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Sample records for chemicals structurally related

  1. Neurotropic Effects in Relation to Chemical Structure.

    DTIC Science & Technology

    ANTISPASMODIC AGENTS, *MOLECULAR STRUCTURE), (*ANALGESICS + ANTIPYRETICS, MOLECULAR STRUCTURE), (*POLYCYCLIC COMPOUNDS, SYNTHESIS(CHEMISTRY...TOXICITY, ANTISPASMODIC AGENTS), MUSCLE RELAXANTS, BIOASSAY, MOLECULAR ISOMERISM, POLYCYCLIC COMPOUNDS, ANHYDRIDES, AMINES, CARBOXYLIC ACIDS, AMIDES, ANTHRACENES, PHENOLS, NAPHTHALENES

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

    PubMed Central

    Zheng, Mingyue; Kong, Xiangyin; Huang, Tao; Cai, Yu-Dong

    2015-01-01

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

  3. 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.

  4. 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).

  5. 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…

  6. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. Macromolecular changes and nano-structural arrangements in gliadin and glutenin films upon chemical modification: Relation to functionality.

    PubMed

    Rasheed, Faiza; Newson, William R; Plivelic, Tomás S; Kuktaite, Ramune; Hedenqvist, Mikael S; Gällstedt, Mikael; Johansson, Eva

    2015-08-01

    Protein macromolecules adopted for biological and bio-based material functions are known to develop a structured protein network upon chemical modification. In this study, we aimed to evaluate the impact of chemical additives such as, NaOH, NH4OH and salicylic acid (SA), on the secondary and nano-structural transitions of wheat proteins. Further, the effect of chemically induced modifications in protein macromolecular structure was anticipated in relation to functional properties. The gliadin-NH4OH-SA film showed a supramolecular protein organization into hexagonal structures with 65 Å lattice parameter, and other not previously observed structural entities having a characteristic distance of 50 Å. Proteins in gliadin-NH4OH-SA films were highly polymerized, with increased amount of disulfide crosslinks and β-sheets, causing improved strength and stiffness. Glutenin and WG proteins with NH4OH-SA showed extensive aggregation and an increase in β-sheet content together with irreversible crosslinks. Irreversible crosslinks hindered a high order structure formation in glutenins, and this resulted in films with only moderately improved stiffness. Thus, formation of nano-hierarchical structures based on β-sheets and disulfide crosslinks are the major reasons of high strength and stiffness in wheat protein based films. Copyright © 2015 Elsevier B.V. All rights reserved.

  15. 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.

  16. Structural Basis for Agonism and Antagonism for a Set of Chemically Related Progesterone Receptor Modulators

    PubMed Central

    Lusher, Scott J.; Raaijmakers, Hans C. A.; Vu-Pham, Diep; Dechering, Koen; Lam, Tsang Wai; Brown, Angus R.; Hamilton, Niall M.; Nimz, Olaf; Bosch, Rolien; McGuire, Ross; Oubrie, Arthur; de Vlieg, Jacob

    2011-01-01

    The progesterone receptor is able to bind to a large number and variety of ligands that elicit a broad range of transcriptional responses ranging from full agonism to full antagonism and numerous mixed profiles inbetween. We describe here two new progesterone receptor ligand binding domain x-ray structures bound to compounds from a structurally related but functionally divergent series, which show different binding modes corresponding to their agonistic or antagonistic nature. In addition, we present a third progesterone receptor ligand binding domain dimer bound to an agonist in monomer A and an antagonist in monomer B, which display binding modes in agreement with the earlier observation that agonists and antagonists from this series adopt different binding modes. PMID:21849509

  17. 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.

  18. 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.

  19. On the structure of palau'amine: evidence for the revised relative configuration from chemical synthesis.

    PubMed

    Lanman, Brian A; Overman, Larry E; Paulini, Ralph; White, Nicole S

    2007-10-24

    Hexacyclic congeners 3 and 4 of palau'amine, which incorporate both guanidine functional groups and have the cis configuration of the azabicyclo[3.3.0]octane core, are prepared in 14 steps from cycloadduct 6. Synthetic access to these analogues allows the first direct comparison of NMR data for hexacyclic diguanidine structures having the originally proposed cis-azabicyclo[3.3.0]octane fragment with data for natural alkaloids of the palau'amine family. This comparison provides convincing evidence in favor of the recently proposed structural revision of these marine alkaloids, fully supporting the trans configuration of the central azabicyclo[3.3.0]octane ring system of palau'amine and congeners.

  20. On the Structure of Palau’amine: Evidence for the Revised Relative Configuration from Chemical Synthesis

    PubMed Central

    Lanman, Brian A.; Overman, Larry E.; Paulini, Ralph; White, Nicole S.

    2008-01-01

    Hexacyclic congeners 2 and 3 of palau’amine, which incorporate both guanidine functional groups and have the cis configuration of the azabicyclo[3.3.0]octane core, are prepared in 14 steps from cycloadduct 6. Synthetic access to these analogs allows the first direct comparison of NMR data for hexacyclic diguanidine structures having the originally proposed cis-azabicyclo[3.3.0]octane fragment with data for natural alkaloids of the palau’amine family. This comparison provides convincing evidence in favor of the recently proposed structural revision of these marine alkaloids, fully supporting the trans configuration of the central azabicyclo[3.3.0]octane ring system of palau’amine and congeners. PMID:17902668

  1. Relating chemical structure to the mechanical and electrical properties in organic crystalline semiconductors

    NASA Astrophysics Data System (ADS)

    Reyes-Martinez, Marcos; Crosby, Alfred; Briseno, Alejandro

    2015-03-01

    The study of the physical properties of organic single crystals (OSCs) has allowed the advent of a new generation of high-performance organic electronic devices. Despite the profound knowledge of the structural and electrical properties of OSCs, there is little research on their mechanical properties and the effects of strain on their electrical properties. This presentation brings new understanding of the intrinsic mechanical properties of organic semiconductors and the effect of deformation in charge transport phenomena. We utilize rubrene single crystals as model systems. Due to the limited dimensions of crystals and the associated handling difficulty, the wrinkling instability is chosen as a metrology tool for the in-plane elastic constants. To elucidate the effects of mechanical strain on charge transport, we take advantage of wrinkling as a unique way to strain the conducting channel of field-effect transistors in a non-destructive, reversible, and predictable manner and demonstrate the mechanical modulation of field-effect mobility. Our contributions are the first to quantitatively correlate the crystal structure and the mechanical properties of OSCs, as well as the first to study their electro-mechanical behavior. They also represent a significant step forward in structure-function relationships in organic semiconductors and lay the foundation for the effective use of organic semiconductors in mechanically demanding applications such as pressure sensors and electronic skins.

  2. 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.

  3. [Relation between the chemical structure of substances and their antimicrobial action against atypical strains. II. 6-acycloamido-2-alkylthiobenzothiazoles, quantitative relation to their effectiveness spectrum].

    PubMed

    Machácek, M; Kunes, J; Sidóová, E; Odlerová, Z; Waisser, K

    1989-02-01

    Forty-six 6-acylamido-2-alkylthiobenzothiazoles were tested in vitro for antimicrobial activity towards Mycobacterium avium. The values of logarithms of the minimal inhibitory concentrations (log MIC) are shown in Table 1. The relationships between chemical structure and the activity under study were studied by the Free-Wilson method. The results, contributions of the substituents in positions 2 and 6 and the contribution of the common benzothiazole part (marked C) to the activity (delta log MIC) are shown in Table 2. Regression equation correlating the contributions and fragmental hydrophobic constants (f) belonging to the unbranched alkyl groups bound to the sulphur atom in position 2 (see Table 2) are not statistically significant (equation 8). The initial data for a complex analysis of the structure--antimycobacterial activity relationships with regard to the equipotency of the activity towards the species mentioned below form the values of log MIC and the derived values delta log MIC towards Mycobacterium tuberculosis, M. kansasii (see ref.9) and M. avium (see above). According to it, to each drug, each molecular fragment, the vector of activities A is attributed (equation 1), or the vector of contributions a (equation 7). Complex analysis is based on the idea of comparison (similarity) of the drug under study with an "ideal" drug, which possesses the required profile of activities. The vector uk corresponding to it is given for the above-considered case (of wide spectrum) by relation 5, for the case of selectivity with regard to the 1st activity by relation 4. The fundamental concepts of vector algebra, particularly the scalar product of vectors (A, uk) (relation 3) are used as the criteria of decision.(ABSTRACT TRUNCATED AT 250 WORDS)

  4. 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.

  5. 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.

  6. Chemical Structural Aging Effects

    DTIC Science & Technology

    1974-10-01

    prediction 20 AIISTRPACT (Continue for reverse aid@ It necessary and lpentity 6v blockA moso&-, Aging studies have been conducted upon one batch of ANB - 3066...correlations can indeed be employed which will allow the use of accelerated surveillance to predict chemical aging rates of ANB -3066 under silo storage...3.2.2 Kinetic Analysis of Parameter Aging Changes 2-4 1.2. 1 Temperature and Strain Dependence of Aging Rates " 3.2.4 Comparison With Other ANB -3066

  7. 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.

  8. Relation between structure and Lewis acidity of Ti-Beta and TS-1 zeolites. A quantum-chemical study

    NASA Astrophysics Data System (ADS)

    Sastre, German; Corma, Avelino

    1999-03-01

    Ab-initio Hartree-Fock and density-functional-theory quantum-chemical calculations have been carried out to characterise the geometry and LUMO energies of two zeolites, Ti-Beta and TS-1. The cluster model has been used and results from classical force-field calculations have also been included for comparison and to guide the definition of the cluster boundaries. The LUMO energy, which is related to the Lewis acidity, is shown to be different for the different T-sites, and, in general, Ti-Beta shows higher Lewis acidity than TS-1. This can explain their behaviour for epoxidation of olefins as well as their catalytic properties for Lewis acid-catalysed reactions such as Meerwein-Ponndorf-Verley reactions.

  9. 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.

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

    PubMed

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

    2016-12-30

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

  11. 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

  12. 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.

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

    PubMed

    Yu, Peiqiang

    2013-02-20

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

  14. Structure validation in chemical crystallography

    PubMed Central

    Spek, Anthony L.

    2009-01-01

    Automated structure validation was introduced in chemical crystallography about 12 years ago as a tool to assist practitioners with the exponential growth in crystal structure analyses. Validation has since evolved into an easy-to-use checkCIF/PLATON web-based IUCr service. The result of a crystal structure determination has to be supplied as a CIF-formatted computer-readable file. The checking software tests the data in the CIF for completeness, quality and consistency. In addition, the reported structure is checked for incomplete analysis, errors in the analysis and relevant issues to be verified. A validation report is generated in the form of a list of ALERTS on the issues to be corrected, checked or commented on. Structure validation has largely eliminated obvious problems with structure reports published in IUCr journals, such as refinement in a space group of too low symmetry. This paper reports on the current status of structure validation and possible future extensions. PMID:19171970

  15. 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.

  16. 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

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

    PubMed

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

    2016-09-06

    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.

  18. 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.

  19. 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

  20. Self-assembly of squalene-based nucleolipids: relating the chemical structure of the bioconjugates to the architecture of the nanoparticles.

    PubMed

    Lepeltier, Elise; Bourgaux, Claudie; Rosilio, Véronique; Poupaert, Jacques H; Meneau, Florian; Zouhiri, Fatima; Lepêtre-Mouelhi, Sinda; Desmaële, Didier; Couvreur, Patrick

    2013-12-03

    Squalene-based nucleolipids, including anticancer or antiviral prodrugs, gave rise to nanoparticles displaying a diversity of structures upon nanoprecipitation in water. Synchrotron small-angle X-ray scattering and cryo-TEM imaging revealed that both the nature of the nucleoside and the position of the squalene moiety relative to the nucleobase determined the self-assembly of the corresponding bioconjugates. It was found that small chemical differences resulted in major differences in the self-organization of nucleolipids when squalene was grafted onto the nucleobase whereas only lamellar phases were observed when squalene was linked to the sugar moiety. The key role of hydrogen bonds between nucleobases in the formation of the lamellar phases was suggested, in agreement with molecular simulations. These findings provide a way to fine tune the supramolecular organization of squalene-based prodrugs, with the aim of improving their pharmacological activity.

  1. Structural and Chemical Biology of Terpenoid Cyclases

    PubMed Central

    2017-01-01

    The year 2017 marks the twentieth anniversary of terpenoid cyclase structural biology: a trio of terpenoid cyclase structures reported together in 1997 were the first to set the foundation for understanding the enzymes largely responsible for the exquisite chemodiversity of more than 80000 terpenoid natural products. Terpenoid cyclases catalyze the most complex chemical reactions in biology, in that more than half of the substrate carbon atoms undergo changes in bonding and hybridization during a single enzyme-catalyzed cyclization reaction. The past two decades have witnessed structural, functional, and computational studies illuminating the modes of substrate activation that initiate the cyclization cascade, the management and manipulation of high-energy carbocation intermediates that propagate the cyclization cascade, and the chemical strategies that terminate the cyclization cascade. The role of the terpenoid cyclase as a template for catalysis is paramount to its function, and protein engineering can be used to reprogram the cyclization cascade to generate alternative and commercially important products. Here, I review key advances in terpenoid cyclase structural and chemical biology, focusing mainly on terpenoid cyclases and related prenyltransferases for which X-ray crystal structures have informed and advanced our understanding of enzyme structure and function. PMID:28841019

  2. 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

  3. 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.

  4. 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.

  5. 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).

  6. 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

  7. 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

    NASA Astrophysics Data System (ADS)

    Xin, Hangshu; Yu, Peiqiang

    2014-12-01

    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. 3010-2765 cm-1, unsaturated lipid band ca. 3043-2987 cm-1 and carbonyl Cdbnd O ester band ca. 1789-1701 cm-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 Cdbnd O 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 48 h 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.

  8. 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.

  9. Image-Based Chemical Structure Determination.

    PubMed

    Ofner, Johannes; Brenner, Florian; Wieland, Karin; Eitenberger, Elisabeth; Kirschner, Johannes; Eisenmenger-Sittner, Christoph; Török, Szilvia; Döme, Balazs; Konegger, Thomas; Kasper-Giebl, Anne; Hutter, Herbert; Friedbacher, Gernot; Lendl, Bernhard; Lohninger, Hans

    2017-07-28

    Chemical imaging is a powerful tool for understanding the chemical composition and nature of heterogeneous samples. Recent developments in elemental, vibrational, and mass-spectrometric chemical imaging with high spatial resolution (50-200 nm) and reasonable timescale (a few hours) are capable of providing complementary chemical information about various samples. However, a single technique is insufficient to provide a comprehensive understanding of chemically complex materials. For bulk samples, the combination of different analytical methods and the application of statistical methods for extracting correlated information across different techniques is a well-established and powerful concept. However, combined multivariate analytics of chemical images obtained via different imaging techniques is still in its infancy, hampered by a lack of analytical methodologies for data fusion and analysis. This study demonstrates the application of multivariate statistics to chemical images taken from the same sample via various methods to assist in chemical structure determination.

  10. 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

  11. 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)

  12. 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)

  13. 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.

  14. 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...

  15. 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...

  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. Chemical weathering within high mountain depositional structures

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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...

  3. 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...

  4. Classification of Chemicals Based On Structured Toxicity ...

    EPA Pesticide Factsheets

    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-based classifications of chemicals were performed as a model application of ToxRefDB. These endpoints will ultimately provide the anchoring toxicity information for the development of predictive models and biological signatures utilizing in vitro assay data. Utilizing query and structured data mining approaches, toxicity profiles were uniformly generated for greater than 300 chemicals. Based on observation rate, species concordance and regulatory relevance, individual and aggregated effects have been selected to classify the chemicals providing a set of predictable endpoints. ToxRefDB exhibits the utility of transforming unstructured toxicity data into structured data and, furthermore, into computable outputs, and serves as a model for applying such data to address modern toxicological problems.

  5. 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.

  6. 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.

  7. The PubChem chemical structure sketcher

    PubMed Central

    2009-01-01

    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. PMID:20298522

  8. 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.

  9. Markov logic networks for optical chemical structure recognition.

    PubMed

    Frasconi, Paolo; Gabbrielli, Francesco; Lippi, Marco; Marinai, Simone

    2014-08-25

    Optical chemical structure recognition is the problem of converting a bitmap image containing a chemical structure formula into a standard structured representation of the molecule. We introduce a novel approach to this problem based on the pipelined integration of pattern recognition techniques with probabilistic knowledge representation and reasoning. Basic entities and relations (such as textual elements, points, lines, etc.) are first extracted by a low-level processing module. A probabilistic reasoning engine based on Markov logic, embodying chemical and graphical knowledge, is subsequently used to refine these pieces of information. An annotated connection table of atoms and bonds is finally assembled and converted into a standard chemical exchange format. We report a successful evaluation on two large image data sets, showing that the method compares favorably with the current state-of-the-art, especially on degraded low-resolution images. The system is available as a web server at http://mlocsr.dinfo.unifi.it.

  10. 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)

  11. 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.

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

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ...) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Definitions and... have related pharmacological effects: Chlorinated organic pesticides, arsenic-containing chemicals... protect the public health, and no additional concurrent tolerances for the organic pesticide chemicals...

  13. 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.

  14. Physico-chemical characteristics and primary structure of an affinity-purified α-D-galactose-specific, jacalin-related lectin from the latex of mulberry (Morus indica).

    PubMed

    Datta, Debparna; Pohlentz, Gottfried; Schulte, Mona; Kaiser, Mathias; Goycoolea, Francisco M; Müthing, Johannes; Mormann, Michael; Swamy, Musti J

    2016-11-01

    An α-D-galactose specific lectin belonging to the family of jacalin-related lectins (JRL) has been purified by affinity chromatography on cross-linked guar-gum. Mass spectrometric data revealed that the protein harbors two chains like all the members of galactose-specific jacalin-related lectins (gJRL). De novo sequencing of proteolytic peptides demonstrated that the heavier chain consists of 133 amino acids and the lighter chain comprises of 21 or 24 amino acids. The heavier chain contains one N-glycosylation site (Asn47) occupied with either pauci-mannose type [GlcNAc2(Fuc)Man3(Xyl)] or complex type [GlcNAc2(Fuc)Man3(Xyl)GlcNAc(Fuc)Gal] N-glycans. Circular dichroism spectroscopy indicated that the secondary structure of the lectin is predominantly made up of β-sheets, and differential scanning calorimetry revealed a thermal denaturation temperature of 77.6 °C. MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) cell viability assays on MCF-7 and MDCK cells showed that the lectin is highly cytotoxic towards both cell lines when dosed at micromolar concentrations, suggesting that it may play a role in the defense mechanism of the plant. Copyright © 2016 Elsevier Inc. All rights reserved.

  15. 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.

  16. 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.

  17. 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.

  18. THE RELATION OF CHEMICAL STRUCTURE IN CATECHOL COMPOUNDS AND DERIVATIVES TO POISON IVY HYPERSENSITIVENESS IN MAN AS SHOWN BY THE PATCH TEST.

    PubMed

    Keil, H; Wasserman, D; Dawson, C R

    1944-10-01

    1. Additional evidence is presented in support of the view which postulates a close chemical and biologic relation between the active ingredients in poison ivy and Japan lac. 2. Biologic evidence, based on the use of the patch test in man, is presented in support of the view that the active ingredient in poison ivy is a catechol derivative with a long, unsaturated side-chain in the 3-position. 3. Of the catechol compounds and derivatives studied, group reactions in patients sensitive to poison ivy leaves or extract were exhibited by the following compounds: 3-pentadecyl catechol (100 per cent of 21 cases), 4-pentadecyl catechol (38 per cent of 21 cases), "urushiol" dimethyl ether (33 per cent of 33 cases), 3-pentadecenyl-1'-veratrole (21 per cent of 14 cases), 3-methyl catechol (14 per cent of 21 cases), and hydrourushiol dimethyl ether (10 per cent of 20 cases). It has been found that 3-geranyl catechol shows a practically constant group reactivity in persons sensitive to poison ivy. 4. The uniformly positive group reaction to 3-pentadecyl catechol is notable since this substance possesses a saturated side-chain, whereas the active ingredient in poison ivy is known to have an unsaturated side-chain. 5. The group reactivity was not restricted to the 3-position, for in some instances 4-pentadecyl catechol also gave group reactions which, however, were less intense and less frequent than those shown by 3-pentadecyl catechol. This indicates that in some cases a long side-chain in the 4 position may be effective in producing group specific reactions. 6. Only an occasional person showed sensitiveness to 3-methyl catechol (short side-chain), and in one instance the group reactivity appeared to be specific for the 3-position. 7. The position of the side-chain in the catechol configuration has some bearing on the degree and incidence of group reactions in persons hypersensitive to poison ivy. 8. Evidence is presented to indicate that the introduction of double bonds in the

  19. THE RELATION OF CHEMICAL STRUCTURE IN CATECHOL COMPOUNDS AND DERIVATIVES TO POISON IVY HYPERSENSITIVENESS IN MAN AS SHOWN BY THE PATCH TEST

    PubMed Central

    Keil, Harry; Wasserman, David; Dawson, Charles R.

    1944-01-01

    1. Additional evidence is presented in support of the view which postulates a close chemical and biologic relation between the active ingredients in poison ivy and Japan lac. 2. Biologic evidence, based on the use of the patch test in man, is presented in support of the view that the active ingredient in poison ivy is a catechol derivative with a long, unsaturated side-chain in the 3-position. 3. Of the catechol compounds and derivatives studied, group reactions in patients sensitive to poison ivy leaves or extract were exhibited by the following compounds: 3-pentadecyl catechol (100 per cent of 21 cases), 4-pentadecyl catechol (38 per cent of 21 cases), "urushiol" dimethyl ether (33 per cent of 33 cases), 3-pentadecenyl-1'-veratrole (21 per cent of 14 cases), 3-methyl catechol (14 per cent of 21 cases), and hydrourushiol dimethyl ether (10 per cent of 20 cases). It has been found that 3-geranyl catechol shows a practically constant group reactivity in persons sensitive to poison ivy. 4. The uniformly positive group reaction to 3-pentadecyl catechol is notable since this substance possesses a saturated side-chain, whereas the active ingredient in poison ivy is known to have an unsaturated side-chain. 5. The group reactivity was not restricted to the 3-position, for in some instances 4-pentadecyl catechol also gave group reactions which, however, were less intense and less frequent than those shown by 3-pentadecyl catechol. This indicates that in some cases a long side-chain in the 4 position may be effective in producing group specific reactions. 6. Only an occasional person showed sensitiveness to 3-methyl catechol (short side-chain), and in one instance the group reactivity appeared to be specific for the 3-position. 7. The position of the side-chain in the catechol configuration has some bearing on the degree and incidence of group reactions in persons hypersensitive to poison ivy. 8. Evidence is presented to indicate that the introduction of double bonds in the

  20. Extracting and connecting chemical structures from text sources using chemicalize.org.

    PubMed

    Southan, Christopher; Stracz, Andras

    2013-04-23

    Exploring bioactive chemistry requires navigating between structures and data from a variety of text-based sources. While PubChem currently includes approximately 16 million document-extracted structures (15 million from patents) the extent of public inter-document and document-to-database links is still well below any estimated total, especially for journal articles. A major expansion in access to text-entombed chemistry is enabled by chemicalize.org. This on-line resource can process IUPAC names, SMILES, InChI strings, CAS numbers and drug names from pasted text, PDFs or URLs to generate structures, calculate properties and launch searches. Here, we explore its utility for answering questions related to chemical structures in documents and where these overlap with database records. These aspects are illustrated using a common theme of Dipeptidyl Peptidase 4 (DPPIV) inhibitors. Full-text open URL sources facilitated the download of over 1400 structures from a DPPIV patent and the alignment of specific examples with IC50 data. Uploading the SMILES to PubChem revealed extensive linking to patents and papers, including prior submissions from chemicalize.org as submitting source. A DPPIV medicinal chemistry paper was completely extracted and structures were aligned to the activity results table, as well as linked to other documents via PubChem. In both cases, key structures with data were partitioned from common chemistry by dividing them into individual new PDFs for conversion. Over 500 structures were also extracted from a batch of PubMed abstracts related to DPPIV inhibition. The drug structures could be stepped through each text occurrence and included some converted MeSH-only IUPAC names not linked in PubChem. Performing set intersections proved effective for detecting compounds-in-common between documents and merged extractions. This work demonstrates the utility of chemicalize.org for the exploration of chemical structure connectivity between documents and

  1. Drop impact on chemically structured arrays

    NASA Astrophysics Data System (ADS)

    Mock, Ulrike; Michel, Tobias; Tropea, Cameron; Roisman, Ilia; Rühe, Jürgen

    2005-03-01

    We describe recent investigations on the impact behaviour of liquid drops onto chemically structured surfaces. The surface patterns were prepared via photochemical attachment of polymer molecules with different hydrophilicities using self-assembled monolayers of benzophenone bearing silanes. Immobilization of the polymer monolayers was followed by an ablation process to generate a chemical surface pattern. Impact experiments on systems consisting of very hydrophobic poly(perfluoroalkylethyl)acrylate coatings and hydrophilic areas show that within certain limitations the water drop has a strong tendency to reach the hydrophilic spots, even for inclined substrates. Impact experiments of drops on arrays of hydrophilic spots on the background of a perfluorinated polymer show that the drops spontaneously self-centre on the lithographically generated pattern. The obtained results suggest that the process can be used to circumvent some of the current problems in micro-array fabrication.

  2. 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…

  3. 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.

  4. 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

  5. 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...

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. Carotenoids Database: structures, chemical fingerprints and distribution among organisms.

    PubMed

    Yabuzaki, Junko

    2017-01-01

    To promote understanding of how organisms are related via carotenoids, either evolutionarily or symbiotically, or in food chains through natural histories, we built the Carotenoids Database. This provides chemical information on 1117 natural carotenoids with 683 source organisms. For extracting organisms closely related through the biosynthesis of carotenoids, we offer a new similarity search system 'Search similar carotenoids' using our original chemical fingerprint 'Carotenoid DB Chemical Fingerprints'. These Carotenoid DB Chemical Fingerprints describe the chemical substructure and the modification details based upon International Union of Pure and Applied Chemistry (IUPAC) semi-systematic names of the carotenoids. The fingerprints also allow (i) easier prediction of six biological functions of carotenoids: provitamin A, membrane stabilizers, odorous substances, allelochemicals, antiproliferative activity and reverse MDR activity against cancer cells, (ii) easier classification of carotenoid structures, (iii) partial and exact structure searching and (iv) easier extraction of structural isomers and stereoisomers. We believe this to be the first attempt to establish fingerprints using the IUPAC semi-systematic names. For extracting close profiled organisms, we provide a new tool 'Search similar profiled organisms'. Our current statistics show some insights into natural history: carotenoids seem to have been spread largely by bacteria, as they produce C30, C40, C45 and C50 carotenoids, with the widest range of end groups, and they share a small portion of C40 carotenoids with eukaryotes. Archaea share an even smaller portion with eukaryotes. Eukaryotes then have evolved a considerable variety of C40 carotenoids. Considering carotenoids, eukaryotes seem more closely related to bacteria than to archaea aside from 16S rRNA lineage analysis. : http://carotenoiddb.jp.

  15. 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.

  16. 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

  17. Electrical and structural properties of chemically modified graphene sheets

    NASA Astrophysics Data System (ADS)

    Dikin, Dmitriy A.; Jung, Inhwa; Ruoff, Rodney S.

    2009-03-01

    The chemical exfoliation of graphite through oxidation and then dispersion in a solvent is one of the methods of achieving scalable production of single graphene sheets. We use this method for making chemically modified graphene (CMG) sheets with tunable electronic properties, which can be placed flat on any surface or dispersed in various matrices. CMG sheets share some similarities with pristine graphene and with carbon nanotubes, e.g. tunable electron- and hole-type conductivity is observed in single CMG sheets just above the percolation threshold. CMGs may also be considered as a template for a bottom up development of a new class of materials. We have performed electrical measurements of individual CMG sheets and will discuss their electronic properties and the possible mechanisms of the charge transport in relation to their atomic structure and chemical composition.

  18. 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.

  19. 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.

  20. Chemical detection system and related methods

    DOEpatents

    Caffrey, Augustine J.; Chichester, David L.; Egger, Ann E.; Krebs, Kenneth M.; Seabury, Edward H.; Van Siclen, Clinton D.; Wharton, C. Jayson; Zabriskie, John M.

    2017-06-27

    A chemical detection system includes a frame, an emitter coupled to the frame, and a detector coupled to the frame proximate the emitter. The system also includes a shielding system coupled to the frame and positioned at least partially between the emitter and the detector, wherein the frame positions a sensing surface of the detector in a direction substantially parallel to a plane extending along a front portion of the frame. A method of analyzing composition of a suspect object includes directing neutrons at the object, detecting gamma rays emitted from the object, and communicating spectrometer information regarding the gamma rays. The method also includes presenting a GUI to a user with a dynamic status of an ongoing neutron spectroscopy process. The dynamic status includes a present confidence for a plurality of compounds being present in the suspect object responsive to changes in the spectrometer information during the ongoing process.

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

    PubMed

    Bratholm, Lars A; Jensen, Jan H

    2017-03-01

    The accurate prediction of protein chemical shifts using a quantum mechanics (QM)-based method has been the subject of intense research for more than 20 years but so far empirical methods for chemical shift prediction have proven more accurate. In this paper we show that a QM-based predictor of a protein backbone and CB chemical shifts (ProCS15, PeerJ, 2016, 3, e1344) is of comparable accuracy to empirical chemical shift predictors after chemical shift-based structural refinement that removes small structural errors. We present a method by which quantum chemistry based predictions of isotropic chemical shielding values (ProCS15) can be used to refine protein structures using Markov Chain Monte Carlo (MCMC) simulations, relating the chemical shielding values to the experimental chemical shifts probabilistically. Two kinds of MCMC structural refinement simulations were performed using force field geometry optimized X-ray structures as starting points: simulated annealing of the starting structure and constant temperature MCMC simulation followed by simulated annealing of a representative ensemble structure. Annealing of the CHARMM structure changes the CA-RMSD by an average of 0.4 Å but lowers the chemical shift RMSD by 1.0 and 0.7 ppm for CA and N. Conformational averaging has a relatively small effect (0.1-0.2 ppm) on the overall agreement with carbon chemical shifts but lowers the error for nitrogen chemical shifts by 0.4 ppm. If an amino acid specific offset is included the ProCS15 predicted chemical shifts have RMSD values relative to experiments that are comparable to popular empirical chemical shift predictors. The annealed representative ensemble structures differ in CA-RMSD relative to the initial structures by an average of 2.0 Å, with >2.0 Å difference for six proteins. In four of the cases, the largest structural differences arise in structurally flexible regions of the protein as determined by NMR, and in the remaining two cases, the large structural

  2. Finding Chemical Structures Corresponding to a Set of Coordinates in Chemical Descriptor Space.

    PubMed

    Miyao, Tomoyuki; Funatsu, Kimito

    2017-08-01

    When chemical structures are searched based on descriptor values, or descriptors are interpreted based on values, it is important that corresponding chemical structures actually exist. In order to consider the existence of chemical structures located in a specific region in the chemical space, we propose to search them inside training data domains (TDDs), which are dense areas of a training dataset in the chemical space. We investigated TDDs' features using diverse and local datasets, assuming that GDB11 is the chemical universe. These two analyses showed that considering TDDs gives higher chance of finding chemical structures than a random search-based method, and that novel chemical structures actually exist inside TDDs. In addition to those findings, we tested the hypothesis that chemical structures were distributed on the limited areas of chemical space. This hypothesis was confirmed by the fact that distances among chemical structures in several descriptor spaces were much shorter than those among randomly generated coordinates in the training data range. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. 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.

  4. 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).

  5. 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.

  6. The Structure of the Chemical Processing Industries.

    ERIC Educational Resources Information Center

    Russell, T. W. F.

    1979-01-01

    Described is a graduate and senior level course utilizing the case study approach in chemical engineering at the University of Delaware that stresses the function and economics of the chemical processing industry. A history of the course development, course outline, and teaching methods used are included. (BT)

  7. 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

  8. 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.

  9. 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

  10. Relative Configuration of Natural Products Using NMR Chemical Shifts

    USDA-ARS?s Scientific Manuscript database

    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...

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

    PubMed Central

    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. PMID:28102265

  12. Thermodynamic derivations of conditions for chemical equilibrium and of Onsager reciprocal relations for chemical reactors.

    PubMed

    Beretta, Gian Paolo; Gyftopoulos, Elias P

    2004-08-08

    For an isolated chemical reactor, we derive the conditions for chemical equilibrium in terms of either energy, volume, and amounts of constituents or temperature, pressure, and composition, with special emphasis on what is meant by temperature and chemical potentials as the system proceeds through nonequilibrium states towards stable chemical equilibrium. For nonequilibrium states, we give both analytical expressions and pictorial representations of the assumptions and implications underlying chemical dynamics models. In the vicinity of the chemical equilibrium state, we express the affinities of the chemical reactions, the reaction rates, and the rate of entropy generation as functions of the reaction coordinates and derive Onsager reciprocal relations without recourse to statistical fluctuations, time reversal, and the principle of microscopic reversibility.

  13. Structural Transformations in Chemically Modified Graphene

    DTIC Science & Technology

    2012-07-16

    unclassified Standard Form 298 (Rev. 8-98) Prescribed by ANSI Std Z39-18 graphene oxide (GO) [13], chemical vapor deposition ( CVD ) onto transition metals [14...significantly. Here we focus on the mechanical aspects of graphene materials primarily using multilayer GO, but we also use single-layer CVD graphene grown on...pressure CVD growth on Cu foils [16] and subsequently transfer graphene from Cu using wet chemical approaches [14]. This includes the use of a poly

  14. 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.

  15. 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

  16. How to add chemical abstracts service registry numbers and structures to databases via chemical names comparison

    PubMed

    Krebs; Jordis

    2000-03-01

    For the conversion of nonstructural chemical databases to structure databases, a series of algorithms to find the closest match between existing names to names in a reference database are described. On the basis of the best match, new fields such as the Chemical Abstracts Service Registry Number (CASRN) or structures were added to the database.

  17. 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.

  18. Crystal structure and chemical bonding of Mg3Ru2.

    PubMed

    Pöttgen, Rainer; Hlukhyy, Viktor; Baranov, Aleksey; Grin, Yuri

    2008-07-07

    Mg 3Ru 2 was prepared by a reaction between the elements in the ideal ratio in a sealed tantalum ampule. Its beta-manganese type crystal structure was refined on the basis of the single-crystal data: space group P4 132, a = 693.52(6) pm, wR2 = 0.024, 168 F (2) values, and 10 parameters. The magnesium (CN = 14) and ruthenium (CN = 12) atoms are completely ordered on the 12d and 8c sites of the crystal structure of beta-manganese. Both environments can be considered as Frank-Kasper related polyhedra. A periodic nodal surface P4 132(110) pi (1) P4 132 separates the magnesium and ruthenium positions in two different labyrinths, suggesting different chemical interactions within different parts of the structural motif. Analysis of the chemical bonding with the electron localizability indicator (ELI-D) reveals covalently interacting three-bonded ruthenium atoms, forming a 3D network. The network interacts with the magnesium substructure by multicenter bonds.

  19. 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.

  20. 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

  1. Influence of chemical structure on carbon isotope composition of lignite

    NASA Astrophysics Data System (ADS)

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

    2017-04-01

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

  2. 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.

  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

    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

  4. 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

  5. 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.

  6. Bayesian inference of protein structure from chemical shift data

    PubMed Central

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

    2015-01-01

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

  7. PETN: Variation in Physical and Chemical Characteristics Related to Aging.

    SciTech Connect

    Monroe, D. C.; Laintz, K. E.; Kramer, J. F.; Peterson, P. D.

    2006-01-01

    Physical and chemical analyses of five PETN (pentaerythritol tetranitrate) batches have been conducted to assist in defining powder acceptance criteria for qualification of newly manufactured powders, as well as for examination of potential changes related to aging and thus changes in performance. Results showed that (1) repeatable Fisher Sub-Sieve Sizer measurements (which relate well to historic performance data) could be obtained with consistent sample setup and measurement techniques; (2) BET nitrogen adsorption estimates of surface area correlate well with Fisher measurements and appear less variable; (3) PharmaVision particle size analyses show promise in discriminating among PETN batches; and (4) SEMs are extremely useful in semi-quantitative discrimination among batches. Physical and chemical data will be related to performance data (to be obtained) to develop quantitative physical and chemical tests useful in predicting performance over time, i.e., as powders age.

  8. 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.

  9. Dissipative structures and related methods

    SciTech Connect

    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.

  10. 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

  11. 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

  12. 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.

  13. 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

  14. Chemical Abstracts Service Chemical Registry System. 11. Substance-related statistics: update and additions.

    PubMed

    Stobaugh, R E

    1988-11-01

    Statistics are updated for types of substances, ring systems, and elemental composition that have been determined for the Chemical Abstracts Service Registry Structure File at different points in time. This paper reports the updated figures and in addition some new statistics and offers some comparisons to show various shifts in file characteristics.

  15. 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

  16. 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.

  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. Miniature photoacoustic chemical sensor using microelectromechanical structures

    NASA Astrophysics Data System (ADS)

    Pellegrino, Paul M.; Polcawich, Ronald G.; Firebaugh, Samara L.

    2004-08-01

    Photoacoustic spectroscopy is a useful monitoring technique that is well suited for trace gas detection. The technique also possesses favorable detection characteristics when the system dimensions are scaled to a micro-system design. The objective of present work is to incorporate two strengths of the Army Research Laboratory (ARL), piezoelectric microelectromechanical systems (MEMS) and chemical and biological sensing into a monolithic MEMS photoacoustic trace gas sensor. A miniaturized macro-cell design was studied as a means to examine performance and design issues as the photoacoustics is scaled to a dimension approaching the MEMS level. Performance of the macro-cell was tested using standard organo-phosphate nerve gas simulants, Dimethyl methyl phosphonate (DMMP) and Diisoprpyl methyl phosphonate (DIMP). Current MEMS work centered on fabrication of a multi-layer cell subsystem to be incorporated in the full photoacoustic device. Preliminary results were very positive for the macro-cell sensitivity (ppb levels) and specificity indicating that the scaled cell maintains sensitivity. Several bonding schemes for a three-dimension MEMS photoacoustic cavity were investigated with initial results of a low temperature AuSn bond proving most feasible.

  19. Prediction of chemical carcinogenicity from molecular structure.

    PubMed

    Sun, Hongmao

    2004-01-01

    Carcinogens represent a serious threat to human health. In vivo determination of carcinogenicity is time-consuming and expensive, thus in silico models to predict chemical carcinogenicity are highly desirable for virtual screening of compound libraries of both pharmaceutically and other commercially interesting molecules. In the present study, a PLS-DA (partial least squares discriminant analysis) model was developed to predict carcinogenicities in each of four rodent models: male mouse (MM), female mouse (FM), male rat (MR), and female rat (FR). The data set that was used contained over 520 compounds from both the NTP and the FDA databases. All the models were built from the same molecular descriptor system, which is based on atom typing [Sun, H. J. Chem. Inf. Comput. Sci. 2004, 44, 748-757], enabling the comparison of atomic contributions to carcinogenicity with respect to species and gender. Using four components, the models were able to achieve excellent fitting and prediction, with r(2) = 0.987 and q(2) = 0.944 for MM, r(2) = 0.985 and q(2) = 0.950 for FM, r(2) = 0.989 and q(2) = 0.962 for MR, and r(2) = 0.990 and q(2) = 0.965 for FR. The models were further validated by response permutation testing and external validation, and the results indicated that the models were both statistically significant and predictive. Variable influence on projection (VIP) analysis identified the key atom types and fragments that contributed to carcinogenicities and response differences across species and gender.

  20. 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.

  1. 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.

  2. Forgotten topological index of chemical structure in drugs.

    PubMed

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

    2016-05-01

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

  3. 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.

  4. 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

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

    DTIC Science & Technology

    1978-04-01

    damage to the ecosystem. At current production levels, the Army uses only 4% of the ttiacetin civilian production capacity. At full mobilization, the...restricting damage to a relatively small area. b. Rocket Motor Grain Loading Most double bass propellant* are formed into grains by hot " extrusions...34Dynamics of Phthalic Acid Esters in Aquatic Organisms," Adv. in Envir . Sci. & Tech., 8, 283. Kasuya, M. (1974), "Toxicity of Phthalate Esters to Nervous

  6. 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.

  7. 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.

  8. 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.

  9. 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.

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

    PubMed

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

    2015-01-01

    There are presently hundreds of online databases hosting millions of chemical compounds and associated data. As a result of the number of cheminformatics software tools that can be used to produce the data, subtle differences between the various cheminformatics platforms, as well as the naivety of the software users, there are a myriad of issues that can exist with chemical structure representations online. In order to help facilitate validation and standardization of chemical structure datasets from various sources we have delivered a freely available internet-based platform to the community for the processing of chemical compound datasets. The chemical validation and standardization platform (CVSP) both validates and standardizes chemical structure representations according to sets of systematic rules. The chemical validation algorithms detect issues with submitted molecular representations using pre-defined or user-defined dictionary-based molecular patterns that are chemically suspicious or potentially requiring manual review. Each identified issue is assigned one of three levels of severity - Information, Warning, and Error - in order to conveniently inform the user of the need to browse and review subsets of their data. The validation process includes validation of atoms and bonds (e.g., making aware of query atoms and bonds), valences, and stereo. The standard form of submission of collections of data, the SDF file, allows the user to map the data fields to predefined CVSP fields for the purpose of cross-validating associated SMILES and InChIs with the connection tables contained within the SDF file. This platform has been applied to the analysis of a large number of data sets prepared for deposition to our ChemSpider database and in preparation of data for the Open PHACTS project. In this work we review the results of the automated validation of the DrugBank dataset, a popular drug and drug target database utilized by the community, and ChEMBL 17 data set

  11. Quantum chemical 13Cα chemical shift calculations for protein NMR structure determination, refinement, and validation

    PubMed Central

    Vila, Jorge A.; Aramini, James M.; Rossi, Paolo; Kuzin, Alexandre; Su, Min; Seetharaman, Jayaraman; Xiao, Rong; Tong, Liang; Montelione, Gaetano T.; Scheraga, Harold A.

    2008-01-01

    A recently determined set of 20 NMR-derived conformations of a 48-residue all-α-helical protein, (PDB ID code 2JVD), is validated here by comparing the observed 13Cα chemical shifts with those computed at the density functional level of theory. In addition, a recently introduced physics-based method, aimed at determining protein structures by using NOE-derived distance constraints together with observed and computed 13Cα chemical shifts, was applied to determine a new set of 10 conformations, (Set-bt), as a blind test for the same protein. A cross-validation of these two sets of conformations in terms of the agreement between computed and observed 13Cα chemical shifts, several stereochemical quality factors, and some NMR quality assessment scores reveals the good quality of both sets of structures. We also carried out an analysis of the agreement between the observed and computed 13Cα chemical shifts for a slightly longer construct of the protein solved by x-ray crystallography at 2.0-Å resolution (PDB ID code 3BHP) with an identical amino acid residue sequence to the 2JVD structure for the first 46 residues. Our results reveal that both of the NMR-derived sets, namely 2JVD and Set-bt, are somewhat better representations of the observed 13Cα chemical shifts in solution than the 3BHP crystal structure. In addition, the 13Cα-based validation analysis appears to be more sensitive to subtle structural differences across the three sets of structures than any other NMR quality-assessment scores used here, and, although it is computationally intensive, this analysis has potential value as a standard procedure to determine, refine, and validate protein structures. PMID:18787110

  12. The Relation between Chemical Bonding and Ultrafast Crystal Growth.

    PubMed

    Lee, Tae Hoon; Elliott, Stephen R

    2017-06-01

    Glasses are often described as supercooled liquids, whose structures are topologically disordered like a liquid, but nevertheless retain short-range structural order. Structural complexity is often associated with complicated electron-charge distributions in glassy systems, making a detailed investigation challenging even for short-range structural order, let alone their atomic dynamics. This is particularly problematic for lone-pair-rich, semiconducting materials, such as phase-change materials (PCMs). Here, this study shows that analytical methods for studying bonding, based on the electron-charge density, rather than a conventional atomic pair-correlation-function approach, allows an in-depth investigation into the chemical-bonding network, as well as lone pairs, of the prototypical PCM, Ge2 Sb2 Te5 (GST). It is demonstrated that the structurally flexible building units of the amorphous GST network, intimately linked to the presence of distinctly coexisting weak covalent and lone-pair interactions, give rise to cooperative structural-ordering processes, by which ultrafast crystal growth becomes possible. This finding may universally apply to other PCMs. © 2017 The Authors. Published by WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  13. 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

  14. 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.

  15. The Surface Structure of Relative Clauses

    ERIC Educational Resources Information Center

    Lucas, Michael A.

    1974-01-01

    This article attempts to show that a more rigorous approach to surface structure analysis can reveal distinctions just as subtle as those discovered through analyzing deep structures or transformations. Relative clauses are examined in relation to nominal constructions, and alternatives to restrictive and non-restrictive classifications are…

  16. 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)

  17. 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)

  18. 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…

  19. 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…

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

    NASA Astrophysics Data System (ADS)

    Werheit, Helmut

    2016-10-01

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

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2014-06-01

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

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

    PubMed

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

    2017-08-25

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

  4. 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.

  5. 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.

  6. 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 .

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

    PubMed Central

    Huang, Jieying; Yu, Zixuan; Gao, Hongjian; Yan, Xiaoming; Chang, Jiang; Wang, Chengming; Hu, Jingwei

    2017-01-01

    Changes in physicochemical characteristics, chemical structures and maturity of swine, cattle and chicken manures and composts during 70-day composting without addition of bulking agents were investigated. Physicochemical characteristics were measured by routine analyses and chemical structures by solid-state 13C NMR and FT-IR. Three manures were of distinct properties. Their changes in physicochemical characteristics, chemical structures, and maturity were different not only from each other but also from those with addition of bulking agents during composting. Aromaticity in chicken manure composts decreased at first, and then increased whereas that in cattle and swine manure composts increased. Enhanced ammonia volatilization occurred without addition of bulking agents. NMR structural information indicated that cattle and chicken composts were relatively stable at day 36 and 56, respectively, but swine manure composts were not mature up to day 70. Finally, the days required for three manures to reach the threshold values of different maturity indices were different. PMID:28604783

  8. 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.

  9. Property distribution of drug-related chemical databases.

    PubMed

    Oprea, T I

    2000-03-01

    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 < or = HDO < or = 2, 2 < or = HAC < or = 9, 2 < or = RTB

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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

  15. (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…

  16. CROSS-DISCIPLINARY PHYSICS AND RELATED AREAS OF SCIENCE AND TECHNOLOGY: A Simple Route of Morphology Control and Structural and Optical Properties of ZnO Grown by Metal-Organic Chemical Vapour Deposition

    NASA Astrophysics Data System (ADS)

    Fan, Hai-Bo; Yang, Shao-Yan; Zhang, Pan-Feng; Wei, Hong-Yuan; Liu, Xiang-Lin; Jiao, Chun-Mei; Zhu, Qin-Sheng; Chen, Yong-Hai; Wang, Zhan-Guo

    2008-08-01

    Employing the metal-organic chemical vapour deposition (MOCVD) technique, we prepare ZnO samples with different morphologies from the film to nanorods through conveniently changing the bubbled diethylzinc flux (BDF) and the carrier gas flux of oxygen (OCGF). The scanning electron microscope images indicate that small BDF and OCGF induce two-dimensional growth while the large ones avail quasi-one-dimensional growth. X-ray diffraction (XRD) and Raman scattering analyses show that all of the morphology-dependent ZnO samples are of high crystal quality with a c-axis orientation. From the precise shifts of the 2θ locations of ZnO (002) face in the XRD patterns and the E2 (high) locations in the Raman spectra, we deduce that the compressive stress forms in the ZnO samples and is strengthened with the increasing BDF and OCGF. Photoluminescence spectroscopy results show all the samples have a sharp ultraviolet luminescent band without any defects-related emission. Upon the experiments a possible growth mechanism is proposed.

  17. 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

  18. 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.

  19. 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.

  20. 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.

  1. Physical-chemical properties studying of molecular structures via topological index calculating

    NASA Astrophysics Data System (ADS)

    Wu, Jianzhang; Farahani, Mohammad Reza; Yu, Xiao; Gao, Wei

    2017-05-01

    It's revealed from the earlier researches that many physical-chemical properties depend heavily on the structure of corresponding moleculars. This fact provides us an approach to measure the physical-chemical characteristics of substances and materials. In our article, we report the eccentricity related indices of certain important molecular structures from mathematical standpoint. The eccentricity version indices of nanostar dendrimers are determined and the reverse eccentric connectivity index for V-phenylenic nanotorus is discussed. The conclusions we obtained mainly use the trick of distance computation and mathematical derivation, and the results can be applied in physics engineering.

  2. 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

  3. 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.

  4. Correlating the structural, chemical, and optical properties at nanometer resolution

    NASA Astrophysics Data System (ADS)

    Gu, L.; Özdöl, V. B.; Sigle, W.; Koch, C. T.; Srot, V.; van Aken, P. A.

    2010-01-01

    Valence electron spectroscopic imaging (VESI) techniques, taking advantages of the energy-losses suffered by inelastic scattering of the fast electrons in the transmission electron microscope, offer an inherently high spatial resolution to characterize the electronic structure of materials close to the Fermi level. Here we demonstrate that the combination of an electron monochromator and a highly dispersive imaging energy filter, which has become available only recently, allows reliable measurements of local bandgaps on the nanometer scale. In addition, the correlations of structural, chemical, and optical properties can be revealed via VESI using monochromated electrons with a high spatial resolution.

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

    PubMed

    Kiener, Joos

    2013-12-11

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

  6. 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

  7. 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.

  8. Modifications of the chemical structure of phenolics differentially affect physiological activities in pulvinar cells of Mimosa pudica L. II. Influence of various molecular properties in relation to membrane transport.

    PubMed

    Rocher, Françoise; Roblin, Gabriel; Chollet, Jean-François

    2017-03-01

    Early prediction of compound absorption by cells is of considerable importance in the building of an integrated scheme describing the impact of a compound on intracellular biological processes. In this scope, we study the structure-activity relationships of several benzoic acid-related phenolics which are involved in many plant biological phenomena (growth, flowering, allelopathy, defense processes). Using the partial least squares (PLS) regression method, the impact of molecular descriptors that have been shown to play an important role concerning the uptake of pharmacologically active compounds by animal cells was analyzed in terms of the modification of membrane potential, variations in proton flux, and inhibition of the osmocontractile reaction of pulvinar cells of Mimosa pudica leaves. The hydrogen bond donors (HBD) and hydrogen bond acceptors (HBA), polar surface area (PSA), halogen ratio (Hal ratio), number of rotatable bonds (FRB), molar volume (MV), molecular weight (MW), and molar refractivity (MR) were considered in addition to two physicochemical properties (logD and the amount of non-dissociated form in relation to pKa). HBD + HBA and PSA predominantly impacted the three biological processes compared to the other descriptors. The coefficient of determination in the quantitative structure-activity relationship (QSAR) models indicated that a major part of the observed seismonasty inhibition and proton flux modification can be explained by the impact of these descriptors, whereas this was not the case for membrane potential variations. These results indicate that the transmembrane transport of the compounds is a predominant component. An increasing number of implicated descriptors as the biological processes become more complex may reflect their impacts on an increasing number of sites in the cell. The determination of the most efficient effectors may lead to a practical use to improve drugs in the control of microbial attacks on plants.

  9. VIPERdb: a relational database for structural virology

    PubMed Central

    Shepherd, Craig M.; Borelli, Ian A.; Lander, Gabriel; Natarajan, Padmaja; Siddavanahalli, Vinay; Bajaj, Chandrajit; Johnson, John E.; Brooks, Charles L.; Reddy, Vijay S.

    2006-01-01

    VIPERdb () is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry. PMID:16381893

  10. VIPERdb: a relational database for structural virology.

    PubMed

    Shepherd, Craig M; Borelli, Ian A; Lander, Gabriel; Natarajan, Padmaja; Siddavanahalli, Vinay; Bajaj, Chandrajit; Johnson, John E; Brooks, Charles L; Reddy, Vijay S

    2006-01-01

    VIPERdb (http://viperdb.scripps.edu) is a database for icosahedral virus capsid structures. Our aim is to provide a comprehensive resource specific to the needs of the structural virology community, with an emphasis on the description and comparison of derived data from structural and energetic analyses of capsids. A relational database implementation based on a schema for macromolecular structure makes the data highly accessible to the user, allowing detailed queries at the atomic level. Together with curation practices that maintain data uniformity, this will facilitate structural bioinformatics studies of virus capsids. User friendly search, visualization and educational tools on the website allow both structural and derived data to be examined easily and extensively. Links to relevant literature, sequence and taxonomy databases are provided for each entry.

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

    PubMed

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

    2013-09-01

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

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

    PubMed

    Jose, Deepthi; Datta, Ayan

    2014-02-18

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

  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 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.

  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. 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.

  18. 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.

  19. 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.

  20. Chemical and structural characterization of boron carbide powders and ceramics

    NASA Astrophysics Data System (ADS)

    Kuwelkar, Kanak Anant

    Boron carbide is the material of choice for lightweight armor applications due to its extreme hardness, high Young's modulus and low specific weight. The homogeneity range in boron carbide extends from 9 to 20 at% carbon with the solubility limits not uniquely defined in literature. Over the homogeneity range, the exact lattice positions of boron and carbon atoms have not been unambiguously established, and this topic has been the consideration of significant debate over the last 60 years. The atomic configuration and positions of the boron and carbon atoms play a key role in the crystal structure of the boron carbide phases. Depending on the atomic structure, boron carbide exhibits different mechanical properties which may alter its ballistic performance under extreme dynamic conditions. This work focusses on refinement and development of analytical and chemical methods for an accurate determination of the boron carbide stoichiometry. These methods were then utilized to link structural changes of boron carbide across the solubility range to variations in mechanical properties. After an extensive assessment of the currently employed characterization techniques, it was discerned that the largest source of uncertainty in the determination of the boron carbide stoichiometry was found to arise from the method utilized to evaluate the free carbon concentration. To this end, a modified spiking technique was introduced for free carbon determination where curve fitting techniques were employed to model the asymmetry of the 002 free carbon diffraction peak based on the amorphous, disordered and graphitic nature of carbon. A relationship was then established between the relative intensities of the carbon and boron carbide peaks to the percentage of added carbon and the free-carbon content was obtained by extrapolation. Samples with varying chemistry and high purity were synthesized across the solubility range by hot pressing mixtures of amorphous boron and boron carbide

  1. 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

  2. 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…

  3. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... salts, optical isomers, or salts of optical isomers, and therapeutically significant quantities of... include their salts, optical isomers, and salts of optical isomers. (ii) Scheduled listed chemical...

  4. 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

  5. Mapping Relational Structure in Spatial Reasoning

    ERIC Educational Resources Information Center

    Gattis, Merideth

    2004-01-01

    Three experiments investigated whether the similarity of relational structures influences the interpretation of spatial representations. Adults were shown diagrams of hand gestures paired with simple statements and asked to judge the meaning of new gestures. In Experiment 1 the gestures were paired with active declarative statements. In Experiment…

  6. 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...

  7. 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...

  8. 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.

  9. 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

  10. 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.

  11. Structural damage and chemical contaminants on reprocessed arthroscopic shaver blades.

    PubMed

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

    2009-02-01

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

  12. Designing ionic liquids: the chemical structure role in the toxicity.

    PubMed

    Ventura, Sónia P M; Gonçalves, Ana M M; Sintra, Tânia; Pereira, Joana L; Gonçalves, Fernando; Coutinho, João A P

    2013-01-01

    Ionic liquids (ILs) are a novel class of solvents with interesting physicochemical properties. Many different applications have been reported for ILs as alternatives to organic solvents in chemical and bioprocesses. Despite the argued advantage of having low vapor pressure, even the most hydrophobic ILs show some degree of solubility in water, allowing their dispersion into aquatic systems and raising concerns on its pollutant potential. Moreover, nowadays most widespread notion concerning the ILs toxicity is that there is a direct relationship with their hydrophobicity/lipophilicity. This work aims at enlarging the currently limited knowledge on ILs toxicity by addressing negative impacts in aquatic ecosystems and investigating the possibility of designing hydrophobic ILs of low ecotoxicity, by the manipulation of their chemical structures. The impact of aromaticity on the toxicity of different cations (pyridinium, piperidinium, pyrrolidinium and imidazolium) and hydrophobic anions (bis(trifluoromethylsulfonyl)imide [NTf(2)] and hexafluorophosphate [PF(6)]) was analysed. Concomitantly, several imidazolium-based ILs of the type [C( n )C( m )C( j )im][NTf(2)] were also studied to evaluate the effects of the position of the alkyl chain on the ILs' toxicity. For that purpose, standard assays were performed using organisms of different trophic levels, Vibrio fischeri, Pseudokirchneriella subcapitata and Daphnia magna, allowing to evaluate the consistency of the structure-activity relationships across different biological targets. The results here reported suggest the possibility of designing ILs with an enhanced hydrophobic character and lower toxicity, by elimination of their aromatic nature.

  13. 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.

  14. 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

  15. 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.

  16. Structuring medication related activities for information management.

    PubMed

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

    2014-01-01

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

  17. Using molecular equivalence numbers to visually explore structural features that distinguish chemical libraries.

    PubMed

    Xu, Yong-Jin; Johnson, Mark

    2002-01-01

    A molecular equivalence number (meqnum) classifies a molecule with respect to a class of structural features or topological shapes such as its cyclic system or its set of functional groups. Meqnums can be used to organize molecular structures into nonoverlapping, yet highly relatable classes. We illustrate the construction of some different types of meqnums and present via examples some methods of comparing diverse chemical libraries based on meqnums. In the examples we compare a library which is a random sample from the MDL Drug Data Report (MDDR) with a library which is a random sample from the Available Chemical Directory (ACD). In our analyses, we discover some interesting features of the topological shape of a molecule and its set of functional groups that are strongly linked with compounds occurring in the MDDR but not in the ACD. We also illustrate the utility of molecular equivalence indices in delineating the structural domain over which an SAR conclusion is valid.

  18. 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.

  19. 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.

  20. 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

  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. 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.

  3. 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

  4. 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...

  5. 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...

  6. Chemical structure determines target organ carcinogenesis in rats

    PubMed Central

    Carrasquer, C. A.; Malik, N.; States, G.; Qamar, S.; Cunningham, S.L.; Cunningham, A.R.

    2012-01-01

    SAR models were developed for 12 rat tumour sites using data derived from the Carcinogenic Potency Database. Essentially, the models fall into two categories: Target Site Carcinogen – Non-Carcinogen (TSC-NC) and Target Site Carcinogen – Non-Target Site Carcinogen (TSC-NTSC). The TSC-NC models were composed of active chemicals that were carcinogenic to a specific target site and inactive ones that were whole animal non-carcinogens. On the other hand, the TSC-NTSC models used an inactive category also composed of carcinogens but to any/all other sites but the target site. Leave one out validations produced an overall average concordance value for all 12 models of 0.77 for the TSC-NC models and 0.73 for the TSC-NTSC models. Overall, these findings suggest that while the TSC-NC models are able to distinguish between carcinogens and non-carcinogens, the TSC-NTSC models are identifying structural attributes that associate carcinogens to specific tumour sites. Since the TSC-NTSC models are composed of active and inactive compounds that are genotoxic and non-genotoxic carcinogens, the TSC-NTSC models may be capable of deciphering non-genotoxic mechanisms of carcinogenesis. Together, models of this type may also prove useful in anticancer drug development since they essentially contain chemicals moieties that target specific tumour site. PMID:23066888

  7. 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

  8. 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

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

    PubMed

    Spížek, Jaroslav; Řezanka, Tomáš

    2017-06-01

    Lincomycin and its derivatives are antibiotics exhibiting biological activity against bacteria, especially Gram-positive ones, and also protozoans. Lincomycin and its semi-synthetic chlorinated derivative clindamycin are widely used in clinical practice. Both antibiotics are bacteriostatic, inhibiting protein synthesis in sensitive bacteria; however, at higher concentrations, they may be bactericidal. Clindamycin is usually much more active than lincomycin in the treatment of bacterial infections, in particular those caused by anaerobic species; it can also be used for the treatment of important protozoal diseases, e.g. malaria, most effectively in combination with other antibiotic or non-antibiotic antimicrobials (primaquine, fosfidomycin, benzoyl peroxide). Chemical structures of lincosamide antibiotics and the biosynthesis of lincomycin and its genetic control have been summarized and described. Resistance to lincomycin and clindamycin may be caused by methylation of 23S ribosomal RNA, modification of the antibiotics by specific enzymes or active efflux from the bacterial cell. Copyright © 2016 Elsevier Inc. All rights reserved.

  10. 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.

  11. 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.

  12. 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.

  13. 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. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  14. 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%.

  15. 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.

  16. Bacterial community succession and chemical profiles of subtidal biofilms in relation to larval settlement of the polychaete Hydroides elegans.

    PubMed

    Chung, Hong Chun; Lee, On On; Huang, Yi-Li; Mok, Siu Yan; Kolter, Roberto; Qian, Pei-Yuan

    2010-06-01

    Earlier studies have shown that biofilms can mediate the larval settlement of the polychaete Hydroides elegans and that changes in the bacterial community structure and density of biofilms often alter the larval settlement response. However, the chemical cues that mediate this response remain unknown. In this study, both successional changes in the bacterial community structure and the chemical profiles of subtidal biofilms are described and related to the larval settlement response. Multispecies biofilms were developed on polystyrene Petri dishes and granite rock in the subtidal zone over a period of 20 days. The effects of the substratum and age on the bacterial community structure and chemical profiles of the biofilms were evaluated with two molecular methods (microarray (PhyloChip) and denaturing gradient gel electrophoresis) and with gas chromatography-mass spectrometry, respectively. Both age and substratum altered the bacterial community structures and chemical profiles of the biofilms. Age had a greater effect in shaping the bacterial community structure than did the substratum. In contrast, the type of substratum more strongly affected the chemical profile. Extracts of biofilms of different ages, which developed on different substrata, were tested for the settlement of H. elegans larvae. The extracts induced larval settlement in a biofilm-age-dependent manner, and extracts originating from different substrata of the same age showed no differences in larval settlement. Our results suggest that the larval settlement response cannot be predicted by the overall chemical composition of the biofilm alone.

  17. 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.

  18. 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.

  19. Chemical Abstracts as a resource for health and safety-related chemical information.

    PubMed

    Moody, R L; Zahm, B C

    1980-02-01

    Documents relevant to the health and safety of the worker or consumer exposed to chemicals or radiation extend over the entire range of the chemical disciplines, and therefore pertinent information can appear throughout the Chemical Abstracts Service information systems. Access routes to such information in both CAS printed publications and computer-readable services are discussed. In the weekly issues of Chemical Abstracts, health and safety information can be accessed through the natural-language Keyword Index. Retrieval of pertinent information through the controlled headings of the CA Volume Indexes in conjunction with the Index Guide is also discussed. CA Selects, a set of current-awareness publications, is described as it pertains to the specialized areas of health and safety.

  20. 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.

  1. 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.

  2. 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. Copyright © 2014 Elsevier Ltd. All rights reserved.

  3. Exotic differentiable structures and general relativity

    NASA Astrophysics Data System (ADS)

    Brans, Carl H.; Randall, Duane

    1993-02-01

    We review recent developments in differential topology with special concern for their possible significance to physical theories, especially general relativity. In particular we are concerned here with the discovery of the existence of non-standard (“fake” or “exotic”) differentiable structures on topologically simple manifolds such asS 7, ℝ4 andS 3 X ℝ1. Because of the technical difficulties involved in the smooth case, we begin with an easily understood toy example looking at the role which the choice of complex structures plays in the formulation of two-dimensional vacuum electrostatics. We then briefly review the mathematical formalisms involved with differentiable structures on topological manifolds, diffeomorphisms and their significance for physics. We summarize the important work of Milnor, Freedman, Donaldson, and others in developing exotic differentiable structures on well known topological manifolds. Finally, we discuss some of the geometric implications of these results and propose some conjectures on possible physical implications of these new manifolds which have never before been considered as physical models.

  4. 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

  5. Designing allosteric control into enzymes by chemical rescue of structure.

    PubMed

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

    2012-06-20

    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 β-glycosidase enzyme (β-gly) and W492G in a β-glucuronidase enzyme (β-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 β-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 β-gly W33G, which together establish the structural basis for enzyme inactivation and rescue. Finally, we use this designed switch to modulate β-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.

  6. 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.

  7. 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

  8. Structural analysis of photosystem I polypeptides using chemical crosslinking

    NASA Technical Reports Server (NTRS)

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

    1994-01-01

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

  9. 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.

  10. Limitations of Structural Superlubricity: Chemical Bonds versus Contact Size.

    PubMed

    Dietzel, Dirk; Brndiar, Ján; Štich, Ivan; Schirmeisen, André

    2017-08-22

    Structural superlubricity describes the state of virtually frictionless sliding if two atomically flat interfaces are incommensurate, that is, they share no common periodicity. Despite the exciting prospects of this low friction phenomenon, there are physical limitations to the existence of this state. Theory predicts that the contact size is one fundamental limit, where the critical size threshold mainly depends on the interplay between lateral contact compliance and interface interaction energies. Here we provide experimental evidence for this size threshold by measuring the sliding friction force of differently sized antimony particles on MoS2. We find that superlubric sliding with the characteristic linear decrease of shear stress with contact size prevails for small particles with contact areas below 15 000 nm(2). Larger particles, however, show a transition toward constant shear stress behavior. In contrast, Sb particles on graphite show superlubricity over the whole size range. Ab initio simulations reveal that the chemical interaction energies for Sb/MoS2 are much stronger than for Sb/HOPG and can therefore explain the different friction properties as well as the critical size thresholds. These limitations must be considered when designing low friction contacts based on structural superlubricity concepts.

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

    PubMed

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

    2011-11-15

    The structural assignment of new natural product molecules supports research in a multitude of disciplines that may lead to new therapeutic agents and or new understanding of disease biology. However, reports of numerous structural revisions, even of recently elucidated natural products, inspired the present survey of techniques used in structural misassignments and subsequent revisions in the context of constitutional or configurational errors. Given the comparatively recent development of marine natural products chemistry, coincident with modern spectroscopy, it is of interest to consider the relative roles of spectroscopy and chemical synthesis in the structure elucidation and revision of those marine natural products that were initially misassigned. Thus, a tabulated review of all marine natural product structural revisions from 2005 to 2010 is organized according to structural motif revised. Misassignments of constitution are more frequent than perhaps anticipated by reliance on HMBC and other advanced NMR experiments, especially when considering the full complement of all natural products. However, these techniques also feature prominently in structural revisions, specifically of marine natural products. Nevertheless, as is the case for revision of relative and absolute configuration, total synthesis is a proven partner for marine, as well as terrestrial, natural products structure elucidation. It also becomes apparent that considerable 'detective work' remains in structure elucidation, in spite of the spectacular advances in spectroscopic techniques. Copyright © 2011 Elsevier Ltd. All rights reserved.

  12. 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.

  13. 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.

  14. 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.

  15. 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...

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

    EPA Science Inventory

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

  17. 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...

  18. 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...

  19. Structural neuroimaging in sport-related concussion.

    PubMed

    Bigler, Erin D

    2017-09-12

    Structural neuroimaging of athletes who have sustained a sports-related concussion (SRC) can be viewed as either standard clinical imaging or with advanced neuroimaging methods that quantitatively assess brain structure. Negative findings from conventional computed tomography (CT) or magnetic resonance imaging (MRI) are the norm in SRC. Nonetheless, these conventional measures remain the first line of neuroimaging of the athlete as they do detect clinically significant pathologies, when present, such as hemorrhagic abnormalities in the form of hematomas, contusions and mircobleeds along with regions of focal encephalomalacia or other signal abnormalities, with CT best capable of detecting skull fractures. However, advanced neuroimaging techniques hold particular promise in detecting subtle neuropathology in the athlete which standard clinical neuroimaging cannot. To best understand what conventional as well as quantitative neuroimaging methods are detecting in SRC, this review begins by covering basic neuroanatomical principles associated with mild traumatic brain injury (mTBI) and the brain regions most vulnerable to injury from SRC, as these regions define where advanced neuroimaging methods most likely detect abnormalities. Advanced MRI techniques incorporate quantitative metrics that include volume, shape, thickness along with diffusion parameters that provide a more fine-grained analysis of brain structure. With advancements in image analysis, multiple quantitative neuroimaging metrics now can be utilized in assessing SRC. Such multimodality approaches are particularly relevant and important for assessing white matter and network integrity of the brain following injury, including SRC. This review focuses just on the structural side of neuroimaging in SRC, but these techniques also are being integrated with functional neuroimaging, where the combination of the two approaches may provide superior methods in assessing the pathological effects of SRC. Copyright

  20. 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.

  1. 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.

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

    PubMed Central

    Stan, Gheorghe; Gates, Richard S; Hu, Qichi; Kjoller, Kevin; Prater, Craig; Jit Singh, Kanwal; Mays, Ebony

    2017-01-01

    The exploitation of nanoscale size effects to create new nanostructured materials necessitates the development of an understanding of relationships between molecular structure, physical properties and material processing at the nanoscale. Numerous metrologies capable of thermal, mechanical, and electrical characterization at the nanoscale have been demonstrated over the past two decades. However, the ability to perform nanoscale molecular/chemical structure characterization has only been recently demonstrated with the advent of atomic-force-microscopy-based infrared spectroscopy (AFM-IR) and related techniques. Therefore, we have combined measurements of chemical structures with AFM-IR and of mechanical properties with contact resonance AFM (CR-AFM) to investigate the fabrication of 20–500 nm wide fin structures in a nanoporous organosilicate material. We show that by combining these two techniques, one can clearly observe variations of chemical structure and mechanical properties that correlate with the fabrication process and the feature size of the organosilicate fins. Specifically, we have observed an inverse correlation between the concentration of terminal organic groups and the stiffness of nanopatterned organosilicate fins. The selective removal of the organic component during etching results in a stiffness increase and reinsertion via chemical silylation results in a stiffness decrease. Examination of this effect as a function of fin width indicates that the loss of terminal organic groups and stiffness increase occur primarily at the exposed surfaces of the fins over a length scale of 10–20 nm. While the observed structure–property relationships are specific to organosilicates, we believe the combined demonstration of AFM-IR with CR-AFM should pave the way for a similar nanoscale characterization of other materials where the understanding of such relationships is essential. PMID:28503397

  3. [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.

  4. 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

  5. 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

  6. 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.

  7. 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.

  8. 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.

  9. 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…

  10. 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…

  11. 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.

  12. 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.

  13. 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...

  14. 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...

  15. Chemicals and Structural Foams to Neutralize or Defeat Anti-Personnel Mines

    DTIC Science & Technology

    1990-10-01

    AD-A256 739 Report# CTI/DAAK7089/002 II 711 _Comprehensive ITechnologies International CHEMICALS AND STRUCTURAL FOAMS II TO NEUTRALIZE OR DEFEAT...CTI/DAAK7089/002 _Cornprehensive Technologies - International CHEMICALS AND STRUCTURAL FOAMS TO NEUTRALIZE OR DEFEAT ANTI-PERSONNEL MINES TECHNICAL...study and analysis of chemical and structural foam products to determine if current technology could be used to defeat/ neutralize anti-personnel

  16. 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.

  17. Topochemical polymerization of dumbbell-shaped diacetylene monomers: relationship between chemical structure, molecular packing structure, and gelation property.

    PubMed

    Kim, Dae-Yoon; Lee, Sang-A; Jung, Daseal; Koo, Jahyeon; Soo Kim, Jin; Yu, Yeon-Tae; Lee, Cheul-Ro; Jeong, Kwang-Un

    2017-08-30

    Herein, we have synthesized novel photopolymerizable dumbbell-shaped diacetylene liquid crystal (LC) monomers by locating a diacetylene dicarboxylic acid group at the center and chemically connecting swallow-tails, such as hydrophobic alkyl chains (abbreviated as AT3DI) and amphiphilic biphenyl mesogens (abbreviated as BP3DI), with bisamide groups. Major phase transitions of dumbbell-shaped diacetylene monomers were identified using differential scanning calorimetry (DSC), polarized optical microscopy (POM), and Fourier transform infrared spectroscopy (FT IR). Molecular packing structures were studied based on structure-sensitive wide-angle X-ray diffraction (WAXD) and small-angle X-ray scattering (SAXS) analyses. Mainly, due to nanophase separations and strong intermolecular hydrogen bonding, AT3DI formed a low-ordered lamellar LC phase at room temperature. BP3DI self-assembled into highly-ordered crystal phases (K1 and K2) at lower temperatures below a low-ordered lamellar LC phase, in which BP3DI were intercalated with each other to compensate the mutual volume differences. From the photopolymerization of AT3DI and BP3DI, it was realized that the topochemical reactions of dumbbell-shaped diacetylene monomers were closely related to their chemical structures as well as molecular packing structures.

  18. The chemical structure of the Main-Belt

    NASA Astrophysics Data System (ADS)

    Carry, Benoit; DeMeo, Francesca

    2015-08-01

    The asteroid main belt between Mars and Jupiter holds evidences from the early Solar System history. The original chemical stratification of the accretion disk has been scrambled by planetary migrations, resulting in a radial mixing of compositions. Since the 1970s, spectral surveys have characterized the surface compositions of the largest members first, then of smaller bodies, slowly tapering into the size-frequency distribution. These surveys led to major discoveries, including the succession of dominating taxonomic classes along heliocentric distances, stained by the presence of interlopers in this over-arching structure. In the 2000s, these results have sustained the emergence of the current paradigm of Solar System formation: the Nice model, in which planets migrated from their formation locations to their current orbits.Since then, all-sky surveys in the visible and mid-infrared, the Sloan Digital Sky Survey and NASA WISE mission, have observed tens of thousands of asteroids, allowing characterization of their surface composition and estimation of their diameter. Simultaneously, our knowledge on asteroid density greatly improved: the sample of density determinations presented a tenfold increase. Such a rich dataset opened the possibility to scrutinize asteroid compositions to smaller sizes and to study the distribution of material in the main belt by mass, rather than by numbers. The picture resulting from these data go back over the previous view, and the few interlopers seem to be rule. The large scale structure seen on the largest bodies holds, but mixing increases at smaller sizes. This detailed picture supports the main results from recent dynamical models of planetary migration and radial mixing of smaller bodies, albeit several observed structures remain yet to be explained: numerous primitive D-type in the inner belt, apparently missing mantle counterpart (A-types) to the crustal and iron core-like (V- and M-types) material.Observational evidences

  19. 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

  20. 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.

  1. 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.

  2. 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.

  3. Relating transition-state spectroscopy to standard chemical spectroscopic processes

    NASA Astrophysics Data System (ADS)

    Reimers, Jeffrey R.; Hush, Noel S.

    2017-09-01

    Transition-state spectra are mapped out using generalized adiabatic electron-transfer theory. This simple model depicts diverse chemical properties, from aromaticity, through bound reactions such as isomerizations and atom-transfer processes with classic transition states, to processes often described as being ;non-adiabatic;, to those in the ;inverted; region that become slower as they are made more exothermic. Predictably, the Born-Oppenheimer approximation is found inadequate for modelling transition-state spectra in the weak-coupling limit. In this limit, the adiabatic Born-Huang approximation is found to perform much better than non-adiabatic surface-hopping approaches. Transition-state spectroscopy is shown to involve significant quantum entanglement between electronic and nuclear motion.

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

    PubMed

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

    2009-08-01

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

  5. Estrogenic activities of chemicals related to food contact plastics and rubbers tested by the yeast two-hybrid assay.

    PubMed

    Ogawa, Yuko; Kawamura, Yoko; Wakui, Chiseko; Mutsuga, Motoh; Nishimura, Tetsuji; Tanamoto, Kenichi

    2006-04-01

    Food contact plastics and rubbers possibly contain many kinds of chemicals such as monomers, oligomers, additives, degradation products of polymers and additives, and impurities. Among them, bisphenol A, nonylphenol, benzylbutyl phthalate, styrene oligomers and hydroxylated benzophenones have been reported to possess estrogenic activities. In this study, other chemicals related to food contact plastics and rubbers, and their metabolites induced by the S9-mixture were tested for their estrogenic activities using the yeast two-hybrid assay. Among the 150 chemicals, 10 chemicals such as bis(4-hydroxyphenyl) methane, 4-cyclohexylphenol, 4-phenylphenol, 4,4'-isopropylidenediphenol alkylphosphite, two type of styrenated phenol (including mono type), tris(nonylphenyl) phosphite, 2,2'-dihydroxy-4-methoxybenzophenone, 2-hydroxy-4-methoxybenzophenone and 2,4-diphenyl-4-methyl-1-pentene, their metabolites and the metabolites of 6 other chemicals, such as 2-(phenylmethyl) phenol, styrenated phenol (di and tri type), 1-(N-phenylamino)naphthalene, 4-tert-butylphenylsalicylate, nonylphenol ethoxylates and 2-methyl-6-tert-butylphenol, displayed estrogenic activities. All of them contained a phenol group in their chemical structures or formed one easily by hydrolysis or metabolism. However, most of the chemicals related to food contact plastics and rubbers, and their metabolites did not show any estrogenicity.

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. Human Metabolism and Interactions of Deployment-Related Chemicals

    DTIC Science & Technology

    2003-08-01

    into the reactive terone or chlorpyrifos metabolism are consistent with the form, aflatoxin B1 -8, 9-epoxide, which is a mutagen (Gal- very recent report...DL (1996) The kinetics of microsomal cytochrome P450 monooxygenasa: structural adaptations for main- aflatoxin B1 oxidation by human eDNA-expressed...toxicity after exposure to OP insecticides. In indicating that the M445T mutation has no effect on testos- addition, CYP3A4 can activate aflatoxin B

  14. 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 ...

  15. 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)

  16. 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 ...

  17. 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)

  18. 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

  19. A structured strategy for assessing chemical risks, suitable for small and medium-sized enterprises.

    PubMed

    Balsat, A; de Graeve, J; Mairiaux, P

    2003-10-01

    A previous study carried out in 20 Belgian companies, especially small and medium-sized enterprises (SMEs), showed that prevention advisors did not use any structured approaches to assess chemical risk. They used their personal judgement and the information contained in manufacturers' Safety Data Sheets to assess the risk. The purpose of the Regetox network is to provide companies with a global approach for assessing chemical health risks. The structured approach proposed consists of two successive steps of increasing complexity. For the first step, we chose a method developed by the INRS (France), the 'ranking of potential risk', which allows the safety officer or staff member to identify hazards and to set priorities among all the supplied products used in the workplace. For the second step, we applied the COSHH method and EASE model established by the UK Health & Safety Executive for assessing 'chemical risk by reference to occupational exposure limits'. The INRS and COSHH Essentials methods were chosen because they define hazards using R-phrases of the European classification system and assess the exposure by using simple information that is easy to collect in the workplace and toxicological databases. A feasibility study conducted in two enterprises shows the usefulness of this approach. In addition to the intrinsic limitations of the methods, the approach showed some limitations related to the inaccuracy of the manufactured safety data sheets and to the collection of the basic information needed for ranking potential risks. The use of the Regetox approach needs training of prevention advisors and a strategy involving employers, staff members and workers in collecting basic information and managing chemical risks. Under these conditions, Regetox seems to be a useful tool for chemical risk assessment in SMEs.

  20. 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...

  1. 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...

  2. 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.

  3. 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.

  4. 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

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

    PubMed

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

    2015-01-01

    Wikipedia, the world's largest and most popular encyclopedia is an indispensable source of chemistry information. It contains among others also entries for over 15,000 chemicals including metabolites, drugs, agrochemicals and industrial chemicals. To provide an easy access to this wealth of information we decided to develop a substructure and similarity search tool for chemical structures referenced in Wikipedia. We extracted chemical structures from entries in Wikipedia and implemented a web system allowing structure and similarity searching on these data. The whole search as well as visualization system is written in JavaScript and therefore can run locally within a web page and does not require a central server. The Wikipedia Chemical Structure Explorer is accessible on-line at www.cheminfo.org/wikipedia and is available also as an open source project from GitHub for local installation. The web-based Wikipedia Chemical Structure Explorer provides a useful resource for research as well as for chemical education enabling both researchers and students easy and user friendly chemistry searching and identification of relevant information in Wikipedia. The tool can also help to improve quality of chemical entries in Wikipedia by providing potential contributors regularly updated list of entries with problematic structures. And last but not least this search system is a nice example of how the modern web technology can be applied in the field of cheminformatics. Graphical abstractWikipedia Chemical Structure Explorer allows substructure and similarity searches on molecules referenced in Wikipedia.

  6. Light Scattering from Systems with Chemical Oscillations and Dissipative Structures.

    DTIC Science & Technology

    splitting in the chemical lines and dispersive (non-Lorentzian) contributions. Two model reaction mechanisms, the Volterra - Lotka model and the Prigogine-Lefever model, are examined in detail. (Author)

  7. From Structural Complexity to Structure-Property Relationships in Intermetallics: Development of Density Functional Theory-Chemical Pressure Analysis

    NASA Astrophysics Data System (ADS)

    Engelkemier, Joshua

    away from each other (negative CP). This technique is used in combination with the concept of structural plasticity (Berns, 2014) to demonstrate how complex intermetallic phases can be understood as a response of simpler structure types to the destabilizing buildup of CP. From this point of view, interfaces created in complex structures relieve the CP manifest in the more basic, parent structures. This is shown specifically for Ca36Sn23 relative to a hypothetical W5Si3-type Ca5Sn3 phase, LnMn xGa3 (Ln = Ho-Tm, x < 0.15) compared to unstuffed AuCu3-type LnGa3 structures, and structural derivatives of CaCu5- and HoCoGa5-type compounds. As a direct result of the technical developments necessitated by these analyses on structural complexity in intermetallics, a further connection is made in this thesis between the calculated CP schemes and the frequencies of vibrational modes in MgCu2-type CaPd2, the Cr 3Si-type superconductor Nb3Ge, and CaCu5-type CaPd5. Local chemical interactions revealed by DFT-CP analysis are used to identify structure-property relationships for the pseudogap in the phonon density of states (DOS) of CaPd2, the higher critical temperature of Nb3Ge vs. Nb3Sn, and the wide diversity of structures based on the CaCu5 type.

  8. 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

  9. 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.

  10. 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

  11. 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.

  12. A probabilistic model for secondary structure prediction from protein chemical shifts.

    PubMed

    Mechelke, Martin; Habeck, Michael

    2013-06-01

    Protein chemical shifts encode detailed structural information that is difficult and computationally costly to describe at a fundamental level. Statistical and machine learning approaches have been used to infer correlations between chemical shifts and secondary structure from experimental chemical shifts. These methods range from simple statistics such as the chemical shift index to complex methods using neural networks. Notwithstanding their higher accuracy, more complex approaches tend to obscure the relationship between secondary structure and chemical shift and often involve many parameters that need to be trained. We present hidden Markov models (HMMs) with Gaussian emission probabilities to model the dependence between protein chemical shifts and secondary structure. The continuous emission probabilities are modeled as conditional probabilities for a given amino acid and secondary structure type. Using these distributions as outputs of first- and second-order HMMs, we achieve a prediction accuracy of 82.3%, which is competitive with existing methods for predicting secondary structure from protein chemical shifts. Incorporation of sequence-based secondary structure prediction into our HMM improves the prediction accuracy to 84.0%. Our findings suggest that an HMM with correlated Gaussian distributions conditioned on the secondary structure provides an adequate generative model of chemical shifts. Copyright © 2013 Wiley Periodicals, Inc.

  13. Factors affecting the use of 13Cα chemical shifts to determine, refine, and validate protein structures

    PubMed Central

    Vila, Jorge A.; Scheraga, Harold A.

    2008-01-01

    Interest centers here on the analysis of two different, but related, phenomena that affect side-chain conformations and consequently 13Cα chemical shifts and their applications to determine, refine, and validate protein structures. The first is whether 13Cα chemical shifts, computed at the DFT level of approximation with charged residues is a better approximation of observed 13Cα chemical shifts than those computed with neutral residues for proteins in solution. Accurate computation of 13Cα chemical shifts requires a proper representation of the charges, which might not take on integral values. For this analysis, the charges for 139 conformations of the protein ubiquitin were determined by explicit consideration of protein binding equilibria, at a given pH, that is, by exploring the 2ξ possible ionization states of the whole molecule, with ξ being the number of ionizable groups. The results of this analysis, as revealed by the shielding/deshield-ing of the 13Cα nucleus, indicated that: (i) there is a significant difference in the computed 13Cα chemical shifts, between basic and acidic groups, as a function of the degree of charge of the side chain; (ii) this difference is attributed to the distance between the ionizable groups and the 13Cα nucleus, which is shorter for the acidic Asp and Glu groups as compared with that for the basic Lys and Arg groups; and (iii) the use of neutral, rather than charged, basic and acidic groups is a better approximation of the observed 13Cα chemical shifts of a protein in solution. The second is how side-chain flexibility influences computed 13Cα chemical shifts in an additional set of ubiquitin conformations, in which the side chains are generated from an NMR-derived structure with the backbone conformation assumed to be fixed. The 13Cα chemical shift of a given amino acid residue in a protein is determined, mainly, by its own backbone and side-chain torsional angles, independent of the neighboring residues; the

  14. 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.

  15. 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.

  16. 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

  17. 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

  18. 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. © 2014 Society for Laboratory Automation and Screening.

  19. The Relationship Between Chemical Structure and Dielectric Properties of Plasma-Enhanced Chemical Vapor Deposited Polymer Thin Films (Postprint)

    DTIC Science & Technology

    2007-01-01

    Materials Sci & Tech Applications, LLC) N. Venkatasubramanian and John T. Grant (University of Dayton) Kurt Eyink, Jesse Enlow, and Timothy J. Bunning...structure and dielectric properties of plasma-enhanced chemical vapor deposited polymer thin films Hao Jiang b,⁎, Lianggou Hong b, N. Venkatasubramanian c

  20. Band structure engineering strategies of metal oxide semiconductor nanowires and related nanostructures: A review

    NASA Astrophysics Data System (ADS)

    Piyadasa, Adimali; Wang, Sibo; Gao, Pu-Xian

    2017-07-01

    The electronic band structure of a solid state semiconductor determines many of its physical and chemical characteristics such as electrical, optical, physicochemical, and catalytic activity. Alteration or modification of the band structure could lead to significant changes in these physical and chemical characteristics, therefore we introduce new mechanisms of creating novel solid state materials with interesting properties. Over the past three decades, research on band structure engineering has allowed development of various methods to modify the band structure of engineered materials. Compared to bulk counterparts, nanostructures generally exhibit higher band structure modulation capabilities due to the quantum confinement effect, prominent surface effect, and higher strain limit. In this review we will discuss various band structure engineering strategies in semiconductor nanowires and other related nanostructures, mostly focusing on metal oxide systems. Several important strategies of band structure modulation are discussed in detail, such as doping, alloying, straining, interface and core-shell nanostructuring.

  1. 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

  2. An Investigative Study of Safety Management Practices in Chemical-Related Industries

    NASA Astrophysics Data System (ADS)

    Lewers, Sarah Grace

    Industrial chemicals are a major part of the United States economic growth and impact every product that we use in everyday life. Some of the major products produced by chemical-related industries are plastics, textiles, petroleum, paper and important metals. Governmental regulations like those created by the Occupational Safety and Health Organization (OSHA), Environmental Protection Agency (EPA) and the U.S. Chemical Safety and Hazard Investigation Board are vital to a chemical-related industries' safety management. Contributing to and helping to drive economic growth, the enforcement of proper safety practices is a necessity. This study was conducted to investigate and assess various safety management practices in selected chemical-related industries. The research design involved the use of a questionnaire/survey method in which a random sample of participants completed a questionnaire related to the variables of interest. Random sampling helps to ensure the generalizability of the survey results. The target population consisted of a subset of employees currently working for plants, businesses and organizations in chemical-related industries. To collect the data, surveys were given to employees in various positions at chemical-related industries such as basic chemicals, specialty chemicals, agricultural chemicals, pharmaceuticals and consumer products. A set of criteria was created to establish the qualification to be recognized as a chemical-related industry. The questionnaire/survey was reviewed by the Institutional Review Board at NC A&T State University to meet necessary regulation guidelines for research involving human subjects. The results showed that 60.22% or more than half of the respondents have worked with their company and organization for over thirty years providing the ability to see the progression of chemical-related industry safety management practices over time. Over eighty percent (80.66%) or 146 respondents agreed that their company or

  3. 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

  4. 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."

  5. 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.

  6. The resource economics of chemical and structural defenses across nitrogen supply gradients.

    PubMed

    Craine, Joseph; Bond, William; Lee, William G; Reich, Peter B; Ollinger, Scott

    2003-12-01

    In order to better understand the role of nutrient supplies in determining the prevalence of plant defense types, we investigated the theoretical relationships between ecosystem N supply and the net C gain of shoots that were undefended or defended in one of three ways: (1) by N-free chemical compounds, (2) by N-containing chemical compounds, or (3) by structural defenses. By extending economic models of shoot resource balance to include the relative value of C and N, depreciation, and amortization, we were able to show that the relative net C gain of the three defense types were similar to changes in their generally understood abundance along an N supply gradient. At low N supply, the additional C acquired when investing C in defense is much higher than investing N in defenses. Only at high N supply is it better to invest large quantities of N in defense rather than additional photosynthesis. In a sensitivity analysis, net C gain of shoots was most sensitive to factors that affect the relative value of C and N and the rate of herbivory. Although there is support for the relative value of C and N influencing defense strategies, more research is necessary to understand why tannins are not more prevalent at high N supply and why moderate amounts of N-based defenses are not used at low N supply.

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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. Copyright © 2013 Elsevier Inc. All rights reserved.

  12. 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)

  13. 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...

  14. 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...

  15. 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…

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

    PubMed

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens.

  17. 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

  18. Identification of novel thyroid cancer-related genes and chemicals using shortest path algorithm.

    PubMed

    Jiang, Yang; Zhang, Peiwei; Li, Li-Peng; He, Yi-Chun; Gao, Ru-jian; Gao, Yu-Fei

    2015-01-01

    Thyroid cancer is a typical endocrine malignancy. In the past three decades, the continued growth of its incidence has made it urgent to design effective treatments to treat this disease. To this end, it is necessary to uncover the mechanism underlying this disease. Identification of thyroid cancer-related genes and chemicals is helpful to understand the mechanism of thyroid cancer. In this study, we generalized some previous methods to discover both disease genes and chemicals. The method was based on shortest path algorithm and applied to discover novel thyroid cancer-related genes and chemicals. The analysis of the final obtained genes and chemicals suggests that some of them are crucial to the formation and development of thyroid cancer. It is indicated that the proposed method is effective for the discovery of novel disease genes and chemicals.

  19. Three-dimensional structure of bidirectional, excitatory chemical synapses in the jellyfish Cyanea capillata.

    PubMed

    Anderson, P A; Grünert, U

    1988-01-01

    Neurons in the ectoderm of the perirhopalial tissue of the jellyfish Cyanea capillata were exposed and fixed for electron microscopy under conditions designed to minimize exocytosis of synaptic vesicles. The structure of the bidirectional chemical synapses that connect neurons was examined and the three-dimensional organization of these synapses was determined from reconstructions of serial sections. Synapses were characterized by the accumulation of a relatively few, large synaptic vesicles. These lie in a single layer against the terminal membrane of each terminal. The cytoplasmic side of the vesicles in any one terminal was covered by a single, large, perforated cisternal sheet. In addition, there were numerous smaller, bulbous cisternae that intermingled with the vesicles in the terminal. The structure of any one terminal was mirrored by that of the opposite terminal of the pair. The organization of these synapses is discussed from the viewpoint of cnidarian synapses in general.

  20. 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

  1. 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.

  2. 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

  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. 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.

  5. 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.

  6. 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.

  7. 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.

  8. 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.

  9. Role of chemical potential in relaxation of faceted crystal structure

    NASA Astrophysics Data System (ADS)

    Schneider, Joshua P.; Nakamura, Kanna; Margetis, Dionisios

    2014-06-01

    Below the roughening transition, crystal surfaces have macroscopic plateaus, facets, whose evolution is driven by the microscale dynamics of steps. A long-standing puzzle was how to reconcile discrete effects in facet motion with fully continuum approaches. We propose a resolution of this issue via connecting, through a jump condition, the continuum-scale surface chemical potential away from the facet, characterized by variations of the continuum surface free energy, with a chemical potential originating from the decay of atomic steps on top of the facet. The proposed condition accounts for step flow inside a discrete boundary layer near the facet. To validate this approach, we implement in a radial geometry a hybrid discrete-continuum scheme in which the continuum theory is coupled with only a few, minimally three, steps in diffusion-limited kinetics with conical initial data.

  10. 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.

  11. 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.

  12. 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.

  13. 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

  14. 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.

  15. Wavy carbon: A new series of carbon structures explored by quantum chemical calculations

    NASA Astrophysics Data System (ADS)

    Ohno, Koichi; Satoh, Hiroko; Iwamoto, Takeaki; Tokoyama, Hiroaki; Yamakado, Hideo

    2015-10-01

    A new carbon family adopting wavy structures has been found by quantum chemical calculations. The key motif of this family is a condensed four-membered ring. Periodically wavy-carbon sheets (wavy-Cn sheets, n = 2, 6, and 8) as well as wavy-C36 tube were found to be very similar to the previously reported prism-Cn carbon tubes (n = 5, 6, and 8) in several respects, including the relative energies per one carbon atom with respect to graphene, CC bond lengths, and CCC bond angles. Because of very high relative energies with respect to graphene (206-253 kJ mol-1), the wavy-carbons may behave as energy reserving materials.

  16. 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

  17. Projective structure and holonomy in general relativity

    NASA Astrophysics Data System (ADS)

    Hall, G. S.; Lonie, D. P.

    2011-04-01

    This review presents a study of the situation when two spacetimes admit the same (unparametrized) geodesics, that is, when they are projectively related. The solution is based on the curvature class and the holonomy type of a spacetime and it transpires that all holonomy possibilities can be solved except the most general one and that the consequence of two spacetimes being projectively related leads, in many cases, to their associated Levi-Civita connections being identical. Some results are also given regarding the general case. It is also shown that the holonomy types of projectively related spacetimes are very closely related. The theory is then applied, with Einstein's principle of equivalence in mind, to 'generic' spacetimes.

  18. 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.

  19. 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

  20. 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

  1. 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.

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

    PubMed

    Cheng, Daojian; Yuan, Shuai; Ferrando, Riccardo

    2013-09-04

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

  3. In silico quantitative structure toxicity relationship of chemical compounds: some case studies.

    PubMed

    Deeb, Omar; Goodarzi, Mohammad

    2012-09-01

    Undesirable toxicity is still a major block in the drug discovery process. Obviously, capable techniques that identify poor effects at a very early stage of product development and provide reasonable toxicity estimates for the huge number of untested compounds are needed. In silico techniques are very useful for this purpose, because of their advantage in reducing time and cost. These case studies give the description of in silico validation techniques and applied modeling methods for the prediction of toxicity of chemical compounds. In silico toxicity prediction techniques can be classified into two categories: Molecular Modeling and methods that derive predictions from experimental data. Molecular modeling is a computational approach to mimic the behavior of molecules, from small molecules (e.g. in conformational analysis) to biomolecules. But the same approaches can also be applied for toxicological purposes, if the mechanism is receptor mediated. Quantitative Structure-Toxicity Relationships (QSTRs) models are typical examples for the prediction of toxicity which relates variations in the molecular structures to toxicity. There are many applied modeling techniques in QSTR such as Partial Least Squares, Artificial Neural Networks, and Principal Component Regression (PCR). The applicability of these techniques in predictive toxicology will be discussed with different examples of sets of chemical compounds.

  4. 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…

  5. 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…

  6. Chemical thermodynamics and elements of structure in oxide melts

    NASA Astrophysics Data System (ADS)

    Novikov, V. K.; Spiridonov, M. A.; Sangalova, I. S.

    2008-02-01

    The data analysis has shown that various structural elements of an oxide melt influence on a concrete property of a system differently. It is interesting to extract the elements with dominating influence on each property and elements with the negligible effect. We show that monomers SiO44- and ring structures Si4O128- do not influence neither on density, nor on the surface tension of the PbO-SiO2 system.

  7. The modeling of the chemical composition and structural transformations in electrode pitches

    SciTech Connect

    Turenko, F.P.; Bochkareva, N.N.

    1984-01-01

    A new method is proposed for studying the composition and physicochemical transformations in pitches - chemical modeling. Correlation relationships have been found between thermochemical properties and composition. A chemical classification of electrode pitches on statistical models is given. The structural transformations taking place on the thermostating of medium-temperature pitches have been shown.

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

    Treesearch

    Nicole Labbe; David Harper; Timothy Rials; Thomas Elder

    2006-01-01

    In this work, the effect of temperature on charcoal structure and chemical composition is investigated for four tree species. Wood charcoal carbonized at various temperatures is analyzed by mid infrared spectroscopy coupled with multivariate analysis and by thermogravimetric analysis to characterize the chemical composition during the carbonization process. The...

  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. 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.

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

    PubMed Central

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

    2015-01-01

    Oxygen is an important element in most biologically significant molecules and experimental solid-state 17O NMR studies have provided numerous useful structural probes to study these systems. However, computational predictions of solid-state 17O NMR chemical shift tensor properties are still challenging in many cases and in particular each of the prior computational work is basically limited to one type of oxygen-containing systems. This work provides the first systematic study of the effects of geometry refinement, method and basis sets for metal and non-metal 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 17O NMR chemical shifts in organic and organometallic compounds. A number of computational factors towards relatively general and accurate predictions of 17O NMR chemical shifts were studied to provide helpful and detailed suggestions for future work. For the studied various kinds of oxygen-containing compounds, the best computational approach results in a theory-versus-experiment correlation coefficient R2 of 0.9880 and mean absolute deviation of 13 ppm (1.9% of the experimental range) for isotropic NMR shifts and R2 of 0.9926 for all shift tensor properties. These results shall facilitate future computational studies of 17O NMR chemical shifts in many biologically relevant systems, and the high accuracy may also help refinement and determination of active-site structures of some oxygen-containing substrate bound proteins. PMID:26274812

  13. 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.

  14. 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.

  15. 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.

  16. 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)

  17. 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...

  18. 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...

  19. 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)

  20. 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...

  1. 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...

  2. Synoptic Mapping of Chemical Composition, Thermal Structure, and Air Motion from UARS Observations

    NASA Technical Reports Server (NTRS)

    Salby, Murry L.

    1999-01-01

    An operational mapping algorithm was developed to process measurements of individual species observed by different satellite instruments on board UARS. Based on Fast Fourier Synoptic Mapping (FFSM), the algorithm accounts for the precessing orbit of UARS, the error of individual instruments, and gaps associated with instrument duty cycle and the satellite yaw maneuver. It provides synoptic structure and evolution on periods as short as 1 day, derived collectively from all observations of an individual species. The algorithm was applied to synoptically map temperature, thickness, and several chemical constituents observed by the instruments: MLS, CLAES, ISAMS, and HALOE. Each field variable observed by these instruments was mapped twice-daily in continuous global time series several months long. Mapped behavior produced via FFSM was compared against standard archived products generated via Kalman filtering. The standard map products reveal similar behavior, but are limited to features of larger scale. Tracer structure that develops through flow deformation and attending transport is therefore represented in those products more coarsely, eventually being sheared down to scales that are no longer represented properly. The synoptic time series also reveal a diurnal cycle for several of the constituents, one that emerges clearly in their space-time spectra. The zonal and meridional structure of diurnal variability was mapped by filtering the space-time spectrum, an intermediate product of FFSM, to those scales resolved by the UARS sampling. Geographical variations of the diurnal cycle have also been evaluated in its seasonal-mean structure by compositing distributions at individual local times. Both were compared to diurnal variations in chemical models and in dynamical models that account for transport by the diurnal tide. Diurnal variations were found to introduce spurious behavior into the archived products generated via Kalman filtering, behavior that is

  3. 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.

  4. 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.

  5. Structural and dynamical properties of water on chemically modified surfaces: The role of the instantaneous surface

    NASA Astrophysics Data System (ADS)

    Bekele, Selemon; Tsige, Mesfin

    Surfaces of polymers such as atactic polystyrene (aPS) represent very good model systems for amorphous material surfaces. Such polymer surfaces are usually modified either chemically or physically for a wide range of applications that include friction, lubrication and adhesion. It is thus quite important to understand the structural and dynamical properties of liquids that come in contact with them to achieve the desired functional properties. Using molecular dynamics (MD) simulations, we investigate the structural and dynamical properties of water molecules in a slab of water in contact with atactic polystyrene surfaces of varying polarity. We find that the density of water molecules and the number distribution of hydrogen bonds as a function of distance relative to an instantaneous surface exhibit a structure indicative of a layering of water molecules near the water/PS interface. For the dynamics, we use time correlation functions of hydrogen bonds and the incoherent structure function for the water molecules. Our results indicate that the polarity of the surface dramatically affects the dynamics of the interfacial water molecules with the dynamics slowing down with increasing polarity. This work was supported by NSF Grant DMR1410290.

  6. 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.

  7. 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

  8. 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.

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

    PubMed Central

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

    2011-01-01

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

  10. 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.

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

    PubMed Central

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

    2014-01-01

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

  12. 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

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

    PubMed

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

    2016-07-19

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

  14. Quantum chemical modeling of UV Spectra of Polyurethane Structural Fragments

    NASA Astrophysics Data System (ADS)

    Ksenofontov, M. A.; Umreiko, D. S.; Shundalau, M. B.

    2012-07-01

    Results of TDDFT calculations of characteristics for excited singlet states of mono- and diisocyanates and carbamates containing from one to three phenyl groups are presented. The influence of the structural composition of the isocyanate/carbamate on the formation of its UV absorption spectrum was analyzed.

  15. 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

  16. 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.

  17. 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...

  18. 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.

  19. 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...

  20. Surface Nano-Structuring by Adsorption and Chemical Reactions

    PubMed Central

    Tanaka, Ken-ichi

    2010-01-01

    Nano-structuring of the surface caused by adsorption of molecules or atoms and by the reaction of surface atoms with adsorbed species is reviewed from a chemistry viewpoint. Self-assembly of adsorbed species is markedly influenced by weak mutual interactions and the local strain of the surface induced by the adsorption. Nano-structuring taking place on the surface is well explained by the notion of a quasi-molecule provided by the reaction of surface atoms with adsorbed species. Self-assembly of quasi-molecules by weak internal bonding provides quasi-compounds on a specific surface. Various nano-structuring phenomena are discussed: (i) self-assembly of adsorbed molecules and atoms; (ii) self-assembly of quasi-compounds; (iii) formation of nano-composite surfaces; (iv) controlled growth of nano-materials on composite surfaces. Nano-structuring processes are not always controlled by energetic feasibility, that is, the formation of nano-composite surface and the growth of nano-particles on surfaces are often controlled by the kinetics. The idea of the “kinetic controlled molding” might be valuable to design nano-materials on surfaces. PMID:28883340

  1. 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

  2. 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...

  3. 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...

  4. 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.

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

    PubMed Central

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

    2016-01-01

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

  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

    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.

  7. 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.

  8. 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.

  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

    2012-06-26

    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.

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

    DOEpatents

    Chiang, Yet-Ming [Framingham, MA; Moorehead, William Douglas [Virginia Beach, VA

    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.

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

    DOEpatents

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

    DOEpatents

    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.

  13. 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...

  14. 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...

  15. 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.

  16. 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

  17. 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.

  18. A quantum chemical study of novel carbon structures: Prism carbon tubes

    NASA Astrophysics Data System (ADS)

    Ohno, Koichi; Tokoyama, Hiroaki; Yamakado, Hideo

    2015-08-01

    A new carbon family with prism-Cn (n = 3-8, 10, 12, 14, 16, 18, and 20) tube structures has been found by quantum chemical calculations. Periodically and axially piled regular polygons were optimized into the prism-Cn tubes, in which all carbon atoms are equivalent and connected with four single bonds of 0.153-0.161 nm. The relative energies per one carbon atom with respect to graphene are 218-354 kJ mol-1. The lowest energy barriers of tri[4]prismane and tri[6]prismane with similar prism-tube skeletons were found to be ca. 80 kJ mol-1, which gives an expectation that carbon skeletons of the prism-Cn tubes are also stable.

  19. 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

  20. Chemical structures, production and enzymatic transformations of sapogenins and saponins from Centella asiatica (L.) Urban.

    PubMed

    Azerad, Robert

    2016-10-01

    Centella asiatica (L.) Urban is a medicinal herb traditionally used in Asiatic countries for its multiple therapeutic properties, essentially due to its accumulation of specific pentacylic triterpenoid saponins, mainly asiaticoside and madecassoside and the corresponding sapogenins. This review summarizes the updated knowledge about the chemical structures of about forty centelloids, found as minor metabolites in Centella, and all derived from ursane and oleane ring patterns. Similarly, the most recent genetic and enzymatic features involved in their biosynthesis is reviewed, in relation with their biotechnological production developed, either from in vitro plant cultures or undifferentiated cells, in order to be independent of natural sources and to provide a continuous and reliable source of centelloids. Finally, a short survey of the biotransformations of some centelloids, either in animal, human or microorganisms is reviewed. Copyright © 2016. Published by Elsevier B.V.

  1. 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.

  2. 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.

  3. 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

  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. Brazilian kefir: structure, microbial communities and chemical composition

    PubMed Central

    Magalhães, Karina Teixeira; de Melo Pereira, Gilberto Vinícius; Campos, Cássia Roberta; Dragone, Giuliano; Schwan, Rosane Freitas

    2011-01-01

    Microbial ecology and chemical composition of Brazilian kefir beverage was performed. The microorganisms associated with Brazilian kefir were investigated using a combination of phenotypic and genotypic methods. A total of 359 microbial isolates were identified. Lactic acid bacteria (60.5%) were the major isolated group identified, followed by yeasts (30.6%) and acetic acid bacteria (8.9%). Lactobacillus paracasei (89 isolates), Lactobacillus parabuchneri (41 isolates), Lactobacillus casei (32 isolates), Lactobacillus kefiri (31 isolates), Lactococcus lactis (24 isolates), Acetobacter lovaniensis (32 isolates), Kluyveromyces lactis (31 isolates), Kazachstania aerobia (23 isolates), Saccharomyces cerevisiae (41 isolates) and Lachancea meyersii (15 isolates) were the microbial species isolated. Scanning electron microscopy showed that the microbiota was dominated by bacilli (short and curved long) cells growing in close association with lemon-shaped yeasts cells. During the 24 h of fermentation, the protein content increased, while lactose and fat content decreased. The concentration of lactic acid ranged from 1.4 to 17.4 mg/ml, and that of acetic acid increased from 2.1 to 2.73 mg/ml. The production of ethanol was limited, reaching a final mean value of 0.5 mg/ml. PMID:24031681

  7. 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.

  8. Multistable Phase Patterns of Spatially Structured Chemical Oscillators

    NASA Astrophysics Data System (ADS)

    Giver, Michael; Goldstein, Daniel; Chakraborty, Bulbul

    2014-03-01

    Recent experiments of two-dimensional microfluidic arrays of droplets containing Belousov-Zhabotinsky reactants show a rich variety of spatio-temporal patterns. Using optical techniques a variety of boundary conditions can be set within the system, including finite rings of droplets. These experiments have provided an interesting and easily reproducible system for probing the effects of nonlinearities and fluctuations in a spatially extended system. Motivated by this experimental set up, we study a simple model of chemical oscillators in the highly nonlinear excitable regime in order to gain insight into the mechanism giving rise to the observed multistable attractors. We map the attractor space of a simple two species activator-inhibitor model coupled via three different coupling mechanism: simple inhibitor diffusion, inhibitor diffusion through an inhomogenous medium where active droplets are separated by inactive holding cells, and coupling through diffusion of an inert signaling species, which arrises through a coarse graining of the inhomogenous medium. Once the attractor space of the mean-field level model has been mapped, we check the robustness of the attractors when subject to intrinsic noise.

  9. 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.

  10. 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

  11. 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.

  12. Chemical thermodynamics of systemic self-organization towards life by nano-structured cosmic dust particles

    NASA Astrophysics Data System (ADS)

    Krueger, F. R.; Kissel, J.

    2001-08-01

    Self-organization of chemicals to living systems demands for several necessary conditions as derived from far-from-equilibrium thermodynamics. Autopoesis is not just self-replication of systems, but is orbital stability of growth, variability, and self-replication. Physically, this means a reaction-diffusion space-time boundary (in/out) problem. The solutions of such a system of related partial non-linear differential coupled equations exhibit orbital stability as needed only if some other conditions are at hand. Of course, template oriented synthesis is needed, however, onset of the cycle demands for high excess reaction energy. The type of non-linearity demands for chirality. The diffusion behaviour needs a nano-grained structure for onset of self-replication, together with critical spatial dimensions in the μm-regime. To meet all chemical and physical requirements the proticity and polarity of a mobile phase (such as liquid water), together with the right heterocatalytic backbone structure and organic precursors are prerequisites, too. To our knowledge only cosmic (esp. cometary or micrometeoritic) dust particles together with liquid water may cause that onset, as we calculated numerically for RNA and peptide life precursors as well. In order to test the dynamics of such a system model grains will be taylored which meet the requirements mentioned. Simple systems are to be prepared on the basis of nano-structured silica spheres. Loading of catalysts and precursors for autocatalytic (peptide or RNA) templates, and furtheron the onset of reaction by changing the liquid phase parameters, will be studied.

  13. 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

  14. Rate of increase of collaboration in chemical physics and related fields

    NASA Astrophysics Data System (ADS)

    Memory, Jasper D.; Lane, Heather M.

    2002-10-01

    As an extension of earlier work on this subject, the rate of increase of collaboration in chemical physics and related fields is estimated by determining the mean number of authors per article in leading journals as a function of time. Those means for the first one hundred articles of the year were determined for the period 1960-2000 in five-year intervals for the Journal of Chemical Physics, the Journal of the American Chemical Society, and the Journal of the American Institute of Chemical Engineers. The results were analyzed by linear regression, and gave increases, in authors per decade, of 0.3, 0.5, and 0.2, with r values of 0.96, 0.97, and 0.94, respectively (p < 0.0001 in each case). Implications for the hypothesis of "critical mass" of research groups are noted.

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

    NASA Astrophysics Data System (ADS)

    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.

    2015-07-01

    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.

  17. Quercetin and related flavonoids conserve their antioxidant properties despite undergoing chemical or enzymatic oxidation.

    PubMed

    Atala, Elías; Fuentes, Jocelyn; Wehrhahn, María José; Speisky, Hernán

    2017-11-01

    Oxidation of a phenolic group in quercetin is assumed to compromise its antioxidant properties. To address this assumption, the ROS-scavenging, Folin-Ciocalteau- and Fe-reducing capacities of quercetin and thirteen structurally related flavonoids were assessed and compared with those of mixtures of metabolites resulting from their chemical and enzymatic oxidation. Regardless of the oxidation mode, the metabolites mixtures largely conserved the antioxidant properties of the parent molecules. For quercetin, 95% of its ROS-scavenging and over 77% of its Folin-Ciocalteau- and Fe-reducing capacities were retained. The susceptibility of flavonoids to oxidative disappearance (monitored by HPLC-DAD) and that of the mixtures to retain their antioxidant capacity was favourably influenced by the presence of a catechol (ring-B) and enol (ring C) function. This is the first study to report that mixtures resulting from the oxidation of quercetin and its analogues largely conserve their antioxidant properties. Copyright © 2017 Elsevier Ltd. All rights reserved.

  18. 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

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

    PubMed

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

    2015-07-30

    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.

  20. 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

  1. 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.

  2. 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.

  3. 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.

  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. 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.

  6. 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

    2017-03-28

    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.

  7. 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

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

    PubMed Central

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

    2011-01-01

    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. PMID:22293396

  9. 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.

  10. Anti-oxidant behavior of functionalized chalcone-a combined quantum chemical and crystallographic structural investigation

    NASA Astrophysics Data System (ADS)

    Mathew, Bijo; Adeniyi, Adebayo A.; Joy, Monu; Mathew, Githa Elizabeth; Singh-Pillay, Ashona; Sudarsanakumar, C.; Soliman, Mahmoud E. S.; Suresh, Jerad

    2017-10-01

    Compound (2E)-3-(methoxyphenyl)-1-(4-methylphenyl) prop-2-en-1-one (Ch) was synthesized by the Claisen-Schmidt condensation reaction between para-methylacetophenone and para-methoxybenzaldehyde under basic condition. The structure of the molecule was elucidated using X-ray diffraction. Compound (Ch) demonstrated higher antioxidant activities in the DPPH test and H2O2 assay (IC50 = 12.23 ± 0.53 and 15.62 ± 0.98) than with the standard ascorbic acid (IC50 = 17.32 ± 0.44 and 19.07 ± 0.35). An evaluation of the atomic and molecular properties of ascorbic acid and Ch were computed based on their antioxidant activities. The molecular properties give insight into possible reasons for the enhanced antioxidant properties of Ch compared to ascorbic acid. The atomic properties provide further insight into chemical changes of the atoms of the compounds. Such changes include electronic shifting of the compounds electrophilic and/or nucleophilic states which highlight chemical moieties which characterize the antioxidant activity but do not directly relate to a variation in their antioxidant activities. The results obtained reflect oxygen atoms having significant nucleophilic interactions of each of the compounds. This was characterized by higher Fukui indices, isotropic and anisotropic hyperfine and orbital coupling stability energy.

  11. 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.

  12. 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.

  13. 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.”

  14. Chemical approaches to the study of supramolecular biological structures with chromatin as an example

    NASA Astrophysics Data System (ADS)

    Knorre, Dmitrii G.; Kobets, Nina D.

    1999-04-01

    Chemical approaches to the study of the chromatin structure and certain aspects of its functioning are reviewed. The main attention is given primarily to those based on the method of 'zero-length cross-linking' aimed at the investigation of the structure of histone complexes within nucleosomes and of the interactions of histones and other proteins with chromosomal DNA. The changes in the nucleosome structure during chromatin transcription are discussed. Recent data on the chemical modification of DNA and several chromatin proteins with reactive oligonucleotide derivatives are considered and analysed. The bibliography includes 89 references.

  15. Quantum chemical studies on structural, vibrational, nonlinear optical properties and chemical reactivity of indigo carmine dye

    NASA Astrophysics Data System (ADS)

    El-Mansy, M. A. M.

    2017-08-01

    Structural and vibrational spectroscopic studies were performed on indigo carmine (IC) isomers using FT-IR spectral analysis along with DFT/B3LYP method utilizing Gaussian 09 software. GaussView 5 program has been employed to perform a detailed interpretation of vibrational spectra. Simulation of infrared spectra has led to an excellent overall agreement with the observed spectral patterns. Mulliken population analyses on atomic charges, MEP, HOMO-LUMO, NLO, first order hyperpolarizability and thermodynamic properties have been examined by (DFT/B3LYP) method with the SDD basis set level. Density of state spectra (DOS) were calculated using GaussSum 3 at the same level of theory. Molecular modeling approved that DOS Spectra are the most significant tools for differentiating between two IC isomers so far. Moreover, The IC isomers (cis-isomer) have shown an extended applicability for manufacturing both NLO and photovoltaic devices such as solar cells.

  16. 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.

  17. 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.

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

    PubMed

    Gawor, Anya; Wania, Frank

    2013-09-01

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

  19. Identifying Metabolically Active Chemicals Using a Consensus Quantitative Structure Activity Model for Estrogen Receptor Binding

    EPA Science Inventory

    Endocrine disrupting chemicals (EDCs) are abundant throughout the environment and can alter neurodevelopment, behavior, and reproductive success of humans and other species by perturbing signaling pathways related to the estrogen receptor (ER). A recent study compared results acr...

  20. 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.

  1. STUDIES ON THE CHEMICAL STRUCTURE OF THE STREPTOCOCCAL CELL WALL

    PubMed Central

    Krause, Richard M.; McCarty, Maclyn

    1961-01-01

    Lysis of trypsinized Group A streptococcal cell walls with phage-associated lysin releases into solution dialyzable and non-dialyzable mucopeptide fractions composed of N-acetylglucosamine, N-acetylmuramic acid and alanine, glutamic acid, lysine, and glycine in addition to the characteristic group-specific carbohydrate. The latter substance contains appreciable amounts of N-acetylmuramic acid and the amino acids as well as N-acetylglucosamine and rhamnose. Hot formamide extraction of the cell walls results in a soluble fraction of group-specific carbohydrate and an insoluble residue. The Group A carbohydrate in this instance is composed of rhamnose and N-acetylglucosamine. The composition of the insoluble residue is similar to that of the mucopeptide fractions released from the cell wall by phage-associated lysin. This residue was shown by electron microscopy to be composed of discrete discs which appear similar in structure to the intact cell wall. The specific carbohydrate obtained by hot formamide extraction of Group A-variant cell walls was composed almost exclusively of rhamnose. The residue fraction was similar to that of Group A. The residue of cell walls extracted with hot formamide is extensively solubilized not only by phage-associated lysin and S. albus enzyme, but also by lysozyme, which has no measurable effect on the intact streptococcal cell wall. PMID:13754097

  2. 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…

  3. 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...

  4. 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...

  5. 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.

  6. [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.

  7. 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

  8. 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.

  9. Hollow-structured mesoporous materials: chemical synthesis, functionalization and applications.

    PubMed

    Li, Yongsheng; Shi, Jianlin

    2014-05-28

    Hollow-structured mesoporous materials (HMMs), as a kind of mesoporous material with unique morphology, have been of great interest in the past decade because of the subtle combination of the hollow architecture with the mesoporous nanostructure. Benefitting from the merits of low density, large void space, large specific surface area, and, especially, the good biocompatibility, HMMs present promising application prospects in various fields, such as adsorption and storage, confined catalysis when catalytically active species are incorporated in the core and/or shell, controlled drug release, targeted drug delivery, and simultaneous diagnosis and therapy of cancers when the surface and/or core of the HMMs are functionalized with functional ligands and/or nanoparticles, and so on. In this review, recent progress in the design, synthesis, functionalization, and applications of hollow mesoporous materials are discussed. Two main synthetic strategies, soft-templating and hard-templating routes, are broadly sorted and described in detail. Progress in the main application aspects of HMMs, such as adsorption and storage, catalysis, and biomedicine, are also discussed in detail in this article, in terms of the unique features of the combined large void space in the core and the mesoporous network in the shell. Functionalization of the core and pore/outer surfaces with functional organic groups and/or nanoparticles, and their performance, are summarized in this article. Finally, an outlook of their prospects and challenges in terms of their controlled synthesis and scaled application is presented. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. 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

  11. 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.

  12. 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

  13. 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.

  14. 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.

  15. Chemical Functionalization of Silicene: Spontaneous Structural Transition and Exotic Electronic Properties

    NASA Astrophysics Data System (ADS)

    Huang, Bing; Xiang, H. J.; Wei, Su-Huai

    2013-10-01

    The use of newly discovered silicene for various optoelectronic applications depends largely on the possibility of controlling its electronic properties by chemical functionalization. To investigate this possibility, we systemically study the structural and electronic properties of chemically functionalized silicene by employing first-principles calculations combined with the cluster expansion approach. Interestingly, we find that chemically functionalized epitaxial silicene is generally accompanied by a spontaneous structural transition, which originates from the preference of sp3 hybridization of silicon. To realized continuously tunable band gaps, chemical functionalization of freestanding silicene at ˜900K is proposed. Finally, we predict that metastable silicene can also be used as an important host material to produce novel functional materials via substitutional doping. For example, the discovered ordered Si8P4 could be a strong candidate for thin-film solar cell absorbers beyond bulk Si.

  16. 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.

  17. 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.

  18. Deuterated detergents for structural and functional studies of membrane proteins: Properties, chemical synthesis and applications.

    PubMed

    Hiruma-Shimizu, Kazumi; Shimizu, Hiroki; Thompson, Gary S; Kalverda, Arnout P; Patching, Simon G

    2015-01-01

    Detergents are amphiphilic compounds that have crucial roles in the extraction, purification and stabilization of integral membrane proteins and in experimental studies of their structure and function. One technique that is highly dependent on detergents for solubilization of membrane proteins is solution-state NMR spectroscopy, where detergent micelles often serve as the best membrane mimetic for achieving particle sizes that tumble fast enough to produce high-resolution and high-sensitivity spectra, although not necessarily the best mimetic for a biomembrane. For achieving the best quality NMR spectra, detergents with partial or complete deuteration can be used, which eliminate interfering proton signals coming from the detergent itself and also eliminate potential proton relaxation pathways and strong dipole-dipole interactions that contribute line broadening effects. Deuterated detergents have also been used to solubilize membrane proteins for other experimental techniques including small angle neutron scattering and single-crystal neutron diffraction and for studying membrane proteins immobilized on gold electrodes. This is a review of the properties, chemical synthesis and applications of detergents that are currently commercially available and/or that have been synthesized with partial or complete deuteration. Specifically, the detergents are sodium dodecyl sulphate (SDS), lauryldimethylamine-oxide (LDAO), n-octyl-β-D-glucoside (β-OG), n-dodecyl-β-D-maltoside (DDM) and fos-cholines including dodecylphosphocholine (DPC). The review also considers effects of deuteration, detergent screening and guidelines for detergent selection. Although deuterated detergents are relatively expensive and not always commercially available due to challenges associated with their chemical synthesis, they will continue to play important roles in structural and functional studies of membrane proteins, especially using solution-state NMR.

  19. 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

  20. Synthesis of cobalt oxides thin films fractal structures by laser chemical vapor deposition.

    PubMed

    Haniam, P; Kunsombat, C; Chiangga, S; Songsasen, A

    2014-01-01

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

  1. Constitutive Relations for Reactive Transport Modeling: Effects of Chemical Reactions on Multi-Phase Flow Properties

    NASA Astrophysics Data System (ADS)

    Zhang, S.; Liu, H. H.; van Dijke, M. I.; Geiger, S.; Agar, S. M.

    2016-12-01

    The relationship between flow properties and chemical reactions is key to modeling subsurface reactive transport. This study develops closed-form equations to describe the effects of mineral precipitation and dissolution on multiphase flow properties (capillary pressure and relative permeabilities) of porous media. The model accounts for the fact that precipitation/dissolution only takes place in the water-filled part of pore space. The capillary tube concept was used to connect pore-scale changes to macroscopic hydraulic properties. Precipitation/dissolution induces changes in the pore radii of water-filled pores and consequently in the pore-size distribution. The updated pore-size distribution is converted back to a new capillary pressure-water saturation relation from which the new relative permeabilities are calculated. Pore network modeling is conducted on a Berea sandstone to validate the new continuum-scale relations. The pore network modeling results are satisfactorily predicted by the new closed-form equations. Currently the effects of chemical reactions on flow properties are represented as a relation between permeability and porosity in reactive transport modeling. Porosity is updated after chemical calculations from the change of mineral volumes, then permeability change is calculated from the porosity change using an empirical permeability-porosity relation, most commonly the Carman-Kozeny relation, or the Verma-Pruess relation. To the best of our knowledge, there are no closed-form relations available yet for the effects of chemical reactions on multi-phase flow properties, and thus currently these effects cannot be accounted for in reactive transport modeling. This work presents new constitutive relations to represent how chemical reactions affect multi-phase flow properties on the continuum scale based on the conceptual model of parallel capillary tubes. The parameters in our new relations are either pre-existing input in a multi-phase flow

  2. 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.

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

    PubMed

    Cortes-Ciriano, Isidro; Bender, Andreas

    2015-12-28

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

  4. Chemical structures of constituents from the flowers of Osmanthus fragrans var. aurantiacus.

    PubMed

    Liu, Jiang; Nakamura, Seikou; Xu, Bin; Matsumoto, Takahiro; Ohta, Tomoe; Fujimoto, Katsuyoshi; Ogawa, Keiko; Fukaya, Masashi; Miyake, Shiori; Yoshikawa, Masayuki; Matsuda, Hisashi

    2015-01-01

    Three new megastigmane glycosides named floraosmanosides I-III and a new γ-decalactone named floraosmanolactone I together with 16 known constituents were isolated from the flowers of Osmanthus fragrans var. aurantiacus cultivated in Guangxi Zhuang Autonomous Region, China. The chemical structures of the new compounds were elucidated on the basis of chemical and physicochemical evidence. Among them, ligustroside and (+)-pinoresinol significantly inhibited nitric oxide production in lipopolysaccharide-activated RAW264.7 macrophages.

  5. 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/.

  6. 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)

  7. 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.

  8. 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.

  9. 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

  10. 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.

  11. 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. © The Author(s) 2016. Published by Oxford University Press.

  12. 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

  13. 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

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

    NASA Astrophysics Data System (ADS)

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

    2017-08-01

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

  15. 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.

  16. 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.

  17. Observations on the chemical structure and cytotoxic activity of marycin, a hematoporphyrin derivative.

    PubMed

    Pinelli, A; Trivulzio, S; Von Hoff, D D; Monti, D; Manitto, P

    1988-01-01

    This paper describes the preparation, chemical structure and cytotoxic activity of marycin, a hematoporphyrin derivative. Marycin has been prepared by condensing hematoporphyrin dimethyl ester in the presence of p-toluenesulfonic acid and reducing the product with lithium aluminum hydride. The product appeared to be pure by thin-layer chromatography (TLC) and high-performance liquid chormatography (HPLC). The product, analyzed by UV-visible absorbance and fluorescence spectra, appears to be related to the parent hematoporphyrin compound. The product was also analyzed by NMR and Mass spectra: a dimeric structure can be assigned to marycin: this appears to have an oxide bridge between C2-chains of two porphyrin units and hydroxyl groups instead of carboxyls. Marycin was screened for cytotoxic activity against ZR-75, MCF-7, HT-29, K-562, human tumor cell lines and the MRC-9 human embryonic cell line. Marycin decreases the growth index, measured in the radiometric assay, as 14CO2 production. The cytotoxic activity was dose-dependent and is attributable to the pure compound, marycin. Marycin is active at low doses but the activity varies with the cell line studied. The compound had low toxicity versus MRC-9 normal cell line. The compound is active without light activation. How marycin acts is a matter of speculation. Marycin is highly liposoluble and would be expected to have high toxicity for tumors.

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

    PubMed

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

    2015-08-01

    Several natural polyketides (PKs) have been associated with important pharmaceutical properties. Type III polyketide synthases (PKS) that generate aromatic PK polyketides have been studied extensively for their substrate promiscuity and product diversity. Stilbene synthase-like (STS) enzymes are unique in the type III PKS class as they possess a hydrogen bonding network, furnishing them with thioesterase-like properties, resulting in aldol condensation of the polyketide intermediates formed. Chalcone synthases (CHS) in contrast, lack this hydrogen-bonding network, resulting primarily in the Claisen condensation of the polyketide intermediates formed. We have attempted to expand the chemical space of this interesting class of compounds generated by creating structure-guided mutants of Vitis vinifera STS. Further, we have utilized a previously established workflow to quickly compare the wild-type reaction products to those generated by the mutants and identify novel PKs formed by using XCMS analysis of LC-MS and LC-MS/MS data. Based on this approach, we were able to generate 15 previously unreported PK molecules by exploring the substrate promiscuity of the wild-type enzyme and all mutants using unnatural substrates. These structures were specific to STSs and cannot be formed by their closely related CHS-like counterparts. Copyright © 2015 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.

  19. 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.

  20. Structural and chemical control in assembly of multicomponent metal-organic coordination networks on a surface.

    PubMed

    Shi, Ziliang; Lin, Nian

    2010-08-11

    Surface-supported supramolecular self-assembly has been used to generate multicomponent two-dimensional metal-organic coordination networks on a Au(111) surface. The networks consist of linker ligands of 4',4''''-(1,4-phenylene)bis(2,2':6',2''-terpyridine) and nodal ligands of 5,10,15,20-tetra(4-pyridyl)porphyrin that are connected by pyridine-Fe-terpyridine motifs. Scanning tunneling microscopy revealed the coexistence of two polymorphic types of network structures (rhombus and Kagome). Through control of the dosage of the constituent ligands, homogeneous structural phases were obtained selectively. In particular, the rhombus structure could be converted into the more complex and more open Kagome structure by inclusion of guest molecules. Finally, coordination networks providing structural and chemical homogeneity were realized by judiciously choosing the dosages of the constituent ligands and the chemical substitution of the porphyrin ligands.