the first to use de novo sequencing and transcriptome assembly for different parts of chemically induced A. sinensis. Results demonstrate that the sesquiterpenoid biosynthesis pathway and WRKY transcription factor play important roles in agarwood formation via chemical induction. The comparative analysis of

  10. A Structural Determinant of Chemical Reactivity and Potential Health Effects of Quinones from Natural Products

    PubMed Central

    Tu, Tingting; Giblin, Daryl; Gross, Michael L.

    2011-01-01

    Although many phenols and catechols found as polyphenol natural products are antioxidants and have putative disease-preventive properties, others have deleterious health effects. One possible route to toxicity is the bioactivation of the phenolic function to quinones that are electrophilic, redox-agents capable of modifying DNA and proteins. The structure-property relationships of biologically important quinones and their precursors may help understand the balance between their health benefits and risks. We describe a mass-spectrometry-based study of four quinones produced by oxidizing flavanones and flavones. Those with a C2-C3 double bond on ring C of the flavonoid stabilize by delocalization an incipient positive charge from protonation and render the protonated quinone particularly susceptible to nucleophilic attack. We hypothesize that the absence of this double bond is one specific structural determinant that is responsible for the ability of quinones to modify biological macromolecules. Those quinones containing a C2-C3 single bond have relative higher aqueous stability and longer half-lives than those with a double bond at the same position; the latter have short half-lives at or below ~ 1 s. Quinones with a C2-C3 double bond show little ability to depurinate DNA because they are rapidly hydrated to unreactive species. Molecular-orbital calculations support that quinone hydration by a highly structure-dependent mechanism accounts for their chemical properties. The evidence taken together support a hypothesis that those flavonoids and related natural products that undergo oxidation to quinones and are then rapidly hydrated are unlikely to damage important biological macromolecules. PMID:21721570

  11. Relative toxicity of pyrolysis gases from materials - Effects of chemical composition and test conditions

    NASA Technical Reports Server (NTRS)

    Hilado, C. J.; Cumming, H. J.

    1978-01-01

    Relative toxicity test data on 270 materials are presented, based on test procedures developed at the University of San Francisco. The effects of chemical composition, using data on 13 types of synthetic polymers and eight types of fabrics, are discussed. Selected materials were evaluated using nine test conditions with the USF method, and using methods developed at the FAA Civil Aeromedical Institute, Douglas Aircraft Company and San Jose State University.

  12. Complex, Dynamic Combination of Physical, Chemical and Nutritional Variables Controls Spatio-Temporal Variation of Sandy Beach Community Structure

    PubMed Central

    Ortega Cisneros, Kelly; Smit, Albertus J.; Laudien, Jürgen; Schoeman, David S.

    2011-01-01

    Sandy beach ecological theory states that physical features of the beach control macrobenthic community structure on all but the most dissipative beaches. However, few studies have simultaneously evaluated the relative importance of physical, chemical and biological factors as potential explanatory variables for meso-scale spatio-temporal patterns of intertidal community structure in these systems. Here, we investigate macroinfaunal community structure of a micro-tidal sandy beach that is located on an oligotrophic subtropical coast and is influenced by seasonal estuarine input. We repeatedly sampled biological and environmental variables at a series of beach transects arranged at increasing distances from the estuary mouth. Sampling took place over a period of five months, corresponding with the transition between the dry and wet season. This allowed assessment of biological-physical relationships across chemical and nutritional gradients associated with a range of estuarine inputs. Physical, chemical, and biological response variables, as well as measures of community structure, showed significant spatio-temporal patterns. In general, bivariate relationships between biological and environmental variables were rare and weak. However, multivariate correlation approaches identified a variety of environmental variables (i.e., sampling session, the C∶N ratio of particulate organic matter, dissolved inorganic nutrient concentrations, various size fractions of photopigment concentrations, salinity and, to a lesser extent, beach width and sediment kurtosis) that either alone or combined provided significant explanatory power for spatio-temporal patterns of macroinfaunal community structure. Overall, these results showed that the macrobenthic community on Mtunzini Beach was not structured primarily by physical factors, but instead by a complex and dynamic blend of nutritional, chemical and physical drivers. This emphasises the need to recognise ocean-exposed sandy

  13. Influence of Transducer Structure on Mechanical and Chemical Effects of 20 kHz Sonication

    NASA Astrophysics Data System (ADS)

    Tran, Khuyen Viet Bao; Asakura, Yoshiyuki; Koda, Shinobu

    2012-07-01

    In this work, we examined the influence of transducer structure on the mechanical and chemical effects of 20 kHz sonication, where the dissipated power measured by calorimetry was kept constant (5 W). The mechanical effects were evaluated from the degradation rate of poly(ethylene oxide) in aqueous solution, and the chemical effects were measured with potassium iodide solution. The mechanical effects for a bath-type apparatus with the transducers fixed at a node with a diameter of 50 mm are nearly equal to those for a horn-type apparatus. The former transducer showed the strongest chemical effects among the transducers investigated here.

  14. Influence of the chemical structure of functional monomers on their adhesive performance.

    PubMed

    Van Landuyt, K L; Yoshida, Y; Hirata, I; Snauwaert, J; De Munck, J; Okazaki, M; Suzuki, K; Lambrechts, P; Van Meerbeek, B

    2008-08-01

    Functional monomers in adhesive systems can improve bonding by enhancing wetting and demineralization, and by chemical bonding to calcium. This study tested the hypothesis that small changes in the chemical structure of functional monomers may improve their bonding effectiveness. Three experimental phosphonate monomers (HAEPA, EAEPA, and MAEPA), with slightly different chemical structures, and 10-MDP (control) were evaluated. Adhesive performance was determined in terms of microtensile bond strength of 4 cements that differed only for the functional monomer. Based on the Adhesion-Decalcification concept, the chemical bonding potential was assessed by atomic absorption spectrophotometry of the dissolution rate of the calcium salt of the functional monomers. High bond strength of the adhesive cement corresponded to low dissolution rate of the calcium salt of the respective functional monomer. The latter is according to the Adhesion-Decalcification concept, suggestive of a high chemical bonding capacity. We conclude that the adhesive performance of an adhesive material depends on the chemical structure of the functional monomer.

  15. Chemical and biological work-related risks across occupations in Europe: a review

    PubMed Central

    2014-01-01

    Background Work-related health inequalities are determined to some extent by an unequal exposure to chemical and biological risk factors of disease. Although their potential economic burden in the European Union (EU-25) might be substantial, comprehensive reviews focusing on the distribution of these risks across occupational groups are limited. Thus, the main objective of this review is to provide a synopsis of the exposure to chemical and biological hazards across occupational groups. In addition, main industrial applications of hazardous substances are identified and some epidemiological evidence is discussed regarding societal costs and incidence rates of work-related diseases. Methods Available lists of carcinogens, sensitisers, mutagens, reprotoxic substances and biological hazards were consulted. For each work-related hazard the main industrial application was identified in order to assess which ISCO occupational groups may be associated with direct exposure. Where available, information on annual tonnage production, risk assessment of the substances and pathogens, and other relevant data were collected and reported. Results Altogether 308 chemical and biological hazards were identified which may account to at least 693 direct exposures. These hazards concentrate on the following major occupational groups: technicians (ISCO 3), operators (ISCO 8), agricultural workers (ISCO 6) and workers in elementary occupations (ISCO 9). Common industrial applications associated with increased exposure rates relate among others to: (1) production or application of pigments, resins, cutting fluids, adhesives, pesticides and cleaning products, (2) production of rubber, plastics, textiles, pharmaceuticals and cosmetics, and (3) in agriculture, metallurgy and food processing industry, Societal costs of the unequal distribution of chemical and biological hazards across occupations depend on the corresponding work-related diseases and may range from 2900 EUR to 126000 EUR per

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

    PubMed

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

    2013-10-09

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

  17. Structural-chemical features and morphology of glauconites in sedimentary iron ore of Bakchar prospect (Western Siberia)

    NASA Astrophysics Data System (ADS)

    Rudmin, M.; Reva, I.; Gunko, A.; Mazurov, A.; Abramova, R.

    2015-11-01

    The research embraces the investigation results of glauconites in Bakchar iron ore occurrences to evaluate the potential diversified commercial application of this mineral. The following lab methods were used to analyze the morphology, chemical composition and structure of glauconites: granulometric analysis, optical microscopy, electron microscopy, X-ray fluorescence analysis, atomic arc-emission analysis and infrared spectroscopy. Glauconite was classified according to morphology and grain color and chemical composition and some specific characteristics were also determined (relative content of absorbed water, random distribution of smectite flakes within the grain structures). The research results showed that pistacho-green glauconite grains are less subjected to alteration than greenish-yellow grains due to the content of potassium, iron, absorbed water and organic impurities.

  18. Agricultural chemicals in groundwater of the midwestern United States: Relations to land use

    USGS Publications Warehouse

    Kolpin, D.W.

    1997-01-01

    To determine the relations between land use and concentrations of selected agricultural chemicals (nitrate, atrazine residue [atrazine (2-chloro-4-ethylamino-6-isopropylamino-s-triazine) + deethylatrazinc (2-amino-4-chloro-6-isopropylamino-s-triazine) + deisopropylatrazine (2-amino-4-chloro-6-ethylamino-s-triazine)], and alachlor residue [alachlor, [2-chloro-2′,6′-diethyl-N-(methoxymethyl) acetanilide] + alachlor ethanesulfonic acid (alachlor-ESA; 2-[(2,6-diethylphenyl)(methoxymethyl)amino]-2-oxoethanesulfonic acid)] in groundwater, detailed land use information based on accurate measurements from aerial photographs for the 1991 growing season was obtained within a 2-km radius surrounding 100 wells completed in near-surface unconsolidated aquifers in the midwestern USA. The most significant land use factors to the agricultural chemicals examined were: nitrate (amount of irrigated crop production, positive relation), atrazine residue (amount of irrigated crop production, positive relation), and alachlor residue (amount of highly erodible land, inverse relation). The investigation of smaller buffer sizes (size of circular area around sampled wells) proved insightful for this study. Additional land use factors having significant relations to all three agricultural chemicals were identified using these smaller buffer radii. The most significant correlations (correlation maxima) generally occurred at ≤500-m for nitrate and ≥1000-m for atrazine residue and alachlor residue. An attempt to improve the statistical relations to land use by taking hydrologic considerations into account (removing land outside the estimated most probable recharge area from the statistical analysis) was not as successful as anticipated. Only 45% of the nitrate, 32% of the atrazine residue, and 20% of the alachlor residue correlations were improved by a consideration of the estimated most probable recharge area.

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

    PubMed

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

    2015-09-01

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

  20. Estimating Relative Positions of Outer-Space Structures

    NASA Technical Reports Server (NTRS)

    Balian, Harry; Breckenridge, William; Brugarolas, Paul

    2009-01-01

    A computer program estimates the relative position and orientation of two structures from measurements, made by use of electronic cameras and laser range finders on one structure, of distances and angular positions of fiducial objects on the other structure. The program was written specifically for use in determining errors in the alignment of large structures deployed in outer space from a space shuttle. The program is based partly on equations for transformations among the various coordinate systems involved in the measurements and on equations that account for errors in the transformation operators. It computes a least-squares estimate of the relative position and orientation. Sequential least-squares estimates, acquired at a measurement rate of 4 Hz, are averaged by passing them through a fourth-order Butterworth filter. The program is executed in a computer aboard the space shuttle, and its position and orientation estimates are displayed to astronauts on a graphical user interface.

  1. Structural, compositional, and photoluminescence characterization of thermal chemical vapor deposition-grown Zn₃N₂ microtips

    SciTech Connect

    Wei, Pai-Chun E-mail: tsengcm@phys.sinica.edu.tw; Chang, Chung-Chieh; Hsu, Chia-Hao; Tong, Shih-Chang; Shen, Ji-Lin; Tseng, Chuan-Ming E-mail: tsengcm@phys.sinica.edu.tw

    2014-10-14

    The catalytic growth of Zn₃N₂ using guided-stream thermal chemical vapor deposition has been investigated within the parameter range of acicular growth to obtain uniform microtips with a high crystalline quality. The cubic anti-bixbyite crystal structure of Zn₃N₂ microtips and its related phonon mode are revealed by X-ray diffraction and Raman spectroscopy, respectively. The surface morphologies of pure and surface-oxidized Zn₃N₂ microtips are depicted by scanning electron microscopy and show the crack formation on the surface-oxidized Zn₃N₂ microtips. The spatial element distribution map confirms the VLS growth mechanism for Zn₃N₂ microtips and reveals the depth profile of zinc, nitrogen, oxygen, and nickel elements. Photoluminescence (PL) spectra of Zn₃N₂ microtips show a sharp infrared band-to-band emission peak at 1.34 eV with a full width at half maximum of ~100 meV and a very broad oxygen-related defect band emission peak centered at ~0.85 eV.

  2. Structure Enhancement Relationship of Chemical Penetration Enhancers in Drug Transport across the Stratum Corneum

    PubMed Central

    Chantasart, Doungdaw; Li, S. Kevin

    2012-01-01

    The stratum corneum is a major barrier of drug penetration across the skin in transdermal delivery. For effective transdermal drug delivery, skin penetration enhancers are used to overcome this barrier. In the past decades, a number of research studies were conducted to understand the mechanisms of skin penetration enhancers and to develop a structure enhancement relationship. Such understanding allows effective prediction of the effects of skin penetration enhancers, assists topical and transdermal formulation development, and avoids extensive enhancer screening in the transdermal delivery industry. In the past two decades, several hypotheses on chemical enhancer-induced penetration enhancement for transport across the skin lipoidal pathway have been examined based on a systematic approach. Particularly, a hypothesis that skin penetration enhancement is directly related to the concentration of the enhancers in the stratum corneum lipid domain was examined. A direct relationship between skin penetration enhancer potency (based on enhancer aqueous concentration in the diffusion cell chamber) and enhancer n-octanol-water partition coefficient was also established. The nature of the microenvironment of the enhancer site of action in the stratum corneum lipid domain was found to be mimicked by n-octanol. The present paper reviews the work related to these hypotheses and the relationships between skin penetration enhancement and enhancer concentration in the drug delivery media and stratum corneum lipids. PMID:24300181

  3. 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.

  4. 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

  5. New clues on carcinogenicity-related substructures derived from mining two large datasets of chemical compounds.

    PubMed

    Golbamaki, Azadi; Benfenati, Emilio; Golbamaki, Nazanin; Manganaro, Alberto; Merdivan, Erinc; Roncaglioni, Alessandra; Gini, Giuseppina

    2016-04-02

    In this study, new molecular fragments associated with genotoxic and nongenotoxic carcinogens are introduced to estimate the carcinogenic potential of compounds. Two rule-based carcinogenesis models were developed with the aid of SARpy: model R (from rodents' experimental data) and model E (from human carcinogenicity data). Structural alert extraction method of SARpy uses a completely automated and unbiased manner with statistical significance. The carcinogenicity models developed in this study are collections of carcinogenic potential fragments that were extracted from two carcinogenicity databases: the ANTARES carcinogenicity dataset with information from bioassay on rats and the combination of ISSCAN and CGX datasets, which take into accounts human-based assessment. The performance of these two models was evaluated in terms of cross-validation and external validation using a 258 compound case study dataset. Combining R and H predictions and scoring a positive or negative result when both models are concordant on a prediction, increased accuracy to 72% and specificity to 79% on the external test set. The carcinogenic fragments present in the two models were compared and analyzed from the point of view of chemical class. The results of this study show that the developed rule sets will be a useful tool to identify some new structural alerts of carcinogenicity and provide effective information on the molecular structures of carcinogenic chemicals.

  6. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints.

    PubMed

    Chen, Jonathan L; Bellaousov, Stanislav; Tubbs, Jason D; Kennedy, Scott D; Lopez, Michael J; Mathews, David H; Turner, Douglas H

    2015-11-17

    Knowledge of RNA structure is necessary to determine structure-function relationships and to facilitate design of potential therapeutics. RNA secondary structure prediction can be improved by applying constraints from nuclear magnetic resonance (NMR) experiments to a dynamic programming algorithm. Imino proton walks from NOESY spectra reveal double-stranded regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs, UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to identify constraints for the 5' to 3' directionality of base pairs in helices. The 5' to 3' directionality constraints were incorporated into an NMR-assisted prediction of secondary structure (NAPSS-CS) program. When it was tested on 18 structures, including nine pseudoknots, the sensitivity and positive predictive value were improved relative to those of three unrestrained programs. The prediction accuracy for the pseudoknots improved the most. The program also facilitates assignment of chemical shifts to individual nucleotides, a necessary step for determining three-dimensional structure.

  7. Chemical separation of primordial Li+ during structure formation caused by nanogauss magnetic field

    NASA Astrophysics Data System (ADS)

    Kusakabe, Motohiko; Kawasaki, Masahiro

    2015-01-01

    During the structure formation, charged and neutral chemical species may have separated from each other at the gravitational contraction in primordial magnetic field (PMF). A gradient in the PMF in a direction perpendicular to the field direction leads to the Lorentz force on the charged species. Resultantly, an ambipolar diffusion occurs, and charged species can move differently from neutral species, which collapses gravitationally during the structure formation. We assume a gravitational contraction of neutral matter in a spherically symmetric structure, and calculate fluid motions of charged and neutral species. It is shown that the charged fluid, i.e. proton, electron, and 7Li+, can significantly decouple from the neutral fluid depending on the field amplitude. The charged species can, therefore, escape from the gravitational collapse. We take the structure mass, the epoch of the gravitational collapse, and the comoving Lorenz force as parameters. We then identify a parameter region for an effective chemical separation. This type of chemical separation can reduce the abundance ratio of Li/H in early structures because of inefficient contraction of 7Li+ ion. Therefore, it may explain Li abundances of Galactic metal-poor stars which are smaller than the prediction in standard big bang nucleosynthesis model. Amplitudes of the PMFs are controlled by a magnetohydrodynamic turbulence. The upper limit on the field amplitude derived from the turbulence effect is close to the value required for the chemical separation.

  8. 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.

  9. Control of the structural stability of α-crystallin under thermal and chemical stress: the role of carnosine.

    PubMed

    Villari, Valentina; Attanasio, Francesco; Micali, Norberto

    2014-11-26

    The structural properties of α-crystallin, the major protein of the eye lens of mammals, in aqueous solution are investigated by means of small angle X-ray and dynamic light scattering. The research interest is devoted in particular to the effect of carnosine in protecting the protein under stress conditions, like temperature increase and presence of denaturant (guanidinium-HCl). The results suggest that carnosine interacts, through mechanisms involving hydrophobic interactions, with α-crystallin and avoids the structural changes in the quaternary structure induced by thermal and chemical stress. It is also shown that, if mediated by carnosine, the self-aggregation of α-crystallin induced by the denaturant at higher temperature can be controlled and even partially reversed. Therefore, carnosine is effective in preserving the structural integrity of the protein, suggesting the possibility of new strategies of intervention for preventing or treating pathologies related to protein aggregation, like cataracts.

  10. Identifying New Candidate Genes and Chemicals Related to Prostate Cancer Using a Hybrid Network and Shortest Path Approach

    PubMed Central

    Yuan, Fei; Zhou, You; Wang, Meng; Yang, Jing; Wu, Kai; Lu, Changhong; Kong, Xiangyin; Cai, Yu-Dong

    2015-01-01

    Prostate cancer is a type of cancer that occurs in the male prostate, a gland in the male reproductive system. Because prostate cancer cells may spread to other parts of the body and can influence human reproduction, understanding the mechanisms underlying this disease is critical for designing effective treatments. The identification of as many genes and chemicals related to prostate cancer as possible will enhance our understanding of this disease. In this study, we proposed a computational method to identify new candidate genes and chemicals based on currently known genes and chemicals related to prostate cancer by applying a shortest path approach in a hybrid network. The hybrid network was constructed according to information concerning chemical-chemical interactions, chemical-protein interactions, and protein-protein interactions. Many of the obtained genes and chemicals are associated with prostate cancer. PMID:26504486

  11. In search of earthquake-related hydrologic and chemical changes along Hayward Fault

    USGS Publications Warehouse

    King, C.-Y.; Basler, D.; Presser, T.S.; Evans, William C.; White, L.D.; Minissale, A.

    1994-01-01

    Flow and chemical measurements have been made about once a month, and more frequently when required, since 1976 at two springs in Alum Rock Park in eastern San Jose, California, and since 1980 at two shallow wells in eastern Oakland in search of earthquake-related changes. All sites are on or near the Hayward Fault and are about 55 km apart. Temperature, electric conductivity, and water level or flow rate were measured in situ with portable instruments. Water samples were collected for later chemical and isotopic analyses in the laboratory. The measured flow rate at one of the springs showed a long-term decrease of about 40% since 1987, when a multi-year drought began in California. It also showed several increases that lasted a few days to a few months with amplitudes of 2.4 to 8.6 times the standard deviations above the background rate. Five of these increases were recorded shortly after nearby earthquakes of magnitude 5.0 or larger, and may have resulted from unclogging of the flow path and increase of permeability caused by strong seismic shaking. Two other flow increases were possibly induced by exceptionally heavy rainfalls. The water in both wells showed seasonal temperature and chemical variations, largely in response to rainfall. In 1980 the water also showed some clear chemical changes unrelated to rainfall that lasted a few months; these changes were followed by a magnitude 4 earthquake 37 km away. The chemical composition at one of the wells and at the springs also showed some longer-term variations that were not correlated with rainfall but possibly correlated with the five earthquakes mentioned above. These correlations suggest a common tectonic origin for the earthquakes and the anomalies. The last variation at the affected well occurred abruptly in 1989, shortly before a magnitude 5.0 earthquake 54 km away. ?? 1993.

  12. A Novel Approach: Chemical Relational Databases, and the Role of the ISSCAN Database on Assessing Chemical Carcinogenity

    EPA Science Inventory

    Mutagenicity and carcinogenicity databases are crucial resources for toxicologists and regulators involved in chemicals risk assessment. Until recently, existing public toxicity databases have been constructed primarily as "look-up-tables" of existing data, and most often did no...

  13. 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.

  14. Phenolic Melatonin-Related Compounds: Their Role as Chemical Protectors against Oxidative Stress.

    PubMed

    Galano, Annia; Castañeda-Arriaga, Romina; Pérez-González, Adriana; Tan, Dun-Xian; Reiter, Russel J

    2016-10-29

    There is currently no doubt about the serious threat that oxidative stress (OS) poses to human health. Therefore, a crucial strategy to maintain a good health status is to identify molecules capable of offering protection against OS through chemical routes. Based on the known efficiency of the phenolic and melatonin (MLT) families of compounds as antioxidants, it is logical to assume that phenolic MLT-related compounds should be (at least) equally efficient. Unfortunately, they have been less investigated than phenols, MLT and its non-phenolic metabolites in this context. The evidence reviewed here strongly suggests that MLT phenolic derivatives can act as both primary and secondary antioxidants, exerting their protection through diverse chemical routes. They all seem to be better free radical scavengers than MLT and Trolox, while some of them also surpass ascorbic acid and resveratrol. However, there are still many aspects that deserve further investigations for this kind of compounds.

  15. Chemical applications of anthocyanins and related compounds. A source of bioinspiration.

    PubMed

    Pina, Fernando

    2014-07-23

    Independently of the natural or synthetic origin, flavylium derivatives follow the same network of chemical reactions. Actually, the flavylium cation is stable only at low pH values. Increasing the pH gives rise to the formation of several species: quinoidal bases, hemiketal, cis- and trans-chalcones, and their deprotonated forms. A deep knowledge of the thermodynamics and kinetics of these species is an essential tool to practical applications of these compounds, in particular, in the domain of food chemistry. In this work the network of chemical reactions involving flavylium derivatives is presented, and the respective thermodynamics and kinetics are discussed in detail, including the mathematical expressions and a step-by-step procedure to calculate all of the rate and equilibrium constants of the system. Examples of systems possessing a high or low cis-trans isomerization barrier are shown. Recent practical applications of anthocyanins and related compounds illustrate the potentialities of the flavylium-based family of compounds.

  16. 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.

  17. 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.

  18. Statistics for the Relative Detectability of Chemicals in Weak Gaseous Plumes in LWIR Hyperspectral Imagery

    SciTech Connect

    Metoyer, Candace N.; Walsh, Stephen J.; Tardiff, Mark F.; Chilton, Lawrence

    2008-10-30

    The detection and identification of weak gaseous plumes using thermal imaging data is complicated by many factors. These include variability due to atmosphere, ground and plume temperature, and background clutter. This paper presents an analysis of one formulation of the physics-based model that describes the at-sensor observed radiance. The motivating question for the analyses performed in this paper is as follows. Given a set of backgrounds, is there a way to predict the background over which the probability of detecting a given chemical will be the highest? Two statistics were developed to address this question. These statistics incorporate data from the long-wave infrared band to predict the background over which chemical detectability will be the highest. These statistics can be computed prior to data collection. As a preliminary exploration into the predictive ability of these statistics, analyses were performed on synthetic hyperspectral images. Each image contained one chemical (either carbon tetrachloride or ammonia) spread across six distinct background types. The statistics were used to generate predictions for the background ranks. Then, the predicted ranks were compared to the empirical ranks obtained from the analyses of the synthetic images. For the simplified images under consideration, the predicted and empirical ranks showed a promising amount of agreement. One statistic accurately predicted the best and worst background for detection in all of the images. Future work may include explorations of more complicated plume ingredients, background types, and noise structures.

  19. Commercial Pesticides Applicator Manual: Industrial, Institutional, Structural and Health Related.

    ERIC Educational Resources Information Center

    Fitzwater, William D.; Renes, Robert

    This training manual provides information needed to meet the minimum EPA standards for certification as a commercial applicator of pesticides in the industrial, institutional, structural and health related pest control category. The text discusses the use and safety of applying pesticides to control invertebrate and vertebrate pests such as ants,…

  20. Using chemical shifts to generate structural ensembles for intrinsically disordered proteins with converged distributions of secondary structure

    PubMed Central

    Ytreberg, F Marty; Borcherds, Wade; Wu, Hongwei; Daughdrill, Gary W

    2015-01-01

    A short segment of the disordered p53 transactivation domain (p53TAD) forms an amphipathic helix when bound to the E3 ubiquitin ligase, MDM2. In the unbound p53TAD, this short segment has transient helical secondary structure. Using a method that combines broad sampling of conformational space with re-weighting, it is shown that it is possible to generate multiple, independent structural ensembles that have highly similar secondary structure distributions for both p53TAD and a P27A mutant. Fractional amounts of transient helical secondary structure were found at the MDM2 binding site that are very similar to estimates based directly on experimental observations. Structures were identified in these ensembles containing segments that are highly similar to short p53 peptides bound to MDM2, even though the ensembles were re-weighted using unbound experimental data. Ensembles were generated using chemical shift data (alpha carbon only, or in combination with other chemical shifts) and cross-validated by predicting residual dipolar couplings. We think this ensemble generator could be used to predict the bound state structure of protein interaction sites in IDPs if there are detectable amounts of matching transient secondary structure in the unbound state.

  1. Structural studies of human glioma pathogenesis-related protein 1.

    PubMed

    Asojo, Oluwatoyin A; Koski, Raymond A; Bonafé, Nathalie

    2011-10-01

    Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn2+ complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn2+ similarly to snake-venom CRISPs, which are involved in Zn2+-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

  2. Synthesis of one-dimensional boron-related nanostructures by chemical vapor deposition

    NASA Astrophysics Data System (ADS)

    Guo, Li

    Motivated by the extensive research on carbon nanotubes (CNTs), boron and its related nano-structures have attracted increasing interest for potential applications in nanodevices and nanotechnologies, due to their extraordinary properties. In this work, different types of B-related nanostructures were successfully grown on oxidized Si substrates with or without transition metal catalysts in CVD processes. The gas chemistry was monitored by in-situ mass-spectroscopy and optical emission spectroscopy. These helped to identify the gas reactive species during the deposition, creating thereby a controllable, optimum synthesis process and helping in identifying the growth mechanism. The boron nitride nanotubes (BNNTs) were successfully synthesized at the low substrate temperatures of 600-800°C by a microwave plasma CVD process, using diborane and ammonia as the gas precursors. The optimum growth conditions of BNNTs were investigated by varying the experimental parameters, such as catalyst film thickness, substrate temperature, diborane flow rate, and growth time. The dense and crystalline BNNT deposits were obtained on 1nm nickel (Ni) or cobalt (Co) thin film coated oxidized Si (111) at a temperature of 800°C, a pressure of 15 torr, microwave power of 800 W, diborane flow rate (5 vol.% in hydrogen) of 5 sccm, ammonia flow rate of 27.5 sccm, hydrogen flow rate of 10sccm, and a deposition time of 1 hour. These nanotubes were either self-assembled in bundles or as a single tube with a diameter less than 10 nm. Raman spectra together with electron diffraction pattern indicated a hexagonal crystalline structure for these BN nanostructures. A growth mechanism of BNNTs involving dissolution-supersaturation-precipitation of BN in the metal catalysts was proposed. It was shown that the growth of BN nanostructures strongly depended on the catalyst and its film thickness, which resulted in the selective growth of BNNTs on the patterned catalyst islands. Ni dots with the diameters

  3. 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.

  4. Structural studies of human glioma pathogenesis-related protein 1

    SciTech Connect

    Asojo, Oluwatoyin A.; Koski, Raymond A.; Bonafé, Nathalie

    2011-10-01

    Structural analysis of a truncated soluble domain of human glioma pathogenesis-related protein 1, a membrane protein implicated in the proliferation of aggressive brain cancer, is presented. Human glioma pathogenesis-related protein 1 (GLIPR1) is a membrane protein that is highly upregulated in brain cancers but is barely detectable in normal brain tissue. GLIPR1 is composed of a signal peptide that directs its secretion, a conserved cysteine-rich CAP (cysteine-rich secretory proteins, antigen 5 and pathogenesis-related 1 proteins) domain and a transmembrane domain. GLIPR1 is currently being investigated as a candidate for prostate cancer gene therapy and for glioblastoma targeted therapy. Crystal structures of a truncated soluble domain of the human GLIPR1 protein (sGLIPR1) solved by molecular replacement using a truncated polyalanine search model of the CAP domain of stecrisp, a snake-venom cysteine-rich secretory protein (CRISP), are presented. The correct molecular-replacement solution could only be obtained by removing all loops from the search model. The native structure was refined to 1.85 Å resolution and that of a Zn{sup 2+} complex was refined to 2.2 Å resolution. The latter structure revealed that the putative binding cavity coordinates Zn{sup 2+} similarly to snake-venom CRISPs, which are involved in Zn{sup 2+}-dependent mechanisms of inflammatory modulation. Both sGLIPR1 structures have extensive flexible loop/turn regions and unique charge distributions that were not observed in any of the previously reported CAP protein structures. A model is also proposed for the structure of full-length membrane-bound GLIPR1.

  5. [DNA and chemical analyses of commercial fly agaric-related products].

    PubMed

    Maruyama, Takuro; Kawahara, Nobuo; Fukiharu, Toshimitsu; Yokoyama, Kazumasa; Makino, Yukiko; Goda, Yukihiro

    2005-04-01

    Since June 6, 2002, psilocin and psilocybin-containing fungi (commonly called "magic mushrooms") have been regulated by the Narcotics and Psychotropics Control Law in Japan. However, various fly agaric-related products are now entering the Japanese market via the internet. In this study, fly agaric-related products available in this way were investigated for raw materials by DNA analysis and for additives by chemical analysis. Nucleotide sequence analysis of the mitochondrial 12S rDNA region suggested that these fly agaric-related products originate from A. muscaria or A. muscaria var. persicina. Furthermore, they were classified into three strains based on the ITS2-LSU nucleotide sequence. Harmine derivatives and/or tryptamine derivatives were detected in some of these products by LC/MS analysis. In accordance with this, the matK gene of Peganum harmala was found in all of the harmine derivative-containing samples.

  6. Relating secondary structure to the mechanical properties of polypeptide hydrogels

    NASA Astrophysics Data System (ADS)

    Hagan, Sharon Anne

    Biomimetic hydrogels are being developed for use in medicine as drug delivery devices and tissue engineering matrices, and the mechanical properties of the materials play an important role in their performance. For example, in tissue engineering, gene expression and cell adhesion have been closely linked to the mechanical properties of the surrounding hydrogel matrix. In poly-L-lysine hydrogels, a five-fold increase in storage modulus, a 50% increase in equilibrium modulus, and a 62% decrease in swelling degree are shown to occur as the hydrogel network chains transition from an alpha-helix to a beta-sheet conformation. The manipulation of the network's mechanical behavior through changes in the secondary structure of the polymer chains offers an additional design variable in the development of biosynthetic materials. Analogous to poly-L-lysine, elastin-mimetic proteins based on the consensus repeat sequence of elastin (VPGVG) undergo a temperature-dependent secondary structure transition from a random coil to a beta-spiral. In this research, chemically-crosslinked poly[(VPGVG)4(VPGKG)] hydrogels are shown to possess temperature- and pH-dependent swelling. Following scaling law predictions (G ˜ φ2n), the hydrogels have been shown to behave as ideal elastic networks when the crosslink density is varied at synthesis (theory: n = 9/4, experimental: n = 2.0 +/- 0.1), and behave as flexible networks above and below their structural transition temperature of 35°C (theory: n = 1/3, experimental: n = 0.45 +/- 0.06). Evaluation of published data on elastin-mimetic hydrogels shows that the hydrogels behave as ideal elastic networks for all crosslinking techniques, crosslink spacings, and crosslink functionalities reported. As a contrast to chemically-crosslinked hydrogels, a novel elastin-mimetic triblock (EMT) copolymer was evaluated because of its potential use in cell encapsulation without potentially harmful side reactions. Unlike other thermally gelling copolymers

  7. 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…

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

    SciTech Connect

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

    1980-03-21

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

  9. 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.

  10. 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,…

  11. Lagrangian space consistency relation for large scale structure

    SciTech Connect

    Horn, Bart; Hui, Lam; Xiao, Xiao E-mail: lh399@columbia.edu

    2015-09-01

    Consistency relations, which relate the squeezed limit of an (N+1)-point correlation function to an N-point function, are non-perturbative symmetry statements that hold even if the associated high momentum modes are deep in the nonlinear regime and astrophysically complex. Recently, Kehagias and Riotto and Peloso and Pietroni discovered a consistency relation applicable to large scale structure. We show that this can be recast into a simple physical statement in Lagrangian space: that the squeezed correlation function (suitably normalized) vanishes. This holds regardless of whether the correlation observables are at the same time or not, and regardless of whether multiple-streaming is present. The simplicity of this statement suggests that an analytic understanding of large scale structure in the nonlinear regime may be particularly promising in Lagrangian space.

  12. Effects of CW (chemical warfare)-related chemicals on social behavior and performance. Annual report, 30 September 1983-29 September 1984

    SciTech Connect

    Bunnell, B.N.; Iturrian, W.B.

    1984-10-01

    This report summarizes work accomplished in the first year of a three-year project aimed at developing a battery of tests of social behavior and and performance that will be sensitive to the effects of chemical warfare-related chemicals considered for use as antidotes or prophylactics against chemical-warfare agents. Procedures for assessing social behavior in nonhuman primates are described and compared. The presence and absence of correlations between social behavior and performance on two operant schedules, a test of complex problem solving, and behavior in a novel environment are reported as are the effects of caffeine (as a control) and atropine on the social and performance variables.

  13. (Impact of energy related pollutants on chromosome structure): Progress report

    SciTech Connect

    Rill, R.L.

    1986-01-01

    Studies of the structure of nucleosome cores using chymotrypsin as a probe of hydrophobic residues showed that only leu-20 of H3 was readily accessible. Primary sites of cleavage of H2a, H2b, and H4 were identified. Chymotrypsin removal of specific histone termini showed that removal of the amino-terminal plus the carboxy-terminal 13 residues of H2a caused little unfolding. Using carbon-13 NMR spectroscopic, about 10% of histone amino acid residues were found to be in termini that are highly mobile. The major mobile segments were amino terminal regions of H3 and H2a, plus a carboxy-terminal region of H2a. The histone variants and developmental changes during embryogenesis of sea urchin were characterized. The early histone gene organization in L. variegatus was characterized, a genomic library was cloned in lambda phage, and several histone gene clones were selected. The nucleosome core length DNA forms crystalline phases at physiological concentrations. Microscopic and NMR spectroscopic methods were used to identify crystalline phases and to establish phase diagrams for transitions between phases as functions of DNA concentration and temperature. The sequence specificities of binding of several polycyclic aromatic chemicals to early H3 and H2a genes were examined. Chemicals studied were the bis-(o-phenanthroline) Cu(I) complex, AAAF, benzopyrene dihydrodiol epoxide, methylene blue, and acridine orange A preliminary map of binding sites of CuOP, AAAF and BPDE in and near the H3 gene showed that several sequence regions were bound preferentially by two or more of these chemicals. CuOP appeared to exhibit the most specificity. 80 refs., 4 figs.

  14. Structure of the lepidopteran proboscis in relation to feeding guild.

    PubMed

    Lehnert, Matthew S; Beard, Charles E; Gerard, Patrick D; Kornev, Konstantin G; Adler, Peter H

    2016-02-01

    Most butterflies and moths (Lepidoptera) use modified mouthparts, the proboscis, to acquire fluids. We quantified the proboscis architecture of five butterfly species in three families to test the hypothesis that proboscis structure relates to feeding guild. We used scanning electron microscopy to elucidate the fine structure of the proboscis of both sexes and to quantify dimensions, cuticular patterns, and the shapes and sizes of sensilla and dorsal legulae. Sexual dimorphism was not detected in the proboscis structure of any species. A hierarchical clustering analysis of overall proboscis architecture reflected lepidopteran phylogeny, but did not produce a distinct group of flower visitors or of puddle visitors within the flower visitors. Specific characters of the proboscis, nonetheless, can indicate flower and nonflower visitors, such as the configuration of sensilla styloconica, width of the lower branches of dorsal legulae, presence or absence of dorsal legulae at the extreme apex, and degree of proboscis tapering. We suggest that the overall proboscis architecture of Lepidoptera reflects a universal structural organization that promotes fluid uptake from droplets and films. On top of this fundamental structural organization, we suggest that the diversity of floral structure has selected for structural adaptations that facilitate entry of the proboscis into floral tubes.

  15. Nature of the binding interaction for 50 structurally diverse chemicals with rat estrogen receptors.

    PubMed

    Laws, Susan C; Yavanhxay, S; Cooper, Ralph L; Eldridge, J Charles

    2006-11-01

    This study was conducted to characterize the estrogen receptor (ER)-binding affinities of 50 chemicals selected from among the high production volume chemicals under the U.S. EPA's (U.S. Environmental Protection Agency's) Toxic Substances Control Act inventory. The chemicals were evaluated using the rat uterine cytosolic (RUC) ER-competitive binding assay, with secondary analysis using Lineweaver-Burk plots and slope replots to confirm true competitive inhibition and to determine an experimental K(i). Data from these ER-competitive binding assays represent the types of competitive binding curves that can be obtained when screening chemicals with broad structural diversity. True competitive inhibition was observed in 17 of 50 chemicals. Binding affinities were much lower than that of estradiol (E(2)) with K(i) concentrations ranging from 0.6 to 373 microM as compared with that of E(2) (0.77 nM). Other chemicals that appeared to displace radiolabeled E(2) binding to ER were, in fact, found not to be competitive inhibitors in the secondary K(i) experiments. These seven chemicals likely altered the stability of the assay by changing the buffer pH, denaturing ER, or disrupting the ER-binding kinetics. Thus, several conditions that may confound interpretation of RUC ER-binding assay data are illustrated. For another group of eight chemicals, neither an IC(50) nor K(i) could be determined due to solubility constraints. These chemicals exhibited slight (20-40%) inhibition at concentrations of 10-100 microM, suggesting that they could be competitors at very high concentrations, yet K(i) experiments were not possible as the limit of chemical solubility in the aqueous assay buffer was well above the IC(50). An additional 18 of the 50 chemicals were classified as nonbinders because in concentrations up to 100 microM they produced essentially no displacement of radiolabeled E(2). These results show that although the ER-competitive binding assay is a valuable tool for screening

  16. First report on development of quantitative interspecies structure-carcinogenicity relationship models and exploring discriminatory features for rodent carcinogenicity of diverse organic chemicals using OECD guidelines.

    PubMed

    Kar, Supratik; Roy, Kunal

    2012-04-01

    Different regulatory agencies in food and drug administration and environmental protection worldwide are employing quantitative structure-activity relationship (QSAR) models to fill the data gaps related with properties of chemicals affecting the environment and human health. Carcinogenicity is a toxicity endpoint of major concern in recent times. Interspecies toxicity correlations may provide a tool for estimating sensitivity towards toxic chemical exposure with known levels of uncertainty for a diversity of wildlife species. In this background, we have developed quantitative interspecies structure-carcinogenicity correlation models for rat and mouse [rodent species according to the Organization for Economic Cooperation and Development (OECD) guidelines] based on the carcinogenic potential of 166 organic chemicals with wide diversity of molecular structures, spanning a large number of chemical classes and biological mechanisms. All the developed models have been assessed according to the OECD principles for the validation of QSAR models. Consensus predictions for carcinogenicity of the individual compounds are presented here for any one species when the data for the other species are available. Informative illustrations of the contributing structural fragments of chemicals which are responsible for specific carcinogenicity endpoints are identified by the developed models. The models have also been used to predict mouse carcinogenicities of 247 organic chemicals (for which rat carcinogenicities are present) and rat carcinogenicities of 150 chemicals (for which mouse carcinogenicities are present). Discriminatory features for rat and mouse carcinogenicity values have also been explored.

  17. Metabolomics relative quantitation with mass spectrometry using chemical derivatization and isotope labeling

    DOE PAGES

    O'Maille, Grace; Go, Eden P.; Hoang, Linh; ...

    2008-01-01

    Comprehensive detection and quantitation of metabolites from a biological source constitute the major challenges of current metabolomics research. Two chemical derivatization methodologies, butylation and amination, were applied to human serum for ionization enhancement of a broad spectrum of metabolite classes, including steroids and amino acids. LC-ESI-MS analysis of the derivatized serum samples provided a significant signal elevation across the total ion chromatogram to over a 100-fold increase in ionization efficiency. It was also demonstrated that derivatization combined with isotopically labeled reagents facilitated the relative quantitation of derivatized metabolites from individual as well as pooled samples.

  18. 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

  19. 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

  20. Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

    SciTech Connect

    Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A.; Heazlewood, Joshua L.; Holmes, Bradley M.; Zabotina, Olga A.

    2012-12-28

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks.

  1. Structural and Chemical Characterization of Hardwood from Tree Species with Applications as Bioenergy Feedstocks

    PubMed Central

    Çetinkol, Özgül Persil; Smith-Moritz, Andreia M.; Cheng, Gang; Lao, Jeemeng; George, Anthe; Hong, Kunlun; Henry, Robert; Simmons, Blake A.; Heazlewood, Joshua L.; Holmes, Bradley M.

    2012-01-01

    Eucalypt species are a group of flowering trees widely used in pulp production for paper manufacture. For several decades, the wood pulp industry has focused research and development efforts on improving yields, growth rates and pulp quality through breeding and the genetic improvement of key tree species. Recently, this focus has shifted from the production of high quality pulps to the investigation of the use of eucalypts as feedstocks for biofuel production. Here the structure and chemical composition of the heartwood and sapwood of Eucalyptus dunnii, E. globulus, E. pillularis, E. urophylla, an E. urophylla-E. grandis cross, Corymbia citriodora ssp. variegata, and Acacia mangium were compared using nuclear magnetic resonance spectroscopy (NMR), X-ray diffraction (XRD) and biochemical composition analysis. Some trends relating to these compositions were also identified by Fourier transform near infrared (FT-NIR) spectroscopy. These results will serve as a foundation for a more comprehensive database of wood properties that will help develop criteria for the selection of tree species for use as biorefinery feedstocks. PMID:23300786

  2. Quantum chemical density functional theory studies on the molecular structure and vibrational spectra of mannitol.

    PubMed

    Moorthi, P P; Gunasekaran, S; Swaminathan, S; Ramkumaar, G R

    2015-02-25

    A collective experimental and theoretical study was conducted on the molecular structure and vibrational spectra of mannitol. The FT-IR and FT-Raman spectra of mannitol were recorded in the solid phase. The molecular geometry, vibrational frequencies, thermodynamic functions and atomic charges of mannitol in the ground state have been calculated by using the ab initio HF (Hartree-Fock) and density functional methods (B3LYP) invoking cc-pVDZ basis set. The complete vibrational assignments were performed on the basis of Total Energy Distribution (TED) of the vibrational modes. The UV absorption spectra of the title compound dissolved in water. Natural bond orbital analysis has been carried out to explain the charge transfer or delocalization of charge due to the intra-molecular interactions. The (1)H and (13)C nuclear magnetic resonance (NMR) chemical shifts of the molecule were calculated by GIAO methods. The first order hyperpolarizability (β0) of this novel molecular system and related properties (β, α0 and Δα) of mannitol are calculated using B3LYP/cc-pVDZ and HF/cc-pVDZ methods on the finite-field approach. By using TD-DFT calculation, electronic absorption spectra of the title compound have been predicted and a good agreement with experimental one is established. In addition, the molecular electrostatic potential (MEP) have been investigated using theoretical calculations, the calculated HOMO and LUMO energies shows that the charge transfer within the molecule.

  3. Structural, ferroelectric and piezoelectric properties of chemically processed, low temperature sintered piezoelectric BZT-BCT ceramics

    NASA Astrophysics Data System (ADS)

    Roy, Subir; Maharana, Rajalaxmi; Rangaswamy Reddy, S.; Singh, Sarabjit; Kumar, Pawan; Karthik, T.; Asthana, Saket; Bhanu Prasad, V. V.; Kamat, S. V.

    2016-03-01

    0.5Ba(Zr0.2Ti0.8)O3-0.5(Ba0.7Ca0.3TiO3) nanopowders were synthesized at very low temperature using a soft chemical approach. The synthesized powders and the consolidated disks were structurally characterized thoroughly by XRD, SEM, TEM and EPMA and also by ultraviolet and Raman spectroscopy. The 1350 °C sintered BZT-BCT disk displayed the highest density, underwent diffused phase transition centered at ˜100 °C and showed the highest dielectric constant (8917) and lowest dielectric loss (0.015). The sintered BZT-BCT sample with the highest density showed a maximum polarization (P max) of 13 μC cm-2 and remnant polarization of 6 μC cm-2. The same sample exhibited very high electrostrain of ˜0.12% under a relatively low electrical field of 3.5 kV mm-1.

  4. Relative Displacement Method for Track-Structure Interaction

    PubMed Central

    Ramos, Óscar Ramón; Pantaleón, Marcos J.

    2014-01-01

    The track-structure interaction effects are usually analysed with conventional FEM programs, where it is difficult to implement the complex track-structure connection behaviour, which is nonlinear, elastic-plastic and depends on the vertical load. The authors developed an alternative analysis method, which they call the relative displacement method. It is based on the calculation of deformation states in single DOF element models that satisfy the boundary conditions. For its solution, an iterative optimisation algorithm is used. This method can be implemented in any programming language or analysis software. A comparison with ABAQUS calculations shows a very good result correlation and compliance with the standard's specifications. PMID:24634610

  5. 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.

  6. 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.

  7. SYBYL line notation (SLN): a single notation to represent chemical structures, queries, reactions, and virtual libraries.

    PubMed

    Homer, R Webster; Swanson, Jon; Jilek, Robert J; Hurst, Tad; Clark, Robert D

    2008-12-01

    SYBYL line notation (SLN) is a powerful way to represent molecular structures, reactions, libraries of structures, molecular fragments, formulations, molecular queries, and reaction queries. Nearly any chemical structure imaginable, including macromolecules, pharmaceuticals, catalysts, and even combinatorial libraries can be represented as an SLN string. The language provides a rich syntax for database queries comparable to SMARTS. It provides full Markush, R-Group, reaction, and macro atom capabilities in a single unified notation. It includes the ability to specify 3D conformations and 2D depictions. All the information necessary to recreate the structure in a modeling or drawing package is present in a single, concise string of ASCII characters. This makes SLN ideal for structure communication over global computer networks between applications sitting at remote sites. Unlike SMILES and its derivatives, SLN accomplishes this within a single unified syntax. Structures, queries, compounds, reactions, and virtual libraries can all be represented in a single notation.

  8. 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.

  9. Structural and diffusional brain abnormality related to relatively low level alcohol consumption.

    PubMed

    Sasaki, Hiroki; Abe, Osamu; Yamasue, Hidenori; Fukuda, Rin; Yamada, Haruyasu; Takei, Kunio; Suga, Motomu; Takao, Hidemasa; Kasai, Kiyoto; Aoki, Shigeki; Ohtomo, Kuni

    2009-06-01

    Chronic excessive alcohol intake results in alcohol-related brain damage. Many previous reports have documented alcohol-related global or local brain shrinkage or diffusional abnormalities among alcoholics and heavy to moderate drinkers; however, the influence of relatively low levels of alcohol consumption on brain structural or diffusional abnormality is unclear. We investigated structural or diffusional abnormalities related to lifetime alcohol consumption (LAC) using voxel-based morphometry (VBM) among Japanese non-alcohol-dependent individuals (114 males, 97 females). High-resolution three-dimensional magnetic resonance images and diffusion tensor imaging were acquired in all subjects. The collected images were normalized, segmented, and smoothed using SPM 5. Gray matter volume (GMV) and white matter volume (WMV) were normalized for each total intracranial volume (TIV), and partial correlation coefficients were estimated between normalized GMV or WMV and lifetime alcohol consumption (LAC) adjusted for age. To investigate regional GMV or WMV abnormalities related to LAC, multiple regression analyses were performed among regional GMV or WMV and LAC, age, and TIV. To investigate subtle regional abnormalities, multiple regression analyses were performed among fractional anisotropy (FA) or mean diffusivity (MD), and LAC and age. No LAC-related global or regional GMV or WMV abnormality or LAC-related regional FA abnormality was found among male or female subjects. Significant LAC-related MD increase was found in the right amygdala among female subjects only. The current results suggest female brain vulnerability to alcohol, and a relation between subtle abnormality in the right amygdala and alcohol misuse.

  10. 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

    2014-07-16

    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.

  11. A script for automated 3-dimentional structure generation and conformer search from 2- dimentional chemical drawing.

    PubMed

    Ishikawa, Yoshinobu

    2013-01-01

    Building 3-dimensional (3D) molecules is the starting point in molecular modeling. Conformer search and identification of a global energy minimum structure are often performed computationally during spectral analysis of data from NMR, IR, and VCD or during rational drug design through ligand-based, structure-based, and QSAR approaches. I herein report a convenient script that allows for automated building of 3D structures and conformer searching from 2-dimensional (2D) drawing of chemical structures. With this Bash shell script, which runs on Mac OS X and the Linux platform, the tasks are consecutively and iteratively executed without a 3D molecule builder via the command line interface of the free (academic) software OpenBabel, Balloon, and MOPAC2012. A large number of 2D chemical drawing files can be processed simultaneously, and the script functions with stereoisomers. Semi-empirical quantum chemical calculation ensures reliable ranking of the generated conformers on the basis of energy. In addition to an energy-sorted list of file names of the conformers, their Gaussian input files are provided for ab initio and density functional theory calculations to predict rigorous electronic energies, structures, and properties. This script is freely available to all scientists.

  12. 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

  13. 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.

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

    PubMed

    Kocsis, Bela; Domokos, J; Szabo, D

    2016-05-23

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

  15. Structural, optical, electrical and thermal properties of zinc oxide thin films by chemical spray pyrolysis

    NASA Astrophysics Data System (ADS)

    Shinde, S. S.; Bhosale, C. H.; Rajpure, K. Y.

    2012-08-01

    Thin films of highly textured ZnO are synthesized by simple chemical spray pyrolysis onto corning glass substrates in aqueous medium. The influence of solution concentration onto photoelectrochemical, structural, morphological, compositional, optical, electrical and thermal properties have been investigated. Structural analysis shows the hexagonal (wurtzite) crystal structure. Electron-phonon-coupling in ZnO films has analyzed using Raman spectroscopy. The chemical composition and valence states of constituent elements in ZnO are analyzed by X-ray photoelectron spectroscopy. The SEM and AFM micrographs depict the films are compact and homogeneous (hexagonal platelets nanostructures) with varying grain sizes (average grain size ˜50-150 nm). The specific heat and thermal conductivity study shows the phonon conduction behavior is dominant in these polycrystalline films.

  16. 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

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

  17. 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.

  18. 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

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

    PubMed Central

    2014-01-01

    Background Sharing sets of chemical data (e.g., chemical properties, docking scores, etc.) among collaborators with diverse skill sets is a common task in computer-aided drug design and medicinal chemistry. The ability to associate this data with images of the relevant molecular structures greatly facilitates scientific communication. There is a need for a simple, free, open-source program that can automatically export aggregated reports of entire chemical data sets to files viewable on any computer, regardless of the operating system and without requiring the installation of additional software. Results We here present a program called WebChem Viewer that automatically generates these types of highly portable reports. Furthermore, in designing WebChem Viewer we have also created a useful online web application for remotely generating molecular structures from SMILES strings. We encourage the direct use of this online application as well as its incorporation into other software packages. Conclusions With these features, WebChem Viewer enables interdisciplinary collaborations that require the sharing and visualization of small molecule structures and associated sets of heterogeneous chemical data. The program is released under the FreeBSD license and can be downloaded from http://nbcr.ucsd.edu/WebChemViewer. The associated web application (called “Smiley2png 1.0”) can be accessed through freely available web services provided by the National Biomedical Computation Resource at http://nbcr.ucsd.edu. PMID:24886360

  20. Impact of steam explosion on biogas production from rape straw in relation to changes in chemical composition.

    PubMed

    Vivekanand, Vivekanand; Ryden, Peter; Horn, Svein J; Tapp, Henri S; Wellner, Nikolaus; Eijsink, Vincent G H; Waldron, Keith W

    2012-11-01

    An 81day trial compared the cumulative production of methane from rape straw pre-treated by steam explosion at 15 levels of severity. The final methane yields were similar. The temporal variation in production rate exhibited two peaks: maximum production occurred in the first peak at around 21days with heights that increased with severity; the height of the second peak reduced with severity and peaked between 32 and 36days. Changes in the straw composition were investigated using mid-infrared spectroscopy. These were also strongly related to the degree of severity, allowing good predictive models to be built of severity and subsequently the rate of methane production. The main spectral changes showed the degradation of cellulose and xylose-containing hemicelluloses and production of furfural-like components commonly associated with biomass pre-treatments. Only small changes to lignin were associated with increased methane generation suggesting a structural rather than chemical role in this process.

  1. The magnetic and chemical structural property of the epitaxially-grown multilayered thin film

    NASA Astrophysics Data System (ADS)

    Lee, Hwachol

    L10 FePt- and Fe-related alloys such as FePtRh, FeRh and FeRhPd have been studied for the high magnetocrystalline anisotropy and magnetic phase transition property for the future application. In this work, the thin film structural and magnetic property is investigated for the selected FePtRh and FeRhPd alloys. The compositionally-modulated L10 FePtRh multilayered structure is grown epitaxially on a-plane Al2O3 with Cr and Pt buffer layer at 600degC growth temperature by DC sputtering technique and examined for the structural, interfacial and magnetic property. For the epitaxially grown L10 [Fe50Pt45Rh5 (FM) (10nm) / Fe50Pt25Rh25 (AFM) (20nm)]x8 superlattice, the magnetically and chemically sharp interface formation between layers was observed in X-ray diffraction, transmission electron microscopy and polarized neutron reflectivity measurements with the negligible exchange bias at room and a slight coupling effect at lower temperature regime. For FeRhPd, the magnetic phase transition of epitaxially-grown 111-oriented Fe46Rh48Pd6 thin film is studied. The applied Rhodium buffer layer on a-plane Al2O3 (11 20) at 600degC shows the extraordinarily high quality of epitaxial film in (111) orientation, where two broad and coherent peak in rocking curve, and Laue oscillations are observed. The epitaxially-grown Pd-doped FeRh on Pt (111) grown at 600degC, 700degC exhibits the co-existing stable L10 (111) and B2 (110) structures and magnetic phase transition around 300degC. On the other hand, the partially-ordered FeRhPd structure grown at 400degC, 500degC shows background high ferromagnetic state over 5K˜350K temperature. For the reduced thickness of Fe46Rh48Pd 6, the ferromagnetic state becomes dominant with a reduced portion of the film undergoing a magnetic phase transition. For some epitaxial FeRhPd film, the spin-glass-like disordered state is also observed in field dependent SQUID measurement. For the tri-layered FeRhPd with thin Pt spacer, the background

  2. Hippocampal structure predicts cortical indices of reactivation of related items.

    PubMed

    Walker, John A; Low, Kathy A; Fletcher, Mark A; Cohen, Neal J; Gratton, Gabriele; Fabiani, Monica

    2017-01-27

    One of the key components of relational memory is the ability to bind together the constituent elements of a memory experience, and this ability is thought to be supported by the hippocampus. Previously we had shown that these relational bindings can be used to reactivate the cortical processors of an absent item in the presence of a relationally bound associate (Walker et al., 2014). Specifically, we recorded the event-related optical signal (EROS) when presenting the scene of a face-scene pair during a preview period immediately preceding a test display, and demonstrated reactivation of a face-processing cortical area (the superior temporal sulcus, STS) for scenes that had been previously paired with faces, relative to scenes that had not. Here we combined the EROS measures during the same preview paradigm with anatomical estimates of hippocampal integrity (structural MRI measures of hippocampal volume and diffusion tensor imaging measures of mean fractional anisotropy and diffusivity) to provide evidence that the hippocampus is mediating this reactivation phenomenon. The study was run in a sample of older adults aged 55-87, taking advantage of the high amount of hippocampal variability present in aging. We replicated the functional reactivation of STS during the preview period, specific to scenes previously paired with faces. Crucially, we also found that this phenomenon is correlated with structural hippocampus integrity. Both STS reactivation and hippocampal structure predicted subsequent recognition performance. These data support the theory that relational memory is sustained by an interaction between hippocampal and cortical sensory processing regions, and that these functions may be at the basis of episodic memory changes in normal aging.

  3. 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.

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

    SciTech Connect

    Not Available

    1992-01-01

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

  5. Unfolding the Therapeutic Potential of Chemical Chaperones for Age-related Macular Degeneration

    PubMed Central

    Sauer, Theodor; Patel, Mrinali; Chan, Chi-Chao; Tuo, Jingsheng

    2008-01-01

    SUMMARY Recent studies suggest that pathological processes involved in age-related macular degeneration (AMD) might induce endoplasmic reticulum (ER) stress. Growing evidence demonstrates the ability of chemical chaperones to decrease ER stress and ameliorate ER stress-related disease phenotypes, suggesting that the field of chaperone therapy might hold novel treatments for AMD. In this review, we examine the evidence suggesting a role for ER stress in AMD. Furthermore, we discuss the use of chaperone therapy for the treatment of ER stress-associated diseases, including other neurodegenerative diseases and retinopathies. Finally, we examine strategies for identifying potential chaperone compounds and for experimentally demonstrating chaperone activity in in vitro and in vivo models of human disease. PMID:18528533

  6. Risk of hypospadias in relation to maternal occupational exposure to potential endocrine disrupting chemicals

    PubMed Central

    Vrijheid, M; Armstrong, B; Dolk, H; van Tongeren, M; Botting, B

    2003-01-01

    Background: Reported rises in the prevalence of hypospadias and other abnormalities of the male reproductive system may be a result of exposure to endocrine disrupting chemicals. Aims: To analyse the relation between risk of hypospadias and maternal occupation, particularly with regard to exposure to potential endocrine disrupting chemicals (EDCs). Methods: Data (1980–96) from the National Congenital Anomaly System (NCAS) were used to analyse the proportion of all congenital anomaly cases (n = 35 962) which were notified with hypospadias (n = 3471) by occupational codes (348 individual job titles) and by categories of exposure to potential EDCs from a job exposure matrix. Results: Five individual occupations (of 348) showed nominally statistically significant excesses, none of which had possible or probable exposure to potential EDCs. Odds ratios for "possible" or "probable" compared to "unlikely" exposure to potential EDCs did not show statistically significant increases in any of the EDC categories after adjustment for social class of the mother and father, nor was there evidence of an upward trend in risk with likelihood of exposure. In the 1992–96 time period odds ratios were increased for hairdressers (the largest group exposed to potential EDCs) and for probable exposure to phthalates (of which hairdressers form the largest group) before social class adjustment. Conclusions: There was little evidence for a relation between risk of hypospadias and maternal occupation or occupational exposure to potential EDCs, but as the exposure classification was necessarily crude, these findings should be interpreted with caution. PMID:12883014

  7. A knowledge-poor approach to chemical-disease relation extraction

    PubMed Central

    Alam, Firoj; Corazza, Anna; Lavelli, Alberto; Zanoli, Roberto

    2016-01-01

    The article describes a knowledge-poor approach to the task of extracting Chemical-Disease Relations from PubMed abstracts. A first version of the approach was applied during the participation in the BioCreative V track 3, both in Disease Named Entity Recognition and Normalization (DNER) and in Chemical-induced diseases (CID) relation extraction. For both tasks, we have adopted a general-purpose approach based on machine learning techniques integrated with a limited number of domain-specific knowledge resources and using freely available tools for preprocessing data. Crucially, the system only uses the data sets provided by the organizers. The aim is to design an easily portable approach with a limited need of domain-specific knowledge resources. In the participation in the BioCreative V task, we ranked 5 out of 16 in DNER, and 7 out of 18 in CID. In this article, we present our follow-up study in particular on CID by performing further experiments, extending our approach and improving the performance. PMID:27189609

  8. Structured IR illumination for relative depth sensing in virtual interfaces

    NASA Astrophysics Data System (ADS)

    Kress, Bernard; Raulot, Victorien; Grossman, Michel

    2012-06-01

    Depth mapping or depth sensing has become a popular field, applied not only to automotive sensing for collision avoidance (radar) but also to gesture sensing for gaming and virtual interfaces (optical). Popular gesture sensing devices such as the Kinect from Microsoft's Xbox gaming device produce a full absolute depth map, which is in most cases not adapted to the task on hand (relative gesture sensing). We propose in this paper a new gesture sensing technique through structured IR illumination to provide a relative depth mapping rather than an absolute one, and this reducing the requirements on computing power and therefore enabling this technology for wearable computing such as see through display.

  9. Modeling the reactivities of hydroxyl radical and ozone towards atmospheric organic chemicals using quantitative structure-reactivity relationship approaches.

    PubMed

    Gupta, Shikha; Basant, Nikita; Mohan, Dinesh; Singh, Kunwar P

    2016-07-01

    The persistence and the removal of organic chemicals from the atmosphere are largely determined by their reactions with the OH radical and O3. Experimental determinations of the kinetic rate constants of OH and O3 with a large number of chemicals are tedious and resource intensive and development of computational approaches has widely been advocated. Recently, ensemble machine learning (EML) methods have emerged as unbiased tools to establish relationship between independent and dependent variables having a nonlinear dependence. In this study, EML-based, temperature-dependent quantitative structure-reactivity relationship (QSRR) models have been developed for predicting the kinetic rate constants for OH (kOH) and O3 (kO3) reactions with diverse chemicals. Structural diversity of chemicals was evaluated using a Tanimoto similarity index. The generalization and prediction abilities of the constructed models were established through rigorous internal and external validation performed employing statistical checks. In test data, the EML QSRR models yielded correlation (R (2)) of ≥0.91 between the measured and the predicted reactivities. The applicability domains of the constructed models were determined using methods based on descriptors range, Euclidean distance, leverage, and standardization approaches. The prediction accuracies for the higher reactivity compounds were relatively better than those of the low reactivity compounds. Proposed EML QSRR models performed well and outperformed the previous reports. The proposed QSRR models can make predictions of rate constants at different temperatures. The proposed models can be useful tools in predicting the reactivities of chemicals towards OH radical and O3 in the atmosphere.

  10. Water relations, thallus structure and photosynthesis in Negev Desert lichens

    NASA Technical Reports Server (NTRS)

    Palmer, R. J. Jr; Friedmann, E. I.

    1990-01-01

    The role of lichen thallus structure in water relations and photosynthesis was studied in Ramalina maciformis (Del.) Bory and Teloschistes lacunosus (Rupr.) Sav. Water-vapour adsorption and photosynthesis are dependent upon thallus integrity and are significantly lower in crushed thalli. Cultured phycobiont (Trebouxia sp.) cells are capable of photosynthesis over the same relative humidity range (> 80% RH) as are intact lichens. Thus, water-vapour adsorption by the thallus and physiological adaptation of the phycobiont contribute to the ability of these lichens to photosynthesize in an arid environment. Despite differences in their anatomical structure and water-uptake characteristics, their CO2 incorporation is similar. The two lichens use liquid water differently and they occupy different niches.

  11. INVESTIGATING PAVEMENT STRUCTURE DETERIORATION WITH A RELATIVE EVALUATION MODEL

    NASA Astrophysics Data System (ADS)

    Mori, Hisashi; Fujiwara, Eigo; Kaito, Kiyoyuki; Kobayashi, Kiyoshi; Hashimoto, Takumi

    The deterioration of pavement structure is a complex phenomenon that follows the deterioration of both pavement surface and pavement sub-surface. In addition, the deterioration progress of pavement sub-surface affects the deterioration speed of pavement surface. The road pavement management is important to determine the optimal repair strategy which considers the deterioration of both pavement surface and sub-surface (hereafter call "pavement structure"). This study proposes pavement repair planning and strategies of 1) extraction of key management section of relative evaluation based on road inspection survey results, and 2) determination of decision-making repair methodologies based on pavement structural soundness survey by FWD (Falling Weight Deflectometer) in key management sections. In addition, the National Highway Route 9 is the target area as empirical study to verify the methodology proposed in this study.

  12. Chemical structure influence on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux.

    PubMed

    Padgett, Mark C; Tick, Geoffrey R; Carroll, Kenneth C; Burke, William R

    2017-03-01

    The influence of chemical structure on NAPL mixture nonideality evolution, rate-limited dissolution, and contaminant mass flux was examined. The variability of measured and UNIFAC modeled NAPL activity coefficients as a function of mole fraction was compared for two NAPL mixtures containing structurally-different contaminants of concern including toluene (TOL) or trichloroethene (TCE) within a hexadecane (HEXDEC) matrix. The results showed that dissolution from the NAPL mixtures transitioned from ideality for mole fractions >0.05 to nonideality as mole fractions decreased. In particular, the TCE generally exhibited more ideal dissolution behavior except at lower mole fractions, and may indicate greater structural/polarity similarity between the two compounds. Raoult's Law and UNIFAC generally under-predicted the batch experiment results for TOL:HEXDEC mixtures especially for mole fractions ≤0.05. The dissolution rate coefficients were similar for both TOL and TCE over all mole fractions tested. Mass flux reduction (MFR) analysis showed that more efficient removal behavior occurred for TOL and TCE with larger mole fractions compared to the lower initial mole fraction mixtures (i.e. <0.2). However, compared to TOL, TCE generally exhibited more efficient removal behavior over all mole fractions tested and may have been the result of structural and molecular property differences between the compounds. Activity coefficient variability as a function of mole fraction was quantified through regression analysis and incorporated into dissolution modeling analyses for the dynamic flushing experiments. TOL elution concentrations were modeled (predicted) reasonable well using ideal and equilibrium assumptions, but the TCE elution concentrations could not be predicted using the ideal model. Rather, the dissolution modeling demonstrated that TCE elution was better described by the nonideal model whereby NAPL-phase activity coefficient varied as a function of COC mole fraction

  13. 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.

  14. Sensor failure detection using generalized parity relations for flexible structures

    NASA Technical Reports Server (NTRS)

    Mercadal, Mathieu

    1989-01-01

    Analytical redundancy may be preferable to hardware redundancy in failure detection/isolation tasks for such large-scale systems as space structures. Generalized single-sensor parity relations are presently applied to this problem; they are noted to yield a very simple isolation logic, and their generation is found to be extremely rapid, even in the case of extremely complex systems, provided only that the eigenstructure of the system be known. Their implementation is, however, extremely sensitive to modeling errors and noise.

  15. Structure-function relations of carbohydrates by neoglycolipid arrays.

    PubMed

    Huang, Gang-Liang; Huang, Hua-Liang; Zhang, Hou-Cheng; Wang, Peng-George

    2006-06-01

    The work presented herein is a new noncovalent glycoarray assembly method for microplates created by simply mixing together a carbohydrate and a tetradecylamine. alpha-D-Mannopyranoside, alpha-D-glucopyranoside, and alpha-D-galactopyranoside were utilized in model studies and product formations were detected by lectin binding. The method can be extended to study the steric hindrance effect of carbohydrate-protein interactions, namely the structure-function relations of carbohydrates.

  16. Process-Structure-Function Relations of Pectin in Food.

    PubMed

    Christiaens, Stefanie; Van Buggenhout, Sandy; Houben, Ken; Jamsazzadeh Kermani, Zahra; Moelants, Katlijn R N; Ngouémazong, Eugénie D; Van Loey, Ann; Hendrickx, Marc E G

    2016-01-01

    Pectin, a complex polysaccharide rich in galacturonic acid, has been identified as a critical structural component of plant cell walls. The functionality of this intricate macromolecule in fruit- and vegetable-based-derived products and ingredients is strongly determined by the nanostructure of its most abundant polymer, homogalacturonan. During food processing, pectic homogalacturonan is susceptible to various enzymatic as well as nonenzymatic conversion reactions modifying its structural and, hence, its functional properties. Consequently, a profound understanding of the various process-structure-function relations of pectin aids food scientists to tailor the functional properties of plant-based derived products and ingredients. This review describes the current knowledge on process-structure-function relations of pectin in foods with special focus on pectin's functionality with regard to textural attributes of solid plant-based foods and rheological properties of particulated fruit- and vegetable-derived products. In this context, both pectin research performed via traditional, ex situ physicochemical analyses of fractionated walls and isolated polymers and pectin investigation through in situ pectin localization are considered.

  17. Designing heterogeneous chemical composition on hierarchical structured copper substrates for the fabrication of superhydrophobic surfaces with controlled adhesion.

    PubMed

    Cheng, Zhongjun; Hou, Rui; Du, Ying; Lai, Hua; Fu, Kewei; Zhang, Naiqing; Sun, Kening

    2013-09-11

    Controlling water adhesion is important for superhydrophobic surfaces in many applications. Compared with numerous researches about the effect of microstructures on the surface adhesion, research relating to the influence of surface chemical composition on the surface adhesion is extremely rare. Herein, a new strategy for preparation of tunable adhesive superhydrophobic surfaces through designing heterogeneous chemical composition (hydrophobic/hydrophilic) on the rough substrate is reported, and the influence of surface chemical composition on the surface adhesion are examined. The surfaces were prepared through self-assembling of mixed thiol (containing both HS(CH2)9CH3 and HS(CH2)11OH) on the hierarchical structured copper substrates. By simply controlling the concentration of HS(CH2)11OH in the modified solution, tunable adhesive superhydrophobic surfaces can be obtained. The adhesive force of the surfaces can be increased from extreme low (about 8 μN) to very high (about 65 μN). The following two reasons can be used to explain the tunable effect: one is the number of hydrogen bond for the variation of surface chemical composition; and the other is the variation of contact area between the water droplet and surface because of the capillary effect that results from the combined effect of hydrophilic hydroxyl groups and microstructures on the surface. Noticeably, water droplets with different pH (2-12) have similar contact angles and adhesive forces on the surfaces, indicating that these surfaces are chemical resistant to acid and alkali. Moreover, the as-prepared surfaces were also used as the reaction substrates and applied in the droplet-based microreactor for the detection of vitamin C. This report provides a new method for preparation of superhydrophobic surfaces with tunable adhesion, which could not only help us further understand the principle for the fabrication of tunable adhesive superhydrophobic surfaces, but also potentially be used in many

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

    PubMed

    Berns, Veronica M; Fredrickson, Daniel C

    2014-10-06

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

  19. Size-Dependent Structure Relations between Nanotubes and Encapsulated Nanocrystals.

    PubMed

    Eliseev, Andrei A; Falaleev, Nikolay S; Verbitskiy, Nikolay I; Volykhov, Andrei A; Yashina, Lada V; Kumskov, Andrei S; Zhigalina, Victoria G; Vasiliev, Alexander L; Lukashin, Alexey V; Sloan, Jeremy; Kiselev, Nikolay A

    2017-02-08

    The structural organization of compounds in a confined space of nanometer-scale cavities is of fundamental importance for understanding the basic principles for atomic structure design at the nanolevel. Here, we explore size-dependent structure relations between one-dimensional PbTe nanocrystals and carbon nanotube containers in the diameter range of 2.0-1.25 nm using high-resolution transmission electron microscopy and ab initio calculations. Upon decrease of the confining volume, one-dimensional crystals reveal gradual thinning, with the structure being cut from the bulk in either a <110> or a <100> growth direction until a certain limit of ∼1.3 nm. This corresponds to the situation when a stoichiometric (uncharged) crystal does not fit into the cavity dimensions. As a result of the in-tube charge compensation, one-dimensional superstructures with nanometer-scale atomic density modulations are formed by a periodic addition of peripheral extra atoms to the main motif. Structural changes in the crystallographic configuration of the composites entail the redistribution of charge density on single-walled carbon nanotube walls and the possible appearance of the electron density wave. The variation of the potential attains 0.4 eV, corresponding to charge density fluctuations of 0.14 e/atom.

  20. Crystalline Structure and Surface Reactivity: Atomistic models are unique tools for dealing with the chemical and physical properties of surfaces.

    PubMed

    Gatos, H C

    1962-08-03

    The role of crystalline structure in the surface reactivity of predominantly covalent materials has been examined in terms of chemical bonding concepts. In this context a solid surface can be viewed as a giant lattice defect characterized by dangling bonds. Although it is difficult, at the present stage of development of the quantum mechanical approach to surfaces, to define precisely the perturbations resulting from the abrupt termination of the lattice at the surface, a host of experimental observations can be understood by assuming displacements of surface atoms and distortions of bonding configurations in accordance with simple chemical bonding principles. A purely atomistic approach has been shown to account not only for the chemical behavior but also for certain structural and electrical characteristics of the surfaces considered. A number of phenomena, such as crystal growth and the behavior of certain lattice defects (for example, dislocations), are intimately related to the presence of dangling bonds and the associated distortions of the lattice at the surface (32).

  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. 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

  3. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure.

    PubMed

    Hollister, Kyle A; Conner, Elizabeth S; Zhang, Xinxing; Spell, Mark; Bernard, Gary M; Patel, Pratik; de Carvalho, Ana Carolina G V; Butcher, Rebecca A; Ragains, Justin R

    2013-09-15

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This panel includes a number of natural ascarosides that were detected in crude pheromone extract, but as yet have no assigned function, as well as many unnatural ascaroside derivatives. Most of these ascarosides, some of which have significant structural similarity to the natural dauer pheromone components, have very little dauer-inducing activity. Our results provide a primer to ascaroside structure-activity relationships and suggest that slight modifications to ascaroside structure dramatically influence binding to the relevant G protein-coupled receptors that control dauer formation.

  4. Ascaroside activity in Caenorhabditis elegans is highly dependent on chemical structure

    PubMed Central

    Hollister, Kyle A.; Conner, Elizabeth S.; Zhang, Xinxing; Spell, Mark; Bernard, Gary M.; Patel, Pratik; de Carvalho, Ana Carolina G.V.; Butcher, Rebecca A.; Ragains, Justin R.

    2015-01-01

    The nematode Caenorhabditis elegans secretes ascarosides, structurally diverse derivatives of the 3,6-dideoxysugar ascarylose, and uses them in chemical communication. At high population densities, specific ascarosides, which are together known as the dauer pheromone, trigger entry into the stress-resistant dauer larval stage. In order to study the structure-activity relationships for the ascarosides, we synthesized a panel of ascarosides and tested them for dauer-inducing activity. This panel includes a number of natural ascarosides that were detected in crude pheromone extract, but as yet have no assigned function, as well as many unnatural ascaroside derivatives. Most of these ascarosides, some of which have significant structural similarity to the natural dauer pheromone components, have very little dauer-inducing activity. Our results provide a primer to ascaroside structure-activity relationships and suggest that slight modifications to ascaroside structure dramatically influence binding to the relevant G protein-coupled receptors that control dauer formation. PMID:23920482

  5. Solid state NMR and IR characterization of wood polymer structure in relation to tree provenance.

    PubMed

    Santoni, Ilaria; Callone, Emanuela; Sandak, Anna; Sandak, Jakub; Dirè, Sandra

    2015-03-06

    (13)C nuclear magnetic resonance and mid-infrared spectroscopies were used for characterizing changes in the chemical structure of wood polymers (cellulose, hemicellulose and lignin) in relation to the tree growth location. Samples of three provenances in Europe (Finland, Poland and Italy) were selected for studies. The requirement was to use untreated solid wood samples to minimize any manipulation to the nanostructure of native wood. The results confirm that the chemical and physical properties of samples belonging to the same wood species (Picea abies Karst.) differ due to the origin. Both FT-IR and dynamic NMR spectroscopies were able to correctly discriminate samples originating from three different provenances in Europe. Such methods might be very useful for both, research and understanding of wood microstructure and its variability due to the growth conditions.

  6. Elucidation of operon structures across closely related bacterial genomes.

    PubMed

    Zhou, Chuan; Ma, Qin; Li, Guojun

    2014-01-01

    About half of the protein-coding genes in prokaryotic genomes are organized into operons to facilitate co-regulation during transcription. With the evolution of genomes, operon structures are undergoing changes which could coordinate diverse gene expression patterns in response to various stimuli during the life cycle of a bacterial cell. Here we developed a graph-based model to elucidate the diversity of operon structures across a set of closely related bacterial genomes. In the constructed graph, each node represents one orthologous gene group (OGG) and a pair of nodes will be connected if any two genes, from the corresponding two OGGs respectively, are located in the same operon as immediate neighbors in any of the considered genomes. Through identifying the connected components in the above graph, we found that genes in a connected component are likely to be functionally related and these identified components tend to form treelike topology, such as paths and stars, corresponding to different biological mechanisms in transcriptional regulation as follows. Specifically, (i) a path-structure component integrates genes encoding a protein complex, such as ribosome; and (ii) a star-structure component not only groups related genes together, but also reflects the key functional roles of the central node of this component, such as the ABC transporter with a transporter permease and substrate-binding proteins surrounding it. Most interestingly, the genes from organisms with highly diverse living environments, i.e., biomass degraders and animal pathogens of clostridia in our study, can be clearly classified into different topological groups on some connected components.

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

    PubMed

    Landy, David; Brookes, David; Smout, Ryan

    2014-09-01

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

  8. Trust, but verify: On the importance of chemical structure curation in cheminformatics and QSAR modeling research

    PubMed Central

    Fourches, Denis; Muratov, Eugene; Tropsha, Alexander

    2010-01-01

    Molecular modelers and cheminformaticians typically analyze experimental data generated by other scientists. Consequently, when it comes to data accuracy, cheminformaticians are always at the mercy of data providers who may inadvertently publish (partially) erroneous data. Thus, dataset curation is crucial for any cheminformatics analysis such as similarity searching, clustering, QSAR modeling, virtual screening, etc., especially nowadays when the availability of chemical datasets in public domain has skyrocketed in recent years. Despite the obvious importance of this preliminary step in the computational analysis of any dataset, there appears to be no commonly accepted guidance or set of procedures for chemical data curation. The main objective of this paper is to emphasize the need for a standardized chemical data curation strategy that should be followed at the onset of any molecular modeling investigation. Herein, we discuss several simple but important steps for cleaning chemical records in a database including the removal of a fraction of the data that cannot be appropriately handled by conventional cheminformatics techniques. Such steps include the removal of inorganic and organometallic compounds, counterions, salts and mixtures; structure validation; ring aromatization; normalization of specific chemotypes; curation of tautomeric forms; and the deletion of duplicates. To emphasize the importance of data curation as a mandatory step in data analysis, we discuss several case studies where chemical curation of the original “raw” database enabled the successful modeling study (specifically, QSAR analysis) or resulted in a significant improvement of model's prediction accuracy. We also demonstrate that in some cases rigorously developed QSAR models could be even used to correct erroneous biological data associated with chemical compounds. We believe that good practices for curation of chemical records outlined in this paper will be of value to all

  9. Controlled Patterning of Vertical Silicon Structures Using Polymer Lithography and Wet Chemical Etching.

    PubMed

    Kim, Han-Jung; Lee, Su-Han; Lee, Jihye; Lee, Eung-Sug; Choi, Jun-Hyuk; Jung, Joo-Yun; Jeong, Jun-Ho; Choi, Dae-Geun

    2015-06-01

    In order to improve their performance for various applications, a facile method for the wafer-scale fabrication of micro/nano-patterned vertical silicon (Si) structures such as silicon nanowires (SiNWs), silicon nanorods (SiNRs), and porous silicon (p-Si) was developed. The method is based on the combination of lithography techniques (photolithography, thermal nano-imprint lithography, nanosphere lithography) and wet chemical etching (electro-chemical etching, metal-assisted chemical etching) processes. Micro-patterned p-Si with various pore diameters from 30 nm to 1.2 um were fabricated via electro-chemical etching. Micro/nano-patterned Si microstructures, nanorods, and nanowires were also successfully fabricated by changing the thickness of the metal layer of 5 nm or 20 nm in the metal-assisted chemical etching process. This study also investigated the effect of the etching time and patterning on the etched SiNWs length. This method provides advantages of simplicity, speed, large-scale production, easy size and shape manipulation, and low cost.

  10. 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.

  11. Morphology tailoring of nano/micro-structured conductive polymers, composites and their applications in chemical sensors.

    PubMed

    Ma, Xingfa; Gao, Mingjun; He, Xiaochun; Li, Guang

    2010-11-01

    Conductive polymer is one of the important multi-functional materials. It has many applications in light-emitting diodes, chemical sensors, biosensors, et al. This paper provides a relatively comprehensive review on the progress of conductive polymer and composite as sensitive film for sensors to chemical vapors including patents, papers and our preliminary research results. Especially, the feature of conjugated polymers, the processing technology, doping characteristics and some factors affecting gas responses are discussed. Otherwise, the developments of nanostructured conductive polymer and organic-inorganic hybrid film sensor with high sensitivity and rapid response to vapors are also described, and some suggestions are proposed.

  12. 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.

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

    PubMed

    Fu, Qianqian; Zhu, Biting; Ge, Jianping

    2017-02-16

    A SiO2 colloidal photonic crystal film with a hierarchical porous structure is fabricated to demonstrate an integrated separation and colorimetric detection of chemical species for the first time. This new photonic crystal based thin layer chromatography process requires no dyeing, developing and UV irradiation compared to the traditional TLC. The assembling of mesoporous SiO2 particles via a supersaturation-induced-precipitation process forms uniform and hierarchical photonic crystals with micron-scale cracks and mesopores, which accelerate the diffusion of developers and intensify the adsorption/desorption between the analytes and silica for efficient separation. Meanwhile, the chemical substances infiltrated to the voids of photonic crystals cause an increase of the refractive index and a large contrast of structural colors towards the unloaded part, so that the sample spots can be directly recognized with the naked eye before and after separation.

  14. Behavioral response of Corophium volutator relative to experimental conditions, physical and chemical disturbances.

    PubMed

    Hellou, Jocelyne; Cheeseman, Kerri; Jouvenelle, Marie-Laure; Robertson, Sarah

    2005-12-01

    The preference/avoidance behavioral response of a widely used amphipod in toxicity tests, Corophium volutator, was investigated in relation to the presence of anthropogenic physical or chemical materials in sediments. Exposure conditions, including the density of amphipods, the depth of sediments, amount of overlying water, and exposure time, were examined for their influence on amphipods' preference for field sediments and avoidance of coarse sand. It was shown that these variables did not affect the response; thus, conditions similar to published standard toxicity tests were chosen. A gradient of sediments spiked with potential habitat disturbances that can be found on a beach or in contaminated sediments, such as those in harbors, were tested. These substances included sand, seaweed, burned wood, coal, crankcase oil, and diesel oil. To enhance the interpretation of results and decrease the variability observed when tests were conducted at different times over the summer, exposures were performed over a gradient of spike material in reference sediments. We conclude that physical obstacles added to reference sediments lead to less correlation with the behavioral response than observed with chemical interferences. Amphipods' behavior ranked harbor sediments similarly to previous studies concerning the health of intertidal mussels collected in proximity to the sediments sites. For five sites, preference of reference sediments was observed until the level of polycyclic aromatic hydrocarbons in diluted harbor sediments reached the Canadian Council of Ministers of the Environment sediment quality guidelines.

  15. [Migration and transformation of marine carbon and related chemical driving factors].

    PubMed

    Zheng, Guoxia; Song, Jinming; Dai, Jicui

    2006-04-01

    The study showed that the migration and transformation of marine carbon had a close relation with the biogeochemical processes driven by various chemical factors. The growth and decline of nutrient concentration, pH, dissolved oxygen (DO), redox potential (Eh), SO4(2-), and sulfur potential (Es) could change marine chemical environment, and thus, affect the migration and transformation of marine carbon. When the nutrient supply was adequate to the nutritional demand of phytoplankton, CO2 was conveyed to deep sea through photosynthesis and organic matter oxidation, which caused the decrease of sea water Pco2 and the increase of sea-air CO2 flux and organic carbon output, making the sea area as a CO2 sink. But, the increasing acidification of marine environment caused by CO2 dissolution and organic matter degradation brought about the solubility augmentation of carbonate in seawater. Moreover, the mineralization of organic carbon was coupled with the changes of DO, Eh, SO4(2-) and Es, and the deposition and burial process of carbon in sediments. In sea water body, high DO and high Eh accelerated the transformation from inorganic carbon to organic carbon, while in sediment, high SO4(2-) was adverse to the burial of organism with low DO and low Eh.

  16. Relation between physico-chemical limnology and crustacean community in Wular Lake of Kashmir Himalaya.

    PubMed

    Shah, Javaid Ahmad; Pandit, Ashok K

    2013-10-01

    The present study scrutinizes the seasonal variation in the distribution of crustacean zooplankton in relation to physico-chemical liminology of Wular lake. Water samples were collected from five study sites during September 2010-August 2011. Remarkable spatial and temporal variations were observed among the different study sites. Among the parameters recorded water temperature showed positive correlation with pH (p<0.01) and orthophosphate (p<0.05).Transparency showed a significant negative correlation with total alkalinity (p<0.01), free carbon dioxide (p<0.01) and ammonical nitrogen (p<0.01). Crustacean zooplankton were collected by filtering 100 L lake water through a 30 microm nytal mesh and preserved in 4% formalin. A total of 42 taxa of crustacean were recorded, among them 23 species belonged to Cladocera, 16 to Copepoda and only 3 to Ostracoda. Species diversity and density depicted an abrupt up surge on the advent of warmer period (extending from March). Among the various sites a maximum of 40 species were recorded from a single biotope (site III) against the minimum of only 17 species being recorded from site I. Bray-Curtis cluster analysis showed close similarity (0.928-0.944%) between summer and autumn in terms of species diversity. Pearson correlation coefficient of the various physico-chemical parameters of water with crustacean zooplankton depicted that not only a single but multiple factors govern over the distribution and diversity of crustacean in the lake.

  17. Structure-property relations in engineered semiconductor nanomaterials (Conference Presentation)

    NASA Astrophysics Data System (ADS)

    Hollingsworth, Jennifer A.; Htoon, Han

    2016-09-01

    Particle-size or `quantum-confinement' effects have been used for decades to tune semiconductor opto-electronic properties. More recently, particle size control as the primary means for properties control has been succeeded by nanoscale hetero-structuring. In this case, the nanosized particle is modified to include internal, nanoscale interfaces, generally defined by compositional variations that induce additional changes to semiconductor properties. These changes can entail enhancements to the size-induced properties as well as unexpected or `emergent' behaviors. Common structural motifs include enveloping a spherical semiconductor nanocrystal, i.e., a quantum dot, within a shell of a different composition. In this talk, I will discuss how solution-phase synthesis can be used to create these structures with precisely `engineered' complexity. Most notably, I will review our experiences with so-called `giant' quantum dots that, due to their internal nanoscale structure, exhibit a range of novel behaviors, including being non-blinking and non-photobleaching (Chen et al. J. Am. Chem. Soc. 2008, 130, 5026; Ghosh et al. J. Am. Chem. Soc. 2012, 134, 9634; Dennis et al. Nano Lett. 2012 12, 5545; Acharya et al. J. Am. Chem. Soc. 2015, 137, 3755), and remarkably efficient emitters of `multi-excitons' due to extreme suppression of Auger recombination (Mangum et al. Nanoscale 2014, 6, 3712; Gao et al. Adv. Optical Mater. 2015, 3, 39). I will discuss recent work extending non-blinking behavior to the blue/green and "dual-color" emission, and show how correlated optical/structural characterization can reveal new information regarding structure-property relations to guide new nanomaterials development (Orfield et al. ACS Nano, Article ASAP).

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

    NASA Astrophysics Data System (ADS)

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

    2016-05-01

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

  19. 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.

  20. Chemically Resolved Interface Structure of Epitaxial Graphene on SiC(0001)

    DTIC Science & Technology

    2013-11-19

    Chemically Resolved Interface Structure of Epitaxial Graphene on SiC(0001) Jonathan D. Emery,1 Blanka Detlefs,2 Hunter J. Karmel,1 Luke O. Nyakiti,3...unique properties that can be significantly modified through interaction with an underlying support. For epitaxial graphene on SiC(0001), the...interface strongly influences the electronic properties of the overlaying graphene . We demonstrate a novel combination of x-ray scattering and spectroscopy

  1. Chemical structure of the O-polysaccharide isolated from Pectobacterium atrosepticum SCRI 1039.

    PubMed

    Czerwicka, Małgorzata; Marszewska, Kinga; Bychowska, Anna; Dziadziuszko, Halina; Brzozowski, Krzysztof; Łojkowska, Ewa; Stepnowski, Piotr; Kaczyński, Zbigniew

    2011-12-27

    The lipopolysaccharide (LPS) of the bacterium Pectobacterium atrosepticum SCRI 1039 was hydrolyzed and the products were separated. A study of the obtained O-polysaccharide by means of chemical methods, GLC, GLC-MS, and NMR spectroscopy allowed us to identify a branched polymer with a pentasaccharide repeating unit of the structure shown below, in which the fucose residue was partially O-acetylated at C-2, C-3 or C-4.

  2. 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.

  3. 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.

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

    PubMed

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

    2010-01-01

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

  5. Chemically gated electronic structure of a superconducting doped topological insulator system

    NASA Astrophysics Data System (ADS)

    Wray, L. A.; Xu, S.; Neupane, M.; Fedorov, A. V.; Hor, Y. S.; Cava, R. J.; Hasan, M. Z.

    2013-07-01

    Angle resolved photoemission spectroscopy is used to observe changes in the electronic structure of bulk-doped topological insulator CuxBi2Se3 as additional copper atoms are deposited onto the cleaved crystal surface. Carrier density and surface-normal electrical field strength near the crystal surface are estimated to consider the effect of chemical surface gating on atypical superconducting properties associated with topological insulator order, such as the dynamics of theoretically predicted Majorana Fermion vortices.

  6. Composition and submicron structure of chemically deposited Cu2Se-In2Se3 films

    NASA Astrophysics Data System (ADS)

    Markov, V. F.; Tulenin, S. S.; Maskaeva, L. N.; Kuznetsov, M. V.; Barbin, N. M.

    2012-03-01

    Films of substitutional solid solutions of the Cu2Se-In2Se3 system containing up to 7.5 at. % In have been obtained by chemical deposition from aqueous media. The composition, structure, and morphology of the films have been studied. Data of X-ray diffraction and X-ray photoelectron spectroscopy showed that copper in the solid solution occurs in a single-valence state (Cu+). The deposited layers possess a globular morphology and are nanostructured.

  7. Epigenome: Biosensor of Cumulative Exposure to Chemical and Nonchemical Stressors Related to Environmental Justice

    PubMed Central

    Gruber, David; Sonawane, Babasaheb

    2014-01-01

    Understanding differential disease susceptibility requires new tools to quantify the cumulative effects of environmental stress. Evidence suggests that social, physical, and chemical stressors can influence disease through the accumulation of epigenetic modifications. Geographically stable epigenetic alterations could identify plausible mechanisms for health disparities among the disadvantaged and poor. Relations between neighborhood-specific epigenetic markers and disease would identify the most appropriate targets for medical and environmental intervention. Complex interactions among genes, the environment, and disease require the examination of how epigenetic changes regulate susceptibility to environmental stressors. Progress in understanding disparities in disease susceptibility may depend on assessing the cumulative effect of environmental stressors on genetic substrates. We highlight key concepts regarding the interface between environmental stress, epigenetics, and chronic disease. PMID:25122010

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

    PubMed Central

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

    2016-01-01

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

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

    PubMed

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

    2016-07-08

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

  10. Improved performance of the microbial electrolysis desalination and chemical-production cell using the stack structure.

    PubMed

    Chen, Shanshan; Liu, Guangli; Zhang, Renduo; Qin, Bangyu; Luo, Yong; Hou, Yanping

    2012-07-01

    The microbial electrolysis desalination and chemical-production cell (MEDCC) is a device to desalinate seawater, and produce acid and alkali. The objective of this study was to enhance the desalination and chemical-production performance of the MEDCC using two types of stack structure. Experiments were conducted with different membrane spacings, numbers of desalination chambers and applied voltages. Results showed that the stack construction in the MEDCC enhanced the desalination and chemical-production rates. The maximal desalination rate of 0.58 ± 0.02 mmol/h, which was 43% higher than that in the MEDCC, was achieved in the four-desalination-chamber MEDCC with the AEM-CEM stack structure and the membrane spacing of 1.5mm. The maximal acid- and alkali-production rates of 0.079 ± 0.006 and 0.13 ± 0.02 mmol/h, which were 46% and 8% higher than that in the MEDCC, respectively, were achieved in the two-desalination-chamber MEDCC with the BPM-AEM-CEM stack structure and the membrane spacing of 3mm.

  11. 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.

  12. Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates.

    PubMed

    Southan, Christopher; Williams, Antony J; Ekins, Sean

    2013-01-01

    There is an expanding amount of interest directed at the repurposing and repositioning of drugs, as well as how in silico methods can assist these endeavors. Recent repurposing project tendering calls by the National Center for Advancing Translational Sciences (USA) and the Medical Research Council (UK) have included compound information and pharmacological data. However, none of the internal company development code names were assigned to chemical structures in the official documentation. This not only abrogates in silico analysis to support repurposing but consequently necessitates data gathering and curation to assign structures. Here, we describe the approaches, results and major challenges associated with this.

  13. Nitridation of Al2O3 surfaces: chemical and structural change triggered by oxygen desorption.

    PubMed

    Akiyama, Toru; Saito, Yasutaka; Nakamura, Kohji; Ito, Tomonori

    2013-01-11

    We present theoretical investigations that clarify elemental nitridation processes of corundum Al2O3(0001) and (1102) surfaces. The calculations within the density functional theory framework reveal that the structures with substitutional N atoms beneath the surface are stabilized under nitridation conditions. We also find that the desorption of O atoms at the topmost layer induces outward diffusion of O atoms as well as inward diffusion of N atoms, leading to the transformation into AlN films. The kinetic Monte Carlo simulations in conjunction with density functional theory results indeed observe a dependence of these chemical and structural changes on temperature and pressure.

  14. Electronic structure of polyimide and related monomers: Theory and experiment

    NASA Astrophysics Data System (ADS)

    Kowalczyk, Steven P.; Stafström, Sven; Brédas, J. L.; Salaneck, William R.; Jordan-Sweet, Jean L.

    1990-01-01

    The electronic structure of polymide and several related compounds was investigated theoretically and experimentally. The compounds include pyromellitic dianhydride, oxydianiline, and polyamic acid. Experimental electronic-structure determinations for poly(methyl phenylene oxide) and poly(vinyl methyl ketone) are also reported. The theoretical approach employed valence-effective-Hamiltonian calculations. Photoelectron spectroscopy (x-ray photoelectron spectroscopy, soft-x-ray photoelectron spectroscopy, and ultraviolet photoelectron spectroscopy) was used to experimentally measure the total valence-band density of states (VBDOS) from thin films of the above compounds. The theoretical VBDOS's were cross-section modulated to facilitate comparison with experiment. Very good agreement is found between the theoretical results and the experimental VBDOS's.

  15. Preparation of melanin from Catharsius molossus L. and preliminary study on its chemical structure.

    PubMed

    Xin, Chao; Ma, Jia-hua; Tan, Cheng-jia; Yang, Zhou; Ye, Feng; Long, Chan; Ye, Shuang; Hou, Da-bin

    2015-04-01

    A great deal of melanin was found in the waste alkali liquor produced by extraction of chitin from Catharsius molossus L. Discarding the lye could harm the environment and cause waste of resources. In this paper, melanin from C. molossus L. was recovered through acid precipitation and purified by pepsin and so on. The purity, chemical composition and structure of the prepared melanin were explored by UV-visible absorption spectroscopy, Fourier transform infrared spectroscopy, proton nuclear magnetic resonance spectroscopy, high resolution (13)C Cross polarization magic angle spinning nuclear magnetic resonance spectroscopy pyrolysis gas chromatography mass spectrometry, X ray diffraction, X ray fluorescence, matrix-assisted laser desorption/ionization time of flight tandem mass spectrometry, thermal analysis, and so on. The results showed that the purity of the prepared melanin was higher than the commercial standard melanin and it was a kind of nanoaggregates composed of a large quantity of 5,6-dihydroxyindole eumelanin and a small amount of phaeomelanin. In addition, the prepared melanin was irregular in shape and its structure could be divided into three levels: advanced structure maintained by polypeptides, substructure maintained by the ferric ion and microstructure. In particular, the smallest structural unit showed the graphite-like layered structure containing five layers linked by non-covalent bonds and each layer mainly consisted of 5,6-dihydroxyindole and its derivatives, which might be connected to each other through various chemical bonds.

  16. Determination of secondary structure populations in disordered states of proteins using nuclear magnetic resonance chemical shifts.

    PubMed

    Camilloni, Carlo; De Simone, Alfonso; Vranken, Wim F; Vendruscolo, Michele

    2012-03-20

    One of the major open challenges in structural biology is to achieve effective descriptions of disordered states of proteins. This problem is difficult because these states are conformationally highly heterogeneous and cannot be represented as single structures, and therefore it is necessary to characterize their conformational properties in terms of probability distributions. Here we show that it is possible to obtain highly quantitative information about particularly important types of probability distributions, the populations of secondary structure elements (α-helix, β-strand, random coil, and polyproline II), by using the information provided by backbone chemical shifts. The application of this approach to mammalian prions indicates that for these proteins a key role in molecular recognition is played by disordered regions characterized by highly conserved polyproline II populations. We also determine the secondary structure populations of a range of other disordered proteins that are medically relevant, including p53, α-synuclein, and the Aβ peptide, as well as an oligomeric form of αB-crystallin. Because chemical shifts are the nuclear magnetic resonance parameters that can be measured under the widest variety of conditions, our approach can be used to obtain detailed information about secondary structure populations for a vast range of different protein states.

  17. In-silico bonding schemes to encode chemical bonds involving sharing of electrons in molecular structures.

    PubMed

    Punnaivanam, Sankar; Sathiadhas, Jerome Pastal Raj; Panneerselvam, Vinoth

    2016-05-01

    Encoding of covalent and coordinate covalent bonds in molecular structures using ground state valence electronic configuration is achieved. The bonding due to electron sharing in the molecular structures is described with five fundamental bonding categories viz. uPair-uPair, lPair-uPair, uPair-lPair, vPair-lPair, and lPair-lPair. The involvement of lone pair electrons and the vacant electron orbitals in chemical bonding are explained with bonding schemes namely "target vacant promotion", "source vacant promotion", "target pairing promotion", "source pairing promotion", "source cation promotion", "source pairing double bond", "target vacant occupation", and "double pairing promotion" schemes. The bonding schemes are verified with a chemical structure editor. The bonding in the structures like ylides, PCl5, SF6, IF7, N-Oxides, BF4(-), AlCl4(-) etc. are explained and encoded unambiguously. The encoding of bonding in the structures of various organic compounds, transition metals compounds, coordination complexes and metal carbonyls is accomplished.

  18. Relationship between chemical structure of soil organic matter and intra-aggregate pore structure: evidence from X-ray computed micro-tomography

    NASA Astrophysics Data System (ADS)

    Kravchenko, Alexandra; Grandy, Stuart A.

    2014-05-01

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

  19. Electronic structure and superconductivity of FeSe-related superconductors.

    PubMed

    Liu, Xu; Zhao, Lin; He, Shaolong; He, Junfeng; Liu, Defa; Mou, Daixiang; Shen, Bing; Hu, Yong; Huang, Jianwei; Zhou, X J

    2015-05-13

    FeSe superconductors and their related systems have attracted much attention in the study of iron-based superconductors owing to their simple crystal structure and peculiar electronic and physical properties. The bulk FeSe superconductor has a superconducting transition temperature (Tc) of ~8 K and it can be dramatically enhanced to 37 K at high pressure. On the other hand, its cousin system, FeTe, possesses a unique antiferromagnetic ground state but is non-superconducting. Substitution of Se with Te in the FeSe superconductor results in an enhancement of Tc up to 14.5 K and superconductivity can persist over a large composition range in the Fe(Se,Te) system. Intercalation of the FeSe superconductor leads to the discovery of the AxFe2-ySe2 (A = K, Cs and Tl) system that exhibits a Tc higher than 30 K and a unique electronic structure of the superconducting phase. A recent report of possible high temperature superconductivity in single-layer FeSe/SrTiO3 films with a Tc above 65 K has generated much excitement in the community. This pioneering work opens a door for interface superconductivity to explore for high Tc superconductors. The distinct electronic structure and superconducting gap, layer-dependent behavior and insulator-superconductor transition of the FeSe/SrTiO3 films provide critical information in understanding the superconductivity mechanism of iron-based superconductors. In this paper, we present a brief review of the investigation of the electronic structure and superconductivity of the FeSe superconductor and related systems, with a particular focus on the FeSe films.

  20. [Structure analysis of disease-related proteins using vibrational spectroscopy].

    PubMed

    Hiramatsu, Hirotsugu

    2014-01-01

    Analyses of the structure and properties of identified pathogenic proteins are important for elucidating the molecular basis of diseases and in drug discovery research. Vibrational spectroscopy has advantages over other techniques in terms of sensitivity of detection of structural changes. Spectral analysis, however, is complicated because the spectrum involves a substantial amount of information. This article includes examples of structural analysis of disease-related proteins using vibrational spectroscopy in combination with additional techniques that facilitate data acquisition and analysis. Residue-specific conformation analysis of an amyloid fibril was conducted using IR absorption spectroscopy in combination with (13)C-isotope labeling, linear dichroism measurement, and analysis of amide I band features. We reveal a pH-dependent property of the interacting segment of an amyloidogenic protein, β2-microglobulin, which causes dialysis-related amyloidosis. We also reveal the molecular mechanisms underlying pH-dependent sugar-binding activity of human galectin-1, which is involved in cell adhesion, using spectroscopic techniques including UV resonance Raman spectroscopy. The decreased activity at acidic pH was attributed to a conformational change in the sugar-binding pocket caused by protonation of His52 (pKa 6.3) and the cation-π interaction between Trp68 and the protonated His44 (pKa 5.7). In addition, we show that the peak positions of the Raman bands of the C4=C5 stretching mode at approximately 1600 cm(-1) and the Nπ-C2-Nτ bending mode at approximately 1405 cm(-1) serve as markers of the His side-chain structure. The Raman signal was enhanced 12 fold using a vertical flow apparatus.

  1. Toward calculations of the 129Xe chemical shift in Xe@C60 at experimental conditions: relativity, correlation, and dynamics.

    PubMed

    Straka, Michal; Lantto, Perttu; Vaara, Juha

    2008-03-27

    We calculate the 129Xe chemical shift in endohedral Xe@C60 with systematic inclusion of the contributing physical effects to model the real experimental conditions. These are relativistic effects, electron correlation, the temperature-dependent dynamics, and solvent effects. The ultimate task is to obtain the right result for the right reason and to develop a physically justified methodological model for calculations and simulations of endohedral Xe fullerenes and other confined Xe systems. We use the smaller Xe...C6H6 model to calibrate density functional theory approaches against accurate correlated wave function methods. Relativistic effects as well as the coupling of relativity and electron correlation are evaluated using the leading-order Breit-Pauli perturbation theory. The dynamic effects are treated in two ways. In the first approximation, quantum dynamics of the Xe atom in a rigid cage takes advantage of the centrosymmetric potential for Xe within the thermally accessible distance range from the center of the cage. This reduces the problem of obtaining the solution of a diatomic rovibrational problem. In the second approach, first-principles classical molecular dynamics on the density functional potential energy hypersurface is used to produce the dynamical trajectory for the whole system, including the dynamic cage. Snapshots from the trajectory are used for calculations of the dynamic contribution to the absorption 129Xe chemical shift. The calculated nonrelativistic Xe shift is found to be highly sensitive to the optimized molecular structure and to the choice of the exchange-correlation functional. Relativistic and dynamic effects are significant and represent each about 10% of the nonrelativistic static shift at the minimum structure. While the role of the Xe dynamics inside of the rigid cage is negligible, the cage dynamics turns out to be responsible for most of the dynamical correction to the 129Xe shift. Solvent effects evaluated with a polarized

  2. Chemical cross-linking and native mass spectrometry: A fruitful combination for structural biology

    PubMed Central

    Sinz, Andrea; Arlt, Christian; Chorev, Dror; Sharon, Michal

    2015-01-01

    Mass spectrometry (MS) is becoming increasingly popular in the field of structural biology for analyzing protein three-dimensional-structures and for mapping protein–protein interactions. In this review, the specific contributions of chemical crosslinking and native MS are outlined to reveal the structural features of proteins and protein assemblies. Both strategies are illustrated based on the examples of the tetrameric tumor suppressor protein p53 and multisubunit vinculin-Arp2/3 hybrid complexes. We describe the distinct advantages and limitations of each technique and highlight synergistic effects when both techniques are combined. Integrating both methods is especially useful for characterizing large protein assemblies and for capturing transient interactions. We also point out the future directions we foresee for a combination of in vivo crosslinking and native MS for structural investigation of intact protein assemblies. PMID:25970732

  3. Electronic structure, chemical bonding, and geometry of pure and Sr-doped CaCO3.

    PubMed

    Stashans, Arvids; Chamba, Gaston; Pinto, Henry

    2008-02-01

    The electronic structure, chemical bonding, geometry, and effects produced by Sr-doping in CaCO(3) have been studied on the basis of density-functional theory using the VASP simulation package and molecular-orbital theory utilizing the CLUSTERD computer code. Two calcium carbonate structures which occur naturally in anhydrous crystalline forms, calcite and aragonite, were considered in the present investigation. The obtained diagrams of density of states show similar patterns for both materials. The spatial structures are computed and analyzed in comparison to the available experimental data. The electronic properties and atomic displacements because of the trace element Sr-incorporation are discussed in a comparative manner for the two crystalline structures.

  4. Benthic invertebrate distributions in the San Joaquin River, California, in relation to physical and chemical factors

    USGS Publications Warehouse

    Leland, H.V.; Fend, S.V.

    1998-01-01

    The invertebrate fauna of nontidal portions of the lower San Joaquin River and its major tributaries is described in relation to water quality and habitat using canonical correspondence analysis, autecological metrics, and indicator species analysis. A large-scale (basin-wide) pattern in community response to salinity (sulfate-bicarbonate type) was detected when standardized, stable substratum was sampled. Community structure, taxa richness, and EPT (ephemeropterans, plecopterans, and trichopterans) richness varied with dissolved solids concentration (55-1700 mg total dissolved solids. L-1), and distributions of many taxa indicated salinity optima. Distinct assemblages associated with either high or low salinity were evident over this range. Large-scale patterns in community structure were unrelated to pesticide distributions. Structure and taxa richness of invertebrate assemblages in sand substratum varied both with salinity and with microhabitat heterogeneity. The benthic fauna generally was dominated by a taxa-poor assemblage of specialized psammophilous species, contributing to a weaker relationship between community structure and water quality than was observed using standardized substratum. Habitat types and associated dominant species were characterized using indicator species analysis. Species assemblages did not vary substantially with irrigation regime or fiver discharge, indicating that structure of invertebrate communities was a conservative measure of water quality.

  5. Polymeric micelles encapsulating photosensitizer: structure/photodynamic therapy efficiency relation.

    PubMed

    Gibot, Laure; Lemelle, Arnaud; Till, Ugo; Moukarzel, Béatrice; Mingotaud, Anne-Françoise; Pimienta, Véronique; Saint-Aguet, Pascale; Rols, Marie-Pierre; Gaucher, Mireille; Violleau, Frédéric; Chassenieux, Christophe; Vicendo, Patricia

    2014-04-14

    Various polymeric micelles were formed from amphiphilic block copolymers, namely, poly(ethyleneoxide-b-ε-caprolactone), poly(ethyleneoxide-b-d,l-lactide), and poly(ethyleneoxide-b-styrene). The micelles were characterized by static and dynamic light scattering, electron microscopy, and asymmetrical flow field-flow fractionation. They all displayed a similar size close to 20 nm. The influence of the chemical structure of the block copolymers on the stability upon dilution of the polymeric micelles was investigated to assess their relevance as carriers for nanomedicine. In the same manner, the stability upon aging was assessed by FRET experiments under various experimental conditions (alone or in the presence of blood proteins). In all cases, a good stability over 48 h for all systems was encountered, with PDLLA copolymer-based systems being the first to release their load slowly. The cytotoxicity and photocytotoxicity of the carriers were examined with or without their load. Lastly, the photodynamic activity was assessed in the presence of pheophorbide a as photosensitizer on 2D and 3D tumor cell culture models, which revealed activity differences between the 2D and 3D systems.

  6. Morphogenesis and morphology of HIV. Structure-function relations.

    PubMed

    Gelderblom, H R; Ozel, M; Pauli, G

    1989-01-01

    Fine structure and antigenic make-up analysis of HIV were combined in a 2D model, from which functional aspects can be deduced. On the envelope 72 probably trimeric surface knobs (gp120) are connected to the virion via the transmembrane protein gp41. Gp120 is shed during ageing of the virion, but host cell antigens stay firmly anchored to the envelope. Underneath the envelope, p17 forms the matrix protein layer, while the capsid of the double cone shaped core is built up of p24. The relation between biochemical findings and morphogenesis and maturation of HIV as well as aspects of pathogenesis and vaccination are discussed.

  7. Examining Similarity Structure: Multidimensional Scaling and Related Approaches in Neuroimaging

    PubMed Central

    Shinkareva, Svetlana V.; Wedell, Douglas H.

    2013-01-01

    This paper covers similarity analyses, a subset of multivariate pattern analysis techniques that are based on similarity spaces defined by multivariate patterns. These techniques offer several advantages and complement other methods for brain data analyses, as they allow for comparison of representational structure across individuals, brain regions, and data acquisition methods. Particular attention is paid to multidimensional scaling and related approaches that yield spatial representations or provide methods for characterizing individual differences. We highlight unique contributions of these methods by reviewing recent applications to functional magnetic resonance imaging data and emphasize areas of caution in applying and interpreting similarity analysis methods. PMID:23662162

  8. Structures of alkali metals in silica gel nanopores: new materials for chemical reductions and hydrogen production.

    PubMed

    Shatnawi, Mouath; Paglia, Gianluca; Dye, James L; Cram, Kevin C; Lefenfeld, Michael; Billinge, Simon J L

    2007-02-07

    Alkali metals and their alloys can be protected from spontaneous reaction with dry air by intercalation (with subsequent heating) into the pores of silica gel (SG) at loadings up to 40 wt %. The resulting loose, black powders are convenient materials for chemical reduction of organic compounds and the production of clean hydrogen. The problem addressed in this paper is the nature of the reducing species present in these amorphous materials. The atomic pair distribution function (PDF), which considers both Bragg and diffuse scattering components, was used to examine their structures. Liquid Na-K alloys added to silica gel at room temperature (stage 0) or heated to 150 degrees C (stage I) as well as stage I Na-SG, retain the overall pattern of pure silica gel. Broad oscillations in the PDF show that added alkali metals remain in the pores as nanoscale metal clusters. 23Na MAS NMR studies confirm the presence of Na(0) and demonstrate that Na+ ions are formed as well. The relative amounts of Na(0) and Na(+) depend on both the overall metal loading and the average pore size. The results suggest that ionization occurs near or in the SiO2 walls, with neutral metal present in the larger cavities. The fate of the electrons released by ionization is uncertain, but they may add to the silica gel lattice, or form an "electride-like plasma" near the silica gel walls. A remaining mystery is why the stage I material does not show a melting endotherm of the encapsulated metal and does not react with dry oxygen. Na-SG when heated to 400 degrees C (stage II) yields a dual-phase reaction product that consists of Na(4)Si(4) and Na(2)SiO(3).

  9. Structure, morphology, and photoluminescence of porous Si nanowires: effect of different chemical treatments

    NASA Astrophysics Data System (ADS)

    Leontis, Ioannis; Othonos, Andreas; Nassiopoulou, Androula G.

    2013-09-01

    The structure and light-emitting properties of Si nanowires (SiNWs) fabricated by a single-step metal-assisted chemical etching (MACE) process on highly boron-doped Si were investigated after different chemical treatments. The Si nanowires that result from the etching of a highly doped p-type Si wafer by MACE are fully porous, and as a result, they show intense photoluminescence (PL) at room temperature, the characteristics of which depend on the surface passivation of the Si nanocrystals composing the nanowires. SiNWs with a hydrogen-terminated nanostructured surface resulting from a chemical treatment with a hydrofluoric acid (HF) solution show red PL, the maximum of which is blueshifted when the samples are further chemically oxidized in a piranha solution. This blueshift of PL is attributed to localized states at the Si/SiO2 interface at the shell of Si nanocrystals composing the porous SiNWs, which induce an important pinning of the electronic bandgap of the Si material and are involved in the recombination mechanism. After a sequence of HF/piranha/HF treatment, the SiNWs are almost fully dissolved in the chemical solution, which is indicative of their fully porous structure, verified also by transmission electron microscopy investigations. It was also found that a continuous porous Si layer is formed underneath the SiNWs during the MACE process, the thickness of which increases with the increase of etching time. This supports the idea that porous Si formation precedes nanowire formation. The origin of this effect is the increased etching rate at sites with high dopant concentration in the highly doped Si material.

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

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

    NASA Astrophysics Data System (ADS)

    Tamulevičius, Tomas; Tamulevičienė, Asta; Virganavičius, Dainius; Vasiliauskas, Andrius; Kopustinskas, Vitoldas; Meškinis, Šarūnas; Tamulevičius, Sigitas

    2014-12-01

    We analyze structuring effects of diamond like carbon based silver nanocomposite (DLC:Ag) thin films by CF4/O2 plasma chemical etching and Ar+ sputtering. DLC:Ag films were deposited employing unbalanced reactive magnetron sputtering of silver target with Ar+ in C2H2 gas atmosphere. Films with different silver content (0.6-12.9 at.%) were analyzed. The films (as deposited and exposed to plasma chemical etching) were characterized employing scanning electron microscopy and energy dispersive X-ray analysis (SEM/EDS), optical microscopy, ultraviolet-visible light (UV-VIS) spectroscopy and Fourier transform infrared (FTIR) spectroscopy. After deposition, the films were plasma chemically etched in CF4/O2 mixture plasma for 2-6 min. It is shown that optical properties of thin films and silver nano particle size distribution can be tailored during deposition changing the magnetron current and C2H2/Ar ratio or during following plasma chemical etching. The plasma etching enabled to reveal the silver filler particle size distribution and to control silver content on the surface that was found to be dependent on Ostwald ripening process of silver nano-clusters. Employing contact lithography and 4 μm period mask in photoresist or aluminum the films were patterned employing CF4/O2 mixture plasma chemical etching, direct Ar+ sputtering or combined etching processes. It is shown that different processing recipes result in different final grating structures. Selective carbon etching in CF4/O2 gas mixture with photoresist mask revealed micrometer range lines of silver nanoparticles, while Ar+ sputtering and combined processing employing aluminum mask resulted in nanocomposite material (DLC:Ag) micropatterns.

  12. Half-Heusler phase related structural perturbations near stoichiometric composition FeZnSb

    SciTech Connect

    Xiong, Ding-Bang; Zhao, Yufeng

    2011-05-15

    Half-Heusler phases XYZ (Pearson symbol cF12) are chemically versatile and rich in physical properties. The half-Heusler phase in the Fe-Zn-Sb ternary system was reported in the year 2000. In this work, two new ternary phases are identified in the vicinity of the equiatomic composition FeZnSb in the same system: Fe{sub 1-x}ZnSb (tetragonal, space group P4/nmm, Pearson symbol tP6-{delta}, Z=2: a=4.1113(6) A, c=6.0127(12) A for x=0.08 (1), and a=4.1274(6) A, c=6.0068(12) A for x=0.12 (2)); and Fe{sub 7.87}Zn{sub 6.72}Sb{sub 8} (Fe{sub 0.98}Zn{sub 0.84}Sb) (3) (cubic, space group Fm-3m, Pearson symbol cF96-{delta}, Z=4, a=11.690(13) A). 1 and 2 crystallize in the PbFCl-type structure, and 3 adopts a unique 2x2x2 supercell of a normal half-Heusler structure. The structures of both the tetragonal and cubic phases can be described as assemblies of half-Heusler structure related subunits. Electrical resistivity measurement on the pure sample of 2 shows it has metallic-like behavior, and its thermal and magnetic properties are also characterized. -- Graphical Abstract: Three types of half-Heusler structure related subunit are identified in the vicinity of the equiatomic composition FeZnSb in the Fe-Zn-Sb system. Display Omitted Highlights: {yields} Two new related phases around equiatomic composition FeZnSb. {yields} Structural perturbation with the small variation of composition. {yields} Magnetic properties of the structure with defects.

  13. Scalable Synthesis of Cortistatin A and Related Structures

    PubMed Central

    Shi, Jun; Manolikakes, Georg; Yeh, Chien-Hung; Guerrero, Carlos A.; Shenvi, Ryan A.; Shigehisa, Hiroki

    2011-01-01

    Full details are provided for an improved synthesis of cortistatin A and related structures as well as the underlying logic and evolution of strategy. The highly functionalized cortistatin A-ring embedded with a key heteroadamantane was synthesized by a simple and scalable 5-step sequence. A chemoselective, tandem geminal dihalogenation of an unactivated methyl group, a reductive fragmentation/trapping/elimination of a bromocyclopropane, and a facile chemoselective etherification reaction afforded the cortistatin A core, dubbed “cortistatinone”. A selective Δ16-alkene reduction with Raney Ni provided cortistatin A. With this scalable and practical route, copious quantities of cortistatinone, Δ16-cortistatin A-the equipotent direct precursor to cortistatin A, and its related analogs were prepared for further biological studies. PMID:21539314

  14. Relating reconnection rate, exhaust structure and effective resistivity

    NASA Astrophysics Data System (ADS)

    Singh, Nagendra

    2014-03-01

    The magnetic reconnection structure consists of a central diffusion region (CDR) and a cone or wedge shaped reconnection exhaust containing accelerated plasma flows and electromagnetic fluctuations. We predict here the relationship among the exhaust half-cone angle (θe), the half width (w) of the CDR, the outflow velocity Vo, and the effective resistivity (ηeff), which includes the effects of all the nonideal terms in the generalized Ohm's law. The effective resistivity is defined as the ratio of reconnection electric field Erec to the current density Jy at the X point and it essentially represents the loss of momentum from the current-carrying plasma particles due to scattering by waves, their inertia or outflux from the CDR. The relation is checked against relevant results previously reported from laboratory experiments, space observations, and simulations, showing excellent agreement. The relation can be used for estimating the ad-hoc effective resistivity often used in magnetohydrodynamic modeling of reconnection.

  15. Rat α-Fetoprotein binding affinities of a large set of structurally diverse chemicals elucidated the relationships between structures and binding affinities.

    PubMed

    Hong, Huixiao; Branham, William S; Dial, Stacey L; Moland, Carrie L; Fang, Hong; Shen, Jie; Perkins, Roger; Sheehan, Daniel; Tong, Weida

    2012-11-19

    Endocrine disrupting chemicals interfere with the endocrine system in animals, including humans, to exert adverse effects. One of the mechanisms of endocrine disruption is through the binding of receptors such as the estrogen receptor (ER) in target cells. The concentration of any chemical in serum is important for its entry into the target cells to bind the receptors. α-Fetoprotein (AFP) is a major transport protein in rodent serum that can bind with estrogens and thus change a chemical's availability for entrance into the target cell. Sequestration of an estrogen in the serum can alter the chemical's potential for disrupting estrogen receptor-mediated responses. To better understand endocrine disruption, we developed a competitive binding assay using rat amniotic fluid, which contains very high levels of AFP, and measured the binding to the rat AFP for 125 structurally diverse chemicals, most of which are known to bind ER. Fifty-three chemicals were able to bind the rat AFP in the assay, while 72 chemicals were determined to be nonbinders. Observations from closely examining the relationship between the binding data and structures of the tested chemicals are rationally explained in a manner consistent with proposed binding regions of rat AFP in the literature. The data reported here represent the largest data set of structurally diverse chemicals tested for rat AFP binding. The data assist in elucidating binding interactions and mechanisms between chemicals and rat AFP and, in turn, assist in the evaluation of the endocrine disrupting potential of chemicals.

  16. Chemical structure elucidation from ¹³C NMR chemical shifts: efficient data processing using bipartite matching and maximal clique algorithms.

    PubMed

    Koichi, Shungo; Arisaka, Masaki; Koshino, Hiroyuki; Aoki, Atsushi; Iwata, Satoru; Uno, Takeaki; Satoh, Hiroko

    2014-04-28

    Computer-assisted chemical structure elucidation has been intensively studied since the first use of computers in chemistry in the 1960s. Most of the existing elucidators use a structure-spectrum database to obtain clues about the correct structure. Such a structure-spectrum database is expected to grow on a daily basis. Hence, the necessity to develop an efficient structure elucidation system that can adapt to the growth of a database has been also growing. Therefore, we have developed a new elucidator using practically efficient graph algorithms, including the convex bipartite matching, weighted bipartite matching, and Bron-Kerbosch maximal clique algorithms. The utilization of the two matching algorithms especially is a novel point of our elucidator. Because of these sophisticated algorithms, the elucidator exactly produces a correct str