Science.gov

Sample records for chemicals structurally related

  1. 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

  2. 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.

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

    ERIC Educational Resources Information Center

    Huang, Chin-Fei; Liu, Chia-Ju

    2012-01-01

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

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    2014-09-01

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

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

    PubMed

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

    2014-09-15

    The stable geometry of 2-hydroxy-4-methoxyacetophenone is optimised by DFT/B3LYP method with 6-311++G(∗∗) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the optimised geometry have been determined. The effects of substituents (hydroxyl, methoxy and acetyl groups) on the benzene ring vibrational frequencies are analysed. The vibrational frequencies of the fundamental modes of 2-hydroxy-4-methoxyacetophenone have been precisely assigned and analysed and the theoretical results are compared with the experimental vibrations. 1H and 13C NMR isotropic chemical shifts are calculated and assignments made are compared with the experimental values. The energies of important MO's, the total electron density and electrostatic potential of the compound are determined. Various reactivity and selectivity descriptors such as chemical hardness, chemical potential, softness, electrophilicity, nucleophilicity and the appropriate local quantities are calculated. PMID:24792193

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

    PubMed

    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

  8. 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

  9. 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

  10. 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. PMID:25936284

  11. 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.

  12. STUDY OF THE BIOLOGICAL ACTIVITY OF ERIONITE IN RELATION TO ITS CHEMICAL AND STRUCTURAL CHARACTERISTICS

    EPA Science Inventory

    Fibrous erionite appears to have many times the mesothelioma induction potential of asbestos. A member of a class of minerals termed zeolites, it differs markedly from asbestos in many physico-chemical characteristics. For preliminary biological studies, experiments were based on...

  13. 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.

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

    PubMed

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

    2013-10-23

    The objectives of this study were to investigate (1) the carbohydrate chemical profile, (2) the energy values, (3) the rumen neutral detergent fiber (NDF) degradation kinetics, (4) the carbohydrate-related functional group structural features using a Fourier transform infrared (FTIR) spectroscopic technique with attenuated total reflectance (ATR), and (5) the correlations between carbohydrate intrinsic structural features and nutritional profiles in three strains of Brassica carinata in yellow and brown seed coats, with comparison to canola seed as a reference. The results showed that yellow B. carinata strains 111000EM and AAC A100 were lower for contents of neutral detergent fiber (NDF), acid detergent fiber (ADF), acid detergent lignin (ADL), and carbohydrate (CHO) and higher for contents of total digestible nutrients (TDN), energy values, and effective degradable NDF (EDNDF) than brown-seeded 110915EM. In comparison, brown canola seed (Brassica napus L.) had more fiber content and less EDNDF. Also, carinata strains showed significantly different IR intensities in structural carbohydrate (SCHO), cellulosic compounds (CELC), and total CHO profiles. These structural variations might be one of the possible reasons for various fiber profile and biodegradation characteristics for ruminants in oilseeds. However, multivariate analyses within carbohydrate regions indicated there were still some structural relationships among the four oilseed samples. Moreover, the correlation study showed that the changes of CELC and CHO peak intensities were highly related with some changes in CHO chemical profile, energy values, and in situ NDF degradation kinetics in B. carinata and canola seeds. Further study with a large sample size is still necessary to figure out whether CHO molecular spectral information could be used to predict nutrient values and biological behavior in oilseeds. PMID:24059242

  15. Quantum chemical calculations to reveal the relationship between the chemical structure and the fluorescence characteristics of phenylquinolinylethynes and phenylisoquinolinylethynes derivatives, and to predict their relative fluorescence intensity.

    PubMed

    Riahi, Siavash; Beheshti, Abolghasem; Ganjali, Mohammad Reza; Norouzi, Parviz

    2009-12-01

    In this paper the relationship between the chemical structure and fluorescence characteristics of 30 phenylquinolinylethyne (PhQE), and phenylisoquinolinylethyne (PhIE) derivatives compounds employing ab initio calculations have been elucidated. Quantum chemical calculations (6-31G) were carried out to obtain: the optimized geometry, energy levels, charges and dipole moments of these compounds, in the singlet (steady and excited states) and triplet states. The relationship between quantum chemical descriptors, and wavelength of maximum excitation and emission indicated that these two parameters have the most correlation with quantum chemical hardness (eta). Also, stokes shift has the most correlation with the square of difference between the maximum of positive charges in the singlet steady and singlet excited states. The quantitative structure-property relationship (QSPR) of PhQE and PhIE was studied for relative fluorescence intensity (RFI). The genetic algorithm (GA) was applied to select the variables that resulted in the best-fit models. After the variable selection, multiple linear regression (MLR) and support vector machine (SVM) were both utilized to construct linear and non-linear QSPR models, respectively. The SVM model demonstrated a better performance than that of the MLR model. The route mean square error (RMSE) in the training and the test sets for the SVM model was 0.195 and 0.324, and the correlation coefficients were 0.965 and 0.960, respectively, thus revealing the reliability of this model. The resulting data indicated that SVM could be used as a powerful modeling tool for QSPR studies. According to the best of our knowledge, this is the first research on QSPR studies to predict RFI for a series of PhQE and PhIE derivative compounds using SVM. PMID:19854100

  16. Semiempirical Predictions of Chemical Degradation Reaction Mechanisms of CL-20 as Related to Molecular Structure

    SciTech Connect

    Qasim, Mohammad M.; Furey, John; Fredrickson, Herbert L.; Szecsody, Jim E.; Mcgrath, Chris J.; Bajpai, Rakesh

    2004-10-01

    Quantum mechanical methods and force field molecular mechanics were used to characterize cage cyclic nitramines and to predict environmental degradation mechanisms. Due to structural similarities it is predicted that, under homologous circumstances, the major environmental RDX degradation pathways should also be effective for CL-20 and similar cyclic nitramines.

  17. Relation of chemical structure to spatial distribution of sensory responses in rat olfactory epithelium.

    PubMed

    Scott, J W; Davis, L M; Shannon, D; Kaplan, C

    1996-05-01

    1. Electroolfactogram (EOG) recordings were made in three configurations from the rat olfactory epithelium. Each configuration compared recordings in the dorsomedial recess of the epithelium with recordings in ventral or lateral parts of the epithelium. Most comparisons were made with simultaneous recordings. The exception was a series in which the dorsal recess and lateral space between the base of two turbinate bones were directly exposed for odor application and recording. The spatial distributions of maximal responses were largely independent of recording configuration. 2. Simultaneous recordings compared dorsomedial and lateral sites in the epithelium during stimulation with a series of 50 odorants. The odorants that evoked larger responses in the lateral sites were usually compounds that lacked oxygen containing functional groups (such as the carbonyl group). This was true for straight chain and cyclic alkanes, for terpine compounds, and for aromatic compounds. The major exception was cineole, a bicyclic compound. All compounds containing ketone groups evoked larger dorsomedial responses. The responses of aldehydes and esters depended upon whether they were attached to aliphatic or aromatic chains. 3. In the three types of preparation, the sites responding best to ketones were in the same expression zone of the epithelium according to published maps for the rat and mouse. The sites responding best to odors without functional groups were in the far lateral or ventral region and corresponded to one of the two most lateral and ventral expression zones. This fact suggests that the receptors in these regions have a preference for particular chemical properties. This level of analysis cannot determine whether all receptors in each zone have a stronger response to certain properties of these odorants or whether each zone contains different proportions of receptors with these properties. PMID:8734602

  18. Chemical structure of interfaces

    NASA Technical Reports Server (NTRS)

    Grunthaner, F. J.

    1985-01-01

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

  19. Equilibrium structure and relative stability of glyceraldehyde conformers: Gas-phase electron diffraction (GED) and quantum-chemical studies

    NASA Astrophysics Data System (ADS)

    Vogt, Natalja; Atavin, Evgenii G.; Rykov, Anatolii N.; Popov, Evgenii V.; Vilkov, Lev V.

    2009-11-01

    For the first time, the five dimensional (5-D) analysis of potential energy surface (PES) from quantum-chemical calculations was carried out to predict reliably the various glyceraldehyde (GLA) conformers. 36 conformers with relative stabilities up to 38 kJ/mol were found in the B3LYP approximation. According to results of MP2/cc-pVQZ calculations, the molecule exists at the experimental temperature of 388 K as a mixture of five conformers in the ratio I:II:III:IV:V = 63:18:4:10:5. Contrary to the theoretical conclusion of Lovas et al., the conformer IV is predicted to be more stable than the conformer III. Our result can explain why the conformer IV could be detected in the microwave (MW) spectroscopic experiment by Lovas et al., whereas the conformer III could not. For the first time, thermal-average and equilibrium structural parameters of GLA (main conformer) have been determined from gas-phase electron diffraction (GED) data. Vibrational corrections to the experimental bond lengths were determined using quadratic and cubic force constants from high-level ab initio calculations (MP2/cc-pVTZ). It was shown that the experimental intensities are sensitive to the contribution of the second conformer (27(15)%). Rotational constants calculated from MP2/cc-pVQZ geometries were found to be in excellent agreement with the experimental rotational constants corrected for anharmonic effects.

  20. Structure of γ-tubulin small complex based on a cryo-EM map, chemical cross-links, and a remotely related structure.

    PubMed

    Greenberg, Charles H; Kollman, Justin; Zelter, Alex; Johnson, Richard; MacCoss, Michael J; Davis, Trisha N; Agard, David A; Sali, Andrej

    2016-06-01

    Modeling protein complex structures based on distantly related homologues can be challenging due to poor sequence and structure conservation. Therefore, utilizing even low-resolution experimental data can significantly increase model precision and accuracy. Here, we present models of the two key functional states of the yeast γ-tubulin small complex (γTuSC): one for the low-activity "open" state and another for the higher-activity "closed" state. Both models were computed based on remotely related template structures and cryo-EM density maps at 6.9Å and 8.0Å resolution, respectively. For each state, extensive sampling of alignments and conformations was guided by the fit to the corresponding cryo-EM density map. The resulting good-scoring models formed a tightly clustered ensemble of conformations in most regions. We found significant structural differences between the two states, primarily in the γ-tubulin subunit regions where the microtubule binds. We also report a set of chemical cross-links that were found to be consistent with equilibrium between the open and closed states. The protocols developed here have been incorporated into our open-source Integrative Modeling Platform (IMP) software package (http://integrativemodeling.org), and can therefore be applied to many other systems. PMID:26968363

  1. Chemical structure-related mechanisms underlying in vivo genotoxicity induced by nitrofurantoin and its constituent moieties in gpt delta rats.

    PubMed

    Kijima, Aki; Ishii, Yuji; Takasu, Shinji; Matsushita, Kohei; Kuroda, Ken; Hibi, Daisuke; Suzuki, Yuta; Nohmi, Takehiko; Umemura, Takashi

    2015-05-01

    Nitrofurans are antimicrobial compounds containing a nitro group at the 5-position of the furan ring and an amine or hydrazide side chain derivative. One member of the nitrofurans, nitrofurantoin (NFT), is a renal carcinogen in male rats despite its still controversial genotoxicity. We investigated chemical structure-related modes of action of NFT, and reporter gene mutation assays for NFT and its constituent moieties were performed. NFT, 5-nitro-2-furaldehyde (NFA), or 1-aminohydantoin (AHD) was administered to male F344 gpt delta rats by gavage for 4 or 13 weeks at a carcinogenic or the maximum tolerated dose. NFT caused a significant increase in gpt mutant frequency (MF) at 13 weeks with G-base substitution mutations. An increase in gpt MF was also observed in the NFA-treated group at 13 weeks, but not in the AHD-treated group. 8-Hydroxydeoxyguanosine (8-OHdG) levels in the kidney DNA of NFT-treated rats were significantly increased after 4 weeks. NFT caused accumulation of hyaline droplets indicated by positive immunostaining and western blot analysis for α2u-globulin in the proximal tubules. An additional study, in which female gpt delta rats were given NFT at the same dose used for males, was performed to mitigate the effect of α2u-globulin. NFT exerted the same effects on female rat kidneys to the same extent as males in terms of gpt MF and 8-OHdG level. Thus, it is highly probable that the structure of the nitro furan plays a key role in NFT-induced genotoxicity and genotoxic mechanisms including oxidative DNA damage are involved in NFT-induced renal carcinogenesis. α2u-globulin-mediated nephropathy may be a prerequisite for NFT-induced renal carcinogenesis in male rats, and additionally NFT could be a latent carcinogen in female rats and other animal species. PMID:25772432

  2. An attempt to study the effects of chemical structure on the affinity and efficacy of compounds related to acetylcholine

    PubMed Central

    Barlow, R. B.; Scott, K. A.; Stephenson, R. P.

    1963-01-01

    Two sets of series of compounds, RN+Me3, RN+Me2Et, RN+MeEt2, RN+Et3, and R'N+Me3, R'N+Me2Et, R'N+MeEt2, R'N+Et3, have been prepared, in which R is a 2-(diphenylacetoxy)ethyl, 2-(benziloyloxy)ethyl, 2-(2,2-diphenylethoxy)ethyl, 3-(diphenylmethoxy)propyl or 3,3-diphenylbutyrylmethyl group, and R' is a 2-acetoxyethyl, 2-ethoxyethyl, 3-methoxypropyl or butyrylmethyl group: compounds of the first set therefore differ from those of the second set in that they contain a diphenylmethyl group (or a benziloyl group) in place of a methyl group. The former compounds are antagonists of acetylcholine whereas most of the latter act like acetylcholine. The affinity constants of the former compounds for the acetylcholine receptors of the guinea-pig ileum have been determined and the equipotent molar ratios relative to acetylcholine have been measured for the latter compounds. The variation of the affinity constant with the constitution of the onium group in the antagonists (the diphenylmethyl compounds) was sufficiently consistent from one series to another for it to seem likely that corresponding changes in affinity with the constitution of the onium group would occur in the agonists. From the relative activity of the agonists and with this knowledge of relative affinity it was possible to assess the effects of their structure on efficacy. Substitution of one methyl in the onium group by an ethyl group in these compounds increased affinity but decreased efficacy. The replacement of a second methyl by a second ethyl group had little effect on affinity but decreased efficacy still further. The replacement of the ester link in acetylcholine by a 4-ether oxygen atom (as in the diphenylmethoxypropyl and methoxypropyl compounds) did not appreciably reduce affinity but markedly reduced efficacy, whereas the replacement of the ester link by a 3-ether oxygen atom (as in the diphenylethoxyethyl and ethoxyethyl compounds) markedly reduced affinity but did not reduce efficacy. The

  3. Gauge theory and chemical structure.

    PubMed

    Mattingly, James

    2003-05-01

    The possibility of chemical structure in the context of quantized matter is examined by way of Richard Bader's Atoms in Molecules. I critically examine his notion of "electronic charge density"-showing that he cannot really mean "density of charge"-and I argue that the appropriate concept is expectation value of charge. This still allows him to define chemical structure, but it makes problematic his appeals to the explanatory power of structure. This is because, as Rosenfeld and Bohr showed, the expectation value of charge cannot be taken as the electronic field experienced by other charges. I suggest that we can recover the efficacy of structure by thinking of chemistry as a gauge theory. Current consensus in the study of gauge theories indicates that gauge potentials represent a new type of property; while no member of the family of functions comprising the gauge potential is real, the potential itself is causally potent. I illustrate this in the case of electrodynamics, where the vector potential can causally influence charges in the absence of electric or magnetic fields. I show how chemical structure can be considered to be a gauge field. Following Bader, I take it to be a family of geometric configurations, no one of which is possessed by a given molecule. I claim that current research in gauge theory licenses the attribution of causal potency to this notion of structure, despite its lack of reality. I thus begin the process of freeing the explanatory resources of gauge theory from physics alone. PMID:12796102

  4. 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

    2016-01-01

    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

  5. 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

  6. InChI - the worldwide chemical structure identifier standard

    PubMed Central

    2013-01-01

    Since its public introduction in 2005 the IUPAC InChI chemical structure identifier standard has become the international, worldwide standard for defined chemical structures. This article will describe the extensive use and dissemination of the InChI and InChIKey structure representations by and for the world-wide chemistry community, the chemical information community, and major publishers and disseminators of chemical and related scientific offerings in manuscripts and databases. PMID:23343401

  7. Associational resistance of fouled blue mussels (Mytilus edulis) against starfish (Asterias rubens) predation: relative importance of structural and chemical properties of the epibionts

    NASA Astrophysics Data System (ADS)

    Laudien, Jürgen; Wahl, Martin

    2004-10-01

    Several epibiotic species reduce starfish (Asterias rubens) preference for the blue mussel Mytilus edulis in the Baltic. The aim of this study was to reveal whether this associational resistance was caused by structural or chemical aspects of the different epibionts. To assess structural epibiont effects, an in situ experiment was conducted with unfouled mussels and mussels equipped with artificial epibionts (`dummies') exposed to natural predation by A. rubens. The chemically inert dummies closely matched the structural properties of the locally common epibionts Balanus improvisus (barnacle), Ceramium strictum (red alga), Halichondria panicea (sponge), and Laomedea flexuosa (hydrozoan). Starfish fed indiscriminately in all treatments. Chemical effects of epibionts on the attractiveness of mussels for A. rubens were investigated by incorporating freeze-dried epibionts or mussel tissue into Phytagel pellets at natural concentrations. Starfish were allowed to choose among these structurally similar but chemically different prey items in an in vitro experiment. The predators exhibited significant preferences among the food pellets, which closely matched their preferences for corresponding natural mussel-epibiont associations. Thus, chemical aspects of epibionts appear to play a larger role in this associational resistance than do structural aspects. Implications of these indirect interactions for benthic communities are discussed.

  8. On reasons of 29Si NMR chemical shift/structure relations for silicon oxides, nitrides, and carbides: an individual-gauge-for-localized-orbitals study.

    PubMed

    Wolff, R; Jancke, H; Radeglia, R

    1997-12-01

    For alpha-quartz, monoclinic ZSM-5, alpha- and beta-Si3N4 and SiC-6H polytype, the silicon chemical shifts have been calculated using the IGLO (individual gauge for localized orbitals) method and models of different size in real crystal geometry. The result is a theoretical chemical shift scale, which is very similar to the corresponding experimental scale from 29Si MAS NMR experiments. It is shown that the assignment of isotropic silicon chemical shifts of crystallized solids based on theory is a method of practical applicability, also in cases where experimental methods or empirical relations fail. The two NMR spectral lines of alpha-Si3N4 are for the first time assigned to the crystallographic positions. The partition of the silicon chemical shifts into localized contributions from different parts of the model allows insight into the interactions around the resonance nucleus due to substituent and geometry variations leading to silicon chemical shifts. PMID:9477448

  9. 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.

  10. Derivatives of 3:4-xylidine and related compounds as inhibitors of influenza virus: relationships between chemical structure and biological activity

    PubMed Central

    Clark, R. J.; Isaacs, A.; Walker, J.

    1958-01-01

    A series of compounds, based primarily on 3:4-xylidine, was examined for inhibitory activity towards the growth of influenza virus in tissue culture. Marked dependence of inhibitory activity upon chemical structure was observed particularly when the 3:4-xylyl group was replaced by other simple aryl radicals. N-(2-Piperidinoethyl)-3:4-xylidine dihydrochloride, a typical compound combining high intrinsic inhibitory activity with no obvious toxicity towards the host tissues, did not inactivate the virus directly before its adsorption, did not interfere with adsorption of virus by the tissues, and did not inhibit the release of freshly synthesized virus by the tissues, but specifically depressed the synthesis of viral haemagglutinin to a greater extent than it depressed the synthesis of complement-fixing soluble antigen. The inhibition of growth of influenza virus caused by this compound in tissue culture was reversed by appropriate addition of 4:5-dimethyl-o-phenylenediamine, but not apparently by riboflavin or by vitamin B12. The action of this substance, and, by inference, of related compounds, in inhibiting viral synthesis may be the result of depressed cytoplasmic protein synthesis. PMID:13618548

  11. 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.

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

    PubMed

    Xin, Hangshu; Yu, Peiqiang

    2014-12-10

    In this experiment, brown- and yellow-seeded Brassica carinata were selected to use as a model to investigate whether there were any changes in lipid-related structure make-up (including CH3 and CH2 asymmetric and symmetric stretching bands ca. 3010-2765cm(-1), unsaturated lipid band ca. 3043-2987cm(-1) and carbonyl CO ester band ca. 1789-1701cm(-1)) of oilseed tissue during rumen in situ incubation using attenuated total reflectance-Fourier transform infrared spectroscopy (ATR-FT/IR). Correlations of lipid spectral characteristics with basic chemical profile and multivariate analyses for clarifying structural differences within lipid regions between two carinata seeds were also measured. The results showed that most spectral parameters in both carinata seeds were reduced as incubation time increased. However, the extent of changes in peak intensity of carbonyl CO ester group of brown-seeded carinata was not in fully accordance with that of yellow-seeded carinata. Additionally, these lipid structure features were highly correlated with the concentrations of OM (positively), CP (positively), NDF (negatively) and EE (positively) in carinata seeds after 0, 12, 24 and 48h of incubation. Based on the results from multivariate analyses, neither AHCA nor PCA could produce any distinctions in rumen residues between brown- and yellow-seeded carinata in spectra at lipid regions. It was concluded that besides for original feed samples, spectroscopic technique of ATR-FT/IR could also be used for rumen degradation residues in detecting changes in lipid-related molecular structure make-up. Further studies are needed to explore more details in lipid metabolism during ruminal fermentation with the combined consideration on both metabolic basis and molecular structural basis. PMID:25000568

  13. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    SD Colson; RS McDowell

    1999-05-10

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

  14. 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.

  15. Annual Report 1998: Chemical Structure and Dynamics

    SciTech Connect

    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).

  16. 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

    2014-07-01

    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. PMID:24836778

  17. Determination of Relative Configuration from Residual Chemical Shift Anisotropy.

    PubMed

    Nath, Nilamoni; Schmidt, Manuel; Gil, Roberto R; Williamson, R Thomas; Martin, Gary E; Navarro-Vázquez, Armando; Griesinger, Christian; Liu, Yizhou

    2016-08-01

    Determination of relative configuration is frequently a rate-limiting step in the characterization of small organic molecules. Solution NMR-based nuclear Overhauser effect and scalar J-coupling constants can provide useful spatial information but often fail when stereocenters are separated by more than 4-5 Å. Residual dipolar couplings (RDCs) can provide a means of assigning relative configuration without limits of distance between stereocenters. However, sensitivity limits their application. Chemical shift is the most readily measured NMR parameter, and partial molecular alignment can reveal the anisotropic component of the chemical shift tensor, manifested as residual chemical shift anisotropy (RCSA). Hence, (13)C RCSAs provide information on the relative orientations of specific structural moieties including nonprotonated carbons and can be used for stereochemical assignment. Herein, we present two robust and sensitive methods to accurately measure and apply (13)C RCSAs for stereochemical assignment. The complementary techniques are demonstrated with five molecules representing differing structural classes. PMID:27294984

  18. 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

  19. Chemical Structure Handling by Computer.

    ERIC Educational Resources Information Center

    Paris, C. Gregory

    1997-01-01

    Organized from the viewpoint of information retrieval theory, this review addresses issues of chemical information representation, comparison and matching, and retrieval strategies. Additional topics include similarity and clustering, visualization, and molecular diversity. Trends in research and application are identified, and gaps in the…

  20. 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)

  1. 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. PMID:26278514

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

    EPA Science Inventory

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

  3. Nanostructured, Gd-doped ceria promoted by Pt or Pd: investigation of the electronic and surface structures and relations to chemical properties.

    PubMed

    Borchert, Holger; Borchert, Yulia; Kaichev, Vasiliy V; Prosvirin, Igor P; Alikina, Galina M; Lukashevich, Anton I; Zaikovskii, Vladimir I; Moroz, Ella M; Paukshtis, Eugenii A; Bukhtiyarov, Valerii I; Sadykov, Vladislav A

    2005-11-01

    Nanostructured ceria doped with other rare earth elements is a good oxygen ion conductor, which gives rise to various catalytic applications such as the construction of membranes for syngas production by partial oxidation of methane. This article focuses on the Gd-doped cerium dioxides, which can be modified with Pt or Pd to enhance the reactivity of the lattice oxygen in interaction with methane. The aim of the work is the elucidation of correlations between the structural, electronic, and chemical properties of these nanomaterials. Detailed studies were performed for a series of samples with and without surface modification by noble metals using a complex combination of physicochemical methods: XRD, TEM, CH(4) TPR, XPS, SIMS, and FTIR spectroscopy of adsorbed CO. XPS and TPR data revealed that surface modification with noble metals enhances the reducibility of the doped ceria support, where the effect is more pronounced for Pd than for Pt. The formation of highly cationic Pd species due to strong metal support interactions provides a possible explanation for this behavior. Furthermore, the results obtained in the present work for the Gd-doped ceria system are compared to those obtained previously for the Pr-doped ceria system. PMID:16853596

  4. 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

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

    NASA Astrophysics Data System (ADS)

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

    1992-05-01

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

  6. 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...

  7. 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.

  8. 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.

  9. 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.

  10. Annual Report 2000. Chemical Structure and Dynamics

    SciTech Connect

    Colson, Steve D; McDowell, Rod 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 and D) program is meeting the need for a fundamental, molecular-level understanding by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes relevant to environmental chemistry; and (3) developing state-of-the-art research and analytical methods for characterizing complex materials of the types found in natural and contaminated systems.

  11. 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.

  12. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  14. 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.

  15. Chemically modified electrodes and related solution studies

    SciTech Connect

    Elliott, C.M.

    1990-01-01

    This report briefly discusses work done in the following areas of chemically modified electrodes: Spectroscopic studies of the modes of interactions of pyridine containing ligands with metal surfaces; attempted synthesis of gem-dihalide containing polymers for attachment of Mo{sub 2}S{sub 4} clusters; Synthesis of oxo-ruthenium dimer complexes as catalysts for H{sub 2} oxidation; and, studies of porphyrin based polymers which catalyze the oxidation (oxygenation) of olefins and benzylic carbons. (JDL)

  16. 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.

  17. 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

  18. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ... the Attorney General (28 CFR 0.100). (4) The terms broker and trader mean any individual, corporation... 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...

  19. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-04-01

    ... has been delegated authority under the Act by the Attorney General (28 CFR 0.100). At retail, with... 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...

  20. 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.

  1. Chemical Structure of Trichomonas vaginalis Surface Lipoglycan

    PubMed Central

    Ryan, Christopher M.; Mehlert, Angela; Richardson, Julia M.; Ferguson, Michael A. J.; Johnson, Patricia J.

    2011-01-01

    The extracellular parasite Trichomonas vaginalis contains a surface glycoconjugate that appears to mediate parasite-host cell interaction via binding to human galectin-1. This glycoconjugate also elicits cytokine production from human vaginal epithelial cells, implicating its role in modulation of host immune responses. We have analyzed the structure of this glycoconjugate, previously described to contain the sugars rhamnose (Rha), N-acetylglucosamine (GlcNAc), galactose (Gal), xylose (Xyl), N-acetylgalactosamine (GalNAc), and glucose (Glc), using gas chromatograph mass spectrometry (GC-MS), matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF), electrospray MS/MS, and nuclear magnetic resonance (NMR), combined with chemical and enzymatic digestions. Our data reveal a complex structure, named T. vaginalis lipoglycan (TvLG), that differs markedly from Leishmania lipophosphoglycan and Entamoeba lipopeptidophosphoglycan and is devoid of phosphosaccharide repeats. TvLG is composed of an α1–3 linked polyrhamnose core, where Rha residues are substituted at the 2-position with either β-Xyl or chains of, on average, five N-acetyllactosamine (-3Galβ1–4GlcNAcβ1-) (LacNAc) units and occasionally lacto-N-biose (-3Galβ1-3GlcNAcβ1-) (LNB). These chains are themselves periodically substituted at the Gal residues with Xyl-Rha. These structural analyses led us to test the role of the poly-LacNAc/LNB chains in parasite binding to host cells. We found that reduction of poly-LacNAc/LNB chains decreased the ability of TvLG to compete parasite binding to host cells. In summary, our data provide a new model for the structure of TvLG, composed of a polyrhamnose backbone with branches of Xyl and poly-LacNAc/LNB. Furthermore, the poly-LacNAc side chains are shown to be involved in parasite-host cell interaction. PMID:21900246

  2. Rectangular groupoids and related structures

    PubMed Central

    Boykett, Tim

    2013-01-01

    The quasivariety of groupoids (N,∗) satisfying the implication a∗b=c∗d⇒a∗d=c∗b=a∗b generalises rectangular semigroups and central groupoids. We call them rectangular groupoids and find three combinatorial structures based upon arrays, matrices and graphs that are closely related. These generalise several groupoids of independent interest. The quasivariety generates the variety of all groupoids; they satisfy no nontrivial equations. We see some strong connections with isotopy, this being one of the classes of algebras (along with quasigroups) closed under isotopy. We investigate some constructions and show that a regular automorphism exists iff the groupoid is derived from a group via a Cayley graph construction. PMID:23836949

  3. 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. PMID:19325749

  4. 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

  5. Chemical syntheses of inulin and levan structures.

    PubMed

    Oscarson, Stefan; Sehgelmeble, Fernando W

    2002-11-29

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

  6. Relative Configuration of Natural Products Using NMR Chemical Shifts

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  7. 40 CFR 180.3 - Tolerances for related pesticide chemicals.

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 40 Protection of Environment 24 2014-07-01 2014-07-01 false Tolerances for related pesticide chemicals. 180.3 Section 180.3 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) PESTICIDE PROGRAMS TOLERANCES AND EXEMPTIONS FOR PESTICIDE CHEMICAL RESIDUES IN FOOD Definitions and Interpretative Regulations § 180.3 Tolerances...

  8. Chemical and structural modifications of RNAi therapeutics.

    PubMed

    Ku, Sook Hee; Jo, Sung Duk; Lee, Yeon Kyung; Kim, Kwangmeyung; Kim, Sun Hwa

    2016-09-01

    Small interfering RNA (siRNA), a 21-23nt double-stranded RNA responsible for post-transcriptional gene silencing, has attracted great interests as promising genomic drugs, due to its strong ability to silence target genes in a sequence-specific manner. Despite high silencing efficiency and on-target specificity, the clinical translation of siRNA has been hindered by its inherent features: poor intracellular delivery, limited blood stability, unpredictable immune responses and unwanted off-targeting effects. To overcome these hindrances, researchers have made various advances to modify siRNA itself and to improve its delivery. In this review paper, first we briefly discuss the innate properties and delivery barriers of siRNA. Then, we describe recent progress in (1) chemically and structurally modified siRNAs to solve their intrinsic problems and (2) siRNA delivery formulations including siRNA conjugates, polymerized siRNA, and nucleic acid-based nanoparticles to improve in vivo delivery. PMID:26549145

  9. Conservation-dissipation structure of chemical reaction systems.

    PubMed

    Yong, Wen-An

    2012-12-01

    In this Brief Report, we show that balanced chemical reaction systems governed by the law of mass action have an elegant conservation-dissipation structure. From this structure a number of important conclusions can be easily deduced. In particular, with the help of this structure we can rigorously justify the classical partial equilibrium approximation in chemical kinetics. PMID:23368081

  10. 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.

  11. Protein Structure Is Related to RNA Structural Reactivity In Vivo.

    PubMed

    Tang, Yin; Assmann, Sarah M; Bevilacqua, Philip C

    2016-02-27

    We assessed whether in vivo mRNA structural reactivity and the structure of the encoded protein are related. This is the first investigation of such a relationship that utilizes information on RNA structure obtained in living cells. Based on our recent genome-wide Structure-seq analysis in Arabidopsis thaliana, we report that, as a meta property, regions of individual mRNAs that code for protein domains generally have higher reactivity to DMS (dimethyl sulfate), a chemical that covalently modifies accessible As and Cs, than regions that encode protein domain junctions. This relationship is prominent for proteins annotated for catalytic activity and reversed in proteins annotated for binding and transcription regulatory activity. Upon analyzing intrinsically disordered proteins, we found a similar pattern for disordered regions as compared to ordered regions: regions of individual mRNAs that code for ordered regions have significantly higher DMS reactivity than regions that code for intrinsically disordered regions. Based on these effects, we hypothesize that the decreased DMS reactivity of RNA regions that encode protein domain junctions or intrinsically disordered regions may reflect increased RNA structure that may slow translation, allowing time for the nascent protein domain or ordered region of the protein to fold, thereby reducing protein misfolding. In addition, a drop in DMS reactivity was observed on portions of mRNA sequences that correspond to the C-termini of protein domains, suggesting ribosome protection at these mRNA regions. Structural relationships between mRNAs and their encoded proteins may have evolved to allow efficient and accurate protein folding. PMID:26598238

  12. 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.

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

    SciTech Connect

    Harris, J.C.

    2001-04-16

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

  14. 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

  15. Sibling Structure and Intergenerational Relations.

    ERIC Educational Resources Information Center

    Spitze, Glenna; Logan, John R.

    1991-01-01

    Examined effects of adult siblings' number, gender, and birth order on their relationships with parents. Analyses showed no evidence for effects of sibling structure through effects on closeness to parents, attitudes about filial responsibilities, or attitudes about gender-typing of responsibilities. Number of siblings had consistent negative…

  16. 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.

  17. 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

  18. 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. PMID:27052618

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

    PubMed Central

    Park, Jungkap; Rosania, Gus R; Shedden, Kerby A; Nguyen, Mandee; Lyu, Naesung; Saitou, Kazuhiro

    2009-01-01

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

  20. Chemical structure representations and applications in computational toxicity.

    PubMed

    Karthikeyan, Muthukumarasamy; Vyas, Renu

    2012-01-01

    Efficient storage and retrieval of chemical structures is one of the most important prerequisite for solving any computational-based problem in life sciences. Several resources including research publications, text books, and articles are available on chemical structure representation. Chemical substances that have same molecular formula but several structural formulae, conformations, and skeleton framework/scaffold/functional groups of the molecule convey various characteristics of the molecule. Today with the aid of sophisticated mathematical models and informatics tools, it is possible to design a molecule of interest with specified characteristics based on their applications in pharmaceuticals, agrochemicals, biotechnology, nanomaterials, petrochemicals, and polymers. This chapter discusses both traditional and current state of art representation of chemical structures and their applications in chemical information management, bioactivity- and toxicity-based predictive studies. PMID:23007430

  1. Symmetry Relations in Chemical Kinetics Arising from Microscopic Reversibility

    NASA Astrophysics Data System (ADS)

    Adib, Artur B.

    2006-01-01

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

  2. 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

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

    NASA Astrophysics Data System (ADS)

    Hay, Mark E.

    2009-01-01

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

  4. 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

  5. The Intersection of Structural and Chemical Biology - An Essential Synergy.

    PubMed

    Zuercher, William J; Elkins, Jonathan M; Knapp, Stefan

    2016-01-21

    The continual improvement in our ability to generate high resolution structural models of biological molecules has stimulated and supported innovative chemical biology projects that target increasingly challenging ligand interaction sites. In this review we outline some of the recent developments in chemical biology and rational ligand design and show selected examples that illustrate the synergy between these research areas. PMID:26933743

  6. 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

  7. PREDICTING MODES OF TOXIC ACTION FROM CHEMICAL STRUCTURE: AN OVERVIEW

    EPA Science Inventory

    In the field of environmental toxicology, and especially aquatic toxicology, quantitative structure activity relationships (QSARS) have developed as scientifically-credible tools for predicting the toxicity of chemicals when little or no empirical data are available. asic and fun...

  8. Relativistic virial relation for cosmological structures

    NASA Astrophysics Data System (ADS)

    Javadinezhad, Reza; Firouzjaee, Javad T.; Mansouri, Reza

    2016-01-01

    Starting with the relativistic Boltzmann equation for a system of particles defined by a distribution function, we have derived the virial relation for a spherical structure within an expanding background in the context of general relativity. This generalized form of the virial relation is then applied to the static case of a spherically symmetric structure to see the difference in the simplest case to the Newtonian relation. A relativistic mass-temperature relation for this simple case is also derived which can be applied to compact objects in astrophysics. Our general virial relation is then applied to the nonstatic case of a structure within an expanding universe where an extra term, usually missed in studies of structures in the presence of the dark energy, appears.

  9. Influence of relative permeabilities on chemical enhanced oil recovery

    NASA Astrophysics Data System (ADS)

    Destefanis, M. F.; Savioli, G. B.

    2011-05-01

    The main objective of chemical flooding is to mobilize the trapped oil remaining after a secondary recovery by waterflooding. This purpose is achieved by lowering the oil-water interfacial tension and producing partial miscibility between both phases. The chemical partition among phases (phase behavior) influences all other physical properties. In particular, it affects residual saturations determining relative permeability curves. Relative permeabilities rule the flow of each phase through the porous medium, so they play an essential role in oil recovery. Therefore, in this work we study the influence of relative permeabilities on the behavior of a surfactant-polymer flooding for the three different types of phase behavior. This analysis is performed applying the 3D compositional numerical simulator UTCHEM developed at the University of Texas at Austin. From the examples studied, we conclude that the influence of relative permeabilities depends on the type of phase behavior, i.e., as microemulsion relative permeability decreases, oil recovery increases for Types II(+) and III while slightly decreases for Type II(-). Moreover, a better displacement efficiency is observed for Types II(+) and III, because they behave similarly to a miscible displacement.

  10. A relationship between chemical structure and the critical temperature

    NASA Technical Reports Server (NTRS)

    Fedors, R. F.

    1982-01-01

    The present investigation is concerned with the effect of both molecular weight and chemical structure on the critical temperature. Using data from the comprehensive compilation of critical constants of Kudchadker et al. (1968), a simple relationship could be developed between the critical temperature and chemical structure. This relationship does not require experimental data such as the normal boiling point. It was found that the critical temperature (Tc) is given by an expression containing m and the sum of delta-i, where m is the total number of atoms in the molecule and delta-i is a number whose value is obtained from a table of additive atomic, group, and structural constants.

  11. Forgotten topological index of chemical structure in drugs.

    PubMed

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

    2016-05-01

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

  12. Specificity of psychiatric manifestations in relation to neurotoxic chemicals.

    PubMed

    Ross, W D; Sholiton, M C

    1983-01-01

    Previous impressions of specificity of psychiatric manifestations in relation to particular chemical intoxications have been confirmed by comparisons of the symptoms and signs of two groups of individuals. Nine persons exposed to inorganic mercury had "erethism" and xenophobia in addition to non-specific features of central nervous system poisoning. Twelve men with heavy exposure to organotins, in contrast to ten men with light or no exposure, more frequently presented an unique alternation between outbursts of range and deep depression, the later lasting from a few hours to a few days. The more heavily exposed men also had a greater number of nonspecific symptoms from neurotoxins. PMID:6575580

  13. Chemical and structural characterization of carbon nanotube surfaces.

    PubMed

    Wepasnick, Kevin A; Smith, Billy A; Bitter, Julie L; Howard Fairbrother, D

    2010-02-01

    To utilize carbon nanotubes (CNTs) in various commercial and scientific applications, the graphene sheets that comprise CNT surfaces are often modified to tailor properties, such as dispersion. In this article, we provide a critical review of the techniques used to explore the chemical and structural characteristics of CNTs modified by covalent surface modification strategies that involve the direct incorporation of specific elements and inorganic or organic functional groups into the graphene sidewalls. Using examples from the literature, we discuss not only the popular techniques such as TEM, XPS, IR, and Raman spectroscopy but also more specialized techniques such as chemical derivatization, Boehm titrations, EELS, NEXAFS, TPD, and TGA. The chemical or structural information provided by each technique discussed, as well as their strengths and limitations. Particular emphasis is placed on XPS and the application of chemical derivatization in conjunction with XPS to quantify functional groups on CNT surfaces in situations where spectral deconvolution of XPS lineshapes is ambiguous. PMID:20052581

  14. 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.

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

    PubMed

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

    2014-07-15

    The Fourier transform infrared and FT-Raman spectra of 2-benzothiazole acetonitrile (BTAN) have been recorded in the range 4000-450 and 4000-100 cm(-1) respectively. The conformational analysis of the compound has been carried out to obtain the stable geometry of the compound. The complete vibrational assignment and analysis of the fundamental modes of the compound are carried out using the experimental FTIR and FT-Raman data and quantum chemical studies. The experimental vibrational frequencies are compared with the wavenumbers derived theoretically by B3LYP gradient calculations employing the standard 6-31G(**), high level 6-311++G(**) and cc-pVTZ basis sets. The structural parameters, thermodynamic properties and vibrational frequencies of the normal modes obtained from the B3LYP methods are in good agreement with the experimental data. The (1)H (400 MHz; CDCl3) and (13)C (100 MHz;CDCl3) nuclear magnetic resonance (NMR) spectra are also recorded. The electronic properties, the energies of the highest occupied and lowest unoccupied molecular orbitals are measured by DFT approach. The kinetic stability of the molecule has been determined from the frontier molecular orbital energy gap. The charges of the atoms and the structure-chemical reactivity relations of the compound are determined by its chemical potential, global hardness, global softness, electronegativity, electrophilicity and local reactivity descriptors by conceptual DFT methods. The non-linear optical properties of the compound have been discussed by measuring the polarisability and hyperpolarisability tensors. PMID:24662754

  16. Structure, Chemical Synthesis, and Biosynthesis of Prodiginine Natural Products.

    PubMed

    Hu, Dennis X; Withall, David M; Challis, Gregory L; Thomson, Regan J

    2016-07-27

    The prodiginine family of bacterial alkaloids is a diverse set of heterocyclic natural products that have likely been known to man since antiquity. In more recent times, these alkaloids have been discovered to span a wide range of chemical structures that possess a number of interesting biological activities. This review provides a comprehensive overview of research undertaken toward the isolation and structural elucidation of the prodiginine family of natural products. Additionally, research toward chemical synthesis of the prodiginine alkaloids over the last several decades is extensively reviewed. Finally, the current, evidence-based understanding of the various biosynthetic pathways employed by bacteria to produce prodiginine alkaloids is summarized. PMID:27314508

  17. 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

  18. 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

  19. Developmental effects of dioxins and related endocrine disrupting chemicals.

    PubMed

    Birnbaum, L S

    1995-12-01

    Alteration of hormones has long been known to affect development. TCDD and related PHAHs modulate the levels of many hormonal systems. Dioxins cause a spectrum of morphological and functional developmental deficits. Fetotoxicity, thymic atrophy, and structural malformations are often noted. Delayed genitourinary tract effects have been observed, and recent studies reported behavioral effects. Highly exposed human offspring have exhibited developmental problems as well. Recently, hormonal and neurological abnormalities have been reported in infants from the general population. The complex alteration of multiple endocrine systems is likely associated with the spectrum of adverse developmental effects caused by dioxin and related compounds. PMID:8597137

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

    ERIC Educational Resources Information Center

    Lo, Mei Ling

    1997-01-01

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

  1. 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)

  2. 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)

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

    ERIC Educational Resources Information Center

    Rzepa, Henry S.

    2016-01-01

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

  4. Establishing relationships between the geometric structure and chemical reactivity of alloy catalysts based on their measured electronic structure.

    SciTech Connect

    Schweitzer, N.; Xin, H.; Nikolla, E.; Miller, J. T.; Linic, S.; Chemical Sciences and Engineering Division; Univ. of Michigan

    2010-01-01

    While it is fairly straightforward to predict the relative chemical reactivity of pure metals, obtaining similar structure-performance relationships for alloys is more challenging. In this contribution we present experimental analysis supported with quantum chemical DFT calculations which allowed us to propose a simple, physically transparent model to predict the impact of alloying on the local electronic structure of different sites in alloys and on the local chemical reactivity. The model was developed through studies of a number of Pt alloys. The central feature of the model is that hybridization of d-orbitals in alloys does not lead to significant charge transfer between the constituent elements in the alloy, and therefore the width of the local density of d-states projected on a site, which is easily calculated from tabulated parameters, is an excellent descriptor of the chemical reactivity of the site.

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

    PubMed

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

    2014-06-01

    The cluster-based compound selection is used in the lead identification process of drug discovery and design. Many clustering methods have been used for chemical databases, but there is no clustering method that can obtain the best results under all circumstances. However, little attention has been focused on the use of combination methods for chemical structure clustering, which is known as consensus clustering. Recently, consensus clustering has been used in many areas including bioinformatics, machine learning and information theory. This process can improve the robustness, stability, consistency and novelty of clustering. For chemical databases, different consensus clustering methods have been used including the co-association matrix-based, graph-based, hypergraph-based and voting-based methods. In this paper, a weighted cumulative voting-based aggregation algorithm (W-CVAA) was developed. The MDL Drug Data Report (MDDR) benchmark chemical dataset was used in the experiments and represented by the AlogP and ECPF_4 descriptors. The results from the clustering methods were evaluated by the ability of the clustering to separate biologically active molecules in each cluster from inactive ones using different criteria, and the effectiveness of the consensus clustering was compared to that of Ward's method, which is the current standard clustering method in chemoinformatics. This study indicated that weighted voting-based consensus clustering can overcome the limitations of the existing voting-based methods and improve the effectiveness of combining multiple clusterings of chemical structures. PMID:24830925

  7. Global Materials Structure Search with Chemically Motivated Coordinates.

    PubMed

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

    2015-12-01

    Identification of relevant reaction pathways in ever more complex composite materials and nanostructures poses a central challenge to computational materials discovery. Efficient global structure search, tailored to identify chemically relevant intermediates, could provide the necessary first-principles atomistic insight to enable a rational process design. In this work we modify a common feature of global geometry optimization schemes by employing automatically generated collective curvilinear coordinates. The similarity of these coordinates to molecular vibrations enhances the generation of chemically meaningful trial structures for covalently bound systems. In the application to hydrogenated Si clusters, we concomitantly observe a significantly increased efficiency in identifying low-energy structures and exploit it for an extensive sampling of potential products of silicon-cluster soft landing on Si(001) surfaces. PMID:26444084

  8. 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. PMID:16729727

  9. 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

  10. 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.

  11. 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.

  12. Development of a chemical structure comparison method for integrated analysis of chemical and genomic information in the metabolic pathways.

    PubMed

    Hattori, Masahiro; Okuno, Yasushi; Goto, Susumu; Kanehisa, Minoru

    2003-10-01

    Cellular functions result from intricate networks of molecular interactions, which involve not only proteins and nucleic acids but also small chemical compounds. Here we present an efficient algorithm for comparing two chemical structures of compounds, where the chemical structure is treated as a graph consisting of atoms as nodes and covalent bonds as edges. On the basis of the concept of functional groups, 68 atom types (node types) are defined for carbon, nitrogen, oxygen, and other atomic species with different environments, which has enabled detection of biochemically meaningful features. Maximal common subgraphs of two graphs can be found by searching for maximal cliques in the association graph, and we have introduced heuristics to accelerate the clique finding and to detect optimal local matches (simply connected common subgraphs). Our procedure was applied to the comparison and clustering of 9383 compounds, mostly metabolic compounds, in the KEGG/LIGAND database. The largest clusters of similar compounds were related to carbohydrates, and the clusters corresponded well to the categorization of pathways as represented by the KEGG pathway map numbers. When each pathway map was examined in more detail, finer clusters could be identified corresponding to subpathways or pathway modules containing continuous sets of reaction steps. Furthermore, it was found that the pathway modules identified by similar compound structures sometimes overlap with the pathway modules identified by genomic contexts, namely, by operon structures of enzyme genes. PMID:14505407

  13. Chemical and biological properties related to toxicity of heated fats.

    PubMed

    Alexander, J C

    1981-01-01

    Heating of fats brings about measurable changes in their chemical and physical characteristics. Heat is applied in processing for food manufacture, such as during hydrogenation of oils with a catalyst, and in frying for meal preparation. Partially hydrogenated products generally contain substantial quantities of geometric and positional isomers of the original unsaturated fatty acids. During deep-fat frying, when the fat is used repeatedly, oxidative and thermal effects result in the formation of many volatile and nonvolatile products, some of which are potentially toxic, depending on the level of intake. Because of concern about the types of changes that take place in fats during oxidative and thermal deterioration and the effects the derivatives could have on the consumer, many chemical and biological studies have been carried out. Experimental findings indicate that any potential danger to the consumer is relative to the severity of the overall treatment of the fat. In some studies we evaluated biological effects on rats of trans fatty acid in the diet and of concentrates of fatty acid derivatives produced in thermally oxidized fats. trans-Octadecenoic acid changed the concentrations of the phospholipid classes in the liver lipids, and interfered with conversion of the essential n - 6 series of fatty acids to higher members. Compared to oleic acid, elaidic acid was preferentially incorporated into the phospholipids instead of the triacylglycerols and was also concentrated in the lipoprotein fractions. Administration of non-urea-adductable concentrates from thermally oxidized fats produced cellular damage in hearts, livers, and kidneys of the animals. Since even practical processing and frying conditions can produce some nutritionally undesirable products, a concerted effort should be made to minimize substantial accumulation of these in our dietary fats. PMID:7265292

  14. 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

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

    PubMed

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

    2010-10-01

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

  16. Fast Optical Chemical and Structural Classification of RNA.

    PubMed

    Morla-Folch, Judit; Xie, Hai-nan; Alvarez-Puebla, Ramon A; Guerrini, Luca

    2016-02-23

    As more biological activities of ribonucleic acids continue to emerge, the development of efficient analytical tools for RNA identification and characterization is necessary to acquire an in-depth understanding of their functions and chemical properties. Herein, we demonstrate the capacity of label-free direct surface-enhanced Raman scattering (SERS) analysis to access highly specific structural information on RNAs at the ultrasensitive level. This includes the recognition of distinctive vibrational features of RNAs organized into a variety of conformations (micro-, fully complementary duplex-, small interfering- and short hairpin-RNAs) or characterized by subtle chemical differences (single-base variances, nucleobase modifications and backbone composition). This method represents a key advance in the ribonucleic acid analysis and will have a direct impact in a wide range of different fields, including medical diagnosis, drug design, and biotechnology, by enabling the rapid, high-throughput, simple, and low-cost identification and classification of structurally similar RNAs. PMID:26831953

  17. 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

  18. 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…

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

    PubMed

    Priyadarsini, K Indira

    2013-01-01

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

  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. 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.

  2. 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

  3. General relativity and cosmic structure formation

    NASA Astrophysics Data System (ADS)

    Adamek, Julian; Daverio, David; Durrer, Ruth; Kunz, Martin

    2016-04-01

    Numerical simulations are a versatile tool for providing insight into the complicated process of structure formation in cosmology. This process is mainly governed by gravity, which is the dominant force on large scales. At present, a century after the formulation of general relativity, numerical codes for structure formation still employ Newton’s law of gravitation. This approximation relies on the two assumptions that gravitational fields are weak and that they originate from non-relativistic matter. Whereas the former seems well justified on cosmological scales, the latter imposes restrictions on the nature of the `dark’ components of the Universe (dark matter and dark energy), which are, however, poorly understood. Here we present the first simulations of cosmic structure formation using equations consistently derived from general relativity. We study in detail the small relativistic effects for a standard lambda cold dark matter cosmology that cannot be obtained within a purely Newtonian framework. Our particle-mesh N-body code computes all six degrees of freedom of the metric and consistently solves the geodesic equation for particles, taking into account the relativistic potentials and the frame-dragging force. This conceptually clean approach is very general and can be applied to various settings where the Newtonian approximation fails or becomes inaccurate, ranging from simulations of models with dynamical dark energy or warm/hot dark matter to core collapse supernova explosions.

  4. 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.

  5. 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

  6. 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

  7. Predictive crystal-chemical relations in Ti-silicates based on the TS block

    NASA Astrophysics Data System (ADS)

    Sokolova, E. V.

    2010-10-01

    In a group of minerals of reasonable complexity in which the structure topology is related but not identical, the general relation between structure topology and chemical composition is not known. This problem is of major significance. The structural hierarchy and stereochemistry are described for 27 titanium disilicate minerals that contain the TS (titanium-silicate) block, a central trioctahedral (O) sheet and two adjacent (H) sheets of [5]- and [6]-coordinated polyhedra and (Si2O7) groups and related delindeite. The TS block is characterized by a planar cell based on translation vectors, t 1 and t 2 , with t 1 ˜ 5.5 and t 2 ˜ 7 Å and t 1 ∧ t 2 close to 90°. The general formula of the TS block is A{2/ P }B{2/ P } M {/2 H } M {/4 O } (Si 2 O 7 ) 2 X 4 + n , where M{2/H} and M{4/O} = cations of the H and O sheets; MH = Ti (= Ti + Nb), Zr, Mn2+, Ca; MO = Ti, Zr, Mn2+, Ca, Na; A P and B P are cations at the peripheral ( P) sites = Na, Ca, Ba; X = anions = O, OH, F; n = 0, 2, 4; the core part of the TS block is shown in bold and is invariant. Cations in each sheet of the TS block form a close-packed layer and the three layers are cubic close packed. There are three topologically distinct TS blocks, depending on the type of linkage of two H sheets and the central O sheet. The H sheets of one TS block attach to the O sheet in the same manner. All structures consist of a TS block and an I (intermediate) block that comprises atoms between two TS blocks. Usually, the I block consists of alkali and alkaline-earth cations, (H2O) groups and oxyanions (PO4)3-, (SO4)2- and (CO3)2-. These structures naturally fall into four groups, based on differences in topology and stereochemistry of the TS block. In Group I, Ti = 1 apfu Ti occurs in the O sheet, and (Si2O7) groups link to a Na polyhedron of the O sheet (linkage 1). In Group II, Ti = 2 apfu, Ti occurs in the H sheet, and (Si2O7) groups link to two M 2+ octahedra of the O sheet adjacent along t 2 (linkage 2). In Group

  8. The expert system for toxicity prediction of chemicals based on structure-activity relationship.

    PubMed Central

    Nakadate, M; Hayashi, M; Sofuni, T; Kamata, E; Aida, Y; Osada, T; Ishibe, T; Sakamura, Y; Ishidate, M

    1991-01-01

    The prediction systems of chemical toxicity has been developed by means of structure-activity relationship based on the computerized fact database (BL-DB). Numbers and ratio of elements, side chains, bonding, position, and microenvironment of side chains were used as structural factors of the chemical for the prediction. Such information was obtained from the BL-DB database by Wiswesser line-formula chemical notation. In the present study, the Salmonella/microsome assay was chosen as indicative of the target toxicity of chemicals. A set of chemicals specified with mutagenicity data was retrieved, and necessary information was extracted and transferred to the working file. Rules of the relations between characteristics of chemical structure and the assay result are extracted as parameters for rules by experts on the rearranged data set. These were analyzed statistically by the discriminant analysis and the prediction with the rules were evaluated by the elimination method. Eight kinds of rules to predict Salmonella/microsome assay were constructed, and currently results of the assay on aliphatic and heterocyclic compounds can be predicted as accurately as +90%. PMID:1820282

  9. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2015-09-01

    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.

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

    PubMed Central

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

    2013-01-01

    Summary A remaining challenge in protein modeling is to predict structures for sequences that do not share recognizable sequence similarity to any experimentally solved structure. This challenge can be addressed by hybrid algorithms that utilize easily obtainable experimental data and carry a limited amount of indirect structural information. Based on earlier observations, the library of protein super-secondary structure motifs (Smotifs) saturated about a decade ago, and new folds discovered since then are novel combinations of existing Smotifs. This observation suggests that it should be possible to build any structure, of either a known or yet to be discovered fold, from a combination of existing Smotifs derived from already known structures. In the absence of any sequence similarity signal, limited experimental data can be used to relate the backbone conformations of Smotifs between target proteins and known experimental structures. Here we present a modeling algorithm that relies on an exhaustive Smotif library and on NMR chemical shift patterns without any input of primary sequence information. In a test of 102 proteins with unique folds, the algorithm delivered 90 homology model quality models, among them 24 high quality ones, and a topologically correct solution for almost all cases. Detailed analysis of the method’s performance suggests that further improvement can be achieved by improving sampling algorithms and developing more precise tools that predict dihedral angle preferences from chemical shift assignments. The current approach opens a venue to address the modeling of larger protein structures for which chemical shifts are available. PMID:23685209

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

    NASA Astrophysics Data System (ADS)

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

    2015-03-01

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

  13. Structural and chemical profiling of the human cytosolic sulfotransferases.

    PubMed

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

    2007-05-01

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

  14. Structural and Chemical Profiling of the Human Cytosolic Sulfotransferases

    PubMed Central

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

    2007-01-01

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

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

    PubMed

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

    2016-01-01

    Identifying chemical-disease relations (CDR) from biomedical literature could improve chemical safety and toxicity studies. This article proposes a novel syntactic and semantic information exploitation method for CDR extraction. The proposed method consists of a feature-based model, a tree kernel-based model and a neural network model. The feature-based model exploits lexical features, the tree kernel-based model captures syntactic structure features, and the neural network model generates semantic representations. The motivation of our method is to fully utilize the nice properties of the three models to explore diverse information for CDR extraction. Experiments on the BioCreative V CDR dataset show that the three models are all effective for CDR extraction, and their combination could further improve extraction performance.Database URL:http://www.biocreative.org/resources/corpora/biocreative-v-cdr-corpus/. PMID:27081156

  16. Chemical composition and temperature structure of Titan's stratosphere

    NASA Astrophysics Data System (ADS)

    Coustenis, A.; Bampasidis, G.; Achterberg, R.; Lavvas, P.; Vinatier, S.; Nixon, C.; Jennings, D.; Teanby, N.; Flasar, F. M.; Orton, G.; Romani, P.; Carlson, R.; Guandique, E. A.

    2013-09-01

    We have explored the thermal and chemical composition of Titan's atmosphere by combining Cassini CIRS recordings and the related ground - and space - based observations. The fulfillment of one Titanian year of space observations provides us for the first time with the opportunity to evaluate the relative role of different physical processes in the long term evolution of this complex environment. We find indication for a weakening of the temperature gradient with warming of the stratosphere and cooling of the lower mesosphere. In addition, we infer precise concentrations for the trace gases and their main isotopologues and find that the chemical composition in Titan's stratosphere varies significantly with latitude during the 6 years investigated here, with increased mixing ratios towards the northern latitudes. In particular, we monitor and quantify the amplitu de of 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 a weakening north polar vortex with reduced lateral mixing across the vortex boundary. By comparing the Cassini/CIRS results from both the limb and the nadir observations with past V1 (1980) and ISO (1997)inferences we find indication for seasonal variations.

  17. Chemical structure and immunobiological activity of Porphyromonas gingivalis lipid A.

    PubMed

    Ogawa, Tomohiko; Asai, Yasuyuki; Makimura, Yutaka; Tamai, Riyoko

    2007-01-01

    In 1933, Boivin et al. extracted an endotoxin from Salmonella typhimurium for the first time, after which a variety of chemical and biological studies on endotoxins have been performed. In 1952, the structural and functional properties of endotoxic lipopolysaccharide (LPS), extracted by a hot phenol and water method devised by Westphal et al., were reported, which led to a number of studies of Gram-negative bacteria in regards to the host defense mechanism. Since 1960, the unique chemical structure and biological activity of Bacteroides species LPS have received a great deal of attention, and there is a long history of such studies. In addition, among oral bacterial strains that have received attention as causative periodontopathic bacteria, many have been classified as Bacteroides species. In particular, a number of researchers have investigated whether LPS of Porphyromonas gingivalis (formerly Bacteroides gingivalis), a black-pigmented oral anaerobic rod, is a virulent factor of the bacterium. The active center of the LPS of these Bacteroides species, the lipid A molecule, is known to be an active participant in endotoxic activation, though its other biological activities are weak, due to its unique chemical structure and action as an antagonist of LPS. On the other hand, many reports have noted that the LPS of those species activate cells in C3H/HeJ mice, which generally do not respond to LPS. We were the first to reveal the chemical structure of P. gingivalis lipid A and, together with other researchers, reported that P. gingivalis LPS and its lipid A have activities toward C3H/HeJ mice. Since that time, because of the popularity of Toll-like receptor (TLR) studies, a great deal of evidence has been reported indicating that P. gingivalis LPS and its lipid A are ligands that act on TLR2. In order to solve such problems as heterogeneity and contamination of the biologically active components of P. gingivalis lipid A, we produced a chemical synthesis counterpart

  18. 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...

  19. AGE-RELATED CHANGES IN SENSITIVITY TO ENVIRONMENTAL CHEMICALS

    EPA Science Inventory

    The processes of aging result in many physiological changes which can lead to alterations in both pharmacokinetic and pharmacodynamic properties. uch changes can result in altered sensitivity to chemicals, whether drugs or environmental agents, in the elderly. t is extremely diff...

  20. SOURCES, EMISSION AND EXPOSURE TO TRICHLOROETHYLENE (TCE) AND RELATED CHEMICALS

    EPA Science Inventory

    This report documents the sources, emission, environmental fate and exposures for TCE, some of its metabolites, and some other chemicals known to produce identical metabolites. The major findings for TCE are:


    1. The primary sources releasing TCE to the environment ...

  1. 21 CFR 1300.02 - Definitions relating to listed chemicals.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ... the Attorney General (28 CFR 0.100). (4) The terms broker and trader mean any individual, corporation... 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...

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

    PubMed

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

    2011-05-16

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

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

    EPA Science Inventory

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

  4. A structured approach to occupational hygiene in the design and operation of fine chemical plant.

    PubMed

    Money, C D

    1992-12-01

    In order to ensure appropriate occupational hygiene controls can be incorporated in the design and operation of fine chemical plant, a structured scheme has been developed based upon the intrinsic hazard of the materials in use. The scheme provides guidelines for managing the inherent risks to health presented by the operation of such plant, including basic recommendations on the selection and operation of selected plant equipment. Although the scheme has focused on a carcinogenic ranking system for aromatic amines and nitro compounds, with suitable modifications its underlying philosophy and principles should be capable of application to any toxicological scheme for ranking the relative hazard of chemical substances. PMID:1471813

  5. 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. PMID:22035594

  6. 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. PMID:16100780

  7. Spectroscopic elucidation of chemical structure of plasma-polymerized pyridine

    SciTech Connect

    Hozumi, K.; Kitamura, K.; Hashimoto, H.; Hamaoka, T.; Fujisawa, H.; Ishizawa, T.

    1983-05-01

    Chemical structure of the plasma-polymerized pyridine film produced on a glass reactor wall by means of the plasma technique in which the pyridine vapor was electronically excited by high-frequency power under a reduced pressure was elucidated. The polymer was highly hydrophilic and was soluble to some of the polar organic solvents so that nitrogen-containing polar functional groups were predicted to participate in the chemical structure of the polymer molecules. /sup 1/H-NMR, /sup 13/CNMR, and IR spectroscopies, high-resolution mass spectral data, and number-average molecular weight determination with some aid of microelemental analysis revealed the presence of various functional groups such as imine, nitrile, amine, pyridine ring, its N-oxide, and even amide. The oxygen atoms involved in the last two groups were supposedly introduced by contact with ambient air after the plasma process. The hydrophilic nature of the polymer which was essential for preparing reverse osmosis membrane was therefore due to the overall hydration effect of these polar functional groups.

  8. Shock induced chemical reactions in energetic structural materials

    NASA Astrophysics Data System (ADS)

    Reding, Derek J.

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

  9. Structure of triadic relations in multiplex networks

    NASA Astrophysics Data System (ADS)

    Cozzo, Emanuele; Kivelä, Mikko; De Domenico, Manlio; Solé-Ribalta, Albert; Arenas, Alex; Gómez, Sergio; Porter, Mason A.; Moreno, Yamir

    2015-07-01

    Recent advances in the study of networked systems have highlighted that our interconnected world is composed of networks that are coupled to each other through different ‘layers’ that each represent one of many possible subsystems or types of interactions. Nevertheless, it is traditional to aggregate multilayer networks into a single weighted network in order to take advantage of existing tools. This is admittedly convenient, but it is also extremely problematic, as important information can be lost as a result. It is therefore important to develop multilayer generalizations of network concepts. In this paper, we analyze triadic relations and generalize the idea of transitivity to multiplex networks. By focusing on triadic relations, which yield the simplest type of transitivity, we generalize the concept and computation of clustering coefficients to multiplex networks. We show how the layered structure of such networks introduces a new degree of freedom that has a fundamental effect on transitivity. We compute multiplex clustering coefficients for several real multiplex networks and illustrate why one must take great care when generalizing standard network concepts to multiplex networks. We also derive analytical expressions for our clustering coefficients for ensemble averages of networks in a family of random multiplex networks. Our analysis illustrates that social networks have a strong tendency to promote redundancy by closing triads at every layer and that they thereby have a different type of multiplex transitivity from transportation networks, which do not exhibit such a tendency. These insights are invisible if one only studies aggregated networks.

  10. 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.

  11. 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...

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

    PubMed

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

    2014-01-01

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

  13. 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

  14. Exploring 3D structural influences of aliphatic and aromatic chemicals on α-cyclodextrin binding.

    PubMed

    Linden, Lukas; Goss, Kai-Uwe; Endo, Satoshi

    2016-04-15

    Binding of solutes to macromolecules is often influenced by steric effects caused by the 3D structures of both binding partners. In this study, the 1:1 α-cyclodextrin (αCD) binding constants (Ka1) for 70 organic chemicals were determined to explore the solute-structural effects on the αCD binding. Ka1 was measured using a three-part partitioning system with either a headspace or a passive sampler serving as the reference phase. The Ka1 values ranged from 1.08 to 4.97 log units. The results show that longer linear aliphatic chemicals form more stable complexes than shorter ones, and that the position of the functional group has a strong influence on Ka1, even stronger than the type of the functional group. Comparison of linear and variously branched aliphatic chemicals indicates that having a sterically unhindered alkyl chain is favorable for binding. These results suggest that only one alkyl chain can enter the binding cavity. Relatively small aromatic chemicals such as 1,3-dichlorobenzene bind to αCD well, while larger ones like tetrachlorobenzene and 3-ring aromatic chemicals show only a weak interaction with αCD, which can be explained by cavity exclusion. The findings of this study help interpret cyclodextrin binding data and facilitate the understanding of binding processes to macromolecules. PMID:26826354

  15. Theoretical spectroscopic studies on chemical and electronic structures of arginylglycine.

    PubMed

    Li, Hongbao; Li, Leilei; Jiang, Jun; Lin, Zijing; Luo, Yi

    2015-10-14

    The energy differences between canonical and zwitterionic isomers of arginylglycine (ArgGly) at the CCSD/aug-cc-pVDZ level are too small (less than 1 kcal mol(-1)) to determine the dominant form in the gas phase from the energetic point of view. First-principles simulations have been performed for near-edge X-ray absorption fine-structure (NEXAFS) spectra and X-ray photoelectron spectra (XPS) at C, N and O K-edges, as well as for infrared (IR) spectra of neutral ArgGly. Noticeable spectral differences were found which enable the unambiguous identification of different neutral groups. We thus demonstrate X-ray spectroscopy as a powerful technique to study the conformation dependent chemical and electronic properties of neutral ArgGly. PMID:26266331

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

    PubMed

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

    2016-01-01

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

  17. 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.

  18. 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. PMID:27016700

  19. 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.

  20. 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

  1. One-pot hydrazide-based native chemical ligation for efficient chemical synthesis and structure determination of toxin Mambalgin-1.

    PubMed

    Pan, Man; He, Yao; Wen, Ming; Wu, Fangming; Sun, Demeng; Li, Sijian; Zhang, Longhua; Li, Yiming; Tian, Changlin

    2014-06-01

    An efficient one-pot chemical synthesis of snake venom toxin Mambalgin-1 was achieved using an azide-switch strategy combined with hydrazide-based native chemical ligation. Synthetic Mambalgin-1 exhibited a well-defined structure after sequential folding in vitro. NMR spectroscopy revealed a three-finger toxin family structure, and the synthetic toxin inhibited human acid-sensing ion channel 1a. PMID:24619065

  2. 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.

  3. 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. PMID:23480816

  4. Electronic structure and chemical bonding in PuO2

    NASA Astrophysics Data System (ADS)

    Teterin, Yu. A.; Maslakov, K. I.; Teterin, A. Yu.; Ivanov, K. E.; Ryzhkov, M. V.; Petrov, V. G.; Enina, D. A.; Kalmykov, St. N.

    2013-06-01

    Quantitative analysis of the x-ray photoelectron spectra structure in the binding energy (BE) range of 0 eV-˜35 eV for plutonium dioxide (PuO2) valence electrons was done. The BEs and structure of the core electronic shells (35 eV-1250 eV BE), as well as the relativistic discrete variation calculation results for the finite fragments of the PuO2 lattice and the data of other authors, were taken into account. The experimental data show that the many-body effects and the multiplet splitting contribute to the spectral structure much less than the outer (0 eV-˜15 eV) and the inner (˜15 eV-˜35 eV) valence molecular orbitals (OVMO and IVMO, respectively). The filled Pu 5f electronic states were shown to form in the PuO2 valence band. The Pu 6p electrons participate in the formation of both the IVMO and the OVMO (bands). The filled Pu 6p3/2 and the O 2s electronic shells were found to take maximum part in the IVMO formation. The MO composition and the sequence order in the BE range of 0 eV-˜35 eV in PuO2 were established. The experimental and theoretical data allowed a quantitative MO scheme for PuO2, which is fundamental for understanding both the chemical bond nature in plutonium dioxide and the interpretation of other x-ray spectra of PuO2.

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

    PubMed Central

    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. PMID:26058041

  6. Commitment in Structurally Enabled and Induced Exchange Relations

    ERIC Educational Resources Information Center

    Lawler, Edward J.; Thye, Shane R.; Yoon, Jeongkoo

    2006-01-01

    Network structures both enable and constrain the development of social relations. This research investigates these features by comparing the development of commitments in structurally enabled and structurally induced exchange relations. We integrate ideas from the theory of relational cohesion and the choice process theory of commitment. In an…

  7. Elucidating the chemical structure of native 1-deoxysphingosine.

    PubMed

    Steiner, Regula; Saied, Essa M; Othman, Alaa; Arenz, Christoph; Maccarone, Alan T; Poad, Berwyck L J; Blanksby, Stephen J; von Eckardstein, Arnold; Hornemann, Thorsten

    2016-07-01

    The 1-deoxysphingolipids (1-deoxySLs) are formed by an alternate substrate usage of the enzyme, serine-palmitoyltransferase, and are devoid of the C1-OH-group present in canonical sphingolipids. Pathologically elevated 1-deoxySL levels are associated with the rare inherited neuropathy, HSAN1, and diabetes type 2 and might contribute to β cell failure and the diabetic sensory neuropathy. In analogy to canonical sphingolipids, it was assumed that 1-deoxySLs also bear a (4E) double bond, which is normally introduced by sphingolipid delta(4)-desaturase 1. This, however, was never confirmed. We therefore supplemented HEK293 cells with isotope-labeled D3-1-deoxysphinganine and compared the downstream formed D3-1-deoxysphingosine (1-deoxySO) to a commercial synthetic SPH m18:1(4E)(3OH) standard. Both compounds showed the same m/z, but differed in their RPLC retention time and atmospheric pressure chemical ionization in-source fragmentation, suggesting that the two compounds are structural isomers. Using dimethyl disulfide derivatization followed by MS(2) as well as differential-mobility spectrometry combined with ozone-induced dissociation MS, we identified the carbon-carbon double bond in native 1-deoxySO to be located at the (Δ14) position. Comparing the chromatographic behavior of native 1-deoxySO to chemically synthesized SPH m18:1(14Z) and (14E) stereoisomers assigned the native compound to be SPH m18:1(14Z). This indicates that 1-deoxySLs are metabolized differently than canonical sphingolipids. PMID:27165858

  8. 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...

  9. 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...

  10. 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

  11. Undergraduate chemistry students' conceptions of atomic structure, molecular structure and chemical bonding

    NASA Astrophysics Data System (ADS)

    Campbell, Erin Roberts

    The process of chemical education should facilitate students' construction of meaningful conceptual structures about the concepts and processes of chemistry. It is evident, however, that students at all levels possess concepts that are inconsistent with currently accepted scientific views. The purpose of this study was to examine undergraduate chemistry students' conceptions of atomic structure, chemical bonding and molecular structure. A diagnostic instrument to evaluate students' conceptions of atomic and molecular structure was developed by the researcher. The instrument incorporated multiple-choice items and reasoned explanations based upon relevant literature and a categorical summarization of student responses (Treagust, 1988, 1995). A covalent bonding and molecular structure diagnostic instrument developed by Peterson and Treagust (1989) was also employed. The ex post facto portion of the study examined the conceptual understanding of undergraduate chemistry students using descriptive statistics to summarize the results obtained from the diagnostic instruments. In addition to the descriptive portion of the study, a total score for each student was calculated based on the combination of correct and incorrect choices made for each item. A comparison of scores obtained on the diagnostic instruments by the upper and lower classes of undergraduate students was made using a t-Test. This study also examined an axiomatic assumption that an understanding of atomic structure is important in understanding bonding and molecular structure. A Pearson Correlation Coefficient, ṟ, was calculated to provide a measure of the strength of this association. Additionally, this study gathered information regarding expectations of undergraduate chemistry students' understanding held by the chemical community. Two questionnaires were developed with items based upon the propositional knowledge statements used in the development of the diagnostic instruments. Subgroups of items from

  12. 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

  13. 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…

  14. 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

  15. 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

  16. 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."

  17. Nanofibers And Related Structures Formed By Polymerization

    NASA Astrophysics Data System (ADS)

    Doiphode, S. V.

    2005-03-01

    Nanofibers of cyanoacrylate were obtained by polymerization from the monomer vapor at a temperature near room temperature. The nanofibers had diameters ranging from 20 nm to 100 nm and lengths of up to several millimeters. Water molecules present on the substrate initiated the living anionic polymerization. As growth continued, the living ends were carried on the tip of each growing nanofiber. These nanofibers formed on glass, metal, plastic, electrospun nanofibers of other polymers, and other surfaces. Some fibers were tapered, some were branched, and some were bent. The number of fibers was varied by controlling the exposure of the substrate to water vapor. Under different conditions the monomer vapor was collected as droplets along electrospun nanofibers, or as droplets at the points where two electrospun nanofibers crossed. The addition of the initiator caused the droplets to polymerize, forming permanent beads on the fibers, and strong mechanical connections at the cross points. This phenomenon provides new ways to construct nanofiber structures engineered on nanometer scales. For example, filters constructed from an open structure of fibers can be coated with nanofibers polymerized from a vapor of nanometer scale droplets flowing through the structure, to improve the capture of molecules or particles.

  18. The bulk and interfacial electronic and chemical structure of amorphous hydrogenated boron carbide

    NASA Astrophysics Data System (ADS)

    Driver, Marcus Sky

    The chemical and electronic structure, as related to the surface, interface and bulk of amorphous hydrogenated boron carbide (a-BxC:H y), is of interest in neutron detection and microelectronics. This dissertation investigates the chemical and electronic structure of semiconducting thin-film a-BxC:Hy grown by plasma enhanced chemical vapor deposition (PECVD) of ortho-carborane (1,2-C2B10H12). Experimental methods used include: x-ray and ultraviolet photoelectron spectroscopies (XPS/UPS) and x-ray absorption/emission spectroscopies (XAS/XES). These methods were used to investigate the chemical species, bonding and hybridizations, and band gaps of a-BxC:Hy prepared or treated under varying conditions. Additionally, a detailed examination of the formation of Schottky barriers was implemented. Throughout this dissertation the chemical structure was studied. One study was to understand various growth conditions. The effects of the PECVD growth parameters were evaluated by comparing changes in atomic percentages (at.%'s) between thin-films from various substrate temperatures. Additionally, detailed studies of the photoelectron core level under two different growth conditions were undertaken to evaluate the effects of pre-/post- argon ion etching (Ar+) for the following: the chemical structural change for both an as grown (AG) and in-situ thermal treatment (500°C), and post Ar+ etch of samples thermally treated ranging from as grown to 850°C. The as grown and in-situ treated samples were used in conjunction to determine the formation of the Schottky barrier. The electronic structure was determined by the changes within the valence band of the thermally treated samples and formation of Schottky barrier. Thermally treated samples (as grown to 850°C) were further evaluated with respect to their occupied and unoccupied electronic states. The atomic percentage gave a stoichiometry range for a-B xC:Hy (given as x=1.5 to 3.0 with y= decreases with thermal treatment and Oz: z

  19. 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)

  20. Annotated bibliography for gas-mask and chemical-defense-gear related papers. Interim report

    SciTech Connect

    Kelly, T.L.; Sucec, A.A.; Englund, C.E.

    1988-01-15

    This is an annotated bibliography of papers that relate to the characteristics and effects of gas masks and other chemical-defense gear. Psychological, physiological, and cognitive performance effects are included.

  1. 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…

  2. 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

  3. 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

    2016-01-01

    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

  4. 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

  5. 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

  6. 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.

  7. 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

  8. 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 ...

  9. 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)

  10. 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

  11. Structure-function relations in flavodoxins.

    PubMed

    Simondsen, R P; Tollin, G

    1980-12-10

    Flavodoxins are low molecular weight, FMN containing, proteins which function as electron transfer agents in a variety of microbial metabolic processes, including nitrogen fixation. Utilizing structural information obtained from x-ray crystal analysis, it has been possible to derive some new and important insights into the relationships which exist between flavin properties and protein environment by comparing the spectroscopic, thermodynamic and kinetic behavior of the flavodoxins with that of free flavin. Thus, for example, a qualitative understanding of the contribution of the protein to flavin redox potentials, semiquinone reactivity and mechanism of electron transfer is beginning to emerge. The highly negative redox potential required for the biochemical activity of the flavodoxins is accomplished by stabilizing the semiquinone via a hydrogen bond to the N-5 position of the flavin and destabilizing the fully-reduced form by constraining it to assume an unfavorable planar conformation. The reactivity of the semiquinone form is lowered by the aforementioned hydrogen bond, as well as by an interaction with a tryptophan residue in the binding site. Electron transfer is accomplished through the exposed dimethylbenzene ring of the bound coenzyme. Although it is not possible at present to determine the extent to which this understanding can be generalized to other flavoproteins, it is clear that a study of the flavodoxins will provide us with at least some of the principles which biological systems have used to modify flavin properties to fulfill a biochemical need. PMID:6782445

  12. Quantum-chemical calculations and electron diffraction study of the equilibrium molecular structure of vitamin K3

    NASA Astrophysics Data System (ADS)

    Khaikin, L. S.; Tikhonov, D. S.; Grikina, O. E.; Rykov, A. N.; Stepanov, N. F.

    2014-05-01

    The equilibrium molecular structure of 2-methyl-1,4-naphthoquinone (vitamin K3) having C s symmetry is experimentally characterized for the first time by means of gas-phase electron diffraction using quantum-chemical calculations and data on the vibrational spectra of related compounds.

  13. 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

  14. STRUCTURE-ACTIVITY RELATIONSHIPS FOR SCREENING ORGANIC CHEMICALS FOR POTENTIAL ECOTOXICITY EFFECTS

    EPA Science Inventory

    The paper presents structure-activity relationships (QSAR) for estimating the bioconcentration factor and acute toxicity of some classes of industrial chemicals using only the n-octanol/water partition coefficient (Log P) which is derived from chemical structure. The bioconcentra...

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

    PubMed

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

    2015-12-01

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

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

    PubMed

    Fourré, Isabelle; Alvarez, Elsa; Chaquin, Patrick

    2014-02-24

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

  17. Applications of LPG fiber optical sensors for relative humidity and chemical-warfare-agents monitoring

    NASA Astrophysics Data System (ADS)

    Luo, Shufang; Liu, Yongcheng; Sucheta, Artur; Evans, Mishell K.; Van Tassell, Roger

    2002-09-01

    A long-period grating (LPG) fiber optic sensor has been developed for monitoring the relative humidity levels and toxic chemicals, especially the chemical warfare agents. The principle of operation of this sensor is based on monitoring the refractive index changes exhibited by the reactive coating applied to the surface of the LPG region in response to analytes. Specific interaction of the analyte with the thin film polymer coating produces as the output a wavelength shift that can be correlated with the concentration of the analyte. Thin polymer coating for relative humidity sensor is made of carboxymethylcellulose (CMC) covalently bound to the surface of the fiber. Coating for chemical warfare agent detection employs metal nanoclusters imbedded in polyethylenimine (PEI) for specific reaction. The relative humidity level can be determined from 0% to 95% and the level of toxic chemicals can be determined is at least on the scale of 1 ppm. This small-size and low-cost LPG fiber optic sensor exhibited high sensitivity, rapid response, repeatability and durability. The goal of developing relative humidity sensor is to produce a fiber optic sensor-based health monitoring system for building, while the chemical sensor has found its application in point detection network for chemical warfare agent monitoring.

  18. 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.

  19. 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.

  20. 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.

  1. 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.

  2. 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.

  3. 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.

  4. 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. PMID:24710340

  5. 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

  6. 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

  7. 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.

  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. PMID:15930646

  9. Advanced exact structure searching in large databases of chemical compounds.

    PubMed

    Trepalin, Sergey V; Skorenko, Andrey V; Balakin, Konstantin V; Nasonov, Anatoly F; Lang, Stanley A; Ivashchenko, Andrey A; Savchuk, Nikolay P

    2003-01-01

    Efficient recognition of tautomeric compound forms in large corporate or commercially available compound databases is a difficult and labor intensive task. Our data indicate that up to 0.5% of commercially available compound collections for bioscreening contain tautomers. Though in the large registry databases, such as Beilstein and CAS, the tautomers are found in an automated fashion using high-performance computational technologies, their real-time recognition in the nonregistry corporate databases, as a rule, remains problematic. We have developed an effective algorithm for tautomer searching based on the proprietary chemoinformatics platform. This algorithm reduces the compound to a canonical structure. This feature enables rapid, automated computer searching of most of the known tautomeric transformations that occur in databases of organic compounds. Another useful extension of this methodology is related to the ability to effectively search for different forms of compounds that contain ionic and semipolar bonds. The computations are performed in the Windows environment on a standard personal computer, a very useful feature. The practical application of the proposed methodology is illustrated by several examples of successful recovery of tautomers and different forms of ionic compounds from real commercially available nonregistry databases. PMID:12767143

  10. 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.

  11. Holistic Structuralism, Elementarism and Piaget's Theory of 'Relationalism'.

    ERIC Educational Resources Information Center

    Kitchener, Richard F.

    1985-01-01

    Contrasts holism, elementarism and Piaget's rationalism. Suggests Piaget's views are close to those of transactionalism and that the key difference between Gestalt holistic structure and Piagetian operatory structure is whether the composition laws are additive or not. Piaget's version of structuralism (relationalism) is distinctive in being…

  12. 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.

  13. 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.

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

    PubMed Central

    Leontis, N B; Westhof, E

    1998-01-01

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

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

    PubMed

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

    2013-09-01

    The research aims to develop global modeling tools capable of categorizing structurally diverse chemicals in various toxicity classes according to the EEC and European Community directives, and to predict their acute toxicity in fathead minnow using set of selected molecular descriptors. Accordingly, artificial intelligence approach based classification and regression models, such as probabilistic neural networks (PNN), generalized regression neural networks (GRNN), multilayer perceptron neural network (MLPN), radial basis function neural network (RBFN), support vector machines (SVM), gene expression programming (GEP), and decision tree (DT) were constructed using the experimental toxicity data. Diversity and non-linearity in the chemicals' data were tested using the Tanimoto similarity index and Brock-Dechert-Scheinkman statistics. Predictive and generalization abilities of various models constructed here were compared using several statistical parameters. PNN and GRNN models performed relatively better than MLPN, RBFN, SVM, GEP, and DT. Both in two and four category classifications, PNN yielded a considerably high accuracy of classification in training (95.85 percent and 90.07 percent) and validation data (91.30 percent and 86.96 percent), respectively. GRNN rendered a high correlation between the measured and model predicted -log LC50 values both for the training (0.929) and validation (0.910) data and low prediction errors (RMSE) of 0.52 and 0.49 for two sets. Efficiency of the selected PNN and GRNN models in predicting acute toxicity of new chemicals was adequately validated using external datasets of different fish species (fathead minnow, bluegill, trout, and guppy). The PNN and GRNN models showed good predictive and generalization abilities and can be used as tools for predicting toxicities of structurally diverse chemical compounds. PMID:23764236

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

    PubMed Central

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

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

    PubMed

    Papamokos, George; Silins, Ilona

    2016-01-01

    There is an increasing need for new reliable non-animal based methods to predict and test toxicity of chemicals. Quantitative structure-activity relationship (QSAR), a computer-based method linking chemical structures with biological activities, is used in predictive toxicology. In this study, we tested the approach to combine QSAR data with literature profiles of carcinogenic modes of action automatically generated by a text-mining tool. The aim was to generate data patterns to identify associations between chemical structures and biological mechanisms related to carcinogenesis. Using these two methods, individually and combined, we evaluated 96 rat carcinogens of the hematopoietic system, liver, lung, and skin. We found that skin and lung rat carcinogens were mainly mutagenic, while the group of carcinogens affecting the hematopoietic system and the liver also included a large proportion of non-mutagens. The automatic literature analysis showed that mutagenicity was a frequently reported endpoint in the literature of these carcinogens, however, less common endpoints such as immunosuppression and hormonal receptor-mediated effects were also found in connection with some of the carcinogens, results of potential importance for certain target organs. The combined approach, using QSAR and text-mining techniques, could be useful for identifying more detailed information on biological mechanisms and the relation with chemical structures. The method can be particularly useful in increasing the understanding of structure and activity relationships for non-mutagens. PMID:27625608

  18. 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

  19. 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. PMID:27087308

  20. 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...

  1. 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

  2. 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. PMID:26184407

  3. 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...

  4. 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.

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

    PubMed Central

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

    2010-01-01

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

  6. 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.

  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. 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.

  9. 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.

  10. 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.

  11. 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

    2015-01-01

    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

  12. 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.

  13. 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

  14. How to link the relative abundances of gas species in coma of comets to their initial chemical composition?

    NASA Astrophysics Data System (ADS)

    Marboeuf, Ulysse; Schmitt, Bernard

    2014-11-01

    Comets are expected to be the most primitive objects in the Solar System. The chemical composition of these objects is frequently assumed to be directly provided by the observations of the abundances of volatile molecules in the coma. The present work aims to determine the relationship between the chemical composition of the coma, the outgassing profile of volatile molecules and the internal chemical composition, and water ice structure of the nucleus, and physical assumptions on comets. To do this, we have developed a quasi 3D model of a cometary nucleus which takes into account all phase changes and water ice structures (amorphous, crystalline, clathrate, and a mixture of them); we have applied this model to the Comet 67P/Churyumov-Gerasimenko, the target of the Rosetta mission. We find that the outgassing profile of volatile molecules is a strong indicator of the physical and thermal properties (water ice structure, thermal inertia, abundances, distribution, physical differentiation) of the solid nucleus. Day/night variations of the rate of production of species helps to distinguish the clathrate structure from other water ice structures in nuclei, implying different thermodynamic conditions of cometary ice formation in the protoplanetary disc. The relative abundance (to H2O) of volatile molecules released from the nucleus interior varies by some orders of magnitude as a function of the distance to the Sun, the volatility of species, their abundance and distribution between the "trapped" and "condensed" states, the structure of water ice, and the thermal inertia and other physical assumptions (dust mantle, …) on the nucleus. For the less volatile molecules such as CO2 and H2S, the relative (to H2O) abundance of species in coma remain similar to the primitive composition of the nucleus (relative deviation less than 25%) only around the perihelion passage (in the range -3 to -2 to +2-3 AU), whatever is the water ice structure and chemical composition, and under

  15. Phase Diagrams of Iron Rich Alloys and Their Influence on the Chemical Structure of Planetary Cores

    NASA Astrophysics Data System (ADS)

    Campbell, A. J.; Miller, N. A.; Fischer, R. A.; Seagle, C. T.; Prakapenka, V. B.

    2008-12-01

    Many planetary bodies are thought to have metallic, iron rich cores, with a significant component of some 'light' alloying element(s). The identity of this light alloying component has a profound effect on the chemical properties of the core, including its melting/crystallization behavior, partitioning of minor and trace elements during core/mantle segregation and core crystallization, and other phase relations. Despite this importance, the light element component(s) of planetary bodies generally remain unknown, apart from those of a few iron meteorite parent bodies. Experimentally determined physical and chemical properties of iron-rich systems can be compared to observations and models of planetary interiors to constrain compositions of planetary cores. Here we summarize our recent high pressure, high temperature experiments on the phase diagrams of iron+light element (Fe-X) binaries, specifically iron-sulfide, iron-silicide, and iron-oxide systems. Melting as well as subsolidus phase relations have been determined in the laser heated diamond anvil cell, using either synchrotron X-ray diffraction or optical methods to establish phase boundaries. X-ray diffraction while laser heating the sample reveals the nature of structural transitions (including partial melting), and optical methods (such as temperature vs. emissivity and related methods) establish the phase boundaries with finer precision. Drawing on these and other recent experimental results, we compare and contrast the binary Fe-X phase diagrams to address such questions as: Which candidate light elements (S, Si, O, C) cause the largest melting point depression, and how does this change with pressure? Which can produce large density constrasts against crystallizing iron metal? and others. These results are compared to thermal and chemical models of terrestrial planet interiors (including Earth's), and important gaps and discrepancies in the available experimental data are highlighted.

  16. Injuries from Methamphetamine-Related Chemical Incidents - Five States, 2001-2012.

    PubMed

    Melnikova, Natalia; Orr, Maureen F; Wu, Jennifer; Christensen, Bryan

    2015-08-28

    Methamphetamine (meth), a highly addictive drug, can be illegally manufactured using easily acquired chemicals; meth production can cause fires, explosions, injuries, and environmental contamination. To analyze injury incidence and trends, data on 1,325 meth-related chemical incidents reported to the Agency for Toxic Substances and Disease Registry's (ATSDR) Hazardous Substances Emergency Events Surveillance (HSEES) system and National Toxic Substance Incidents Program (NTSIP) by the five participating states (Louisiana, Oregon, Utah, New York, and Wisconsin) with complete information during 2001-2012 were examined. The findings suggested that meth-related chemical incidents increased with the drug's popularity (2001-2004), declined with legislation limiting access to precursor chemicals (2005-2007), and increased again as drug makers circumvented precursor restrictions (2008-2012). Seven percent of meth-related chemical incidents resulted in injuries to 162 persons, mostly members of the general public (97 persons, including 26 children) and law enforcement officials (42). Recent trends suggest a need for efforts to protect the general public, particularly children and law enforcement officials. Because individual state legislative actions can result in increased illegal meth production in neighboring states, a regional approach to prevention is recommended. PMID:26313473

  17. Similarity graphing and enzyme-reaction database: methods to detect sequence regions of importance for recognition of chemical structures.

    PubMed

    Sumi, K; Nishioka, T; Oda, J

    1991-04-01

    We developed a new method which searches sequence segments responsible for the recognition of a given chemical structure. These segments are detected as those locally conserved among a sequence to be analyzed (target sequence) and a set of sequences (reference sequences). Reference sequences are the sequences of functionally related proteins, ligands of which contain a common chemical substructure in their molecular structures. 'Similarity graphing' cuts target sequences into segments, aligns them with reference sequence pairwise, calculates the degree of similarity for each alignment, and shows graphically cumulative similarity values on target sequence. Any locally conserved regions, short or long in length and weak or strong in similarity, are detected at their optimal conditions by adjusting three parameters. The 'enzyme-reaction database' contains chemical structures and their related enzymes. When a chemical substructure is input into the database, sequences of the enzymes related to the input substructure are systematically searched from the NBRF sequence database and output as reference sequences. Examples of analysis using similarity graphing in combination with the enzyme-reaction database showed a great potentiality in the systematic analysis of the relationships between sequences and molecular recognitions for protein engineering. PMID:1881867

  18. 77Se Chemical Shift Tensor of L-selenocystine: Experimental NMR Measurements and Quantum Chemical Investigations of Structural Effects

    PubMed Central

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-01-01

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

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

    PubMed

    Struppe, Jochem; Zhang, Yong; Rozovsky, Sharon

    2015-03-01

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

  20. Simultaneous mapping of chemical abundances and magnetic field structure in Ap stars

    NASA Astrophysics Data System (ADS)

    Lueftinger, T.

    2014-11-01

    Magnetic A stars represent about 5 highly ordered, very stable and often very strong magnetic fields. They frequently show variations in both brightness and spectral line profiles that are synchronised to stellar rotation. Those variations are believed to be produced by atomic diffusion operating in the stellar atmospheres which have become stabilized by multi-kG magnetic fields. In recent years, with the development and application of the Doppler and magnetic-Doppler imaging techniques and the availability of high-precision spectroscopic and spectropolarimetric data, it has became possible to map the chemical abundances and magnetic field structures of Ap stars simultaneously and in increasing detail, based on full Stokes vector observations. I review the state-of-the-art understanding pf Ap star spots and their relation to magnetic fields, the development of Doppler and magnetic-Doppler imaging into one of the most powerful remote sensing methods for astrophysics, and the physics of Ap stars atmospheres that we can deduce from simultaneous mapping of magnetic field structure and chemical abundances.

  1. Provenance of Corexit-related chemical constituents found in nearshore and inland Gulf Coast waters.

    PubMed

    Hayworth, Joel S; Clement, T Prabakhar

    2012-10-01

    The dispersants Corexit 9527 and Corexit 9500 were extensively used during the response to the Deepwater Horizon accident in 2010. In addition to the monitoring programs established by federal and state governments, local communities also conducted studies to determine if chemical constituents from these dispersants impacted nearshore and inland waters. One community (the City of Orange Beach, Alabama) collected water samples between September, 2010 and January, 2011, and found the dispersant-related chemicals propylene glycol, 2-butoxyethanol, and dioctyl sodium sulfosuccinate at nearshore and inland water sampling sites. In this paper, we examine their dataset in an attempt to discern the origin of these chemicals. Our assessment indicates that these compounds are unlikely to be present as a result of the use of Corexit dispersants; rather, they are likely related to point and non-point source stormwater discharge. PMID:22959174

  2. 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.

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

    NASA Technical Reports Server (NTRS)

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

    1984-01-01

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

  4. Fatal work-related injuries in the U.S. chemical industry 1984-89.

    PubMed

    Suruda, A; Wallace, D

    1996-01-01

    Several mortality studies of the chemical industry have examined fatal injuries, but most of these studies have been of employees of large chemical firms and have not separated work-related from non-work-related injuries. We examined all U.S. Occupational Safety and Health Administration (OSHA) investigation files in 1984-89 in 47 U.S. states of fatal injuries in the chemical industry, Standard Industrial Classification (SIC) 2800-2899. OSHA investigates all reported deaths over which it has jurisdiction; this includes most causes of work-related death except for homicide and motor vehicle crashes. For the 6 year period, there were 234 fatalities in the chemical industry, for a work-related fatality rate of 0.55 per 10,000 workers/year. The largest category of deaths was from explosions, with 99 (42%), followed by fire & burns, with 32 (14%), poisoning, with 31 (13%), and falls, with 18 (8%). Of the 99 deaths from explosions, 45 (45%) involved manufacture or handling of fireworks or other explosives. The fatality rate at firms with fewer than 50 employees was more than twice that of larger firms (P < 0.05) and employees at small firms were less likely to have been covered by a union contract (P < 0.05). OSHA issued citations for safety violations in 73% of the deaths. While regulatory authorities and the media often focus attention on large, multinational chemical corporations, the highest worker fatality rates are found at the smallest chemical firms. PMID:8891780

  5. 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. PMID:24852611

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

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

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

  7. 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...

  8. 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

  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. 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.